Articles

Mammalian Argonaute-DNA binding?

When a field shares the consensus that a particular phenomenon does NOT occur, this may reflect extensive experimental investigations with negative outcomes, or may represent the “common sense” position based ...

Authors: Neil R Smalheiser and Octavio L A Gomes

Microbes on the edge of Occam’s razor

Our body harbors hundreds of microbial species and contains many more bacterial than human cells. These microbes are not passive riders but rather a vital component of the organism. The human microbiota affect...

Authors: Petro Starokadomskyy

Cooperation and selfishness both occur during molecular evolution

Perhaps the ‘selfish’ aspect of evolution has been over-emphasised, and organisms considered as basically selfish. However, at the macromolecular level of genes and proteins the cooperative aspect of evolution...

Authors: David Penny

Modeling the population dynamics of lemon sharks

Long-lived marine megavertebrates (e.g. sharks, turtles, mammals, and seabirds) are inherently vulnerable to anthropogenic mortality. Although some mathematical models have been applied successfully to manage ...

Authors: Easton R White, John D Nagy and Samuel H Gruber

Minimization of extracellular space as a driving force in prokaryote association and the origin of eukaryotes

Internalization-based hypotheses of eukaryotic origin require close physical association of host and symbiont. Prior hypotheses of how these associations arose include chance, specific metabolic couplings betw...

Authors: Scott L Hooper and Helaine J Burstein

Chordopoxvirus protein F12 implicated in enveloped virion morphogenesis is an inactivated DNA polymerase

Through the course of their evolution, viruses with large genomes have acquired numerous host genes, most of which perform function in virus reproduction in a manner that is related to their original activitie...

Authors: Natalya Yutin, Guilhem Faure, Eugene V Koonin and Arcady R Mushegian

Putative roles of purinergic signaling in human immunodeficiency virus-1 infection

This article was reviewed by Neil S. Greenspan and Rachel Gerstein.

Authors: Paulo AF Pacheco, Robson X Faria, Leonardo GB Ferreira and Izabel CNP Paixão

A new rhesus macaque assembly and annotation for next-generation sequencing analyses

The rhesus macaque (Macaca mulatta) is a key species for advancing biomedical research. Like all draft mammalian genomes, the draft rhesus assembly (rheMac2) has gaps, sequencing errors and misassemblies that hav...

Authors: Aleksey V Zimin, Adam S Cornish, Mnirnal D Maudhoo, Robert M Gibbs, Xiongfei Zhang, Sanjit Pandey, Daniel T Meehan, Kristin Wipfler, Steven E Bosinger, Zachary P Johnson, Gregory K Tharp, Guillaume Marçais, Michael Roberts, Betsy Ferguson, Howard S Fox, Todd Treangen…

Mycobacteriophage-drived diversification of Mycobacterium abscessus

Mycobacterium abscessus is an emerging opportunistic pathogen which diversity was acknowledged by the recent description of two subspecies accommodating M. abscessus, Mycobacterium bolletii and Mycobacterium mass...

Authors: Mohamed Sassi, Philippe Gouret, Olivier Chabrol, Pierre Pontarotti and Michel Drancourt

Parallel universes of Black Six biology

Creation of lethal and synthetic lethal mutations in an experimental organism is a cornerstone of genetic dissection of gene function, and is related to the concept of an essential gene. Common inbred mouse st...

Authors: Alexander Kraev

Translational selection in human: more pronounced in housekeeping genes

Translational selection is a ubiquitous and significant mechanism to regulate protein expression in prokaryotes and unicellular eukaryotes. Recent evidence has shown that translational selection is weakly oper...

Authors: Lina Ma, Peng Cui, Jiang Zhu, Zhihua Zhang and Zhang Zhang

Impairment of translation in neurons as a putative causative factor for autism

A dramatic increase in the prevalence of autism and Autistic Spectrum Disorders (ASD) has been observed over the last two decades in USA, Europe and Asia. Given the accumulating data on the possible role of tr...

Authors: Eugenia Poliakov, Eugene V Koonin and Igor B Rogozin

Exploring the stability of long intergenic non-coding RNA in K562 cells by comparative studies of RNA-Seq datasets

The stability of long intergenic non-coding RNAs (lincRNAs) that possess tissue/cell-specific expression, might be closely related to their physiological functions. However, the mechanism associated with stabi...

