Transcriptome-wide association mapping provides insights into the genetic basis and candidate genes governing flowering, maturity and seed weight in rice bean (Vigna umbellata).

BACKGROUND: Rice bean (Vigna umbellata), an underrated legume, adapts to diverse climatic conditions with the potential to support food and nutritional security worldwide. It is used as a vegetable, minor food crop and a fodder crop, being a rich source of proteins, minerals, and essential fatty acids. However, little effort has been made to decipher the genetic and molecular basis of various useful traits in this crop. Therefore, we considered three economically important traits i.e., flowering, maturity and seed weight of rice bean and identified the associated candidate genes employing an associative transcriptomics approach on 100 diverse genotypes out of 1800 evaluated rice bean accessions from the Indian National Genebank. RESULTS: The transcriptomics-based genotyping of one-hundred diverse rice bean cultivars followed by pre-processing of genotypic data resulted in 49,271 filtered markers. The STRUCTURE, PCA and Neighbor-Joining clustering of 100 genotypes revealed three putative sub-populations. The marker-trait association analysis involving various genome-wide association study (GWAS) models revealed significant association of 82 markers on 48 transcripts for flowering, 26 markers on 22 transcripts for maturity and 22 markers on 21 transcripts for seed weight. The transcript annotation provided information on the putative candidate genes for the considered traits. The candidate genes identified for flowering include HSC80, P-II PsbX, phospholipid-transporting-ATPase-9, pectin-acetylesterase-8 and E3-ubiquitin-protein-ligase-RHG1A. Further, the WRKY1 and DEAD-box-RH27 were found to be associated with seed weight. Furthermore, the associations of PIF3 and pentatricopeptide-repeat-containing-gene with maturity and seed weight, and aldo-keto-reductase with flowering and maturity were revealed. CONCLUSION: This study offers insights into the genetic basis of key agronomic traits in rice bean, including flowering, maturity, and seed weight. The identified markers and associated candidate genes provide valuable resources for future exploration and targeted breeding, aiming to enhance the agronomic performance of rice bean cultivars. Notably, this research represents the first transcriptome-wide association study in pulse crop, uncovering the candidate genes for agronomically useful traits.

In silico and network pharmacology analysis of fucosterol: a potent anticancer bioactive compound against HCC.

The Fucaceae family of marine brown algae includes Ascophyllum nodosum. Fucosterol (FSL) is a unique bioactive component that was identified through GC-MS analysis of the hydroalcoholic extract of A. nodosum. Fucosterol's mechanism of action towards hepatocellular cancer was clarified using network pharmacology and docking study techniques. The probable target gene of FSL has been predicted using the TargetNet and SwissTargetPred databases. GeneCards and the DisGNet database were used to check the targeted genes of FSL. By using the web programme Venny 2.1, the overlaps of FSL and HCC disease demonstrated that 18 genes (1.3%) were obtained as targeted genes Via the STRING database, a protein-protein interaction (PPI) network with 18 common target genes was constructed. With the aid of CytoNCA, hub genes were screened using the Cytoscape software, and the targets' hub genes were exported into the ShinyGo online tool for study of KEGG and gene ontology enrichment. Using the software AutoDock, a hub gene molecular docking study was performed. Ten genes, including AR, CYP19A1, ESR1, ESR2, TNF, PPARA, PPARG, HMGCR, SRC, and IGF1R, were obtained. The 10 targeted hubs docked with FSL successfully. The active components FSL of ASD, the FSL, are engaged in fatty liver disease, cancer pathways, and other signalling pathways, which could prove beneficial for the management of HCC.

Therapeutic Potential of Morin Hydrate Against Rifampicin Induced Hepato and Renotoxicity in Albino Wistar Rats: Modulation of Organ Function, Oxidative Stress and Inflammatory Response.

