A comprehensive analysis of NAC gene family in Oryza sativa japonica: a structural and functional genomics approach.

NAC gene family regulates diverse aspects of plant growth and developmental processes. The NAC DNA binding domains together with cis-acting elements play inter-related roles in regulating gene expression. In this study, an in silico approach for genome wide analysis of NAC gene in Oryza sativa japonica lead to an identification of 11 NAC genes, distributed over 12 chromosomes. A detailed analysis of phylogenetic relationship, motifs, gene structure, duplication patterns, positive-selection pressure and cis-elements of 11 OsNAC genes were performed. Three pairs of NAC genes with a high degree of homology in terminal nodes were observed and were inferred to be paralogous pairs. One conserved NAC domain was analyzed in all the NAC proteins. Only one gene was studied to be intronless and the majority had 2 introns. Segmental gene duplication pattern was predominant in 11 NAC genes. Ka/Ks ratio of 3 pairs of segmentally duplicated gene was substantially lower than 1, suggesting that the OsNAC sequences are under strong purifying selection pressure. NAC74 and NAC71 gene showed the maximum responsiveness for several factors. The paralogous genes, NAC2 and NAC67 were found to have maximum mya values, respectively. They showed maximum difference amongst themselves in all the categories of responsiveness. Responsiveness towards abscisic acid was observed to be absent in NAC67, but present in NAC2, while responsiveness to meristem inducibility was observed to remain absent in NAC2 but present in NAC67. These results would provide a platform for the future identification and analysis of NAC genes in Oryza sativa japonica.Communicated by Ramaswamy H. Sarma.

Dengue Associated Demyelinating Disorders - A Report of 2 Cases.

Dengue is a common viral infection worldwide, though its neurological manifestations are infrequent (2%-11% in recent years) and can be varied as the Dengue virus per se is a non-neurotropic virus. Neurological manifestations of Dengue usually result from multisystem dysfunction which may be secondary to vascular leak or it can be due to direct virus invasion (dengue encephalitis) or an immunological phenomenon which is triggered by dengue infection (demyelinating disorders). Here we present two cases of dengue fever associated demyelinating disorders in two pediatric patients aptly depicting the two spectra of the disease. One of them is a case of fatal acute hemorrhagic leukoencephalopathy (AHLE) in a 3-year-old girl, that developed severe neurological sequelae while the other one is a case of an Acute disseminated Encephalomyelitis (ADEM) in a 3-year-old boy who had recovered with timely immunomodulatory therapy and appropriate management.

Randomized trial of high-dose pyridoxine in combination with standard hormonal therapy in West syndrome.

OBJECTIVE: To determine whether high-dose, oral pyridoxine in combination with standard adrenocorticotropic hormone (ACTH) therapy has superior effectiveness than ACTH therapy alone in increasing cessation of epileptic spasms for children with West syndrome. METHODS: This study was an open-label, randomized controlled trial with masked endpoint assessments. Eligible children with West syndrome, age ranged 3-18 months, were randomized into the intervention (n = 43) and the standard arm (n = 37) of therapy. The intervention group received oral pyridoxine at 100-300 mg/kg/day in addition to standard therapy of intramuscular ACTH at 150 IU/m2/day. Primary effectiveness outcome was a complete cessation of spasms at two weeks and sustained till six weeks. RESULTS: Comparison of effectiveness measures between intervention and standard groups were : complete cessation of epileptic spasms (48.8% vs 58.3%; group difference -9.6%; 95% confidence interval [CI] -30% to 12.3%; p = 0.4), median EEG scores (Q1-Q3) by Jeavons Score at six weeks [3 (1-5) vs 3 (1-5); p = 0.6], median motor scores (Q1-Q3) by DASII (Development Assessment Scales for Indian Infants) at 12 weeks [35 (29-49) vs 42 (34.3-63.8), p = 0.04], and median mental scores (Q1-Q3) by DASII at 12 weeks [35 (29.5-46) vs 41.5 (31.3-60), p = 0.02]. Adverse events were comparable in both arms. CONCLUSIONS: There was no evidence to suggest the superiority of high-dose pyridoxine in combination with ACTH versus ACTH alone for the treatment of West syndrome, considering the limitations of the study design.

