scholarly journals In Silico Experiments in Scientific Papers on Molecular Biology

2011 ◽  
Vol 24 (2) ◽  
pp. 23-42
Author(s):  
Sabrina Moretti
Keyword(s):  
Molecular Biology ◽  
In Silico ◽  
In Vitro Experiments ◽  
Technical Object ◽  
Experimental Conditions ◽  
Biological Phenomena ◽  
Scientific Papers

This article explores the role of the so-called in silico experiments used in molecular biology. It is based on the analysis of some papers that present scientific applications which rely on in silico experiments. By means of this study I found two basic ways of viewing them. According to the first view, the in silico experiment is a computer program that realizes some specific operations: it constitutes some particular experimental conditions, which allow us to investigate biological phenomena, and which complement those present in in vivo and in vitro experiments. According to the second view, in silico experimentation has a different meaning, which corresponds more closely to the meaning of “simulation”: its identity is linked to that of the “model” used to construct such simulation. The authors of the analysed papers never express an intention to standardize a model, so its meaning remains contingent, and cannot be turned into a technical object.

Factors affecting in vitro and in vivo antioxidant effects. Experimental conditions and nature of oxidants determine antioxidant efficacy

2021 ◽  
pp. 1-9
Author(s):  
Etsuo Niki
Keyword(s):  
Biological Molecules ◽  
Experimental Conditions ◽  
Factors Affecting ◽  
Beneficial Effects ◽  
Multiple Oxidants ◽  
Antioxidant Effects

Reactive oxygen and nitrogen species have been implicated in the onset and progression of various diseases and the role of antioxidants in the maintenance of health and prevention of diseases has received much attention. The action and effect of antioxidants have been studied extensively under different reaction conditions in multiple media. The antioxidant effects are determined by many factors. This review aims to discuss several important issues that should be considered for determination of experimental conditions and interpretation of experimental results in order to understand the beneficial effects and limit of antioxidants against detrimental oxidation of biological molecules. Emphasis was laid on cell culture experiments and effects of diversity of multiple oxidants on antioxidant efficacy.

scholarly journals Antidiabetic activity of some pentacyclic acid triterpenoids, role of PTP–1B: In vitro, in silico, and in vivo approaches

2011 ◽  
Vol 46 (6) ◽  
pp. 2243-2251 ◽  
Author(s):  
Juan José Ramírez-Espinosa ◽  
Maria Yolanda Rios ◽  
Sugey López-Martínez ◽  
Fabian López-Vallejo ◽  
José L. Medina-Franco ◽  
...  
Keyword(s):  
In Silico ◽  
Antidiabetic Activity ◽  
Ptp 1B

scholarly journals Trophectoderm-Specific Knockdown of LIN28 Decreases Expression of Genes Necessary for Cell Proliferation and Reduces Elongation of Sheep Conceptus

2020 ◽  
Vol 21 (7) ◽  
pp. 2549 ◽  
Author(s):  
Asghar Ali ◽  
Mark Stenglein ◽  
Thomas Spencer ◽  
Gerrit Bouma ◽  
Russell Anthony ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Critical Period ◽  
In Vitro Experiments ◽  
Placental Development ◽  
Expression Of Genes ◽  
Trophectoderm Cells ◽  
Successful Establishment

LIN28 inhibits let-7 miRNA maturation which prevents cell differentiation and promotes proliferation. We hypothesized that the LIN28-let-7 axis regulates proliferation-associated genes in sheep trophectoderm in vivo. Day 9-hatched sheep blastocysts were incubated with lentiviral particles to deliver shRNA targeting LIN28 specifically to trophectoderm cells. At day 16, conceptus elongation was significantly reduced in LIN28A and LIN28B knockdowns. Let-7 miRNAs were significantly increased and IGF2BP1-3, HMGA1, ARID3B, and c-MYC were decreased in trophectoderm from knockdown conceptuses. Ovine trophoblast (OTR) cells derived from day 16 trophectoderm are a useful tool for in vitro experiments. Surprisingly, LIN28 was significantly reduced and let-7 miRNAs increased after only a few passages of OTR cells, suggesting these passaged cells represent a more differentiated phenotype. To create an OTR cell line more similar to day 16 trophectoderm we overexpressed LIN28A and LIN28B, which significantly decreased let-7 miRNAs and increased IGF2BP1-3, HMGA1, ARID3B, and c-MYC compared to control. This is the first study showing the role of the LIN28-let-7 axis in trophoblast proliferation and conceptus elongation in vivo. These results suggest that reduced LIN28 during early placental development can lead to reduced trophoblast proliferation and sheep conceptus elongation at a critical period for successful establishment of pregnancy.

