Proteomic changes associated with deletion of the Magnaporthe oryzae conidial morphology-regulating gene COM1.

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: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: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: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: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:Currently a huge amount of protein-protein interaction data is available therefore extracting meaningful ones are a challenging task. In a protein-protein interaction network, hubs are considered as key proteins maintaining function and stability of the network. Therefore, studying protein-protein complexes ...

journal_title：Biology direct

authors： Choura M,Rebaï A

更新日期：2011-10-05 00:00:00

abstract：:LINE-1 (L1) retrotransposons are repetitive elements in mammalian genomes. They are capable of synthesizing DNA on their own RNA templates by harnessing reverse transcriptase (RT) that they encode. Abundantly expressed full-length L1s and their RT are found to globally influence gene expression profiles, differentiati...

journal_title：Biology direct

authors： Belan E

更新日期：2013-09-13 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: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: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: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:Microbial communities play a crucial role in our environment and may influence human health tremendously. Despite being the place where human interaction is most abundant we still know little about the urban microbiome. This is highlighted by the large amount of unclassified DNA reads found in urban metageno...

journal_title：Biology direct

authors： Gerner SM,Rattei T,Graf AB

更新日期：2018-10-12 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：BACKGROUND:The costs and benefits of spliceosomal introns in eukaryotes have not been established. One recognized effect of intron splicing is its known enhancement of gene expression. However, the mechanism regulating such splicing-mediated expression enhancement has not been defined. Previous studies have shown that ...

journal_title：Biology direct

authors： Niu DK,Yang YF

更新日期：2011-05-18 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：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: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：: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：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: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 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:Phagocytosis, that is, engulfment of large particles by eukaryotic cells, is found in diverse organisms and is often thought to be central to the very origin of the eukaryotic cell, in particular, for the acquisition of bacterial endosymbionts including the ancestor of the mitochondrion. RESULTS:Comparisons...

journal_title：Biology direct

authors： Yutin N,Wolf MY,Wolf YI,Koonin EV

更新日期：2009-02-26 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: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. RESULTS:The first terrestrial hyperthermophilic member of the Nanoarchaeota was collected from Obsidian Pool, a ...

journal_title：Biology direct

authors： Podar M,Makarova KS,Graham DE,Wolf YI,Koonin EV,Reysenbach AL

更新日期：2013-04-22 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

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：BACKGROUND:Telocytes (TCs) is an interstitial cell with extremely long and thin telopodes (Tps) with thin segments (podomers) and dilations (podoms) to interact with neighboring cells. TCs have been found in different organs, while there is still a lack of TCs-specific biomarkers to distinguish TCs from the other cells...

journal_title：Biology direct

authors： Wang J,Ye L,Jin M,Wang X

更新日期：2015-03-11 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：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