BLoG ONE

Gut Pathogens making a positive impact in 2012

2012-01-26T17:35:00.001+05:30

The year has started positively for Gut Pathogens with the news that the journal will receive its first Impact Factor in June 2012.Gut Pathogens is aiming to be ranked in the first quartile of Gastroenterology and Hepatology journals.

Gut Pathogens, an internationally recognized journal, boasts an Editorial Board consisting of leading researchers from around the world. A key factor in the journal's success has been its commitment to publishing articles that are topical and relevant to researchers in this field. In particular, Gut Pathogens has consistently published highly popular articles on probiotics, and is becoming a key journal for researchers in the field to submit their research. The journal will continue to publish high quality articles on probiotics in the future. (Image credit: Probiotic Lactobacillus salivarius. Sleator, Gut Pathogens 2010 2:5)

There has been an increasing interest in pathogens such as Clostridium difficile, E. coli and Salmonella because of the significant emerging health problems they are causing in western countries. Gut Pathogens would like to invite scientists to submit their research on these and similar themes to the journal for publication in 2012.

Posted by Srimathy Sriskantharajah at Biomed Central Blog on 26/1/2012

Open Access versus ‘doing business on corpses’: Is PLoS ONE the choicest journal of the TB community?

2011-12-06T23:14:00.005+05:30

It is heartening to see PLoS ONE emerge as a preferred destination for tuberculosis and lung diseases research and the journal has already published >1300 articles in this area (http://tinyurl.com/cvnvdnb), a volume equivalent to a 13 year output of the journal Tuberculosis (@ 100 articles per year) and of 6 years output of the International Journal of Tuberculosis and Lung Disease (IJTLD) (@ 240 articles per year).
Given this, I must congratulate all those authors who have by publishing in ONE in a way dumped the might of the journals that block Open Access to TB research - something like 'doing business on the corpses'. They have for years blocked access to TB works - the situation worsened in high burden countries such as India (where 320000 people died of TB in 2010 alone). Very surprising and painful is the reality that one of these journals, the IJTLD is published by the International Union Against TB and Lung Disease or the Union (www.theunion.org), one of the major champions of the cause of TB. While the Union is doing very laudable efforts in the area of TB control and prevention, I would urge them to consider widening unconditional Open Access to the IJTLD contents by the Indian TB communities (rather than linking access to membership/subscription). Why would someone become a member of the Union just to read an article in need? Currently, the Union makes available the journal through Ingenta Connect who charge about USD 40.00 per view, per article when accessed directly. The cost per view charged thereby is equivalent of the cost of food/ration for one month for a mid size, lower middle class family in India. The same is true with Tuberculosis articles, each accessible at the cost of USD 35.00 levied by Elsevier. The Union receives huge funding and donations from various sources and they should seriously think on converting their journal in to an Open Access, online only journal to better serve the down trodden.
World over, the research on TB is mainly funded by tax payers' money and in no way the TB community should allow these journals to carve business out of this dreaded epidemic. PLoS ONE on the other hand generously waives off cost of article processing for all the authors who request for the same. Each article is available free of cost for unlimited download and distribution with no strings attached. That's why PLoS ONE stands today as one of the choicest journal of the TB researchers.

German cows get clean chit for the outbreak of Shiga toxin-producing E. coli O104:H4

2011-11-10T18:10:00.001+05:30

No evidence of the Shiga toxin-producing E. coli O104:H4 outbreak strain or enteroaggregative E. coli (EAEC) found in cattle faeces in northern Germany, the hotspot of the 2011 HUS outbreak area

Lothar H Wieler, Torsten Semmler, Inga Eichhorn, Esther M Antao, Bianca Kinnemann, Lutz Geue, Helge Karch, Sebastian Guenther and Astrid Bethe Gut Pathogens 2011, 3:17 doi:10.1186/1757-4749-3-17 Published: 3 November 2011

Ruminants, in particular bovines, are the primary reservoir of Shiga toxin-producing E. coli (STEC), but whole genome analyses of the current German ESBL-producing O104:H4 outbreak strain of sequence type (ST) 678 showed this strain to be highly similar to enteroaggregative E. coli (EAEC). Strains of the EAEC pathotype are basically adapted to the human host. To clarify whether in contrast to this paradigm, the O104:H4 out-break strain and/or EAEC may also be able to colonize ruminants, we screened a total of 2.000 colonies from faecal samples of 100 cattle from 34 different farms - all located in the HUS outbreak region of Northern Germany - for genes associated with the O104:H4 HUS outbreak strain (stx2, terD, rfbO104, fliCH4), STEC (stx1, stx2, escV), EAEC (pAA, aggR, astA), and ESBL-production (blaCTX-M, blaTEM, blaSHV). Results: The faecal samples contained neither the HUS outbreak strain nor any EAEC. As the current outbreak strain belongs to ST678 and displays an enteroaggregative and ESBL-producing phenotype, we additionally screened selected strains for ST678 as well as the aggregative adhesion pattern in HEp-2 cells. However, we were unable to find any strains belonging to ST678 or showing an aggregative adhesion pattern. A high percentage of animals (28%) shed STEC, corroborating previous knowledge and thereby proving the validity of our study. One of the STEC also harboured the LEE pathogenicity island. In addition, eleven animals shed ESBL-producing E. coli. Conclusions: While we are aware of the limitations of our survey, our data support the theory, that, in contrast to other Shiga-toxin producing E. coli, cattle are not the reservoir for the O104:H4 outbreak strain or other EAEC, but that the outbreak strain seems to be adapted to humans or might have yet another reservoir, raising new questions about the epidemiology of STEC O104:H4. Access full article free of cost

Feast of the Open Access Week: PLoS Won

2011-10-26T21:02:00.001+05:30

By Michael Eisen | October 25, 2011 (Courtesy: it is NOT junk)

When Pat Brown, Harold Varmus and I started the Public Library of Science (PLoS) 10 years ago with the goal of making the scientific and medical literature a universally freely available resource, most people in the science publishing industry dismissed us as naive idealists who didn't understand that publishing is a business that has to make money, or derided us as dangerous radicals hellbent on destroying them.

So it has given me considerable pleasure to watch, over the past year or so, as one traditional publisher after another has responded to the smashing success of PLoS One by launching direct ripoffs that seek to capitalize on the business model we have established.

For those of you who don't know, PLoS One, launched in 2006, does things a bit differently than most scientific journals. Every paper submitted to the journal is peer reviewed, but the reviewers and editors consider only the technical merits of the paper in deciding whether or not it should be published – they do not attempt (as virtually all other journals do) to gauge the potential significance or sexiness of the paper. The result is a simple and objective peer review process that gets papers published quickly and, because it is an open access journal, in a place where it is accessible for anyone to find and read. To cover the costs of running the journal and handling the paper, authors of accepted papers pay a fee (currently $1,350 – he money comes from their research grants or institutions, not from their own pockets, and any authors who say they can not pay are granted waivers).

And apparently authors love PLoS One, because they are sending us lots of paper. The journal published 6,700 articles in 2010 and will publish around 12,000 in 2011. This has clearly caught the attention of lots of established publishers, as the past year has seen the launch of a series of PLoS One clones, including:

The American Society for Microbiology's mBio
The Genetics Society of America's G3
BMJ Open
Company of Biologists Biology Open
Nature's Scientific Reports
Cell Press's Cell Reports
The Royal Society's Open Biology
SAGE Open

joining already existing offerings from open access publishers BioMed Central, Hindawi and others.

This is, in many ways, exactly what we hoped would happen. In 2001 most publishers lacked both the foresight to see how publishing could better serve the research community, and the incentive to bother figuring it out. Now, PLoS One's volume, and the threat it poses to their existing journals, provides the motivation, and PLoS One's financial success (it is profitable) serves as an inspiration. Our goal was always to see that papers were published in open access journals. If they were PLoS journals – great. But if they were from other publishers – that's great too.

And here, there is a bit of a rub. PLoS and BMC established the standard for open access publishing by adopting the Creative Commons Attribution License (CC-BY), which allows for unrestricted reuse and redistribution subject only to the constraint that the original authors and source be cited. Several of the new journals follow our lead and use CC-BY, including G3, Open Biology and SAGE Open. I fully endorse what these publishers are doing, and have already published one paper in G3.

The others have not been so enlightened, using exclusively (or in one case optionally) licenses that restrict commercial reuse or the generation of derivitive works.

CC-BY-NC – BMJ Open

CC-NC-SA – mBio, Biology Open

CC-BY-NC-ND – Scientific Reports

CC-BY or CC-BY-NC-ND – Cell Reports

This is a very misguided decision on the part of these publishers. The rules governing reuse of content matter a lot if we are ever going to start making more effective use of the published scientific literature. The non-commercial licenses employed by BMJ, Nature, ASM, Company of Biologists, Cell Press and Nature all – rather absurdly – prevent PLoS from reusing their content in tools we are developing to help researchers organize literature in their fields and make the contents of papers they care about more useful. I hope this is a short-lived mistake and that, following Netflix, they realize the error of their ways and switch to a CC-BY license (in the meantime, I urge people who care about open access to continue supporting only those journals that use the CC-BY license).

There is, obviously, still a long way to go before we achieve our original goal of making every paper immediately freely available. Buit it's hard not to see events of the last year as anything but a major victory for PLoS and open access.

Happy Open Access Week!

[UPDATE: I want to clarify that Cell Reports does not view itself as a PLoS One clone, as it will be rejecting papers on the basis of impact/importance. I also want to commend them for offering the CC-BY license to authors, although I think that many will naively choose the NC version].

PLoSONE: Global Conservation Priorities for Marine Turtles

2011-09-30T11:50:00.002+05:30

Wallace BP, DiMatteo AD, Bolten AB, Chaloupka MY, Hutchinson BJ, et al. (2011) Global Conservation Priorities for Marine Turtles. PLoS ONE 6(9): e24510 - Read full article here for free

Where conservation resources are limited and conservation targets are diverse, robust yet flexible priority-setting frameworks are vital. Priority-setting is especially important for geographically widespread species with distinct populations subject to multiple threats that operate on different spatial and temporal scales. Marine turtles are widely distributed and exhibit intra-specific variations in population sizes and trends, as well as reproduction and morphology. However, current global extinction risk assessment frameworks do not assess conservation status of spatially and biologically distinct marine turtle Regional Management Units (RMUs), and thus do not capture variations in population trends, impacts of threats, or necessary conservation actions across individual populations. To address this issue, we developed a new assessment framework that allowed us to evaluate, compare and organize marine turtle RMUs according to status and threats criteria. Because conservation priorities can vary widely (i.e. from avoiding imminent extinction to maintaining long-term monitoring efforts) we developed a "conservation priorities portfolio" system using categories of paired risk and threats scores for all RMUs (n = 58). We performed these assessments and rankings globally, by species, by ocean basin, and by recognized geopolitical bodies to identify patterns in risk, threats, and data gaps at different scales. This process resulted in characterization of risk and threats to all marine turtle RMUs, including identification of the world's 11 most endangered marine turtle RMUs based on highest risk and threats scores. This system also highlighted important gaps in available information that is crucial for accurate conservation assessments. Overall, this priority-setting framework can provide guidance for research and conservation priorities at multiple relevant scales, and should serve as a model for conservation status assessments and priority-setting for widespread, long-lived taxa. Image coutesy: WWF. Read full article here for free

Aligarh sherwani is shining in Montreal!

2011-09-17T23:05:00.001+05:30

'Zara nam ho toh yeh mittee badee zarkhez hai saaqui'

My congratulations to Dr Hammad Shadab of AMU for his best presentation award at Alternatives Congress.

Hot in PLoS ONE: Do Facial Expressions Develop before Birth?

2011-09-06T19:45:00.000+05:30

Citation: Reissland N, Francis B, Mason J, Lincoln K (2011) Do Facial Expressions Develop before Birth? PLoS ONE 6(8): e24081. doi:10.1371/journal.pone.0024081

Background

Fetal facial development is essential not only for postnatal bonding between parents and child, but also theoretically for the study of the origins of affect. However, how such movements become coordinated is poorly understood. 4-D ultrasound visualisation allows an objective coding of fetal facial movements.

Methodology/Findings

Based on research using facial muscle movements to code recognisable facial expressions in adults and adapted for infants, we defined two distinct fetal facial movements, namely "cry-face-gestalt" and "laughter- gestalt," both made up of up to 7 distinct facial movements. In this conceptual study, two healthy fetuses were then scanned at different gestational ages in the second and third trimester. We observed that the number and complexity of simultaneous movements increased with gestational age. Thus, between 24 and 35 weeks the mean number of co-occurrences of 3 or more facial movements increased from 7% to 69%. Recognisable facial expressions were also observed to develop. Between 24 and 35 weeks the number of co-occurrences of 3 or more movements making up a "cry-face gestalt" facial movement increased from 0% to 42%. Similarly the number of co-occurrences of 3 or more facial movements combining to a "laughter-face gestalt" increased from 0% to 35%. These changes over age were all highly significant.

Significance

This research provides the first evidence of developmental progression from individual unrelated facial movements toward fetal facial gestalts. We propose that there is considerable potential of this method for assessing fetal development: Subsequent discrimination of normal and abnormal fetal facial development might identify health problems in utero.

From PLoS Blogs: Ramadan: Holy month and field experiment

2011-08-10T19:52:00.001+05:30

By Emily Anthes

Ramadan, the Islamic holy month during which Muslims fast during daylight hours, began last week. But Ramadan is more than a holiday–it's also a unique research opportunity. The month provides a large population of people who are fighting against their normal circadian rhythms, eating and being active mostly when it's dark. Back in 2007, I wrote a story for The Boston Globe about what scientists were learning by studying how the body adjusts to this topsy-turvy month. In honor of Ramadan, here's a good chunk of that story:

During Ramadan, Muslims eat and get more active just when their bodies are used to winding down, creating sleep disruptions, hormonal changes, and sometimes mood impacts.

"Their biological clocks are no longer in harmony with their watches," said Yvan Touitou, a chronobiologist at Pierre and Marie Curie University in Paris. "Ramadan is capable of desynchronizing people."

Touitou's research has illustrated that Ramadan can alter the usual circadian patterns of cortisol, a stress hormone, and testosterone, with sharper decreases of these hormones in the morning and later rises at night – though the impact of these rhythm disruptions is unclear.

The holiday also changes the schedule of the release of leptin, a hormone that regulates appetite and weight, and decreases the peak levels of melatonin, a hormone released at night to induce sleep. Interestingly, despite the disruption in leptin and in daily eating patterns, Ramadan rarely causes significant changes in body weight. Investigating why this is the case could yield useful insights into human energy metabolism, said Tom Reilly, a sports scientist at Liverpool John Moores University in England who has studied circadian rhythms and Ramadan.

"Normally, your body clock is affected by the alternation of light and darkness – light is the signal to become alert. With Ramadan, fasting is obligatory at exactly the time the body is gearing up for activity," Reilly said. "It's an exact reversal of the usual pattern."

Florian Chapotot, a neuroscientist at the University of Chicago, found that subjects showed an overall decrease in the amount of sleep they got during the holiday – not surprising given that typically, Ramadan adherents often fit in two or three meals between sunset and sunrise.

What was most interesting, Chapotot said, was the finding that subjects also spent a smaller proportion of their sleep time in slow-wave and REM sleep, both of which "are important because they have restorative functions."

It's still not clear, however, whether sleep disruptions are a result of changes in melatonin secretion, other physiological rhythms or behavioral patterns during the holiday.

The effects of all these physiological changes are unknown. Research has shown that motor skills, such as reaction times, muscle, and learning performance decrease significantly during the holiday and that sleepiness and traffic accidents increase. But scientists are investigating whether these changes are direct results of circadian rhythm disruption.

And despite its usefulness, Ramadan is difficult to study, partly because of the sheer number of variables. The month, part of the lunar Islamic calendar, moves forward by about 11 days every year, and the length of daily fasting can range from 12 hours upward, depending on location and time of year.

Additionally, those who observe the holiday have wildly different ways of coping with the altered hours – some take naps during the day and stay up most of the night, while others only slightly alter their usual sleeping patterns.

"The use of Ramadan as a chronobiological model is a little bit messy. We cannot get control of all of the variables," Reilly said. But, "it's a beautiful field experimental condition."

E. coli genome crowd-sourcing consortium publishes their data: why choose a closed access magazine for an Open Source project?

2011-07-28T21:32:00.001+05:30

The E. coli O104:H4 Genome Analysis Crowd-Sourcing Consortium today published their findings in the New England Journal of Medicine. The paper ignores previous authors' published efforts on the similar lines and the findings reported are not surprising and not newer than the data published by two German groups in Archives Microbiology and PLoS ONE; I handled peer review for the latter study. Having said this, what is disgusting is that the crowd-sourcing consortium have in a way strengthened the agenda of closed access publishing syndicates who run the 'glamour magazines' of science and medicine! As a consequence, the entire purpose of the idea of an Open Source platform for the analysis of the E. coli epidemic stands defeated. The journal may not allow universal access to the article by holding copy right over the much acclaimed 'Open Source' data of this consortium - meaning that no unrestricted access and creative reuse will be possible as against the practice of most Open Access journals.

Prevent leptospirosis: wear good quality shoes during Monsoon

2011-07-21T13:12:00.000+05:30

These pics explain why we get lepto outbreaks each year in June-July. The leptospira penetrate wet skin by by their cork-screw like action. No vaccine is needed as long as you wear long shoes and do not expose to contaminated water spills.

Prospective genomics in epidemics – lessons from the German E. coli outbreak

2011-07-21T06:13:00.001+05:30

By Jennifer Laloup (EveryONE)

Today we published an article by Mellmann et al. entitled, Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology. The following is an opinion piece by Dr. Niyaz Ahmed, a section editor for PLoS ONE and the academic editor of this paper. He is an expert in the area of molecular epidemiology and genomics of bacterial pathogens at the University of Hyderabad, India.

When a monstrously virulent strain of never-before-seen E. coli suddenly appeared in Germany last month, the rush to decode became an immediate focus. Several groups became engaged simultaneously to crack the genome of the underlying bug and then followed a huge crowd-sourcing effort on the internet as soon as the genome sequences were made available. Given that reasonable data were made available by these authors within 60 hours of the outbreak, not much of the evolutionary history of the organism had been dissected and a great deal of the interpretation remained vague.

An informed, scientific treatise was needed to help health control authorities and policy makers launch a serious mitigation campaign; this work, in that sense, constitutes the first official report on the genomic footprint of the underlying E. coli strain. The authors report chronological (step-wise) recombination of the genome in the outbreak strains over a period of ten years. This reveals the extraordinary capability of certain pathogens to recombine so that a devastating phenotype finally emerges with a multi-dimensional fitness advantage. Further, the study of Mellmann et al. demonstrates the might of present-day sequencing technologies such as Ion Torrent in enabling genome-guided epidemiology, diagnostics, and interventions.

I have no hesitation to say that the study carried out by Mellmann et al. is truly a technical masterpiece, a first time proof-of-principle whereby next generation sequencing could be harnessed in real-time when certain 'gold standards' such as serotyping failed miserably. This report has an important bearing on the new proposed field of 'epidemic forecasting' in which the spread potentials of a pathogen could be predicted based on genomic fingerprints – in other words, predicting if the infection will assume pandemic proportions. The finding that the E. coli strains analyzed were enteroaggregative (EAEC) could explain this. EAECs could persist in recovered or subclinical cases and that they could be carried by the latter on travel routes worldwide.

