African Swine Fever (ASF) causes severe economic losses in the global pig industry, characterized by high mortality rates and lack of an effective vaccine. Interestingly, India's indigenous Doom pig breed has displayed tolerance to ASF, remaining seropositive without detectable viremia. This study investigated the genetic basis of ASFV tolerance, focusing on the STING1 gene, a key component of the cGAS-STING antiviral signaling pathway. In-silico docking identified a potential ASFV protein binding site within exon 5 of STING1. A non-synonymous SNP (CGG/TGG; R→W) at position 148 in this region was selected for genotyping. We genotyped 119 pigs, representing tolerant (Doom), susceptible, and ASFV-infected groups, using allele-specific PCR and Sanger sequencing. Doom pigs and most other breeds, including ASFV-infected samples, displayed a conserved GG genotype. Susceptible Manipuri Black and Ghoongroo pigs, however, displayed both AA and GG genotypes, yet still succumbed to the disease. A significant downregulation (0.436-fold) of STING1 was observed in ASFV-infected spleen tissue, indicating active immune evasion by the virus. The lack of a unique allele in Doom pigs compared to susceptible breeds indicates that ASFV tolerance is unlikely to be associated with this STING1 SNP. Therefore, genome-wide studies are recommended to identify markers truly associated with ASFV tolerance in this resilient breed.

African Swine Fever (ASF) is a highly contagious transboundary viral disease affecting domestic pigs worldwide, often resulting in nearly 100 % mortality due to the lack of effective vaccines. However, wild species such as warthogs (Phacochoerus sp.) and bush pigs (Potamochoerus sp.) do not exhibit clinical symptoms of the disease, previous studies showed that amino acid substitutions in a proto-oncogene, RelA, a subunit of NF-κB found in warthogs might be responsible for their resistance. Expanding this study over an Indian breed named Doom which was considered tolerant due to lack of much information regarding their ASFV-positive cases and identifying the genetic basis of tolerance might help in creating a tolerant breed, thereby controlling the spread of the disease. So, this study was initiated to investigate the polymorphic signature in RelA gene of Doom breed similar to warthogs. Initially molecular docking studies identified a potential interaction between the N-terminal sub-domain of Rel homology domain of porcine RELA and the African Swine Fever Viral (ASFV) protein A238L, a hypothetical viral protein of unknown function. This amino acid interaction corresponds to a nucleotide sequence of exon 10 of porcine RelA gene. Further, ARMS-PCR (Amplification Refractory Mutation System-PCR) and PCR-RFLP (Restriction Fragment Length Polymorphism) were optimized to target a single nucleotide polymorphism (SNP, CCT/GCT: Pro→Ala) identified in the exon 10 region through Ensemble genome browser. PCR results showed the presence of homozygous CC genotype, coding for proline, in all pig breeds tested, including Doom. Sanger sequencing confirmed the CC genotype across all breeds, indicating that amino acid substitutions in this RELA domain were not present in Doom and therefore may not be responsible for ASF tolerance. Since disease tolerance is a polygenic trait relying on one gene might not reveal the exact cause for their tolerance against ASFV. Future research can be targeted on other set of genes playing important role in innate immune pathways or Genome Wide Association Study can be preferred to identify and associate SNPs with Doom's tolerance against ASFV.

Background: Endometriosis is a chronic inflammatory condition of high incidence and with serious consequences. Several synthetic compounds proved to be useful in treating its symptoms by inhibiting aromatase, which is responsible for the pathogenesis of this painful illness. Nevertheless, synthetic drugs inflict several side effects, including headaches, osteoporosis, and so on. This scenario advocates the search for therapeutic formulations based on natural compounds. Thus, the present study was hypothesized to evaluate the comparative efficacy of the synthetic and natural drugs used in endometriosis, using the bioinformatics approach. Methods: CB-Dock was employed to perform molecular docking of the aromatase enzyme with two synthetic and three natural drugs for predicting their molecular interactions, and binding affinities. The curcumin-aromatase complex was further subjected to MD simulations to determine its stability, and to apply it to natural compound-based computer-aided drug discovery. Results: Curcumin was observed to dock with a greater binding interaction with aromatase. The RMSD profile, hydrogen bonds, and the RMSF and Rg values of the complex were stabilised after 50 ns, which was an indicator of the stable binding pose of the curcumin-aromatase complex. Conclusion: These in-silico findings are the basis for proposing that curcumin can be considered as a potential binding agent to inhibit the aromatase enzyme in the treatment of endometriosis. Molecular modelling and dynamics results suggest that curcumin and aromatase form a stable complex and that curcumin can be targeted as a drug in the treatment of endometriosis