Authors: Lei Wang, Dequan Zhou, Jing Tu, Yan Wang and Zuhong Lu

Pseudo-chaotic oscillations in CRISPR-virus coevolution predicted by bifurcation analysis

The CRISPR-Cas systems of adaptive antivirus immunity are present in most archaea and many bacteria, and provide resistance to specific viruses or plasmids by inserting fragments of foreign DNA into the host g...

Authors: Faina S Berezovskaya, Yuri I Wolf, Eugene V Koonin and Georgy P Karev

Midichlorians - the biomeme hypothesis: is there a microbial component to religious rituals?

Cutting edge research of human microbiome diversity has led to the development of the microbiome-gut-brain axis concept, based on the idea that gut microbes may have an impact on the behavior of their human ho...

Authors: Alexander Y Panchin, Alexander I Tuzhikov and Yuri V Panchin

Selecting biologically informative genes in co-expression networks with a centrality score

Measures of node centrality in biological networks are useful to detect genes with critical functional roles. In gene co-expression networks, highly connected genes (i.e., candidate hubs) have been associated ...

Authors: Francisco J Azuaje

The Rodin-Ohno hypothesis that two enzyme superfamilies descended from one ancestral gene: an unlikely scenario for the origins of translation that will not be dismissed

Because amino acid activation is rate-limiting for uncatalyzed protein synthesis, it is a key puzzle in understanding the origin of the genetic code. Two unrelated classes (I and II) of contemporary aminoacyl-...

Authors: Charles W Carter Jr, Li Li, Violetta Weinreb, Martha Collier, Katiria Gonzalez-Rivera, Mariel Jimenez-Rodriguez, Ozgün Erdogan, Brian Kuhlman, Xavier Ambroggio, Tishan Williams and S Niranj Chandrasekharan

Profiling the orphan enzymes

The emergence of Next Generation Sequencing generates an incredible amount of sequence and great potential for new enzyme discovery. Despite this huge amount of data and the profusion of bioinformatic methods ...

Authors: Maria Sorokina, Mark Stam, Claudine Médigue, Olivier Lespinet and David Vallenet

A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs

We have previously suggested a method for proteome wide analysis of variation at functional residues wherein we identified the set of all human genes with nonsynonymous single nucleotide variation (nsSNV) in t...

Authors: Hayley Dingerdissen, Daniel S Weaver, Peter D Karp, Yang Pan, Vahan Simonyan and Raja Mazumder

Endothelial function is impaired in conduit arteries of pannexin1 knockout mice

Pannexin1 is ubiquitously expressed in vertebrate tissues, but the role it plays in vascular tone regulation remains unclear. We found that Pannexin1 expression level is much higher in the endothelium relative...

Authors: Dina Gaynullina, Olga S Tarasova, Oxana O Kiryukhina, Valery I Shestopalov and Yuri Panchin

Hemoglobins in the genome of the cryptomonad Guillardia theta

Cryptomonads, are a lineage of unicellular and mostly photosynthetic algae, that acquired their plastids through the “secondary” endosymbiosis of a red alga — and still retain the nuclear genome (nucleomorph) ...

Authors: David R Smith, Serge N Vinogradov and David Hoogewijs

Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses

This article was reviewed by Lakshminarayan M. Iyer and I. King Jordan. For complete reviews, see the Reviewers’ Reports section.

Authors: Mart Krupovic, Dennis H Bamford and Eugene V Koonin

Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions

H. sapiens-M. tuberculosis H37Rv protein-protein interaction (PPI) data are essential for understanding the infection mechanism of the formidable pathogen M. tuberculosis H37Rv. Computational prediction is an imp...

Authors: Hufeng Zhou, Shangzhi Gao, Nam Ninh Nguyen, Mengyuan Fan, Jingjing Jin, Bing Liu, Liang Zhao, Geng Xiong, Min Tan, Shijun Li and Limsoon Wong

A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data

ChIP-Seq (chromatin immunoprecipitation sequencing) has provided the advantage for finding motifs as ChIP-Seq experiments narrow down the motif finding to binding site locations. Recent motif finding tools fac...

Authors: Ngoc Tam L Tran and Chun-Hsi Huang

The human platelet: strong transcriptome correlations among individuals associate weakly with the platelet proteome

For the anucleate platelet it has been unclear how well platelet transcriptomes correlate among different donors or across different RNA profiling platforms, and what the transcriptomes’ relationship is with t...

