Articles

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

Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park

A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes.

Authors: Mircea Podar, Kira S Makarova, David E Graham, Yuri I Wolf, Eugene V Koonin and Anna-Louise Reysenbach

Invasive cells in animals and plants: searching for LECA machineries in later eukaryotic life

Invasive cell growth and migration is usually considered a specifically metazoan phenomenon. However, common features and mechanisms of cytoskeletal rearrangements, membrane trafficking and signalling processe...

Authors: Katarína Vaškovičová, Viktor Žárský, Daniel Rösel, Margaret Nikolič, Roberto Buccione, Fatima Cvrčková and Jan Brábek

Invariance and optimality in the regulation of an enzyme

The Michaelis-Menten equation, proposed a century ago, describes the kinetics of enzyme-catalyzed biochemical reactions. Since then, this equation has been used in countless, increasingly complex models of cel...

Authors: Ed Reznik, Stefan Yohe and Daniel Segrè

Description of plant tRNA-derived RNA fragments (tRFs) associated with argonaute and identification of their putative targets

tRNA-derived RNA fragments (tRFs) are 19mer small RNAs that associate with Argonaute (AGO) proteins in humans. However, in plants, it is unknown if tRFs bind with AGO proteins. Here, using public deep sequenci...

Authors: Guilherme Loss-Morais, Peter M Waterhouse and Rogerio Margis

GABBR1 has a HERV-W LTR in its regulatory region – a possible implication for schizophrenia

Schizophrenia is a complex disease with uncertain aetiology. We suggest GABBR1, GABA receptor B1 implicated in schizophrenia based on a HERV-W LTR in the regulatory region of GABBR1. Our hypothesis is supporte...

Authors: Hedi Hegyi

Surprisingly high number of Twintrons in vertebrates

Twintrons represent a special intronic arrangement in which introns of two different types occupy the same gene position. Consequently, alternative splicing of these introns requires two different spliceosomes...

Authors: Jessin Janice, Marcin Jąkalski and Wojciech Makałowski

Next-generation phylogenomics

Thanks to advances in next-generation technologies, genome sequences are now being generated at breadth (e.g. across environments) and depth (thousands of closely related strains, individuals or samples) unimagin...

Authors: Cheong Xin Chan and Mark A Ragan

Deep transcriptome-sequencing and proteome analysis of the hydrothermal vent annelid Alvinella pompejana identifies the CvP-bias as a robust measure of eukaryotic thermostability

Alvinella pompejana is an annelid worm that inhabits deep-sea hydrothermal vent sites in the Pacific Ocean. Living at a depth of approximately 2500 meters, these worms experience extreme environmental conditions,...

Authors: Thomas Holder, Claire Basquin, Judith Ebert, Nadine Randel, Didier Jollivet, Elena Conti, Gáspár Jékely and Fulvia Bono

Microevolutionary, macroevolutionary, ecological and taxonomical implications of punctuational theories of adaptive evolution

Punctuational theories of evolution suggest that adaptive evolution proceeds mostly, or even entirely, in the distinct periods of existence of a particular species. The mechanisms of this punctuated nature of ...

Authors: Jaroslav Flegr

Detection of a common chimeric transcript between human chromosomes 7 and 16

Interchromosomal chimeric RNA molecules are often transcription products from genomic rearrangement in cancerous cells. Here we report the computational detection of an interchromosomal RNA fusion between ZC3HAV1...

Authors: Wenwen Fang, Yong Wei, Yibin Kang and Laura F Landweber

Cubic time algorithms of amalgamating gene trees and building evolutionary scenarios

A long recognized problem is the inference of the supertree S that amalgamates a given set {G _j } of trees G _j , with leaves in each G _...

Authors: Vassily A Lyubetsky, Lev I Rubanov, Leonid Y Rusin and Konstantin Yu Gorbunov

AID/APOBEC cytosine deaminase induces genome-wide kataegis

Clusters of localized hypermutation in human breast cancer genomes, named “kataegis” (from the Greek for thunderstorm), are hypothesized to result from multiple cytosine deaminations catalyzed by AID/APOBEC pr...

Authors: Artem G Lada, Alok Dhar, Robert J Boissy, Masayuki Hirano, Aleksandr A Rubel, Igor B Rogozin and Youri I Pavlov

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer

Collections of Clusters of Orthologous Genes (COGs) provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made...

Authors: Yuri I Wolf, Kira S Makarova, Natalya Yutin and Eugene V Koonin

Ethanolamine utilization in Vibrio alginolyticus

Ethanolamine is used as an energy source by phylogenetically diverse bacteria including pathogens, by the concerted action of proteins from the eut-operon. Previous studies have revealed the presence of eutBC gen...

Authors: Neelam Khatri, Indu Khatri, Srikrishna Subramanian and Saumya Raychaudhuri

Harnessing the complexity of gene expression data from cancer: from single gene to structural pathway methods

High-dimensional gene expression data provide a rich source of information because they capture the expression level of genes in dynamic states that reflect the biological functioning of a cell. For this reaso...

Authors: Frank Emmert-Streib, Shailesh Tripathi and Ricardo de Matos Simoes

Bioinformatics clouds for big data manipulation

As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computin...

Authors: Lin Dai, Xin Gao, Yan Guo, Jingfa Xiao and Zhang Zhang

The origin of life is a spatially localized stochastic transition

Life depends on biopolymer sequences as catalysts and as genetic material. A key step in the Origin of Life is the emergence of an autocatalytic system of biopolymers. Here we study computational models that a...

Authors: Meng Wu and Paul G Higgs

Somatic transposition in the brain has the potential to influence the biosynthesis of metabolites involved in Parkinson’s disease and schizophrenia

It has been recently discovered that transposable elements show high activity in the brain of mammals, however, the magnitude of their influence on its functioning is unclear so far. In this paper, I use flux ...