One of the possible shortcomings of the study could be that it is silent on the mechanistic details of 'adornment' of these bacteria with several layers of fitness – multiple antibiotic resistance, acid tolerance, enteroaggregative capacity and shigatoxin production all bundled up in one 'naturally' chimeric strain in just 10 years is extremely dramatic! The pace of evolution of the German outbreak strains has surpassed even Helicobacter pylori, an organism notorious for its speed of recombination, recasting its entire genome every forty years. We recently had an opportunity to sequence and look at H. pylori genomes hierarchically obtained across ten years. We did not find major insertion, deletion and substitution events.

Technology helped with the dissection of the E. coli epidemic in hours and days, but the editorial process also was seamless and prompt enough to enable rapid dissemination of results. Open and early access is very important for the dissemination of findings during epidemic times because much of the control and mitigation measures need planning in the light of latest research findings.

Impact Factors of Biomed Central journals

2011-07-10T20:33:00.000+05:30

The 2010 edition of Thomson Reuters' Journal Citation Reports, released on June 28th 2011, provides further evidence that open access journals are delivering not only high visibility but also high rates of citation and impact.

Altogether, 101 BioMed Central journals now have official impact factors. 21 journals recorded their first impact factors this year. Meanwhile, among the 80 journals which already had impact factors, 52 increased while only 28 declined. The average change in impact factor was an increase of 0.19 points.

Some highlights:

BMC Medicine (IF 5.75) saw a huge jump in its impact factor and is now in the top 10% of journals in the General Medicine category
Retrovirology (IF 5.24), is now 4^th of 32 in the Virology category, overtaking Journal of Virology
Malaria Journal (IF 3.49) recorded its third successive increase and remains the 2^nd most highly ranked journal in the Tropical Medicine category
Journal of Cardiovascular Magnetic Resonance (IF 4.33), official journal of the Society for Cardiovascular Magnetic Resonance, almost doubled its previous impact factor of 2.28
BMC Plant Biology (IF 4.09) increased from 3.77 to confirm its ranking in the top 10% of the Plant Science category
BMC Veterinary Research (IF 2.37) makes an exceptionally strong start, ranking 8^th of 145 in the Veterinary Sciences category
Frontiers of Zoology (IF 2.42) debuts in the JCR in the top 10% of the Zoology category
Particle and Fibre Toxicology (IF 4.91) ranks 4th of 83 in the Toxicology category
Cell Division (IF 4.09) and Epigenetics & Chromatin (IF 4.73) also both make strong starts

Full list of 2010 impact factors for BioMed Central journals
(journals listed in bold have new or improved impact factors)

Journal	2010 IF
Acta Veterinaria Scandinavica	1.20
Algorithms for Molecular Biology	2.80
Arthritis Research & Therapy	4.36
Behavioral Brain Functions	2.31
Biology Direct	3.74
Biological Procedures Online	0.74
BioMedical Engineering OnLine	1.12
Biotechnology for Biofuels	4.15
BMC Bioinformatics	3.03
BMC Biology	5.20
BMC Biotechnology	2.86
BMC Cancer	3.15
BMC Cardiovascular Disorders	2.02	New
BMC Cell Biology	2.46
BMC Complementary and Alternative Medicine	2.20	New
BMC Developmental Biology	2.78
BMC Evolutionary Biology	3.70
BMC Family Practice	1.47
BMC Gastroenterology	2.47
BMC Genetics	2.49
BMC Genomics	4.21
BMC Health Services Research	1.72
BMC Immunology	3.00
BMC Infectious Diseases	2.83
BMC Medical Education	1.20	New
BMC Medical Genetics	2.44
BMC Medical Genomics	3.77
BMC Medical Informatics and Decision Making	2.23
BMC Medical Research Methodology	2.15
BMC Medicine	5.75
BMC Microbiology	2.96
BMC Molecular Biology	3.19
BMC Musculoskeletal Disorders	1.94
BMC Nephrology	2.14	New
BMC Neurology	2.80
BMC Neuroscience	3.09
BMC Pediatrics	1.90	New
BMC Plant Biology	4.09
BMC Psychiatry	2.89
BMC Public Health	2.36
BMC Structural Biology	2.26
BMC Systems Biology	3.57
BMC Veterinary Research	2.37	New
Breast Cancer Research	5.79
Cardiovascular Diabetology	2.72
Cardiovascular Ultrasound	1.56	New
Cell Division	4.09	New
Chemistry Central Journal^*	1.12
Critical Care	4.60
Diagnostic Pathology	1.39
Environmental Health	2.45
Epigenetics & Chromatin	4.73	New
Frontiers in Zoology	2.52	New
Genetics Selection Evolution	1.48
Genome Biology	6.89
Geochemical Transactions	1.92
Harm Reduction Journal	1.46	New
Human Resources for Health	1.38	New
Health and Quality of Life Outcomes	1.86
Hereditary Cancer in Clinical Practice	0.96
Implementation Science	2.51
International Journal for Equity in Health	1.30	New
International Journal of Behavioral Nutrition and Physical Activity	3.17
International Journal of Health Geographics	2.34
Irish Veterinary Journal	0.33
Journal of Biomedical Science	1.96
Journal of Cardiothoracic Surgery	0.91
Journal of Cardiovascular Magnetic Resonance	4.33
Journal of Experimental & Clinical Cancer Research	1.92
Journal of Hematology & Oncology	2.93
Journal of Inflammation	2.02	New
Journal of Neurodevelopmental Disorders	1.27	New
Journal of NeuroEngineering and Rehabilitation	2.64
Journal of Neuroinflammation	5.79
Journal of the International Society for Sports Nutrition	2.68	New
Journal of Translational Medicine	3.51
Lipids in Health and Disease	2.24
Malaria Journal	3.49
Microbial Cell Factories	4.54
Molecular Cancer	3.78
Molecular Neurodegeneration	5.36
Molecular Pain	4.15
Neural Development	3.40
Nutrition & Metabolism	2.35
Nutrition Journal	2.56	New
Orphanet Journal of Rare Diseases	5.93
Parasites and Vectors	2.13
Particle and Fibre Toxicology	4.91	New
Plant Methods	3.28
Proteome Science	2.49
Radiation Oncology	2.41
Reproductive Biology and Endocrinology	1.70
Respiratory Research	2.86
Retrovirology	5.24
Scandinavian Journal of Trauma, Resuscitation and Emergency Medicine	2.18	New
Substance AbuseTreatment, Prevention, and Policy	1.58
Theoretical Biology and Medical Modelling	1.60	New
Trials	2.08
Veterinary Research	3.77
Virology Journal	2.55
World Journal of Surgical Oncology	1.12	New

* Based on Web of Science data, the impact factor listed for Chemistry Central Journal appears to be erroneously low and has been queried with Thomson Reuters.

For further information on impact factors and journal tracking, see BioMed Central's impact factor FAQ.

Posted by Matt Cockerill

Words to avoid in presentations and in speech

2011-07-06T11:01:00.001+05:30

Barry J Marshall (courtesy: http://barryjmarshall.blogspot.com/)

This month I have decided to go public with my list of "meaningless words" which should no longer be used in public, especially not in meetings or presentations and never on TV or radio. Here are the ones I recall today.

1. Basically
a. This word has become a favourite of scientific people especially when they are answering questions. I am also guilty. Example as follows - Question: If the DNA is copied until the primer just falls off, how is it that all the pieces of DNA end up exactly the same length? Answer: Well, basically, you are almost correct however, only the first copy gives a random length. After that, basically, the primer in the next cycle has to start 637 base pairs from the start point of the first copy. So, basically, all except the first copy are the same length, basically 637.
2. I mean
a. This seems to be used as a spacer between sentences, where the speaker continually likes to embellish details and add ideas. I mean, just as one would normally give the listener person a chance to talk by leaving a short gap in the conversation, by using "I mean" the gap is stolen back so that the normal person might not get a word in edgeways. I mean, let's say that it was you being the listener, and you are a nice polite person; I mean, like Marj in the Simpsons. Then you never have a chance to speak because ...
3. Sort of
a. A vague term implying that the speaker has not put any thought into the discussion and is sort of making stuff up as he goes along. This seams to be common in presentations from young artists.
4. Yeah
a. Australians have become adept at placing this word in the middle of sentences as some kind of emphasis. I think it is very common in interviews with surfers; yeah – .
5. Absolutely
a. Television personalities, especially on gardening shows, continually say absolutely. Then the show "Absolutely Fabulous" started up perhaps as a send up of this trend. Recently it has been used more and more by almost everyone. By adding this word, a very vague concept suddenly becomes absolutely correct and proven beyond all doubt. Also, other words can be added to it, especially "fabulous" to make something rather mundane and boring into something apparently exciting. Take the concept of picking up handfuls of animal poo. We don't have smellovision yet, and the warm temperature of a putrefying heap is hard to transmit to the gardening audience. But I can call it compost and say how this material is absolutely the best thing for your garden. How absolutely fabulous it is to feel the warmth as you thrust your hands into the pile in order to experience nature as the good bacteria convert biodegradeable organic material into absolutely perfect plant nutrients. Actually, it sounds rather attractive as I write this.
6. Umm
a. A non word, also used as a spacer to stop other people butting in. Luckily there is no need to use this on TV interviews because a smart editor will cut out all the wasted time anyway, so as to add more content, or another "non umming" person to the time allocated for the story.
7. Like
a. This word is more often used by teenagers – or even myself actually – as emphasis in a story. But it is used rather informally, among friends, with alcohol on board usually, and often as a preamble to an acted out part of the story telling. I am having trouble explaining it but here goes. Just say that I am telling you about a scene from the movie Avatar. So the main actor Sam Worthington is just a dumb marine so he's like, "I need to walk again so I will do anything to pay for an operation"; but Sigourney weaver, she's like some kind of genius professor so she's like "don't break the machinery you dumbass!" etc.
8. You know
a. Everyone uses this Phrase, again a spacer to show that you probably don't know all the facts but what you say is probably about right. Of course, as the brainy listener, you probably have more information or already have heard this story, but if you do know it you would not be so rude as to correct the speaker or embellish his own story. You know.

I think it might be fun to add a few more of these and give funny examples. It would be good practice for a screen writer in a sitcom. My son reminded me of a program we used to have which converted normal speech to "Jive" which was a kind of black American street gang speech which most Australians would hardly ever hear but probably rappers and people from Los Angeles might be familiar with. Time is up – I can't spend my life just doing a blog. Back to real life.

SPARC Innovator Award for PLoS ONE

2011-07-03T18:50:00.001+05:30

Because the concept of PLoS ONE was so simple, yet so revolutionary, its launch in December 2006 was met with equal parts excitement and skepticism. In the PLoS ONE model, editors and reviewers would not attempt to assess the potential importance of the work. Rather, as long as the research was determined to be solid, the author would pay a flat fee, and up it would go on the Web. Could something as simple as publishing articles just because they were "good science" really work?

"The idea was to decouple impact assessment and technical assessment," says Mark Patterson, director of publishing for the Public Library of Science, who was one of the staff involved with the journal from the beginning. "We were also trying to take the hassle out of publishing."

PLoS co-founders Pat Brown, Michael Eisen, and Harold Varmus were also the visionaries behind PLoS ONE, once again creating a new channel by viewing publishing through the lens of scientists. Their vision was to do away with the redundant process of submitting a paper to a journal, waiting for a rejection that was so often based on subjective qualities such as impact, and then resubmitting to a new title. Instead, research would be peer-reviewed against objective criteria and published after it was deemed worthy of joining the scientific literature—often with just one round of revisions. New technology would be leveraged so readers could add value to the content. Those comments would then help to indicate the importance of the work to the body of scientific knowledge.

When the concept was first introduced, it created a lot of chatter—especially in the blogosphere, says Patterson. And, as with any new journal, no one knew what the response would be. Even supporters of PLoS ONE wondered if the model would be seen as selective and prestigious in the scientific community. "I found it very exciting at the time," says Cameron Neylon, a biochemist at the Rutherford Appleton Laboratory in Didcot, England, and member of the PLoS ONE Academic Editor board. "But I was less than convinced it would take off."

It didn't take long before PLoS ONE began emphatically to answer the skeptics.

In 2007, the journal received about 2,500 submissions and published 1,200 articles. In 2010, PLoS ONE received nearly 13,560 articles and published 6,800—with about 60 being published daily. It is now the single largest journal being published today.

The PLoS ONE business model is scalable. Its publishing costs have always been fully covered by the publication fees and it became a financial success. In 2010, due in part to this meteoric rise, PLoS became self-sustaining. The innovative concept and its capacity for rapid growth have caught the attention of other publishers. In a clear nod to the success of PLoS ONE, "clones" are popping up —from SAGE Open, to BMJ Open to Scientific Reports by Nature.

For its groundbreaking model of open-access publishing success, SPARC (the Scholarly Publishing and Academic Resources Coalition), has named PLoS ONE as its July 2011 Innovator.

"PLoS ONE is a game-changer," said Heather Joseph, SPARC's Executive Director. "It breaks through the preconception that authors— and readers—require a journal to determine the significance of scientific research, and demonstrates that the community is ready and willing to take on that role."

PLoS ONE has made a powerful—and quick—change in scientific publishing, which is a conventional industry, says Peter Jerram, chief executive officer of PLoS. "It's a testament to the idea," he says. "If you only look at how rigorous the science is and whether the conclusions are supported by the data, then a lot of great science gets out there more quickly, including some that wouldn't otherwise see the light of day."

The model represents something completely new and has attracted staff from more traditional publishers, such as Peter Binfield. In early 2008, Binfield succeeded Chris Surridge as managing editor of PLoS ONE. Binfield had been a career publisher who had always worked with the traditional subscription model. While he was one of the initial PLoS ONE skeptics, he felt Open Access was a better way to accelerate advancement in science and he very quickly became a fan of the journal.

"It seemed self-evident to me that this was the future of academic publishing," says Binfield.

It was groundbreaking to establish a journal that would publish first and only then figure out impact. With PLoS ONE, the author didn't get kudos or a badge of honor for being accepted to the journal. Rather, in this model the reader would make the judgment call as to how important the research was, from their unique vantage point.

The PLoS ONE process is more efficient and transparent than the traditional, subjective journal peer review process. "Not asking the impact question makes it a cleaner and more objective review," says Binfield.

And, contrary to early concerns that anything could make its way onto PLoS ONE, significant filters were established. On average, two external reviewers read every paper, and most are sent back to the author for revision. The journal applies stringent policies dealing with items such as disclosure requirements, data deposition standards, and ethical concerns. In addition, every paper has to pass a detailed technical checklist of over 40 items before even entering the peer review process. About 65-70 percent of submissions end up being published, says Binfield. Online tools are then used to evaluate, sort, and filter content after publication, not before.

There are approximately 10,000 publishers today, producing 25,000 journals with about 1.5 million articles per year. In an industry that has been slow to change, PLoS ONE is proving that new business models that don't charge subscription fees can survive—and thrive, says Binfield. In four years, this one journal has become the largest peer-reviewed journal in existence. On its current trajectory, PLoS ONE could be responsible for publishing fully 3 percent of the biomedical literature in 2012.

Looking ahead, Binfield sees the potential that, rather than having thousands of smaller journals, the vast majority of the world's literature could eventually be in as few as 100 journals, all with a similar profile to PLoS ONE. "It's moving very rapidly. It feels like a tipping point in the industry," he says.

The draw

Surveys of PLoS ONE authors help shed light on the journal's phenomenal success. The number one reason scientists submit is because it is open-access. They want their work to be freely accessible and widely available. The second draw is speed. Rather than waiting months or years to get a paper accepted in a traditional journal, PLoS ONE gets researchers' work out quickly. Finally, the quality of the PLoS brand is an important factor and the objective peer review is also appreciated, says Binfield.

Gary Ward, professor of microbiology and molecular genetics at the University of Vermont, who became Chair of the PLoS board of directors in January, just had his first paper accepted to PLoS ONE.

He and other researchers welcome the relief that PLoS ONE provides from the "treadmill" of submitting and resubmitting to traditional journals, says Ward.

"I love the concept of eliminating this huge waste of time by simply removing subjective evaluations of importance from the review process," says Ward. "If the paper is well-written and the conclusions don't overreach, then let the community decide the impact."

Ward calls the PLoS ONE approach the ultimate in "crowd sourcing" that also contains rigorous review—just a different kind of peer review.

PLoS ONE features original research from all disciplines within science and medicine (although most submissions are in life and health sciences). By providing an interdisciplinary platform, the hope is to facilitate discovery of connections between papers and subject areas. "The fact that you can read around the edges of a field is a big deal," says Binfield. "PLoS ONE forms a home for any article; it no longer has to have a journal of its own."

Behind the success

The concept of publishing without having to battle the system was the big driver behind the explosive growth of PLoS ONE. The trust of the PLoS brand also helped, says Patterson. Of course, there is the human capital that has had to expand to keep up with the rapidly growing journal.

Handling 2,000 submissions a month and publishing 60 articles daily takes a substantial group of people. The paid staff on the journal, which handles the checks and balances of the system, has increased to handle the growing number of submissions. There are about 35 full-time equivalents, with some positions contracted out. Then there are 1,700 academic editors on the journal, individually handling each paper and finding peer reviewers so that every paper is appropriately reviewed.

"We have been up to the challenge; we've kept pace," says Patterson.

CEO Jerram says he is amazed at the dedication of the people who work for PLoS ONE and that has made a palpable difference in the journal's success. "There is a real passion and commitment there," he says.

Binfield says while the staff works hard and the work can be stressful, it is a mission-driven organization, and they are energized by what they are doing. "We feel like we are doing the right thing for the right reasons," he says.

The process has worked because the model scales with the volume of submissions: Every article adds more work, but also adds revenue. The publication fee for each published paper is $1,350, which is usually covered by grant money. Unlike a traditional journal, PLoS ONE allows researchers to publish papers of unlimited length, with full color throughout and containing any amount of supplemental material such as spreadsheets or videos. Occasionally authors take fee waivers, but about 90 percent of authors pay the full amount.

The goal of making PLoS self-sustaining was met last year. The organization was originally established with the help of foundations and outsider support, but as the suite of publications has grown to make PLoS self-sustaining, they have been able to develop additional innovations such as article-level metrics, PLoS Currents and PLoS Hubs.

The followers and the future

"The model is working beautifully. It's financially sustainable and there is increasing rapid growth. This is something science is really embracing," says Ward. "The competition is crazy not to go this way," says Ward. The mission of PLoS is to make as much of the literature open-access as possible, and to show how Open Access can transform the literature into a more powerful resource for education and research.

While PLoS ONE pioneered coverage of the whole of science, many who have adapted the model are using it for single subject areas, says Binfield. "We are encouraged and excited to see these clones launched," he says. "It validates that this model is here to stay … We can see the future path and the launch of these clones just cements it."

Will PLoS adopt the PLoS ONE model for its other journals?

Chairman of the Board Ward says that the history of PLoS, (which is based in San Francisco and Cambridge, England and is the world's largest not-for-profit open-access journal publisher) has always been one of an organization pushing the envelope. "We are constantly looking at the editorial structure, the business model," he says. However, once a journal is established, it is harder to make wholesales changes. Ward says PLoS will continue to consider what works best for all of its titles and the organization is committed to being innovative. "We want to keep PLoS on the cutting edge," says Ward.

A goal of PLoS is to help publishers move into Open Access and PLoS ONE is indeed a new model for publishing, says Jerram. In the future, he says there may be better ways to communicate science than through journals. The real power and promise of Open Access is to make scientific information and data not only able to be read, but also re-used. "Open Access is the enabler that makes other things possible," says Jerram.