Tuberculosis (TB) is a challenging public health issue, particularly in poor and developing countries. Rifampicin (RIF) is one of the most common first-line anti-TB drugs but it is known for its adverse effects on the hepato-renal system. The present study investigated the efficacy of morin hydrate (MH) in protecting hepato-renal damage inflicted by RIF in rats. RIF (50 mg/kg), and a combination of RIF (50 mg/kg) and MH (50 mg/kg) were administered orally for 4 weeks in rats. Silymarin (50 mg/kg) was used as a positive control. Increased levels of serological parameters such as AST, ALT, ALP, LDH, GGT, bilirubin, triglyceride, total cholesterol, urea, uric acid, creatinine, TNF-α, IFN-γ, IL-6 along with the decreased level of IL-10, total protein and albumin were used as markers of hepatic and renal injury. Oxidative damage in the tissues was measured by the increase in lipid peroxidation and decline in GSH, SOD and catalase activities. Histopathology of liver slices was used to study hepatic architecture. Four-week RIF treatment produced altered serological parameters with an increase in pro-inflammatory cytokines in serum suggesting hepatotoxicity and nephrotoxicity. The antioxidant status of the liver and kidney (increased lipid peroxidation and decline in GSH, SOD and catalase) was compromised. Cellular damage and necrosis were observed in liver slices. MH supplementation with RIF improved hepato-renal functions by restoring the serum and tissue markers towards normal values. Histological observations authenticated the results. MH supplementation also reduced the production of pro-inflammatory cytokines. Thus, the results revealed that MH provides protection against RIF-induced hepato-renal injury.

Genome-Wide Comparative Analysis of Five Amaranthaceae Species Reveals a Large Amount of Repeat Content.

Amaranthus is a genus of C4 dicotyledonous herbaceous plant species that are widely distributed in Asia, Africa, Australia, and Europe and are used as grain, vegetables, forages, and ornamental plants. Amaranth species have gained significant attention nowadays as potential sources of nutritious food and industrial products. In this study, we performed a comparative genome analysis of five amaranth species, namely, Amaranthus hypochondriacus, Amaranthus tuberculatus, Amaranthus hybridus, Amaranthus palmeri, and Amaranthus cruentus. The estimated repeat content ranged from 54.49% to 63.26% and was not correlated with the genome sizes. Out of the predicted repeat classes, the majority of repetitive sequences were Long Terminal Repeat (LTR) elements, which account for about 13.91% to 24.89% of all amaranth genomes. Phylogenetic analysis based on 406 single-copy orthologous genes revealed that A. hypochondriacus is most closely linked to A. hybridus and distantly related to A. cruentus. However, dioecious amaranth species, such as A. tuberculatus and A. palmeri, which belong to the subgenera Amaranthus Acnida, have formed their distinct clade. The comparative analysis of genomic data of amaranth species will be useful to identify and characterize agronomically important genes and their mechanisms of action. This will facilitate genomics-based, evolutionary studies, and breeding strategies to design faster, more precise, and predictable crop improvement programs.

In silico strategies for identifying therapeutic candidates against Acinetobacter baumannii: spotlight on the UDP-N-acetylmuramoyl-L-alanine-D-glutamate:meso-diaminopimelate ligase (MurE).

The opportunistic bacterium Acinetobacter baumannii, which belongs to ESKAPE group of pathogenic bacteria, is leading cause of infections associated with gram-negative bacteria. Acinetobacter baumannii causes severe diseases, such as VAP (ventilator-associated pneumonia), meningitis, and UTI (urinary tract infections) among the nosocomial infections contracted in hospitals. The high infection rate and growing resistance to the vast array of antibiotics makes it paramount to look for new therapeutic strategies against this pathogen. The most promising therapeutic targets are the proteins involved in the synthesis of peptidoglycan which is chief component of bacterial cell wall, MurE is one of those enzymes and is responsible for the addition of one unit of meso-diaminopimelic acid (meso-A2pm) to the nucleotide precursor, UDPMurNAc-L-Ala-D-Glu, and aids in the formation of crosslinker pentapeptide chain. The three-dimensional structure of MurE was modelled using homology modelling technique and then vHTS was performed using this model against Approved Drug Library on DrugRep server using AutoDock Vina. Out of 500 drug molecules, two were selected based on estimated binding affinity, interaction pattern, interacting residues, etc. The selected drug molecules are DB12887 (Tazemetostat) and DB13879 (Glecaprevir). Then, MD simulations were performed on native MurE and its complexes with ligands to examine their dynamical behaviour, stability, integrity, compactness, and folding properties. The protein-ligand complexes were then subjected to binding free energy calculations using the MM/PBSA-based binding free energy analysis and the values are -109.788 ± 8.03 and -152.753 ± 11.98 kcal for MurE-DB12887 and MurE-DB13879 complex, respectively. All the analysis performed on MD trajectories for the complexes of these ligands with protein provided plenty of dependable evidences to consider these molecules for inhibition of MurE enzyme from A. baumannii. Communicated by Ramaswamy H. Sarma.