Anionic and cationic exchange mechanisms in the skin of anurans, with special reference to Leptodactylidae in vivo

1971 ◽  
Vol 262 (842) ◽  
pp. 163-174 ◽  
Keyword(s):  
Transport Mechanism ◽  
Selective Inhibition ◽  
The Other ◽  
Sodium Absorption ◽  
Experimental Conditions ◽  
Net Flux ◽  
Cationic Exchange

In several species of anurans, the in vivo skin has been shown to absorb Na + and Cl - independently from dilute external solutions. That the mechanism for sodium absorption is different from that of chloride absroption is born out by the following: (1) Either of these ions is absorbed without an accompanying ion when this latter is impermeant. (2) From NaCl solutions there can be an unequal absorption of sodium and chloride. (3) A selective inhibition of the absorption of one of the ions can be produced experimentally, while the net flux of the other remains unchanged. In all these situations, the absorbed ion has to be exchanged against an endogenous ion of the same charge. In Calyptocephalella gayi , H + and HCO - 3 are exchanged against sodium and chloride respectively. A comparison of the relationships between H + excretion and Na + absorption in vivo skins and shortcircuited in vitro skins shows that in the latter no H + excretion occurs, only the Na + transport being maintained under these experimental conditions. From this, one must conclude that the active Na + transport is the motive factor of the transport mechanism. H + excretion by the in vivo skin plays the role of physiologically short-circuiting the Na + transport.

Role of Activated Platelets in the Homing, Maturation, and Differentiation of Endotheleal Progenitor Cells (EPCs) to Vascular Subendotheleal Matrix.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 3938-3938
Author(s):  
Eli I. Lev ◽  
Jing-fei Dong ◽  
Marcin Bujak ◽  
Khatira Aboulfatova ◽  
Neal S. Kleiman ◽  
...  
Keyword(s):  
Progenitor Cells ◽  
Vascular Injury ◽  
Human Platelets ◽  
In Vitro Experiments ◽  
Cell Markers ◽  
Femoral Arteries ◽  
In Vivo Experiments

Abstract We and others have found that platelets play an important role in the recruitment of endothelial progenitor cells to sights of vascular injury. However, it is not clear whether the EPCs mature and differentiate to endothelial cells following recruitment to the vascular injury sites. In addition, there is limited in vivo data to support the role of EPCs in re-endothlialization following vascular injury. We conducted in vitro experiments to investigate the maturation of EPCs on platelet based-media and in vivo experiments to evaluate the recruitment of EPCs following vascular injury. In in vitro experiments human EPCs were isolated from donated buffy coats by magnetic microbeads and flow cytometry cell sorting using CD133 and VEGFR-2, respectively, as cell markers. Isolated viable EPCs (CD133+, VEGFR-2+ cells) were plated on human fibronectin or a monolayer of washed human platelets. Cell colonies were counted 7 days after plating and stained for the endothelial cell markers CD31 (PECAM-1) and CD144 (VE-cadherin). The mean number of colony-forming cells was 35±2.6 colonies/106 cells on platelets, which was significantly higher than 18±4.2 colonies/106 cells on fibronectin (n = 4, P<0.01). Apart from the difference in colony numbers, the EPC colonies grew faster on the platelet substrate, were larger, and had more spindle-shaped cells (Figure 1 - staining of EPC colonies for CD31 and CD144). In the in vivo experiments a model of transluminal injury to mouse femoral arteries was used. Femoral artery denudation was performed by 0.25-mm-diameter angioplasty guidewire. Injured femoral arteries were compared to the contra-lateral controls (uninjured), and were harvested 1.5 hours following the injury and immunostaining performed with an anti-VEGFR-2 antibody. Four experiments showed a markedly higher number of VEGFR-2+ cells in the artery that has undergone denudation. These experiments indicate that a media composed of platelets promotes the maturation and differentiation of EPCs. Furthermore, in vivo, EPCs are recruited early following vascular injury. Thus, homing, maturation, and differentiation of EPCs are mediated by platelets.

Inhibin-like activity in Sertoli cell culture media and testicular homogenates from rats of various ages

1987 ◽  
Vol 113 (1) ◽  
pp. 103-110 ◽  
Author(s):  
A. M. Ultee-van Gessel ◽  
F. H. de Jong
Keyword(s):  
Sertoli Cells ◽  
Culture Media ◽  
Reciprocal Relationship ◽  
Pituitary Cells ◽  
In Vitro Experiments ◽  
Old Rats ◽  
Lh Secretion

ABSTRACT The influence of age on testicular inhibin in untreated, neonatally hemicastrated and prenatally irradiated rats was studied using in-vivo and in-vitro experiments. In testicular cytosols prepared from 1-, 7-, 14-, 21-, 42- and 63-day-old rats concentrations of testicular inhibin could be measured with an in-vitro bioassay method using dispersed pituitary cells. Preparations of testicular cytosols caused a dose-dependent suppression of pituitary FSH secretion, whereas no effects were found on LH secretion. Testicular content of inhibin increased gradually with age, while after 14 days of age a relatively large increase of peripheral FSH concentrations occurred in all experimental groups. Neonatal hemicastration or prenatal irradiation resulted in decreased inhibin content of the testis and increased plasma FSH levels. The production of inhibin activity by Sertoli cells obtained from 7-, 14-, 21-, 42- and 63-day-old normal rats was measured during a 24-h incubation period on the third day of culture. The inhibin production per 106 plated Sertoli cells decreased rapidly after 14 days of age and the lowest production of inhibin was found in Sertoli cells from rats of 63 days of age. After preincubation with ovine FSH significantly larger amounts of inhibin activity were detected in spent media from 21-day-old rat testes. In contrast, suppression of inhibin production was found after preculture in the presence of testosterone at most of the ages studied. These data from in-vivo and in-vitro experiments indicate that a reciprocal relationship exists between pituitary FSH secretion and inhibin production before the age of 21 days. This relationship supports the concept that inhibin is a physiologically important modulator of FSH secretion before puberty, while the role of the large amount of testicular inhibin present at the older ages remains to be determined. J. Endocr. (1987) 113, 103–110

