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1
Artykuł dostępny w postaci pełnego tekstu - kliknij by otworzyć plik
Content available

Applying In Silico approaches for designing a chimeric InaV/N-DFPase protein and evaluating its binding with diisopropyl-fluorophosphate

100%
Allahyari H., Karami A., Tebyanian H., Nouri H. R., Khodi S., Farnoosh G., Arab S. S., Latifi A. M.
International Letters of Natural Sciences
|
2019
|
tom 75
The N-terminal domain of the ice-nucleation protein InaV (InaV-N) of Pseudomonas syringae was applied to display the DFPase on the cell surface. In silico techniques were used to generate a model in order to examine the possibility of DFPase exhibition on the cell surface. The secondary and tertiary structures of a chimeric protein were determined and then, the predicted model was subjected to several repeated cycles of stereochemical evaluation and energy minimization. The homology-modeled structure of the InaV/N-DFPase protein was docked to DFP. The optimized inaV/N-dfpase gene was translated to 519 amino acids. The minimum free energy of the best-predicted secondary structures was formed by RNA molecules (-215.45 kcal/mol). SOPMA analysis results showed that the main helix peak corresponded to the anchor fragment. Validation of the 3D model indicated that 86.1% of amino acid residues were incorporated into the favored regions. The moldock score was 360.22 for DFP. Results of this study indicated that according to in silico analysis, all of these findings were effective in targeting DFPase.
2

Application of bioinformatics in GMO detection

100%
Nenov A., Vassilev D.
Biotechnologia
|
2006
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nr 3
3
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Content available

Epitope prediction, modeling, and docking studies for H3L protein as an agent of smallpox

86%
Mohammadi E., Dashty S.
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
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2019
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tom 100
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nr 1
4
Artykuł dostępny w postaci pełnego tekstu - kliknij by otworzyć plik
Content available

Determining the structural amino acid attributes which are important in both protein thermostability and alkalophilicity: a case study on xylanase

86%
Delavari A., Zare S., Ghaemi M. R., Kashfi R., Ebrahimi M., Tahmasebi A., Ebrahimi M., Ebrahimie E.
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
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2014
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tom 95
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nr 2
5
Content available remote

Where are we in genomics?

72%
Hocquette J.-F.
Journal of Physiology and Pharmacology. Supplement
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2005
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tom 56
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nr 3
37-70
Genomic studies provide scientists with methods to quickly analyse genes and their products en masse. The first high-throughput techniques to be developed were sequencing methods. A great number of genomes from different organisms have thus been sequenced. Genomics is now shifting to the study of gene expression and function. In the past 5-10 years genomics, proteomics and high-throughput microarray technologies have fundamentally changed our ability to study the molecular basis of cells and tissues in health and diseases, giving a new comprehensive view. For example, in cancer research we have seen new diagnostic opportunities for tumour classification, and prognostication. A new exciting development is metabolomics and lab-on-a-chip techniques (which combine miniaturisation and automation) for metabolic studies. However, to interpret the large amount of data, extensive computational development is required. In the coming years, we will see the study of biological networks dominating the scene in Physiology. The great accumulation of genomics information will be used in computer programs to simulate biologic processes. Originally developed for genome analysis, bioinformatics now encompasses a wide range of fields in biology from gene studies to integrated biology (i.e. combination of different data sets from genes to metabolites). This is systems biology which aims to study biological organisms as a whole. In medicine, scientific results and applied biotechnologies arising from genomics will be used for effective prediction of diseases and risk associated with drugs. Preventive medicine and medical therapy will be personalised. Widespread applications of genomics for personalised medicine will require associations of gene expression pattern with diagnoses, treatment and clinical data. This will help in the discovery and development of drugs. In agriculture and animal science, the outcomes of genomics will include improvement in food safety, in crop yield, in traceability and in quality of animal products (dairy products and meat) through increased efficiency in breeding and better knowledge of animal physiology. Genomics and integrated biology are huge tasks and no single lab can pursue this alone. We are probably at the end of the beginning rather than at the beginning of the end because Genomics will probably change Biology to a greater extent than previously forecasted. In addition, there is a great need for more information and better understanding of genomics before complete public acceptance.
6

Profiling of regulatory microRNA transcriptomes in various biological processes: a review