Evaluation of hydrogeochemical processes and saltwater intrusion in the coastal aquifers in the southern part of Puri District, Odisha, India.

Groundwater is widely regarded as being among the freshwater natural resources with the lowest levels of contamination. Nevertheless, the saltwater intrusion has resulted in the contamination of groundwater in coastal regions with lower elevation. The rationale of the present work is to investigate the chemistry of groundwater, to identify the various facies of groundwater, to identify the processes that influence groundwater chemistry and saltwater intrusion, and to evaluate the groundwater's aptness for use in drinking and farming. In order to gain an understanding of the groundwater quality as well as the salinization process that occurs in coastal aquifers as a result of hydrogeochemical processes, a total of 108 groundwater samples (54 each in pre- and post-monsoon) were taken and analyzed for several physiochemical parameters in the southern part of the Puri district in the Indian state of Odisha. The data has undergone analysis and examination to identify the factors (such as hydrological facies, potential solute source in water, and salinization process) that contribute to groundwater salinity. The result showed the chemistry controlling processes of rock-water interaction as per Gibbs diagram. The majority of shallow aquifers exhibit the Na-Cl type of facies as per the Piper plot. A total of 37% pre-monsoon and 33% post-monsoon samples having Na+/Cl- ratio below the threshold of 0.86 indicating the influence of saltwater intrusion. In both seasons, it was observed that 74% of the samples exhibited a Na+ concentration that exceeded the permissible limit set by the World Health Organization (WHO) for drinking purposes. The findings indicate that most groundwater failed to pass safe drinking water and irrigation standards due to saltwater intrusion. Consequently, the monitoring of coastal aquifer quality has become imperative in order to ensure the sustainability of aquifers and the development of groundwater resources. This is because coastal aquifers are highly vulnerable to saltwater intrusion, primarily as a result of the extensive extraction of groundwater for diverse purposes.

Computational identification of candidate inhibitors for Dihydrofolate reductase in Acinetobacter baumannii.

Acinetobacter baumannii is one of the emerging causes of hospital acquired infections and this bacterium, due to multi-drug resistant and Extensive Drug resistant has been able to develop resistance against the antimicrobial agents that are being used to eliminate it. A.baumannii has been the cause of death in immune compromised patients in hospitals. Hence it is the urgent need of time to find potential inhibitors for this bacterium to cease its virulence and affect its survival inside host organisms. The Dihydrofolate reductase enzyme, which is an important biocatalyst in the conversion of Dihydrofolate to Tetrahydrofolate, is an important drug target protein. In the present study high throughput screening is used to identify the inhibitors of this enzyme. The prioritized ligand molecular candidates identified through virtual screening for the substrate binding site of the predicted model are Z1447621107, Z2604448220 and Z1830442365. The Molecular Dynamics Simulation study suggests that potential inhibitor of the Dihydrofolate reductase enzyme would prevent bacteria from completing its life cycle, affecting its survival. Finally the complexes were analysed for binding free energy of the Dihydrofolate reductase enzyme complexes with the ligands.

Squamous cell carcinoma of skin in a case of post-filariasis chronic lower limb lymphedema- a case study and review of literature.

