A minimal physics-based model for musical perception.

Some people, entirely untrained in music, can listen to a song and replicate it on a piano with unnerving accuracy. What enables some to "hear" music so much better than others? Long-standing research confirms that part of the answer is undoubtedly neurological and can be improved with training. However, are there structural, physical, or engineering attributes of the human hearing mechanism apparatus (i.e., the hair cells of the internal ear) that render one human innately superior to another in terms of propensity to listen to music? In this work, we investigate a physics-based model of the electromechanics of the hair cells in the inner ear to understand why a person might be physiologically better poised to distinguish musical sounds. A key feature of the model is that we avoid a "black-box" systems-type approach. All parameters are well-defined physical quantities, including membrane thickness, bending modulus, electromechanical properties, and geometrical features, among others. Using the two-tone interference problem as a proxy for musical perception, our model allows us to establish the basis for exploring the effect of external factors such as medicine or environment. As an example of the insights we obtain, we conclude that the reduction in bending modulus of the cell membranes (which for instance may be caused by the usage of a certain class of analgesic drugs) or an increase in the flexoelectricity of the hair cell membrane can interfere with the perception of two-tone excitation.

The giant flexoelectric effect in a luffa plant-based sponge for green devices and energy harvesters.

Soft materials that can produce electrical energy under mechanical stimulus or deform significantly via moderate electrical fields are important for applications ranging from soft robotics to biomedical science. Piezoelectricity, the property that would ostensibly promise such a realization, is notably absent from typical soft matter. Flexoelectricity is an alternative form of electromechanical coupling that universally exists in all dielectrics and can generate electricity under nonuniform deformation such as flexure and conversely, a deformation under inhomogeneous electrical fields. The flexoelectric coupling effect is, however, rather modest for most materials and thus remains a critical bottleneck. In this work, we argue that a significant emergent flexoelectric response can be obtained by leveraging a hierarchical porous structure found in biological materials. We experimentally illustrate our thesis for a natural dry luffa vegetable-based sponge and demonstrate an extraordinarily large mass- and deformability-specific electromechanical response with the highest-density-specific equivalent piezoelectric coefficient known for any material (50 times that of polyvinylidene fluoride and more than 10 times that of lead zirconate titanate). Finally, we demonstrate the application of the fabricated natural sponge as green, biodegradable flexible smart devices in the context of sensing (e.g., for speech, touch pressure) and electrical energy harvesting.

Genome and transcriptome based comparative analysis of Tilletia indica to decipher the causal genes for pathogenicity of Karnal bunt in wheat.

Tilletia indica Mitra causes Karnal bunt (KB) in wheat by pathogenic dikaryophase. The present study is the first to provide the draft genomes of the dikaryon (PSWKBGD-3) and its two monosporidial lines (PSWKBGH-1 and 2) using Illumina and PacBio reads, their annotation and the comparative analyses among the three genomes by extracting polymorphic SSR markers. The trancriptome from infected wheat grains of the susceptible wheat cultivar WL711 at 24 h, 48h, and 7d after inoculation of PSWKBGH-1, 2 and PSWKBGD-3 were also isolated. Further, two transcriptome analyses were performed utilizing T. indica transcriptome to extract dikaryon genes responsible for pathogenesis, and wheat transcriptome to extract wheat genes affected by dikaryon involved in plant-pathogen interaction during progression of KB in wheat. A total of 54, 529, and 87 genes at 24hai, 48hai, and 7dai, respectively were upregulated in dikaryon stage while 21, 35, and 134 genes of T. indica at 24hai, 48hai, and 7dai, respectively, were activated only in dikaryon stage. While, a total of 23, 17, and 52 wheat genes at 24hai, 48hai, and 7dai, respectively were upregulated due to the presence of dikaryon stage only. The results obtained during this study have been compiled in a web resource called TiGeR ( http://backlin.cabgrid.res.in/tiger/ ), which is the first genomic resource for T. indica cataloguing genes, genomic and polymorphic SSRs of the three T. indica lines, wheat and T. indica DEGs as well as wheat genes affected by T. indica dikaryon along with the pathogenecity related proteins of T. indica dikaryon during incidence of KB at different time points. The present study would be helpful to understand the role of dikaryon in plant-pathogen interaction during progression of KB, which would be helpful to manage KB in wheat, and to develop KB-resistant wheat varieties.