Development of new vaccine target against SARS-CoV2 using envelope (E) protein: An evolutionary, molecular modeling and docking based study.

COVID-19 is one of the fatal pandemic throughout the world. For cellular fusion, its antigenic peptides are presented by major histocompatibility complex (MHC) in humans. Therefore, exploration into residual interaction details of CoV2 with MHCs shall be a promising point for instigating the vaccine development. Envelope (E) protein, the smallest outer surface protein from SARS-CoV2 genome was found to possess the highest antigenicity and is therefore used to identify B-cell and T-cell epitopes. Four novel mutations (T55S, V56F, E69R and G70del) were observed in E-protein of SARS-CoV2 after evolutionary analysis. It showed a coil➔helix transition in the protein conformation. Antigenic variability of the epitopes was also checked to explore the novel mutations in the epitope region. It was found that the interactions were more when SARS-CoV2 E-protein interacted with MHC-I than with MHC-II through several ionic and H-bonds. Tyr42 and Tyr57 played a predominant role upon interaction with MHC-I. The higher ΔG values with lesser dissociation constant values also affirm the stronger and spontaneous interaction by SARS-CoV2 proteins with MHCs. On comparison with the consensus E-protein, SARS-CoV2 E-protein showed stronger interaction with the MHCs with lesser solvent accessibility. E-protein can therefore be targeted as a potential vaccine target against SARS-CoV2.

ADSL Deficiency - The Lesser-Known Metabolic Epilepsy in Infancy.

Adenylosuccinate lyase deficiency is a rare inherited disorder of purine metabolism causing severe neurological impairment ranging from early-onset neonatal epileptic encephalopathy to progressive psychomotor retardation and autism in later life. Diagnostic workup involves the measurement of toxic succinyl purines in body fluids and gene sequencing. The authors describe a 13-mo-old girl with compound heterozygous variants in the ADSL gene, presenting as early-onset seizures, severe neurological impairment, development delay, and hypotonia. Neuroimaging revealed cerebral atrophy, delayed myelination and diffusion restriction in bilateral basal ganglia, thalamus and periventricular white matter. The present case highlights ADSL deficiency as a rare cause of metabolic epilepsy that needs timely recognition and prevention of unnecessary investigations.

Exploring Single Nucleotide Polymorphisms in ITGAV for Gastric, Pancreatic and Liver Malignancies: An Approach Towards the Discovery of Biomarker.

BACKGROUND: Integrin αV, encoded by ITGAV gene, is one of the most studied protein subunits, closely associated with liver, pancreatic and stomach cancer progression and metastasis via regulation of angiogenesis. The occurrence of Single Nucleotide Polymorphisms (SNPs) in cancer- associated proteins is a key determinant for varied susceptibility of an individual towards cancer. METHODOLOGY: The study investigated the deleterious effects of these cancer-associated SNPs on the protein's structure, stability and cancer causing potential using an in silico approach. Numerous computational tools were employed that identified the most deleterious cancer-associated SNPs and those to get actively involved in post-translational modifications. The impact of these SNPs on the protein structure, function and stability was also examined. Conclusion and Future Scope: A total 63 non-synonymous SNPs in ITGAV gene were observed to be associated in these three gastrointestinal cancers and among this, 63, 19 were the most deleterious ones. The structural and functional importance of residues altered by most damaging SNPs was analyzed through evolutionary conservation and solvent accessibility. The study also elucidated three-dimensional structures of the 19 most damaging mutants. The analysis of conformational variation identified 5 SNPs (D379Y, G188E, G513V, L950P, and R540L) in integrin αV, which influence the protein's structure. Three calcium binding sites were predicted at residues: D379, G384 and G408 and a peptide binding site at residue: R369 in integrin αV. Therefore, SNPs D379Y, G384C, G408R and R369W have the potential to alter the binding properties of the protein. Screening and characterization of deleterious SNPs could advance novel biomarker discovery and therapeutic development in the future.