INTRODUCTION AND IMPORTANCE: Filariasis, predominantly caused by the parasite Wuchereria Bancrofti, is a key etiological factor in lymphedema development. Lymphedema, characterized by persistent lymphatic obstruction, leads to significant changes in immunological factors and protein composition. These alterations play a crucial role in the delayed diagnosis of squamous cell carcinoma within chronic lymphedema contexts. Notably, chronic lymphedema is an infrequent but significant precursor to squamous cell carcinoma, with fewer than 20 cases reported in medical literature, including only 11 cases affecting the lower limbs. The management of squamous cell carcinoma in lymphedema is challenging due to the rarity of cases and the resulting lack of experience among clinicians. CASE PRESENTATION: The report focuses on a 69-year-old woman with long-standing right lower limb lymphedema following filariasis. She underwent treatment for a non-healing ulcer in the right gluteal region, diagnosed as moderately differentiated squamous cell carcinoma. Following a wide local excision with primary closure, her lower limb swelling persisted, and subsequent diagnosis confirmed regional lymph node metastasis. The patient was then considered for immunotherapy. CLINICAL DISCUSSION: This case emphasizes the link between chronic lymphedema and squamous cell carcinoma. It highlights the necessity for a multidisciplinary approach for timely and effective treatment, addressing the rarity and complexity of such cases. CONCLUSION: The successful application of immunotherapy in this case illustrates a favorable clinical outcome, marking a significant advancement in treating similar conditions. This finding contributes to the evolving knowledge in this medical field, suggesting immunotherapy as a promising treatment option. METHODS: This case report meticulously follows the SCARE 2023 guidelines: updating consensus Surgical Case Report guidelines (Sohrabi et al., 2023) [1]. These guidelines ensure high-quality reporting in surgical case reports. The report details the evaluation, diagnosis, and a comprehensive review of the literature pertaining to a patient with squamous cell carcinoma of the skin and regional nodal metastasis, which developed in the context of post-filariasis chronic lower limb lymphedema. By employing a multidisciplinary approach, this report achieves a thorough and standardized presentation of the case, serving as a benchmark and an additional tool for raising awareness about such rare medical conditions.

A critical review on fate, behavior, and ecotoxicological impact of zinc oxide nanoparticles on algae.

The rapid inclusion of zinc oxide nanoparticles (ZnO NPs) in nanotechnology-based products over the last decade has generated a new threat in the apprehension of the environment. The massive use of zinc nanosized products will certainly be disposed of and be released, eventually entering the aquatic ecosystem, posing severe environmental hazards. Moreover, nanosized ZnO particles owing the larger surface area per volume exhibit different chemical interactions within the aquatic ecosystem. They undergo diverse potential transformations because of their unique physiochemical properties and the feature of receiving medium. Therefore, assessment of their impact is critical not only for scavenging the present situation but also for preventing unintended environmental hazards. Algae being a primary producer of the aquatic ecosystem help assess the risk of massive NPs usage in environmental health. Because of their nutritional needs and position at the base of aquatic food webs, algal indicators exhibit relatively unique information concerning ecosystem conditions. Moreover, algae are presently the most vital part of the circular economy. Hence, it is imperative to understand the physiologic, metabolic, and morphologic changes brought by the ZnO NPs to the algal cells along with the development of the mechanism imparting toxicity mechanism. We also need to develop an appropriate scientific strategy in the innovation process to restrain the exposure of NPs at safer levels. This review provides the details of ZnO NP interaction with algae. Moreover, their impact, mechanism, and factors affecting toxicity to the algae are discussed.

Exploration of potential hit compounds targeting 1-deoxy-d-xylulose 5-phosphate reductoisomerase (IspC) from Acinetobacter baumannii: an in silico investigation.

The emergence of carbapenem-resistant Acinetobacter baumannii, a highly concerning bacterial species designated as a Priority 1: Critical pathogen by the WHO, has become a formidable global threat. In this study, we utilised computational methods to explore the potent molecules capable of inhibiting the IspC enzyme, which plays a crucial role in the methylerythritol 4-phosphate (MEP) biosynthetic pathway. Employing high-throughput virtual screening of small molecules from the Enamine library, we focused on the highly conserved substrate binding site of the DXR target protein, resulting in the identification of 1000 potential compounds. Among these compounds, we selected the top two candidates (Z2615855584 and Z2206320703) based on Lipinski's rule of Five and ADMET filters, along with FR900098, a known IspC inhibitor, and DXP, the substrate of IspC, for molecular dynamics (MD) simulations. The MD simulation trajectories revealed remarkable structural and thermodynamic stability, as well as strong binding affinity, for all the IspC-ligand complexes. Furthermore, binding free energy calculations based on MM/PBSA (Molecular Mechanics/Poisson-Boltzmann Surface Area) methodology demonstrated significant interactions between the selected ligand molecules and IspC. Taking into consideration all the aforementioned criteria, we suggest Z2206320703 as the potent lead candidate against IspC. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-024-03923-w.

A Dual Therapeutic Approach to Diabetes Mellitus via Bioactive Phytochemicals Found in a Poly Herbal Extract by Restoration of Favorable Gut Flora and Related Short-Chain Fatty Acids.

