Peer review of scholarly communication in health: Perspectives in the Internet age

Peer review is an established form of trust-marking and ensuring quality of scholarly communications. The advent of Internet has had its impact on peer review also. This paper examines the existing approaches of peer review utilizing the Internet. Future approaches, challenges and proposal of a framework for open peer review of directly published scholarly communication on the Internet is also discussed

Cyber-pharmacies and emerging concerns on marketing drugs Online

The booming e-commerce and a regulation-less environment online have led to the rise of a new generation of websites that market drugs and other products over the Internet. Some of these drugs are often herbal products or of dubious quality, often marketed with a mix of professional design and unverified/fraudulent claims. Several concerns have arisen from different corners and evidence of malpractice has emerged. But there is a lack of sufficient evidence confirming the concerns

Open, Online and Global: Benefits of BioMedical Journals Going Online and Open

The emergence of Internet affords the immense possibility for scientific publications to be indexed, linked, copied, archived, redistributed and searched at ease and at a lower production cost. This has paved the way for the emergence of Online-Only Journals like the Online Journal of Health and Allied Sciences. This has also spurred the rise of Open Access movements spearheaded by the Budapest Open Access Initiative and the Public Library of Science. 'Open Access' means immediate, permanent, toll-free, non-gerrymandered, online access to the full-text. Open Access can be considered as borne on three major pillars of Open Access Publishing, Open Access Archiving and Open Access Support and Open Access publishing is perhaps the future of scientific communicatio

microRNAs in viral oncogenesis

MicroRNAs are a recently discovered class of small noncoding functional RNAs. These molecules mediate post-transcriptional regulation of gene expression in a sequence specific manner. MicroRNAs are now known to be key players in a variety of biological processes and have been shown to be deregulated in a number of cancers. The discovery of viral encoded microRNAs, especially from a family of oncogenic viruses, has attracted immense attention towards the possibility of microRNAs as critical modulators of viral oncogenesis. The host-virus crosstalk mediated by microRNAs, messenger RNAs and proteins, is complex and involves the different cellular regulatory layers. In this commentary, we describe models of microRNA mediated viral oncogenesis

Long Non-Coding RNAs in Infection Biology

Long non-coding RNA have emerged as an increasingly well studied subset of non-coding RNAs (ncRNAs) following their recent discovery in a number of organisms including humans and characterization of their functional and regulatory roles in variety of distinct cellular mechanisms. The recent annotations of long noncoding RNAs in humans peg their numbers as similar to protein-coding genes. However, despite the rapid advancements in the field the functional characterization and biological roles of most of the long noncoding RNAs still remain unidentified, although some candidate long noncoding RNAs have been extensively studied for their roles in cancers and biological phenomena such as X-inactivation and epigenetic regulation of genes. A number of recent reports suggest an exciting possibility of long noncoding RNAs mediating host-response and immune function, suggesting an elaborate network of regulatory interactions mediated through ncRNAs in infection. The present role of long noncoding RNAs in host-pathogen cross talk is limited to a handful of mechanistically distinct examples. The current commentary chronicles the findings of these reports on the role of long noncoding RNAs in infection biology and further highlights the bottlenecks and future directions towards understanding the biological significance of the role of long noncoding RNAs in infection biology

dbSMR: a novel resource of genome-wide SNPs affecting microRNA mediated regulation

Background: MicroRNAs (miRNAs) regulate several biological processes through post-transcriptional gene silencing. The efficiency of binding of miRNAs to target transcripts depends on the sequence as well as intramolecular structure of the transcript. Single Nucleotide Polymorphisms (SNPs) can contribute to alterations in the structure of regions flanking them, thereby influencing the accessibility for miRNA binding. Description: The entire human genome was analyzed for SNPs in and around predicted miRNA target sites. Polymorphisms within 200 nucleotides that could alter the intramolecular structure at the target site, thereby altering regulation were annotated. Collated information was ported in a MySQL database with a user-friendly interface accessible through the URL: http://miracle.igib.res.in/ dbSMR. Conclusion: The database has a user-friendly interface where the information can be queried using either the gene name, microRNA name, polymorphism ID or transcript ID. Combination queries using 'AND' or 'OR' is also possible along with specifying the degree of change of intramolecular bonding with and without the polymorphism. Such a resource would enable researchers address questions like the role of regulatory SNPs in the 3' UTRs and population specific regulatory modulations in the context of microRNA targets

Prediction of viral microRNA precursors based on human microRNA precursor sequence and structural features

MicroRNAs (small ~22 nucleotide long non-coding endogenous RNAs) have recently attracted immense attention as critical regulators of gene expression in multi-cellular eukaryotes, especially in humans. Recent studies have proved that viruses also express microRNAs, which are thought to contribute to the intricate mechanisms of host-pathogen interactions. Computational predictions have greatly accelerated the discovery of microRNAs. However, most of these widely used tools are dependent on structural features and sequence conservation which limits their use in discovering novel virus expressed microRNAs and non-conserved eukaryotic microRNAs. In this work an efficient prediction method is developed based on the hypothesis that sequence and structure features which discriminate between host microRNA precursor hairpins and pseudo microRNAs are shared by viral microRNA as they depend on host machinery for the processing of microRNA precursors. The proposed method has been found to be more efficient than recently reported ab-initio methods for predicting viral microRNAs and microRNAs expressed by mammals

Quadfinder: server for identification and analysis of quadruplex-forming motifs in nucleotide sequences

G-quadruplex secondary structures, which play a structural role in repetitive DNA such as telomeres, may also play a functional role at other genomic locations as targetable regulatory elements which control gene expression. The recent interest in application of quadruplexes in biological systems prompted us to develop a tool for the identification and analysis of quadruplex-forming nucleotide sequences especially in the RNA. Here we present Quadfinder, an online server for prediction and bioinformatics of uni-molecular quadruplex-forming nucleotide sequences. The server is designed to be user-friendly and needs minimal intervention by the user, while providing flexibility of defining the variants of the motif. The server is freely available at URL

A Case for Pharmacogenomics in Management of Cardiac Arrhythmias

Disorders of the cardiac rhythm are quite prevalent in clinical practice. Though the variability in drug response between individuals has been extensively studied, this information has not been widely used in clinical practice. Rapid advances in the field of pharmacogenomics have provided us with crucial insights on inter-individual genetic variability and its impact on drug metabolism and action. Technologies for faster and cheaper genetic testing and even personal genome sequencing would enable clinicians to optimize prescription based on the genetic makeup of the individual, which would open up new avenues in the area of personalized medicine. We have systematically looked at literature evidence on pharmacogenomics markers for anti-arrhythmic agents from the OpenPGx consortium collection and reason the applicability of genetics in the management of arrhythmia. We also discuss potential issues that need to be resolved before personalized pharmacogenomics becomes a reality in regular clinical practice