Authors: György Abrusán

Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes

The virus-host arms race is a major theater for evolutionary innovation. Archaea and bacteria have evolved diverse, elaborate antivirus defense systems that function on two general principles: i) immune system...

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

ALOG domains: provenance of plant homeotic and developmental regulators from the DNA-binding domain of a novel class of DIRS1-type retroposons

Members of the Arabidopsis LSH1 and Oryza G1 (ALOG) family of proteins have been shown to function as key developmental regulators in land plants. However, their precise mode of action remains unclear. Using sens...

Authors: Lakshminarayan M Iyer and L Aravind

Early evolution of efficient enzymes and genome organization

Cellular life with complex metabolism probably evolved during the reign of RNA, when it served as both information carrier and enzyme. Jensen proposed that enzymes of primordial cells possessed broad specifici...

Authors: András Szilágyi, Ádám Kun and Eörs Szathmáry

Thousands of missed genes found in bacterial genomes and their analysis with COMBREX

The dramatic reduction in the cost of sequencing has allowed many researchers to join in the effort of sequencing and annotating prokaryotic genomes. Annotation methods vary considerably and may fail to identi...

Authors: Derrick E Wood, Henry Lin, Ami Levy-Moonshine, Rajiswari Swaminathan, Yi-Chien Chang, Brian P Anton, Lais Osmani, Martin Steffen, Simon Kasif and Steven L Salzberg

Distinct groups of repetitive families preserved in mammals correspond to different periods of regulatory innovations in vertebrates

Mammalian genomes are repositories of repetitive DNA sequences derived from transposable elements (TEs). Typically, TEs generate multiple, mostly inactive copies of themselves, commonly known as repetitive fam...

Authors: Jerzy Jurka, Weidong Bao, Kenji K Kojima, Oleksiy Kohany and Matthew G Yurka

Constructive neutral evolution: exploring evolutionary theory’s curious disconnect

Constructive neutral evolution (CNE) suggests that neutral evolution may follow a stepwise path to extravagance. Whether or not CNE is common, the mere possibility raises provocative questions about causation:...

Authors: Arlin Stoltzfus

Proteorhodopsin genes in giant viruses

Viruses with large genomes encode numerous proteins that do not directly participate in virus biogenesis but rather modify key functional systems of infected cells. We report that a distinct group of giant vir...

Authors: Natalya Yutin and Eugene V Koonin

Stable feature selection and classification algorithms for multiclass microarray data

Recent studies suggest that gene expression profiles are a promising alternative for clinical cancer classification. One major problem in applying DNA microarrays for classification is the dimension of obtaine...

Authors: Sebastian Student and Krzysztof Fujarewicz

Comparative genomic analysis of the DUF71/COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage

The availability of over 3000 published genome sequences has enabled the use of comparative genomic approaches to drive the biological function discovery process. Classically, one used to link gene with functi...

Authors: Valérie de Crécy-Lagard, Farhad Forouhar, Céline Brochier-Armanet, Liang Tong and John F Hunt

Evasion of tumours from the control of the immune system: consequences of brief encounters

In this work a mathematical model describing the growth of a solid tumour in the presence of an immune system response is presented. Specifically, attention is focused on the interactions between cytotoxic T-l...

Authors: Mohannad Al-Tameemi, Mark Chaplain and Alberto d’Onofrio

Stop codons in bacteria are not selectively equivalent

The evolution and genomic stop codon frequencies have not been rigorously studied with the exception of coding of non-canonical amino acids. Here we study the rate of evolution and frequency distribution of st...

Authors: Inna S Povolotskaya, Fyodor A Kondrashov, Alice Ledda and Peter K Vlasov

Identifying the mechanisms of intron gain: progress and trends

Continued improvements in Next-Generation DNA/RNA sequencing coupled with advances in gene annotation have provided researchers access to a plethora of annotated genomes. Subsequent analyses of orthologous gen...

Authors: Paul Yenerall and Leming Zhou

Novel and unexpected bacterial diversity in an arsenic-rich ecosystem revealed by culture-dependent approaches

Acid Mine Drainages (AMDs) are extreme environments characterized by very acid conditions and heavy metal contaminations. In these ecosystems, the bacterial diversity is considered to be low. Previous culture-...

Authors: François Delavat, Marie-Claire Lett and Didier Lièvremont

Does the central dogma still stand?

Prions are agents of analog, protein conformation-based inheritance that can confer beneficial phenotypes to cells, especially under stress. Combined with genetic variation, prion-mediated inheritance can be c...

Authors: Eugene V Koonin

Modeling RNA polymerase interaction in mitochondria of chordates

In previous work, we introduced a concept, a mathematical model and its computer realization that describe the interaction between bacterial and phage type RNA polymerases, protein factors, DNA and RNA seconda...

Authors: Vassily A Lyubetsky, Oleg A Zverkov, Sergey A Pirogov, Lev I Rubanov and Alexandr V Seliverstov

Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs

The availability of sequencing technology has enabled understanding of transcriptomes through genome-wide approaches including RNA-sequencing. Contrary to the previous assumption that large tracts of the eukar...

Authors: Saakshi Jalali, Gopal Gunanathan Jayaraj and Vinod Scaria

CRISPR transcript processing: a mechanism for generating a large number of small interfering RNAs

CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated sequences) is a recently discovered prokaryotic defense system against foreign DNA, including viruses and plasmids. CRISP...

Authors: Marko Djordjevic, Magdalena Djordjevic and Konstantin Severinov

The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others)^a

The problems associated with the RNA world hypothesis are well known. In the following I discuss some of these difficulties, some of the alternative hypotheses that have been proposed, and some of the problems...

Authors: Harold S Bernhardt