A computational approach to identify phytochemicals as potential inhibitor of acetylcholinesterase: Molecular docking, ADME profiling and molecular dynamics simulations.

Inhibition of acetylcholinesterase (AChE) is a crucial target in the treatment of Alzheimer's disease (AD). Common anti-acetylcholinesterase drugs such as Galantamine, Rivastigmine, Donepezil, and Tacrine have significant inhibition potential. Due to side effects and safety concerns, we aimed to investigate a wide range of phytochemicals and structural analogues of these compounds. Compounds similar to the established drugs, and phytochemicals were investigated as potential inhibitors for AChE in treating AD. A total of 2,270 compound libraries were generated for further analysis. Initial virtual screening was performed using Pyrx software, resulting in 638 molecules showing higher binding affinities compared to positive controls Tacrine (-9.0 kcal/mol), Donepezil (-7.3 kcal/mol), Galantamine (-8.3 kcal/mol), and Rivastigmine (-6.4 kcal/mol). Subsequently, ADME properties were assessed, including blood-brain barrier permeability and Lipinski's rule of five violations, leading to 88 compounds passing the ADME analysis. Among the rivastigmine analogous, [3-(1-methylpiperidin-2-yl)phenyl] N,N-diethylcarbamate showed interaction with Tyr123, Tyr336, Tyr340, Phe337, Trp285 residues of AChE. Tacrine similar compounds, such as 4-amino-2-styrylquinoline, exhibited bindings with Tyr123, Phe337, Tyr336, Trp285, Trp85, Gly119, and Gly120 residues. A phytocompound (bisdemethoxycurcumin) showed interaction with Trp285, Tyr340, Trp85, Tyr71, and His446 residues of AChE with favourable binding. These findings underscore the potential of these compounds as novel inhibitors of AChE, offering insights into alternative therapeutic avenues for AD. A 100ns simulation analysis confirmed the stability of protein-ligand complex based on the RMSD, RMSF, ligand properties, PCA, DCCM and MMGBS parameters. The investigation suggested 3 ligands as a potent inhibitor of AChE which are [3-(1-methylpiperidin-2-yl)phenyl] N,N-diethylcarbamate, 4-Amino-2-styrylquinoline and bisdemethoxycurcumin. Furthermore, investigation, including in-vitro and in-vivo studies, is needed to validate the efficacy, safety profiles, and therapeutic potential of these compounds for AD treatment.

Methylglyoxal detoxifying gene families in tomato: Genome-wide identification, evolution, functional prediction, and transcript profiling.

Methylglyoxal (MG) is a highly cytotoxic molecule produced in all biological systems, which could be converted into non-toxic D-lactate by an evolutionarily conserved glyoxalase pathway. Glutathione-dependent glyoxalase I (GLYI) and glyoxalase II (GLYII) are responsible for the detoxification of MG into D-lactate in sequential reactions, while DJ-1 domain containing glyoxalase III (GLYIII) catalyzes the same reaction in a single step without glutathione dependency. Afterwards, D-lactate dehydrogenase (D-LDH) converts D-lactate into pyruvate, a metabolically usable intermediate. In the study, a comprehensive genome-wide investigation has been performed in one of the important vegetable plants, tomato to identify 13 putative GLYI, 4 GLYII, 3 GLYIII (DJ-1), and 4 D-LDH genes. Expression pattern analysis using microarray data confirmed their ubiquitous presence in different tissues and developmental stages. Moreover, stress treatment of tomato seedlings and subsequent qRT-PCR demonstrated upregulation of SlGLYI-2, SlGLYI-3, SlGLYI-6A, SlGLYII-1A, SlGLYII-3B, SlDJ-1A, SlDLDH-1 and SlDLDH-4 in response to different abiotic stresses, whereas SlGLYI-6B, SlGLYII-1B, SlGLYII-3A, SlDJ-1D and SlDLDH-2 were downregulated. Expression data also revealed SlGLYII-1B, SlGLYI-1A, SlGLYI-2, SlDJ-1D, and SlDLDH-4 were upregulated in response to various pathogenic infections, indicating the role of MG detoxifying enzymes in both plant defence and stress modulation. The functional characterization of each of these members could lay the foundation for the development of stress and disease-resistant plants promoting sustainable agriculture and production.

