рН-зависимая регуляция электронного и протонного транспорта в хлоропластах in situ и in silico

Author(s):  
А. В. Вершубский ◽  
А. Н. Тихонов
Keyword(s):  
2020 ◽  
Vol 40 (04) ◽  
pp. 524-535
Author(s):  
Dmitry Y. Nechipurenko ◽  
Aleksey M. Shibeko ◽  
Anastasia N. Sveshnikova ◽  
Mikhail A. Panteleev

AbstractComputational physiology, i.e., reproduction of physiological (and, by extension, pathophysiological) processes in silico, could be considered one of the major goals in computational biology. One might use computers to simulate molecular interactions, enzyme kinetics, gene expression, or whole networks of biochemical reactions, but it is (patho)physiological meaning that is usually the meaningful goal of the research even when a single enzyme is its subject. Although exponential rise in the use of computational and mathematical models in the field of hemostasis and thrombosis began in the 1980s (first for blood coagulation, then for platelet adhesion, and finally for platelet signal transduction), the majority of their successful applications are still focused on simulating the elements of the hemostatic system rather than the total (patho)physiological response in situ. Here we discuss the state of the art, the state of the progress toward the efficient “virtual thrombus formation,” and what one can already get from the existing models.


2014 ◽  
Vol 73 ◽  
pp. 250-257 ◽  
Author(s):  
Verónica Carrasco-Sánchez ◽  
Ariela Vergara-Jaque ◽  
Matías Zuñiga ◽  
Jeffrey Comer ◽  
Amalraj John ◽  
...  
Keyword(s):  

2021 ◽  
Author(s):  
Evangelos Bisyris ◽  
Eleni Zingkou ◽  
Golfo G Kordopati ◽  
Minos-Timotheos Matsoukas ◽  
Plato A. Magriotis ◽  
...  

We applied a new in silico approach for fishing protease-substrate motifs to design a kallirein 7 (KLK7)-specific phosphonate activity-based probe (ABP) to quantify the active KLK7 in situ. Epidermal application...


Author(s):  
Zatty Zawani Zaidi ◽  
Fahrul Huyop

Halogenated compound such as 2,2-dichloropropionic acid is known for its toxicity and polluted many areas especially with agricultural activities. This study focused on the isolation and characterization of the bacterium that can utilise 2,2-dichloropropionic acid from palm oil plantation in Lenga, Johor and in silico analysis of putative dehalogenase obtained from NCBI database of the same genus and species. The bacterium was isolated using an enrichment culture media supplemented with 20 mM 2,2-dicholoropropionic acid as a carbon source.  The cells were grown at 30˚C with cells doubling time of 2.00±0.005 hours with the maximum growth at A680nm of 1.047 overnight. The partial biochemical tests and morphological examination concluded that the bacterium belongs to the genus Staphylococcus sp.. This is the first reported studies of  Staphylococcus sp. with the ability to grow on 2,2-dichloropropionic acid. The genomic DNA from NCBI database of the same species was analysed assuming the same genus and has identical genomic sequence.  The full genome of Staphylococcus sp. was screened for dehalogenase gene and  haloacid dehalogenase gene was detected in the mobile genetic element of the species revealed that the dehalogenase sequence has little identities to the previously reported dehalogenases.The main outcome of the studies suggesting an in situ bioremediation can be regarded as a natural process to detoxify the contaminated sites provided that the microorganisms contained a specialised gene sequence within its genome that served the nature for many long years. Whether microorganisms will be successful in destroying man-made contaminants entirely rely on what types of organisms play a role in in situ bioremediation and which contaminants are most susceptible to bioremediation. 


2012 ◽  
Vol 302 (1) ◽  
pp. F29-F37 ◽  
Author(s):  
Silvia Medrano ◽  
Maria C. Monteagudo ◽  
Maria Luisa S. Sequeira-Lopez ◽  
Ellen S. Pentz ◽  
R. Ariel Gomez

We have shown that microRNAs (miRNAs) are necessary for renin cell specification and kidney vascular development. Here, we used a screening strategy involving microarray and in silico analyses, along with in situ hybridization and in vitro functional assays to identify miRNAs important for renin cell identity. Microarray studies using vascular smooth muscle cells (SMCs) of the renin lineage and kidney cortex under normal conditions and after reacquisition of the renin phenotype revealed that of 599 miRNAs, 192 were expressed in SMCs and 234 in kidney cortex. In silico analysis showed that the highly conserved miR-330 and miR-125b-5p have potential binding sites in smoothelin ( Smtn), calbindin 1, smooth muscle myosin heavy chain, α-smooth muscle actin, and renin genes important for the myoepithelioid phenotype of the renin cell. RT-PCR studies confirmed miR-330 and miR-125b-5p expression in kidney and SMCs. In situ hybridization revealed that under normal conditions, miR-125b-5p was expressed in arteriolar SMCs and in juxtaglomerular (JG) cells. Under conditions that induce reacquisition of the renin phenotype, miR-125b-5p was downregulated in arteriolar SMCs but remained expressed in JG cells. miR-330, normally absent, was expressed exclusively in JG cells of treated mice. In vitro functional studies showed that overexpression of miR-330 inhibited Smtn expression in SMCs. On the other hand, miR-125b-5p increased Smtn expression, whereas its inhibition reduced Smtn expression. Our results demonstrate that miR-330 and miR-125b-5p are markers of JG cells and have opposite effects on renin lineage cells: one inhibiting and the other favoring their smooth muscle phenotype.


2021 ◽  
pp. 016224392110556
Author(s):  
Ana Delgado

In view of the end of the golden years of the Norwegian oil economy, ocean genetic resources are being advertised in policy environments as holding great potential for the future of the country. Microbes have increased in popularity as promising agents of the Norwegian new bioeconomy, as advances in gene sequencing technologies and genomics have made them more accessible. This paper examines the turn toward digital sequence data in bioprospecting to inquire about its political implications. It draws on a combination of empirical materials to describe the infrastructural work that goes into extracting microbes from their in situ locations in arctic and subarctic waters to in silico collections and databases. I argue that in that infrastructural work, microbes may become both more promising and more elusive public and political matters. As biodiversity is turned into data, bioprospecting appears as less dependent on material samples, which may ultimately render policy frameworks for biodiversity governance obsolete. The shift toward big sequence data in bioprospecting entails shifts in how promise is attributed to biodiversity, which life forms appear to be more promising, and how such life forms come to appear as public good.


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