In silico functional, structural and pathogenicity analysis of missense single nucleotide polymorphisms in human MCM6 gene.

Single nucleotide polymorphisms (SNPs) are one of the most common determinants and potential biomarkers of human disease pathogenesis. SNPs could alter amino acid residues, leading to the loss of structural and functional integrity of the encoded protein. In humans, members of the minichromosome maintenance (MCM) family play a vital role in cell proliferation and have a significant impact on tumorigenesis. Among the MCM members, the molecular mechanism of how missense SNPs of minichromosome maintenance complex component 6 (MCM6) contribute to DNA replication and tumor pathogenesis is underexplored and needs to be elucidated. Hence, a series of sequence and structure-based computational tools were utilized to determine how mutations affect the corresponding MCM6 protein. From the dbSNP database, among 15,009 SNPs in the MCM6 gene, 642 missense SNPs (4.28%), 291 synonymous SNPs (1.94%), and 12,500 intron SNPs (83.28%) were observed. Out of the 642 missense SNPs, 33 were found to be deleterious during the SIFT analysis. Among these, 11 missense SNPs (I123S, R207C, R222C, L449F, V456M, D463G, H556Y, R602H, R633W, R658C, and P815T) were found as deleterious, probably damaging, affective and disease-associated. Then, I123S, R207C, R222C, V456M, D463G, R602H, R633W, and R658C missense SNPs were found to be highly harmful. Six missense SNPs (I123S, R207C, V456M, D463G, R602H, and R633W) had the potential to destabilize the corresponding protein as predicted by DynaMut2. Interestingly, five high-risk mutations (I123S, V456M, D463G, R602H, and R633W) were distributed in two domains (PF00493 and PF14551). During molecular dynamics simulations analysis, consistent fluctuation in RMSD and RMSF values, high Rg and hydrogen bonds in mutant proteins compared to wild-type revealed that these mutations might alter the protein structure and stability of the corresponding protein. Hence, the results from the analyses guide the exploration of the mechanism by which these missense SNPs of the MCM6 gene alter the structural integrity and functional properties of the protein, which could guide the identification of ways to minimize the harmful effects of these mutations in humans.

Influence of Ca doping in structural, electronic, optical and mechanical properties of Ba1-xCaxTiO3 perovskite from first-principles investigation.

Nowadays, perovskite materials are well known for electronics and optoelectronics applications. We have investigated a potential candidate for those applications to compare the applicability in optoelectronics, photorefractive and photovoltaic (PV) devices. The systematic comparative study of the structural, electronic, optical, mechanical, and thermodynamic properties of pure BaTiO3 and Ca doped BaTiO3 (Ba1-xCaxTiO3 where x = 0.125, 0.25, 0.375, 0.500, 0.625) perovskite have been carried out using first-principles and density-functional-theory calculations as recently this material was mostly experimented. The measured structural parameters from the geometrically optimized structure of cubic BT ceramic compared with the other theoretical values. A crystal phase transition occurs when doping content x = 0.25. The electronic band structure shows that the nature of the bandgap is changed from indirect bandgap to direct bandgap energy at G-point after doping the Ca atom into BaTiO3 (BT) crystal. Doping of Ca into BT has led to bandstructure modification including conduction band (CB) shifting toward the higher energy level. Electronic properties have been reported to examine the contribution of different orbitals to the CB and to the valance band (VB). This study investigated the modification of optical properties such as absorption, reflectivity, refractive index, extinction coefficient, conductivity, dielectric function and loss function at the energy range from 0 to 30 eV. The prominent absorption peak and optical energy were observed at the UV light energy region. Based on the optical behavior of the material this theoretical research suggests that the doped BT solution is a suitable candidate for photorefractive and optoelectronic devices. Different elastic constants reveal mechanical stability and the existence of the covalent bond of those compounds. Debye temperature increases with doping content. Hence modification of BaTiO3 crystal by Ca atom significantly develop various properties that led it to multifunctional applications.

Molecular Characterization and Phylogenetic Analysis of MADS-Box Gene VroAGL11 Associated with Stenospermocarpic Seedlessness in Muscadine Grapes.

