scholarly journals In silico characterization and homology modeling of cytosolic APX gene predicts novel glycine residue modulating waterlogging stress response in pigeon pea

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10888
Author(s):  
Anshika Tyagi ◽  
Sandhya Sharma ◽  
Harsha Srivastava ◽  
Nagendra Kumar Singh ◽  
Kishor Gaikwad
Keyword(s):  
Md Simulation ◽  
Simulation Analysis ◽  
Pigeon Pea ◽  
Waterlogging Stress ◽  
The Family ◽  
Key Factor ◽  
Alignment Coverage ◽  
Binding Residues ◽  
In Silico Characterization ◽  
High Binding Affinity

Ascorbate peroxidase (APX) is a member of the family of heme-containing peroxidases having a similar structure with Cytochrome c peroxidase (CCP) that effectively scavenge cytosolic and chloroplastic hydrogen peroxide (H2O2) under various stresses. In this study, computational characterization and homology analysis of APX protein from waterlogging tolerant (ICPL 84023) and sensitive (ICP 7035) pigeon pea genotypes were carried out resulting in 100% homology with Glycine max in case of former and 99% in later genotypes respectively with 97.39% alignment coverage among each other. The model structure was further refined by various tools like PROCHECK, ProSA, and Verify3D. The planned model of the APX enzyme was then tested to dock with H2O2along with molecular dynamics (MD) simulation analysis. The docked complex of ICPL 84023 showed the best G-score (23.39 kcal/mol) in comparison to ICP 7035 (16.74 kcal/mol) depicting the higher production of APX for scavenging reactive oxygen species (ROS) production making this genotype more tolerant. The important binding residues in the ICPL 84023-H2O2complex (SER1, THR4, GLU23, and GLY13) have shown less fluctuation than the ICP 7035-H2O2 complex (SER1, THR4, and GLU23). Overall, our results showed that amino acid residue glycine in ICPL 84023 APX gene has a high binding affinity with H2O2 which could be a key factor associated with waterlogging stress tolerance in pigeon pea.

scholarly journals Public Views on Priority Groups for COVID-19 Vaccination: A Survey from Iran

2021 ◽  
Vol In Press (In Press) ◽  
Author(s):  
Najmeh Moradi ◽  
Seyyed Taghi Heydari ◽  
Leila Zarei ◽  
Jalal Arabloo ◽  
Aziz Rezapour ◽  
...  
Keyword(s):  
Online Survey ◽  
Univariate Analysis ◽  
Random Order ◽  
The Elderly ◽  
Iranian Population ◽  
Vulnerable Groups ◽  
Vaccination Programs ◽  
The Family ◽  
Key Factor ◽  
Allocation Strategies

Background: In the initial coronavirus disease 2019 (COVID-19) vaccination program, prioritizing vulnerable groups is inevitable due to limited supply. Currently, most of the allocation strategies are focused on individuals’ characteristics. Objectives: The present study aimed to assess the opinions of Iranian population in specifying high-priority individuals and groups for COVID-19 vaccination. Methods: An online survey was conducted using some popular social media in Iran. The data was collected from Iranian population (878 individuals) aged 18 years and older during the COVID-19 pandemic (2 - 20 May 2020) to investigate their opinions towards vaccine allocation strategies at the family and society levels. In vaccine prioritizing within family three option and in vaccine prioritizing within society, seven population groups were introduced by the respondents in a random order, respectively. To analyze the data, mean rank and univariate analysis was used. Results: Healthcare workers, high-risk patients, and the elderly were the first priority groups for a vaccination with a mean rank of 2.8, 2.8, and 3.8, respectively. The least priority group was policymakers and executive managers (mean rank = 5.75). At the family level, 64% of the respondents introduced one of the family members as the first priority for vaccination, followed by their children (29%) and themselves (7%). No significant relationship was observed between respondents’ characteristics and their prioritization in vaccine prioritizing within society. Conclusions: Although involving public preference in decision-making is a key factor for the success of policies, careful design and implementation of vaccination programs through considering risk-benefit assessment is strongly recommended.