Viral informatics: bioinformatics-based solution for managing viral infections.

Several new viral infections have emerged in the human population and establishing as global pandemics. With advancements in translation research, the scientific community has developed potential therapeutics to eradicate or control certain viral infections, such as smallpox and polio, responsible for billions of disabilities and deaths in the past. Unfortunately, some viral infections, such as dengue virus (DENV) and human immunodeficiency virus-1 (HIV-1), are still prevailing due to a lack of specific therapeutics, while new pathogenic viral strains or variants are emerging because of high genetic recombination or cross-species transmission. Consequently, to combat the emerging viral infections, bioinformatics-based potential strategies have been developed for viral characterization and developing new effective therapeutics for their eradication or management. This review attempts to provide a single platform for the available wide range of bioinformatics-based approaches, including bioinformatics methods for the identification and management of emerging or evolved viral strains, genome analysis concerning the pathogenicity and epidemiological analysis, computational methods for designing the viral therapeutics, and consolidated information in the form of databases against the known pathogenic viruses. This enriched review of the generally applicable viral informatics approaches aims to provide an overview of available resources capable of carrying out the desired task and may be utilized to expand additional strategies to improve the quality of translation viral informatics research.

Structure of a novel form of phosphopantetheine adenylyltransferase from Klebsiella pneumoniae at 2.59 Å resolution.

Phosphopantetheine adenylyltransferase (EC. 2.7.7.3, PPAT) catalyzes the penultimate step of the multistep reaction in the coenzyme A (CoA) biosynthesis pathway. In this step, an adenylyl group from adenosine triphosphate (ATP) is transferred to 4'-phosphopantetheine (PNS) yielding 3'-dephospho-coenzyme A (dpCoA) and pyrophosphate (PPi). PPAT from strain C3 of Klebsiella pneumoniae (KpPPAT) was cloned, expressed and purified. It was crystallized using 0.1 M HEPES buffer and PEG10000 at pH 7.5. The crystals belonged to tetragonal space group P41212 with cell dimensions of a = b = 72.82 Å and c = 200.37 Å. The structure was determined using the molecular replacement method and refined to values of 0.208 and 0.255 for Rcryst and Rfree factors, respectively. The structure determination showed the presence of three crystallographically independent molecules A, B and C in the asymmetric unit. The molecules A and B are observed in the form of a dimer in the asymmetric unit while molecule C belongs to the second dimer whose partner is related by crystallographic twofold symmetry. The polypeptide chain of KpPPAT folds into a ß/α structure. The conformations of the side chains of several residues in the substrate binding site in KpPPAT are significantly different from those reported in other PPATs. As a result, the modes of binding of substrates, phosphopantetheine (PNS) and adenosine triphosphate (ATP) differ considerably. The binding studies using fluorescence spectroscopy indicated a KD value of 3.45 × 10-4 M for ATP which is significantly lower than the corresponding values reported for PPAT from other species.

Bifurcation dissecting aneurysm: tips and tricks to differentiate from saccular aneurysm.

Bifurcations are a common site for saccular aneurysms, but rarely can be a site for dissecting aneurysms. Identification of these aneurysms is extremely important because the management plan depends on it. We describe a rare case of a ruptured dissecting aneurysm at the right ICA bifurcation in a pre-teen child which posed a diagnostic dilemma but ultimately was successfully managed with flow diversion.

Flexoelectricity in soft elastomers and the molecular mechanisms underpinning the design and emergence of giant flexoelectricity.

