scholarly journals CellNetVis: a web tool for visualization of biological networks using force-directed layout constrained by cellular components

2017 ◽  
Author(s):  
Henry Heberle ◽  
Marcelo Falsarella Carazzolle ◽  
Guilherme P. Telles ◽  
Gabriela Vaz Meirelles ◽  
Rosane Minghim
Keyword(s):  
Biological Networks ◽  
Visual Exploration ◽  
Web Tool ◽  
Biomolecular Interaction ◽  
Dense Networks ◽  
A Cell ◽  
Visualization Of Data ◽  
Cellular Compartments ◽  
Cellular Components ◽  
Dynamic Investigation

AbstractBackgroundThe advent of “omics” science has brought new perspectives in contemporary biology through the high-throughput analyses of molecular interactions, providing new clues in protein/gene function and in the organization of biological pathways. Biomolecular interaction networks, or graphs, are simple abstract representations where the components of a cell (e.g. proteins, metabolites etc.) are represented by nodes and their interactions are represented by edges. An appropriate visualization of data is crucial for understanding such networks, since pathways are related to functions that occur in specific regions of the cell. The force-directed layout is an important and widely used technique to draw networks according to their topologies. Placing the networks into cellular compartments helps to quickly identify where network elements are located and, more specifically, concentrated. Currently, only a few tools provide the capability of visually organizing networks by cellular compartments. Most of them cannot handle large and dense networks. Even for small networks with hundreds of nodes the available tools are not able to reposition the network while the user is interacting, limiting the visual exploration capability.ResultsHere we propose CellNetVis, a web tool to easily display biological networks in a cell diagram employing a constrained force-directed layout algorithm. The tool is freely available and open-source. It was originally designed for networks generated by the Integrated Interactome System and can be used with networks from others databases, like InnateDB.ConclusionsCellNetVis has demonstrated to be applicable for dynamic investigation of complex networks over a consistent representation of a cell on the Web, with capabilities not matched elsewhere.

scholarly journals CellNetVis: a web tool for visualization of biological networks using force-directed layout constrained by cellular components

2017 ◽  
Vol 18 (S10) ◽  
Author(s):  
Henry Heberle ◽  
Marcelo Falsarella Carazzolle ◽  
Guilherme P. Telles ◽  
Gabriela Vaz Meirelles ◽  
Rosane Minghim
Keyword(s):  
Biological Networks ◽  
Web Tool ◽  
Cellular Components

scholarly journals Subcellular Localization of Disease-Associated Proteins in Psoriasis

2020 ◽  
Vol 2 (1) ◽  
pp. 8
Keyword(s):  
Subcellular Localization ◽  
Metabolic Pathways ◽  
Inflammatory Disorder ◽  
Protein Protein Interaction ◽  
Extracellular Region ◽  
Associated Proteins ◽  
A Cell ◽  
Pathway Analyses ◽  
Cellular Compartments ◽  
Molecular Pathophysiology

Psoriasis is an autoimmune, persisting, inflammatory disorder that extremely affects the skin and joints of the system. In spite of the field under investigation across the globe roots toward the origin and the molecular pathophysiology of the disease, yet, the mechanism is vaguely presumed. The pathology has its basis in the underlying genes, the protein interactomes, and the metabolic pathways. Subcellular localization of the proteins (Sl) imparts geometrical details of proteins in a cell. In Sl, Proteins conjoin with suitable proteins to assemble into active complexes in signaling routes and metabolic pathways. Variations in the disease set of genes modify the production of gene outcomes as well alters the choosing steps of appropriate Sl, which interrupts the vital roles of the proteins. Proteins related to the disease are predominantly accumulated in typical Sl, which is why apt recognition of protein Sl guides to track down disease bound proteins and the interdependence between them. To do so, in the current investigation, the GOnet tool has been utilized to identify Sl of the proteins by the input of genes and by modeling and visualizing collaborative graphs in conjunction with GO terms and genes. The results obtained displays that the Psoriasis proteins have been localized in respective cellular compartments such as Golgi apparatus, cytoplasm, nucleolus, mitochondria, peroxisomes cytoskeleton, cytoplasm, endosomes, endoplasmic reticulum, extracellular region, nucleoplasm, cilium, vacuole, protein-containing complex, and nuclear chromosome. Further exploration of subcellular localization followed by protein-protein interaction and molecular pathway analyses may be the bedrock to a deeper insight towards disease development and molecular centered relations alongside multimorbidity interactions in Psoriasis.

The nuclear pore complex, nuclear transport, and apoptosisThis paper is one of a selection of papers published in this Special Issue, entitled The Nucleus: A Cell Within A Cell.