Binfield envisions more and more journals following PLoS ONE's lead and he says that it is very exciting to see the transformations that are underway. "I come into work every day with the knowledge that I am helping to advance science by accelerating and improving the process of disseminating scientific results," he says. "It's an important thing to have the knowledge that what we are doing is making a big difference in the world."

by Caralee Adams

Impact Factors of Indian Science Journals in 2011

2011-06-30T16:35:00.001+05:30

Year	Impact Factor (IF)	Total Articles	Total Cites
2010	1.826	166	3169
2009	1.516	178	2812
2008	1.883	178	2458

Indian Journal of Medical Research

Year	Impact Factor (IF)	Total Articles	Total Cites
2010	1.494	77	414
2009	0.813	77	194
2008	0.358	77	58

Journal of Genetics

Year	Impact Factor (IF)	Total Articles	Total Cites
2010	1.888	60	1630
2009	1.956	82	1274
2008	1.703	82	1045

Journal of Biosciences

Year	Impact Factor (IF)	Total Articles	Total Cites
2010	0.824	58	696
2009	0.574	59	696
2008	0.579	59	603

Indian Journal of Biochemistry and Biophysics

Journal of Biosciences Impact Factor reversing

2011-06-30T16:19:00.001+05:30

Year	Impact Factor (IF)	Total Articles	Total Cites
2010	1.888	60	1630
2009	1.956	82	1274
2008	1.703	82	1045

PLoS ONE's 2010 Impact Factor is 4.411

2011-06-29T20:19:00.001+05:30

PLoS ONE received its 2010 journal impact factor today, 4.411, placing the open access journal in 12th spot among 85 Biology journals.

The open access journal, published by the Public Library of Science, has grown rapidly since its launch in December, 2006. In 2010, it published nearly 7,000 articles and became the largest scientific journal in the world. Based on this trajectory, the publisher predicts 12,000 published articles by the end of 2011.

PLoS ONE is based on a scalable publishing model with an editorial board of 1,300 volunteer academics. As an online-only publication, the growth of the journal is nearly limitless: The journal is purposefully interdisciplinary in nature, bases criteria for inclusion primarily on "sound methodology," not novelty, and pays for itself through individual article fees. At the 2011 SSP Annual Conference, PLoS ONE publisher, Peter Binfield, believes that we've entered the era of the "OA Mega Journal." According to his predictions, by 2016, 50% of all STM articles will be published by 100 of these mega journals.

The metaphor to describe this new publishing model could go both ways: For the cynical, PLoS ONE is an alien Blob that is bent on devouring the publishing landscape; for its supporters, it represents a successful model to be emulated — and emulated it has. In the last two years, many subscription publishers have launched PLoS ONE-like journals (SAGE Open, BMJ Open,Biology Open, and Open Biology, to name a few) into the growing market, promising similar services–fast publication, high-acceptance, and article-level metrics — at competing prices.

Expect several more entrants this year.

To continue reading this article by Phil Davis please visit The Scholarly Kitchen

'Indians could actually be refrectory to the German E. coli strain' - Lothar Wieler

2011-06-08T23:28:00.004+05:30

My friend, Lothar Wieler, called this evening from Berlin and informed that they are now tracing the history of the bacteria, and will be out in the field going after cows, trash and soil to know the natural descent of the outbreak strain! so that its kinships are established. This is now the natural scientific way out as the latest analysis released by the BJI indicates that the two German strains (01-09591 originally isolated in 2001 and TY2482 from the 2011 outbreak) have clonal profiles for all 12 virulence/fitness genes and 7 MLST housekeeping genes (100% identity). However, at some point over this 10-year period, the new 2011 outbreak strain might have accumulated mutations/plasmids that conferred ability to resist many additional types of antibiotics. In simple words, the source of the German EHEC outbreak is home grown - their own EAEC strain from a 2001 outbreak.

I am hopeful Lothar and his team will succeed in their efforts. We discussed also the possibility that the new isolate being interoaggregative could become pandemic if certain patients turn chronic carriers and could take the bug with them on travel routes. The EU therefore should be proactive on containment of this outbreak within the boundaries of Germany. Lothar, (who is always surprised and amused on visibly unhygienic conditions in certain parts of India, such as heaps of garbage, open drains etc., and apparently healthy people with no institutionalized outbreaks! ) then laughed loud to say Indians could actually be immune to the EHEC like strains - so no worries!! and, I agree. So sometimes the cow dung around us could be 'auspicious' in many ways!

Crowdsourcing annotation of the German (monster-) E. coli (STEC O104:H4)?

2011-06-06T14:08:00.001+05:30

By Mariam Rizkallah - Open Source Pharmacist

(added by Niyaz Ahmed ->> Gut Pathogens will consider to publish any such annotation study on priority!)

As soon as Beijing Genomics Institute has finished sequencing the E. coli strain that is responsible for the outbreak in Europe, BGI made the "draft assembly" available for download. I didn't know the difference between a draft and the elegant assembled genome I used to work on while annotating phage capsid proteins, but I did believe that this outbreak idea is a phage thing, you know, "Cherchez le phage!" I wanted to annotate this E. coli.

I suggested to Dr. Aziz that this "genome sequence" may benefit from RAST (Rapid Annotation using Subsystem Technology – http://rast.nmpdr.org), the tool developed by Dr. Edwards' Lab and ANL for rapid and accurate annotation of bacterial and archaeal genomes. Dr. Aziz replied "Then what are you waiting for? Upload it to RAST". Then he told me how the draft is in "FASTQ" format, a machine output format that can not be an input for RAST (and for Real-Time Metagenomics.web in particular http://edwards.sdsu.edu/rtmg/). Dr. Aziz explained to me that each "run/genome fragment" will be treated as metagenome, that's why I should use RTMg.

Step1: Convert sequences from fastq to fasta: I searched the web for the problem, then I found this one-line program in Perl by Robert Schmeider, PhD student at Dr. Edwards' lab on his lab blog. I am very grateful, Robert!

Step2: Uploading the draft in fasta format to RTMg as separate "runs". I don't know if it's the right measure, or I should've collected all "runs" in one big fasta file and let RTMg process them.

Step3:I made use of the "tab-separated" output of RTMg and saved it to a spreadsheet (I do apologize, but the spreadsheet on Google is not viewable, please download it to edit it). I saved the results sorted by "function" and by "3-level subsystem".

Step4: ??? I don't know really. I do want to make use of RTMg data, but I don't know where to start. I guess aligning the 5 runs as well as the strain vs other E. coli strains will be the answer. Community will take STEC O104:H4 down sooner than "it thought".

I quote Dr. Aziz here:

"RTMg is mainly a tool for metagenomics analysis, and it treats every sequence read as an environmental gene tag (EGT) or simply as an independent fragment. It cannot be really used to explain a genome; however, it gives a really quick ideaof what each sequence looks like, of the ratio of different genes, of the most frequent protein-encoding genes in this strain, the density of phage proteins (for example, you can write a script to count the word phage and calculate its percent to the overall genome), etc.

There are two main things needed though before this: 1) is to clean up the sequence fragments; 2) is to assemble them (using, for example, NEWBLER). To check the sequence and clean it up check: Prinseq and Tagcleaner then re-run. Another way to benefit from RTMg would be to compare that strain with another one sequenced exactly the same way, which is not relevant here."

Naked dance of E. coli in the land of Theodor Escherich and Robert Koch

2011-05-27T19:52:00.003+05:30

I arrived in Berlin and Jena on a collaborative mission amidst the EHEC infection epidemic developing in Germany. My German cooperation partner, Lothar Wieler, an expert of pathogenic E. coli is busy all days giving interviews and briefings to the charged German media. It is very strange and unexpected that the severity of the infection by enterohaemorrhagic E. coli (EHEC) could be so deadly to kill half a dozen people in a highly developed setting such as Germany - the land of Robert Koch, Escherich and Loeffler. Due to a strange serotype, many labs could not identify the organism involved, while 5 cases succumbed already. The beauty, however, is that the Germans could isolate the bug and sequence entire genome of the underlying EHEC in just 2 days! Now they have all the high-tech arsenal for diagnostic and the cases are being reported left and right, exceeding nearly 300. It is said the bacteria are ESBL producers and are hitting women harder than men. The origin is unclear but Spanish cucumbers are blamed amidst arguments and counter arguments passed on the source of infection. I think it will be important now to see how Germany (a country bestowed with age old knowledge and institutions specializing in microbiology and a very strong healthcare setup with a perfect antibiotic policy) deals with this scourge in time to remain an acclaimed champion of microbiology and hygiene. My stomach is making strange -- gur gur gud --- (sounds) when I write this blog although I am not such a big fan of salads! I think I got in to psychosis of EHEC myself, imagine the psyche of the public at large! and that of babes who only eat salads to keep slim! I hope all will be well and good sense prevails - Amen.

New in Gut Pathogens: Metagenome of the gut of a malnourished child

2011-05-21T11:37:00.001+05:30

Sen Gupta et al., Gut Pathogens 2011, 3:7doi:10.1186/1757-4749-3-7 (Access free full paper here)

Background

Malnutrition, a major health problem, affects a significant proportion of preschool children in developing countries. The devastating consequences of malnutrition include diarrhoea, malabsorption, increased intestinal permeability and suboptimal immune response etc. Nutritional interventions and dietary solutions have not been effective for treatment of malnutrition till date. Metagenomic procedures allow one to access the complex cross-talk between the gut and its microbial flora and understand how a different community composition affects various states of human health. In this study, a metagenomic approach was employed for analysing the differences between gut microbial communities obtained from a malnourished and an apparently healthy child.

Results

Our results indicate that the malnourished child gut has an abundance of enteric pathogens which are known to cause intestinal inflammation resulting in malabsorption of nutrients. We also identified a few functional sub-systems from these pathogens, which probably impact the overall metabolic capabilities of the malnourished child gut.

Conclusion

The present study comprehensively characterizes the microbial community resident in the gut of a malnourished child. This study has attempted to extend the understanding of the basis of malnutrition beyond nutrition deprivation.

PLoS ONE: How Citation Boosts Promote Scientific Paradigm Shifts and Nobel Prizes

2011-05-06T13:42:00.001+05:30

Nobel Prizes are commonly seen to be among the most prestigious achievements of our times. Based on mining several million citations, we quantitatively analyze the processes driving paradigm shifts in science. We find that groundbreaking discoveries of Nobel Prize Laureates and other famous scientists are not only acknowledged by many citations of their landmark papers. Surprisingly, they also boost the citation rates of their previous publications. Given that innovations must outcompete the rich-gets-richer effect for scientific citations, it turns out that they can make their way only through citation cascades. A quantitative analysis reveals how and why they happen. Science appears to behave like a self-organized critical system, in which citation cascades of all sizes occur, from continuous scientific progress all the way up to scientific revolutions, which change the way we see our world. Measuring the "boosting effect" of landmark papers, our analysis reveals how new ideas and new players can make their way and finally triumph in a world dominated by established paradigms. The underlying "boost factor" is also useful to discover scientific breakthroughs and talents much earlier than through classical citation analysis, which by now has become a widespread method to measure scientific excellence, influencing scientific careers and the distribution of research funds. Our findings reveal patterns of collective social behavior, which are also interesting from an attention economics perspective. Understanding the origin of scientific authority may therefore ultimately help to explain how social influence comes about and why the value of goods depends so strongly on the attention they attract.

Mazloumian A, Eom Y-H, Helbing D, Lozano S, Fortunato S (2011) How Citation Boosts Promote Scientific Paradigm Shifts and Nobel Prizes. PLoS ONE 6(5): e18975. doi:10.1371/journal.pone.0018975 Read Free Full Text

Latent TB of Indians worries UK: some issues to ponder

2011-04-23T21:21:00.001+05:30

Diagnosis and treatment of latent tuberculosis are both difficult and uneconomical. The Monteux test based on skin reaction to mycobacterial protein components is seriously cross-reactive and could produce false positive and false negative results in case of 70% of the Indians. Similar difficulties could be encountered with Interferon – gamma test. The reasons for this diagnostic failure vis-à-vis latent TB could be due to many immunological confounders such as the past vaccination (with BCG) and exposure to environmental mycobacteria (there are 300 different saprophytic mycobacterial species which impact our immune system exposure). Moreover, other chronic pathogens such as Helicobacter pylori which inflict nearly 80% of all Indians in its benign form could also interfere with immunological testing for latent tuberculosis due to their bystander effects.

It is in-correct ethically to impose prophylactic therapy upon individuals who have no clinical disease and who might never get it in their lifetime. Anti TB drugs are hepatotoxic in long course and low dosage or short course could select out drug resistant bacteria. In my opinion, treatment of millions of putative, latent TB cases will inflict the government exchequer enormously and only the pharma companies who are pushing for a few years for the treatment of latent TB as a standard regimen will only benefit from it. It will shift focus from the management of clinically ailing patients which in itself is a mammoth task for a high burden country like India

As far as the India centric Lancet article on latent TB detection in prospective immigrants in the UK is concerned, it is merely sensationalization of the issue. Now a days, in the infection epidemiology arena, it has become a fashion in the West to project India as a source of infection. There could be some truth in the scenario given our high infection burden, however, the story is worst in case of countries of the world that are dubiously known for their highly virulent MDR and XDR strains such as South Africa, Russia and the countries of the former USSR. In fact UK should happily give immigrant status to Indians because it is proved already that the Indian strains of Mycobacteria are of ancestral type (genotype TbD1+) and the treatment success rates of up to 95% have been recorded under the DOTS program in India. These strains are theorized as 'shy' in terms of dissemination as compared to some of the very aggressive genotypes such as Beijing, Africa and Haarlem. India has so far not experienced any institutionalized outbreak as against the famous fatal outbreaks of New York and Kwazulu Natal. That means the Indian strains are less aggressive and controllable. Indians enjoy a distinct natural protection from latent TB due to the facts that their genetic makeup is different, their strains are different and their immune system is already primed due to a saprophytic antigenic background and/or by Helicobacter infection. UK should therefore not be worried for Indians. They should in fact be worried about the Pakistanis and Sri Lankans who do not have the ancestral strains of TB bacteria (TbD1+) in their countries and could proceed to full blown TB more rapidly than Indians. It will be interesting if the Health Protection Agency of the UK comes up with clear statistics on how many Indians, Pakistanis, and Sri Lankans have progressed to full blown TB per year after their arrival in UK and how many of them were infected with which type of strain and whether or not they were diabetics or living with HIV/AIDS.

There is however, one important angle to the conversion of Indians from latent to open TB cases while in the UK – it is Vitamin D, an important determinant of resistance or susceptibility to TB and which is synthesized naturally by the body when exposed to sunlight. Due to poor sunlight in UK, it is possible that deficiency of Vitamin D might build up especially in cases of vegetarian people who may not be able to maintain their dietary intake of vitamin D. UK Immigrant authorities should therefore, pay more attention to the food and lifestyle of these immigrants so that they keep their immune system stepped –up as they do back home in India.

Deccan Chronicle: UK blames India for rise in TB cases

2011-04-23T09:56:00.001+05:30

Hyderabad, April 23, 2011. Health experts from Hyderabad have taken strong exception to the charge that Indians harbouring tuberculosis germ in its latent form are responsible for the spread of TB in the United Kingdom.The UK is regarded as the TB capital of the world, and a team of UK-based researchers is blaming the Indians for it. This is the third serious medical allegation against India by Lancet, a UK-based peer reviewed medical journal, in the last eight months. Two earlier studies by Lancet too had angered the medical and health authorities in the country. They had forced the Indian Council of Medical Research to take up a comprehensive research on the superbug that was wrongly named New Delhi metallo beta lactamase. The present Lancet study is on tuberculosis allegedly being spread by Indians visiting the UK. "The charge is baseless and deliberate attempt to defame India. The Lancet studies have not conclusively proved that India or Indians are responsible" said the senior biologist, Dr Duggaraju Srinivas Rao. "The Lancet team wants all Indians visiting the UK to be screened for latent tuberculosis though tests are not always accurate," said the senior microbial scientist, Dr Niyaz Ahmed. By Syed Akbar - Science and Technology Correspondent, DC and Asian Age.

Well - Its not the case always. It is possible that resistance genes are abundant in normal intestinal flora in Indians

2011-04-17T09:52:00.001+05:30

New Delhi Superbug is no threat to Europe: Deccan Chronicle

2011-04-16T12:48:00.000+05:30

Experts question the sampling strategy of the UK superbug study: The Asian Age/Deccan Chronicle

2011-04-13T20:06:00.000+05:30

World Health Day: Drug resistance - No action today, No cure tomorrow

2011-04-07T09:17:00.002+05:30

The joy of handling peer review of 200 articles

2011-03-23T22:48:00.004+05:30

Below is my 200th editorial assignment at PLoS ONE which went live recently. On this occasion, I am grateful to the management, in house editors and staff of PLoS ONE for entrusting and reposing their confidence in me, and for the authors who did not loose patience, and for hundreds of colleagues who reviewed these manuscripts on more than one occasion and assisted me in keeping to the time frames. All the articles handled by me at ONE can be accessed here. Below is the 200th article signed off by me as an Academic Editor.

Molecular Analysis of Microbial Communities in Endotracheal Tube Biofilms

Cairns S, Thomas JG, Hooper SJ, Wise MP, Frost PJ, et al. (2011) Molecular Analysis of Microbial Communities in Endotracheal Tube Biofilms. PLoS ONE 6(3): e14759. doi:10.1371/journal.pone.0014759

Background

Ventilator-associated pneumonia is the most prevalent acquired infection of patients on intensive care units and is associated with considerable morbidity and mortality. Evidence suggests that an improved understanding of the composition of the biofilm communities that form on endotracheal tubes may result in the development of improved preventative strategies for ventilator-associated pneumonia.

Methodology/Principal Findings

The aim of this study was to characterise microbial biofilms on the inner luminal surface of extubated endotracheal tubes from ICU patients using PCR and molecular profiling. Twenty-four endotracheal tubes were obtained from twenty mechanically ventilated patients. Denaturing gradient gel electrophoresis (DGGE) profiling of 16S rRNA gene amplicons was used to assess the diversity of the bacterial population, together with species specific PCR of key marker oral microorganisms and a quantitative assessment of culturable aerobic bacteria. Analysis of culturable aerobic bacteria revealed a range of colonisation from no growth to 2.1×10⁸ colony forming units (cfu)/cm² of endotracheal tube (mean 1.4×10⁷ cfu/cm²). PCR targeting of specific bacterial species detected the oral bacteria Streptococcus mutans (n = 5) and Porphyromonas gingivalis (n = 5). DGGE profiling of the endotracheal biofilms revealed complex banding patterns containing between 3 and 22 (mean 6) bands per tube, thus demonstrating the marked complexity of the constituent biofilms. Significant inter-patient diversity was evident. The number of DGGE bands detected was not related to total viable microbial counts or the duration of intubation.

Conclusions/Significance

Molecular profiling using DGGE demonstrated considerable biofilm compositional complexity and inter-patient diversity and provides a rapid method for the further study of biofilm composition in longitudinal and interventional studies. The presence of oral microorganisms in endotracheal tube biofilms suggests that these may be important in biofilm development and may provide a therapeutic target for the prevention of ventilator-associated pneumonia.

The PLoS ONE tale of a Phantom limb!

2011-03-05T09:46:00.002+05:30

Arvid Guterstam, Valeria I. Petkova and H. Henrik Ehrsson recently published a paper entitled, The Illusion of Owning a Third Arm. Their manuscript received media attention from: NPR, New York Times, Not Exactly Rocket Science, Times of India, and Scientific American.