72%
Shah A. A., Meese E., Blin N.
Journal of Applied Genetics
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2010
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tom 51
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nr 4
A class of small, non-coding ribonucleic acids, termed microRNA (miRNA), has recently emerged as a new key player in the cellular control of gene expression. By either blocking translation or inducing target mRNA degradation, miRNA not only participates in regular biological processes within cells and tissues but is also involved in pathological processes. Many human malignancies have been linked to specific miRNA expression patterns, raising hopes for new approaches to therapy. While such human disease-related mechanisms have been widely discussed and frequently reviewed, miRNA's general significance in animals has been less in editorial focus, despite its obvious role in basic physiological processes, e.g. neurosensory maturation, development of fertility, and hibernation. Using selected examples, this review highlights our current knowledge of miRNA's potential and its promise as a new tool for gene regulation.
7
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Databases and associated bioinformatic tools in studies of food allergens, epitopes and haptens - a review

72%
Bucholska J., Minkiewicz P., Darewicz M., Iwaniak A.
Polish Journal of Food and Nutrition Sciences
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2018
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tom 68
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nr 2
Allergies and/or food intolerances are a growing problem of the modern world. Diffi culties associated with the correct diagnosis of food allergies result in the need to classify the factors causing allergies and allergens themselves. Therefore, internet databases and other bioinformatic tools play a special role in deepening knowledge of biologically-important compounds. Internet repositories, as a source of information on different chemical compounds, including those related to allergy and intolerance, are increasingly being used by scientists. Bioinformatic methods play a signifi cant role in biological and medical sciences, and their importance in food science is increasing. This study aimed at presenting selected databases and tools of bioinformatic analysis useful in research on food allergies, allergens (11 databases), epitopes (7 databases), and haptens (2 databases). It also presents examples of the application of computer methods in studies related to allergies.
8

Molecular cloning and bioinformatic characterisation of FhPcW1, a new isoform of cathepsin L from adult Fasciola hepatica

72%
Jaros S., Zygner W., Januszkiewicz K., Jaros D., Wedrychowicz H.
Bulletin of the Veterinary Institute in Puławy
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2010
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tom 54
|
nr 4
The aim of this study was to clone new secretory antigen of Fasciola hepatica and to predict its availability for immune system. The new cathepsin L - FhPcW1 (F. hepatico cysteine proteinase Warsaw 1), GenBank accession: EF407948, cDNA was cloned from adult F. hepatica flukes using RACE-PCR method. FhPcW1 is encoded by a 1,066 bp mRNA with a predicted open reading frame (ORF) of 326 amino acids (predicted pl = 5.41, m.w. = 37.137 kDa). Performed bioinformatic analysis included alignments of the nucleotide and amino acid sequences, the ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics and National Center for Biotechnology Information. Performed analyses allowed to suppose that FhPcW1 is a secreted protein, which contains signal peptide, serine, threonine, tyrosine phosphorylation sites and four tyrosine sulfation sites, and does not contain glycosylation sites. The ORF corresponding to FhPcW1 exhibited strong similarity to previously cloned cathepsins L from the F. hepatico as well as F. gigantica. Predicted biochemical characteristics fits to the described before F. hepatica cathepsin Ls. Moreover, three dimensional model and MHC types ligation strength prediction were performed. Analysis of MHC type I and II peptide binding suggests that FhPcW1 may have significant immunogenic potential. The potential HLA II epitopes are situated at the outer surface of this protein. Thus, these epitopes seems to be available for immune response, especially for antibodies. This result may show that FhPcW1 seems to be a promising antigen for vaccination against F. hepatica.
9

Cloning and partial characterization of a gene in Bombyx mori homologous to a human adiponectin receptor

72%
Zhu M., Chen K., Wang Y., Guo Z., Yin H., Yao Q., Chen H.
Acta Biochimica Polonica
|
2008
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tom 55
|
nr 2
241-249
In this study, we report the cloning and characteristics of an adiponectin-like receptor gene from Bombyx mori (BmAdipoR) with highly conserved deduced amino-acid sequences and similar structure to the human adiponectin receptor (AdipoR). Structural analysis of the translated cDNA suggested it encoded a membrane protein with seven transmembrane domains. BmAdipoR was found to be expressed in multiple tissues and highly expressed in Malpighian tubules, fat body and testis. BmNPV (Bombyx morinucleopolyhedrovirus) bacmid system combined with confocal microscopy revealed that BmAdipoR was targeted to the cell membrane. We also found that infection with BmNPV did not have an effect on BmAdipoR mRNA quantity in the midgut of susceptible Bombyx moristrain (306) at 48 h, but BmAdipoR mRNA quantity increased significantly at 72 h. We concluded that BmAdipoR gene was a membrane protein ubiquitously expressed in Bombyx moritissues and that its expression was altered by treating with BmNPV.
10

Theoretical model explaining the relationship between the molecular mass and the activation energy of the enzyme revealed by a large-scale analysis of bioinformatics data

