RT-PCR Amplification and in-silico Analysis of Water Stress-Responsive Hydrophilic TaDreb, TaDHN and TaWCS20 Genes from Triticum aestivum

Migraine is a re-occurring type of headache and causes moderate-to-severe pain that is troubling or pulsing. The pain occurs in half of the head, and common symptoms are photophobia, phonophobia, nausea, depression, anxiety, vomiting, etc. This study evaluates the prevalence of migraine and responsible genes through molecular modeling in the region of Bahawalpur, Pakistan. This research was aimed to determine the prevalence of migraine-causing genes in the population of Bahawalpur and also to do molecular and in-silico analysis of migraine-causing gene as no similar research was conducted before. The disease was characterized and diagnosed under the criteria of the Second Edition of the International Classification of Headache Disorders and molecular identification of migraine-causing genes, i.e. GRIA1, GRIA3, and ESR1, by PCR amplification. The total number of samples collected for migraine patients was 230, out of which 30 were positive for PCR amplification of the genes GRIA1, GRIA3, and ESR1. Therapeutic potentials of commercial drugs, namely Cyclobenzaprine, Divalproex, Ergotamine, and Sumatriptan, were analyzed in silico through molecular docking. Ergotamine demonstrated the highest binding affinity of [Formula: see text]8.4 kcal/mol for the target molecule and, hence, the highest potential. The bivariate analysis showed that the prevalence of migraine concerning gender and age was significantly correlated ([Formula: see text], [Formula: see text]). It was observed that almost 31.4% of women suffered from headaches daily, 70% weekly, 28.1% monthly, and 23.5% rarely. Comparatively, only 8.3% of males suffered from daily headaches, 34% weekly, 12.8% monthly, and 14.9% rarely. The study shows promising results and encourages future researchers to conduct such a comprehensive epidemiological study on an even larger population to justify a more precise association of risk factors involved in migraine pathophysiology.

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Evaluation of the effects of SARS-CoV-2 genetic mutations on diagnostic RT-PCR assays

10.1101/2021.01.19.426622 ◽

2021 ◽

Author(s):

Takeru Nakabayashi ◽

Yuki Kawasaki ◽

Koichiro Murashima ◽

Kazuya Omi ◽

Satoshi Yuhara

Keyword(s):

In Silico ◽

In Silico Analysis ◽

Detection Sensitivity ◽

Genetic Mutations ◽

Rt Pcr ◽

Mutant Strains ◽

Binding Regions ◽

Control And Prevention ◽

Pcr Assays ◽

Silico Analysis

AbstractSeveral mutant strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are emerging. Mismatch(es) in primer/probe binding regions would decrease the detection sensitivity of the PCR test, thereby affecting the results of clinical testing. In this study, we conducted an in silico survey on SARS-CoV-2 sequence variability within the binding regions of primer/probe published by the Japan National Institute of Infectious Diseases (NIID) and Centers for Disease Control and Prevention (CDC). In silico analysis revealed the presence of mutations in the primer/probe binding regions. We performed RT-PCR assays using synthetic RNAs containing the mutations and showed that some mutations significantly decreased the detection sensitivity of the RT-PCR assays.Our results highlight the importance of genomic monitoring of SARS-CoV-2 and evaluating the effects of mismatches on PCR testing sensitivity.

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Changes in secondary metabolites and fiber quality of cotton (Gossypium hirsutum) seed under consecutive water stress and in silico analysis of cellulose synthase and xyloglucan endotransglucosylase

Physiology and Molecular Biology of Plants ◽

10.1007/s12298-021-01033-y ◽

2021 ◽

Author(s):

Maryam Kolahi ◽

Elham Faghani ◽

Mina Kazemian ◽

Andrea Goldson-Barnaby ◽

Sedighe Dodangi

Keyword(s):

Water Stress ◽

Secondary Metabolites ◽

Gossypium Hirsutum ◽

In Silico ◽

Fiber Quality ◽

In Silico Analysis ◽

Cellulose Synthase ◽

Silico Analysis

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Validation Study for VERIPRO® SARS-CoV-2 Env Assay for the Detection of SARS-CoV-2 from Stainless Steel Environmental Surface Swabs: Emergency Response Validation-AOAC—AOAC Performance Tested MethodSM 122001

Journal of AOAC International ◽

10.1093/jaoacint/qsab048 ◽

2021 ◽

Author(s):

Adam Joelsson ◽

Shannon Green ◽

Nicholas Siciliano ◽

Vikrant Dutta ◽

Ron Johnson

Keyword(s):

Stainless Steel ◽

Emergency Response ◽

Causative Agent ◽

In Silico ◽

Reference Method ◽

In Silico Analysis ◽

Accurate Method ◽

Rt Pcr ◽

Environmental Surface ◽

Silico Analysis

Abstract Background The VERIPRO SARS-CoV-2 Env assay uses reverse transcriptase PCR (RT-PCR) to detect SARS-CoV-2, the causative agent of COVID-19, from stainless steel environmental sample swabs. Objective To validate the VERIPRO SARS-CoV-2 Env assay as part of the AOAC Research Institute’s Emergency Response Validation Performance Tested MethodSM program. Methods The VERIPRO SARS-CoV-2 Env assay was evaluated for specificity using in silico analysis of 15 764 SARS-CoV-2 sequences and 65 exclusivity organisms (both near neighbors and background organisms). The candidate method was evaluated in an unpaired study design for one environmental surface (stainless steel) and compared to the U.S. Centers for Disease Control and Prevention 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel, Instructions for Use (Revision 4, Effective 6/12/2020). Results Results of the in silico analysis demonstrated the specificity of the method in being able to detect target sequences and discriminate them from near neighbors. In the matrix study, the candidate method demonstrated statistically significant better recovery of the target analyte than the reference method. Conclusions The VERIPRO SARS-CoV-2 Env assay is a rapid and accurate method that can be utilized by food producers to detect the causative agent of COVID-19 on food contact surfaces. Highlights The VERIPRO SARS-CoV-2 Env assay can be performed without the need for an optional RNA purification step to detect SARS-CoV-2 from environmental surfaces.

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