Pushker's Blog

Argala Magazine

2008-10-16T08:00:00.000-07:00

We are about to release the first issue of a Hindi magazine called "Argala" ( www.argala.org ). It will be online for first few months and later from January 2009 onwards we will go for print issue. We are very much in favour of contributions from young people specially who are less than 30 years old or don't have any publication history. All other contributions are by invitation only. We welcome all kind of contribution related to Hindi literature such as, Kavita, Kahani, Lekh, Sameeksha or anything which suggest how to promote Hindi or Hindi literature. There is one column which is dedicated to Translated articles from other languages to Hindi.

In the first issue of Argala some of the highlights are, Interview of India's biggest award in literature ie Sahitya Academy Award winner Amarkant, Interview of Dr. Soumyabrata Chowdhury, a famous theater director and writer, article of Late Acharya Ramchandra Shukla and a few contributions from some of the most famous personalities in this field - Dr. Varyam Singh, Dr. Ganga Prasad Vimal, Dr. Anand Kumar and Dr. Devendra Chowbey.

Hoping to hear from you soon.

Regards,

Ravindra Pushker

Member, Editorial Board

Argala

The Neolithic revolution of Bacterial genomes

2006-02-23T09:36:00.000-08:00

Finally the most awaited article "The Neolithic revolition of bacterial genomes" has been accepted for publication in Trends in Microbiology.

Abstract

Current human activities undoubtedly impact natural ecosystems. However, the influence of Homo sapiens on living organisms must have also occurred in the past. We show that certain genomic characteristics of prokaryotes can be used to study the impact of ancient human activities on microorganisms. By analysing DNA sequence similarity features of transposable elements we have identified dramatic genomic changes in bacteria associated with human populations, agriculture and farming, three activities unequivocally linked to the Neolithic Revolution. We hypothesize that bacteria specialised in human-associated niches underwent an intense transformation after the social and demographic changes that took place with the first neolithic settlements. These genomic changes are absent in related species that are not specialised in humans.

Citation

Mira A., Pushker R. and Rodríguez-Valera F. (2006) The Neolithic revolution of bacterial genomes. Trends in Microbiology, In press

IWoCS is accepted

2005-12-29T05:56:00.000-08:00

There can't be anything better to end this year. Today one research article IWoCS has been accpeted for publication in Bioinformatics.

Abstract

In the last ten years the use of ITS sequences for bacterial typing purposes has increased. The 16S-23S Intergenic Transcribed Spacers (ITS) are characterized by a high variability that allows performing intraspecic discrimination of very close bacterial strains. The presence of conserved regions like tRNA genes or boxes together with hyper variable regions makes the ITS a very complex sequence dificult to analyze and compare. A software to study Intergenic Transcribed Spacers by a Word Count based System (IWoCS) has been proposed. A wide dataset of ITS was created (comprising 6,398 sequences) jointly with a n-mer (with n going from 5 to 10) database where all the occurrences of possible mer, describing each ITS sequence, were collected including 16,509,227 entries. The database allows to analyze ITS sequences submitted by users using a web based interface. The abundance in the database of each n-mer is given in a one-base sliding frame. The obtained profile identifies common n-mers as conserved regions (like tRNA or boxes) or rare n-mers as unique regions with corresponding taxonomic specificity. The study of the obtained profile highlights conserved or strain specific regions with a concomitant taxonomy report. Each mer could be used to retrieve the corresponding sequences for subsequent taxonomy or relationship analysis.

Micro-Mar is published

2005-09-09T17:36:00.000-07:00

Pushker R., D'Auria G., Alba-Casado J.C. and Rodriguez-Valera F. (2005) Micro-Mar: a database for dynamic representation of marine microbial biodiversity. BMC Bioinformatics, 6:222

Background: The cataloging of marine prokaryotic DNA sequences is a fundamental aspect for bioprospecting and also for the development of evolutionary and speciation models. However, large amount of DNA sequences used to quantify prokaryotic biodiversity requires proper tools for storing, managing and analyzing these data for research purposes.

Description: The Micro-Mar database has been created to collect DNA diversity information from marine prokaryotes for biogeographical and ecological analyses. The database currently includes 11874 sequences corresponding to high resolution taxonomic genes (16S rRNA, ITS and 23S rRNA) and many other genes including CDS of marine prokaryotes together with available biogeographical and ecological information.

Conclusions: The database aims to integrate molecular data and taxonomic affiliation with biogeographical and ecological features that will allow to have a dynamic representation of the marine microbial diversity embedded in a user friendly web interface. It is available online at http://egg.umh.es/micromar/

Micro-Mar is accepted

2005-08-23T08:55:00.000-07:00

Peer Review of "Micro-Mar: a database for dynamic representation of marine microbial biodiversity" is complete and it has been accepted for publication in BMC Bioinformatics.

Hi to Nijmegen, The Netherlands

2005-08-21T08:08:00.000-07:00

I am in Nijmegen, Netherlands. It was raining all the day so couldn't see much of Nijmegen.

Hi to Dublin, Ireland

2005-08-11T19:39:00.000-07:00

I am in Dublin, Ireland. I went to Galway also with my friends. The weather was not that bad. Sometimes a bit cloudy but no rains.