Article summary:

Could it be possible that, in the not-so-distant future, we will be able to reshape the human body so as to have extra limbs? A third arm helping us out with the weekly shopping in the local grocery store, or an extra artificial limb assisting a paralysed person? Here we report a perceptual illusion in which a rubber right hand, placed beside the real hand in full view of the participant, is perceived as a supernumerary limb belonging to the participant's own body. This effect was supported by questionnaire data in conjunction with physiological evidence obtained from skin conductance responses when physically threatening either the rubber hand or the real one. In four well-controlled experiments, we demonstrate the minimal required conditions for the elicitation of this "supernumerary hand illusion". In the fifth, and final experiment, we show that the illusion reported here is qualitatively different from the traditional rubber hand illusion as it is characterised by less disownership of the real hand and a stronger feeling of having two right hands. These results suggest that the artificial hand 'borrows' some of the multisensory processes that represent the real hand, leading to duplication of touch and ownership of two right arms. This work represents a major advance because it challenges the traditional view of the gross morphology of the human body as a fundamental constraint on what we can come to experience as our physical self, by showing that the body representation can easily be updated to incorporate an additional limb.

Looking for a paper that has been covered by the media? Try out PLoS ONE search functionality.

PLoS ONE at BBC: Did ancient Britons 'drank from skulls'?

2011-02-28T19:37:00.003+05:30

Earliest Directly-Dated Human Skull-Cups

Background

The use of human braincases as drinking cups and containers has extensive historic and ethnographic documentation, but archaeological examples are extremely rare. In the Upper Palaeolithic of western Europe, cut-marked and broken human bones are widespread in the Magdalenian (~15 to 12,000 years BP) and skull-cup preparation is an element of this tradition.

Principal Findings

Here we describe the post-mortem processing of human heads at the Upper Palaeolithic site of Gough's Cave (Somerset, England) and identify a range of modifications associated with the production of skull-cups. New analyses of human remains from Gough's Cave demonstrate the skilled post-mortem manipulation of human bodies. Results of the research suggest the processing of cadavers for the consumption of body tissues (bone marrow), accompanied by meticulous shaping of cranial vaults. The distribution of cut-marks and percussion features indicates that the skulls were scrupulously 'cleaned' of any soft tissues, and subsequently modified by controlled removal of the facial region and breakage of the cranial base along a sub-horizontal plane. The vaults were also ‘retouched’, possibly to make the broken edges more regular. This manipulation suggests the shaping of skulls to produce skull-cups.

Conclusions

Three skull-cups have been identified amongst the human bones from Gough's Cave. New ultrafiltered radiocarbon determinations provide direct dates of about 14,700 cal BP, making these the oldest directly dated skull-cups and the only examples known from the British Isles.

Citation: Bello SM, Parfitt SA, Stringer CB (2011) Earliest Directly-Dated Human Skull-Cups. PLoS ONE 6(2): e17026. doi:10.1371/journal.pone.0017026

Read Media coverage at BBC: http://www.bbc.co.uk/news/science-environment-12478115

Watch BBC report below.

Remembering CV Raman and his Raman Effect: India's National Science Day

2011-02-28T19:12:00.001+05:30

Each year, we Indians, celebrate February 28 as National Science Day to commemorate the discovery of the Raman effect in 1928 and to remember the hard work of CV Raman, the great son of India who won the first Nobel for India in Sciences. India desperately need continue the legacy of Sir Raman. Is young India serious of taking that forward?

New journal “Nature ONE” launched: that means PLoS ONE rocks at the end!

2011-02-22T17:48:00.001+05:30

New journal “Nature ONE” launched

Exciting in PLoS ONE: Chernobyl Birds Have Smaller Brains

2011-02-19T10:31:00.002+05:30

'Animals living in areas contaminated by radioactive material from Chernobyl suffer from increased oxidative stress and low levels of antioxidants. Therefore, normal development of the nervous system is jeopardized as reflected by high frequencies of developmental errors, reduced brain size and impaired cognitive abilities in humans. Alternatively, associations between psychological effects and radiation have been attributed to post-traumatic stress in humans.

Here we used an extensive sample of 550 birds belonging to 48 species to test the prediction that even in the absence of post-traumatic stress, there is a negative association between relative brain size and level of background radiation. We found a negative association between brain size as reflected by external head volume and level of background radiation, independent of structural body size and body mass. The observed reduction in brain size in relation to background radiation amounted to 5% across the range of almost a factor 5,000 in radiation level. Species differed significantly in reduction in brain size with increasing background radiation, and brain size was the only morphological character that showed a negative relationship with radiation. Brain size was significantly smaller in yearlings than in older individuals.

Low dose radiation can have significant effects on normal brain development as reflected by brain size and therefore potentially cognitive ability. The fact that brain size was smaller in yearlings than in older individuals implies that there was significant directional selection on brain size with individuals with larger brains experiencing a viability advantage'.

Read full story here: Møller AP, Bonisoli-Alquati A, Rudolfsen G, Mousseau TA (2011) Chernobyl Birds Have Smaller Brains. PLoS ONE 6(2): e16862. doi:10.1371/journal.pone.0016862

Read related coverage at BBC: http://news.bbc.co.uk/earth/hi/earth_news/newsid_9387000/9387395.stm

PLoS ONE gains further ground: PLoS author survey 2010

2011-02-12T11:46:00.000+05:30

According to PLoS Author Survey 2010, one of the more explicit observations was the finding that PLoS ONE gained further ground as an attractive venue to publish primary research. In the 2009 survey 23% of authors preferred PLoS ONE as first port to dock at, and in the 2010 data this figure had increased to 37%.

Hot in PLoS ONE: Added Value Measures in Education Show Genetic as Well as Environmental Influence

2011-02-12T10:55:00.001+05:30

Does achievement independent of ability or previous attainment provide a purer measure of the added value of school? In a study of 4000 pairs of 12-year-old twins in the UK, we measured achievement with year-long teacher assessments as well as tests. Raw achievement shows moderate heritability (about 50%) and modest shared environmental influences (25%). Unexpectedly, we show that for indices of the added value of school, genetic influences remain moderate (around 50%), and the shared (school) environment is less important (about 12%). The pervasiveness of genetic influence in how and how much children learn is compatible with an active view of learning in which children create their own educational experiences in part on the basis of their genetic propensities. [Read the full report]

Haworth CMA, Asbury K, Dale PS, Plomin R (2011) Added Value Measures in Education Show Genetic as Well as Environmental Influence. PLoS ONE 6(2): e16006. doi:10.1371/journal.pone.0016006

Read the coverage of this article at BBC: http://www.bbc.co.uk/news/education-12339798

Read New in Gut Pathogens: Acne vulgaris, probiotics and the gut-brain-skin axis - back to the future?

2011-02-01T23:23:00.000+05:30

Over 70 years have passed since dermatologists John H. Stokes and Donald M. Pillsbury first proposed a gastrointestinal mechanism for the overlap between depression, anxiety and skin conditions such as acne. Stokes and Pillsbury hypothesized that emotional states might alter the normal intestinal microflora, increase intestinal permeability and contribute to systemic inflammation. Among the remedies advocated by Stokes and Pillsbury were Lactobacillus acidophilus cultures. Many aspects of this gut-brain-skin unifying theory have recently been validated. The ability of the gut microbiota and oral probiotics to influence systemic inflammation, oxidative stress, glycemic control, tissue lipid content and even mood itself, may have important implications in acne. The intestinal microflora may also provide a twist to the developing diet and acne research. Here we provide a historical perspective to the contemporary investigations and clinical implications of the gut-brain-skin connection in acne [Whitney P Bowe and Alan C Logan, 2011].
Free full text: http://www.gutpathogens.com/content/3/1/1/

Pioneers of Malaysian goodness in PLoS ONE: Mohamed Rais Mustafa

2010-12-10T17:23:00.000+05:30

Achoui M, Appleton D, Abdulla MA, Awang K, Mohd MA, et al. (2010) In Vitro and In Vivo Anti-Inflammatory Activity of 17-O-Acetylacuminolide through the Inhibition of Cytokines, NF-κB Translocation and IKKβ Activity. PLoS ONE 5(12): e15105. doi:10.1371/journal.pone.0015105

17-O-acetylacuminolide (AA), a diterpenoid labdane, was isolated for the first time from the plant species Neouvaria foetida. The anti-inflammatory effects of this compound were studied both in vitro and in vivo.
Plant extracts were initially tested against LPS-stimulated release of tumor necrosis factor alpha (TNF-α) from murine macrophages (RAW264.7 cells). Based on bioassay-guided fractionation, the active compound was identified as AA. AA was tested for its ability to reduce nitric oxide (NO) production, and the inducible nitric oxide synthase (iNOS) expression. The inhibition of a panel of inflammatory cytokines (TNF, IL-1β, IL-6, KC, and GM-CSF) by AA was assessed at the expression and the mRNA levels. Moreover, the effect of AA on the translocation of the transcription factor nuclear factor kappa B (NF-κB) was evaluated in LPS-stimulated RAW264.7 cells and in TNF-stimulated L929 cells. Subsequently, AA was tested in the inhibitor of NF-κB kinase beta (IKKβ) activity assay. Lastly, the anti-inflammatory activity of AA in vivo was evaluated by testing TNF production in LPS-stimulated Balb/c mice.
AA effectively inhibited TNF-α release with an IC₅₀ of 2.7 µg/mL. Moreover, AA significantly inhibited both NO production and iNOS expression. It significantly and dose-dependently inhibited TNF and IL-1β proteins and mRNA expression; as well as IL-6 and KC proteins. Additionally, AA prevented the translocation of NF-κB in both cell lines; suggesting that it is acting at a post receptor level. This was confirmed by AA's ability to inhibit IKKβ activity, a kinase responsible for activating NF-κB, hence providing an insight on AA's mechanism of action. Finally, AA significantly reduced TNF production in vivo.
This study presents the potential utilization of this compound, as a lead for the development of an anti-inflammatory drug.
--------------
Professor Rais Mustafa (in picture) is a smiling, calm person who has the responsibility of being the Deputy Dean (Research) of the Medical Faculty at the UM Kuala Lumpur. Professor Rais was recently 'baptized' by us to get his research showcased in PLoS ONE! His paper published in PLoS ONE just a few days ago has already put him at an advantage of being at the forefront of the proposed 'International Network of Excellence on goodness of Malaysian natural compounds'.

The art of giving: Azim Premji shows the way!

2010-12-04T21:44:00.001+05:30

Click on the latest Forbes List of Top 10 Billionaires in the world and there are two Indian names, both within the top five. Now do the same with the list of top 10 philanthropists in the world and not a single Indian name emerges! Why? What explains this huge disconnect between wealth and giving? Why are Indians more niggardly when it comes to parting with their wealth? One reason could be cultural. We tend to be much more inward-looking and family-oriented than our western counterparts, notwithstanding the Vasudhaiva Kutumbakam (the world is one family) worldview that many Indians profess. Another could be that many of the newer Indian billionaires are yet to get comfortable with their wealth. And a third, no less important, could be our unimaginative tax policies that almost dissuade charitable donations. In a rational world, you would expect those who have more to give more, even if it was Karl Marx, the avowed enemy of capitalism who said, 'from each according to his ability … Those whom fortune has favoured must be more willing to share their wealth with those less privileged. That has been the guiding philosophy of many American philanthropists who set up some of its great universities. But not in India, or so it seemed! Till now when, thanks to an astoundingly generous act from Azim Premji, chairman, Wipro Foundation, an Indian is all set to make it to the list of top philanthropists in the world. Compare the size of Premji's endowment (approx $2 billion) with the average $ 4.1 billion given by top 50 US philanthropists last year (according to the Chronicle of Philanthropy) and the scale of his generosity is manifest. The Azim Premji Foundation has been engaged in improving the quality of schooling in Karnataka and with this latest endowment should now be able to contribute even more. Admittedly, it may be difficult for many of India's corporate leaders to match Premji's generosity, though it is worth noting that the top donors in the US last year Stanley and Fiona Druckenmiller — are not the richest. But the good thing is, over the years, there has definitely been more giving than in the past. Now with Premji showing the way, will others follow? And will tax policy foster the culture of giving to advance the collective good? (in syndication with - The economic times)

The beauty of Mathematics!

2010-11-06T11:37:00.001+05:30

1 x 8 + 1 = 9

12 x 8 + 2 = 98

123 x 8 + 3 = 987

1234 x 8 + 4 = 9876

12345 x 8 + 5 = 98765

123456 x 8 + 6 = 987654

1234567 x 8 + 7 = 9876543

12345678 x 8 + 8 = 98765432

123456789 x 8 + 9 = 987654321

1 x 9 + 2 = 11

12 x 9 + 3 = 111

123 x 9 + 4 = 1111

1234 x 9 + 5 = 11111

12345 x 9 + 6 = 111111

123456 x 9 + 7 = 1111111

1234567 x 9 + 8 = 11111111

12345678 x 9 + 9 = 111111111

123456789 x 9 +10= 1111111111

9 x 9 + 7 = 88

98 x 9 + 6 = 888

987 x 9 + 5 = 8888

9876 x 9 + 4 = 88888

98765 x 9 + 3 = 888888

987654 x 9 + 2 = 8888888

9876543 x 9 + 1 = 88888888

98765432 x 9 + 0 = 888888888

Brilliant, isn't it?

And look at this symmetry:

1 x 1 = 1

11 x 11 = 121

111 x 111 = 12321

1111 x 1111 = 1234321

11111 x 11111 = 123454321

111111 x 111111 = 12345654321

1111111 x 1111111 = 1234567654321

11111111 x 11111111 = 123456787654321

111111111 x 111111111 = 12345678987654321

Now, take a look at this...

101%

From a strictly mathematical viewpoint:

What Equals 100%?

What does it mean to give MORE than 100%?

Ever wondered about those people who say they are giving more than 100%?

We have all been in situations where someone wants you to GIVE OVER 100%.

How about ACHIEVING 101%?

What equals 100% in life?

Here's a little mathematical formula that might help answer these questions:

If:

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

is represented as:

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26.

then:

H-A-R-D-W-O- R- K

8+1+18+4+23+ 15+18+11 = 98%

and:

K-N-O-W-L-E- D-G-E

11+14+15+23+ 12+5+4+7+ 5 = 96%

but:

A-T-T-I-T-U- D-E

1+20+20+9+20+ 21+4+5 = 100%

THEN, look how far the love of God will take you:

L-O-V-E-O-F- G-O-D

12+15+22+5+15+ 6+7+15+4 = 101%

Therefore, one can conclude with mathematical certainty that:

While Hard Work and Knowledge will get you close, and Attitude will get you there, It's the Love of God that will put you over the top!

Biodiversity on Broadway - Enigmatic Diversity of the Societies of Ants (Formicidae) on the Streets of New York City

2010-10-07T22:10:00.000+05:30

'Each year, a larger proportion of the Earth's surface is urbanized, and a larger proportion of the people on Earth lives in those urban areas. The everyday nature, however, that humans encounter in cities remains poorly understood. Here, we consider perhaps the most urban green habitat, street medians. We sampled ants from forty-four medians along three boulevards in New York City and examined how median properties affect the abundance and species richness of native and introduced ants found on them. Ant species richness varied among streets and increased with area but was independent of the other median attributes measured. Ant assemblages were highly nested, with three numerically dominant species present at all medians and additional species present at a subset of medians. The most common ant species were the introduced Pavement ant (Tetramorium caespitum) and the native Thief ant (Solenopsis molesta) and Cornfield ant (Lasius neoniger). The common introduced species on the medians responded differently to natural and disturbed elements of medians. Tetramorium caespitum was most abundant in small medians, with the greatest edge/area ratio, particularly if those medians had few trees, whereas Nylanderia flavipes was most abundant in the largest medians, particularly if they had more trees. Many of the species encountered in Manhattan were similar to those found in other large North American cities, such that a relatively small subset of ant species probably represent most of the encounters humans have with ants in North America'.

Read this article for free here: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013222

Dr Harald Labischinski tribute

2010-10-05T22:07:00.001+05:30

We are very sorry to hear that Harald Labischinski, Faculty Member for Pharmacology @ Faculty of 1000, former CEO of MerLion Pharmaceuticals and member of the ICAAC Program Committee, has sadly died. Dr Labischinski was a great asset to anti-infective research throughout his distinguished career and was strongly involved in the development of a number of significant anti-infective programs. Beyond his retirement, he continued to follow his passion for drug research and provided invaluable help and support to several companies in drug discovery and development, as well as being a committed and passionate teacher at the Free University of Berlin. His contribution to the field will be greatly missed.

Rhesus Monkeys (Macaca mulatta) Do Recognize Themselves in the Mirror: Implications for the Evolution of Self-Recognition

2010-10-04T23:48:00.001+05:30

Rajala AZ, Reininger KR, Lancaster KM, Populin LC (2010) Rhesus Monkeys (Macaca mulatta) Do Recognize Themselves in the Mirror: Implications for the Evolution of Self-Recognition. PLoS ONE 5(9): e12865. doi:10.1371/journal.pone.0012865

Self-recognition in front of a mirror is used as an indicator of self-awareness. Along with humans, some chimpanzees and orangutans have been shown to be self-aware using the mark test. Monkeys are conspicuously absent from this list because they fail the mark test and show persistent signs of social responses to mirrors despite prolonged exposure, which has been interpreted as evidence of a cognitive divide between hominoids and other species. In stark contrast with those reports, the rhesus monkeys in this study, who had been prepared for electrophysiological recordings with a head implant, showed consistent self-directed behaviors in front of the mirror and showed social responses that subsided quickly during the first experimental session. The self-directed behaviors, which were performed in front of the mirror and did not take place in its absence, included extensive observation of the implant and genital areas that cannot be observed directly without a mirror. We hypothesize that the head implant, a most salient mark, prompted the monkeys to overcome gaze aversion inhibition or lack of interest in order to look and examine themselves in front of the mirror. The results of this study demonstrate that rhesus monkeys do recognize themselves in the mirror and, therefore, have some form of self-awareness. Accordingly, instead of a cognitive divide, they support the notion of an evolutionary continuity of mental functions.

PLoS ONE: Fine-Scale Bacterial Beta Diversity within a Complex Ecosystem (Zodletone Spring, OK, USA): The Role of the Rare Biosphere

2010-09-09T23:00:00.001+05:30

by Mostafa El-Shahed and colleagues

Abstract: Background

The adaptation of pyrosequencing technologies for use in culture-independent diversity surveys allowed for deeper sampling of ecosystems of interest. One extremely well suited area of interest for pyrosequencing-based diversity surveys that has received surprisingly little attention so far, is examining fine scale (e.g. micrometer to millimeter) beta diversity in complex microbial ecosystems.

Methodology/Principal Findings

We examined the patterns of fine scale Beta diversity in four adjacent sediment samples (1mm apart) from the source of an anaerobic sulfide and sulfur rich spring (Zodletone spring) in southwestern Oklahoma, USA. Using pyrosequencing, a total of 292,130 16S rRNA gene sequences were obtained. The beta diversity patterns within the four datasets were examined using various qualitative and quantitative similarity indices. Low levels of Beta diversity (high similarity indices) were observed between the four samples at the phylum-level. However, at a putative species (OTU_0.03) level, higher levels of beta diversity (lower similarity indices) were observed. Further examination of beta diversity patterns within dominant and rare members of the community indicated that at the putative species level, beta diversity is much higher within rare members of the community. Finally, sub-classification of rare members of Zodletone spring community based on patterns of novelty and uniqueness, and further examination of fine scale beta diversity of each of these subgroups indicated that members of the community that are unique, but non novel showed the highest beta diversity within these subgroups of the rare biosphere.

