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Results for “connectivity mapping”

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At least 91 records · Page 5Linked to original sources
PubMed2000

Learning-induced synchronization of a globally coupled excitable map system.

We propose a pulse-coupled neural network model in which one-dimensional excitable maps connected in a time-delayed network serve as the neural processing units. Although the individual processing unit has simple dynamical properties, the network exhibits collective chaos in the active states. Introducing a Hebbian learning algorithm for synaptic connections enhances the synchronization of excitation timing of the units within a subpopulation. The synchronizing clusters approximately exhibit a power-law size distribution, suggesting a hierarchy of synchronization. After applying a stationary signal to a subpopulation of the units with learning, the network then reproduces the signal. The learnable time range is much longer than the inherent time scale of the processing units, i.e., the synaptic delay time. Also, the network can reproduce periodic signals with time resolution finer than the delay time. Our present network model can be considered as a temporal association device which operates in chaotic states.

Animals↗
PubMed2001

Direct-method-aided phasing of MAD data.

The direct methods of breaking the phase ambiguity intrinsic in one-wavelength anomalous scattering (OAS) data and MAD phasing are powerful methods in their own rights. In a different context, in addition to their success in phasing OAS data, direct methods can also be useful in the treatment of MAD data. The idea has been tested with the MAD data at 2.5 A resolution from the protein human adenosine kinase [Mathews et al. (1998), Biochemistry, 37, 15607--15620]. The results showed that the incorporation of direct methods in MAD phasing led to a significant improvement of phases over those obtained from the conventional MAD phasing method alone, as indicated by improved map correlation coefficients (with the existing model), reduced phase errors by 4.5 degrees and improved map connectivity.

Adenosine Kinase↗
PubMed2002

B cell antigen receptor signaling: roles in cell development and disease.

Signals propagated through the B cell antigen receptor (BCR) are vital for the development and survival of B lymphocytes in both the bone marrow and the periphery. These signals not only guide maturation and activation but also affect the removal of potentially self-reactive B lymphocytes. Interestingly, these signals are known to be either ligand-independent ("tonic" signals) or induced by ligand (antigen) binding to the BCR. We focus on the problems that occur in B cell development due to defects in signals emanating from the BCR. In addition, we present the B Cell Antigen Receptor Pathway, an STKE Connections Map that illustrates the events involved in B cell signaling.

Animals↗
PubMed2002

The jasmonate pathway.

Plants are faced with many of the same problems as animals-a need for regulation of metabolic processes and reproduction and for defense against enemies. Jasmonates in plants serve key roles in gene and metabolic regulation, defense, responses to trauma, reproduction, and possibly communication. Some remarkable features of plant responses, such as production of repellent volatiles as a defense against herbivorous insects, or the massive transcriptional reprogramming that occurs in response to wounding, are under the control of the jasmonate pathway. Details of the jasmonate signaling pathway are currently at the center of active research that is generating exciting results. The Jasmonate Biochemical Pathway at the STKE Connections Maps is designed to present and keep pace with these developments.

Cyclopentanes↗
PubMed2002

The promise and perils of Wnt signaling through beta-catenin.

Wnt pathways are involved in the control of gene expression, cell behavior, cell adhesion, and cell polarity. In addition, they often operate in combination with other signaling pathways. The Wnt/beta-catenin pathway is the best studied of the Wnt pathways and is highly conserved through evolution. In this pathway, Wnt signaling inhibits the degradation of beta-catenin, which can regulate transcription of a number of genes. Some of the genes regulated are those associated with cancer and other diseases (for example, colorectal cancer and melanomas). As a result, components of the Wnt/beta-catenin pathway are promising targets in the search for therapeutic agents. Information about Wnt pathways is available both in canonical terms and at the species level. In addition to the canonical Wnt/beta-catenin pathway, information is now available for Drosophila, Caenorhabditis elegans, and Xenopus. The STKE Connections Maps for these pathways provide an important tool in accessing this large body of complex information.