2006 ◽  
Vol 84 (3-4) ◽  
pp. 279-286 ◽  
Author(s):  
Birthe Fahrenkrog
Keyword(s):  
Nuclear Pore Complex ◽  
Nuclear Import ◽  
Morphological Changes ◽  
Nuclear Transport ◽  
Nuclear Pore ◽  
Simple Fact ◽  
Cell Death Program ◽  
A Cell ◽  
Cellular Compartments ◽  
Selection Of

The nuclear pore complex (NPC) is the sole gateway between the nucleus and the cytoplasm of interphase eukaryotic cells, and it mediates all trafficking between these 2 cellular compartments. As such, the NPC and nuclear transport play central roles in translocating death signals from the cell membrane to the nucleus where they initiate biochemical and morphological changes occurring during apoptosis. Recent findings suggest that the correlation between the NPC, nuclear transport, and apoptosis goes beyond the simple fact that NPCs mediate nuclear transport of key players involved in the cell death program. In this context, the accessibility of key regulators of apoptosis appears to be highly modulated by nuclear transport (e.g., impaired nuclear import might be an apoptotic trigger). In this review, recent findings concerning the unexpected tight link between NPCs, nuclear transport, and apoptosis will be presented and critically discussed.

scholarly journals Building of the Tetraspanin Web: Distinct Structural Domains of CD81 Function in Different Cellular Compartments

2006 ◽  
Vol 26 (4) ◽  
pp. 1373-1385 ◽  
Author(s):  
Tsipi Shoham ◽  
Ranjani Rajapaksa ◽  
Chiung-Chi Kuo ◽  
Joseph Haimovich ◽  
Shoshana Levy
Keyword(s):  
Transmembrane Domain ◽  
Multiple Roles ◽  
Cellular Interactions ◽  
Structural Domains ◽  
Large Extracellular Loop ◽  
A Cell ◽  
Surface Signaling ◽  
Cell Surface Signaling ◽  
Cellular Compartments ◽  
Partner Proteins

ABSTRACT The tetraspanin web is composed of a network of tetraspanins and their partner proteins that facilitate cellular interactions and fusion events by an unknown mechanism. Our aim was to unravel the web partnership between the tetraspanin CD81 and CD19, a cell surface signaling molecule in B lymphocytes. We found that CD81 plays multiple roles in the processing, intracellular trafficking, and membrane functions of CD19. Surprisingly, these different roles are embodied in distinct CD81 domains, which function in the different cellular compartments: the N-terminal tail of CD81 has an effect on the glycosylation of CD19; the first transmembrane domain of CD81 is sufficient to support the exit of CD19 from the endoplasmic reticulum, although the large extracellular loop (LEL) of CD81 associates physically with CD19 early during biosynthesis; and finally, the TM2 and TM3 domains of CD81 play a role in the transmission of signals initiated upon engagement of the LEL. The participation of distinct CD81 domains in varied functions may explain the pleiotropic effects of CD81 within the tetraspanin web.

scholarly journals FluxMap: A VANTED add-on for the visual exploration of flux distributions in biological networks

2012 ◽  
Vol 6 (1) ◽  
pp. 33 ◽  
Author(s):  
Hendrik Rohn ◽  
Anja Hartmann ◽  
Astrid Junker ◽  
Björn H Junker ◽  
Falk Schreiber
Keyword(s):  
Biological Networks ◽  
Visual Exploration

scholarly journals Mutations in the Lipopolysaccharide Biosynthesis Pathway Interfere with Crescentin-Mediated Cell Curvature in Caulobacter crescentus

2010 ◽  
Vol 192 (13) ◽  
pp. 3368-3378 ◽  
Author(s):  
Matthew T. Cabeen ◽  
Michelle A. Murolo ◽  
Ariane Briegel ◽  
N. Khai Bui ◽  
Waldemar Vollmer ◽  
...  
Keyword(s):  
Cell Wall ◽  
Caulobacter Crescentus ◽  
Cell Envelope ◽  
Cellular Systems ◽  
Biosynthesis Pathway ◽  
Cell Morphogenesis ◽  
Division Site ◽  
Growth Properties ◽  
A Cell ◽  
Cellular Components