Structural impact due to PPQEE deletion in multiple cancer associated protein - Integrin αV: An In silico exploration.

A heterodimeric receptor subunit, Integrin αV, often complexed with Integrin ß3 plays a vital role in cell signaling to regulate angiogenesis and promote cancer progression. The paramount ß-turn formed from pentapeptide residues (PPQEE) in the cytoplasmic domain of Integrin αV was previously reported as crucial for cell signaling and its deletion was proved deleterious for protein's cell membrane adhesion and ligand binding properties. This study revealed conformational changes in the Integrin αV subunit upon deletion of PPQEE residues through in silico structural modelling approach followed by analysis of alteration of binding sites. Human Protein Atlas database helped to identify the association of Integrin αV to the unfavourable prognosis of three gastrointestinal cancers: stomach, liver and pancreatic cancers. Molecular modelling and docking techniques were carried out for the necessary complex formations (wild-type and mutant-type). Further comparison was performed for the complexes. The changes in protein's conformation and stability due to PPQEE deletion were observed in both independent subunit and heterodimer. The most noteworthy conformational shift was the disruption of a transmembrane helix into coil, which accounted for protein's impaired cell membrane adhesion, increased solvent accessibility and decreased stability. The deletion also caused a reduction of beta-turn regions, which disrupted ligand binding in the cytoplasmic domain of Integrin αV subunit. This study emphasized on structural basis of how the deletion of PPQEE residues alters stability, ligand binding and signaling activity of Integrin αV subunit highlighting the importance of these residues in maintenance of protein's native structure.

Identification of novel therapeutic target and epitopes through proteome mining from essential hypothetical proteins in Salmonella strains: An In silico approach towards antivirulence therapy and vaccine development.

Salmonella strains are responsible for a huge mortality rate through foodborne ailment in the world that necessitated the discovery of novel drugs and vaccines. Essential hypothetical proteins (EHPs), whose structures and functions were previously unknown, could serve as potential therapeutic and vaccine targets. Antivirulence therapy shall emerge as a superior therapeutic approach that uses virulence factors as drug targets. This study annotated the biological functions of 96 out of total 106 essential hypothetical proteins in five strains of Salmonella and classified into nine important protein categories. 34 virulence factors were predicted among the EHPs, out of which, 11 were identified to be pathogen specific potential drug targets for antivirulence therapy. These targets were non-homologous to both human and gut microbiota proteome to avoid cross-reactivity with them. Seven identified targets had druggable property, while the rest four targets were novel targets. Four identified targets (DEG10320148, DEG10110027, DEG10110040 and DEG10110142) had antigenic properties and were further classified as: two membrane-bound Lipid-binding transmembrane proteins, a Zinc-binding membrane protein and an extracellular glycosylase. These targets could be potentially used for the development of subunit vaccines. The study further identified 11 highly conserved and exposed epitope sequences from these 4 vaccine targets. The three-dimensional structures of the vaccine targets were also elucidated along with highlighting the conformation of the epitopes. This study identified potential therapeutic targets for antivirulence therapy against Salmonella. It would therefore instigate in novel drug designing as well as provide important leads to new Salmonella vaccine development.

In Silico Drug Target Discovery Through Proteome Mining from M. tuberculosis: An Insight into Antivirulent Therapy.