Animals↗
PubMed2002

Control of T cell function by positive and negative regulators.

T cells are an essential element of the body's immune system. Engagement of the T cell receptor is responsible for initiating the signaling events that can activate, inactivate, or eliminate T cells, depending on the magnitude and duration of the signal. Control of T cell signaling occurs through both positive and negative regulation, as well as through the actions of molecular scaffolds that contribute to the formation of signaling complexes. The T Cell Signal Transduction Pathway at the STKE Connections Maps highlights the molecular components that are responsible for T cell activation. Understanding the mechanisms that regulate T cell responsiveness will aid in the development of therapeutic agents to treat infection, cancer, and autoimmune disease and immune deficiency.

Animals↗
PubMed2002

Signaling pathways for PC12 cell differentiation: making the right connections.

A key issue in signal transduction is how signaling pathways common to many systems-so-called canonical signaling cassettes-integrate signals from molecules having a wide spectrum of activities, such as hormones and neurotrophins, to deliver distinct biological outcomes. The neuroendocrine cell line PC12, derived from rat pheochromocytoma, provides an example of how one canonical signaling cassette-the Raf --> mitogen-activated protein kinase kinase (MEK) --> extracellular signal-regulated kinase (ERK) pathway-can promote distinct outcomes, which in this case include neuritogenesis, gene induction, and proliferation. Two growth hormones, epidermal growth factor (EGF) and nerve growth factor (NGF), use the same pathway to cause PC12 proliferation and differentiation, respectively. In addition, pituitary adenylate cyclase-activating polypeptide (PACAP), a neurotransmitter that also causes differentiation, uses the same canonical cassette as NGF but in a different way. The Connections Map for PC12 Cell Differentiation brings into focus the complex array of specific cellular responses that rely on canonical signal transduction systems.

Animals↗
PubMed2002

Deciphering the cross-talk of implantation: advances and challenges.

Implantation involves a series of steps leading to an effective reciprocal signaling between the blastocyst and the uterus. Except for a restricted period when ovarian hormones induce a uterine receptive phase, the uterus is an unfavorable environment for blastocyst implantation. Because species-specific variations in implantation strategies exist, these differences preclude the formulation of a unifying theme for the molecular basis of this event. However, an increased understanding of mammalian implantation has been gained through the use of the mouse model. This review summarizes recognized signaling cascades and new research in mammalian implantation, based primarily on available genetic and molecular evidence from implantation studies in the mouse. Although the identification of new molecules associated with implantation in various species provides valuable insight, important questions remain regarding the common molecular mechanisms that govern this process. Understanding the mechanisms of implantation promises to help alleviate infertility, enhance fetal health, and improve contraceptive design. The success of any species depends on its reproductive efficiency. For sexual reproduction, an egg and sperm must overcome many obstacles to fuse and co-mingle their genetic material at fertilization. The zygote develops into a blastocyst with two cell lineages (the inner cell mass and the trophectoderm), migrates within the reproductive tract, and ultimately implants into a transiently permissive host tissue, the uterus. However, the molecular basis of the road map connecting the blastocyst with the endometrium across species is diverse (1) and not fully understood. Recent advances have identified numerous molecules involved in implantation (1-4), yet new discoveries have not yielded a unifying scheme for the mechanisms of implantation.

Animals↗
PubMed2002

Phosphorelay and transcription control in cytokinin signal transduction.

The past decade has seen substantial advances in knowledge of molecular mechanisms and actions of plant hormones, but only in the past few years has research on cytokinins begun to hit its stride. Cytokinins are master regulators of a large number of processes in plant development, which is known to be unusually plastic and adaptive, as well as resilient and perpetual. These characteristics allow plants to respond sensitively and quickly to their environments. Recent studies have demonstrated that cytokinin signaling involves a multistep two-component signaling pathway, resulting in the development of a canonical model of cytokinin signaling that is likely representative in plants. This Viewpoint outlines this general model, focusing on the specific example of Arabidopsis, and introduces the STKE Connections Maps for both the canonical module and the specific Arabidopsis Cytokinin Signaling Pathway.