Authors: Eric R Londin, Eleftheria Hatzimichael, Phillipe Loher, Leonard Edelstein, Chad Shaw, Kathleen Delgrosso, Paolo Fortina, Paul F Bray, Steven E McKenzie and Isidore Rigoutsos

Faster evolving Drosophilaparalogs lose expression rate and ubiquity and accumulate more non-synonymous SNPs

Duplicated genes can indefinately persist in genomes if either both copies retain the original function due to dosage benefit (gene conservation), or one of the copies assumes a novel function (neofunctionaliz...

Authors: Lev Y Yampolsky and Michael A Bouzinier

Earth before life

A recent study argued, based on data on functional genome size of major phyla, that there is evidence life may have originated significantly prior to the formation of the Earth.

Authors: Caren Marzban, Raju Viswanathan and Ulvi Yurtsever

Models of gene gain and gene loss for probabilistic reconstruction of gene content in the last universal common ancestor of life

The problem of probabilistic inference of gene content in the last common ancestor of several extant species with completely sequenced genomes is: for each gene that is conserved in all or some of the genomes,...

Authors: Lavanya Kannan, Hua Li, Boris Rubinstein and Arcady Mushegian

Input-output relations in biological systems: measurement, information and the Hill equation

Biological systems produce outputs in response to variable inputs. Input-output relations tend to follow a few regular patterns. For example, many chemical processes follow the S-shaped Hill equation relation ...

Authors: Steven A Frank

Designing of interferon-gamma inducing MHC class-II binders

The generation of interferon-gamma (IFN-γ) by MHC class II activated CD4⁺ T helper cells play a substantial contribution in the control of infections such as caused by Mycobacterium tuberculosis. In the past, num...

Authors: Sandeep Kumar Dhanda, Pooja Vir and Gajendra PS Raghava

Highly homologous eEF1A1 and eEF1A2 exhibit differential post-translationalmodification with significant enrichment around localised sites of sequence variation

Translation elongation factors eEF1A1 and eEF1A2 are 92% identical but exhibit non-overlapping expression patterns. While the two proteins are predicted to have similar tertiary structures, it is notable that ...

Authors: Dinesh C Soares and Catherine M Abbott

DrugMint: a webserver for predicting and designing of drug-like molecules

Identification of drug-like molecules is one of the major challenges in the field of drug discovery. Existing approach like Lipinski rule of 5 (Ro5), Operea have their own limitations. Thus, there is a need to...

Authors: Sandeep Kumar Dhanda, Deepak Singla, Alok K Mondal and Gajendra PS Raghava

Identification of B-cell epitopes in an antigen for inducing specific class of antibodies

In the past, numerous methods have been developed for predicting antigenic regions or B-cell epitopes that can induce B-cell response. To the best of authors’ knowledge, no method has been developed for predic...

Authors: Sudheer Gupta, Hifzur Rahman Ansari, Ankur Gautam and Gajendra PS Raghava

A new piece in the puzzle of the novel avian-origin influenza A (H7N9) virus

This article was reviewed by Prof Xiufan Liu (nominated by Dr Purificacion Lopez-Garcia) and Prof Sandor Pongor.

Authors: Raphael Tze Chuen Lee, Vithiagaran Gunalan, Thanh Dac Van, Ly Thi Le, Frank Eisenhaber and Sebastian Maurer-Stroh

Pandoraviruses are highly derived phycodnaviruses

The recently discovered Pandoraviruses are by far the largest viruses known, with their 2 megabase genomes exceeding in size the genomes of numerous bacteria and archaea. Pandoraviruses show a distant relation...

Authors: Natalya Yutin and Eugene V Koonin

Interaction-based evolution: how natural selection and nonrandom mutation work together

The modern evolutionary synthesis leaves unresolved some of the mostfundamental, long-standing questions in evolutionary biology: What is therole of sex in evolution? How does complex adaptation evolve? How ca...

Authors: Adi Livnat

Recognizing short coding sequences of prokaryotic genome using a novel iteratively adaptive sparse partial least squares algorithm

Significant efforts have been made to address the problem of identifying short genes in prokaryotic genomes. However, most known methods are not effective in detecting short genes. Because of the limited infor...

Authors: Sun Chen, Chun-ying Zhang and Kai Song

LINEs of evidence: noncanonical DNA replication as an epigenetic determinant

LINE-1 (L1) retrotransposons are repetitive elements in mammalian genomes. They arecapable of synthesizing DNA on their own RNA templates by harnessing reversetranscriptase (RT) that they encode. Abundantly ex...