Identification of m6A RNA methylation genes in Oryza sativa and expression profiling in response to different developmental and environmental stimuli.

Eukaryotic messenger RNAs (mRNAs) transcend their predominant function of protein encoding by incorporating auxiliary components that ultimately contribute to their processing, transportation, translation, and decay. In doing so, additional layers of modifications are incorporated in mRNAs at post-transcriptional stage. Among them, N6-methyladenosine (m6A) is the most frequently found mRNA modification that plays crucial roles in plant development and stress response. In the overall mechanism of m6A methylation, key proteins classified based on their functions such as writers, readers, and erasers dynamically add, read, and subtract methyl groups respectively to deliver relevant functions in response to external stimuli. In this study, we identified 30 m6A regulatory genes (9 writers, 5 erasers, and 16 readers) in rice that encode 53 proteins (13 writers, 7 erasers, and 33 readers) where segmental duplication was found in one writer and four reader gene pairs. Reproductive cells such as sperm, anther and panicle showed high levels of expression for most of the m6A regulatory genes. Notably, writers like OsMTA, OsMTD, and OsMTC showed varied responses in different stress and infection contexts, with initial upregulation in response to early exposure followed by downregulation later. OsALKBH9A, a noteworthy eraser, displayed varied expression in response to different stresses at different time intervals, but upregulation in certain infections. Reader genes like OsECT5, OsCPSF30-L3, and OsECT8 showed continuous upregulation in exertion of all kinds of stress relevant here. Conversely, other reader genes along with OsECT11 and OsCPSF30-L2 were observed to be consistently downregulated. The apparent correlation between the expression patterns of m6A regulatory genes and stress modulation pathways in this study underscores the need for additional research to unravel their intricate regulatory mechanisms that could ultimately contribute to the substantial development of enhanced stress tolerance in rice through mRNA modification.

Evolutionary expansion, functional diversification, and transcript profiling of plant Glutathione Peroxidases.

Glutathione peroxidases (GPXs) play a crucial role in combating activated oxygen species and have been widely studied for their involvement in stress responses. In addition to their stress-related functions, GPXs exhibit diverse roles such as immunological response, and involvement in growth and development. These enzymes are found in both animals and plants, with multiple families identified in the evolutionarily diverse species. These families consist of conserved genes as well as unique members, highlighting the evolutionary diversification of GPX members. While animals have eight GPX families, plants possess five families. Notably, plant genomes undergo duplication and expansion events, leading to an increase in the number of GPX genes and the overall size of the GPX superfamily. This expansion suggests a wide range of functional roles for GPX. In this study, the evolutionary diversification, family expansion, and diverse functional roles of GPX enzymes have been investigated. Additionally, the expression profile of Arabidopsis and Oryza sativa GPX genes were analyzed in different developmental stages, tissues, and abiotic stress conditions. Further extensive research has been required to unravel the intricate interplay between GPX and other proteins, to gain the comprehensive mechanism governing the physiological and developmental roles of GPX.

Synthesis and biological evaluation of Ribo 7-N/O/S pyrimidine 9-deaza C-nucleoside analogs as new antiviral agents for inhibiting HCV RNA-dependent RNA polymerases.

Hepatitis C infection is caused by the bloodborne pathogen hepatitis C virus (HCV) and can lead to serious liver diseases and, ultimately, death if the treatment is ineffective. This work reports the synthesis and preclinical evaluation of 7 novel 9-O/N/S pyrimidine nucleosides, including compound 12, the triphosphate of known compound 7b. The nucleosides are 9-deaza modifications of adenosine and guanosine with ß-2'-C-methyl substituent on the ribose. Within this series of compounds, a 9-deaza furopyrimidine analog of adenosine, compound 7b, showed high anti-HCV activity in vitro, good stability, low toxicity, and low genotoxicity when administrated in low doses, and an adequate pharmacokinetics profile. An improved synthesis of compound 7b compared to a previous study is also reported. Compound 12 was synthesized as a control to verify phosphorylation of 7b occurred in vivo.

Variant-specific deleterious mutations in the SARS-CoV-2 genome reveal immune responses and potentials for prophylactic vaccine development.