scholarly journals Energy Saving Potential from Shading Design for Residential House in Rural Area

2018 ◽  
Vol 164 ◽  
pp. 01007
Author(s):  
Dany Perwita Sari ◽  
Yun-shang Chiou
Keyword(s):  
Energy Saving ◽  
Rural Area ◽  
Energy Savings ◽  
Simulation Analysis ◽  
Residential Buildings ◽  
Substantial Impact ◽  
Energy Saving Potential ◽  
Key Factor ◽  
Residential House ◽  
Shading Devices

There are some architectural factors in the energy saving design of residential houses in Taiwan. In addition, in rural area, window glazing is a key factor to reducing electricity. For these purposes, a simulation model of exterior shading has been done in this study. Various types of shading devices have been analysed and compared in terms of energy savings. Simulation analysis by DesignBuilder reveals that shading devices has substantial impact to minimizing energy consumption. The results derived in this paper could provide useful suggestions for the shading design of residential buildings at rural area in Taiwan.

scholarly journals Study of Caspase 8 Inhibition for the Management of Alzheimer’s Disease: A Molecular Docking and Dynamics Simulation

Molecules ◽  
2020 ◽  
Vol 25 (9) ◽  
pp. 2071
Author(s):  
Syed Sayeed Ahmad ◽  
Meetali Sinha ◽  
Khurshid Ahmad ◽  
Mohammad Khalid ◽  
Inho Choi
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Molecular Docking ◽  
Md Simulation ◽  
Simulation Analysis ◽  
Dynamics Simulation ◽  
Caspase 8 ◽  
Amino Acid Residues ◽  
The Stability ◽  
Molecular Docking And Dynamics

Alzheimer’s disease (AD) is the most common type of dementia and usually manifests as diminished episodic memory and cognitive functions. Caspases are crucial mediators of neuronal death in a number of neurodegenerative diseases, and caspase 8 is considered a major therapeutic target in the context of AD. In the present study, we performed a virtual screening of 200 natural compounds by molecular docking with respect to their abilities to bind with caspase 8. Among them, rutaecarpine was found to have the highest (negative) binding energy (−6.5 kcal/mol) and was further subjected to molecular dynamics (MD) simulation analysis. Caspase 8 was determined to interact with rutaecarpine through five amino acid residues, specifically Thr337, Lys353, Val354, Phe355, and Phe356, and two hydrogen bonds (ligand: H35-A: LYS353:O and A:PHE355: N-ligand: N5). Furthermore, a 50 ns MD simulation was conducted to optimize the interaction, to predict complex flexibility, and to investigate the stability of the caspase 8–rutaecarpine complex, which appeared to be quite stable. The obtained results propose that rutaecarpine could be a lead compound that bears remarkable anti-Alzheimer’s potential against caspase 8.

scholarly journals Mechanism for APOBEC3G catalytic exclusion of RNA and non-substrate DNA

2019 ◽  
Vol 47 (14) ◽  
pp. 7676-7689 ◽  
Author(s):  
William C Solomon ◽  
Wazo Myint ◽  
Shurong Hou ◽  
Tapan Kanai ◽  
Rashmi Tripathi ◽  
...  
Keyword(s):  
Md Simulation ◽  
Catalytic Domain ◽  
Simulation Analysis ◽  
Binding Mode ◽  
Hydroxyl Group ◽  
Hiv Replication ◽  
Ssdna Binding ◽  
Dna And Rna ◽  
Multiple Substrate ◽  
Sugar Conformation

