Structural analysis of hubs in human NR-RTK network.

abstract：BACKGROUND:Synthesis of proteins is based on the genetic code - a nearly universal assignment of codons to amino acids (aas). A major challenge to the understanding of the origins of this assignment is the archetypal "key-lock vs. frozen accident" dilemma. Here we re-examine this dilemma in light of 1) the fundamental ...

journal_title：Biology direct

authors： Rodin AS,Szathmáry E,Rodin SN

更新日期：2011-02-22 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：: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：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: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: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:In eukaryotes, RNA interference (RNAi) is a major mechanism of defense against viruses and transposable elements as well of regulating translation of endogenous mRNAs. The RNAi systems recognize the target RNA molecules via small guide RNAs that are completely or partially complementary to a region of the ta...

journal_title：Biology direct

authors： Makarova KS,Wolf YI,van der Oost J,Koonin EV

更新日期：2009-08-25 00:00:00

abstract：INTRODUCTION:Three major outer membrane protein genes of Escherichia coli, ompF, ompC, and ompA respond to stress factors. Transcripts from these genes are regulated by the small non-coding RNAs micF, micC, and micA, respectively. Here we examine Photorhabdus luminescens, an organism that has a different habitat from E...

journal_title：Biology direct

authors： Papamichail D,Delihas N

更新日期：2006-05-22 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

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: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: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：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: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：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: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: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: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: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:Drug-induced liver injury (DILI) is a major safety concern characterized by a complex and diverse pathogenesis. In order to identify DILI early in drug development, a better understanding of the injury and models with better predictivity are urgently needed. One approach in this regard are in silico models w...

journal_title：Biology direct

authors： Liu A,Walter M,Wright P,Bartosik A,Dolciami D,Elbasir A,Yang H,Bender A

更新日期：2021-01-18 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: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:Domains containing the beta-grasp fold are utilized in a great diversity of physiological functions but their role, if any, in soluble or small molecule ligand recognition is poorly studied. RESULTS:Using sensitive sequence and structure similarity searches we identify a novel superfamily containing the bet...

journal_title：Biology direct

authors： Burroughs AM,Balaji S,Iyer LM,Aravind L

更新日期：2007-01-24 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：:ᅟ: Some tumor cells can evolve into transmissible parasites. Notable examples include the Tasmanian devil facial tumor disease, the canine transmissible venereal tumor and transmissible cancers of mollusks. We present a hypothesis that such transmissible tumors existed in the past and that some modern animal taxa are ...

journal_title：Biology direct

authors： Panchin AY,Aleoshin VV,Panchin YV

更新日期：2019-01-23 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:The gammadelta T cells serve as early immune defense against certain encountered microbes. Only a few gammadelta T cell-recognized ligands from microbial antigens have been identified so far and the mechanisms by which gammadelta T cells recognize these ligands remain unknown. Here we explored the mechanism ...

journal_title：Biology direct

authors： Cui Y,Kang L,Cui L,He W

更新日期：2009-12-01 00:00:00

abstract：BACKGROUND:In the past, many methods have been developed for peptide tertiary structure prediction but they are limited to peptides having natural amino acids. This study describes a method PEPstrMOD, which is an updated version of PEPstr, developed specifically for predicting the structure of peptides containing natur...

journal_title：Biology direct

authors： Singh S,Singh H,Tuknait A,Chaudhary K,Singh B,Kumaran S,Raghava GP

更新日期：2015-12-21 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:Drug-induced liver injury (DILI) is a major concern in drug development, as hepatotoxicity may not be apparent at early stages but can lead to life threatening consequences. The ability to predict DILI from in vitro data would be a crucial advantage. In 2018, the Critical Assessment Massive Data Analysis gro...

journal_title：Biology direct

authors： Chierici M,Francescatto M,Bussola N,Jurman G,Furlanello C

更新日期：2020-02-13 00:00:00