Introduction: Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has had a disastrous effect worldwide during the previous three years due to widespread infections with SARS-CoV-2 and its emerging variations. More than 674 million confirmed cases and over 6.7 million deaths have been attributed to successive waves of SARS-CoV-2 infections as of 29th January 2023. Similar to other RNA viruses, SARS-CoV-2 is more susceptible to genetic evolution and spontaneous mutations over time, resulting in the continual emergence of variants with distinct characteristics. Spontaneous mutations of SARS-CoV-2 variants increase its transmissibility, virulence, and disease severity and diminish the efficacy of therapeutics and vaccines, resulting in vaccine-breakthrough infections and re-infection, leading to high mortality and morbidity rates. Materials and methods: In this study, we evaluated 10,531 whole genome sequences of all reported variants globally through a computational approach to assess the spread and emergence of the mutations in the SARS-CoV-2 genome. The available data sources of NextCladeCLI 2.3.0 (https://clades.nextstrain.org/) and NextStrain (https://nextstrain.org/) were searched for tracking SARS-CoV-2 mutations, analysed using the PROVEAN, Polyphen-2, and Predict SNP mutational analysis tools and validated by Machine Learning models. Result: Compared to the Wuhan-Hu-1 reference strain NC 045512.2, genome-wide annotations showed 16,954 mutations in the SARS-CoV-2 genome. We determined that the Omicron variant had 6,307 mutations (retrieved sequence:1947), including 67.8% unique mutations, more than any other variant evaluated in this study. The spike protein of the Omicron variant harboured 876 mutations, including 443 deleterious mutations. Among these deleterious mutations, 187 were common and 256 were unique non-synonymous mutations. In contrast, after analysing 1,884 sequences of the Delta variant, we discovered 4,468 mutations, of which 66% were unique, and not previously reported in other variants. Mutations affecting spike proteins are mostly found in RBD regions for Omicron, whereas most of the Delta variant mutations drawn to focus on amino acid regions ranging from 911 to 924 in the context of epitope prediction (B cell & T cell) and mutational stability impact analysis protruding that Omicron is more transmissible. Discussion: The pathogenesis of the Omicron variant could be prevented if the deleterious and persistent unique immunosuppressive mutations can be targeted for vaccination or small-molecule inhibitor designing. Thus, our findings will help researchers monitor and track the continuously evolving nature of SARS-CoV-2 strains, the associated genetic variants, and their implications for developing effective control and prophylaxis strategies.

Synthesis of novel azasugar-containing 2'ß-C-Me 9-deaza nucleosides as potential anti-hepatitis C virus agents.

As a part of our ongoing discovery efforts exploring azasugar as agents for treating various unmet medical needs, we prepared analogs of azasugar as potential anti-hepatitis C virus (HCV) agents. Herein we describe the synthesis of novel 2'ß-C-Me 9-deazanucleoside azasugar analogs.

Transcript profiling of glutathione metabolizing genes reveals abiotic stress and glutathione-specific alteration in Arabidopsis and rice.

Homoeostasis of glutathione (GSH) is crucial for plant survival and adaptability against stress. Despite the presence of complete Arabidopsis and rice genome sequence, the comprehensive analysis of the GSH metabolizing genes is still missing. This research concentrated on the comprehensive understanding of GSH metabolizing genes in two model plants-Arabidopsis and rice in terms of their subcellular localization, exon-intron distribution, protein domain structure, and transcript abundance. Expression profiling using the microarray data provided significant evidence of their participation in response to various abiotic stress conditions. Besides, some of these GSH metabolizing genes revealed their expression alteration in several developmental changes and tissue diversification. The presence of various stress-specific cis-regulatory elements in the promoter region of GSH metabolizing genes could be directly correlated with their stress-specific transcript alteration. Moreover, the application of exogenous GSH significantly downregulated GSH synthesizing genes and upregulated GSH metabolizing genes in Arabidopsis with few exceptions indicating a product-dependent regulation of GSH metabolizing genes. Interestingly, validation of rice GSH metabolizing genes in response to drought and salinity showed an almost similar pattern of expression in quantitative real-time as observed by microarray data. Altogether, GSH metabolizing members are a promising and underutilized genetic source for plant improvement that could be used to enhance stress tolerance in plants. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-022-01220-5.

