Orphan SelD proteins and selenium-dependent molybdenum hydroxylases.

abstract：BACKGROUND: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 function by genetic or biochemical approaches, a lengthy process that often took years. Phylogenetic distr...

journal_title：Biology direct

authors： de Crécy-Lagard V,Forouhar F,Brochier-Armanet C,Tong L,Hunt JF

更新日期：2012-09-26 00:00:00

abstract：BACKGROUND:The transition from premalignant to invasive tumour growth is a prolonged multistep process governed by phenotypic adaptation to changing microenvironmental selection pressures. Cancer prevention strategies are required to interrupt or delay somatic evolution of the malignant invasive phenotype. Empirical st...

journal_title：Biology direct

authors： Smallbone K,Maini PK,Gatenby RA

更新日期：2010-04-20 00:00:00

abstract：BACKGROUND:Accurate estimation of the isoelectric point (pI) based on the amino acid sequence is useful for many analytical biochemistry and proteomics techniques such as 2-D polyacrylamide gel electrophoresis, or capillary isoelectric focusing used in combination with high-throughput mass spectrometry. Additionally, p...

journal_title：Biology direct

authors： Kozlowski LP

更新日期：2016-10-21 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: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：UNLABELLED:In this work we review past articles that have mathematically studied cancer heterogeneity and the impact of this heterogeneity on the structure of optimal therapy. We look at past works on modeling how heterogeneous tumors respond to radiotherapy, and take a particularly close look at how the optimal radiot...

journal_title：Biology direct

authors： Badri H,Leder K

更新日期：2016-08-23 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:It is common belief that all cellular life forms on earth have a common origin. This view is supported by the universality of the genetic code and the universal conservation of multiple genes, particularly those that encode key components of the translation system. A remarkable recent study claims to provide...

journal_title：Biology direct

authors： Koonin EV,Wolf YI

更新日期：2010-11-18 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：: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: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: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：:All modern cells are bounded by cell membranes best described by the fluid mosaic model. This statement is so widely accepted by biologists that little attention is generally given to the theoretical importance of cell membranes in describing the cell. This has not always been the case. When the Cell Theory was first ...

journal_title：Biology direct

authors： Lombard J

更新日期：2014-12-19 00:00:00

abstract：BACKGROUND:The rice blast disease caused by Magnaporthe oryzae is a major constraint on world rice production. The conidia produced by this fungal pathogen are the main source of disease dissemination. The morphology of conidia may be a critical factor in the spore dispersal and virulence of M. oryzae in the field. Del...

journal_title：Biology direct

authors： Bhadauria V,Wang LX,Peng YL

更新日期：2010-11-02 00:00:00

abstract：BACKGROUND:The elucidation of the dominant role of horizontal gene transfer (HGT) in the evolution of prokaryotes led to a severe crisis of the Tree of Life (TOL) concept and intense debates on this subject. CONCEPT:Prompted by the crisis of the TOL, we attempt to define the primary units and the fundamental patterns ...

journal_title：Biology direct

authors： Koonin EV,Wolf YI

更新日期：2009-09-29 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: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：UNLABELLED:Primase and GINS are essential factors for chromosomal DNA replication in eukaryotic and archaeal cells. Here we describe a previously undetected relationship between the C-terminal domain of the catalytic subunit (PriS) of archaeal primase and the B-domains of the archaeo-eukaryotic GINS proteins in the for...

journal_title：Biology direct

authors： Swiatek A,Macneill SA

更新日期：2010-04-12 00:00:00

abstract：BACKGROUND:Our current understanding of evolution is so tightly linked to template-dependent replication of DNA and RNA molecules that the old idea from Oparin of a self-reproducing 'garbage bag' ('coacervate') of chemicals that predated fully-fledged cell-like entities seems to be farfetched to most scientists today. ...

journal_title：Biology direct

authors： Vasas V,Fernando C,Santos M,Kauffman S,Szathmáry E

更新日期：2012-01-05 00:00:00

abstract：BACKGROUND:Chlamydia trachomatis is an obligate intracellular bacterial parasite, which causes several severe and debilitating diseases in humans. This study uses comparative genomic analyses of 12 complete published C. trachomatis genomes to assess the contribution of recombination and selection in this pathogen and t...

journal_title：Biology direct

authors： Joseph SJ,Didelot X,Gandhi K,Dean D,Read TD

更新日期：2011-05-26 00:00:00

abstract：UNLABELLED:Pseudogenes arise from the decay of gene copies following either RNA-mediated duplication (processed pseudogenes) or DNA-mediated duplication (nonprocessed pseudogenes). Here, we show that long protein-coding genes tend to produce more nonprocessed pseudogenes than short genes, whereas the opposite is true f...

journal_title：Biology direct

authors： Khachane AN,Harrison PM

更新日期：2009-10-06 00:00:00

abstract：BACKGROUND:BLAST is a commonly-used software package for comparing a query sequence to a database of known sequences; in this study, we focus on protein sequences. Position-specific-iterated BLAST (PSI-BLAST) iteratively searches a protein sequence database, using the matches in round i to construct a position-specific...

journal_title：Biology direct

authors： Boratyn GM,Schäffer AA,Agarwala R,Altschul SF,Lipman DJ,Madden TL

更新日期：2012-04-17 00:00:00

abstract：BACKGROUND:Identifying group-specific characteristics in metabolic networks can provide better insight into evolutionary developments. Here, we present an approach to classify the three domains of life using topological information about the underlying metabolic networks. These networks have been shown to share domain-...

journal_title：Biology direct

authors： Mueller LA,Kugler KG,Netzer M,Graber A,Dehmer M

更新日期：2011-10-13 00:00:00

abstract：BACKGROUND:In the presence of horizontal gene transfer (HGT), the concepts of lineage and genealogy in the microbial world become more ambiguous because chimeric genomes trace their ancestry from a myriad of sources, both living and extinct. RESULTS:We present the evolutionary histories of three aminoacyl-tRNA synthet...

journal_title：Biology direct

authors： Andam CP,Gogarten JP

更新日期：2011-09-23 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 basic tenet of protein science is that all information about the spatial structure of proteins is present in their sequences. Nonetheless, many proteins fail to attain native structure upon experimental denaturation and refolding in vitro, raising the question of the specific role of cellular machinery in ...

journal_title：Biology direct

authors： Sorokina I,Mushegian A

更新日期：2017-05-31 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：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：:Two apparently irreconcilable models dominate research into the origin of eukaryotes. In one model, amitochondrial proto-eukaryotes emerged autogenously from the last universal common ancestor of all cells. Proto-eukaryotes subsequently acquired mitochondrial progenitors by the phagocytic capture of bacteria. In the s...

journal_title：Biology direct

authors： Bateman A

更新日期：2020-04-28 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