African swine fever (ASF) has emerged as a threat to swine production worldwide. Evasion of host immunity by ASF virus (ASFV) is well understood. However, the role of ASFV in triggering oncogenesis is still unclear. In the present study, ASFV-infected kidney tissue samples were subjected to Illumina-based transcriptome analysis. A total of 2463 upregulated and 825 downregulated genes were differentially expressed (p < 0.05). A literature review revealed that the majority of the differentially expressed host genes were key molecules in signaling pathways involved in oncogenesis. Bioinformatic analysis indicated the activation of certain oncogenic KEGG pathways, including basal cell carcinoma, breast cancer, transcriptional deregulation in cancer, and hepatocellular carcinoma. Analysis of host-virus interactions revealed that the upregulated oncogenic RELA (p65 transcription factor) protein of Sus scrofa can interact with the A238L (hypothetical protein of unknown function) of ASFV. Differential expression of oncogenes was confirmed by qRT-PCR, using the H3 histone family 3A gene (H3F3A) as an internal control to confirm the RNA-Seq data. The levels of gene expression indicated by qRT-PCR matched closely to those determined through RNA-Seq. These findings open up new possibilities for investigation of the mechanisms underlying ASFV infection and offer insights into the dynamic interaction between viral infection and oncogenic processes. However, as these investigations were conducted on pigs that died from natural ASFV infection, the role of ASFV in oncogenesis still needs to be investigated in controlled experimental studies.

The present study aimed to generate antibodies against predicted B cell epitopic peptides encoding bAMH for developing different ELISA models. Sandwich ELISA was determined to be an excellent technique for assessing bAMH in bovine plasma based on sensitivity tests. The assay's specificity, sensitivity, inter- and intra-assay CV, recovery

This chapter deals with the topic of bioinformatics approaches applied to biology, essentially for the analysis and characterization of protein. Protein is a large and diverse class of biomolecules, involved in various functional and structural parts in all forms of life. Advances in the experimental techniques and computational methodology have facilitated a relevant understanding of the 3D arrangement of the protein structures and the molecular level insight of the protein function. The collective exponential growth of the solved 3D structures has been utilized extensively to develop an advanced computational program to classify the structure information in different hierarchical levels, to develop more accurate machine learning-based protocols for 3D-structure prediction and scoring function, and to understand the mysterious protein folding problem. This chapter discusses the state-of-the-art computational techniques oriented toward the protein structure and function prediction from the sequence. These methods, if used appropriately, can provide valuable indicators of protein structure and prediction.

The goal of this study was to compare the global gene expression profile in cardiac tissues of pig infected with porcine circovirus 2 (PCV2) to that of healthy cells. Since PCV2 infection causes severe cardiovascular lesions, the myocardial tissue model was chosen for this study. In High-throughput transcriptome analysis, DESeq2 and CLC genomics workbench analyses revealed a total of 196 significantly differentially expressed genes (DEGs) (p-value < 0.05). Furthermore, 194 transcripts were upregulated, while only two were downregulated (HSPA6 and DNAJA1), with fold changes ranging from 16.293 to -10.002. Among the KEGG canonical pathways targeted by the DEGs in the functional analysis, adrenergic signalling in cardiomyocytes, Cardiac Muscle Contraction, Hypertrophic Cardiomyopathy (HCM), and Dilated Cardiomyopathy (DCM) tends to be enriched. The differentially expressed highly connected (DEHC) biomarker genes in pathogenicity of PCV2 infection, such as LDB3, MYOZ2, CASQ2, TNNT2, MLC2V, MYBPC3, ACTC1, TCAP, TNNI3, TRDN, CSRP3, MYL3, RYR2, LMOD2, MYH7, etc., were identified using protein-protein interaction (PPI) network analysis. The study might provide detailed information on the dysregulated genes and biological pathways in infected myocardial tissues that may be essential for PCV2-related heart pathology.