Soft robotics requires materials that are capable of large deformation and amenable to actuation with external stimuli such as electric fields. Energy harvesting, biomedical devices, flexible electronics, and sensors are some other applications enabled by electroactive soft materials. The phenomenon of flexoelectricity is an enticing alternative that refers to the development of electric polarization in dielectrics when subjected to strain gradients. In particular, flexoelectricity offers a direct linear coupling between a highly desirable deformation mode (flexure) and electric stimulus. Unfortunately, barring some exceptions, the flexoelectric effect is quite weak and rather substantial bending curvatures are required for an appreciable electromechanical response. Most experiments in the literature appear to confirm modest flexoelectricity in polymers although perplexingly, a singular work has measured a "giant" effect in elastomers under some specific conditions. Due to the lack of an understanding of the microscopic underpinnings of flexoelectricity in elastomers and a commensurate theory, it is not currently possible to either explain the contradictory experimental results on elastomers or pursue avenues for possible design of large flexoelectricity. In this work, we present a statistical-mechanics theory for the emergent flexoelectricity of elastomers consisting of polar monomers. The theory is shown to be valid in broad generality and leads to key insights regarding both giant flexoelectricity and material design. In particular, the theory shows that, in standard elastomer networks, combining stretching and bending is a mechanism for obtaining giant flexoelectricity, which also explains the aforementioned, surprising experimental discovery.

Comprehensive Computational Screening and Analysis of Natural Compounds Reveals Promising Estrogen Receptor Alpha Inhibitors for Breast Cancer Therapy.

Breast cancer remains a leading cause of death among women, with estrogen receptor alpha (ERα) overexpression playing a pivotal role in tumor growth and progression. This study aimed to identify novel ERα inhibitors from a library of 561 natural compounds using computational techniques, including virtual screening, molecular docking, and molecular dynamics simulations. Four promising candidates-Protopine, Sanguinarine, Pseudocoptisine, and Stylopine-were selected based on their high binding affinities and interactions with key ERα residues. Molecular dynamics simulations conducted over 500 nanoseconds revealed that Protopine and Sanguinarine exhibited more excellent stability with minimal fluctuations, suggesting strong and stable binding. In contrast, Pseudocoptisine and Stylopine showed higher flexibility, indicating less stable interactions. Binding free energy calculations further supported the potential of Protopine and Sanguinarine as ERα inhibitors, though their binding strength was slightly lower than that of the reference compound. These findings highlight Protopine and Sanguinarine as leading candidates for further investigation, and in vitro and in vivo studies are recommended to evaluate their therapeutic potential in breast cancer treatment.

Effect of boron fertilization on productivity and sustainability of rice-wheat cropping system in Tarai region, North-West India.

Extensive global dependency on rice and wheat crops has necessitated the adoption of intensive cultivation practices, thereby compelling to closely monitor the potential yield-limiting factors, among which, boron (B) deficiency stands out to be a prime concern. The present study explores the effects of B fertilization strategies within the Rice-Wheat Cropping System (RWCS) in the Tarai region of North-West India. A comprehensive six-year field experiment was conducted (2013-2019) at G.B. Pant University of Agriculture and Technology, Uttarakhand, India. The experiment tested graded B doses (0.5, 1.0, 1.5, and 2.0 kg ha-1) at varied frequencies (single, alternate, and annual) in a factorial design. The study revealed significant impacts of alternate B application at 1.5 kg ha-1 on crop yields and the Sustainable Yield Index (SYI). The System Rice Equivalent Yield (SREY) exhibited an increase of 6.7% with B supplementation over B-deprived plots, highlighting the pivotal role of B fertilizer in enhancing productivity within the RWCS. The economic optimum B dose was found to be 1.422 kg ha-1 using a linear plus plateau model, resulting in a calculated annual SREY of 9.73 t ha-1 when applied alternately to the cropping system. Continuous application and higher B rates demonstrated substantial increases in various B fractions, while the mobility factor remained within 10%, depicting safe ecological limits. The distribution of fractions in B-treated plots on average followed the order: residual B > organically-bound B > oxide bound B > specifically adsorbed B > readily soluble B. Similarities in the distribution patterns of B fractions between B-treated plots and the control indicated potential influence of biotic or abiotic processes on B fraction dynamics, even in the absence of external B application. To sum up, B application in alternate years at 1.5 kg ha-1 was most sustainable in enhancing the SREY, SYI, available soil B, and B fractions and lowering the environmental hazards.

End-of-life Care Patient Information Leaflets-A Comparative Evaluation of Artificial Intelligence-generated Content for Readability, Sentiment, Accuracy, Completeness, and Suitability: ChatGPT vs Google Gemini.