Abstract The potent antiretroviral protein APOBEC3G (A3G) specifically targets and deaminates deoxycytidine nucleotides, generating deoxyuridine, in single stranded DNA (ssDNA) intermediates produced during HIV replication. A non-catalytic domain in A3G binds strongly to RNA, an interaction crucial for recruitment of A3G to the virion; yet, A3G displays no deamination activity for cytidines in viral RNA. Here, we report NMR and molecular dynamics (MD) simulation analysis for interactions between A3Gctd and multiple substrate or non-substrate DNA and RNA, in combination with deamination assays. NMR ssDNA-binding experiments revealed that the interaction with residues in helix1 and loop1 (T201-L220) distinguishes the binding mode of substrate ssDNA from non-substrate. Using 2′-deoxy-2′-fluorine substituted cytidines, we show that a 2′-endo sugar conformation of the target deoxycytidine is favored for substrate binding and deamination. Trajectories of the MD simulation indicate that a ribose 2′-hydroxyl group destabilizes the π-π stacking of the target cytosine and H257, resulting in dislocation of the target cytosine base from the catalytic position. Interestingly, APOBEC3A, which can deaminate ribocytidines, retains the ribocytidine in the catalytic position throughout the MD simulation. Our results indicate that A3Gctd catalytic selectivity against RNA is dictated by both the sugar conformation and 2′-hydroxyl group.

Application of Simulation Technology on the Design of One Special Expandable Tubular Thread

2014 ◽  
Vol 607 ◽  
pp. 257-263 ◽  
Author(s):  
Yong Gang Liu ◽  
Zhang Hua Lian ◽  
Xiao Jun Li ◽  
Ding Peng Ye
Keyword(s):  
Finite Element ◽  
Finite Element Simulation ◽  
Simulation Analysis ◽  
Structure Design ◽  
Thread Connection ◽  
Expansion Test ◽  
Element Simulation ◽  
Metal Seal ◽  
Key Factor ◽  
Sealing Ring

(minimum 200words, maximum 300-500words) The solid expandable tubular technology is one of the most important ones which play key role in 21st century’s oil drilling industry. The expandable thread connection is one of the key factor of the technology which decide the success or failure of expansion casing site construction. Finite element simulation can help analyze the feasibility effectively on expandable casing thread connection structure design and save a lot of material and financial resources. According to a special expansion casing thread which with single hook thread characteristics, metal seal cylinder and seal ring, this paper use the finite element simulation analysis method to learn the stress, strain and displacement being occurred in thread connection during the process of expansion. The finite element simulation analysis results shown that the wall thickness decreased about 0.66mm after the expansion, the maximum stress of expandable casing connection during expansion was 494 MPa which between the yield stress(ss= 380MPa) and ultimate strength(sb= 650MPa) of the casing material, the most dangerous place of thread connection was the roots of thread, there was gapless between contact surfaces of the messing thread with contact pressure during the expansion, and the rubber sealing ring kept the state with the minimum 4.64 MPa compress stress during the expansion. Through the simulation, It can come to a conclusion that the special thread structure could meet the expected connection and seal function effectively during the expansion process, which provides an important basis for the following thread processing and expansion test.

scholarly journals The impact of the live-in housemaids intervention in family affairs and in the interactive relationship between couples in the Kuwaiti society

2016 ◽  
Vol 6 (2) ◽  
pp. 5
Author(s):  
Amer Al-Saleh
Keyword(s):  
Statistical Significance ◽  
Social Survey ◽  
The Social ◽  
The Family ◽  
Key Factor ◽  
Interactive Relationship ◽  
Sample Application ◽  
Independent Variable ◽  
Post Hoc ◽  
The Impact

The aim of the present study is to clarify the effect of the intervention of live-in maids in the family affairs and especially in the interactive relationship between couples whether by revealing respect or by their position in quarrels. The maid is a key factor in the domestic life of the host family; she plays a role in the food preparation and the cleaning, gives medicine to the children, resolves their problems and helps with their homework. The method and methodology for this study was the social survey and stratified random sample application. A questionnaire was used for the current study to collect data from 1,800 families consisting of a husband and a wife who live with the maid in the same house. The statistical package that was used in this study was SPSS for analyzing the collected data applying statistical equations such as the Independent Sample T-test for the two independent samples of the husbands and wives. Additionally, the Multivariate Analysis of Variance (MANOVA) and the Post Hoc Multiple Comparison for Observed Means for comparisons between the averages of arithmetical means of the data of the study were used to investigate the effect of independent variables. The scale for the independent variable related to the maid’s interference in the family affairs included three levels as follows: (a –high intervention b – medium intervention c-absolute no intervention). The purpose was to know the effect of the independent variable on the two dependent variables which are 1 -respect between spouses 2 – fights between spouses). The findings of the study suggest that there is a statistical significance between the feelings of respect between spouses as well as the quarrels between the couple and the live-in maid’s interference in family affairs. Finally, the study recommends that future studies and research shed more light on the various problems with house servants like crimes and theft. 