In India, during the second wave of the COVID-19 pandemic, the breakthrough infections were mainly caused by the SARS-COV-2 delta variant (B.1.617.2). It was reported that, among majority of the infections due to the delta variant, only 9.8% percent cases required hospitalization, whereas only 0.4% fatality was observed. Sudden dropdown in COVID-19 infections cases were observed within a short timeframe, suggesting better host adaptation with evolved delta variant. Downregulation of host immune response against SARS-CoV-2 by ORF8 induced MHC-I degradation has been reported earlier. The Delta variant carried mutations (deletion) at Asp119 and Phe120 amino acids which are critical for ORF8 dimerization. The deletions of amino acids Asp119 and Phe120 in ORF8 of delta variant resulted in structural instability of ORF8 dimer caused by disruption of hydrogen bonds and salt bridges as revealed by structural analysis and MD simulation studies. Further, flexible docking of wild type and mutant ORF8 dimer revealed reduced interaction of mutant ORF8 dimer with MHC-I as compared to wild-type ORF8 dimer with MHC-1, thus implicating its possible role in MHC-I expression and host immune response against SARS-CoV-2. We thus propose that mutant ORF8 of SARS-CoV-2 delta variant may not be hindering the MHC-I expression thereby resulting in a better immune response against the SARS-CoV-2 delta variant, which partly explains the possible reason for sudden drop of SARS-CoV-2 infection rate in the second wave of SARS-CoV-2 predominated by delta variant in India.

Different human races across the globe responded in a different way to the SARS-CoV-2 infection leading to different disease severity. Therefore, it is anticipated that host genetic factors have a straight association with the COVID-19. We identified a total 6, 7, and 6 genomic loci for deceased-recovered, asymptomatic-recovered, and deceased-asymptomatic group comparison, respectively. Unfavourable alleles of the markers nearby the genes which are associated with lung and heart diseases such as Tumor necrosis factor superfamily (TNFSF4&18), showed noteworthy association with the disease severity and outcome for the COVID-19 patients in the western Indian population. The markers found with significant association with disease prognosis or recovery are of value in determining the individual's response to SARS-CoV-2 infection and can be used for the risk prediction in COVID-19. Besides, GWAS study in other populations from India may help to strengthen the outcome of this study.

Porcine reproductive and respiratory syndrome (PRRS) is an important economical disease in the global swine industry. The accurate detection of the PRRS virus (PRRSV) antigen is essential for the disease control and prevention programme. In this study, an indirect enzyme-linked immunosorbent test (PRRSVCD163-iELISA) was developed for the detection of the PRRSV antigen in samples of post-mortem swine tissue using the recombinant pig CD163 receptor protein as the capture ligand. The test was found to be specific for PRRSV, with no cross-reactions with other prevalent pig viral pathogens. The assay was validated by testing 217 post-mortem porcine tissue samples and the results were found to be satisfactory with a relative accuracy of 88.88%. Our assay is also quite precise, with intra- and inter-assay CVs of 6% and 10%, respectively. These findings imply that the PRRSVCD163-iELISA developed is capable of detecting the PRRSV antigen in swine post-mortem tissue samples. This research showed that porcine CD163, the PRRSV cellular receptor, can be exploited to build a diagnostic technique for the detection of PRRSV antigen.

In India, the breakthrough infections during second wave of COVID-19 pandemic was due to SARS-COV-2 delta variant (B.1.617.2). It was reported that majority of the infections were caused by the delta variant and only 9.8% percent cases required hospitalization whereas, only 0.4% fatality was observed. Sudden dropdown in COVID-19 infections was observed within a short timeframe, suggesting better host adaptation with evolved delta variant. Down regulation of host immune response against SARS-CoV-2 by ORF8 induced MHC-I degradation has been reported earlier. The Delta variant carried mutations (deletion) at Asp119 and Phe120 amino acids which are critical for ORF8 dimerization. The deletions of amino acids Asp119 and Phe120 in ORF8 of delta variant results in structural instability of ORF8 dimer caused by disruption of hydrogen bonding and salt bridges as revealed by structural analysis and MD simulation studies of ORF8 dimer. Further, flexible docking of wild type and mutant ORF8 dimer revealed reduced interaction of mutant ORF8 dimer with MHC-I as compared to wild type ORF8 dimer with MHC-1, thus implicating its possible role in MHC-I expression and host immune response against SARS-CoV-2. We thus propose that mutant ORF8 may not hindering the MHC-I expression thereby resulting in better immune response against SARS-CoV-2 delta variant, which partly explains the sudden drop of SARS-CoV-2 infection rate in the second wave of SARS-CoV-2 predominated by delta variant in India Graphical Abstract

