scholarly journals Downregulation of miR‑224‑5p in prostate cancer and its relevant molecular mechanism via TCGA, GEO database and in�silico analyses

2018 ◽  
Author(s):  
Bin‑Liang Gan ◽  
Li‑Jie Zhang ◽  
Li Gao ◽  
Fu‑Chao Ma ◽  
Rong‑Quan He ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Molecular Mechanism ◽  
In Silico ◽  
In Silico Analyses ◽  
Geo Database

scholarly journals Frequency of KLK3 gene deletions in the general population

2016 ◽  
Vol 54 (4) ◽  
pp. 472-480
Author(s):  
Santiago Rodriguez ◽  
Osama A Al-Ghamdi ◽  
Philip AI Guthrie ◽  
Hashem A Shihab ◽  
Wendy McArdle ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Control System ◽  
General Population ◽  
Prostate Specific Antigen ◽  
In Silico ◽  
Prostate Cancer Screening ◽  
False Negative ◽  
Specific Antigen ◽  
Serum Prostate Specific Antigen ◽  
In Silico Analyses

Background One of the kallikrein genes ( KLK3) encodes prostate-specific antigen, a key biomarker for prostate cancer. A number of factors, both genetic and non-genetic, determine variation of serum prostate-specific antigen concentrations in the population. We have recently found three KLK3 deletions in individuals with very low prostate-specific antigen concentrations, suggesting a link between abnormally reduced KLK3 expression and deletions of KLK3. Here, we aim to determine the frequency of kallikrein gene 3 deletions in the general population. Methods The frequency of KLK3 deletions in the general population was estimated from the 1958 Birth Cohort sample ( n = 3815) using amplification ratiometry control system. In silico analyses using PennCNV were carried out in the same cohort and in NBS-WTCCC2 in order to provide an independent estimation of the frequency of KLK3 deletions in the general population. Results Amplification ratiometry control system results from the 1958 cohort indicated a frequency of KLK3 deletions of 0.81% (3.98% following a less stringent calling criterion). From in silico analyses, we found that potential deletions harbouring the KLK3 gene occurred at rates of 2.13% (1958 Cohort, n = 2867) and 0.99% (NBS-WTCCC2, n = 2737), respectively. These results are in good agreement with our in vitro experiments. All deletions found were in heterozygosis. Conclusions We conclude that a number of individuals from the general population present KLK3 deletions in heterozygosis. Further studies are required in order to know if interpretation of low serum prostate-specific antigen concentrations in individuals with KLK3 deletions may offer false-negative assurances with consequences for prostate cancer screening, diagnosis and monitoring.

scholarly journals Molecular Mechanism Underlying Hesperetin-induced Apoptosis by in silico Analysis and in Prostate Cancer PC-3 Cells

2013 ◽  
Vol 14 (7) ◽  
pp. 4347-4352 ◽  
Author(s):  
Shanmugam Sambantham ◽  
Mahendran Radha ◽  
Arumugam Paramasivam ◽  
Balakrishnan Anandan ◽  
Ragunathan Malathi ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Molecular Mechanism ◽  
In Silico ◽  
In Silico Analysis ◽  
Induced Apoptosis ◽  
Silico Analysis

Molecular mechanism in the development and progression of prostate cancer

2014 ◽  
Vol 35 (12) ◽  
pp. 1310
Author(s):  
Ji LIN ◽  
Jian-guo HOU ◽  
Tong SU ◽  
Hong-wei ZHANG
Keyword(s):  
Prostate Cancer ◽  
Molecular Mechanism

In-silico Analyses of Natural Products on Leishmania Enzyme Targets

2015 ◽  
Vol 15 (3) ◽  
pp. 253-269 ◽  
Author(s):  
L. Scotti ◽  
H. Ishiki ◽  
F.J.B. Mendonca ◽  
M.S. Silva ◽  
M.T. Scotti
Keyword(s):  
Natural Products ◽  
In Silico ◽  
In Silico Analyses