Development of Multi-epitope Based Subunit Vaccine Against Crimean-Congo Hemorrhagic Fever Virus Using Reverse Vaccinology Approach.

Crimean-Congo hemorrhagic fever (CCHF) is a viral disease caused by the Crimean-Congo hemorrhagic fever virus (CCHFV) of the Nairovirus genus. CCHF has occurred endemically in several regions of Africa, Southern Europe, and Central and Southeast Asia, with a case fatality rate of 5 to 80%. The World health organization enlisted CCHF as one of the top prioritized diseases for research and development in emergency contexts that making it a public health concern as no effective vaccine is available till date. Therefore, the present study aims to develop an effective multi-epitope subunit vaccine using immunoinformatics and reverse vaccinology approach against this virus. The B-cell and T-cell epitopes were predicted from structural and non-structural proteins, and filtered by immunogenicity, allergenicity, toxicity, conservancy, and cross-reactivity. The computational analysis revealed that the epitopes could induce an adequate immune response and had strong associations with their respective human leukocyte antigen (HLA) alleles with 98.94% of total world population coverage. Finally, the vaccine with 427 amino acids was constructed by connecting 8 cytotoxic T-lymphocytes, 4 helper T-lymphocytes, and 10 B-cell epitopes with appropriate linkers and ß-defensin as an adjuvant. The antigenicity, allergenicity, solubility, and physiochemical properties of the vaccine were evaluated, followed by structural modelling, refinement, and validation. In addition, molecular docking and molecular dynamic simulations revealed a robust binding affinity and stability of the vaccine-immune receptor complex. Moreover, the codons were optimized for its higher expression in Escherichia coli (E. coli) K12 strain followed by in silico cloning. The proposed subunit vaccine developed in this study could be a potential candidate against CCHFV. However, further experimental validation is required to ensure the immunogenicity and safety profile of the proposed vaccine for combating and eradicating CCHFV. Supplementary Information: The online version contains supplementary material available at 10.1007/s10989-022-10430-0.

Aldehyde dehydrogenase superfamily in sorghum: genome-wide identification, evolution, and transcript profiling during development stages and stress conditions.

BACKGROUND: Aldehyde dehydrogenases (ALDHs) are a family of NAD(P)+ dependent enzymes that detoxify aldehydes by promoting their oxidation to respective carboxylic acids. The role of ALDH enzymes in various plant species has been extensively studied, revealing their critical role in salinity, drought, heat, and heavy metal stress tolerance. Despite their physiological significance, ALDH genes in Sorghum bicolor have yet to be studied thoroughly. RESULTS: In this study, a total of 19 ALDH genes have been identified that have been grouped into ten families based on the criteria of the ALDH gene nomenclature committee. Segmental duplication assisted more in the enhancement of SbALDH gene family members than tandem duplication. All the identified SbALDH members made a cluster with monocot rice and maize in the phylogenetic tree rather than dicot species, suggesting the pre-eudicot-monocot separation of the ALDH superfamily members. The gene structure and protein domain were found to be mostly conserved in separate phylogenetic classes, indicating that each family played an important role in evolution. Expression analysis revealed that several SbALDHs were expressed in various tissues, developmental stages, and in response to abiotic stresses, indicating that they can play roles in plant growth, development, or stress adaptation. Interestingly, the majority of the SbALDH genes were found to be highly responsive to drought stress, and the SbALDH18B1 transcript showed maximum enhancement in all the stress conditions. The presence of cis-acting elements (mainly ABRE and MBS) in the promoter region of these genes might have a significant role in drought tolerance. CONCLUSIONS: Our findings add to the current understanding, evolutionary history, and contribution of SbALDHs in stress tolerance, and smooth the path of further functional validation of these genes.

Genome wide analysis of the heavy-metal-associated (HMA) gene family in tomato and expression profiles under different stresses.

