Strong association between pseudogenization mechanisms and gene sequence length.

abstract：:Bacterial and Archaeal cells use selenium structurally in selenouridine-modified tRNAs, in proteins translated with selenocysteine, and in the selenium-dependent molybdenum hydroxylases (SDMH). The first two uses both require the selenophosphate synthetase gene, selD. Examining over 500 complete prokaryotic genomes fi...

journal_title：Biology direct

authors： Haft DH,Self WT

更新日期：2008-02-20 00:00:00

abstract：BACKGROUND:Oil palm is an important source of edible oil. The importance of the crop, as well as its long breeding cycle (10-12 years) has led to the sequencing of its genome in 2013 to pave the way for genomics-guided breeding. Nevertheless, the first set of gene predictions, although useful, had many fragmented genes...

journal_title：Biology direct

authors： Chan KL,Tatarinova TV,Rosli R,Amiruddin N,Azizi N,Halim MAA,Sanusi NSNM,Jayanthi N,Ponomarenko P,Triska M,Solovyev V,Firdaus-Raih M,Sambanthamurthi R,Murphy D,Low EL

更新日期：2017-09-08 00:00:00

abstract：BACKGROUND:Glycogen synthase kinase-3 (GSK-3) is a ubiquitously expressed serine/threonine (Ser/Thr) kinase comprising two isoforms, GSK-3α and GSK-3β. Both enzymes are similarly inactivated by serine phosphorylation (GSK-3α at Ser21 and GSK-3β at Ser9) and activated by tyrosine phosphorylation (GSK-3α at Tyr279 and GS...

journal_title：Biology direct

authors： Campa VM,Kypta RM

更新日期：2011-01-24 00:00:00

abstract：: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 sequencing libraries of immunoprecipitated Argonaute proteins (AGO-IP) and bioinformatics approaches, we identified th...

journal_title：Biology direct

authors： Loss-Morais G,Waterhouse PM,Margis R

更新日期：2013-02-12 00:00:00

abstract：BACKGROUND:The prokaryotic toxin-antitoxin systems (TAS, also referred to as TA loci) are widespread, mobile two-gene modules that can be viewed as selfish genetic elements because they evolved mechanisms to become addictive for replicons and cells in which they reside, but also possess "normal" cellular functions in v...

journal_title：Biology direct

authors： Makarova KS,Wolf YI,Koonin EV

更新日期：2009-06-03 00:00:00

abstract：BACKGROUND:The current analysis of transposon elements (TE) in Drosophila melanogaster at Evolution Canyon, (EC), Israel, is based on data and analysis done by our collaborators (Drs. J. Gonzalez, J. Martinez and W. Makalowski, this issue). They estimated the frequencies of 28 TEs (transposon elements) in fruit flies (...

journal_title：Biology direct

authors： Beiles A,Raz S,Ben-Abu Y,Nevo E

更新日期：2015-10-14 00:00:00

abstract：BACKGROUND:Several computational candidate gene selection and prioritization methods have recently been developed. These in silico selection and prioritization techniques are usually based on two central approaches--the examination of similarities to known disease genes and/or the evaluation of functional annotation of...

journal_title：Biology direct

authors： Lombard Z,Park C,Makova KD,Ramsay M

更新日期：2011-06-13 00:00:00

abstract：BACKGROUND:While all codons that specify amino acids are universally recognized by tRNA molecules, codons signaling termination of translation are recognized by proteins known as class-I release factors (RF). In most eukaryotes and archaea a single RF accomplishes termination at all three stop codons. In most bacteria,...

journal_title：Biology direct

authors： Baranov PV,Vestergaard B,Hamelryck T,Gesteland RF,Nyborg J,Atkins JF

更新日期：2006-09-13 00:00:00

abstract：BACKGROUND: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 obtained data sets. In this paper we propose a multiclass gene selection method based on Partial Least Squa...