scholarly journals Complex role of NK cells in regulation of oncolytic virus–bortezomib therapy

2018 ◽  
Vol 115 (19) ◽  
pp. 4927-4932 ◽  
Author(s):  
Yangjin Kim ◽  
Ji Young Yoo ◽  
Tae Jin Lee ◽  
Joseph Liu ◽  
Jianhua Yu ◽  
...  
Keyword(s):  
Mathematical Model ◽  
Tumor Microenvironment ◽  
Nk Cells ◽  
Proteasome Inhibitor ◽  
Oncolytic Virus ◽  
In Vitro Experiments ◽  
Hematological Cancers

In the present work, we investigated the role of natural killer (NK) cells in combination therapy with oncolytic virus (OV) and bortezomib, a proteasome inhibitor. NK cells display rapid and potent immunity to metastatic and hematological cancers, and they overcome immunosuppressive effects of tumor microenvironment. We developed a mathematical model to address the question of how the density of NK cells affects the growth of the tumor. We found that the antitumor efficacy increases when the endogenous NKs are depleted and also when exogenous NK cells are injected into the tumor. These predictions were validated by our in vivo and in vitro experiments.

Melanophore β-adrenoceptors in patterning in a flatfish, Pseudopleuronectes americanus

2007 ◽  
Vol 85 (6) ◽  
pp. 695-702 ◽  
Author(s):  
D. Burton
Keyword(s):  
Salt Solution ◽  
Winter Flounder ◽  
Dark Band ◽  
Pigment Dispersion ◽  
In Vitro Experiments ◽  
Pseudopleuronectes Americanus ◽  
Adrenoceptor Agonists

In vitro experiments were performed on melanophores bourne on scale slips sampled from three major areas (general background, dark band, and white spot) of the integumentary pattern of winter flounder, Pseudopleuronectes americanus (Walbaum, 1792). The effects of the respective β1- and β2-adrenoceptor agonists dobutamine and terbutaline and antagonists atenolol and ICI 118551 on pattern-related melanosome aggregation in response to exogenously applied L-noradrenaline were determined, as well as their effects on melanosome dispersion in balanced salt solution. The results demonstrate β1-adrenoceptor mediation in flatfish melanosome dispersion, with pattern-related variation, and also provide further evidence for β2-subtype involvement. Based on mammalian physiology, two β-subtypes will facilitate melanophore responsiveness to both neural and circulatory catecholamines. The in vivo role of these β-subtypes is discussed in relation to previously described attributes of the patterning behaviour of this species, which incorporates balances between α- and β-adrenoceptors. Dark band melanophores display a β-adrenoceptor bias, in contrast with other areas of the pattern, which would be consistent with their capacity for pigment dispersion in stressed flounders and with the slow paling of these bands during background-related responses.

In Vitro Models for Studying Renal Stone Formation: A Clear Alternative

1998 ◽  
Vol 26 (4) ◽  
pp. 481-503
Author(s):  
Felix Grases ◽  
Rafael M. Prieto ◽  
Antonia Costa-Bauzá
Keyword(s):  
Renal Stone ◽  
Stone Formation ◽  
Renal Stones ◽  
Renal Calculi ◽  
In Vitro Models ◽  
Laboratory Animals ◽  
In Vitro Experiments ◽  
Experimental Conditions

This paper discusses the limitations of using laboratory animals for direct in vivo observation of the development of renal stones. In fact, the majority of hypotheses related to mechanisms of stone formation have been based on the results of in vitro experiments. The relevance of in vitro experiments that allow the study of urolithiasis depends upon the degree of correspondence between the experimental conditions and those prevailing in the stone-forming kidney in vivo. For this reason, several in vitro experimental systems that attempt to reproduce the conditions found in vivo have been developed in order to study renal stone formation, which have been classified into two main groups: a) models to study papillary stone formation; and b) models to study “sedimentary” stone formation. These models are briefly described in this paper, and the information obtained was compared with that resulting from a study of the fine structure of real human renal calculi, in order to prove the validity of the models. It was concluded that the experimental in vitro models can closely reproduce the renal conditions under which human calculi are developed. This allows important data to be obtained about the aetiology of renal lithiasis, which is of great relevance to the development of effective treatments for this disease. Therefore, experimental in vitro models constitute a clear alternative to the use of laboratory animals.

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