Background: End-of-life care (EOLC) is a critical aspect of healthcare, yet accessing reliable information remains challenging, particularly in culturally diverse contexts like India. Objective: This study investigates the potential of artificial intelligence (AI) in addressing the informational gap by analyzing patient information leaflets (PILs) generated by AI chatbots on EOLC. Methodology: Using a comparative research design, PILs generated by ChatGPT and Google Gemini were evaluated for readability, sentiment, accuracy, completeness, and suitability. Readability was assessed using established metrics, sentiment analysis determined emotional tone, accuracy, and completeness were rated by subject experts, and suitability was evaluated using the Patient Education Materials Assessment Tool (PEMAT). Results: Google Gemini PILs exhibited superior readability and actionability compared to ChatGPT PILs. Both conveyed positive sentiments and high levels of accuracy and completeness, with Google Gemini PILs showing slightly lower accuracy scores. Conclusion: The findings highlight the promising role of AI in enhancing patient education in EOLC, with implications for improving care outcomes and promoting informed decision-making in diverse cultural settings. Ongoing refinement and innovation in AI-driven patient education strategies are needed to ensure compassionate and culturally sensitive EOLC. How to cite this article: Gondode PG, Khanna P, Sharma P, Duggal S, Garg N. End-of-life Care Patient Information Leaflets-A Comparative Evaluation of Artificial Intelligence-generated Content for Readability, Sentiment, Accuracy, Completeness, and Suitability: ChatGPT vs Google Gemini. Indian J Crit Care Med 2024;28(6):561-568.

Chloroquine synergizes doxorubicin efficacy in cervical cancer cells through flux impairment and down regulation of proteins involved in the fusion of autophagosomes to lysosomes.

Drug repurposing holds abundant opportunity in the development of novel anticancer drugs. Chloroquine (CQ), a FDA approved anti-malarial drug, is demonstrated to enhance anticancer efficacy of standard anticancer drugs including doxorubicin (DOX) in several types of cancer cells. Here, we aimed to exploit the chemosensitizing effects of CQ against DOX in human cervical cancer (HeLa) cells that remains to be investigated yet. We show that a combination of DOX (40 nM) and CQ (40 µM) resulted in a synergistic cytotoxicity (combination index; CI < 1) in HeLa cells compared to the DOX or CQ alone. Synergistic effect of the combination (DOX + CQ) was associated with the impaired autophagic flux and enhanced apoptosis. Following treatment with the combination (DOX + CQ), the level of p62/SQSTM and LC-3II proteins was increased, while a decrease was noted in the expression of LAMP-2, Syntaxin17, Rab 5, and Rab 7 proteins that play critical roles in the fusion of autophagosomes to lysosomes. Autophagy inhibition by combination (DOX + CQ) enhanced the apoptotic cell death synergistically by increasing the cleavage of procaspase-3 and PARP1. Further, a prior incubation of HeLa cells with Z-VAD-FMK (a pan-caspase inhibitor) for 4 h, suppressed the combination (DOX + CQ)-induced cell death. Our data suggest that a combination of DOX + CQ had a better anti-cancer efficacy in HeLa cells than either of the drugs alone. Thus, CQ, as a repurposed drug, may hold the potential to synergize anticancer effects of DOX in cervical cancer cells.

Defective quality control autophagy in Hyperhomocysteinemia promotes ER stress and consequent neuronal apoptosis through proteotoxicity.

Homocysteine (Hcy), produced physiologically in all cells, is an intermediate metabolite of methionine and cysteine metabolism. Hyperhomocysteinemia (HHcy) resulting from an in-born error of metabolism that leads to accumulation of high levels of Hcy, is associated with vascular damage, neurodegeneration and cognitive decline. Using a HHcy model in neuronal cells, primary cortical neurons and transgenic zebrafish, we demonstrate diminished autophagy and Hcy-induced neurotoxicity associated with mitochondrial dysfunction, fragmentation and apoptosis. We find this mitochondrial dysfunction is due to Hcy-induced proteotoxicity leading to ER stress. We show this sustained proteotoxicity originates from the perturbation of upstream autophagic pathways through an aberrant activation of mTOR and that protetoxic stress act as a feedforward cues to aggravate a sustained ER stress that culminate to mitochondrial apoptosis in HHcy model systems. Using chemical chaperones to mitigate sustained ER stress, Hcy-induced proteotoxicity and consequent neurotoxicity were rescued. We also rescue neuronal lethality by activation of autophagy and thereby reducing proteotoxicity and ER stress. Our findings pave the way to devise new strategies for the treatment of neural and cognitive pathologies reported in HHcy, by either activation of upstream autophagy or by suppression of downstream ER stress. Video Abstract.