72%
Pawlowski P. H., Zielenkiewicz P.
Acta Biochimica Polonica
|
2013
|
tom 60
|
nr 2
 A general dependence of the enzyme catalytic rate on its mass was revealed when a statistical analysis of 17065 records from the EMP database was performed. The estimated activation energy of the catalytic process decreases asymptotically with the enzyme molecular mass increase. The proposed theoretical model postulates the existence of an intermediate complex of the enzyme and the departing product. It allows for the explanation of the discovered mass-energy relationship, as an effect of the global enzyme-product interactions during complex dissociation. Fitted parameters of the model seem to be in agreement with those widely accepted for the van der Waals energy of molecular interactions. Their values also agree with the picture of the hydrogen bonding in the catalytic process and suggest that surface walk can be the favorable way of the product departure.
11

Molecular cloning, expression and characterization of Bmserpin-2 gene from Bombyx mori

72%
Pan Y., Xia H., Lu P., Chen K., Yao Q., Chen H., Gao L., He Y., Wang L.
Acta Biochimica Polonica
|
2009
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tom 56
|
nr 4
671-677
Serpins are a broadly distributed family of protease inhibitors. In this study, the gene encoding Bombyx mori serpin-2 (Bmserpin-2) was cloned and expressed in E. coli. The Bmserpin-2 cDNA contains a 1125 bp open reading frame (ORF). The deduced protein has 374 amino-acid residues, contains a conserved SERPIN domain and shares extensive homology with other invertebrate serpins. RT-PCR analysis showed that Bmserpin-2 was expressed in all developmental stages of B. mori larvae and various larval tissues. Subcellular localization analysis indicated that Bmserpin-2 protein was located in the cytoplasm. Interestingly, real-time quantitative PCR revealed that the expression of Bmserpin-2 in the midgut of susceptible B. mori strain 306 significantly increased at 72 hours post inoculation (hpi) when infected with BmNPV. However, there was no significant increase of the Bmserpin-2 expression in resistant strain NB infected with BmNPV. Thus, our data indicates that Bmserpin-2 may be involved in B. mori antiviral response.
12

Cytomegalovirus immediate early gene UL37 encodes a novel MHC-like protein

72%
Wyrwicz L. S., Rychlewski L.
Acta Biochimica Polonica
|
2008
|
tom 55
|
nr 1
The cytomegalovirus (CMV) genome encodes four clusters of genes expressed immediately after infection — i.e.: UL36-38, UL122-123, TRS1-IRS1, and US3. The general function of these genes is associated with inhibition of cellular mechanisms of antiviral response. Although several biological processes have been mapped onto specific gene products, the knowledge of the molecular mechanism of their activity remains fragmentary. Here, we report the application of protein structure prediction methods in assigning the function to a glycosylated domain encoded by UL37 of CMV (gpUL37, UL37x3). The discerned similarity clearly points out that this domain represents a novel type of a major histocompatibility complex (MHC)-like protein, and consequently may play a central role in an additional mechanism of escape from antiviral response.
13

Metabolomics and metabolite prolifing - can we achieve the goal?

72%
Stobiecki M., Kachlicki P.
Acta Physiologiae Plantarum
|
2005
|
tom 27
|
nr 1
Deciphering of the plant metabolome is one of the most difficult analytical tasks in functional genomic research. Studies directed at the gene or protein expression are well established, sequencing analyses of these kinds of biopolymers on genome or proteome level are possible. This is not the case for metabolites, where identification in single sample of many chemical entities of different elemental composition and structures and various physicochemical properties is necessary. Different instrumental methods are applied for identification of metabolites but none of them allows obtaining unambiguous structural information about more than 500 compounds in single mixture (metabolite profiling). This is a much smaller number of metabolites than is predicted for single plant metabolome. However, instrumental approaches were proposed (metabolite fingerprinting) in which biochemical phenotype of an organism may be estimated, but identification of individual compounds is not possible.
14

Homologues of HSV-1 nuclear egress factor UL34 are potential phosphoinositide-binding proteins

72%
Wyrwicz L. S., Koczyk G., Rychlewski L.
Acta Biochimica Polonica
|
2008
|
tom 55
|
nr 1
15