journal_title：Biology direct

authors： Student S,Fujarewicz K

更新日期：2012-10-02 00:00:00

abstract：:It is well-known that Charles Darwin sketched abstract trees of relationship in his 1837 notebook, and depicted a tree in the Origin of Species (1859). Here I attempt to place Darwin's trees in historical context. By the mid-Eighteenth century the Great Chain of Being was increasingly seen to be an inadequate descript...

journal_title：Biology direct

authors： Ragan MA

更新日期：2009-11-16 00:00:00

abstract：:Chron's Disease is a chronic inflammatory intestinal disease, first described at the beginning of the last century. The disease is characterized by the alternation of periods of flares and remissions influenced by a complex pathogenesis in which inflammation plays a key role. Crohn's disease evolution is mediated by a...

journal_title：Biology direct

authors： Petagna L,Antonelli A,Ganini C,Bellato V,Campanelli M,Divizia A,Efrati C,Franceschilli M,Guida AM,Ingallinella S,Montagnese F,Sensi B,Siragusa L,Sica GS

更新日期：2020-11-07 00:00:00

abstract：UNLABELLED:Recently Mycobacterium tuberculosis was shown to possess a novel protein modification, in which a small protein Pup is conjugated to the epsilon-amino groups of lysines in target proteins. Analogous to ubiquitin modification in eukaryotes, this remarkable modification recruits proteins for degradation via ar...

journal_title：Biology direct

authors： Iyer LM,Burroughs AM,Aravind L

更新日期：2008-11-03 00:00:00

abstract：BACKGROUND:An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on suc...

journal_title：Biology direct

authors： Makarova KS,Sorokin AV,Novichkov PS,Wolf YI,Koonin EV

更新日期：2007-11-27 00:00:00

abstract：:A widespread and highly conserved family of apparently inactivated derivatives of archaeal B-family DNA polymerases is described. Phylogenetic analysis shows that the inactivated forms comprise a distinct clade among archaeal B-family polymerases and that, within this clade, Euryarchaea and Crenarchaea are clearly sep...

journal_title：Biology direct

authors： Rogozin IB,Makarova KS,Pavlov YI,Koonin EV

更新日期：2008-08-06 00:00:00

abstract：BACKGROUND: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 genome and then utilizing transcripts of these spacers to inactivate the cognate foreign genome. The ...

journal_title：Biology direct

authors： Berezovskaya FS,Wolf YI,Koonin EV,Karev GP

更新日期：2014-07-02 00:00:00

abstract：BACKGROUND: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 translation in the etiology of ASD, we analyzed potential effects of rare synonymous substitutions ass...

journal_title：Biology direct

authors： Poliakov E,Koonin EV,Rogozin IB

更新日期：2014-07-10 00:00:00

abstract：:Plant viruses of the recently recognized family Amalgaviridae have monopartite double-stranded (ds) RNA genomes and encode two proteins: an RNA-dependent RNA polymerase (RdRp) and a putative capsid protein (CP). Whereas the RdRp of amalgaviruses has been found to be most closely related to the RdRps of dsRNA viruses o...

journal_title：Biology direct

authors： Krupovic M,Dolja VV,Koonin EV

更新日期：2015-03-29 00:00:00

abstract：:The concept of developmental constraints has been central to understand the role of development in morphological evolution. Developmental constraints are classically defined as biases imposed by development on the distribution of morphological variation.This opinion article argues that the concepts of developmental co...

journal_title：Biology direct

authors： Salazar-Ciudad I

更新日期：2021-01-09 00:00:00

abstract：:Shannon entropy is used to provide an estimate of the number of interpretable components in a principal component analysis. In addition, several ad hoc stopping rules for dimension determination are reviewed and a modification of the broken stick model is presented. The modification incorporates a test for the presenc...

journal_title：Biology direct

authors： Cangelosi R,Goriely A

更新日期：2007-01-17 00:00:00

abstract：BACKGROUND:Many studies of biochemical networks have analyzed network topology. Such work has suggested that specific types of network wiring may increase network robustness and therefore confer a selective advantage. However, knowledge of network topology does not allow one to predict network dynamical behavior--for e...

