Abstract:
:Gene regulatory networks constitute the first layer of the cellular computation for cell adaptation and surveillance. In these webs, a set of causal relations is built up from thousands of interactions between transcription factors and their target genes. The large size of these webs and their entangled nature make it difficult to achieve a global view of their internal organisation. Here, this problem has been addressed through a comparative study of Escherichia coli, Bacillus subtilis and Saccharomyces cerevisiae gene regulatory networks. We extract the minimal core of causal relations, uncovering the hierarchical and modular organisation from a novel dynamical/causal perspective. Our results reveal a marked top-down hierarchy containing several small dynamical modules for E. coli and B. subtilis. Conversely, the yeast network displays a single but large dynamical module in the middle of a bow-tie structure. We found that these dynamical modules capture the relevant wiring among both common and organism-specific biological functions such as transcription initiation, metabolic control, signal transduction, response to stress, sporulation and cell cycle. Functional and topological results suggest that two fundamentally different forms of logic organisation may have evolved in bacteria and yeast.
journal_name
Mol Biosystjournal_title
Molecular bioSystemsauthors
Rodríguez-Caso C,Corominas-Murtra B,Solé RVdoi
10.1039/B904960fsubject
Has Abstractpub_date
2009-12-01 00:00:00pages
1617-29issue
12eissn
1742-206Xissn
1742-2051journal_volume
5pub_type
杂志文章abstract::Cycloserine (CS, 4-amino-3-isoxazolidone) is a cyclic amino acid mimic that is known to inhibit many essential pyridoxal 5'-phosphate (PLP)-dependent enzymes. Two CS enantiomers are known; D-cycloserine (DCS, also known as Seromycin) is a natural product that is used to treat resistant Mycobacterium tuberculosis infec...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c003743e
更新日期:2010-09-01 00:00:00
abstract::We explain that part of the reduction in the parameter uncertainties in the computations of Apgar et al. (Mol. Biosyst. 2010, 6, 1890-900) is due to a greatly increased number of effective data points. ...
journal_title:Molecular bioSystems
pub_type: 评论,信件
doi:10.1039/c1mb05046j
更新日期:2011-08-01 00:00:00
abstract::Proteomics is the study of proteins and their interactions within complex biological systems. While this field is often associated with mass spectrometry, it is more useful to consider proteomics in the context of an objective: to identify and understand the molecular basis of health and disease at the protein level i...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/b611446f
更新日期:2007-01-01 00:00:00
abstract::The pro-inflammatory cytokines interleukin 1 (IL-1) and 6 (IL-6) are crucially involved in the regulation of a multitude of physiological processes, in particular coordinating the immune response upon bacterial infection and tissue injury. Both interleukins induce complex signalling cascades and trigger the production...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c1mb05261f
更新日期:2011-12-01 00:00:00
abstract::Unstable angina (UA) is one of the most dangerous types of coronary heart disease and has high mortality and morbidity rates worldwide. However, the diagnostic accuracy for UA is unsatisfactory in clinical practice. In this study, we investigated the application of plasma metabolomics in discovering potential biomarke...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c3mb70216b
更新日期:2013-12-01 00:00:00
abstract:BACKGROUND:Candida albicans, the most common fungal pathogen related to colonization and biofilm formation on the surfaces of indwelling medical devices, shows high resistance to the most commonly used antifungal drugs. In this study, an ion-pairing chromatography-porous graphitic carbon column coupled with a time-of-f...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c3mb70240e
更新日期:2014-01-01 00:00:00
abstract::Mirror image phage display is a straightforward approach to identify new potentially therapeutically active D-enantiomeric peptides. Such D-peptides are more resistant to proteolytic degradation compared to L-peptides. In this review, several examples of mirror image phage display derived D-peptides with therapeutical...
journal_title:Molecular bioSystems
pub_type: 杂志文章,评审
doi:10.1039/b904138a
更新日期:2009-08-01 00:00:00
abstract::Many Gram-negative bacterial pathogens use type III secretion systems (TTSSs) for subverting the normal cellular functions of their target eukaryotic cells. The type III secretion apparatus (TTSA) functions like a syringe to inject proteins through an external needle and into a target cell's membrane and cytosol. The ...