Diabetes mellitus (DM), a metabolic and endocrine condition, poses a serious threat to human health and longevity. The emerging role of gut microbiome associated with bioactive compounds has recently created a new hope for DM treatment. UHPLC-HRMS methods were used to identify these compounds in a poly herbal ethanolic extract (PHE). The effects of PHE on body weight (BW), fasting blood glucose (FBG) level, gut microbiota, fecal short-chain fatty acids (SCFAs) production, and the correlation between DM-related indices and gut microbes, in rats were investigated. Chebulic acid (0.368%), gallic acid (0.469%), andrographolide (1.304%), berberine (6.442%), and numerous polysaccharides were the most representative constituents in PHE. A more significant BW gain and a reduction in FBG level towards normal of PHE 600 mg/kg treated rats group were resulted at the end of 28th days of the study. Moreover, the composition of the gut microbiota corroborated the study's hypothesis, as evidenced by an increased ratio of Bacteroidetes to Firmicutes and some beneficial microbial species, including Prevotella copri and Lactobacillus hamster. The relative abundance of Bifidobacterium pseudolongum, Ruminococcus bromii, and Blautia producta was found to decline in PHE treatment groups as compared to diabetic group. The abundance of beneficial bacteria in PHE 600 mg/kg treatment group was concurrently associated with increased SCFAs concentrations of acetate and propionate (7.26 nmol/g and 4.13 nmol/g). The findings of this study suggest a promising approach to prevent DM by demonstrating that these naturally occurring compounds decreased FBG levels by increasing SCFAs content and SCFAs producing gut microbiota.

Comparative transcriptome profiling of contrasting finger millet (Eleusine coracana (L.) Gaertn) genotypes under heat stress.

BACKGROUND: Eleusine coracana (L.) Gaertn is a crucial C4 species renowned for its stress robustness and nutritional significance. Because of its adaptability traits, finger millet (ragi) is a storehouse of critical genomic resources for crop improvement. However, more knowledge about this crop's molecular responses to heat stress needs to be gained. METHODS AND RESULTS: In the present study, a comparative RNA sequencing analysis was done in the leaf tissue of the finger millet, between the heat-sensitive (KJNS-46) and heat-tolerant (PES-110) cultivars of Ragi, in response to high temperatures. On average, each sample generated about 24 million reads. Interestingly, a comparison of transcriptomic profiling identified 684 transcripts which were significantly differentially expressed genes (DEGs) examined between the heat-stressed samples of both genotypes. The heat-induced change in the transcriptome was confirmed by qRT-PCR using a set of randomly selected genes. Pathway analysis and functional annotation analysis revealed the activation of various genes involved in response to stress specifically heat, oxidation-reduction process, water deprivation, and changes in heat shock protein (HSP) and transcription factors, calcium signaling, and kinase signaling. The basal regulatory genes, such as bZIP, were involved in response to heat stress, indicating that heat stress activates genes involved in housekeeping or related to basal regulatory processes. A substantial percentage of the DEGs belonged to proteins of unknown functions (PUFs), i.e., not yet characterized. CONCLUSION: These findings highlight the importance of candidate genes, such as HSPs and pathways that can confer tolerance towards heat stress in ragi. These results will provide valuable information to improve the heat tolerance in heat-susceptible agronomically important varieties of ragi and other crops.

Effect of salt, alkali and combined stresses on root system architecture and ion profiling in a diverse panel of oat (Avena spp.).