Authors: Ekaterina Belan

Circularity and self-cleavage as a strategy for the emergence of a chromosome in the RNA-based protocell

It is now popularly accepted that an “RNA world” existed in early evolution. During division of RNA-based protocells, random distribution of individual genes (simultaneously as ribozymes) between offspring mig...

Authors: Wentao Ma, Chunwu Yu and Wentao Zhang

Novel autoproteolytic and DNA-damage sensing components in the bacterial SOS response and oxidized methylcytosine-induced eukaryotic DNA demethylation systems

The bacterial SOS response is an elaborate program for DNA repair, cell cycle regulation and adaptive mutagenesis under stress conditions. Using sensitive sequence and structure analysis, combined with context...

Authors: L Aravind, Swadha Anand and Lakshminarayan M Iyer

Parabolic replicator dynamics and the principle of minimum Tsallis information gain

Non-linear, parabolic (sub-exponential) and hyperbolic (super-exponential) models of prebiological evolution of molecular replicators have been proposed and extensively studied. The parabolic models appear to ...

Authors: Georgy P Karev and Eugene V Koonin

How protein targeting to primary plastids via the endomembrane system could have evolved? A new hypothesis based on phylogenetic studies

It is commonly assumed that a heterotrophic ancestor of the supergroup Archaeplastida/Plantae engulfed a cyanobacterium that was transformed into a primary plastid; however, it is still unclear how nuclear-enc...

Authors: Przemysław Gagat, Andrzej Bodył and Paweł Mackiewicz

The mechanistic and evolutionary aspects of the 2′- and 3′-OH paradigm in biosynthetic machinery

The translation machinery underlies a multitude of biological processes within the cell. The design and implementation of the modern translation apparatus on even the simplest course of action is extremely com...

Authors: Mark Safro and Liron Klipcan

RNaseIII and T4 Polynucleotide Kinase sequence biases and solutions during RNA-seq library construction

RNA-seq is a next generation sequencing method with a wide range of applications including single nucleotide polymorphism (SNP) detection, splice junction identification, and gene expression level measurement....

Authors: Changhoon Lee, R Adron Harris, Jason K Wall, R Dayne Mayfield and Claus O Wilke

Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing

The major role of enzymatic toxins that target nucleic acids in biological conflicts at all levels has become increasingly apparent thanks in large part to the advances of comparative genomics. Typically, toxi...

Authors: Vivek Anantharaman, Kira S Makarova, A Maxwell Burroughs, Eugene V Koonin and L Aravind

Methylation kinetics and CpG-island methylator phenotyope status in colorectal cancer cell lines

Hypermethylation of CpG islands is thought to contribute to carcinogenesis through the inactivation of tumor suppressor genes. Tumor cells with relatively high levels of CpG island methylation are considered C...

Authors: Dominik Wodarz, C Richard Boland, Ajay Goel and Natalia L Komarova

Two novel PIWI families: roles in inter-genomic conflicts in bacteria and Mediator-dependent modulation of transcription in eukaryotes

The PIWI module, found in the PIWI/AGO superfamily of proteins, is a critical component of several cellular pathways including germline maintenance, chromatin organization, regulation of splicing, RNA interfer...

Authors: A Maxwell Burroughs, Lakshminarayan M Iyer and L Aravind

Exosomes secreted by human cells transport largely mRNA fragments that are enriched in the 3′-untranslated regions

Small secreted membrane vesicles called exosomes have recently attracted a great interest after the discovery that they transfer mRNA that can be translated into protein in recipient cells. Surprisingly, we fo...

Authors: Arsen O Batagov and Igor V Kurochkin

Biology Direct:celebrating 7 years of open, published peer review

Authors: Eugene V Koonin, Laura F Landweber and David J Lipman

Genome-wide analysis reveals downregulation of miR-379/miR-656 cluster in human cancers

MicroRNAs (miRNAs) are non-uniformly distributed in genomes and ~30% of the miRNAs in the human genome are clustered. In this study we have focused on the imprinted miRNA cluster miR-379/miR-656 on 14q32.31 (h...

Authors: Saurabh V Laddha, Subhashree Nayak, Deepanjan Paul, Rajasekhara Reddy, Charu Sharma, Prerana Jha, Manoj Hariharan, Anurag Agrawal, Shantanu Chowdhury, Chitra Sarkar and Arijit Mukhopadhyay