Conclusions/Significance

The results demonstrate the occurrence of high inter-sample diversity within seemingly identical samples from a complex habitat. We reason that such unexpected diversity should be taken into consideration when exploring gamma diversity of various ecosystems, as well as planning for sequencing-intensive metagenomic surveys of highly complex ecosystems.

Read the open-access, full-text article here:
http://dx.plos.org/10.1371/journal.pone.0012414

Now the Indian probiotic trial: would it help prevent diarrhea in the poor?

2010-08-31T21:18:00.001+05:30

Are probiotics a feasible intervention for prevention of diarrhoea in the developing world?

N Hajela, GB Nair and NK Ganguly

Gut Pathogens 2010, 2:10doi:10.1186/1757-4749-2-10

With about 1.4 million of the just under 9 million child deaths attributed to diarrhoea in 2008 and 49% of them occurring in five countries namely, India, Nigeria, Democratic Republic of the Congo, Pakistan and China, there is an urgent need for interventions to prevent and control diarrhoeal diseases. Of the various interventions to prevent diarrhoea, probiotics offer potential. The past decade has witnessed the validation of their utility for the prevention, treatment and management of a variety of infective and non infective disorders. The most investigated field continues to remain infectious diarrhoea and compelling evidence comes from randomized placebo controlled trails. While results from these studies are encouraging, most of them reflect the outcomes of the developed world. Developing countries like India continue to struggle with nutritional and health challenges and bear the greatest burden of diarrhoea. A paucity of data from the developing countries limits the definite recommendation of probiotics. In these countries curd, often confused for a probiotic, is practiced as an integral part of the culture. While the nutritional benefits of these products cannot be understated, it is still uncertain whether these products can be classified as a probiotic. The emergence of probiotic foods which are scientifically validated for their efficacy and impart defined health benefits offer an excellent opportunity to improve public health. A recent randomized controlled trial conducted by the National Institute of Cholera and Enteric Diseases in Kolkata, India demonstrated a protective efficacy of 14% in preventing diarrhoea among children who received a probiotic. For the developing world, however, the vision for probiotics would mean a fundamental change in perception and developing a well-planned strategy to allow interventions like probiotics to permeate to impoverished settings, where the assault of micro organisms is on a daily basis. This would mean that probiotics be ingrained into the public health system without being seen as a medicine.

Read complete article here: http://www.gutpathogens.com/content/2/1/10/

Faculty of 1000’s most viewed top 10 evaluations: Evaluation of Aziz and Nizet, Sci Transl Med 2010 Jan 27 2(16):16ps4

2010-08-19T20:13:00.001+05:30

Pathogen Micro-evolution in High Resolution (see the evaluation at F1000)

This perspective by Aziz and Nizet stresses that key hypotheses regarding microbial strain evolution or virulence cannot be addressed through conventional genotyping methods that often do not offer enough resolution of minor changes between closely related strains, such as insertion, deletion and substitution polymorphisms. Just like siblings and identical twins having their own personalities and phenotypes due to genetic, epigenetic or environmental confounders, paired/clonal isolates of bacteria, even if genetically identical, have their own colonization traits and pathogenic potentials due to their 'variome'.

Previously, people used to 'characterize' and individualize strains and isolates of bacterial pathogens by means of genetic fingerprinting or DNA profiling. However, recent revelations based on whole genome sequencing have showed that any two strains, even if (seemingly clonal) could be dramatically different in their functional capabilities, owing mainly to the single nucleotide polymorphisms (SNPs). This article, thus, potentially brings about the importance of a 'variome' in understanding evolution of pathogens, rather than putting emphasis on the core genome. In our own experience, Helicobacter pylori serially isolated from a single patient over a decade were different in containing or losing as much as ~51 open reading frames (ORFs) when whole genomes were sequenced (N Ahmed, T Taylor, F Megraud, unpublished data). These isolates were previously shown to belong to only one parental strain and were clonal according to the randomly amplified polymorphic DNA (RAPD), and MLST based genotyping {1}. As suggested in this paper, genome-wide analyses of SNPs between paired strains isolated from the same patient, or between input vs. output strains generated in a suitable animal model, could reveal important genetic 'switch' mechanisms critical for survival, adaptation and invasion potentials of the bacterial pathogens.

References: {1} Prouzet-Mauléon et al. J Clin Microbiol 2005, 43:4237-41 [PMID:16081988].

Evaluated 10 Aug 2010

New at PLoS ONE: From Grazing Resistance to Pathogenesis: The Coincidental Evolution of Virulence Factors

2010-08-19T19:59:00.001+05:30

Sandrine Adiba et al., 2010. PLoS ONE 5(8): e11882. doi:10.1371/journal.pone.0011882

"If you happen to be stranded in a building, it's probably not the occasion to start setting fire to things. But this is perhaps what some bacteria do when they find themselves challenged inside a human; they cause then the diseases that are potentially fatal but not contagious. Loosing thus an opportunity to escape (transmission), they risk getting perished with their host. This seems like a ludicrous strategy but we're looking at it from the wrong perspective – our own. By analogy, we just suffer a collateral damage in an invisible war (caution: this is an oversimplification of the process!). Like all living things, bacteria have to protect themselves against predators such as protists (amoebae). Some microorganisms do so by turning their repertoire of certain genes on, and, by that, they transform them from passive victims into aggressive fighters. And by coincidence, these same adaptations make them more virulent (better survival advantage and colonization traits) in human bodies. We're just caught in the crossfire! " (in syndication with talkrational.org)

Read the abstract of Adiba et al., below:

To many pathogenic bacteria, human hosts are an evolutionary dead end. This begs the question what evolutionary forces have shaped their virulence traits. Why are these bacteria so virulent? The coincidental evolution hypothesis suggests that such virulence factors result from adaptation to other ecological niches. In particular, virulence traits in bacteria might result from selective pressure exerted by protozoan predator. Thus, grazing resistance may be an evolutionarily exaptation for bacterial pathogenicity.

This hypothesis was tested by subjecting a well characterized collection of 31 Escherichia coli strains (human commensal or extra-intestinal pathogenic) to grazing by the social haploid amoeba Dictyostelium discoideum. We then assessed how resistance to grazing correlates with some bacterial traits, such as the presence of virulence genes. Whatever the relative population size (bacteria/amoeba) for a non-pathogenic bacteria strain, D. discoideum was able to phagocytise, digest and grow. In contrast, a pathogenic bacterium strain killed D. discoideum above a certain bacteria/amoeba population size. A plating assay was then carried out using the E. coli collection faced to the grazing of D. discoideum. E. coli strains carrying virulence genes such as iroN, irp2, fyuA involved in iron uptake, belonging to the B2 phylogenetic group and being virulent in a mouse model of septicaemia were resistant to the grazing from D. discoideum. Experimental proof of the key role of the irp gene in the grazing resistance was evidenced with a mutant strain lacking this gene. Such determinant of virulence may well be originally selected and (or) further maintained for their role in natural habitat: resistance to digestion by free-living protozoa, rather than for virulence per se.

This is an Open Access article and available therefore free of cost from PLoS ONE journal website.

India-centric Lancet ‘superbug’ story: a murky ‘courier express’ collaboration?

2010-08-15T07:35:00.002+05:30

Amid huge media frenzy over the LANCET Infectious Diseases article that appeared on August 11, 2010, there are reasons why India should try retracting the story 'Emergence of a new antibiotic resistance mechanism in India…' (sorry, it's a closed access article despite that it was funded by EU and Wellcome Trust, and you will have to shed ample money to read it in full!). On a quick, editorial read out, it appears that the authors have possibly flouted several pre-publishing requirements:

None of the Indian and other South Asian authors is very well known researcher or clinician (by their publication record); why were they invited for this study and their trips paid out by Pharma players; just for hunting isolates?
Why convenient sampling at tertiary hospitals?
Who cleared transfer of isolates from India to UK? Do Indian hospitals mentioned in the study hold export licenses for classified biological agents? Do they have HMSC [an Indian Council of Medical Research (ICMR) watch-dog] clearances?
Were the culture and antibiotic sensitivity screening protocols approved by biosafety committees at respective Indian centers and hospitals?
Why Hinduja Hospital Team dropped for authorships when there were analyses of isolates presented from Mumbai? How many isolates did Hinduja ship to UK and how?
How the isolates got shipped to UK? Did the first author Kumarasamy carried them over to UK and his trip funded by Wyeth as mentioned?
If my doubts above are genuine, then, should they be overlooked, especially, when the study falls within the ambit of prestigious funding agencies such as EU and Wellcome Trust?

There are additional problems:

(a) No mention of how many isolates supplied by whom? (b) much of the discussion directed towards denting medical tourism in India and the premise based on popular media reports and articles from 'God-forsaken' journals (J Assoc Physician India and J Infect Dev Ctries ) (c) it seems that the involvement of Indian centers was merely for collecting the isolates and such a research collaboration can not be justified. Authorships should not be given just for the isolation of cultures and provision of demographic and patient data.

The above points must be investigated and taken up (by the ICMR and the Indian Health Ministry) with the journal and the Indian institutions/hospitals that cleared implementation of the study. Unless documents supporting ethical and biosafety clearances produced, the journal should be asked to retract the report with apology. Moreover, the ICMR and the Indian agencies should formulate concrete policies on such ad-hoc collaborations which are meant only for hunting and exporting the genetic material and patient isolates.

GRK1674: German Research Foundation's New International Research Training Group at Freie Universität Berlin/University of Hyderabad

2010-08-08T19:37:00.001+05:30

29 June 2010 Freie Universitaet Berlin

06 August 2010 University of Hyderabad

(Press Release)

Research in Collaboration with Indian University of Hyderabad Studies Expression of Infectious Diseases as a Function of Genetic Factors.

The German Research Foundation (DFG) has set up a new international research training group (GRK) at Freie Universität Berlin. The projects of GRK 1673 "Functional Molecular Epidemiology Infection" at the Department of Veterinary Medicine (Speaker, Lothar H Wieler) deal with the factors that determine the severity and the geographic spread of infectious diseases. Among other things, the research deals with the immediate causes of tuberculosis, filariasis, or malaria. The University of Hyderabad in India is the cooperation partner (Speaker, Niyaz Ahmed).
Research at the joint facilities of Freie Universität Berlin, which acts as the host university, and the University of Hyderabad focuses on the areas of host-pathogen genomics and economic analysis of genetic variations. The comparative analysis of infectious diseases in Germany and India will provide information on the pathogen and host factors that influence the disease. "The outstanding expertise of the Indian partner(s) in the areas of bioinformatics and disease cohorts managed in Greater Hyderabad coupled with the extensive expertise of the Berlin partner in infection biology and epidemiology are a wonderful basis for an exciting and successful intercultural collaboration for the benefit of patients," said Professor Lothar H. Wieler, director of the research training group.
The new DFG research training groups offer graduate students an opportunity to complete their doctorates in a structured research and training program at a highly specialized level. "Students of medicine, veterinary medicine, or biology will find excellent conditions at Freie Universität," said Professor Wieler. "Our new international research training center offers outstanding conditions for completing a doctorate in one of these areas." This also means the opportunity to gain international experience: the program at Freie Universität includes a stay in India.
Overall, the DFG has set up 12 new research training groups to further improve conditions for young researchers in Germany. During the first funding period of four and a half years, they are being supported by the DFG with a sum of around 45 million euros. Three of the new facilities are international research training groups, which cooperate closely with foreign universities. The DFG currently funds 219 research training groups, including 55 international ones.

(www.vetmed.fu-berlin.de/v/grk1673/)

Phew! New Impact Factor for PLoS ONE: Guess how much?

2010-06-20T00:04:00.000+05:30

Finally, Thomson Reuters have released the cat out of their bag. PLoS ONE's IF is cool at a respectable 4.351. IF really does not matter to us PLoSians but for those who really were dying for it since the last 3 years will be reason to celebrate. Enjoy with it and - Ciao!

A New Era For Indian Farms - Sponsored By Craig Venter

2010-05-29T17:06:00.003+05:30

Survivor bacteria linked to diabetes, say experts | Deccan Chronicle | 2010-05-06

2010-05-06T15:29:00.001+05:30

Hyderabad, May 5: Researches in the city have found a link between a notorious bacterium that lives in milk and the type 1 diabetes which mostly affects children.
Though the exact cause of type 1 diabetes is yet to be ascertained, doctors generally blame genetics and environmental factors.
For the first time, a group of researchers from Hyderabad have gathered concrete proof of a link between the bacterium and type 1 diabetes. The bacterium infects people through milk and contaminated water.
The study was carried out by Dr P. Sandhya Rani and Dr Niyaz Ahmed of the University of Hyderabad, in collaboration with Dr L.A. Sechi, from the University of Sassari, Italy. The bacterium, mycobacterium avium sub-species paratuberculosis, or simply MAP, is very dangerous as it survives in milk even after pasteurisation.
MAP causes chronic infection in the intestines of cattle (Johne’s Disease) and causes enteritis in human beings (Crohn’s Disease).
“With increasing recognition of the link between MAP and Crohn’s Disease, it has been postulated that MAP is an occult antigen which, like Crohn’s, could trigger type 1 diabetes.
Studies implicate MAP as one of the triggers of diabetes. Also laboratory analyses in diabetic patients from Sardinia (Italy) point a finger at the bacterium,” Dr Sechi said.The study is significant as the type 1 diabetes is the second most common chronic disease during childhood and the most common form of diabetes affecting three out of every 2,000 children world-wide.
In the South Indian urban population, the type 1 diabetes occurs in 26 out of every 10,000 children under 15 years of age. The MAP bacterium enters the human body through the faecal-oral route. Infected animals release MAP in their milk and faeces.
The bacterium is found to be present in untreated water and in water-bodies contaminated by agricultural runoff. The treatment of water to make it potable by the processes of sedimentation, filtration and chlorination has little or no effect on the bacteria.
Though the team has identified MAP as a trigger for the type 1 diabetes, it will take further research to unravel the puzzle of how the bacterium damages the production of insulin.

New article added to PLoS ONE Prokaryotic Genome Collection

2010-05-04T18:10:00.000+05:30

One Bacterial Cell, One Complete Genome

'While the bulk of the finished microbial genomes sequenced to date are derived from cultured bacterial and archaeal representatives, the vast majority of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes from these environmental species. Single cell genomics is a novel culture-independent approach, which enables access to the genetic material of an individual cell. No single cell genome has to our knowledge been closed and finished to date. Here we report the completed genome from an uncultured single cell of Candidatus Sulcia muelleri DMIN. Digital PCR on single symbiont cells isolated from the bacteriome of the green sharpshooter Draeculacephala minerva bacteriome allowed us to assess that this bacteria is polyploid with genome copies ranging from approximately 200–900 per cell, making it a most suitable target for single cell finishing efforts. For single cell shotgun sequencing, an individual Sulcia cell was isolated and whole genome amplified by multiple displacement amplification (MDA). Sanger-based finishing methods allowed us to close the genome. To verify the correctness of our single cell genome and exclude MDA-derived artifacts, we independently shotgun sequenced and assembled the Sulcia genome from pooled bacteriomes using a metagenomic approach, yielding a nearly identical genome. Four variations we detected appear to be genuine biological differences between the two samples. Comparison of the single cell genome with bacteriome metagenomic sequence data detected two single nucleotide polymorphisms (SNPs), indicating extremely low genetic diversity within a Sulcia population. This study demonstrates the power of single cell genomics to generate a complete, high quality, non-composite reference genome within an environmental sample, which can be used for population genetic analyzes'.

Woyke T, Tighe D, Mavromatis K, Clum A, Copeland A, et al. (2010) One Bacterial Cell, One Complete Genome. PLoS ONE 5(4): e10314. doi:10.1371/journal.pone.0010314

New articles added to PLoS ONE Prokaryotic Genome Collection

2010-04-11T22:28:00.001+05:30

The Complete Multipartite Genome Sequence of Cupriavidus necator JMP134, a Versatile Pollutant Degrader

Athanasios Lykidis, Danilo Pérez-Pantoja, Thomas Ledger, Kostantinos Mavromatis, Iain J. Anderson, Natalia N. Ivanova, Sean D. Hooper, Alla Lapidus, Susan Lucas, Bernardo González, Nikos C. Kyrpides

PLoS ONE:
Published 22 Mar 2010 | info:doi/10.1371/journal.pone.0009729

Genome Sequence of Cronobacter sakazakii BAA-894 and Comparative Genomic Hybridization Analysis with Other Cronobacter Species

Eva Kucerova, Sandra W. Clifton, Xiao-Qin Xia, Fred Long, Steffen Porwollik, Lucinda Fulton, Catrina Fronick, Patrick Minx, Kim Kyung, Wesley Warren, Robert Fulton, Dongyan Feng, Aye Wollam, Neha Shah, Veena Bhonagiri, William E. Nash, Kymberlie Hallsworth-Pepin, Richard K. Wilson, Michael McClelland, Stephen J. Forsythe

PLoS ONE:
Published 08 Mar 2010 | info:doi/10.1371/journal.pone.0009556

The Genome of Streptococcus mitis B6 - What Is a Commensal?

Dalia Denapaite, Reinhold Brückner, Michael Nuhn, Peter Reichmann, Bernhard Henrich, Patrick Maurer, Yvonne Schähle, Peter Selbmann, Wolfgang Zimmermann, Rolf Wambutt, Regine Hakenbeck

PLoS ONE:
Published 25 Feb 2010 | info:doi/10.1371/journal.pone.0009426

Large Direct Repeats Flank Genomic Rearrangements between a New Clinical Isolate of Francisella tularensis subsp. tularensis A1 and Schu S4

Ufuk Nalbantoglu, Khalid Sayood, Michael P. Dempsey, Peter C. Iwen, Stephen C. Francesconi, Ravi D. Barabote, Gary Xie, Thomas S. Brettin, Steven H. Hinrichs, Paul D. Fey

PLoS ONE:
Published 03 Feb 2010 | info:doi/10.1371/journal.pone.0009007

PLoS ONE published its 10000th article

2010-04-04T13:39:00.001+05:30

PLoS ONE has just published its 10,000th article! Since its birth in December 2006, PLoS ONE has put up a formidable competition to the print copy science publishers, and this recent milestone shows that open-access publication of "not so novel and subjective based research" is indeed a viable and scientifically justified project and which enjoys wide support within the academic community. Following the success of PLoS ONE, more such publication projects [including few from PLoS ONE's vocal critics] have recently mushroomed. It ill be interesting to know how far the new projects will be successful fishing inside the catchment of PLoS ONE. Below is the 10000th PLoS ONE article that appeared on April 2, 2010:

Immunoproteomics Analysis of the Murine Antibody Response to Vaccination with an Improved Francisella tularensis Live Vaccine Strain (LVS) Susan M. Twine, Mireille D. Petit, Kelly M. Fulton, Robert V. House, J. Wayne Conlan Research Article, published 02 Apr 2010 doi:10.1371/journal.pone.0010000

For more coverage of this news and an interview with the authors of the above article please see the PLoS ONE community blog: http://everyone.plos.org/2010/04/02/plos-one-publishes-10000th-article/

New PLoS ONE articles evaluated at Faculty of 1000

2010-02-04T07:26:00.001+05:30

Faculty of 1000 Biology
search alert

New PLoS ONE Articles Evaluated at F1000

	Recommended
F1000 Factor 3.0

Hypothesis
New Finding
Controversial

Infection with Helicobacter pylori is associated with protection against tuberculosis.
Perry S, de Jong BC, …, Canfield D, Parsonnet J
PLoS One 2010 5(1):e8804 [abstract on PubMed] [related articles] [FREE full text]

Selected by | Niyaz Ahmed
Evaluated 3 Feb 2010

	Recommended
F1000 Factor 3.0

Confirmation
New Finding

Quantifying the extent of North American mammal extinction relative to the pre-anthropogenic baseline.
Carrasco MA, Barnosky AD, Graham RW
PLoS One 2009 4(12):e8331 [abstract on PubMed] [related articles] [FREE full text]

Selected by | Barry Brook with Lochran Traill
Evaluated 3 Feb 2010

	Recommended
F1000 Factor 3.0

New Finding
Controversial

Self-medication as adaptive plasticity: increased ingestion of plant toxins by parasitized caterpillars.
Singer MS, Mace KC, Bernays EA
PLoS One 2009 4(3):e4796 [abstract on PubMed] [related articles] [FREE full text]

Selected by | Jon Harrison with Arianne Cease
Evaluated 2 Feb 2010

	Recommended
F1000 Factor 3.0

Confirmation

Marine reserves enhance the recovery of corals on Caribbean reefs.
Mumby PJ, Harborne AR
PLoS One 2010 5(1):e8657 [abstract on PubMed] [related articles] [FREE full text]

Selected by | John Pandolfi with Ruth Reef
Evaluated 2 Feb 2010

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To help you and your colleagues keep up-to-date with the most interesting biology papers --- regardless of in which journal they appear --- as evaluated continuously by over a thousand of the world's leading researchers click here to fill out our simple librarian recommendation form.