AIM AND OBJECTIVE: One of the challenges to conventional therapies against Mycobacterium tuberculosis is the development of multi-drug resistant pathogenic strains. This study was undertaken to explore new therapeutic targets for the revolutionary antivirulence therapy utilizing the pathogen's essential hypothetical proteins, serving as virulence factors, which is the essential first step in novel drug designing. METHODS: Functional annotations of essential hypothetical proteins from Mycobacterium tuberculosis (H37Rv strain) were performed through domain annotation, Gene Ontology analysis, physicochemical characterization and prediction of subcellular localization. Virulence factors among the essential hypothetical proteins were predicted, among which pathogen-specific drug target candidates, non-homologous to human and gut microbiota, were identified. This was followed by druggability and spectrum analysis of the identified targets. RESULTS AND CONCLUSION: The study successfully assigned functions of 83 essential hypothetical proteins of Mycobacterium tuberculosis, among which 25 were identified as virulence factors. Out of 25, 12 virulence factors were observed as potential pathogen-specific drug target candidates. Nine potential targets had druggable properties and rest three were considered as novel targets. Exploration of these targets will provide new insights into future drug development. Characterization of subcellular localizations revealed that most of the predicted targets were cytoplasmic which could be ideal for intracellular drugs, while two drug targets were membranebound, ideal for vaccines. Spectrum analysis identified one broad-spectrum and 11 narrowspectrum targets. This study would, therefore, instigate designing novel therapeutics for antivirulence therapy, which have the potential to serve as revolutionary treatment instead of conventional antibiotic therapies to overcome the lethality of antibiotic-resistant strains.

Detailed Molecular Biochemistry for Novel Therapeutic Design Against Nipah and Hendra Virus: A Systematic Review.

BACKGROUND: Nipah virus (NiV) and Hendra virus (HeV) of genus Henipavirus are the deadliest zoonotic viruses, which cause severe respiratory ailments and fatal encephalitis in humans and other susceptible animals. The fatality rate for these infections had been alarmingly high with no approved treatment available to date. Viral attachment and fusion with host cell membrane is essential for viral entry and is the most essential event of viral infection. Viral attachment is mediated by interaction of Henipavirus attachment glycoprotein (G) with the host cell receptor: Ephrin B2/B3, while viral fusion and endocytosis are mediated by the combined action of both viral glycoprotein (G) and fusion protein (F). CONCLUSION: This review highlights the mechanism of viral attachment, fusion and also explains the basic mechanism and pathobiology of this infection in humans. The drugs and therapeutics used either experimentally or clinically against NiV and HeV infection have been documented and classified in detail. Some amino acid residues essential for the functionality of G and F proteins were also emphasized. Therapeutic designing to target and block these residues can serve as a promising approach in future drug development against NiV and HeV.

Structural, functional, and evolutionary analysis of late embryogenesis abundant proteins (LEA) in Triticum aestivum: A detailed molecular level biochemistry using in silico approach.

LEA (Late Embryogenesis Abundant) proteins are abundant in plants and play a crucial role in abiotic stress tolerance. In our work, we primarily focused on the variations in physiochemical properties, conserved domains, secondary structure, gene ontology and evolutionary relationships among 40 LEA proteins of Triticum aestivum (common wheat). Wheat LEA protein belongs to first 6 classes out of the 13 classes present in LEApdB, the comprehensive database for LEA proteins. Proteins belonging to each LEApdB class have structures and functions distinguished from other classes. The study found three different conserved LEA domains in Triticum aestivum. One important domain was dehydrin, present in wheat proteins of classes 1, 2 and 4, though varied in sequence level, have similar biological processes. The study also found sequence level and phylogenetic similarity between dehydrin domains of class 1 and 4, but distinct from that of LEApdB class 2. This study also demonstrated functional diversity in two class 6 proteins occurred due to many destabilizing mutations in the LEA4 domain that caused alteration of ligand binding and conformational shift from 310-helix → turn within the domain. The LEA4 domains of these proteins also showed functional similarity and evolutionary relatedness with three other proteins of genus Aegilops, denoting that these proteins in Triticum aestivum were derived from its ancestor Aegilops. The study also assigned LEApdB class 4 to an unclassified LEA protein 'WZY2-1' based on amino acid composition, conserved domain, motif architecture and phylogenetic relatedness with class 4 proteins. Our study has revealed a detailed analysis of LEA proteins in Triticum aestivum and can serve as a pillar for further investigations and comparative analysis of wheat LEA proteins with other cereal or plant types.