ABSTRACT Bacterial cell morphogenesis requires coordination among multiple cellular systems, including the bacterial cytoskeleton and the cell wall. In the vibrioid bacterium Caulobacter crescentus, the intermediate filament-like protein crescentin forms a cell envelope-associated cytoskeletal structure that controls cell wall growth to generate cell curvature. We undertook a genetic screen to find other cellular components important for cell curvature. Here we report that deletion of a gene (wbqL) involved in the lipopolysaccharide (LPS) biosynthesis pathway abolishes cell curvature. Loss of WbqL function leads to the accumulation of an aberrant O-polysaccharide species and to the release of the S layer in the culture medium. Epistasis and microscopy experiments show that neither S-layer nor O-polysaccharide production is required for curved cell morphology per se but that production of the altered O-polysaccharide species abolishes cell curvature by apparently interfering with the ability of the crescentin structure to associate with the cell envelope. Our data suggest that perturbations in a cellular pathway that is itself fully dispensable for cell curvature can cause a disruption of cell morphogenesis, highlighting the delicate harmony among unrelated cellular systems. Using the wbqL mutant, we also show that the normal assembly and growth properties of the crescentin structure are independent of its association with the cell envelope. However, this envelope association is important for facilitating the local disruption of the stable crescentin structure at the division site during cytokinesis.

scholarly journals NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks

2017 ◽  
Vol 10 (1) ◽  
Author(s):  
Theodosios Theodosiou ◽  
Georgios Efstathiou ◽  
Nikolas Papanikolaou ◽  
Nikos C. Kyrpides ◽  
Pantelis G. Bagos ◽  
...  
Keyword(s):  
Network Analysis ◽  
Biological Networks ◽  
Topological Analysis ◽  
Web Tool ◽  
Medium Scale

scholarly journals Compartment-Restricted Biotinylation Reveals Novel Features of Prion Protein Metabolism in Vivo

2010 ◽  
Vol 21 (24) ◽  
pp. 4325-4337 ◽  
Author(s):  
Amy B. Emerman ◽  
Zai-Rong Zhang ◽  
Oishee Chakrabarti ◽  
Ramanujan S. Hegde
Keyword(s):  
Cell Surface ◽  
Prion Protein ◽  
Protein Metabolism ◽  
Selective Detection ◽  
Wild Type ◽  
Selective Labeling ◽  
A Cell ◽  
Cellular Compartments ◽  
Made In

Proteins are often made in more than one form, with alternate versions sometimes residing in different cellular compartments than the primary species. The mammalian prion protein (PrP), a cell surface GPI-anchored protein, is a particularly noteworthy example for which minor cytosolic and transmembrane forms have been implicated in disease pathogenesis. To study these minor species, we used a selective labeling strategy in which spatially restricted expression of a biotinylating enzyme was combined with asymmetric engineering of the cognate acceptor sequence into PrP. Using this method, we could show that even wild-type PrP generates small amounts of the CtmPrP transmembrane form. Selective detection of CtmPrP allowed us to reveal its N-terminal processing, long half-life, residence in both intracellular and cell surface locations, and eventual degradation in the lysosome. Surprisingly, some human disease-causing mutants in PrP selectively stabilized CtmPrP, revealing a previously unanticipated mechanism of CtmPrP up-regulation that may contribute to disease. Thus, spatiotemporal tagging has uncovered novel aspects of normal and mutant PrP metabolism and should be readily applicable to the analysis of minor topologic isoforms of other proteins.

scholarly journals Quantitative understanding of molecular competition as a hidden layer of gene regulatory network

2018 ◽  
Author(s):  
Ye Yuan ◽  
Lei Wei ◽  
Tao Hu ◽  
Shuailin Li ◽  
Tianrun Cheng ◽  
...  
Keyword(s):  
Biological Networks ◽  
Regulatory Mechanism ◽  
Response Speed ◽  
Coarse Grained ◽  
Motif Model ◽  
Molecular Systems ◽  
Trade Offs ◽  
Quantitative Understanding ◽  
Hidden Layer ◽  
Cellular Components

AbstractMolecular competition is ubiquitous, essential and multifunctional throughout diverse biological processes. Competition brings about trade-offs of shared limited resources among the cellular components, and it thus introduce a hidden layer of regulatory mechanism by connecting components even without direct physical interactions. By abstracting the analogous competition mechanism behind diverse molecular systems, we built a unified coarse-grained competition motif model to systematically compare experimental evidences in these processes and analyzed general properties shared behind them. We could predict in what molecular environments competition would reveal threshold behavior or display a negative linear dependence. We quantified how competition can shape regulator-target dose-response curve, modulate dynamic response speed, control target expression noise, and introduce correlated fluctuations between targets. This work uncovered the complexity and generality of molecular competition effect, which might act as a hidden regulatory mechanism with multiple functions throughout biological networks in both natural and synthetic systems.

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