New articles added to the 'PLoS Prokaryotic Genome Collection'

2010-01-27T12:52:00.000+05:30

Complete Genome Sequence of the Multiresistant Taxonomic Outlier Pseudomonas aeruginosa PA7

Paul H. Roy, Sasha G. Tetu, André Larouche, Liam Elbourne, Simon Tremblay, Qinghu Ren, Robert Dodson, Derek Harkins, Ryan Shay, Kisha Watkins, Yasmin Mahamoud, Ian T. Paulsen

PLoS ONE: published 22 Jan 2010 | info:doi/10.1371/journal.pone.0008842

Complete Genome Sequence and Comparative Metabolic Profiling of the Prototypical Enteroaggregative Escherichia coli Strain 042

Roy R. Chaudhuri, Mohammed Sebaihia, Jon L. Hobman, Mark A. Webber, Denisse L. Leyton, Martin D. Goldberg, Adam F. Cunningham, Anthony Scott-Tucker, Paul R. Ferguson, Christopher M. Thomas, Gad Frankel, Christoph M. Tang, Edward G. Dudley, Ian S. Roberts, David A. Rasko, Mark J. Pallen, Julian Parkhill, James P. Nataro, Nicholas R. Thomson, Ian R. Henderson

PLoS ONE: published 20 Jan 2010 | info:doi/10.1371/journal.pone.0008801

Genome Sequence of the Endosymbiont Rickettsia peacockii and Comparison with Virulent Rickettsia rickettsii: Identification of Virulence Factors

Roderick F. Felsheim, Timothy J. Kurtti, Ulrike G. Munderloh

PLoS ONE: published 21 Dec 2009 | info:doi/10.1371/journal.pone.0008361

--------

The PLoS ONE Prokaryotic Genome Collection is an attempt to present and highlight a number of important articles that describe whole genome sequence and/or comparative genomics of important prokaryotic organisms. We believe that this collection will be able to facilitate understanding of the biology and lifestyle of the underlying organisms not only through the content of the Research Articles, but also from the external information sources which are linked to from the original articles. Editorial oversight and coordination of the peer-review for most of the articles was provided by Niyaz Ahmed, PLoS ONE Section Editor for Genomics and Microbiology. Articles are presented in order of publication date and new articles will be added to the collection as they are published. We welcome submissions in this field.

PLoS ONE indexed by Web of Science (Thomson Reuters)

2010-01-09T15:09:00.001+05:30

[by Mark Patterson | reposted here from PLoS BLog]

Today we learned that by the end of this week PLoS ONE (in keeping with all other PLoS journals) will be indexed by the Web of Science – this is an important literature discovery tool that many people use and so we are pleased to be indexed. PLoS ONE is also indexed by a host of other services such as PubMed, MEDLINE, PubMed Central, Scopus, Google Scholar, the Chemical Abstracts Service (CAS), EMBASE, AGRICOLA, PsycINFO, Zoological Records, FSTA (Food Science and Technology Abstracts), GeoRef, and RefAware.

Initially, coverage in the Web of Science will include new PLoS ONE articles plus those published in 2008 and 2009, and will be expanded to the articles published in 2006 (when PLoS ONE was launched) and 2007 in the coming weeks. Inclusion in the Web of Science also means that in June 2010 PLoS ONE will receive journal-level citation data from Thomson Reuters including a 2- and 5-year Impact Factor and Eigenfactor metrics.

As we have previously indicated, PLoS believes that research articles are best assessed on their own merits, rather than on the basis of the journal (and its impact factor) where the work happens to be published. While we are happy that PLoS ONE articles will become more discoverable as a result of their inclusion in the Web of Science, we will continue to push forward with our Article-Level Metrics program.

Naturally, we understand that inclusion in the Web of Science is significant for many academics whose research output is still measured by traditional means. We hope that this news encourages even more scientists to publish their work in PLoS journals, to benefit from the article-level metrics that are provided for every PLoS article (for example, this PLoS ONE article), and to ensure that all interested users have open access to their research.

PLoS ONE Review of 2009

2009-12-30T09:39:00.001+05:30

[By Peter Binfield, Managing Editor - PLoS ONE | originally posted at Everyone - PLoS ONE community blog]

'It was on Dec 20^th, 2006 that PLoS ONE launched, and 2009 (only our third full year of publication) has been packed full of exciting developments. To note our birthday, I took the opportunity to round up the major events of the past 12 months. There have been an awful lot of them and it is a tribute to our staff and academic editors that we were able to achieve all of the following while increasing our publication volume from 2,726 articles published in 2008 to 4,400 expected in 2009 (something which, we believe, now makes us the third largest journal in the world, by publication volume).

The start of the year saw us developing new functionality, with the launch of Collections on PLoS ONE. This began with the publication of the ''Stress-Induced Depression and Comorbidities'' Collection in January, followed by our second in February – the PLoS ONE Paleontology Collection. We subsequently launched the Prokaryotic Genome Collection in June and the Structural Genomics Consortium Collection in October (a collection which provides 'enhanced versions' of papers, incorporating advanced 3D interactive simulation software – an excellent example of the creative re-use of Open Access content).

In March, we launched everyONE, our community blog site; we announced our ability to accept LaTeX submissions; and we upgraded our site with a redesigned 'tabbed' user interface to accommodate our newly launched Article-Level Metrics functionality (of which more later).

In April, we announced our ''Blog Post of the Month Competition'' (in collaboration with researchblogging.org) which has since gone on to award a winner every month.

In May, we redesigned our email Table of Contents alerts so that recipients now receive an email categorized by subject area, and this was also the month in which we publicly thanked the 9,000 peer reviewers who gave us their expert opinions during 2008.

Our 2009 media coverage will be reviewed by Bex in a different post, but in May we published a paper that sparked our largest media story of the year – the Darwinius masillae (or 'Ida') paper – "Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology". The coverage of this paper was overviewed in three separate blog posts.

May also saw a major event in the development of PLoS's technology platform – with the migration of PLoS Biology and PLoS Medicine, we were finally able to have all seven of our titles on Topaz, which is now our shared online platform.

In July, we began a partnership with DeepDyve to improve our search capabilities and we also launched the "Worth a Thousand Words" blog series (featuring a selected image from each week's publications). July also saw PLoS publicly express our opinion that there is more value in measuring impact at the article level than at the journal level – something which coincided with the announcement that we would no longer be promoting Impact Factors on our sites.

In August, PLoS ONE was featured in the popular internet comic, "PhD Comics" as part of their "Nature vs Science" series, and in the same month PLoS launched an important experiment in rapid publication – PLoS Currents: Influenza, a collaboration between PLoS, Google Knol and the NCBI

In September, PLoS ONE was immensely proud to win the ALPSP Award for Publishing Innovation, 2009 – this is a major industry award and a testament to the rapid pace of innovation that the journal has pioneered in the 3 years since launch.

September was also the month that saw our Article-Level Metrics program expand in a significant way, by displaying usage data on every article in the PLoS corpus. In December, we also added data from ResearchBlogging.org to the program. We regard Article-Level Metrics as a significant new development in academic publishing and we expect to significantly expand it in 2010. Several presentations were made through the year on the topic of Article-level Metrics, for example to NISO, to the ElPub Conference, and to UCSF/Berkeley and these are all archived with audio if you wanted to delve into the details.

In October, OASPA, the new association for Open Access Scholarly Publishers was launched and PLoS was proud to be a founding member. This coincided with Open Access Week, 2009. And in November, in response to many requests over the years, we launched our new PLoS store.

And finally, after a year of incredible developments, 2009 has culminated with what may yet turn out to be the most significant development of all – the request by the White House Office of Science and Technology Policy (OSTP) for public comments on the issue of broadening public access to publicly funded research. You still have time to provide your feedback and there would be no better New Year resolution than to make your voice heard in this forum.

Thank you to everyone who has supported us in 2009, and over the last three years – in particular thank you to our (almost) 1,000 Academic Editors, all of our peer reviewers and of course, all of our authors. We look forward to publishing more great science in 2010'.

Happy third birth day, PLoS ONE!

2009-12-22T12:00:00.001+05:30

This is the time all supporters of OA should celebrate - for the great, unparallel success that PLoS ONE has achieved in three years: more than 8000 articles, an extended editorial force of 1000 Academic Editors, innovative article-level metrics, thematic collections, etc. We would like to thank all the reviewers who volunteered to review manuscripts within a very short time window of 10 days! The editorial staff deserve a big thank you for the hard work and readiness to help and solve problems. We must also thank our authors who have shown faith in PLoS ONE and submitted their high quality work to this journal. I hope next year will be even better.

New addition to Article-Level Metrics - blog posts from ResearchBlogging.org

2009-12-18T07:26:00.001+05:30

(By Liz Allen, Thu 2009-12-17 12:19 | in syndication with PLoS Blog)

Throughout the course of 2009, PLoS has been adding a range of Metrics to each and every article that it has published. In addition to the many metrics already displayed (article pageviews and downloads, citations, social bookmarks, notes, comments and ratings), we are pleased to now add data relating to the blog coverage of any article, as measured by ResearchBlogging.org. You can find out more about the Article Level Metrics program here.

Every interested author and user can now see how many times an article has been downloaded (split into HTML Pageviews, PDF and XML downloads and displayed in a month-by-month format); how often an article has been cited (as measured by PubMed Central, Scopus and CrossRef); how many times it has been 'socially bookmarked' (at CiteULike and Connotea); how many times users have Commented, or left Notes, or provided Ratings; and how many blog articles have been written about it (as measured by the blog aggragators Postgenomic, Blog Lines, Nature Blogs and, from today, ResearchBlogging.org).

We've created a 2.4 minute screen shot video (with audio commentary) that you can watch to familiarize yourself with the blog aggregation functionality from ResearchBlogging.org so you can see for yourself the benefits of this part of the Article-Level Metrics program.

On launching this new functionality, Pete Binfield, Publisher of PLoS ONE and the Community Journals said:

"We're delighted to add data from ResearchBlogging.org to the Article Level Metrics program because the blogs that they index are mainly written by practicing scientists, who are well versed at providing readable summaries of the research that we publish".

Bloggers who regularly write about scientific research are able to register with ResearchBlogging.org and (provided they qualify) they are then entitled to indicate that their blog entries refer to peer reviewed scientific research by adding an icon to their posts. As a result, the ResarchBlogging.org service represents a high quality source of highly relevant articles, typically written by practicing scientists, on the topic of peer reviewed research. Since all PLoS content is peer reviewed and free to read, PLoS articles tend to be regularly covered by their bloggers. You can find the current list of qualified ResearchBlogging.org bloggers here.

Dave Munger, the co-founder of ResearchBlogging.org, said:

"We're pleased to be working with PLoS to assess the impact of its articles. PLoS journals do a great job publishing and making research accessible to everyone, and we think coverage in thoughtful blog posts is an important component of the impact of a peer-reviewed journal article". You can read more in this blog post.

PLoS ONE and ResearchBlogging.org also collaborate on a monthly "Blog Pick of the Month" competition that we feature on everyONE, the PLoS ONE community blog. Every month, Bora Zivkovic, the Online Discussion Expert for PLoS, chooses the best blog about a PLoS ONE article that has appeared in ResearchBlogging.org and we feature it on our blog. The winning blogger and all the authors of the original PLoS ONE research article all win t-shirts. To enter, you simply need to be a ResearchBlogging.org blogger and start writing about PLoS ONE articles.

We welcome feedback and questions on any aspect of this program to alm@plos.org.

Open Access Workshop at the University of Hyderabad

2009-11-25T21:39:00.000+05:30

One day Open Access Workshop was organized on November 18, 2009 at the University of Hyderabad at the initiative of the Indira Gandhi Memorial Library of the University. Professor Seyed E Hasnain, Vice-Chancellor, inaugurated the workshop and delivered his keynote speech. He stressed for the need to make the scientific literature open and free of cost. The university is planning to usher into green open access very soon.

Designer probiotics: the future or too much to stomach?

2009-11-25T21:26:00.001+05:30

Although the benefits of probiotics have been postulated for more than 100 years, there has been an increasing interest in the effects of probiotics on ill health and general well being over recent years.
Studies have shown positive outcomes of probiotics in the treatment and prevention of gastrointestinal infections and disease. But are generic probiotics enough? In the review "Probiotics and gastrointestinal disease: successes, problems and future prospects" published in Gut Pathogens, Eamonn Culligan et al. review the treatment of various GI disorders with specific probiotic strains. They also discuss whether the future lies with designer probiotics, which are engineered to specifically target a particular toxin or pathogen, but raise concerns of a negative public reaction to the development of this possible course of treatment.
Will designer probiotics be the future treatment of GI disorders? Or will public resistance for genetically modified organisms hinder its progress? (Source: Biomed Central Blog)

Open Access, PLoS article level metrics part of syllabus for PhD course at Uni Hyderabad

2009-09-18T23:13:00.001+05:30

Impressed by PLoS style, our university here decided to teach Open Access, creative reuse and article level metrics to entry level PhD students in Life Sciences. I am grateful to the university authorities for enabling us to direct such a timely and important course for the first time in the history of graduate teaching in India; see the course curriculum approved by the university below. I hope many other universities and institutes will be able to replicate this course:

Course name: Scientific writing; Course director: Dr Niyaz Ahmed; Course credits: 1 (12 lectures in a semester)

1. Documentation of scientific observations and maintenance of raw data in a biology lab
2. Primary research articles and secondary content - commentaries, reviews, book length evaluations
3. Creative re-use, semantic enhancements and reproduction of open access scientific material
4. Copyright and Creative Commons attribution licences
5. Publication ethics
6. Malpractices in scientific reporting - examples and case studies
7. Citations, evaluations, article-specific metrics and impact factors
8. Scientific deliberations

Coveted Industry Award to PLoS ONE for Publishing Innovation

2009-09-12T06:12:00.002+05:30

PLoS ONE achieved yet another milestone yesterday by receiving an award from the ALPSP (the Association of Learned and Professional Society Publishers) for Publishing Innovation of the Year, 2009. The award is given in recognition of a truly innovative approach to any aspect of publication as adjudged from originality and innovative qualities, together with utility, benefit to the community and long term prospects. This prestigious industry award is therefore, a proof of the hard work of all the editors, managers, staff, authors, and reviewers! The award is a formal recognition of the fact that PLoS ONE has spearheaded a radical departure from traditional scientific publishing in a number of ways, from its pioneering editorial policies to its regular technical innovations, including the commentary and rating features available on all of its articles—in short, PLoS ONE now means 'new generation scientific publishing in a most innovative and interactive style'.

200th PLoS ONE article evaluated at Faculty of 1000

2009-09-08T05:26:00.002+05:30

It is heartening to note that 200th article from PLoS ONE has now been evaluated at the Faculty of 1000 Biology. Last year on July 17, a report on the evaluation of 100th article from PLoS ONE was posted on this blog. It is about in a year's time that further one hundred articles were evaluated; a remarkable achievement despite a very high volume publishing in diverse areas. Since the number of articles almost tripled in a year (6000 in August 2009 versus 2600 in July 2008), the number of evaluations touched almost 10 per month (3.3% of total articles published). For a broad based and high volume journal such as PLoS ONE, the F1000 evaluations serve as an important quality index for individual articles.

'Fine Reading: The Biocentric View of the Microbial World'

2009-09-04T06:39:00.001+05:30

By - Elio (Moselio Schaechter)

"How does anthropocentrism apply to microbiologists? In a current commentary in the new journal Gut Pathogens, Ramy Aziz reminds us that it shows up all over the place. Take the very term microbe, meaning small living thing. 'Small,' says who? Not the microbes. To them, other microbes would be of 'normal' size and we humans Rabelaisian gargantuas. This wouldn't much matter if it stopped there, with our choice of words alone. Aziz points out that anthropocentrism in microbiology can have serious consequences. For instance, 'pathogens' have been considered to be special group of microbes, separate from the rest. Nothing could be farther from the truth, and nothing could be more objectionable than to consider the human body to be anything but another habitat.

In recent years, it has been increasingly realized that pathogenic microbiology is merely another branch of microbial ecology. However, a gentle reminder in Aziz' well-turned words is welcomed. A truly integrated view of the microbial world, or of the biological world in general, cannot be anthropocentric but can only be, as Aziz says, biocentric".

[In syndication with ASM blog - 'Small things considered', original post here]. Ramy K Aziz is an Editorial Board Member of PLoS ONE.

The Journal of Biosciences, India: kicking and alive, or struggling to excel?

2009-07-04T18:57:00.002+05:30

The Journal of Biosciences is the only 'high impact' journal of life sciences published from India under the aegis of the Indian Academy of Sciences. The journal has established an impressive rapport among life sciences communities in India and elsewhere. Sadly, however, it was flagged recently in a meeting (read ahead) that not many of its well-wishers themselves consider to publish their best of the best research in J Biosci. I attended the meeting of the Editors of the J Biosci recently wherein all interested to the cause of the journal were invited. I found morale of the associates of the journal and the authors quite upbeat, also in the aftermath of recently released 'journal impact factors' – JIF 2008; the J Biosci has recorded a 'comfortable' IF of 1.7! However, I think they need to be careful on the statistics part because the number of papers published by the journal has been traditionally very low; it published about 70 citable articles in a 2 year period. Given this, I thought it will not be appropriate to celebrate the jacked up IF, but to introspect as to why the acceptance rate is so low (just 7%) and why so many commentaries and secondary content being published and not much original research? I guess the board members, might consider to follow the example of PLoS journals wherein many of the PLoS advocates first published their high quality (the so called 'Nature, Cell, Science, PNAS quality' of stuff??) research in the journals they stood for. Well, this proposition didn't go well – there were arguments in favor and against and the excuses given were vivid. We can understand the hesitation, but as someone said, 'charity begins at home'! Other hindering things could be the extraordinarily long time taken by the journal, as told, for completing the peer review (somewhere near 3-4 months) and for eventual publication after acceptance (2 more months). Keeping aside these deficiencies, I think we are looking at an emerging journal coming up from a developing country domain and I am all in favor of publishing there as long as the journal follows an Open Access policy although Springer has already started selling the contents through paid views/downloads under an agreement with the journal/academy.