Active Transport, Cell Nucleus↗
PubMed2002

TNF-R1 signaling: a beautiful pathway.

Tumor necrosis factor (TNF) is a major mediator of apoptosis as well as inflammation and immunity, and it has been implicated in the pathogenesis of a wide spectrum of human diseases, including sepsis, diabetes, cancer, osteoporosis, multiple sclerosis, rheumatoid arthritis, and inflammatory bowel diseases. The interaction of TNF with TNF receptor-1 (TNF-R1) activates several signal transduction pathways. A common feature of each pathway is the TNF-induced formation of a multiprotein signaling complex at the cell membrane. Over the past decade, many of the components and mechanisms of these signaling pathways have been elucidated. We provide an overview of current knowledge of TNF signaling and introduce an STKE Connections Map that depicts a canonical view of this process.

Animals↗
PubMed2003

Myocyte adrenoceptor signaling pathways.

Adrenoceptors (ARs), members of the G protein-coupled receptor superfamily, form the interface between the sympathetic nervous system and the cardiovascular system, with integral roles in the rapid regulation of myocardial function. However, in heart failure, chronic catecholamine stimulation of adrenoceptors has been linked to pathologic cardiac remodeling, including myocyte apoptosis and hypertrophy. In cardiac myocytes, activation of AR subtypes results in coupling to different G proteins and induction of specific signaling pathways, which is partly regulated by the subtype-specific distribution of receptors in plasma membrane compartments containing distinct complexes of signaling molecules. The Connections Maps of the Adrenergic and Myocyte Adrenergic Signaling Pathways bring into focus the specific signaling pathways of individual AR subtypes and their relevant functions in vivo.

Animals↗
PubMed2003

Regulators of cerebellar granule cell development act through specific signaling pathways.

The proper development of the central nervous system depends upon a finely tuned balance between cell proliferation and programmed cell death (PCD). Although PCD was initially believed to depend solely on the inability of certain neurons to obtain access to a limited supply of trophic factors, it has become apparent that the local production of death signals is also critical. In this Viewpoint, we discuss several pathways implicated in the survival of cerebellar granule cells- both pathways that protect from apoptosis and pathways that promote apoptosis-and describe how these disparate pathways converge on the final common mediators of PCD. Information on other important pathways implicated in granule cell survival may be found in the Connections Maps.

Animals↗
PubMed2003

The signal to move: D. discoideum go orienteering.

Cells migrating directionally toward a chemoattractant source display a highly polarized cytoskeletal organization, with F-actin localized predominantly at the anterior and myosin II at the lateral and posterior regions. Dictyostelium discoideum has proven a useful system for elucidating signaling pathways that regulate this chemotactic response. During development, extracellular adenosine 3', 5' monophosphate (cAMP) functions as a primary signal to activate cell surface cAMP receptors (cARs). These receptors transduce different signals depending on whether or not they are coupled to heterotrimeric guanine nucleotide-binding proteins (G proteins) (see the STKE Connections Maps). Multiple G protein-stimulated pathways interact to establish polarity in chemotaxing D. discoideum cells by localizing F-actin at their leading edge and by regulating the phosphorylation state and assembly of myosin II. Many of the molecular interactions described are fundamental to the regulation of chemotaxis in other eukaryotic cells.

Actins↗
PubMed2003

Circadian rhythms: in the loop at last.

The basic molecular mechanisms underlying circadian oscillators follow the same general plan across the phylogenetic spectrum: oscillating feedback loops in which clock gene products negatively regulate their own expression. The circadian clocks of animals involve at least two interacting feedback loops. This Viewpoint compares and contrasts the circadian clocks of mammals and of Drosophila, emphasizing how different players are used to create the same basic script. Both the general script and the specific details of the murine and Drosophila circadian pathways are available at Science's Signal Transduction Knowledge Environment Connections Maps.