journal_title：Biology direct

authors： McDonald D,Waterbury L,Knight R,Betterton MD

更新日期：2008-12-04 00:00:00

abstract：BACKGROUND: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 important strategy to fill the gap in experimental H. sapiens-M. tuberculosis H37Rv PPI data. Homolo...

journal_title：Biology direct

authors： Zhou H,Gao S,Nguyen NN,Fan M,Jin J,Liu B,Zhao L,Xiong G,Tan M,Li S,Wong L

更新日期：2014-04-08 00:00:00

abstract：BACKGROUND:The evidence for universal common ancestry (UCA) is vast and persuasive. A phylogenetic test has been proposed for quantifying its odds against independently originated sequences based on the comparison between one versus several trees. This test was successfully applied to a well-supported homologous sequen...

journal_title：Biology direct

authors： de Oliveira Martins L,Posada D

更新日期：2016-04-07 00:00:00

abstract：BACKGROUND:The origin of eukaryotic cells was an important transition in evolution. The factors underlying the origin and evolutionary success of the eukaryote lineage are still discussed. One camp argues that mitochondria were essential for eukaryote origin because of the unique configuration of internalized bioenerge...

journal_title：Biology direct

authors： Gerlitz M,Knopp M,Kapust N,Xavier JC,Martin WF

更新日期：2018-10-03 00:00:00

abstract：BACKGROUND:While the local-mode HMMER3 is notable for its massive speed improvement, the slower glocal-mode HMMER2 is more exact for domain annotation by enforcing full domain-to-sequence alignments. Since a unit of domain necessarily implies a unit of function, local-mode HMMER3 alone remains insufficient for precise ...

journal_title：Biology direct

authors： Yap CK,Eisenhaber B,Eisenhaber F,Wong WC

更新日期：2016-11-29 00:00:00

abstract：BACKGROUND: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 complex, and involves different RNA and protein factors. According to the "RNA world" idea, the critica...

journal_title：Biology direct

authors： Safro M,Klipcan L

更新日期：2013-07-08 00:00:00

abstract：BACKGROUND:The N-end rule pathway is a part of the ubiquitin-dependent proteolytic system wherein N-recognin proteins recognize the amino terminal degradation signals (N-degrons) of the substrate. The type 1 N-degron recognizing UBR-box domain of the eukaryotic Arg/N-end rule pathway is known to possess a novel three-z...

journal_title：Biology direct

authors： Kaur G,Subramanian S

更新日期：2015-07-17 00:00:00

abstract：BACKGROUND: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 these animals, more detailed treatments are often needed to assess potential drivers of population d...

journal_title：Biology direct

authors： White ER,Nagy JD,Gruber SH

更新日期：2014-11-18 00:00:00

abstract：BACKGROUND:The advent of metagenomic sequencing provides microbial abundance patterns that can be leveraged for sample origin prediction. Supervised machine learning classification approaches have been reported to predict sample origin accurately when the origin has been previously sampled. Using metagenomic datasets p...

journal_title：Biology direct

authors： Chen JC,Tyler AD

更新日期：2020-12-10 00:00:00

abstract：BACKGROUND:The origin of the selective nuclear protein import machinery, which consists of nuclear pore complexes and adaptor molecules interacting with the nuclear localization signals (NLSs) of cargo molecules, is one of the most important events in the evolution of eukaryotic cells. How proteins were selected for im...

journal_title：Biology direct

authors： Lisitsyna OM,Kurnaeva MA,Arifulin EA,Shubina MY,Musinova YR,Mironov AA,Sheval EV

更新日期：2020-04-28 00:00:00

abstract：BACKGROUND:In genetics it is customary to refer to double-stranded DNA as containing a "Watson strand" and a "Crick strand." However, there seems to be no consensus in the literature on the exact meaning of these two terms, and the many usages contradict one another as well as the original definition. Here, we review t...

journal_title：Biology direct

authors： Cartwright RA,Graur D

更新日期：2011-02-08 00:00:00