journal_title:Molecular bioSystems
pub_type: 杂志文章,评审
doi:10.1039/b808271p
更新日期:2008-12-01 00:00:00
abstract::Bacterial resistance to β-lactam antibiotics poses a serious threat to human health. Penicillin binding proteins (PBPs) and β-lactamases are involved in both antibacterial activity and mediation of β-lactam antibiotic resistance. The two major reasons for resistance to β-lactams include: (i) pathogenic bacteria expres...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c3mb70537d
更新日期:2014-04-01 00:00:00
abstract::α-Alkylidene-γ-butyrolactones are quite common in nature and exhibit a broad spectrum of biological activities. We therefore synthesized a small library of xanthatine inspired α-alkylidene-γ-butyrolactones to screen non-pathogenic and uropathogenic E. coli strains by activity based protein profiling (ABPP). The identi...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c2mb25313e
更新日期:2012-11-01 00:00:00
abstract::Abundant information about the nucleotide sequence of the human genome has become readily available and it is now necessary to develop methods for the identification of genes that are involved in important cellular, developmental and disease-related processes. Identification methods based on the activities of hammerhe...
journal_title:Molecular bioSystems
pub_type: 杂志文章,评审
doi:10.1039/b503235k
更新日期:2005-05-01 00:00:00
abstract::In actively proliferating cells, such as the cells of the developing embryo, DNA repair is crucial for preventing the accumulation of mutations and synchronizing cell division. Sea urchin embryo growth was analyzed and extracts were prepared. The relative activity of DNA polymerase, apurinic/apyrimidinic (AP) endonucl...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c5mb00906e
更新日期:2016-06-21 00:00:00
abstract::Herein, we demonstrate that the bacterial signaling molecule, c-di-GMP, can enhance the peroxidation of hemin when proflavine is present. The c-di-GMP-proflavine-hemin nucleotidezyme can oxidize the colorless compound 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid), ABTS, to the colored radical cation ABTS˙(+) ...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c2mb05430b
更新日期:2012-03-01 00:00:00
abstract::Disordered regions within proteins have increasingly been associated with various cellular functions. Identifying the specific roles played by disorder in these functions has proved difficult. However, the development of reliable prediction algorithms has expanded the study of disorder from a few anecdotal examples to...
journal_title:Molecular bioSystems
pub_type: 杂志文章,评审
doi:10.1039/c1mb05235g
更新日期:2012-01-01 00:00:00
abstract::Glucocorticoids (GCs) have been proved to be an important pathogenic factor of some neuropsychiatric disorders. Usually, a classical injury model based on corticosterone-induced cytotoxicity of differentiated rat pheochromocytoma (PC12) cells was used to stimulate the state of GC damage of hippocampal neurons and inve...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c5mb00642b
更新日期:2016-03-01 00:00:00
abstract::Lovastatin and other statins inhibit HMG-CoA reductase, which carries out an early step in the sterol biosynthesis pathway. Statins lower cholesterol and are widely prescribed to prevent heart disease, but like many drugs, they can interact with nutritionally acquired metabolites. To probe these interactions, we explo...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c0mb00166j
更新日期:2011-02-01 00:00:00
abstract::Epigenetic regulation by histone methylation is crucial for proper programming of the genome during development. Homeostasis of histone methylation is balanced by the activities of histone methyltransferases and demethylases. Although these methyltransferases and demethylases represent logical targets for potential dr...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c3mb70413k
更新日期:2014-02-01 00:00:00
abstract::α-Anomers of 2'-deoxyadenosine (αdA) are major products of deoxyadenosine damage when DNA is γ-irradiated under anoxic conditions. Such lesions are a threat to genomic stability and are known to be processed by human apurinic/apyrimidinic endonuclease 1 (APE1). The aim of this study was to determine whether the α-anom...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c6mb00511j
更新日期:2016-10-18 00:00:00
abstract::Low transfection efficiency and inactivation by serum are the major drawbacks for cationic polymers when used as non-viral gene vectors. Here, a series of N-succinyl-chitosan-graft-polyethylenimine (NSC-g-PEI) copolymers with different compositions were synthesized through grafting low molecular weight PEI (800 Da) to...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/b822505b
更新日期:2009-06-01 00:00:00
abstract::Enediyne natural product biosynthesis is characterized by a convergence of multiple pathways, generating unique peripheral moieties that are appended onto the distinctive enediyne core. Kedarcidin (KED) possesses two unique peripheral moieties, a (R)-2-aza-3-chloro-β-tyrosine and an iso-propoxy-bearing 2-naphthonate m...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c3mb25523a
更新日期:2013-03-01 00:00:00
abstract::Biotin is an enzyme cofactor indispensable to metabolic fixation of carbon dioxide in all three domains of life. Although the catalytic and physiological roles of biotin have been well characterized, the biosynthesis of biotin remains to be fully elucidated. Studies in microbes suggest a two-stage biosynthetic pathway...