In vivo and in silico analyses of estrogenic potential of equine estrogens in medaka (Oryzias latipes)

2021 ◽  
Vol 767 ◽  
pp. 144379
Author(s):  
Hiroshi Ishibashi ◽  
Masaya Uchida ◽  
Masashi Hirano ◽  
Taka Hayashi ◽  
Ryoko Yamamoto ◽  
...  
Keyword(s):  
In Silico ◽  
Oryzias Latipes ◽  
Estrogenic Potential ◽  
Equine Estrogens ◽  
In Silico Analyses

scholarly journals How to Use Online Tools to Generate New Hypotheses for Mammary Gland Biology Research: A Case Study for Wnt7b

2021 ◽  
Author(s):  
Yorick Bernardus Cornelis van de Grift ◽  
Nika Heijmans ◽  
Renée van Amerongen
Keyword(s):  
Mammary Gland ◽  
In Silico ◽  
Online Tools ◽  
Mammary Gland Biology ◽  
User Friendly ◽  
In Silico Analyses ◽  
Biology Research ◽  
Selection Of

AbstractAn increasing number of ‘-omics’ datasets, generated by labs all across the world, are becoming available. They contain a wealth of data that are largely unexplored. Not every scientist, however, will have access to the required resources and expertise to analyze such data from scratch. Fortunately, a growing number of investigators is dedicating their time and effort to the development of user friendly, online applications that allow researchers to use and investigate these datasets. Here, we will illustrate the usefulness of such an approach. Using regulation of Wnt7b expression as an example, we will highlight a selection of accessible tools and resources that are available to researchers in the area of mammary gland biology. We show how they can be used for in silico analyses of gene regulatory mechanisms, resulting in new hypotheses and providing leads for experimental follow up. We also call out to the mammary gland community to join forces in a coordinated effort to generate and share additional tissue-specific ‘-omics’ datasets and thereby expand the in silico toolbox.

scholarly journals In Silico Analyses of Rice Thionin Genes and the Antimicrobial Activity of OsTHION15 Against Phytopathogens

2019 ◽  
Vol 109 (1) ◽  
pp. 27-35
Author(s):  
Krissana Boonpa ◽  
Suparuk Tantong ◽  
Kamonwan Weerawanich ◽  
Pawinee Panpetch ◽  
Onanong Pringsulaka ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Stress Responses ◽  
In Silico ◽  
Pathogenic Bacteria ◽  
Hyphal Growth ◽  
In Planta ◽  
Recombinant Peptide ◽  
Plant Disease Control ◽  
Helminthosporium Oryzae ◽  
In Silico Analyses

Thionins are a family of antimicrobial peptides. We performed in silico expression analyses of the 44 rice (Oryza sativa) thionins (OsTHIONs). Modulated expression levels of OsTHIONs under different treatments suggest their involvement in many processes, including biotic, abiotic, and nutritional stress responses, and in hormone signaling. OsTHION15 (LOC_Os06g32600) was selected for further characterization based on several in silico analyses. OsTHION15 in O. sativa subsp. indica ‘KDML 105’ was expressed in all of the tissues and organs examined, including germinating seed, leaves, and roots of seedlings and mature plants, and inflorescences. To investigate the antimicrobial activity of OsTHION15, we produced a recombinant peptide in Escherichia coli Rosetta-gami (DE3). The recombinant OsTHION15 exhibited inhibitory activities toward rice-pathogenic bacteria such as Xanthomonas oryzae pv. oryzae and Pectobacterium carotovorum pv. atroseptica, with minimum inhibitory concentrations of 112.6 and 14.1 µg ml−1, respectively. A significant hyphal growth inhibition was also observed toward Fusarium oxysporum f. sp. cubense and Helminthosporium oryzae. In addition, we demonstrated the in planta antibacterial activity of this peptide in Nicotiana benthamiana against X. campestris pv. glycines. These activities suggest the possible application of OsTHION15 in plant disease control.

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