Application of population physiologically based pharmacokinetic modelling to optimize target expression and clearance mechanisms of therapeutic monoclonal antibodies.

AIMS: To use population physiologically based pharmacokinetic (PopPBPK) modelling to optimize target expression, kinetics and clearance of HER1/2 directed therapeutic monoclonal antibodies (mAbs). Thus, to propose a general workflow of PopPBPK modelling and its application in clinical pharmacology. METHODS: Full PBPK model of pertuzumab (PTZ) was developed in patient population using Simcyp V21R1 incorporating mechanistic targeted-mediated drug disposition process by fitting known clinical PK and sparse receptor proteomics data to optimize target expression and kinetics of HER2 receptor. Trastuzumab (TTZ) PBPK modelling was used to validate the optimized HER2 target. Additionally, the simulator was also used to develop a full PBPK model for the HER1-directed mAb cetuximab (CTX) to assess the underlying targeted-mediated drug disposition-independent elimination mechanisms. RESULTS: HER2 final parameterisation coming from the PBPK modelling of PTZ was successfully cross validated through PBPK modelling of TTZ with average fold error (AFE), absolute AFE and percent prediction error values for area under the concentration-time curve (AUC) and maximum plasma concentration (Cmax ) of 1.13, 1.16 and 16, and 1.01, 1.07 and 7, respectively. CTX PBPK model performance was validated after the incorporation of an additional systemic clearance of 0.033 L/h as AFE and absolute AFE showed an acceptable predictive power of AUC and Cmax with percent prediction error of 13% for AUC and 10% for Cmax . CONCLUSIONS: Optimisation of both system and drug related parameters were performed through PBPK modelling to improve model performance of therapeutic mAbs (PTZ, TTZ and CTX). General workflow was proposed to develop and apply PopPBPK to support clinical development of mAbs targeting same receptor.

Temporal expression analysis of microRNAs and their target GRAS genes induced by osmotic stress in two contrasting wheat genotypes.

BACKGROUND: MicroRNAs (miRNAs) are important nonprotein-coding genes in plants which participate in almost all biological processes during abiotic and biotic stresses. Understanding how plants respond to various environmental conditions requires the identification of stress-related miRNAs. In recent years, there has been an increased interest in studying miRNA genes and gene expression. Drought is one of the common environmental stresses limiting plant growth and development. Stress-specific miRNAs and their GRAS gene targets were validated to understand the role of miRNAs in response to osmotic stress. RESULTS: In this study, expression patterns of the ten stress-responsive miRNAs involved in osmotic stress adaptation were examined in order to undertand the regulation behavior of abiotic stress and miRNAs in two contrasting wheat genotype C-306 (drought tolerant) and WL-711 (drought sensitive). Three miRNAs were discovered to be upregulated under stress, whereas seven miRNAs were showed to be down-regulated as a consequence of the study. In contrast to miRNA, it was also discovered that GRAS genes as their targets were up-regulated during osmotic stress. In addition, the expression level of miR159, miR408 along with their targets, TaGRAS178 and TaGRAS84 increased in response to osmotic stress. Nevertheless, miR408 is highly conserved miRNA that regulates plant growth, development and stress response. As a result, variation in the expression levels of studied miRNAs in the presence of target genes provides a plausible explanation for miRNA-based abiotic stress regulation. A regulatory network of miRNA and their targets revealed that fourteen miRNA interact with 55 GRAS targets from various subfamilies that contribute in the plant growth and development. CONCLUSIONS: These findings provide evidence for temporal and variety-specific differential regulation of miRNAs and their targets in wheat in response to osmotic shock, and they may aid in determining the potential.

AMMI and GGE biplot analysis of yield under terminal heat tolerance in wheat.

