Friday, May 27, 2011

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

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.

Saturday, May 21, 2011

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

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


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.


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.


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.

Friday, May 6, 2011

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

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