The heavy-metal-associated (HMA) family plays a major role in the transportation of metals. Despite having the genome sequence of the tomato (Solanum lycopersicum), the HMA gene family has not been studied yet. In this study, we identified 48 HMA genes and categorized them into Cu/Ag P1B-ATPase and Zn/Co/Cd/Pb P1BATPase sub-families according to their phylogenic relationship with Arabidopsis and rice. The SlHMA genes were distributed throughout the 12 chromosomes. Analysis of gene structure, chromosomal position, and synteny, revealed that segmental duplications bestowed their evolution. The high numbers of stress-related cis-elements were found to be present in the putative promoter regions indicate the involvement of SlHMAs in stress modulation pathways. RNA-seq data revealed that SlHMAs had divergent expression in different tissues and developmental stages, where members of Cu/Ag P1B-ATPase subfamily were strongly expressed in the roots. RT-qPCR analysis of nine selected SlHMAs showed that most of the genes were up-regulated in response to heavy metals and moderately regulated in response to different abiotic stresses such as salt, drought, and cold.

Plant Gene Modification by BAC Recombineering.

Recombineering approaches exploiting the bacteriophage λ Red recombination functions are widely used for versatile modification of eukaryotic genes carried by bacterial artificial chromosomes (BACs) in E. coli. Whereas BAC transformation provides a simple means for integration of modified genes into the genomes of animal cells to generate knock-in and knockout lines, successful application of this strategy is hampered by low frequency of homologous recombination in higher plants. However, plant cells can be transformed at a high frequency using the transferred DNA (T-DNA) of Agrobacterium, which is stably and randomly integrated into the plant genome. The function of plant genes that are modified by recombineering and transferred by Agrobacterium T-DNA vectors into plant cells can thus be suitably studied using genetic complementation of knockout mutations induced by either T-DNA insertions or genome editing with T-DNA-based Crisp/Cas9 constructs. Here we describe two recombineering protocols for modification and transfer of plant genes from BACs into Agrobacterium T-DNA plant transformation vectors. The first protocol uses a conditional suicide ccdB gene cassette to assist the genetic complementation assays by generation of point mutations, deletions, and insertions at any gene position. The second "turbo"-recombineering protocol exploits various I-SceI insertion cassettes for fusing of fluorescent protein tags to the plant gene products to facilitate the characterization of their in vivo interacting partners by affinity purification, mass spectrometry, and cellular localization studies.

Glyoxalase III enhances salinity tolerance through reactive oxygen species scavenging and reduced glycation.

Methylglyoxal (MG) is a metabolically generated highly cytotoxic compound that accumulates in all living organisms, from Escherichia coli to humans, under stress conditions. To detoxify MG, nature has evolved reduced glutathione (GSH)-dependent glyoxalase and NADPH-dependent aldo-keto reductase systems. But both GSH and NADPH have been reported to be limiting in plants under stress conditions, and thus detoxification might not be performed efficiently. Recently, glyoxalase III (GLY III)-like enzyme activity has been reported from various species, which can detoxify MG without any cofactor. In the present study, we have tested whether an E. coli gene, hchA, encoding a functional GLY III, could provide abiotic stress tolerance to living systems. Overexpression of this gene showed improved tolerance in E. coli and Saccharomyces cerevisiae cells against salinity, dicarbonyl, and oxidative stresses. Ectopic expression of the E. coli GLY III gene (EcGLY-III) in transgenic tobacco plants confers tolerance against salinity at both seedling and reproductive stages as indicated by their height, weight, membrane stability index, and total yield potential. Transgenic plants showed significantly increased glyoxalase and antioxidant enzyme activity that resisted the accumulation of excess MG and reactive oxygen species (ROS) during stress. Moreover, transgenic plants showed more anti-glycation activity to inhibit the formation of advanced glycation end product (AGE) that might prevent transgenic plants from stress-induced senescence. Taken together, all these observations indicate that overexpression of EcGLYIII confers salinity stress tolerance in plants and should be explored further for the generation of stress-tolerant plants.

Evolution, family expansion, and functional diversification of plant aldehyde dehydrogenases.