BACKGROUND: Wheat is an important cereal crop that helps to meet the food grain needs of people all over the world. Heat stress is one of the most significant abiotic stresses that wheat crops face during terminal growth stages in the wheat growing regions like India. It is very important to identify heat tolerant genotypes to be used as donors for breeding tolerant varieties. METHODS: Thirty-six wheat genotypes were evaluated under different sowing dates viz., Timely sown (TS), Late sown (LS) and very late sown (VLS), and the fourth was sown in the Temperature controlled phenotyping facility (TCPF) across two years. Genotypes were planted following lattice square design with two replications. Data was recorded for yield and yield contributing traits and analysed using selection indices as well AMMI and GGE biplot stability models. RESULTS: Heat stress affected all the traits under different heat environments which ranged from 1.6% (Spikelet number) to 37.2% (grain yield). Regression analysis indicated that the thousand grains weight (R2 = 0.50) contributed significantly towards grain yield under heat stress. Stress susceptibility index (SSI) found genotypes GW322, RAJ3765, Raj4037and MACS6145 as heat tolerant whereas, Stress Tolerance Index (STI) identified C306, HD2967, WH1080, WH730, DBW90, HD2932, DBW17, RAJ3765 as heat tolerant and high yielding. AMMI biplot analysis indicated stable genotypes DBW90, WH730, RAJ4083, CBW38, HD2932, NI5439, WR544, whereas GGE biplot analysis revealed stable genotypes NIAW34, NI5439, RAJ4083, DBW90, PBW590, Raj3765, HUW 510, WH730, HD2967 and UP2382. CONCLUSION: Heat stress affects significantly all yield contributing traits. Thousand grain weight was the most important trait that can be used as a selection criterion for selecting tolerant lines. Based on selection indices and both AMMI and GGE analysis, genotype RAJ3765 was identified to be highly heat tolerant with good grain yield.

Development and evaluation of Hedyotis corymbosa (L.) extract containing phytosomes: a preclinical approach for treatment of neuropathic pain in rodent model.

PURPOSE: The study was aimed to encapsulate Hedyotis corymbosa extract (HCE) into phytosomes to improve its therapeutic efficacy in neuropathic pain by enhancing the bioavailability of chief chemical constituent Hedycoryside -A (HCA). METHODS: For preparing phytosomes complexes (F1, F2, and F3), HCE and phospholipids were reacted in disparate ratio. F2 was chosen to assess its therapeutic efficacy in neuropathic pain induced by partial sciatic nerve ligation. Nociceptive threshold and oral bioavailability were also estimated for F2. RESULTS: Particle size, zeta potential and entrapment efficiency for F2 were analysed as 298.1 ± 1.1 nm, -3.92 ± 0.41 mV and 72.12 ± 0.72% respectively. F2 gave enhanced relative bioavailability (158.92%) of HCA along with a greater neuroprotective potential showing a significant antioxidant effect and augmentation (p < 0.05) in nociceptive threshold with the diminution in damage to nerves. CONCLUSION: F2 is an optimistic formulation for enhancing the HCE delivery for the effective treatment of neuropathic pain.

Genome-wide identification of DCL, AGO, and RDR gene families in wheat (Triticum aestivum L.) and their expression analysis in response to heat stress.

Key components of the RNA interference (RNAi) pathway include the Dicer-like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) gene families. While these components have been studied in various plant species, their functional validation in wheat remains unexplored particularly under heat stress. In this study, a comprehensive genome-wide analysis to identify, and characterize DCL, AGO, and RDR genes in wheat and their expression patterns was carried out. Using phylogenetic analysis with orthologous genes from Arabidopsis and rice, we identified a total of 82 AGO, 31 DCL, and 31 RDR genes distributed across the 21 chromosomes of wheat. To understand the regulatory network, a network analysis of miRNAs that target RNA-silencing genes was performed. Our analysis revealed that 13 miRNAs target AGO genes, 8 miRNAs target DCL genes, and 10 miRNAs target RDR genes at different sites, respectively. Additionally, promoter analysis of the RNA-silencing genes was done and identified the presence of 132 cis-elements responsive to stress and phytohormones. To examine their expression patterns, we performed RNA-seq analysis in the flag leaf samples of wheat exposed to both normal and heat stress conditions. To understand the regulation of RNA silencing, we experimentally analysed the transcriptional changes in response to gradient heat stress treatments. Our results showed constitutive expression of the AGO1, AGO9, and DCL2 gene families, indicating their importance in the overall biological processes of wheat. Notably, RDR1, known to be involved in small interfering RNA (siRNA) biogenesis, exhibited higher expression levels in wheat leaf tissues. These findings suggest that these genes may play a role in responses to stress in wheat, highlighting their significance in adapting to environmental challenges. Overall, our study provides additional knowledge to understand the mechanisms underlying heat stress responses and emphasizes the essential roles of these gene families in wheat. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-023-01362-0.