Due to continuous anthropogenic activities and other natural changes, aquatic ecosystems are under increasing stress. Metagenomics aided by next-generation sequencing techniques provides in-depth insights into microbiome dynamics from multitude of aquatic resources thus contributes in understanding the physiological, metabolic, and ecological roles of microbial assemblies. Monitoring of diverse aquatic resources using metagenomics has the potential to efficiently characterize diverse range of microbiomes with relevant functional pathways. Contributions made by high-throughput second and third generation sequencing platforms are noteworthy in monitoring aquatic microbial biodiversity through characterization of genetic variations which is indicative of changing environmental adaptations. Analysis of sequence and function driven metagenomics enable elucidation of enzymatic pathways leading to the discovery of novel gene sequences with desired functions having ecological, industrial and pharmaceutical importance. This review seeks to define the role of metagenomics in exploring aquatic microbiota in terms of toxicological exposure, genome heterogeneity, assessment, and the management of aquatic ecosystem by utilizing microbial bio-indicators. We have also enlisted various high-throughput computational biology packages and tools exclusively used to handle metagenomic data along with the challenges and future perspectives. Owing to global climate change and massive human-induced alterations in aquatic ecosystems, we expect that the on-going whole-genome metagenomics studies in combination with "meta-OMICS" approaches would transform our comprehension of microbiome community structure, function and ecology at high resolution.

COVID-19 is a highly contagious viral infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is declared pandemic by the World Health Organization (WHO). The spike protein of SARS-CoV-2 is a key component playing a pivotal role in facilitating viral fusion as well as release of genome into the host cell. Till date there is no clinically approved vaccine or drug available against Covid-19. We designed four hydrophobic inhibitory peptides (ITPs) based on WWIHS (Wimley and White interfacial hydrophobicity scale) score, targeting the HR1 domain of spike protein. Two inhibitory peptides out of four have a strong affinity to the hydrophobic surface of HR1 domain in pre-fusion spike protein. The MD simulation result showed the strong accommodation of ITPs with HR1 domain surface. These self-inhibitory peptides mimic the function of HR2 by binding to HR1 domain, thus inhibiting the formation of HR1-HR2 post-fusion complex, which is a key structure for virus-host tropism.Communicated by Ramaswamy H. Sarma.

The WRKY family of transcription factors modulates the host defense mechanisms in response to various environmental stresses. The role of WRKY33 in plant defense and its crosstalk with defense hormone was well established in Arabidopsis but very few information was noted in Sinapis alba. The present study was carried out in 2017, in which computational approaches to characterize the structural and functional features of SaWRKY33 transcription factor was used. Full length WRKY33 coding sequence (1509 bp) from S. alba has been cloned, sequenced and identified as AtWRKY33 homolog. The expression of SaWRKY33 was scored higher in fungal pathogen challenged and jasmonate-treated samples while lower expression was noticed in salicylate-treated samples. Phylogenetic classification, sequence alignment and MEME-based motif scanning demonstrated the remarkable sequential conservation in the WRKY domains and SaWRKY33 clusters with Crambe abyssinica exhibiting the monophyletic origin and paraphyletic evolution from their wild relatives. STRING data showed SaWRKY33 were interacted with MKS1, MPK3, SIB1, and those are involved in plant defense responses against diverse stress conditions. The homology-based modeling of SaWRKY33 functional WRKY domains showed acceptable Ramachandran statistics and satisfies all the necessary energy parameters. The Hex Docking server-based analysis of DNA-protein interaction showed that WRKY domain binds to the W-box through WRKYGQK along with few conserved amino acid residues in the flanking sequences and zinc finger motifs.

•The effect of 50 µM exogenous sodium nitroprusside on rice cv. HUR 3022 exposed to 50 µM Cd was examined.•Cd alone led to increase in activity of antioxidant enzymes- guaiacol peroxidize, ascorbate peroxidase, glutathione reductase and production of reactive oxygen species.•Decreased level of antioxidants- glutathione and ascorbate was noted under Cd stress.•50 µM SNP-treatments to Cd-exposed rice lowered the activity of antioxidant enzymes and production of reactive oxygen species.•The decreased antioxidant levels under Cd-stress alone considerably recovered upon SNP treatment.