Failures of citation based rating - new analysis

2009-06-27T18:46:00.003+05:30

Ramy Aziz, one of the most enthusiastic members of the PLoS ONE Editorial Board has very nicely commented on a recently published PLoS ONE article which highlights the failures of the so called 'impact factor' based rating of the value of science journals. The journal impact factors were released last week itself and thus the analysis presented in the article is very timely, indeed. Below are Ramy's comments to which I agree 100%:

"The presented results pertain to what we believe to be the largest and most thorough survey of usage- and citation based measures of scientific impact."

I agree with the above statement and I definitely like this thorough comparison of a large number of "impact measures." The article is also informative and has introduced in detail many methods for evaluation of scientific literature with which I was not familiar.

However, on reading the article, I had the following concerns regarding its reliability:

1) Most of the readers will only read the abstract, especially because the article is full of statistical and technical terms. The conclusion of the abstract is not so informative and poorly represents the insightful discussion at the end of the article.
In particular, I would have preferred a positive than a negative conclusion. I would have preferred a recommendation of which measures correlate better with each of the multiple dimensions of scientific attributes (e.g., quality, prestige, impact, immediacy, etc.) rather than the--rather obsolete--conclusion that JIF is not optimal and should be "used with caution." I have read more than 20 articles and editorials (including those in Science, JBC, JCI, PLoS) written in the past two years and stating that JIF should be used with caution.

2) I agree with the authors that JIF is misused; however, a value cannot be blamed for what it does not stand for. I believe the authors have given more importance to JIF (probably because of its "impact" on the scientific community), and I think that this has affected the objectiveness of the paper.

3) As the authors state in the introduction, until now I'm not sure whether how "scientific impact" is defined. Is it "journal impact", "article impact", or "scientist impact"? And which of these matters more? However, the authors seem to have committed the same unfair comparison that JIF and SJR do: measuring articles, scientists, and even "science" itself by the journals rather than by the articles. Journal-level metrics simply mean that an article is evaluated mostly prior to its publication. Once a scientist "makes it to Science or Nature," he or she celebrates even if the article will never be cited again!

4) Once more I declare my agreement with the authors that JIF is neither the most accurate nor the fairest way to measure scientists, articles, or even journals. However, this "conclusion" is clearly stated in the introduction (quoted below). Why the analysis then?

"The JIF is now commonly used to measure the impact of journals and by extension the impact of the articles they have published, and by even further extension the authors of these articles, their departments, their universities and even entire countries. However, the JIF has a number of undesirable properties which have been extensively discussed in the literature [2], [3], [4], [5], [6]. This had led to a situation in which most experts agree that the JIF is a far from perfect measure of scientific impact but it is still generally used because of the lack of accepted alternative"

5) One final concern/question.
Citation-based metrics take into consideration journals that are technologically behind (for many "non-science-related" reasons, including funding problems, poor management, being published in a developing country, etc.) and thus do not have well established web sites but are still citable and cited. Do the "usage-based metrics" just ignore those journals?

Need for qualitative assessment of biomedical research

2009-06-20T14:31:00.003+05:30

Here comes a new PLoS ONE article describing one of the most authoritative analyses of the research impact - by none other than the Wellcome Trust. The research conducted by experts of the Trust summates that authoritative opinions about a published research finding constitute important benchmark of the quality of biomedical research. These data vindicate stand of the advocates of post publication peer review (and I am one humble volunteer) that modern day qualitative indicators are extremely necessary to judge the impact of biomedical research findings. Not only that this article supports and strengthens cause of the 'Faculty of 1000' but also that of PLoS ONE, although indirectly. The latter is no doubt the most successful forerunner of the idea of post-publication peer review and qualitative assessment while harnessing the web2.0 based semantic tools for such purposes. At this critical juncture, it is time for the concerned institutions to retrospect about their practices of evaluating research productivity of scientists based on bibliometric indices (such as the 'impact factor') alone.

New genome article added to 'PLoS ONE prokaryotic genome collection'

2009-06-19T16:03:00.001+05:30

A new PLoS ONE article describing whole genome sequence of a contaminating mycobacterial species, Mycobacterium abscessus is the most recent addition to the 'PLoS ONE Prokaryotic Genome Collection'.

The article presents most important observations such as those related to the presence of several novel virulence determinants of non-mycobacterial origins and that these were perhaps acquired from other environmental organisms and pathogens including Rhodococcus sp., Streptomyces sp., pseudomonads and Burkholderia cepacia.

Standards for genome data reporting: should we go about it?

2009-06-19T12:21:00.001+05:30

Within my overview article that accompanies the PLoS ONE Prokaryotic Genome Collection, one thing that I did not touch base with was the standards for genome data reporting. The Genome Standards Consortium (GSC) is now already in place (and I am one proud member of the same!) and they strongly advocate that certain standards be introduced (at the least) at the level of genome meta data. The consortium has recently published aims and objectives, prospective guidelines and envisaged benefits of such 'would be' mandatory standards (http://www.pubmedcentral....).

As a next critical step, the GSC are now starting to ask journals to require that new genome/metagenome publications be accompanied by completed 'Minumum Information about a Genome Sequence (MIGS/MIMS)' reports.

This sounds a wonderful proposition and I guess PLoS journals in this connection could lead headway as they already insist for adherence to certain other standards such as MIAME for reporting microarray data). Until this point, it is all OK. But some people feel that 'monopolizing' standards could be a kind of 'suffocation'. However, I am sure this will not lead to the kind of 'suffocating monopoly' created by certain 'nomenclature commissions' and their 'mouthpiece journals' in the area of taxonomy and systematics.

I discussed this with one of my friend, a genomic/bioinformatics expert and he says ".. my problem with standards is also not only the monopoly, but that it is also really hard to set a minimal role of meta data that need to be entered per genome. I suffer from the lack of organized meta data; but once the entry is enforced, people will just start putting anything to fill the tables and get their data out, which will lead to the opposite of what standards are supposed to achieve".

Given above, it is clear that some discussion and brainstorming is nevertheless required before journals start insisting for the MIGS/MIMS reports. I can not find a better place than PLoS ONE (sandbox) to discuss and resolve such issues.

New F1000 Evaluation of a PLoS ONE article

2009-06-13T18:24:00.001+05:30

Yet another PLoS ONE article was evaluated by F1000 Biology, making the total number of evaluated articles to 180. At any given time, about 3-4% of PLoS ONE articles are evaluated at F1000. Below is a simplified version of the evaluation of the article by Myers et al. The article was evaluated by Felix Viana of the UMH Instituto de Neurociencias, Spain.

Evolution of thermal response properties in a cold-activated TRP channel.
Myers BR, Sigal YM, Julius D
PLoS ONE 2009 4(5):e5741 [abstract on PubMed] [citations on Google Scholar] [related articles] [FREE full text]

"This is an interesting study, comparing functional properties of ortholog thermosensitive TRPM8 channels in frogs and rats. It suggests that intrinsic thermosensitivity is tuned to the normal operating range of body temperature. Animals populate different ecological niches. Survival in these environments is strongly dependent on properly tuned sensory systems that allow the rapid detection of food and the avoidance of dangerous situations, like predators or exposure to extreme temperatures. TRPM8 is a transient receptor potential activated by cold temperatures and cooling compounds like menthol {1, 2}. In mice, TRPM8 is critical for the detection of mild cold temperatures, and perhaps for unpleasant or noxious cold. In this paper, the authors cloned and characterized the functional properties of frog, specifically Xenopus laevis and Xenopus tropicalis, TRPM8. These aquatic frogs are poikilotherms, their core body temperature fluctuates with environmental temperature, in a range clearly below the core body temperature of mammals and birds. While various properties (i.e. menthol sensitivity and voltage-dependence) of frog TRPM8 were similar to those described for rat and mice, there was a clear shift in the thermal response of the channel towards temperatures below their "normal" core temperature. The amino acid sequence of Xenopus TRPM8 displays 75% identity to the rat sequence. This result suggests that this thermo TRP is under strong evolutionary pressure, likely reflecting an important role in temperature sensing in species other than mammals. Besides the intrinsic interest of this novel information for thermosensory biology in general, a careful analysis of the differences in sequence between different species, and the construction of chimeras, may provide additional insights into the mechanism of temperature gating of TRPs, an important unsolved question".

References: {1} McKemy et al. Nature 2002, 416:52-8 [PMID:11882888]. {2} Peier et al. Cell 2002, 108:705-15 [PMID:11893340].

Single Cell Genomics: New PLoS ONE article evaluated at Faculty of 1000

2009-06-10T21:59:00.001+05:30

I recently handled an interesting article at PLoS ONE [Assembling the marine metagenome, one cell at a time. Woyke T, et al., PLoS ONE 2009 4(4):e5299].

As for the other high ranking PLoS ONE articles, this article too was evaluated at the Faculty of 1000 Biology and was rated with a F1000 Factor of 6.0 (Must Read). A redacted version of the evaluation by Douglas Bartlett is here:

'This work details the use of single cell genomics from two uncultured marine Flavobacteria to recruit considerable sequence data from the Global Ocean Survey (GOS) compared to genome sequences from cultured Flavobacteria isolates. The genome reconstruction and stringent quality control of the two SAGs (single amplified genomes) are well handled, considering contamination and chimeras associated with the amplification process. The analyses of the two SAGs indicate unique metabolic features such as hydrogen oxidation, proteorhodopsin photometabolism, and biopolymer hydrolysis. Also of interest is the genome streamlining in the ...' ..... Full evaluation of the article is available here (http://www.f1000biology.com/article/id/1160822).

BLoG ONE has moved to Word Press

2009-06-10T16:14:00.001+05:30

A mirror of BLoG ONE now operates from WordPress. All contents from this site will be mirrored from there.

PLoS ONE Prokaryotic Genome Collection - now launched

2009-06-10T13:22:00.007+05:30

I am excited to tell you of the latest collection of some of the high-impact articles, the PLoS ONE Prokaryotic Genome Collection. Liz Allen of PLoS, has some more things to say …read her full blog post here.

There is an editorial overview that accompanies the new collection; it’s written by me. Comments related to the collection and the ‘overview’ have started to trickle in, such as this one by Dr Ramy Aziz:

“This article lists very interesting challenges and questions that will be answered in the next decade of this millennium. With the revolution stirred by next-gen sequencing machines, sequencing/resequencing steps have become quick and cheap. Thus, data generation is the least part to worry about. However, as the article appropriately discusses, the problem is what to sequence and then how to make sense out of the piles.

We will very soon have 5,000 fully sequenced prokaryotic genomes, but, as quick annotation tools are being developed, we realize very well that more genomes annotated = more errors propagated.

In addition to high-speed and high-performance …” … Read more here.

Evidence of Leprosy in Ancient India

2009-06-03T13:39:00.003+05:30

In a recent PLoS ONE article, Gwen Robbins and colleagues reported analysis of a 4000-year-old skeleton from India, which represents both the earliest archaeological evidence for human infection with Mycobacterium leprae in the world and the first evidence for the disease in prehistoric India. I think the authors need to have clear definitions of 'ancient origins' and 'historic presence'. Leprosy has clear origins from Africa as for tubeculosis (TB). After spreading from Africa the disease may have assumed endemic potentials in certain countries such as India. Therefore, the findings here should be consistent with our own research, published back in 2006 about TB, wherein we suggested that India was a historic cradle for mycobacterial infections and that she served as an ancient corridor for an early worldwide spread of TB. The authors did not cite our work; may be an oversight! But, I am more concerned that they as well forgot to refer to an important PLoS ONE paper which recently attempted to characterize about 9000 year old skeletons from submerged, ancient burials in Israel using paleopathology and DNA based evidence.

How to get cited one hundred times?

2009-03-03T20:13:00.005+05:30

Exactly 2 years ago, PLoS ONE published this superb article (Fahlgren N, et al., 2007 High-throughput sequencing of Arabidopsis microRNAs: Evidence for frequent birth and death of MIRNA genes. PLoS ONE 2: e219), a citation classic. Thanks to its being published via Open Access, today it crossed the landmark of one hundred citations in Google Scholar. The paper thus became one of the star articles of PLoS series and the first one from PLoS ONE to log 3 digit citations in a record time of 2 years. The article was also evaluated in F1000 Biology and its corresponding author interviewed at PLoS blog.

Gut Pathogens: a new forum for enteric health at the interface of changing microbiology

2009-02-03T23:03:00.005+05:30

Today is the special day for us and the ISOGEM; we launched Gut Pathogens, the 200th Open Access journal of the Biomed Central. Gut Pathogens is a new OA journal publishing articles on all aspects of the biology and pathogenesis of bacterial, parasitic and viral infections of the gut, including their diagnosis and clinical management.

Gut Pathogens shall be the official journal of The International Society for Genomic and Evolutionary Microbiology (ISOGEM) and is supported by a qualified Editorial Board of active scientists and clinicians. We have detailed in the launch Editorial how we hope that an open access journal in this field will provide a high-quality forum for research on enteric infections of humans and animals, facilitating the practice of preventive and social medicine for the benefit of the patients.

Novel ‘replication check mechanism’ key to dormant Tuberculosis

2009-01-07T21:50:00.006+05:30

Tuberculosis is a major communicable disease expanding globally and is caused by Mycobacterium tuberculosis (M. tb). The disease is a main killer among infectious diseases in the world with the occurrence of 2 million deaths each year and 8 million cases of active disease. The biggest challenge of tuberculosis (TB) is its ability to survive in dormant form in apparently healthy individuals for decades. M.tb, the diehard pathogen that causes tuberculosis, is capable of staying asymptomatically in a latent form, persisting for years in very low replicating state, before getting reactivated to cause active infection.

M.tb is known to survive for extended periods during the latency phase without any replication. During this phase the bacterium senses the surrounding environmental conditions such as availability of nutrients, immune cell preponderance etc. and if needed puts its machinery back in action to grow and replicate. The regulation of chromosomal DNA replication therefore is a very important switch to maintain dormancy. While the bacterium is dormant replication is bare minimum.

A new study published by PLoS ONE (In-vitro helix opening of M. tuberculosis oriC by DnaA occurs at precise location and is inhibited by IciA like protein) provides some fresh insights into maintenance of dormancy by the pathogenic mycobacteria. Professor Seyed E. Hasnain (Distinguished Professor at the Institute of Life Sciences at the Hyderabad University campus, Hyderabad, India) who led the study said ‘the dormant state of the bacterium is maintained by a novel protein called as Inhibitor of Chromosomal initiation (IciA), which our group has rigorously characterized and which binds to the A+T rich region of the origin of replication’. ‘This binding blocks helix opening of the A+T rich region, a step critical for chromosomal replication initiation to occur’ says Hasnain. This represents the first evidence that chromosomal DNA replication control is a critical molecular switch in the form of IciA protein, which the TB bacteria over express to remain dormant.

Besides identification of the replication check phenomenon by the IciA, the study also generated an in vitro model of mycobacterial replication which will be a very important tool in the hands of infection biologists trying to understand intricacies of microbial acquisition, survival and adaptation under different stress conditions and in different hosts. Although the present study largely represents laboratory based observations, direct evidence for the role of the IciA like protein will come from M.tb iciA knockout experiments to be performed in an animal infection model. While such experiments are underway at Hasnain labs, it will be interesting to see if quantitative expression of IciA in tuberculosis patient’s material could effectively be harnessed as a molecular marker of M.tb activation.

Songs that thronged PLoS ONE through 2008

2009-01-04T14:05:00.011+05:30

Well, we listened a lot to bird songs last year at PLoS ONE forums and journal clubs. After birds, mice arrived on the scene to sing and squeal, meaning that rodents could as well joyfully sing, and that their songs to prospective mates are as likely complex as those of birds. However, unlike birds, their vocalizations are discharged at ultrasonic frequencies, and that is why no one noticed them, nor was anyone motivated to celebrate them. But, as one of the many celebrated PLoS ONE stories (DOI: 10.1371/journal.pone.0001893) echoes in popular media and blogosphere, we may hope they will likely find a place in romantic poetry! The article was published by H. Wang and colleagues quite some time back (in April 2008), but was recently showcased in a recent news round-up by New Scientist of the top ten genetics stories of the year. Alison Motluk of New Scientist discussed this research and also provided recordings of the squeaks of male mice in a human audible format.

“Most musical, most melancholy bird,” said Samuel Taylor Coleridge of the nightingale ‘but whether birdsong can affect us in the same way as a beautiful sonata played by a human musician is another matter’ said Rebecca Walton in her blog post summating another celebrated article by Stefan Koelsch of the University of Sussex, wherein his team, investigated differential response to instrumental and computerised music. According to this research, volunteers who listened to recordings of professional pianists showed more emotional activity of the brain than did those who listened to recordings made by computer. This article was covered in different headlines by the Chronicle of Higher Education (Don't Cry For Me, R2D2), The Telegraph (Sweaty music find could help develop new treatments), The Guardian (Music that brings a tear to the eye), Wired (Study: Computer Musicians Ain't Got No Soul) and PsychCentral (Computer Music Not As Calming).

At the end of the year, one more article ("Practicing a musical instrument in childhood is associated with enhanced verbal ability and nonverbal reasoning" PLoS ONE, 2008) dominated the blogosphere, this time for another reason, to celebrate the second birthday of PLoS ONE! This was all about an excellent blog by SciCurious of the Neurotopia 2.0 (Einstein was smart, but Could He Play the Violin?) who won the PLoS ONE second birthday synchroblogging competition organized on December 20, 2008.

All content published in PLoS ONE, from dinosaurs to elephants to chimps to birds to bats and about mice to butterflies and bees is freely available online. Rate them and comment and discuss yourself to enjoy the full power of Web 2.0 technology that PLoS ONE harnesses. Here at PLoS ONE is certainly quite diverse food for thought and you can always join in the discussion by creating an account on the journal site and posting your comments for others to read.

New PLoS ONE articles evaluated at F1000 Biology

2008-12-24T20:38:00.002+05:30

It appears that the year 2008 is closing on a good note - in the last 6 days three important articles from PLoS ONE were evaluated by the F1000 Biology faculty. These articles were graded as significantly novel reports (see below).

Rapid SNP discovery and genetic mapping using sequenced RAD markers. Baird NA, Etter PD, …, Cresko WA, Johnson EA PLoS ONE 2008 3(10):e3376

Evaluated by: Tony Long on December 23, 2008

F1000 Factor: 6.0 (Must Read)

If I were you: perceptual illusion of body swapping. Petkova VI, Ehrsson HH PLoS ONE 2008 3(12):e3832

Evaluated by: Aina Puce on December 19, 2008

F1000 Factor: 6.0 (Must Read)

The zinc transporter SLC39A13/ZIP13 is required for connective tissue development; its involvement in BMP/TGF-beta signaling pathways. Fukada T, Civic N, …, Superti-Furga A, Hirano T PLoS ONE 2008 3(11):e3642

Evaluated by Bruce Pitt on December 18, 2008

F1000 Factor: 9.0 (Exceptional)

All PLoS ONE content is freely available on the web and readers could themselves rate and evaluate the articles. However, those evaluated on F1000 are certainly the crème de la crème kind of material; at any given time about 4% of the PLoS ONE articles are evaluated at the F1000.