journal_title:Molecular bioSystems
pub_type: 杂志文章,评审
doi:10.1039/c1mb05022b
更新日期:2011-06-01 00:00:00
abstract::The chemical composition of the cervical mucus (CM), its physical characteristics and the volume of secretion change cyclically throughout the menstrual cycle. The aim of this study was to identify the constitutive protein composition of CM of fertile women and the changes in the CM proteome throughout the menstrual c...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c5mb00071h
更新日期:2015-06-01 00:00:00
abstract::Infections caused by human parasites (HPs) affect the poorest 500 million people worldwide but chemotherapy has become expensive, toxic, and/or less effective due to drug resistance. On the other hand, many 3D structures in Protein Data Bank (PDB) remain without function annotation. We need theoretical models to quick...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c1mb05069a
更新日期:2011-06-01 00:00:00
abstract::CC chemokine receptor 5 (CCR5), a member of G protein-coupled receptors (GPCRs), plays a vital role in inflammatory responses to infection. Alterations in the expression of CCR5 have been correlated with disease progression in many types of cancers. The idea of using CCR5 as a target for therapeutic intervention has b...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c6mb00577b
更新日期:2016-10-18 00:00:00
abstract::Extracellular electron transfer (EET) is the key feature of some bacteria, such as Geobacter sulfurreducens and Shewanella oneidensis. Via EET processes, these bacteria can grow on electrode surfaces and make current output of microbial fuel cells. c-Type cytochromes can be used as carriers to transfer electrons, whic...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c4mb00386a
更新日期:2014-12-01 00:00:00
abstract::The emerging field of synthetic biology is generating insatiable demands for synthetic genes, which far exceed existing gene synthesis capabilities. This review discusses the current methods of chemical DNA synthesis and gene assembly, as well as the latest engineering tools, technologies and trends which could potent...
journal_title:Molecular bioSystems
pub_type: 杂志文章,评审
doi:10.1039/b822268c
更新日期:2009-07-01 00:00:00
abstract::Thyroid carcinoma is a common endocrine malignancy worldwide, accounting for approximately 1% of all diagnosed cancers and about 91.5% of the malignancies of head and neck. However, differentiating malignant thyroid nodules from benign ones remains a diagnostic challenge. Thus, novel molecular markers that enable non-...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c1mb05029j
更新日期:2011-09-01 00:00:00
abstract::Single molecule observation of fluorescence resonance energy transfer can be used to provide insight into the structure and dynamics of proteins. Using a straightforward triple-colour labelling strategy, we present a measurement and analysis scheme that can simultaneously study multiple regions within single intrinsic...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c2mb25135c
更新日期:2012-10-01 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::MicroiRNAs are genome encoded small double stranded RNAs that regulate expression of homologous mRNAs. With approximately 2500 human miRNAs and each having hundreds of potential mRNA targets, miRNA based gene regulation is quite pervasive in both development and disease. While there are numerous studies investigating ...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c5mb00415b
更新日期:2016-01-01 00:00:00