scholarly journals Homocysteine and Asymmetric Dimethylarginine (ADMA) in Neurological Diseases

2017 ◽  
Vol 6 (2) ◽  
pp. 930-939
Author(s):  
Jolanta Dorszewska
Keyword(s):  
Neurodegenerative Diseases ◽  
Metabolic Pathways ◽  
Asymmetric Dimethylarginine ◽  
Neurological Diseases ◽  
No Synthase ◽  
Lipid Lowering ◽  
Endogenous Inhibitor ◽  
Pathological Conditions ◽  
The Family ◽  
Key Factor

Homocysteine (Hcy) is formed from methionine (Met) and is distributed in two metabolic pathways: in the process of remethylation to Met and in the process of transsulfuration to cysteine. Hyperhomocysteinemia (HHcy) is a risk factor for cardiovascular and neurological diseases such as: Alzheimer’s and Parkinson’s diseases, multiple sclerosis, and stroke. Increased Hcy level may lead to endothelial dysfunction due to impaired bioavailability of endothelium-derived nitric oxide (NO). The molecular mechanism decreasing the levels of NO in HHcy conditions is incompletely understood, but it seems that asymmetric dimethylarginine (ADMA), an endogenous inhibitor of NO synthase, may be a key factor. ADMA is formed from L-arginine by enzymes in the family of protein N-methyltransferases (PRMT) and may undergo hydrolysis to L-citrulline and dimethylamine with the participation of dimethylaminohydrolase (DDAH). In pathological conditions such as neurodegenerative diseases, Hcy may lead to increased ADMA concentrations by inhibiting the activity of DDAH. Several drugs, such L-dopa, antiepileptic drugs, and lipid-lowering drugs, may interfere with the metabolic pathways of thiols, leading to an alteration of plasma Hcy and ADMA levels. It seems that administration of L-arginine, in conjunction with B vitamins, to patients with HHcy may be a new method in the treatment of neurodegenerative diseases.

scholarly journals A CONCEPTUAL REVIEW ON TREATMENT MODALITIES FOR RAKTAPRADAR W.S.R. TO DUB

2021 ◽  
Vol 9 (12) ◽  
pp. 3038-3048
Author(s):  
Himani Gupta ◽  
Poonam Bamola ◽  
Nikita Jaiswal
Keyword(s):  
Quality Of Life ◽  
Sustainable Development ◽  
Iron Deficiency ◽  
Treatment Modalities ◽  
Deficiency Anemia ◽  
Common Cause ◽  
The Family ◽  
Key Factor ◽  
The Common

Women are the pioneers and key to sustainable development and quality of life in the family. Hindu culture respects women as Goddess due to this power of creativity of life inside her womb. This energy of procreation starts with menarche and ends with menopause. Ayurveda focusses on preventive and curative measures of female health. Acharya Charak mentioned “Yonishu Shuddhasu Garbham Vindati Yoshitaha” i.e., normal healthy status of Yoni (vagina) is the key factor for achieving the conception. Various gynaecological disorders like Yoni Rogas, Artava Doshas and Raktapradar hampers the achievement of conception. Raktapradar i.e., excessive excretion of men- strual blood, either in quantity or in duration is explained in Ayurvedic Classics. It is the common cause of Iron deficiency anemia & general debility. Ayurvedic intervention mentioned can be recommended as safer, feasible and effective therapy for management of Raktapradar. Keywords: Shudha Yoni, Yoni Roga, Artava Dosha, Raktapradar.

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