PLoS ONE second birthday blogging competition: winners in waiting

2008-12-20T17:24:00.004+05:30

A blogging competition to mark second birthday of the revolutionary Open Access publishing project by name PLoS ONE, was organized on December 18. Bora Zivkovic has posted on his blog the final list of eligible posts that discuss some of the most interesting articles published in recent times in PLoS ONE. I have read all the posts and they are really very nice. I think the jury will have a tough time deciding the winner. Here are the winners in waiting:

Barn Owl of Guadalupe Storm-Petrel: DNA Repair During Spermatogenesis: Gimme a Break! about the article: Deletion of Genes Implicated in Protecting the Integrity of Male Germ Cells Has Differential Effects on the Incidence of DNA Breaks and Germ Cell Loss

Ed Yong of Not Exactly Rocket Science: Predatory slime mould freezes prey in large groups about the article: Exploitation of Other Social Amoebae by Dictyostelium caveatum

Scicurious of Neurotopia (version 2.0): Why Did the Dolphin Carry a Sponge? about the article: Why Do Dolphins Carry Sponges?

Scicurious of Neurotopia (version 2.0): Einstein was smart, but Could He Play the Violin? about the article: Practicing a Musical Instrument in Childhood is Associated with Enhanced Verbal Ability and Nonverbal Reasoning

Allyson of Systems Biology & Bioinformatics (Semantically Speaking) on One way for RDF to help a bioinformatician build a database: S3DB (also cross-posted on The mind wobbles: One way for RDF to help a bioinformatician build a database: S3DB) about the article: A Semantic Web Management Model for Integrative Biomedical Informatics

Simon Cockell of Fuzzier Logic: Contextual Specificity in Peptide-Mediated Protein Interactions about the article: Contextual Specificity in Peptide-Mediated Protein Interactions

Mike Haubrich of Tangled Up in Blue Guy : Small-Bodied Humans on Palau - A Disagreement about the articles: Small-Bodied Humans from Palau, Micronesia and Small Scattered Fragments Do Not a Dwarf Make: Biological and Archaeological Data Indicate that Prehistoric Inhabitants of Palau Were Normal Sized

Martin of The Lay Scientist : Catching Snowflakes: The Media and Public Perceptions of Disease about the article: Medicine in the Popular Press: The Influence of the Media on Perceptions of Disease

Nir London of Macromolecular Modeling Blog: Model for the Peptide-Free Conformation of Class II MHC Proteins about the article: Model for the Peptide-Free Conformation of Class II MHC Proteins

Greg Laden of Greg Laden's blog: How to make an elephant turn invisible about the articles: Risk and Ethical Concerns of Hunting Male Elephant: Behavioural and Physiological Assays of the Remaining Elephants, Roadless Wilderness Area Determines Forest Elephant Movements in the Congo Basin, Elephant (Loxodonta africana) Home Ranges in Sabi Sand Reserve and Kruger National Park: A Five-Year Satellite Tracking Study and Population and Individual Elephant Response to a Catastrophic Fire in Pilanesberg National Park.

The Neurocritic of The Neurocritic blog: Can You Reread My Mind? about the article: Using fMRI Brain Activation to Identify Cognitive States Associated with Perception of Tools and Dwellings

Moneduloides of Moneduloides blog: A trypanosome and a tsetse walk into a bar... about the article: Factors Affecting Trypanosome Maturation in Tsetse Flies

El-Ho of Pas d'il y'on que nous: The Etiology of Fear about the article: Coupled Contagion Dynamics of Fear and Disease: Mathematical and Computational Explorations

Ian of Further thoughts: Evolution and conservation in Mexican dry forests about the article: Sources and Sinks of Diversification and Conservation Priorities for the Mexican Tropical Dry Forest

Alun Salt of Archaeoastronomy: If you put a snail shell to your ear can you hear the sound of your thoughts? about the article: Climate Change, Genetics or Human Choice: Why Were the Shells of Mankind's Earliest Ornament Larger in the Pleistocene Than in the Holocene?

Michael Tobis of Only In It For The Gold: The Singularity about the article: Ecosystem Overfishing in the Ocean

PodBlack Cat of PodBlack blog: Pet Ownership - Maybe Not For Better Health, Perhaps Sense Of Humour? about the article: To Have or Not To Have a Pet for Better Health?

Juan Nunez-Iglesias of I Love Symposia!: Randomise your samples! about the article: Randomization in Laboratory Procedure Is Key to Obtaining Reproducible Microarray Results

Munger of Cognitive Daily is one of the judges: Make sure you get some sleep -- or at least some caffeine -- before that test about the article: Sleep Loss Produces False Memories

A PLoS ONE article that is hot favourite of F1000 Editors

2008-12-12T20:05:00.003+05:30

Last month I evaluated on F1000 an article from PLoS ONE that addressed infection as a driving force for the extinction of rats native of Christmas Island. The importance of this timely study was also discussed on BLoG ONE. Apparently, it appears that the F1000 evaluation of this article has been taken on quite a good note. It just appeared in the latest issue of the F1000 update wherein the Editors of F1000 reinforce the opinion that the PLoS ONE paper indeed provides important evidence that infectious diseases are a potential cause of future extinctions of endangered mammalian species. The original article is freely available for anyone to read, rate and comment.

Good-bye CDFD

2008-12-12T01:22:00.004+05:30

Finally, today I said good-bye to CDFD, the institute where I worked for more than 10 years. It has been a wonderful experience being there and having enjoyed each and every moment of a busy scientific career. The University of Hyderabad, my new employer, extended a warm welcome also to my advocacy of Science 2.0, PLoS ONE and Open Access in general. Change is for the betterment - lets see how true.

The first case of mammalian extinction due to an exotic disease – an alarm bell for conservation efforts?

2008-11-18T22:01:00.005+05:30

An interesting article that we accepted last month for PLoS ONE describes a very fine DNA detective work to put forth the hypothesis of mammalian extinction due to an introduced infectious disease. The research published on November 6 suggests that a century ago the black rat species, which led to the emergence of the bubonic plague in Medieval Europe and considered one of the worst invasive species on the planet, sheltered a parasitic disease that eliminated two immunologically naive rat species native to the Christmas Island in the Indian Ocean.

Alex Greenwood from the Old Dominion University in Norfolk, Virginia, and colleagues brilliantly attempted to solve the mystery of the mammalian extinctions. They collected samples from 21 historical rat specimens from Christmas Island stored at natural history museums across the United Kingdom. These researchers analyzed preserved remains of black rats, the extinct species, and the crosses of the two. The century old specimens were then analyzed for genetic signatures of crossbreeding as well as for the presence of Trypanosoma lewisi, the close relative of the sleeping sickness pathogen, T. evansii.

The interesting part of the story is that the authors argue they did not find any evidence of hybridization between black rats and Christmas Island rats. They emphasize that mere invasion does not necessarily lead to extinction and, that on Christmas Island, the Christmas Island shrew survived until 1985 even in the presence of black rats, arguing against general competitive exclusion or predation. Therefore, it appears that their data are more consistent with disease as a reason for extinction rather than competition.

The authors speculate that the extinction of Christmas Island rats (Rattus macleari) was due to a trypanosome pathogen present in fleas carried by black rats introduced to the island (Rattus rattus). The study presents acceptable evidence for the presence of trypanosome infection in the Christmas Island rats after black rats have been introduced to the island, but not before.

However, if we consider some of the arguments, the scenario becomes little implausible - Trypanosome diseases do not normally have short and acute progression and T. lewisi (which the authors tested for) is not reported to be acutely pathogenic in rats. The other question could be - what is the reason to believe that the Christmas Island rats would reveal a different pathology compared with the black rats which were putatively carrying the disease? Nevertheless, it is possible that R. macleari would have been immunologically naïve to black rat pathogens which acted more deadly in a naïve host compared to its natural host or to a host adapted to it. But the next argument could be - why the Christmas Island rats were not killed by some other pathogen (for example a rodent virus) introduced by the black rats? Also, it is possible that the authors missed a possible interspecific ecological competition that might have served as an important extinction force. But no one knows ways to test that!

Leaving this debate to the scientific community (and the PLoS ONE readership at large) to choose among different explanations, I thought the paper was indeed worthy of publication because some of the emerging and re-emerging infectious diseases could possibly serve as a strong force to future extinctions, especially of the wildlife that are increasingly threatened and we thus have a warning bell in the form of this important study.

The Cancer Week - Nagoya: Paradigm shift in Japanese Science Communication

2008-10-31T16:37:00.002+05:30

Traditionally, a majority of the Japanese researchers and clinicians have been shying off the mainstream communication skills in science and technology. However, this seems fast becoming history. The Japanese Cancer Association (JCA) meeting, a grand annual event in cancer science and medicine, started this year with a new trend – compulsory communication in English!

The cancer week witnessing the annual congregations of the JCA and the Japan Society for Clinical Oncology began on October 27 this year in Nagoya. The twin meeting was attended by 5000 attendees comprising of cancer specialists, doctors, basic researchers and students. Reportedly, for the first time in the last 66 years’ history of the Japanese cancer meetings, it was made compulsory for the presenters to write their abstracts in English only and 12 dedicated International sessions (with English only presentations) were organized. Also, the aspects of World Cancer Declaration were presented for the want of advocacy and solidarity of the Japanese cancer community to the cause of global cancer prevention.

This new beginning has also made possible for International academics and doctors to participate and communicate through the platform of JCA. It was especially a great opportunity for me to have shaped, participated and chaired one of their international sessions. This was also a nice platform for Open Access advocacy and I was excited to note the growing interest of Japanese biosciences community towards OA journals in general and PLoS ONE in particular.

The next JCA meeting is planned in Tokyo in 2009. Let us hope it will be equally successful and rewarding.

PLoS ONE - what is going unnoticed?

2008-10-28T13:30:00.006+05:30

I feel so proud each time PLoS ONE is attached to some high profile science personalities. Françoise Barré-Sinoussi is one such icon - Nobel Laureate and a PLoS ONE author. This was announced and highlighted soon after she won the Nobel Prize, earlier this month. The other great thing that happened during the same time-period (and went largely unnoticed!) was the F1000 evaluation (of a PLoS ONE article) by none other than Rino Rappuoli !

Here is his evaluation:

Extensive adaptive changes occur in the transcriptome of Streptococcus agalactiae (group B streptococcus) in response to incubation with human blood. Mereghetti L, Sitkiewicz I, Green NM, Musser JM. PLoS ONE 2008 3(9):e3143

'In this work, the group of James Musser applied a microarray approach in order to understand how Streptococcus agalactiae (GBS) adapts its transcriptional profile to growth in human blood during invasive disease. The authors observe the up-regulation of GBS virulence genes involved in host-bacteria interaction, such as factors involved in the interaction with the complement system and the coagulation/fibrinolysin system. Ex-vivo blood cultures were used to mimic sepsis and overcome the limitations of animal models (i.e. bias due to species-specific differences, appropriate volumes of blood and adaptation throughout time during animal blood exposure). The findings validate the use of ex-vivo human blood cultures as a surrogate of the invasive infection. Approaches like this one, pioneered by the group of James Musser, will be instrumental to understanding the mechanisms by which bacterial pathogens evade the host immune system leading to survival and proliferation in the human body'.

Complete evaluation of this article including ratings etc. is available via F1000 Biology. A total of 130 articles from PLoS ONE have been evaluated at F1000.

TB and Mycobacteria community publishes in PLoS ONE

2008-08-22T21:02:00.002+05:30

Tuberculosis (TB) continues to cause increasing deaths globally and last year alone about 1.7 million lives were lost (The World Health Organization, 2006). The human immunodeficiency virus (HIV) epidemic has worsened the situation as the incidence rates dramatically jumped in recent times (http://www.globalhealthfacts.org). Most countries that are crippled by the menace of TB have negligible flow of international funding for research and new fruits of post genomic discovery are yet to percolate to these zones. Library budgets are seriously dwindling and the researchers, clinicians and higher degree students have no access to TB research that has been traditionally published in ‘closed access’ journals. I recall my days (1997) at the National Dairy Research Institute, Karnal (India), where, I had to run on almost weekly basis to the National Medical Library in Delhi (100 Kilometers) or to the library of the Post Graduate Institute of Medical Research (PGI) at Chandigarh (~100 Kilometers) to refer to some of the 'print only' journals for my dissertation work on TB. The situation has not improved much even today. Thankfully, Open Access publishing has arrived as the new ray of hope for many who hold dear to their hearts the cause of poverty alleviation through epidemic control. PLoS ONE has been seriously partnering this cause since its inception in 2006 and has since then published about 73 landmark articles addressing the broad areas of TB control, mycobacterial biology and medicine. We at PLoS ONE are overwhelmed with this response of the TB and mycobacteria community and thank the authors who opted for the journal to showcase their research and to widen access to those who desperately need it - the developing world. In particular, it is quite pleasing for me to put on record the patronage extended by the mycobacterial research community from India by publishing highest number of papers on the topic from a high burden country.

Exciting and noteworthy in PLoS ONE: My picks

2008-07-31T20:21:00.001+05:30

There are 62 brand new articles published at PLoS ONE this week which certainly reflects quite diverse food for thought. You can always join in discussion on interesting articles by creating an account on the journal site and posting your comments for others to read. Also, you may like to rate the articles. Ratings are the quickest and easiest way for users to indicate their support for the authors and to highlight which articles are of potential impact for the readers and the community. I suggest why not to begin with these exciting ones?

Dinosaurian Soft Tissues Interpreted as Bacterial Biofilms:

A scanning electron microscope survey was initiated to determine if the previously reported findings of "dinosaurian soft tissues" could be identified in situ within the bones. The results obtained allowed a reinterpretation of the formation and preservation of several types of these "tissues" and their content. Mineralized and non-mineralized coatings were found extensively in the porous trabecular bone of a variety of dinosaur and mammal species across time. They represent bacterial biofilms common throughout nature. Biofilms form endocasts and once dissolved out of the bone, mimic real blood vessels and osteocytes. Bridged trails observed in biofilms indicate that a previously viscous film was populated with swimming bacteria. Carbon dating of the film points to its relatively modern origin. A comparison of infrared spectra of modern biofilms with modern collagen and fossil bone coatings suggests that modern biofilms share a closer molecular make-up than modern collagen to the coatings from fossil bones. Blood cell size iron-oxygen spheres found in the vessels were identified as an oxidized form of formerly pyritic framboids. Our observations appeal to a more conservative explanation for the structures found preserved in fossil bone.

Remodeling of the Streptococcus agalactiae Transcriptome in Response to Growth Temperature

To act as a commensal bacterium and a pathogen in humans and animals, Streptococcus agalactiae (group B streptococcus, GBS) must be able to monitor and adapt to different environmental conditions. Temperature variation is a one of the most commonly encountered variables. To understand the extent to which GBS modify gene expression in response to temperatures encountered in the various hosts, we conducted a whole genome transcriptome analysis of organisms grown at 30°C and 40°C. We identified extensive transcriptome remodeling at various stages of growth, especially in the stationary phase (significant transcript changes occurred for 25% of the genes). A large proportion of genes involved in metabolism was up-regulated at 30°C in stationary phase. Conversely, genes up-regulated at 40°C relative to 30°C include those encoding virulence factors such as hemolysins and extracellular secreted proteins with LPXTG motifs. Over-expression of hemolysins was linked to larger zones of hemolysis and enhanced hemolytic activity at 40°C. A key theme identified by our study was that genes involved in purine metabolism and iron acquisition were significantly up-regulated at 40°C. Growth of GBS in vitro at different temperatures resulted in extensive remodeling of the transcriptome, including genes encoding proven and putative virulence genes. The data provide extensive new leads for molecular pathogenesis research.

Streptococcus iniae M-Like Protein Contributes to Virulence in Fish and Is a Target for Live Attenuated Vaccine Development

Streptococcus iniae is a significant pathogen in finfish aquaculture, though knowledge of virulence determinants is lacking. Through pyrosequencing of the S. iniae genome we have identified two gene homologues to classical surface-anchored streptococcal virulence factors: M-like protein (simA) and C5a peptidase (scpI). S. iniae possesses a Mga-like locus containing simA and a divergently transcribed putative mga-like regulatory gene, mgx. In contrast to the Mga locus of group A Streptococcus (GAS, S. pyogenes), scpI is located distally in the chromosome. Comparative sequence analysis of the Mgx locus revealed only one significant variant, a strain with an insertion frameshift mutation in simA and a deletion mutation in a region downstream of mgx, generating an ORF which may encode a second putative mga-like gene, mgx2. Allelic exchange mutagenesis of simA and scpI was employed to investigate the potential role of these genes in S. iniae virulence. Our hybrid striped bass (HSB) and zebrafish models of infection revealed that M-like protein contributes significantly to S. iniae pathogenesis whereas C5a peptidase-like protein does not. Further, in vitro cell-based analyses indicate that SiMA, like other M family proteins, contributes to cellular adherence and invasion and provides resistance to phagocytic killing. Attenuation in our virulence models was also observed in the S. iniae isolate possessing a natural simA mutation. Vaccination of HSB with the ΔsimA mutant provided 100% protection against subsequent challenge with a lethal dose of wild-type (WT) S. iniae after 1,400 degree days, and shows promise as a target for live attenuated vaccine development. Analysis of M-like protein and C5a peptidase through allelic replacement revealed that M-like protein plays a significant role in S. iniae virulence, and the Mga-like locus, which may regulate expression of this gene, has an unusual arrangement. The M-like protein mutant created in this research holds promise as live-attenuated vaccine.

Effect of Attenuation of Treg during BCG Immunization on Anti-Mycobacterial Th1 Responses and Protection against Mycobacterium tuberculosis

The functional equilibrium between natural regulatory T cells (Treg) and effector T cells can affect the issue of numerous infections. In unvaccinated mice, the influence of Treg in the control of primary infection with mycobacteria remains controversial. Here, we evaluated the role of Treg during prophylactic vaccination with Mycobacterium bovis BCG (Bacillus Calmette-Guérin) on the induction of T cell responses and on the protective effect against subsequent M. tuberculosis challenge in mice. We demonstrated that, subsequent to BCG injection, Treg were recruited to the draining lymph nodes and negatively control anti-mycobacterial CD4+ — but not CD8+ — T-cell responses. Treatment of BCG-immunized mice with an anti-CD25 mAb (PC61) induced an increase IFN-γ response against both subdominant and immunodominant regions of the protective immunogen TB10.4. In Treg-attenuated, BCG-immunized mice, which were then infected with M. tuberculosis, the lung mycobacterial load was significantly, albeit moderately, reduced compared to the control mice. Our results provide the first demonstration that attenuation of Treg subset concomitant to BCG vaccination has a positive, yet limited, impact on the protective capacity of this vaccine against infection with M. tuberculosis. Thus, for rational design of improved BCG, it should be considered that, although the action of Treg does not represent the major cause of the limited efficiency of BCG, the impact of this cell population on the subsequent control of M. tuberculosis growth is significant and measurable.

Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing

Humans host complex microbial communities believed to contribute to health maintenance and, when in imbalance, to the development of diseases. Determining the microbial composition in patients and healthy controls may thus provide novel therapeutic targets. For this purpose, high-throughput, cost-effective methods for microbiota characterization are needed. We have employed 454-pyrosequencing of a hyper-variable region of the 16S rRNA gene in combination with sample-specific barcode sequences which enables parallel in-depth analysis of hundreds of samples with limited sample processing. In silico modeling demonstrated that the method correctly describes microbial communities down to phylotypes below the genus level. Here we applied the technique to analyze microbial communities in throat, stomach and fecal samples. Our results demonstrate the applicability of barcoded pyrosequencing as a high-throughput method for comparative microbial ecology.