Abstract:
BACKGROUND:Microscopic examination of living cells often reveals that cells from some cell strains appear to be in a permanent state of disarray without obvious reason. In all probability such a disorderly state affects cell functioning. The aim of this study was to establish whether a disorderly state could occur that adversely affects gene expression profiles and whether such a state might have biomedical consequences. To this end, the expression profiles of the 14 genes of the proteasome derived from the GEO SAGE database were utilized as a model system. RESULTS:By adopting the overall expression profile as the standard for normal expression, deviation in transcription was frequently observed. Each deviating tissue exhibited its own characteristic profile of over-expressed and under-expressed genes. Moreover such a specific deviating profile appeared to be epigenetic in origin and could be stably transmitted to a clonal derivative e.g. from a precancerous normal tissue to its tumor. A significantly greater degree of deviation was observed in the expression profiles from the tumor tissues. The changes in the expression of different genes display a network of interdependencies. Therefore our hypothesis is that deviating profiles reflect disorder in the localization of genes within the nucleus. The underlying cause(s) for these disorderly states remain obscure; it could be noise and/or deterministic chaos. Presence of mutational damage does not appear to be predominantly involved. CONCLUSION:As disturbances in expression profiles frequently occur and have biomedical consequences, its determination could prove of value in several fields of biomedical research.
journal_name
Biol Directjournal_title
Biology directauthors
Simons JWdoi
10.1186/1745-6150-1-9keywords:
subject
Has Abstractpub_date
2006-04-02 00:00:00pages
9issn
1745-6150pii
1745-6150-1-9journal_volume
1pub_type
杂志文章相关文献
Biology Direct文献大全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
pub_type: 杂志文章
doi:10.1186/1745-6150-8-9
更新日期:2013-04-22 00:00:00
abstract::The provenance and biochemical roles of eukaryotic MORC proteins have remained poorly understood since the discovery of their prototype MORC1, which is required for meiotic nuclear division in animals. The MORC family contains a combination of a gyrase, histidine kinase, and MutL (GHKL) and S5 domains that together co...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-3-8
更新日期:2008-03-17 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
pub_type: 杂志文章,评审
doi:10.1186/s13062-016-0142-5
更新日期:2016-08-23 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
pub_type: 杂志文章
doi:10.1186/s13062-015-0066-5
更新日期:2015-07-17 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
pub_type: 杂志文章
doi:10.1186/1745-6150-6-30
更新日期:2011-06-13 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
pub_type: 杂志文章
doi:10.1186/1745-6150-3-49
更新日期:2008-12-04 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
pub_type: 杂志文章,评审
doi:10.1186/s13062-020-00280-5
更新日期:2020-11-07 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
pub_type: 历史文章,杂志文章,评审
doi:10.1186/1745-6150-4-43
更新日期:2009-11-16 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
pub_type: 杂志文章
doi:10.1186/s13062-020-00285-0
更新日期:2021-01-18 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
pub_type: 杂志文章
doi:10.1186/s13062-016-0120-y
更新日期:2016-04-07 00:00:00
abstract::Functional biologists, like Claude Bernard, ask "How?", meaning that they investigate the mechanisms underlying the emergence of biological functions (proximal causes), while evolutionary biologists, like Charles Darwin, asks "Why?", meaning that they search the causes of adaptation, survival and evolution (remote cau...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/s13062-016-0109-6
更新日期:2016-02-09 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
pub_type: 杂志文章
doi:10.1186/s13062-018-0221-x
更新日期:2018-10-03 00:00:00
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
pub_type: 杂志文章
doi:10.1186/1745-6150-6-14
更新日期:2011-02-22 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
pub_type: 杂志文章
doi:10.1186/1745-6150-2-4
更新日期:2007-01-24 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
pub_type: 杂志文章
doi:10.1186/1745-6150-9-13
更新日期:2014-07-02 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
pub_type: 杂志文章
doi:10.1186/1745-6150-9-23
更新日期:2014-11-18 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
pub_type: 杂志文章
doi:10.1186/1745-6150-4-9
更新日期:2009-02-26 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
pub_type: 杂志文章
doi:10.1186/1745-6150-5-17
更新日期:2010-04-12 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
pub_type: 杂志文章
doi:10.1186/1745-6150-6-49
更新日期:2011-10-05 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
pub_type: 杂志文章
doi:10.1186/1745-6150-6-47
更新日期:2011-09-23 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
pub_type: 杂志文章
doi:10.1186/1745-6150-8-6
更新日期:2013-02-12 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
pub_type: 杂志文章
doi:10.1186/1745-6150-4-47
更新日期:2009-12-01 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
pub_type: 杂志文章
doi:10.1186/s13062-020-00260-9
更新日期:2020-04-28 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
pub_type: 杂志文章
doi:10.1186/1745-6150-5-22
更新日期:2010-04-20 00:00:00
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
pub_type: 杂志文章
doi:10.1186/1745-6150-3-4
更新日期:2008-02-20 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
pub_type: 杂志文章
doi:10.1186/s13062-018-0209-6
更新日期:2018-05-09 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
pub_type: 杂志文章
doi:10.1186/1745-6150-6-28
更新日期:2011-05-26 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
pub_type: 杂志文章
doi:10.1186/1745-6150-7-12
更新日期:2012-04-17 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
pub_type: 杂志文章
doi:10.1186/1745-6150-4-33
更新日期:2009-09-29 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
pub_type: 杂志文章
doi:10.1186/s13062-019-0233-1
更新日期:2019-01-23 00:00:00