ARNTL Transcription Factors↗
PubMed2003

Toll-like receptor signaling pathways.

Members of the Toll-like receptor (TLR) family recognize conserved microbial structures, such as bacterial lipopolysaccharide and viral double-stranded RNA, and activate signaling pathways that result in immune responses against microbial infections. All TLRs activate MyD88-dependent pathways to induce a core set of stereotyped responses, such as inflammation. However, individual TLRs can also induce immune responses that are tailored to a given microbial infection. Thus, these receptors are involved in both innate and adaptive immune responses. The mechanisms and components of these varied responses are only partly understood. Given the importance of TLRs in host defense, dissection of the pathways they activate has become an important emerging research focus. TLRs and their pathways are numerous; Science's Signal Transduction Knowledge Environment's TLR Connections Map provides an immediate, clear overview of the known components and relations of this complex system.

Adaptor Proteins, Signal Transducing↗
PubMed2003

Insulin signaling in health and disease.

The signaling pathways used by insulin have been identified [M. White, Insulin Signaling Pathway, Sci. STKE (Connections Map, as seen November 2003), http://stke.sciencemag.org/cgi/cm/cmp_12069]. Now our challenge is to understand how the failure of these signals is associated with obesity and the progressive failure of pancreatic beta cells that leads to diabetes. Whether better management of chronic inflammation can improve insulin action is an important area of investigation. Drugs that stimulate IRS2 (insulin receptor substrate protein 2) synthesis or signaling might be a good starting point. This knowledge will lead to rational strategies that prevent or cure diabetes.

Animals↗
PubMed2004

Keeping the leaves green above us.

The plant immune system relies to a great extent on the highly regulated expression of hundreds of defense genes encoding antimicrobial proteins, such as defensins, and antiherbivore proteins, such as lectins. The expression of many of these genes is controlled by a family of mediators known as jasmonates; these cyclic oxygenated fatty acid derivatives are reminiscent of prostaglandins. The roles of jasmonates also extend to the control of reproductive development. How are these complex events regulated? Nearly 20 members of the jasmonate family have been characterized. Some, like jasmonic acid, exist in unmodified forms, whereas others are conjugated to other lipids or to hydrophobic amino acids. Why do so many chemically different forms of these mediators exist, and do individual jasmonates have unique signaling properties or are they made to facilitate transport within and between cells? Key features of the jasmonate signal pathway have been identified and include the specific activation of E3-type ubiquitin ligases thought to target as-yet-undescribed transcriptional repressors for modification or destruction. Several classes of transcription factor are known to function in the jasmonate pathway, and, in some cases, these proteins provide nodes that integrate this network with other important defensive and developmental pathways. Progress in jasmonate research is now rapid, but large gaps in our knowledge exist. Aimed to keep pace with progress, the ensemble of jasmonate Connections Maps at the Signal Transduction Knowledge Environment describe (i) the canonical signaling pathway, (ii) the Arabidopsis signaling pathway, and (iii) the biogenesis and structures of the jasmonates themselves.

Arabidopsis↗
PubMed2004

The ethylene signaling pathway.

Plants use a structurally very simple gas molecule, the hydrocarbon ethylene, to modulate various developmental programs and coordinate responses to a multitude of external stress factors. How this simple molecule generates such a diverse array of effects has been the subject of intense research for the past two decades. A fascinating signaling pathway, with classical as well as novel plant-specific signaling elements, is emerging from these studies. We describe the four main modules that constitute this signaling pathway: a phosphotransfer relay, an EIN2-based unit, a ubiquitin-mediated protein degradation component, and a transcriptional cascade. The canonical and Arabidopsis ethylene signaling pathways in the Signal Transduction Knowledge Environment Connections Maps provide a complete panoramic view of these signaling events in plants.

Arabidopsis↗