Fold recognition insights into function of herpes ICP4 protein

72%
Wyrwicz L. S., Rychlewski L.
Acta Biochimica Polonica
|
2007
|
tom 54
|
nr 3
ICP4 is an important factor regulating the life cycle of HSV1. This conserved protein has several molecular functions, including activation of expression of viral late gene transcripts and inhibition of immediate early genes. Although ICP4 and its Alphaherpesvirinae homologs (eg.: IE62 of VZV) have been subjects of various molecular studies, a complete view of their molecular function is lacking. Here we present the results of fold recognition and molecular modelling of ICP4 functional domains. The performed state-of-the-art bioinformatic fold recognition analysis identified a dual helix-turn-helix motif as a binding module of repressor activities (so called region 2 domain). The mapping of distant homology identified that a segment responsible for activation of late gene promoters (region 4) exhibits folding of uracil DNA glycosylase (UDG), but seems to be a non-functional homolog of UDG. Potential implications of the results are discussed.
16
Artykuł dostępny w postaci pełnego tekstu - kliknij by otworzyć plik
Content available

A green light for plants

58%
Jasinski M.
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
|
2011
|
tom 92
|
nr 2
17
Artykuł dostępny w postaci pełnego tekstu - kliknij by otworzyć plik
Content available

On the border between biology, mathematics and computer science

58%
Formanowicz P.
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
|
2011
|
tom 92
|
nr 3
18

Unexpected domain composition of MACC1 links MET signaling and apoptosis

58%
Kokoszynska K., Krynski J., Rychlewski L., Wyrwicz L. S.
Acta Biochimica Polonica
|
2009
|
tom 56
|
nr 2
317-323
Colorectal cancer, one of the most challenging malignancies, still has a limited number of recognized prognostic and predictive markers indicating appropriate treatment. MACC1 (metastasis-associated in colon cancer-1), a novel regulator of tumor growth and metastasis has recently been identified as an important prognostic factor of metastatic disease in colorectal cancer. The mechanism of MACC1 activity remains undetermined. Here we apply a combination of fold recognition and homology modeling algorithms to draft MACC1 function. The applied methods revealed that the MACC1 protein consists of four domains: ZU5, SH3, and two C-terminal death domains (DD). Previously a similar domain architecture (ZU5-DD) was observed in other proteins, involved mainly in signal transduction and apoptosis regulation. Based on the specific aspects of the closest homologues' biology functional hypotheses on MACC1 are proposed. A broad range of bioinformatic analyzes indicates that MACC1, besides its involvement in signal transduction from the MET receptor, links MET signaling and apoptosis.
19

Prediction of the structure of the common perimitochondrial localization signal of nuclear transcripts in yeast

58%
Ejsmont R. K., Golik P., Stepien P. P.
Acta Biochimica Polonica
|
2007
|
tom 54
|
nr 1
Many nuclear genes encoding mitochondrial proteins require specific localization of their mRNAs to the vicinity of mitochondria for proper expression. Studies in Saccharomyces cerevisiae have shown that the cis-acting signal responsible for subcellular localization of mRNAs is localized in the 3' UTR of the transcript. In this paper we present an in silico approach for prediction of a common perimitochondrial localization signal of nuclear transcripts encoding mitochondrial proteins. We computed a consensus structure for this signal by comparison of 3' UTR models for about 3000 yeast transcripts with known localization. Our studies show a short stem-loop structure which appears in most mRNAs localized to the vicinity of mitochondria. The degree of similarity of a given 3' UTR to our consensus structure strongly correlates with experimentally determined perimitochondrial localization of the mRNA, therefore we believe that the structure we predicted acts as a subcellular localization signal. Since our algorithm operates on structures, it seems to be more reliable than sequence-based algorithms. The good predictive value of our model is supported by statistical analysis.
20

A common cis-element in promoters of protein synthesis and cell cycle genes

58%
Wyrwicz L. S., Gaj P., Hoffmann M., Rychlewski L., Ostrowski J.
Acta Biochimica Polonica
|
2007
|
tom 54
|
nr 1
Gene promoters contain several classes of functional sequence elements (cis elements) recognized by protein agents, e.g. transcription factors and essential components of the transcription machinery. Here we describe a common DNA regulatory element (tandem TCTCGCGAGA motif) of human TATA-less promoters. A combination of bioinformatic and experimental methodology suggests that the element can be critical for expression of genes involved in enhanced protein synthesis and the G1/S transition in the cell cycle. The motif was identified in a substantial fraction of promoters of cell cycle genes, like cyclins (CCNC, CCNG1), as well as transcription regulators (TAF7, TAF13, KLF7, NCOA2), chromatin structure modulators (HDAC2, TAF6L), translation initiation factors (EIF5, EIF2S1, EIF4G2, EIF3S8, EIF4) and previously reported 18 ribosomal protein genes. Since the motif can define a subset of promoters with a distinct mechanism of activation involved in regulation of expression of about 5% of human genes, further investigation of this regulatory element is an emerging task.
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