Friday, December 10, 2010

Pioneers of Malaysian goodness in PLoS ONE: Mohamed Rais Mustafa

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'.

Saturday, December 4, 2010

The art of giving: Azim Premji shows the way!

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)

Saturday, November 6, 2010

The beauty of Mathematics!

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...




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:






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.





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


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





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


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





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!

Thursday, October 7, 2010

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

'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:

Tuesday, October 5, 2010

Dr Harald Labischinski tribute

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.


Monday, October 4, 2010

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

 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.

Thursday, September 9, 2010

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

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 (OTU0.03) 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.


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:

Tuesday, August 31, 2010

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

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.

Thursday, August 19, 2010

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

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

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

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.

Sunday, August 15, 2010

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

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:

  1. 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?
  2. Why convenient sampling at tertiary hospitals?
  3. 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?
  4. Were the culture and antibiotic sensitivity screening protocols approved by biosafety committees at respective Indian centers and hospitals?
  5. 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?
  6. 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?
  7. 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.

Sunday, August 8, 2010

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

Sunday, June 20, 2010

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

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!

Thursday, May 6, 2010

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

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.

Tuesday, May 4, 2010

New article added to PLoS ONE Prokaryotic Genome Collection

'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

Sunday, April 11, 2010

New articles added to PLoS ONE Prokaryotic Genome Collection

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

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

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

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

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

Sunday, April 4, 2010

PLoS ONE published its 10000th article

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:

Thursday, February 4, 2010

New PLoS ONE articles evaluated at Faculty of 1000


  Faculty of 1000 Biology search alert  Faculty of 1000 Biology
search alert

New PLoS ONE Articles Evaluated at F1000

F1000 Factor 3.0

New Finding
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
F1000 Factor 3.0

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
F1000 Factor 3.0

New Finding
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
F1000 Factor 3.0

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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Wednesday, January 27, 2010

New articles added to the 'PLoS Prokaryotic Genome Collection'

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.

Saturday, January 9, 2010

PLoS ONE indexed by Web of Science (Thomson Reuters)

[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.