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

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：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：: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：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：BACKGROUND:Knowledge of the protein structure is a pre-requisite for improved understanding of molecular function. The gap in the sequence-structure space has increased in the post-genomic era. Grouping related protein sequences into families can aid in narrowing the gap. In the Pfam database, structure description is ...

journal_title：Biology direct

authors： Kumar G,Mudgal R,Srinivasan N,Sandhya S

更新日期：2018-05-09 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: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：: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：: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: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: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：: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: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: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：: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: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: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: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 overwhelming majority of animal species exhibit bilateral symmetry. However, the precise evolutionary importance of bilateral symmetry is unknown, although elements of the understanding of the phenomenon have been present within the scientific community for decades. PRESENTATION OF THE HYPOTHESIS:Here w...

journal_title：Biology direct

authors： Holló G,Novák M

更新日期：2012-07-12 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: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: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: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 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: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 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 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 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: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