Open Bioinformatics Journal最新文献

{"title":"Emergent Principles in Gene Expression Dynamics","authors":"J. Nacher, T. Ochiai","doi":"10.2174/1875036201105010034","DOIUrl":"https://doi.org/10.2174/1875036201105010034","url":null,"abstract":"Rapid advances in data processing of genome-wide gene expression have allowed us to get a first glimpse of some fundamental laws and principles involved in the intra-cellular organization as well as to investigate its complex regulatory architecture. However, the identification of commonalities in dynamical processes involved in networks has not followed the same development. In particular, the coupling between dynamics and structural features remains largely uncovered. Here, we review several works that have addressed the issue of uncovering the gene expression dynamics and principles using micro-array time series data at different environmental conditions and disease states as well as the emer- gence of criticality in gene expression systems by using information theory. Moreover, we also describe the efforts done to explore the question of characterizing gene networks by using transcriptional dynamics information. The combination of the emergent principles uncovered in the transcriptional organization with dynamic information, may lead to recon- struct, characterize and complete gene networks. We also discuss several methods based on simulations of a series of en- zyme-catalyzed reaction routes and Markov processes as well as combination of complex network properties with sto- chastic theory.","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68106211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stability and Flexibility from a System Analysis of Gene Regulatory Networks Based on Ordinary Differential Equations","authors":"M. Gustafsson, Michael Hörnquist","doi":"10.2174/1875036201105010026","DOIUrl":"https://doi.org/10.2174/1875036201105010026","url":null,"abstract":"The inference of large-scale gene regulatory networks from high-throughput data sets has revealed a diverse picture of only partially overlapping descriptions. Nevertheless, several properties in t ...","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68106727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Topological determinants of synchronizability of oscillators on large complex networks","authors":"Weihan Li, Changsong Zhou","doi":"10.2174/1875036201105010042","DOIUrl":"https://doi.org/10.2174/1875036201105010042","url":null,"abstract":"Synchronized oscillations play an important role in many biological systems. In recent years, much work has been done on oscillating biomolecular systems, both experimentally and theoretically. A better insight into oscillation mechanisms, coupling strategies and related biological processes is gained by quantitative analysis. Here we summarized some of recent work on oscillation and synchronization in biological systems and reviewed the basic concepts of synchronization of coupled oscillators and dynamics on complex networks.","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68106226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Boolean modeling of biochemical networks","authors":"T. Helikar, Naomi Kochi, J. Konvalina, J. Rogers","doi":"10.2174/1875036201105010016","DOIUrl":"https://doi.org/10.2174/1875036201105010016","url":null,"abstract":"The use of modeling to observe and analyze the mechanisms of complex biochemical network function is be- coming an important methodological tool in the systems biology era. Number of different approaches to model these net- works have been utilized-- they range from analysis of static connection graphs to dynamical models based on kinetic in- teraction data. Dynamical models have a distinct appeal in that they make it possible to observe these networks in action, but they also pose a distinct challenge in that they require detailed information describing how the individual components of these networks interact in living cells. Because this level of detail is generally not known, dynamic modeling requires simplifying assumptions in order to make it practical. In this review Boolean modeling will be discussed, a modeling method that depends on the simplifying assumption that all elements of a network exist only in one of two states.","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68106682","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the Dynamics of Large-Scale Biochemical Networks: A Computational Perspective","authors":"R. Steuer","doi":"10.2174/1875036201105010004","DOIUrl":"https://doi.org/10.2174/1875036201105010004","url":null,"abstract":"The complexity of even comparatively simple biochemical systems necessitates a computational description to explore and eventually understand the dynamics emerging from the underlying networks of cellular interactions. Within this contribution, several aspects relating to a computational description of large-scale biochemical networks are discussed. Topics range from a brief description of the rationales for computational modeling to the utilization of Monte Carlo methods to explore dynamic properties of biochemical networks. The main focus is to outline a path towards the construction of large-scale kinetic models of metabolic networks in the face of incomplete and uncertain knowledge of kinetic parameters. It is argued that a combination of phenotypic data, large-scale measurements, heuristic assumptions about generic rate equations, together with appropriate numerical schemes, allows for a fast and efficient way to explore the dynamic properties of biochemical networks. In this respect, several recently proposed strategies that are based on Monte Carlo methods are an important step towards large-scale kinetic models of cellular metabolism.","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68106661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial: Structure, Dynamics and Function - Dynamical Properties of Large Bio-Molecular Networks","authors":"A. Fuente","doi":"10.2174/1875036201104010001","DOIUrl":"https://doi.org/10.2174/1875036201104010001","url":null,"abstract":"Bio-molecular systems consist of tens of thousands of molecular species of different chemical nature. These systems have been described as networks, such as metabolic networks [1, 2], protein-interaction networks [3], and transcriptional regulatory networks [4]. The nodes in these networks represent bio-molecular species (e.g. metabolites, proteins, RNAs) and the edges represent functional, causal or physical interactions between the nodes. The abstract representation of bio-molecular regulatory systems