Cadmium is a well known toxic heavy metal, which has various detrimental effects on plant system. In plants an important enzyme involved in the production of nitric oxide, nitrate reductase, is also affected by cadmium toxicity. According to many studies cadmium has an inhibitory effect on nitrate reductase activity. Similar effect of cadmium was found in our study where an inhibitory effect of cadmium on nitrate reductase activity was noted. However, the mechanism behind this inhibition has not been explored. With the help of homology, 3-D structure of rice-nitrate reductase is modeled in this study. Its binding with nitrate, nitrite and cadmium metal in silico has been explored. The bonds formed between the enzyme-substrate complex, enzyme-cadmium and differences in interactions in presence of cadmium has been studied in detail. The present study should help in understanding the modeled structure of rice-nitrate reductase in 3-D which may in turn guide enzyme related studies in silico. The present study also provides an insight as to how cadmium interacts with nitrate reductase to alter the enzyme activity.

Terminal heat stress has detrimental effect on the growth and yield of wheat. Very limited information is available on heat stress-associated active proteins (SAAPs) in wheat. Here, we have identified 159 protein groups with 4271 SAAPs in control (22 ± 3 °C) and HS-treated (38 °C, 2 h) wheat cvs. HD2985 and HD2329 using iTRAQ. We identified 3600 proteins to be upregulated and 5825 proteins to be downregulated in both the wheat cvs. under HS. We observed 60.3% of the common SAAPs showing upregulation in HD2985 (thermotolerant) and downregulation in HD2329 (thermosusceptible) under HS. GO analysis showed proton transport (molecular), photosynthesis (biological), and ATP binding (cellular) to be most altered under HS. Most of the SAAPs identified were observed to be chloroplast localized and involved in photosynthesis. Carboxylase enzyme was observed most abundant active enzymes in wheat under HS. An increase in the degradative isoenzymes (α/β-amylases) was observed, as compared to biosynthesis enzymes (ADP-glucophosphorylase, soluble starch synthase, etc.) under HS. Transcript profiling showed very high relative fold expression of HSP17, CDPK, Cu/Zn SOD, whereas downregulation of AGPase, SSS under HS. The identified SAAPs can be used for targeted protein-based precision wheat-breeding program for the development of 'climate-smart' wheat.

The pattern of interactions between foot and mouth disease (FMD) viral protein 1 (VP1) with susceptible and resistant host integrins were deciphered. The putative effect of site-directed mutation on alteration of interaction is illustrated using predicted and validated 3D structures of VP1, mutated VP1 and integrins of Bos taurus, Gallus and Canis. Strong interactions were observed between FMDV-VP1 protein motifs at conserved tripeptide, Arg-Gly-Asp (143)RGD(145) and at domain (676)SIPLQ(680) in alpha-integrin of B. taurus. Notably, in-silico site-directed mutation in FMDV-VP1 protein led to complete loss of interaction between FMD-VP1 protein and B. taurus integrin, which confirmed the active role of arginine-glycine-aspartic acid (RGD) domain. Interestingly, in-vitro analysis demonstrates the persistence of the putative tropism site 'SIPLQ' in different cattle breeds undertaken. Thus, the attempt to decipher the tropism of FMDV at host receptor level interaction might be useful for future FMD control strategies through development of mimetic marker vaccines and/or host receptor manipulations. Communicated by Ramaswamy H. Sarma

In this paper, we are proposing a 1 bit full adder using multi-threshold complementary metal oxide semiconductor (MTCMOS) full adder. We have improved the figure of merit (Power Delay Product) of the proposed full adder and analyze it with other 12 different types of full adders. The simulation environment is cadence virtuoso in 45 nm technology using BSIM 4 model. Twelve different full adder cells, collected from the literature are evaluated and ranked using the framework, which ensures fair comparison basis. Apart from this we are using transistor sizing and critical path delay technique for the performance enhancement of all the full adders. In similarity with the existing full adder designs, the present proposed circuit was found to offer significant improvement in terms of power, speed and Power Delay Product (PDP).

MicroRNAs (miRNAs) are ~22nt long non-coding RNAs, which regulate the gene regulation at the post transcriptional level in both plants and animals. These miRNA are conserved in nature and hence potential base for new miRNA prediction through homology search. No miRNAs in this species are identified so far in economically important water buffalo (Bubalus bubalis). In this study, EST-based homology search, an established computational approach is used to find the potential miRNAs in buffalo. Six potential miRNA in buffalo were identified utilizing publicly available buffalo ESTs against the already known mature miRNAs of closely related species i.e. Bos taurus. Based on their sequence complementarity, target genes were identified which encode transcription factors (8%), enzymes (30%) and transporters (14%) as well as other proteins involved in physiological and metabolic processes (48%). These target genes also encode the proteins for signal transduction and normal development. This study will accelerate the way for further research on miRNAs and their functions in Bubalus bubalis.