Abstract:
:Escherichia coli has evolved an intracellular pathway to regulate its motion termed as chemotaxis so as to move towards a favorable environment such as regions with higher concentration of nutrients. Chemotaxis is a response to temporal and spatial variation of extracellular ligand concentration and randomness in motion induced by collisions with solvent molecules. Previous studies have reported average drift velocities for a given gradient and do not measure drift velocities as a function of time and space. To address this issue, a novel experimental technique was developed to quantify the motion of E. coli cells to varying concentrations and gradients of methyl-aspartate so as to capture the spatial and temporal variation of the drift velocity. A two-state receptor model accounting for the intracellular signaling pathway predicted the experimentally observed increase in drift velocity with gradient and the subsequent adaptation. Our study revealed that the rotational diffusivity induced by the extracellular environment is crucial in determining the drift velocity of E. coli. The model predictions matched with experimental observations only when the response of the intracellular pathway was highly ultra-sensitive to overcome the extracellular randomness. The parametric sensitivity of the pathway indicated that the dissociation constant for the binding of the ligand and the rate constants of the methylation/demethylation of the receptor are key to predict the performance of the chemotactic behavior. The study also indicates a possible role of oxygen in the chemotaxis response and that the response to a ligand may have to account for effects of oxygen.
journal_name
Mol Biosystjournal_title
Molecular bioSystemsauthors
Vuppula RR,Tirumkudulu MS,Venkatesh KVdoi
10.1039/b924368bsubject
Has Abstractpub_date
2010-06-01 00:00:00pages
1082-92issue
6eissn
1742-206Xissn
1742-2051journal_volume
6pub_type
杂志文章abstract::Precise quantification of endogenous protein-protein interactions across live cells would be a major boon to biology. Such precise measurement is theoretically possible with fluorescence lifetime imaging microscopy (FLIM) but requires first properly addressing multiple biological, instrumental, statistical, and photop...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c0mb00132e
更新日期:2011-02-01 00:00:00
abstract::Bacterial biofilms are defined as a community of surface-attached bacteria that are protected by an extracellular matrix of biomolecules. We have recently reported the synthesis of a small molecule, denoted TAGE, based on the natural product bromoageliferin and demonstrated that TAGE has anti-biofilm activity against ...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/b719989a
更新日期:2008-06-01 00:00:00
abstract::Despite many prior studies on microbial response to oxidative stress, our understanding of microbial tolerance against oxidative stress is currently limited to aerobic conditions, and few engineering strategies have been devised to resolve toxicity issues of oxidative stress under anaerobic conditions. Since biologica...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c2mb25259g
更新日期:2013-02-02 00:00:00
abstract::Cellular heterogeneity and stochastic fluctuation play key roles in biological processes. Single molecule approaches have the key advantage of avoiding ensemble averaging, allowing the observation of transient intermediates and heterogeneity (both static and dynamic). Thus they have revolutionised the way many biologi...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/b702845h
更新日期:2007-06-01 00:00:00
abstract::Stochastic fluctuations (noise) in gene expression can cause members of otherwise genetically identical populations to display drastically different phenotypes. An understanding of the sources of noise and the strategies cells employ to function reliably despite noise is proving to be increasingly important in describ...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/b801245h
更新日期:2008-07-01 00:00:00
abstract::Inferring metabolic networks from metabolite concentration data is a central topic in systems biology. Mathematical techniques to extract information about the network from data have been proposed in the literature. This paper presents a critical assessment of the feasibility of reverse engineering of metabolic networ...
