004 Datenverarbeitung; Informatik
Refine
Has Fulltext
- yes (27)
Is part of the Bibliography
- yes (27)
Year of publication
Document Type
- Journal article (27) (remove)
Language
- English (27)
Keywords
- database (3)
- resistance (3)
- engineering (2)
- genetics (2)
- 26S RDNA Data (1)
- ACKR4 (1)
- AI (1)
- AKT (1)
- Analysis (1)
- Barcodes (1)
- Biology (1)
- Boolean function (1)
- Boolean tree (1)
- CD4+T cells (1)
- CD8+T cells (1)
- CD95 (1)
- CETCH cycle (1)
- CO2-sequestration (1)
- COVID-19 (1)
- Caenorhabditis elegans (1)
- Colonial volvocales chlorophyta (1)
- Computer software (1)
- DNA (1)
- DNA storage (1)
- Dasycladales chlorophyta (1)
- FLIMbee (1)
- HGPS (1)
- HHblits (1)
- I-tasser (1)
- ICEP (1)
- IGFBP2 (1)
- III secretion (1)
- ImageJ (1)
- IronChip Evaluation Package (1)
- Java 3D (1)
- LC-MS/MS (1)
- Land plants (1)
- Measurement (1)
- Microarray (1)
- Molecular systematics (1)
- Mycoplasma (1)
- Neuromuscular junctions (1)
- Nuclear RDNA (1)
- Profile distances (1)
- Programmierbare logische Anordnung (1)
- RBCL Gene-sequences (1)
- RNA sequencing (1)
- SARS-CoV-2 (1)
- SMLM (1)
- Secondary structure (1)
- Septins (1)
- Software product lines (1)
- Synapses (1)
- Synaptic vesicles (1)
- V-antigen (1)
- Variability (1)
- Vesicles (1)
- Visualisierung (1)
- WH2 domain (1)
- WNT (1)
- Yersinia enterocolitica (1)
- Yolk protein (1)
- Zebrafish (1)
- actin nucleation (1)
- adaptation (1)
- aging (1)
- alignment (1)
- apixaban (1)
- arabidopsis thaliana (1)
- arabidpsis thaliana (1)
- behavior (1)
- binary decision diagram (1)
- biofuel (1)
- bioinformatics (1)
- biomanufacturing (1)
- brain (1)
- caenorhabditis elegans (1)
- carboxylation (1)
- caspase-3 (1)
- cell membranes (1)
- cerebral ischemia (1)
- cisplatin (1)
- classification (1)
- colony-stimulating factor (1)
- combination therapy (1)
- comparative sequence analysis (1)
- complex traits (1)
- compressed sensing (1)
- computational (1)
- connector (1)
- corticotropin-releasing hormone (1)
- crosstalk (1)
- cytokine profiling (1)
- dSTORM (1)
- design (1)
- diagnostic accuracy (1)
- differentiation (1)
- direct oral anticoagulants (1)
- direct thrombin inhibitor (1)
- disease (1)
- disruption project (1)
- drug (1)
- drug-minded protein (1)
- electrolytes (1)
- elementary mode analysis (1)
- elementary modes (1)
- enzyme (1)
- evolution (1)
- expression (1)
- expression signature (1)
- factor XA inhibitor (1)
- flies (1)
- framework (1)
- functional analysis (1)
- gamma (1)
- genes (1)
- genetic regulatory network (1)
- hepatotoxicity (1)
- histidine kinase (1)
- homology modeling (1)
- hypotonic (1)
- hypotonic solutions (1)
- immunity (1)
- inhibitor (1)
- intermediate host (1)
- internal transcribed spacer 2 (1)
- interpolation (1)
- isotonic (1)
- life-span regulation (1)
- light-gated proteins (1)
- lymphotoxicity (1)
- malaria (1)
- markers (1)
- membrane proteins (1)
- memory immune responses (1)
- metabolic flux (1)
- metabolic modeling (1)
- metabolism (1)
- metastasis (1)
- methylene blue (1)
- mice (1)
- microbes (1)
- modules (1)
- molecular systematics (1)
- mouse (1)
- mutation (1)
- nanocellulose (1)
- natural variation (1)
- networks (1)
- nonhuman-primates (1)
- omics (1)
- organogenesis (1)
- origin (1)
- oxidative stress (1)
- painful (1)
- pangolin (1)
- pathway (1)
- performance liquid chromatography (1)
- permeability (1)
- pestis infection (1)
- photorespiration (1)
- phylogenetic tree (1)
- phylogeny (1)
- pneumonic plague (1)
- progeria (1)
- promoter (1)
- protein (1)
- protein chip (1)
- protein-interaction networks (1)
- pseudomas-syringae (1)
- quantification (1)
- receptor (1)
- recombinant protein rVE (1)
- recombination (1)
- response regulator (1)
- ribosomal RNA (1)
- richtersius coronifer (1)
- secondary structure (1)
- sensor (1)
- sequence alignment (1)
- serum (1)
- set (1)
- shootin-1 (1)
- single-electron transistors (1)
- spire (1)