Reduced expression of MADS-box gene AGAMOUS-LIKE11 (VviAGL11) is responsible for stenospermocarpic seedlessness in bunch grapes. This study is aimed to characterize the VviAGL11 orthologous gene (VroAGL11) in native muscadine grapes (Vitis rotundifolia) at the molecular level and analyze its divergence from other plants. The VroAGL11 transcripts were found in all muscadine cultivars tested and highly expressed in berries while barely detectable in leaves. RT-PCR and sequencing of predicted ORFs from diverse grape species showed that AGL11 transcripts were conservatively spliced. The encoded VroAGL11 protein contains highly conserved MADS-MEF2-like domain, MADS domain, K box, putative phosphorylation site and two sumoylation motifs. The muscadine VroAGL11 proteins are almost identical (99%) to that of seeded bunch cultivar, Chardonnay, except in one amino acid (A79G), but differs from mutant protein of seedless bunch grape, Sultanina, in two amino acids, R197L and T210A. Phylogenetic analysis showed that AGL11 gene of muscadine and other Vitis species formed a separate clade than that of other eudicots and monocots. Muscadine grape cultivar "Jane Bell" containing the highest percentage of seed content in berry (7.2% of berry weight) had the highest VroAGL11 expression, but almost none to nominal expression in seedless cultivars Fry Seedless (muscadine) and Reliance Seedless (bunch). These findings suggest that VroAGL11 gene controls the seed morphogenesis in muscadine grapes like in bunch grape and can be manipulated to induce stenospermocarpic seedlessness using gene editing technology.

Influence of molybdenum and technetium doping on visible light absorption, optical and electronic properties of lead-free perovskite CsSnBr3 for optoelectronic applications.

Lead-free metal halide perovskites have nowadays become familiar owing to their potential use in solar cells and other optoelectronic applications. In this study, we carried out the structural, elastic, electronic, and optical properties of pure and metal (Mo/Tc) doped CsSnBr3 by using the density functional theory. The metal doping CsSnBr3 displays a narrowing band gap and as a result the optical functions exhibit high absorption and high conductivity in the visible region. Metal doping samples also reveal a high dielectric constant which indicates a low charge-carrier recombination rate and hence enhances the device performance. The optical absorption spectra of metal doped samples greatly shifted (red-shift) towards the lower energy region compared with the pure sample which creates a high-intensity peak in the visible region. The mechanical parameter reveals a highly ductile, soft, and flexible nature which indicates the suitability for use in thin films. The electronic band structure of metal-doped CsSnBr3 shows an intermediate state that assists the excited electron to pass on from valence band to conduction band. The overall study suggests that lead-free CsSn0.875Tc0.125Br3 perovskite is a promising candidate for solar cells and other optoelectronic applications.

Comparative Physiological and Metabolic Analysis Reveals a Complex Mechanism Involved in Drought Tolerance in Chickpea (Cicer arietinum L.) Induced by PGPR and PGRs.

The plant growth promoting rhizobacteria (PGPR) and plant growth regulators (PGRs) can be applied to improve the growth and productivity of plants, with potential to be used for genetic improvement of drought tolerance. However, for genetic improvement to be achieved, a solid understanding of the physiological and biochemical changes in plants induced by PGPR and PGR is required. The present study was carried out to investigate the role of PGPR and PGRs on the physiology and biochemical changes in chickpea grown under drought stress conditions and their association with drought tolerance. The PGPR, isolated from the rhizosphere of chickpea, were characterized on the basis of colony morphology and biochemical characters. They were also screened for the production of indole-3-acetic acid (IAA), hydrogen cyanide (HCN), ammonia (NH3), and exopolysaccharides (EPS) production. The isolated PGPR strains, named P1, P2, and P3, were identified by 16S-rRNA gene sequencing as Bacillus subtilis, Bacillus thuringiensis, and Bacillus megaterium, respectively. The seeds of two chickpea varieties, Punjab Noor-2009 (drought sensitive) and 93127 (drought tolerant) were soaked for 2-3 h prior to sowing in 24 h old cultures of isolates. The salicylic acid (SA) and putrescine (Put) were sprayed (150 mg/L) on 25 day old chickpea seedlings. The results showed that chickpea plants treated with a consortium of PGPR and PGRs significantly enhanced the chlorophyll, protein, and sugar contents compared to irrigated and drought conditions. Leaf proline content, lipid peroxidation, and activities of antioxidant enzymes (CAT, APOX, POD, and SOD) all increased in response to drought stress but decreased due to the PGPR and PGRs treatment. An ultrahigh performance liquid chromatography-high resolution mass spectrometry (UPLC-HRMS) analysis was carried out for metabolic profiling of chickpea leaves planted under controlled (well-irrigated), drought, and consortium (drought plus PGPR and PGRs) conditions. Proline, L-arginine, L-histidine, L-isoleucine, and tryptophan were accumulated in the leaves of chickpea exposed to drought stress. Consortium of PGPR and PGRs induced significant accumulation of riboflavin, L-asparagine, aspartate, glycerol, nicotinamide, and 3-hydroxy-3-methyglutarate in the leaves of chickpea. The drought sensitive chickpea variety showed significant accumulation of nicotinamide and 4-hydroxy-methylglycine in PGPR and PGR treated plants at both time points (44 and 60 days) as compared to non-inoculated drought plants. Additionally, arginine accumulation was also enhanced in the leaves of the sensitive variety under drought conditions. Metabolic changes as a result of drought and consortium conditions highlighted pools of metabolites that affect the metabolic and physiological adjustments in chickpea that reduce drought impacts.