Molecular interactions and mutational impact upon rhodopsin (G90→D90) for hindering dark adaptation of eye: A comparative structural level outlook for signaling mechanism in night blindness.

For night blindness, a detailed structural exploration of the interactions among G-protein receptor rhodopsin, transducin and arrestin was performed. Rhodopsin is responsible for dim light vision while a point mutation (G90→D90) results in an adverse change in its photo-transduction. The validated 3D models of the three proteins were utilized, and upon mutation and interactions, rhodopsin attained higher stability (evaluated through thermodynamic energy calculations, electrostatic surface potential and solvent accessible area), thereby participating strongly with transducin. Conformational switches in mutated rhodopsin also depicted a firm conformation with few 310 helices accompanied by increased percentage of pure α-helices and sheets. All evaluations were corroborated through paired T-tests. Glu33 (glycosylated unit in the N-terminal zone) of rhodopsin plays a chief role in the overall interaction pattern. Arg69 and Glu33 from wild-type rhodopsin participated in ionic interactions, while the latter set of ionic interaction remained preserved even after mutation. Cys323 (C-terminal residue) and Arg69 formed H-bonds from the wild-type rhodopsin. Cys323 exceptionally supports cellular signaling pattern in the non-mutated situation and for the non-sufferers of night-blindness. Ser297 and Tyr43 from mutated rhodopsin reside in helices and interact with Thr32 of transducin, preserving the steady conformation in activated interacted state, even in the dark. Ser297 lies adjoined to Lys296 (retinal attachment site), which resides in NPXXY motif (an "activation switch" for signal transduction). Thus, the molecular facet for involvement of photo-transduction, which holds a paramount zone in ophthalmology, was dealt with. This might instigate the future prospect for drug discovery to prevent such mutations.

Acute disseminated encephalomyelitis: complication of a vaccine preventable disease.

Acute disseminated encephalomyelitis (ADEM) is a rare inflammatory-demyelinating disease of central nervous system. Several viral infections and vaccines act as precipitating factor for ADEM. We report an 8-year-old girl presenting with acute-onset flaccid paraparesis and bilateral painless vision loss. MRI brain showed extensive multifocal patchy demyelination and she made good clinical recovery with steroids and intravenous immunoglobulin therapy. She had history of bilateral parotid swelling before the onset of neurological symptoms and diagnosis of mumps was confirmed by positive ELISA in serum. Mumps, usually a benign and self-limited viral infection, rarely can cause severe neurological complications. Hence, we report this case to emphasise the importance of mumps vaccination and the need to strengthen the health policy system for the prevention of disease.

Mutations and functional analysis of 14-3-3 stress response protein from Triticum aestivum: An evolutionary analysis through in silico structural biochemistry approach.

Wheat (Triticum aestivum), having high nutritional values is one of the staple food of most of the countries in the world. The productivity of the crop decreases drastically when it encounters various abiotic stresses, most common of which are heat, drought, flood and salinity. There is a crucial role of stress response proteins for the survival of the crops in stress conditions. So the study of wheat stress response proteins is of great importance to raise wheat production in different stress conditions. In this study, we analysed 14-3-3 protein, a stress response protein that is expressed in three major stresses, for example heat, drought and salinity and helps the plants to survive in those conditions. Effect of mutations in the 14-3-3 sequence was predicted using its domain, secondary structure and multiple sequence alignment of amino acid sequences from wheat and its related species. The functional diversity of the protein in different species was correlated with mutations, change in secondary structure and the evolutionary relatedness of the protein in different species. This is the first novel work for analysing the mutational effect on the structure and function of a stress response protein (14-3-3) from Triticum aestivum and its related species.