Discovery of the Lead Molecules Targeting the First Step of the Histidine Biosynthesis Pathway of Acinetobacter baumannii.

Acinetobacter baumannii is a multidrug-resistant, opportunistic, nosocomial pathogen for which a new line of treatments is desperately needed. We have targeted the enzyme of the first step of the histidine biosynthesis pathway, viz., ATP-phosphoribosyltransferase (ATP-PRT). The three-dimensional structure of ATP-PRT was predicted on the template of the known three-dimensional structure of ATP-PRT from Psychrobacter arcticus (PaATPPRT) using a homology modeling approach. High-throughput virtual screening (HTVS) of the antibacterial library of Life Chemicals Inc., Ontario, Canada was carried out followed by molecular dynamics simulations of the top hit compounds. In silico results were then biochemically validated using surface plasmon resonance spectroscopy. We found that two compounds, namely, F0843-0019 and F0608-0626, were binding with micromolar affinities to the ATP-phosphoribosyltransferase from Acinetobacter baumannii (AbATPPRT). Both of these compounds were binding in the same way as AMP in PaATPPRT, and the important residues of the active site, viz., Val4, Ser72, Thr76, Tyr77, Glu95, Lys134, Val136, and Tyr156, were also interacting via hydrogen bonds. The calculated binding energies of these compounds were -10.5 kcal/mol and -11.1 kcal/mol, respectively. These two compounds can be used as the potential lead molecules for designing antibacterial compounds in the future, and this information will help in drug discovery programs against Acinetobacter worldwide.

WheatQTLdb V2.0: a supplement to the database for wheat QTL.

We recently developed a database for hexaploid wheat QTL (WheatQTLdb; www.wheatqtldb.net), which included 11,552 QTL affecting various traits of economic importance. However, that database did not include valuable QTL from other wheat species and/or progenitors of hexaploid wheat. Therefore, an updated and improved version of wheat QTL database (WheatQTLdb V2.0) was developed, which now includes information on hexaploid wheat (Triticum aestivum) and the following seven other related species: T. durum, T. turgidum, T. dicoccoides, T. dicoccum, T. monococcum, T. boeoticum, and Aegilops tauschii. WheatQTLdb V2.0 includes a much-improved list of QTL, including 27,518 main effect QTL, 202 epistatic QTL, and 1321 metaQTL. This newly released WheatQTLdb V2.0 also has additional valuable options to search and choose the QTL, category-wise, and trait-wise data for their use in research or breeding programs.

Epigenetic regulation of salinity stress responses in cereals.

Cereals are important crops and are exposed to various types of environmental stresses that affect the overall growth and yield. Among the various abiotic stresses, salt stress is a major environmental factor that influences the genetic, physiological, and biochemical responses of cereal crops. Epigenetic regulation which includes DNA methylation, histone modification, and chromatin remodelling plays an important role in salt stress tolerance. Recent studies in rice genomics have highlighted that the epigenetic changes are heritable and therefore can be considered as molecular signatures. An epigenetic mechanism under salinity induces phenotypic responses involving modulations in gene expression. Association between histone modification and altered DNA methylation patterns and differential gene expression has been evidenced for salt sensitivity in rice and other cereal crops. In addition, epigenetics also creates stress memory that helps the plant to better combat future stress exposure. In the present review, we have discussed epigenetic influences in stress tolerance, adaptation, and evolution processes. Understanding the epigenetic regulation of salinity could help for designing salt-tolerant varieties leading to improved crop productivity.