- stability (1)
- stable state (1)
- sun exposure (1)
- superoxide-dismutase (1)
- survival (1)
- synthetic biology (1)
- synthetic pathways (1)
- temperature (1)
- tolerance (1)
- tonicity (1)
- transcription (1)
- transmission (1)
- vaccine (1)
- validation (1)
- vitellogenin (1)
- water stress (1)
Institute
- Theodor-Boveri-Institut für Biowissenschaften (27) (remove)
EU-Project number / Contract (GA) number
- 835102) (1)
Swelling-activated pathways for myo-inositol, one of the most abundant organic osmolytes in mammalian cells, have not yet been identified. The present study explores the SLC5A3 protein as a possible transporter of myo-inositol in hyponically swollen HEK293 cells. To address this issue, we examined the relationship between the hypotonicity-induced changes in plasma membrane permeability to myo-inositol Pino [m/s] and expression/localization of SLC5A3. Pino values were determined by cell volumetry over a wide tonicity range (100–275 mOsm) in myo-inositol-substituted solutions. While being negligible under mild hypotonicity (200–275 mOsm), Pino grew rapidly at osmolalities below 200 mOsm to reach a maximum of ∼3 nm/s at 100–125 mOsm, as indicated by fast cell swelling due to myo-inositol influx. The increase in Pino resulted most likely from the hypotonicity-mediated incorporation of cytosolic SLC5A3 into the plasma membrane, as revealed by confocal fluorescence microscopy of cells expressing EGFP-tagged SLC5A3 and super-resolution imaging of immunostained SLC5A3 by direct stochastic optical reconstruction microscopy (dSTORM). dSTORM in hypotonic cells revealed a surface density of membrane-associated SLC5A3 proteins of 200–2000 localizations/μm2. Assuming SLC5A3 to be the major path for myo-inositol, a turnover rate of 80–800 myo-inositol molecules per second for a single transporter protein was estimated from combined volumetric and dSTORM data. Hypotonic stress also caused a significant upregulation of SLC5A3 gene expression as detected by semiquantitative RT-PCR and Western blot analysis. In summary, our data provide first evidence for swelling-mediated activation of SLC5A3 thus suggesting a functional role of this transporter in hypotonic volume regulation of mammalian cells.
The ITS2 Database
(2012)
The internal transcribed spacer 2 (ITS2) has been used as a phylogenetic marker for more than two decades. As ITS2 research mainly focused on the very variable ITS2 sequence, it confined this marker to low-level phylogenetics only. However, the combination of the ITS2 sequence and its highly conserved secondary structure improves the phylogenetic resolution1 and allows phylogenetic inference at multiple taxonomic ranks, including species delimitation.
The ITS2 Database presents an exhaustive dataset of internal transcribed spacer 2 sequences from NCBI GenBank accurately reannotated. Following an annotation by profile Hidden Markov Models (HMMs), the secondary structure of each sequence is predicted. First, it is tested whether a minimum energy based fold (direct fold) results in a correct, four helix conformation. If this is not the case, the structure is predicted by homology modeling. In homology modeling, an already known secondary structure is transferred to another ITS2 sequence, whose secondary structure was not able to fold correctly in a direct fold.
The ITS2 Database is not only a database for storage and retrieval of ITS2 sequence-structures. It also provides several tools to process your own ITS2 sequences, including annotation, structural prediction, motif detection and BLAST search on the combined sequence-structure information. Moreover, it integrates trimmed versions of 4SALE and ProfDistS for multiple sequence-structure alignment calculation and Neighbor Joining tree reconstruction. Together they form a coherent analysis pipeline from an initial set of sequences to a phylogeny based on sequence and secondary structure.