as networks is fruitful because it provides the ability to study the systems as a whole while ignoring many irrelevant details [5, 6]. All chemistry and physics is removed (or considered only implicitly) in order to concentrate on the essence of the system: the 'wiring scheme'. As for all abstractions of natural systems, we are doomed to lose some information when we represent bio-molecular regulatory systems as networks [6-8]. Large bio-molecular network have been subjected extensively to topological analysis for over a decade now. Many interesting topological features have been identified and their potential functions have been proposed [5, 6]. However, relating the structure of large bio-molecular network to dynamics and function is still a largely unexplored subject. Studies on dynamical properties have mostly been restricted to very small bio-molecular networks, due to the limited amount of quantitative data. Fortunately, several studies have shown that even without detailed quantitative knowledge, much can still be learned about the dynamical properties of large bio-molecular networks [9-13]. This special issue provides a recent update of the current state of art in relating structure to dynamics applied to large bio-molecular networks. The goal of the studies reviewed in this special issue is not to study the dynamics of any specific bio-molecular network, but rather to identify topological patterns which imply the possibility of certain dynamical/functional behaviors. By no means can we definitely state that 'structure determines function' as networks with the same structure could display distinct dynamics depending on their parameter values (for instance the strength or signs of interactions). Networks could for instance display oscillations or reach a stable steady state depending on the specific model parameters. To be able to characterize the true behavior of bio-molecular networks we need the quantitative information of all the parameters. Experimental identification of the large numbers of parameters is currently infeasible, even with modern high throughput techniques. Nevertheless, we can still learn much about dynamics from topology alone. Inspection of the network topology can immediately exclude certain dynamical behaviors completely …","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68106567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Protein Kinase-Regulated Inwardly Rectifying Anion and Organic Osmolyte Channels in Malaria-Infected Erythrocytes","authors":"G. Bouyer, Serge L. Y. Thomas, S. Egée","doi":"10.2174/1874196701104010010","DOIUrl":"https://doi.org/10.2174/1874196701104010010","url":null,"abstract":"The intraerythrocytic amplification of the malaria parasite Plasmodium falciparum induces new pathways of solute permeability in the host cell's membrane. These pathways play a pivotal role in parasite development by supplying the parasite with nutrients, disposing of the parasite's metabolic waste and organic osmolytes, and adapting the host's electrolyte composition to the parasite's needs. During the last ten years, electrophysiological investigations strongly supported earlier evidence obtained by transport and pharmacological studies that this new permeability pathway, which is induced by the parasite in the host cell membrane, is constituted by anion-selective channels. This review surveys the evidences acquired using the patch-clamp technique and discuss the hypothesis that protein kinase A is an effector of the signalling pathway leading to the activation of endogenous channels upon infection.","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68052932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Outward Rectifying Anions and Organic Osmolytes Conductance in Malaria-Infected Erythocytes: Myth or Reality?","authors":"C. Duranton, Tanneur Valerie, Tauc Michel","doi":"10.2174/1874196701104010003","DOIUrl":"https://doi.org/10.2174/1874196701104010003","url":null,"abstract":"Malaria-infected erythrocytes acquired New Permeability Pathways (NPPs) to meet the needs in nutrients and disposal of waste products of the intraerythocytic parasite development. The NPPs have been intensively studied for their putative interest as therapeutic targets for malaria treatment. Over the past 10 years, many electrophysiological studies have identified novel ion conductances (reflecting a part of the NPPs activities) in the host plasma membrane of Plasmodium falciparum-infected erythrocytes. In this article, we review the electrophysiological/biophysical properties of the malaria-induced outwardly rectifying anion conductance and compare this conductance to the other anion conductances and permeabilities already described in the literature.","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68052918","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ClC-2 Channels in Erythrocytes","authors":"E. Shumilina, S. Huber","doi":"10.2174/1874196701104010018","DOIUrl":"https://doi.org/10.2174/1874196701104010018","url":null,"abstract":"ClC-2 is a ubiquitously expressed plasma membrane Cl - channel that reportedly controls the ionic environment in mouse retina and testis. Beyond that, ClC-2 might sense cellular energy status and cellular stress by its carboxy- terminal cystathionine-beta-synthase (CBS) domains and by its molecular interaction with the heat shock protein Hsp90, respectively. In mature human and mouse erythrocytes, ClC-2 is activated by oxidative stress and by malaria infection. This article describes possible function of erythrocyte ClC-2 channels for the programmed death of oxidatively injured erythrocytes and for the regulatory volume decrease of malaria-infected erythrocytes.","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68052942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial: Ion Channels of Mature Human Erythrocytes","authors":"H. Stephan","doi":"10.2174/18750362010040100001","DOIUrl":"https://doi.org/10.2174/18750362010040100001","url":null,"abstract":"Ion channels in the plasma membrane serve multiple functions such as setting the membrane potential, adjusting the cell volume and the intracellular electrolyte concentrations or eliciting versatile cytosolic Ca signals. Channel activities regulate many basic cellular processes. Among those are cell proliferation, migration, differentiation and apoptotic cell death. Although devoid of nuclei and mitochondria, mature mammalian erythrocytes maintain a full set of functional ion channels in their plasma membrane.","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68106349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}