Aldehyde dehydrogenases (ALDHs) act as "aldehyde scavengers" in plants, eliminating reactive aldehydes and hence performing a crucial part in response to stress. ALDH has been specified multiple activities since its identification in the mammalian system 72 years ago. But the most widely researched role in plants is their engagement in stress tolerance. Multiple ALDH families are found in both animals and plants, and many genes are substantially conserved within these two evolutionary diverse taxa, yet both have their unique members/families. A total of twenty-four ALDH protein family has been reported across organisms, where plants contain fourteen families. Surprisingly, the number of genes in the ALDH superfamily has risen in the higher plants because of genome duplication and expansion, indicating the functional versatilely. Observed expansion in the ALDH isoforms might provide high plasticity in their actions to achieve diversified roles in the plant. The physiological importance and functional diversity of ALDHs including plant development and environmental stress adaptability, and their evolution in plants has been studied extensively. Future investigations need to focus on evaluating the individual and interconnecting function of multiple ALDH isoforms across organisms in providing plants with proper development, maturation, and adaptability against harsh environmental conditions.

Investigating the possible origin and transmission routes of SARS-CoV-2 genomes and variants of concern in Bangladesh.

The COVID-19 pandemic induced by the SARS-CoV-2 virus and its variants has ravaged most countries around the world including Bangladesh. We have analyzed publicly available genomic data to understand the current COVID-19 outbreak scenario as well as the evolutionary origin and transmission routes of SARS-CoV-2 isolates in Bangladesh. All the early isolates as well as recent B.1.1.7 and B.1.351 variants had already spread across the major divisional cities of Bangladesh. A sex biasness towards male COVID-19 patient samples sequencing has been observed over female patient samples in all age-group, that could be the trend in infection rate. Phylogenetic analysis indicated a total of 13 estimated countries, including Italy, India, United Kingdom, Saudi Arabia, United Arab Emirates, Germany, Australia, New Zealand, South Africa, Democratic Republic of the Congo, United States, Russia, and Denmark, could be the possible origin introduced SARS-CoV-2 isolates in Bangladesh because of regional and intercontinental travel. Recent, B.1.1.7 variant could be imported from a total of 7 estimated countries including UK, India, Nigeria, Spain, Ireland, Australia, and Indonesia, while South Africa and the United States are the most likely sources of B.1.351 variant in Bangladesh. Based on these findings, public health strategies could be designed and implemented to reduce the local transmission of the virus.

Genome-wide identification, evolution, and transcript profiling of Aldehyde dehydrogenase superfamily in potato during development stages and stress conditions.

The Aldehyde dehydrogenase (ALDH) superfamily comprises a group of enzymes involved in the scavenging of toxic aldehyde molecules by converting them into their corresponding non-toxic carboxylic acids. A genome-wide study in potato identified a total of 22 ALDH genes grouped into ten families that are presented unevenly throughout all the 12 chromosomes. Based on the evolutionary analysis of ALDH proteins from different plant species, ALDH2 and ALDH3 were found to be the most abundant families in the plant, while ALDH18 was found to be the most distantly related one. Gene expression analysis revealed that the expression of StALDH genes is highly tissue-specific and divergent in various abiotic, biotic, and hormonal treatments. Structural modelling and functional analysis of selected StALDH members revealed conservancy in their secondary structures and cofactor binding sites. Taken together, our findings provide comprehensive information on the ALDH gene family in potato that will help in developing a framework for further functional studies.

Identification and expression profiling of proline metabolizing genes in Arabidopsis thaliana and Oryza sativa to reveal their stress-specific transcript alteration.

The amino acid, proline, is utilized by different organisms to offset cellular imbalances caused by environmental stresses. The wide use of proline as a stress adaptor molecule indicates that proline has a fundamental biological role in stress response. A comprehensive analysis of the transcript abundance of proline metabolizing genes is fundamental for the assessment of function and regulation of each gene. Using available microarray data and quantitative real-time RT-PCR, the expression profiles of gene encoding key proline biosynthesis and degradation enzymes i.e., OAT, P5CS, P5CR and PDH were examined. Interestingly, validation of candidate genes in rice using in-silico data provided strong evidence for their involvement in stress response. Note that, OsOAT, OsP5CS1, OsP5CS2, OsP5CR showed similar expression pattern in quantitative real-time RT-PCR results as compared to microarray data. However, OsPDH showed a different expression pattern which may be due to the genotypic variation. Furthermore, a biochemical assay measuring proline content gave us a proper indication of the accumulation of proline under stressed conditions. Identification of key proline metabolizing genes from rice and Arabidopsis provides insights on the molecular regulation of proline homeostasis, to initiate metabolic engineering to develop stress-resilient plants. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-01023-0.

