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Understanding the exacerbating role of the metalloproteinase meprin during AKI, an in silico approach

100%

Chatterjee D.

International Letters of Natural Sciences

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2016

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tom 57

Acute kidney injury (AKI) is a syndrome characterised by the rapid loss of the kidney’s excretory function and is typically diagnosed by the accumulation of end products of nitrogen metabolism (urea and creatinine) or decreased urine output, or both. It is the clinical manifestation of several disorders that affect the kidney acutely. No specific therapies have yet emerged that can attenuate AKI or expedite recovery; thus, the only treatment is supportive therapies and intensive care. The present study was aimed to provide an insight into the importance of a metalloproteinase involved in the pathological conditions of AKI and potentially is a unique target for therapeutic intervention during the disease; Meprin. The data obtained using literature search from PubMed and interaction networks analysis software STRING strongly support the concept that meprin acts as a major matrix degrading enzyme in the kidney, and thus creating an environment that leads to impairment in cellular function rather than cellular stability in response to AKI. The present study discerns the structure of meprin alpha subunit using in silico tools SWISSMODE, Phyre2 web server and identify the active site and critical amino acid residues in the active site using AADS (IIT Delhi), 3DLigandSite and DoGSiteScorer. Further it is documented that actinonin, a naturally occurring antibacterial agent as a pharmacologically active intervention for the metalloproteinase’s α subunit by blocking its active sites from the environment which was validated using molecular docking algorithms of SWISS-DOCK and FlexX.

2

Identification of anti-cyanobacterial leads targeting carbonic anhydrase from phytochemical database using in silico approach

88%

Padhiary A., Mir S. A., Tete S. S., Baitharu I., Nayak B.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2023

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tom 104

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nr 2

3

In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species

75%

Varshney R. K., Thiel T., Stein N., Langridge P., Graner A.

Cellular and Molecular Biology Letters

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2002

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tom 07

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nr 2A

During the last decade microsatellites or SSRs (simple sequence repeats) have been proven to be the markers of choice in plant genetics research and for breeding purposes because of their hypervariability and ease of detection. However, development of these markers is expensive, labour intensive and time consuming, in particular, if they are being developed from genomie libraries. In the context of large-scale sequencing and genomics programmes in various cereal species at different laboratories, a large set of expressed sequence tags (ESTs) is being generated, which can be used to search for microsatellites. Keeping in view the importance of such type of SSRs, available ESTs of some cereal species like barley, maize, oats, rice, rye and wheat were investigated for a study of abundance, frequency and distribution of various types of microsatellites. SSRs were present in about 7% to 10% of the total ESTs in the investigated cereal genomes. On the basis of surveying EST sequences amounting to 75.2 Mb in barley, 54.7 Mb in maize, 43.9 Mb in rice, 3.7 Mb in rye, 41.6 Mb in sorghum and 37.5 Mb in wheat, the frequency of SSRs was 1/7.5 kb in barley, 1/7.5 kb in maize, 1/6.2 kb in wheat, 1/5.5 kb in rye and sorghum and 1/3.9 kb in rice. The overall average SSR frequency for these species is 1/6.0 kb. Trimeric repeats are the most abundant (54% to 78%) class of microsatellites followed by dimeric repeats (17% to 40%). Among the trimeric repeats the motifs CCG are the most common in all the cases ranging from 32% in wheat to 49% in sorghum. When all these SSRs were analysed for assessing their potential to develop new markers, unique primer pairs could be designed for 30% to 70% of the total non-redundant microsatellites which are up to 3% of total ESTs in the studied species.

4

Cellular identification and in silico characterization of protein phosphatase 2C (PP2C) of Cryptosporidium parvum

63%

Gomez-Sandoval J. N., Okhuysen P., Mondragon-Flores R., Escalona-Montano A. R., Aguirre-Garcia M. M.

Acta Parasitologica

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2020

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tom 65

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nr 3

5

In silico and in vitro cytotoxic effect of prodigiosin-conjugated silver nanoparticles on liver cancer cells (HepG2)

63%

El-Batal A. I., El-Hendawy H. H., Faraag A. H. I.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2017

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tom 98

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nr 3

6

Cloning and characterization of the yak gene coding for calpastatin and in silico analysis of its putative product

63%

Zhang L., Ma B., Wu J., Fei C., Yang L., Wan H.

Acta Biochimica Polonica

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2010

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tom 57

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nr 1

35-41

The calcium-activated neutral proteases, μ- and m-calpain, along with their inhibitor, calpastatin, have been demonstrated to mediate a variety of Ca2+-dependent processes including signal transduction, cell proliferation, cell cycle progression, differentiation, apoptosis, membrane fusion, platelet activation and skeletal muscle protein degradation. The cDNA coding for yak calpastatin was amplified and cloned by RT-PCR to investigate and characterize the nucleotide/amino-acid sequence and to predict structure and function of the calpastatin. The present study suggests that the yak calpastatin gene encodes a protein of 786 amino acids that shares 99 % sequence identity with the amino-acid sequence of cattle calpastatin, and that the yak protein is composed of an N-terminal region (domains L and XL) and four repetitive homologous C-terminal domains (d1–d4), in which several prosite motifs are present including short peptide L54–64 (EVKPKEHTEPK in domain L) and GXXE/ DXTIPPXYR (in subdomain B), where X is a variable amino acid. Our results suggest the existence of other functional sites including potential phosphorylation sites for protein kinase C, cAMP- and cGMP-dependent protein kinase, casein kinase II, as well as N-myristoylation and amidation sites that play an important role in molecular regulation of the calpain/calpastatin system. The regulation of the calpain/calpastatin system is determined by the interaction between dIV and dVI in calpains and subdomains A, B, and C in calpastatin.

7

In silico analysis of the biodiversity and conservation status of mitochondrial cytochrome C oxidase subunit 1 (CO1) gene of Taenia multiceps

51%

Kilinc S. G., Celik F., Kesik H. K., Simsek S.

Acta Parasitologica

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2020

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tom 65

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nr 4

8

Identification of potential CD8+ epitopes in pp62 polyprotein of African swine fever virus using computational immunology

51%

Galicia M. L. C., Morales D. J. M., Pogado P. G. B., Quebrado A. L., Herrera-Ong L. R.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2023

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tom 104

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nr 3

Ograniczanie wyników

Understanding the exacerbating role of the metalloproteinase meprin during AKI, an in silico approach

Identification of anti-cyanobacterial leads targeting carbonic anhydrase from phytochemical database using in silico approach

In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species

Cellular identification and in silico characterization of protein phosphatase 2C (PP2C) of Cryptosporidium parvum

In silico and in vitro cytotoxic effect of prodigiosin-conjugated silver nanoparticles on liver cancer cells (HepG2)

Cloning and characterization of the yak gene coding for calpastatin and in silico analysis of its putative product

In silico analysis of the biodiversity and conservation status of mitochondrial cytochrome C oxidase subunit 1 (CO1) gene of Taenia multiceps

Identification of potential CD8+ epitopes in pp62 polyprotein of African swine fever virus using computational immunology