In a nutshell, this workbench simplifies first phylogenetic analyses to only a few mouse-clicks, while additionally providing tools and data for comprehensive large-scale analyses.
BACKGROUND: In the face of growing resistance in malaria parasites to drugs, pharmacological combination therapies are important. There is accumulating evidence that methylene blue (MB) is an effective drug against malaria. Here we explore the biological effects of both MB alone and in combination therapy using modeling and experimental data.
RESULTS: We built a model of the central metabolic pathways in P. falciparum. Metabolic flux modes and their changes under MB were calculated by integrating experimental data (RT-PCR data on mRNAs for redox enzymes) as constraints and results from the YANA software package for metabolic pathway calculations. Several different lines of MB attack on Plasmodium redox defense were identified by analysis of the network effects. Next, chloroquine resistance based on pfmdr/and pfcrt transporters, as well as pyrimethamine/sulfadoxine resistance (by mutations in DHF/DHPS), were modeled in silico. Further modeling shows that MB has a favorable synergism on antimalarial network effects with these commonly used antimalarial drugs.
CONCLUSIONS: Theoretical and experimental results support that methylene blue should, because of its resistance-breaking potential, be further tested as a key component in drug combination therapy efforts in holoendemic areas.
Two-component systems (TCS) are short signalling pathways generally occurring in prokaryotes. They frequently regulate prokaryotic stimulus responses and thus are also of interest for engineering in biotechnology and synthetic biology. The aim of this study is to better understand and describe rewiring of TCS while investigating different evolutionary scenarios. Based on large-scale screens of TCS in different organisms, this study gives detailed data, concrete alignments, and structure analysis on three general modification scenarios, where TCS were rewired for new responses and functions: (i) exchanges in the sequence within single TCS domains, (ii) exchange of whole TCS domains; (iii) addition of new components modulating TCS function. As a result, the replacement of stimulus and promotor cassettes to rewire TCS is well defined exploiting the alignments given here. The diverged TCS examples are non-trivial and the design is challenging. Designed connector proteins may also be useful to modify TCS in selected cases.
This article is about a measurement analysis based approach to help software practitioners in managing the additional level complexities and variabilities in software product line applications. The architecture of the proposed approach i.e. ZAC is designed and implemented to perform preprocessesed source code analysis, calculate traditional and product line metrics and visualize results in two and three dimensional diagrams. Experiments using real time data sets are performed which concluded with the results that the ZAC can be very helpful for the software practitioners in understanding the overall structure and complexity of product line applications. Moreover the obtained results prove strong positive correlation between calculated traditional and product line measures.
The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays
(2010)
Background: Gene expression studies greatly contribute to our understanding of complex relationships in gene regulatory networks. However, the complexity of array design, production and manipulations are limiting factors, affecting data quality. The use of customized DNA microarrays improves overall data quality in many situations, however, only if for these specifically designed microarrays analysis tools are available. Results: The IronChip Evaluation Package (ICEP) is a collection of Perl utilities and an easy to use data evaluation pipeline for the analysis of microarray data with a focus on data quality of custom-designed microarrays. The package has been developed for the statistical and bioinformatical analysis of the custom cDNA microarray IronChip but can be easily adapted for other cDNA or oligonucleotide-based designed microarray platforms. ICEP uses decision tree-based algorithms to assign quality flags and performs robust analysis based on chip design properties regarding multiple repetitions, ratio cut-off, background and negative controls. Conclusions: ICEP is a stand-alone Windows application to obtain optimal data quality from custom-designed microarrays and is freely available here (see “Additional Files” section) and at: http://www.alice-dsl.net/evgeniy. vainshtein/ICEP/
Background: Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set. Results: Here we present a platform-independent framework based on Java and Java 3D for accelerated rendering of biological images. Our framework is seamlessly integrated into ImageJ, a free image processing package with a vast collection of community-developed biological image analysis tools. Our framework enriches the ImageJ software libraries with methods that greatly reduce the complexity of developing image analysis tools in an interactive 3D visualization environment. In particular, we provide high-level access to volume rendering, volume editing, surface extraction, and image annotation. The ability to rely on a library that removes the low-level details enables concentrating software development efforts on the algorithm implementation parts. Conclusions: Our framework enables biomedical image software development to be built with 3D visualization capabilities with very little effort. We offer the source code and convenient binary packages along with extensive documentation at http://3dviewer.neurofly.de.