journal_title:Molecular bioSystems
pub_type: 杂志文章,评审
doi:10.1039/c0mb00083c
更新日期:2011-02-01 00:00:00
abstract::Transcription factors (TFs) and microRNAs (miRNAs) can jointly regulate transcriptional networks in the form of recurrent circuits or motifs. A motif can be divided into a feedforward loop (FFL) and a feedback loop (FBL). Incoherent FFLs have been the recent focus due to their potential to dampen gene expression noise...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c4mb00526k
更新日期:2014-12-01 00:00:00
abstract::Plant stress hormones, such as jasmonates (JAs) and ethylene (ET) are essential in plant defence against stress conditions. JAs are used in cosmetics and food flavouring, and the recently demonstrated anti-cancer activity of JAs highlights their potential in health protection. It reinforces the need for a better under...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/b718578m
更新日期:2008-08-01 00:00:00
abstract::All trans-retinoic acid (ATRA) is widely used to direct the differentiation of cultured stem cells. When exposed to the pluripotent human embryonal carcinoma (EC) stem cell line, TERA2.cl.SP12, ATRA induces ectoderm differentiation and the formation of neuronal cell types. We report in this study that novel polyene ch...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c3mb70273a
更新日期:2013-12-01 00:00:00
abstract::Here, we used stopped-flow fluorescence techniques to conduct a comparative kinetic analysis of the conformational transitions in human apurinic/apyrimidinic endonuclease 1 (APE1) and in DNA containing an abasic site in the course of their interaction. Effects of monovalent (K(+)) and divalent (Mg(2+), Mn(2+), Ca(2+),...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c6mb00128a
更新日期:2016-05-26 00:00:00
abstract::Unbalanced uptake of Omega 6/Omega 3 (ω-6/ω-3) ratios could increase chronic disease occurrences, such as inflammation, atherosclerosis, or tumor proliferation, and methylation methods for measuring the ruminal microbiome fatty acid (FA) composition/distribution play a vital role in discovering the contribution of foo...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c5mb00325c
更新日期:2015-11-01 00:00:00
abstract::Large combinatorial libraries of macrocyclic peptides are a useful source of bioactive compounds. However, peptides are not generally cell permeable, so there is great interest in the development of methods to create large libraries of modified peptides. In particular, N-alkylation of peptides is known to improve thei...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c5mb00308c
更新日期:2015-10-01 00:00:00
abstract::It is now widely accepted that microRNAs (miRNAs or miRs) along with transcription factors (TFs) weave a complex inter-regulatory network within the cell that is responsible for the combinatorial regulation of gene expression. Recently we have shown that miRNAs and TFs that form network clusters are also associated wi...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c3mb25518b
更新日期:2013-06-01 00:00:00
abstract::The biosynthesis of the endocannabinoid anandamide (AEA) and related N-acyl ethanolamine (NAE) lipids is complex and appears to involve multiple pathways, including: (1) direct release of NAEs from N-acyl phosphatidyl ethanolamine (NAPE) precursors by the phosphodiesterase NAPE-PLD, and (2) double O-deacylation of NAP...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c000237b
更新日期:2010-08-01 00:00:00
abstract::Plant aquaporins belong to a large superfamily of conserved proteins called the major intrinsic proteins (MIPs). There is limited information about the diversity of MIPs and their water transport capacity in broccoli (Brassica oleracea) plants. In this study, the cDNAs of isoforms of Plasma Membrane Intrinsic Proteins...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c0mb00285b
更新日期:2011-04-01 00:00:00
abstract::Intrinsically disordered regions in proteins are known to evolve rapidly while maintaining their function. However, given their lack of structure and sequence conservation, the means through which they stay functional is not clear. Poor sequence conservation also hampers the classification of these regions into functi...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c2mb25202c
更新日期:2012-10-30 00:00:00
abstract::In the present study, we focused on the expression and biological functions of TMEM45B in pancreatic cancer tissues and cell lines. Real-time PCR and Western blotting were used to examine the expression levels of TMEM45B in pancreatic cancer tissues and cell lines. The functions of TMEM45B were evaluated using CCK-8, ...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c6mb00203j
更新日期:2016-05-24 00:00:00
abstract::Mimicking receptor flexibility during receptor-ligand binding is a challenging task in computational drug design since it is associated with a large increase in the conformational search space. In the present study, we have devised an in silico design strategy incorporating receptor flexibility in virtual screening to...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c4mb00307a
更新日期:2014-10-01 00:00:00
abstract::Nitronyl nitroxides are capable of preventing cells, tissues, and organs from radical-induced damage through scavenging NO˙, ˙O(2)(-) and ˙OH. In order to explore the conversions of nitronyl nitroxides in biological systems with and without NO˙, HPLC-MS aided PC12 cell systems were developed, and the conversions of 2-...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c1mb05037k
更新日期:2011-05-01 00:00:00
abstract::The neuroscientific community rapidly adopted RNA interference techniques as an experimental tool for the dissection of gene function in vitro and in animal models of neurological disease in vivo. Here, we discuss recent advances in the biotechnical implementation of siRNA/shRNA-mediated gene silencing focusing on iss...
