OperonDB: a comprehensive database of predicted operons in microbial genomes

The fast pace of bacterial genome sequencing and the resulting dependence on highly automated annotation methods has driven the development of many genome-wide analysis tools. OperonDB, first released in 2001, is a database containing the results of a computational algorithm for locating operon structures in microbial genomes. OperonDB has grown from 34 genomes in its initial release to more than 500 genomes today. In addition to increasing the size of the database, we have re-designed our operon finding algorithm and improved its accuracy. The new database is updated regularly as additional genomes become available in public archives. OperonDB can be accessed at: http://operondb.cbcb.umd.ed

Magnetic force microscopy of modified multilayer structures Co/Pt

В докладе представлены результаты МСМ исследований доменной структуры многослойных пленок Co/Pt с перпендикулярной анизотропией, модифицированных посредством осаждения на их поверхность дополнительного покрывающего слоя Со и посредством облучения ионами Не+.We present the results of MFM investigations of domain structure in the multilayer films Co/Pt with perpendicular anisotropy modified by deposition of additional covering Co layer and by the local irradiation with He+ beams.Работа поддерживается Российским Научным Фондом (проект № 16-12-10254)

Anti-vortex state in cross-like nanomagnets

We report on results of computer micromodelling of anti-vortex states in asymmetrical cross-like ferromagnetic nanostructures and their practical realization. The arrays of cobalt crosses with 1 mkm branches, 100 nm widths of the branches and 40 nm thicknesses were fabricated using e-beam lithography and ion etching. Each branch of the cross was tapered at one end and bulbous at the other. The stable formation of anti-vortex magnetic states in these nanostructures during magnetization reversal was demonstrated experimentally using magnetic force microscopy.Comment: 19 pages, 9 figure

Correlation between nucleotide composition and folding energy of coding sequences with special attention to wobble bases

Background: The secondary structure and complexity of mRNA influences its accessibility to regulatory molecules (proteins, micro-RNAs), its stability and its level of expression. The mobile elements of the RNA sequence, the wobble bases, are expected to regulate the formation of structures encompassing coding sequences. Results: The sequence/folding energy (FE) relationship was studied by statistical, bioinformatic methods in 90 CDS containing 26,370 codons. I found that the FE (dG) associated with coding sequences is significant and negative (407 kcal/1000 bases, mean +/- S.E.M.) indicating that these sequences are able to form structures. However, the FE has only a small free component, less than 10% of the total. The contribution of the 1st and 3rd codon bases to the FE is larger than the contribution of the 2nd (central) bases. It is possible to achieve a ~ 4-fold change in FE by altering the wobble bases in synonymous codons. The sequence/FE relationship can be described with a simple algorithm, and the total FE can be predicted solely from the sequence composition of the nucleic acid. The contributions of different synonymous codons to the FE are additive and one codon cannot replace another. The accumulated contributions of synonymous codons of an amino acid to the total folding energy of an mRNA is strongly correlated to the relative amount of that amino acid in the translated protein. Conclusion: Synonymous codons are not interchangable with regard to their role in determining the mRNA FE and the relative amounts of amino acids in the translated protein, even if they are indistinguishable in respect of amino acid coding.Comment: 14 pages including 6 figures and 1 tabl

Magnetic force microscope tip-induced remagnetization of CoPt nanodisks with perpendicular anisotropy

We report on the results of a magnetic force microscopy investigation of remagnetization processes in arrays of CoPt nanodisks with diameters of 35 and 200 nm and a thickness of 9.8 nm fabricated by e-beam lithography and ion etching. The controllable magnetization reversal of individual CoPt nanodisks by the magnetic force microscope (MFM) tip-induced magnetic field was demonstrated. We observed experimentally two essentially different processes of tip-induced remagnetization. Magnetization reversal of 200 nm disks was observed when the probe moved across the particle while in case of 35 nm nanodisks one-touch remagnetization was realized. Micromagnetic modeling based on the Landau-Lifshitz-Gilbert (LLG) equation demonstrated that the tip-induced magnetization reversal occurs through the essentially inhomogeneous states. Computer simulations confirmed that in case of 200 nm disks the mechanism of embryo nucleation with reversed magnetization and further dynamic propagation following the probe moving across the particle was realized. On the other hand one-touch remagnetization of 35 nm disks occurs through the inhomogeneous vortexlike state. Micromagnetic LLG simulations showed that magnetization reversal in an inhomogeneous MFM probe field has a lower energy barrier in comparison with the mechanism of coherent rotation, which takes place in a homogeneous external magnetic field