Genome-wide identification and expression profiling of glutathione S-transferase family under multiple abiotic and biotic stresses in Medicago truncatula L.

Glutathione transferases (GSTs) constitute an ancient, ubiquitous, multi-functional antioxidant enzyme superfamily that has great importance on cellular detoxification against abiotic and biotic stresses as well as plant development and growth. The present study aimed to a comprehensive genome-wide identification and functional characterization of GST family in one of the economically important legume plants-Medicago truncatula. Here, we have identified a total of ninety-two putative MtGST genes that code for 120 proteins. All these members were classified into twelve classes based on their phylogenetic relationship and the presence of structural conserved domain/motif. Among them, 7 MtGST gene pairs were identified to have segmental duplication. Expression profiling of MtGST transcripts revealed their high level of organ/tissue-specific expression in most of the developmental stages and anatomical tissues. The transcripts of MtGSTU5, MtGSTU8, MtGSTU17, MtGSTU46, and MtGSTU47 showed significant up-regulation in response to various abiotic and biotic stresses. Moreover, transcripts of MtGSTU8, MtGSTU14, MtGSTU28, MtGSTU30, MtGSTU34, MtGSTU46 and MtGSTF8 were found to be highly upregulated in response to drought treatment for 24h and 48h. Among the highly stress-responsive MtGST members, MtGSTU17 showed strong affinity towards its conventional substrates reduced glutathione (GSH) and 1-chloro-2,4-dinitrobenzene (CDNB) with the lowest binding energy of-5.7 kcal/mol and -6.5 kcal/mol, respectively. Furthermore, the substrate-binding site residues of MtGSTU17 were found to be highly conserved. These findings will facilitate the further functional and evolutionary characterization of GST genes in Medicago.

Genome-wide in silico identification and characterization of Simple Sequence Repeats in diverse completed SARS-CoV-2 genomes.

Simple sequence repeats (SSRs) or, Microsatellites are short repeat sequences that have been extensively studied in eukaryotic (plants) and prokaryotic (bacteria) organisms. Compared to other organisms, the presence and incidence of SSR on viral genomes are less studied. With the emergence of novel infectious viruses over the past few decades, it is imperative to study the genetic diversity in such viruses to predict their evolutionary and functional changes over time. Following the emergence of SARS-CoV-2, we have assembled 121 complete genomes reported from 31 countries across the six continents for the identification and characterization of SSR repeats. Using two independent SSR identification tools, we have found remarkable consistency in the diversity of microsatellites pattern (38-42 per genome) found in the 121 analyzed SARS-CoV-2 genomes indication their important role for genome stability. Among the identified motifs, trinucleotide and hexanucleotide repeats were found to be the most abundant form followed by mono- and di-nucleotide. There were no tetra- or penta-nucleotide repeats in the analyzed SARS-CoV-2 genomes. The discovery of microsatellites in SARS-CoV-2 genomes may become useful for the population genetics, evolutionary analysis, strain identification and genetic variation.

Impact of Lockdown Measures and Meteorological Parameters on the COVID-19 Incidence and Mortality Rate in Bangladesh.

The coronavirus disease 2019 (COVID-19) pandemic has become a public health crisis and a global catastrophe for human societies. In the absence of a vaccine, non-pharmaceutical interventions have been implemented across the world to reduce COVID-19 transmission. Recently, several studies have articulated the influence of meteorological parameters on COVID-19 infections in several countries. The purpose of this study was to investigate the effect of lockdown measures and meteorological parameters on COVID-19 daily confirmed cases and deaths in Bangladesh. Different parameters, such as case fatality rate, recovery rate, number of polymerase chain reaction tests, and percentages of confirmed cases were calculated for data covering March to September 2020. The meteorological data include daily average temperature, humidity, and wind speed, and their effects on COVID-19 data were analyzed after 0, 3, 7, and 14 days. A linear regression analysis revealed that all the studied meteorological parameters were positively correlated with the daily new cases and deaths in Bangladesh, while the highest correlations were observed for the 14 days incubation period. These results provide useful implications for the healthcare authorities to contain the pandemic in Bangladesh and beyond.