journal_title:Molecular bioSystems
pub_type: 杂志文章,评审
doi:10.1039/b701169e
更新日期:2007-11-01 00:00:00
abstract::The non-classical zinc finger protein, Neural Zinc Finger Factor-1, contains six Cys2His2Cys domains. All three cysteines and the second histidine directly bind Zn(II). Using a combination of mutagenesis, metal coordination and DNA binding studies, we report that the first histidine is involved in a functionally impor...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c4mb00246f
更新日期:2014-07-01 00:00:00
abstract::There are clearly many different philosophies associated with adapting fragment screening into mainstream Drug Discovery Lead Generation strategies. Scientists at Astex, for instance, focus entirely on strategies involving use of X-ray crystallography and NMR. However, AstraZeneca uses a number of different fragment s...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/b610069b
更新日期:2006-09-01 00:00:00
abstract::Conversion of the predominantly α-helical cellular prion protein (PrP(C)) to the misfolded β-sheet enriched Scrapie form (PrP(Sc)) is a critical event in prion pathogenesis. However, the conformational triggers that lead to the isoform conversion (PrP(C) to PrP(Sc)) remain obscure, and conjectures about the role of un...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c4mb00689e
更新日期:2015-05-01 00:00:00
abstract::Cervical cancer is initiated by infection with high-risk human papillomavirus (HPV). The viral E6 and E7 oncogenes are required for the initiation of cervical epithelial cell immortalization, but do not suffice to cause cervical cancer. Human oncogenes and tumor suppressor genes with altered activity in cervical carci...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c0mb00284d
更新日期:2011-05-01 00:00:00
abstract::Plasma membrane translocation is challenging due to the barrier of the cell membrane. Contrary to the synthetic cell-penetrating materials, tailed bacteriophages use cell-puncturing protein needles to puncture the cell membranes as an initial step of the DNA injection process. Cell-puncturing protein needles are thoug...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c4mb00293h
更新日期:2014-10-01 00:00:00
abstract::The first fluorescent labeling technology, which can induce not only an increase in the fluorescence intensity but also a shift in the fluorescence spectrum, has been developed for "ratiometric" measurements for a protein by utilizing a newly designed "field-sensitive" fluorescent probe and its corresponding unique am...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/b515777c
更新日期:2006-02-01 00:00:00
abstract::The dairy bacterium Lactococcus lactis has to master a complicated task. It must control its essentially linear glycolytic pathway in such a fashion that, when the substrate, glucose, runs out, it retains enough phosphoenolpyruvate and fructose-1,6-bisphosphate to be able to restart glycolysis as soon as new glucose b...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c5mb00726g
更新日期:2016-01-01 00:00:00
abstract::We demonstrate the expected preference of an immobilised oligosaccharide Man(9)(GlcNAc)(2) upon a 96-well photochemical array, for its known receptor, the cell-surface lectin Dendritic Cell-Specific ICAM3 Grabbing Nonintegrin (DC-SIGN) when compared to immobilised competing monosaccharides. ...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c0mb00118j
更新日期:2011-01-01 00:00:00
abstract::The transforming growth factor beta (TGF-β) signaling pathway plays myriad roles in development and disease. TGF-β isoforms initiate signaling by organizing their cell surface receptors TβRI and TβRII. Exploration and exploitation of the versatility of TGF-β signaling requires an enhanced understanding of structure-fu...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c0mb00115e
更新日期:2010-12-01 00:00:00
abstract::The adaptation of the cellular network to functional changes, timing and patterning of gene expression is regulated by binding of transcription factors to gene regulatory elements, which in turn depends on co-occurring histone modifications. These two layers influence each other, enabling a further level of regulatory...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c1mb05363a
更新日期:2012-02-01 00:00:00