Bidirectional best hit r-window gene clusters

<p>Abstract</p> <p>Background</p> <p><it>Conserved gene clusters </it>are groups of genes that are located close to one another in the genomes of several species. They tend to code for proteins that have a functional interaction. The identification of conserved gene clusters is an important step towards understanding genome evolution and predicting gene function.</p> <p>Results</p> <p>In this paper, we propose a novel pairwise gene cluster model that combines the notion of bidirectional best hits with the <it>r</it>-window model introduced in 2003 by Durand and Sankoff. The bidirectional best hit (BBH) constraint removes the need to specify the minimum number of shared genes in the <it>r</it>-window model and improves the relevance of the results. We design a subquadratic time algorithm to compute the set of BBH <it>r</it>-window gene clusters efficiently.</p> <p>Conclusion</p> <p>We apply our cluster model to the comparative analysis of <it>E. coli </it>K-12 and <it>B. subtilis </it>and perform an extensive comparison between our new model and the gene teams model developed by Bergeron <it>et al</it>. As compared to the gene teams model, our new cluster model has a slightly lower recall but a higher precision at all levels of recall when the results were ranked using statistical tests. An analysis of the most significant BBH <it>r</it>-window gene cluster show that they correspond to known operons.</p

Database resources of the National Center for Biotechnology Information

In addition to maintaining the GenBank(®) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link(BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace and Assembly Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Viral Genotyping Tools, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at

Identification of conserved gene clusters in multiple genomes based on synteny and homology

<p>Abstract</p> <p>Background</p> <p>Uncovering the relationship between the conserved chromosomal segments and the functional relatedness of elements within these segments is an important question in computational genomics. We build upon the series of works on <it>gene teams</it> and <it>homology teams.</it></p> <p>Results</p> <p>Our primary contribution is a local sliding-window SYNS (SYNtenic teamS) algorithm that refines an existing family structure into orthologous sub-families by analyzing the neighborhoods around the members of a given family with a locally sliding window. The neighborhood analysis is done by computing conserved gene clusters. We evaluate our algorithm on the existing homologous families from the Genolevures database over five genomes of the Hemyascomycete phylum.</p> <p>Conclusions</p> <p>The result is an efficient algorithm that works on multiple genomes, considers paralogous copies of genes and is able to uncover orthologous clusters even in distant genomes. Resulting orthologous clusters are comparable to those obtained by manual curation.</p

TNF-induced necroptosis in L929 cells is tightly regulated by multiple TNFR1 complex I and II members

TNF receptor 1 signaling induces NF-κB activation and necroptosis in L929 cells. We previously reported that cellular inhibitor of apoptosis protein-mediated receptor-interacting protein 1 (RIP1) ubiquitination acts as a cytoprotective mechanism, whereas knockdown of cylindromatosis, a RIP1-deubiquitinating enzyme, protects against tumor necrosis factor (TNF)-induced necroptosis. We report here that RIP1 is a crucial mediator of canonical NF-κB activation in L929 cells, therefore questioning the relative cytoprotective contribution of RIP1 ubiquitination versus canonical NF-κB activation. We found that attenuated NF-κB activation has no impact on TNF-induced necroptosis. However, we identified A20 and linear ubiquitin chain assembly complex as negative regulators of necroptosis. Unexpectedly, and in contrast to RIP3, we also found that knockdown of RIP1 did not block TNF cytotoxicity. Cell death typing revealed that RIP1-depleted cells switch from necroptotic to apoptotic death, indicating that RIP1 can also suppress apoptosis in L929 cells. Inversely, we observed that Fas-associated protein via a death domain, cellular FLICE inhibitory protein and caspase-8, which are all involved in the initiation of apoptosis, counteract necroptosis induction. Finally, we also report RIP1-independent but RIP3-mediated necroptosis in the context of TNF signaling in particular conditions