The co-occurrence of salinisation and alkalisation is quite frequent in problematic soils and poses an immediate threat to food, feed and nutritional security. In the present study, root system architectural traits (RSAs) and ion profiling were evaluated in 21 genotypes of Avena species to understand the effect of salinity-alkalinity stress. The oat genotypes were grown on germination paper and 5-day-old seedlings were transferred to a hydroponic system for up to 30days. These seedlings were subjected to seven treatments: T0 , treatment control (Hoagland solution); T1 , moderate salinity (50mM); T2 , high salinity (100mM); T3 , moderate alkalinity (15mM); T4 , high alkalinity (30mM); T5 , combined moderate salinity-alkalinity (50mM+15mM); and T6 , combined high salinity-alkalinity (100mM and 30mM) by using NaCl+Na2 SO4 (saline) and NaHCO3 +Na2 CO3 (alkaline) salts equivalently. The root traits, such as total root area (TRA), total root length (TRL), total root diameter (TRD), total root volume (TRV), root tips (RT), root segments (RS), root fork (RF) and root biomass (RB) were found to be statistically significant (P + and K+ content analysis in root and shoot tissues revealed the ion homeostasis capacity of different Avena accessions under stress treatments. Principal component analysis (PCA) covered almost 83.0% of genetic variation and revealed that the sharing of TRA, RT, RS and RF traits was significantly high. Biplot analysis showed a highly significant correlation matrix (P <0.01) between the pairs of RT and RS, TRL and RS, and RT and RF. Based on PCA ranking and relative value for stress tolerance, IG-20-1183, IG-20-894, IG-20-718 and IG-20-425 expressed tolerance to salinity (T2), IG-20-425 (alkalinity; T4) and IG-20-1183, IG-20-894 and IG-20-1004 were tolerant to salt-alkali treatment (T6). Multi-trait stability index (MTSI) analysis identified three stable oat genotypes (IG-20-714, IG-20-894 and IG-20-425) under multiple environments and these lines can be used in salinity-alkalinity affected areas after yield trials or as donor lines for combined stresses in future breeding programs.

Antitubercular drugs: possible role of natural products acting as antituberculosis medication in overcoming drug resistance and drug-induced hepatotoxicity.

Mycobacterium tuberculosis (Mtb) is a pathogenic bacterium which causes tuberculosis (TB). TB control programmes are facing threats from drug resistance. Multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mtb strains need longer and more expensive treatment with many medications resulting in more adverse effects and decreased chances of treatment outcomes. The World Health Organization (WHO) has emphasised the development of not just new individual anti-TB drugs, but also novel medication regimens as an alternative treatment option for the drug-resistant Mtb strains. Many plants, as well as marine creatures (sponge; Haliclona sp.) and fungi, have been continuously used to treat TB in various traditional treatment systems around the world, providing an almost limitless supply of active components. Natural products, in addition to their anti-mycobacterial action, can be used as adjuvant therapy to increase the efficacy of conventional anti-mycobacterial medications, reduce their side effects, and reverse MDR Mtb strain due to Mycobacterium's genetic flexibility and environmental adaptation. Several natural compounds such as quercetin, ursolic acid, berberine, thymoquinone, curcumin, phloretin, and propolis have shown potential anti-mycobacterial efficacy and are still being explored in preclinical and clinical investigations for confirmation of their efficacy and safety as anti-TB medication. However, more high-level randomized clinical trials are desperately required. The current review provides an overview of drug-resistant TB along with the latest anti-TB medications, drug-induced hepatotoxicity and oxidative stress. Further, the role and mechanisms of action of first and second-line anti-TB drugs and new drugs have been highlighted. Finally, the role of natural compounds as anti-TB medication and hepatoprotectants have been described and their mechanisms discussed.

Graded levels of Eimeria infection modulated gut physiology and temporarily ceased the egg production of laying hens at peak production.

An experiment was conducted to investigate the changes in gastrointestinal physiology, including intestinal leakage, immune response, oxidative stress, along with performance traits, of Hy-Line W-36 laying hens following Eimeria infection at peak egg production. A total of 360 laying hens, at 25 wk of age, were assigned randomly to 5 treatment groups, each consisting of 6 replicate cages, including a nonchallenged control group. The other 4 groups were inoculated with graded levels of mixed Eimeria species as high, medium-high, medium-low, and low doses, respectively. The body weight (BW) and body weight gain (BWG) of laying hens were measured from 0 to 14 days postinoculation (DPI). Average daily feed intake (ADFI) and hen-day egg production (HDEP) were measured from 0 to 15 and 0 to 28 DPI, respectively. Gut permeability was measured on 5 DPI, whereas oxidative stress, immune response, and expression of nutrient transporter genes were measured on 6 and 14 DPI. A significant linear reduction in BW and BWG was observed with increased Eimeria inoculation dosage on both 6 and 14 DPI (P < 0.001, P-Lin < 0.0001). An interaction between the Eimeria dosages and DPI was observed for ADFI (P < 0.0001). Feed intake in the challenged groups decreased starting at 4 DPI, with the most significant drop occurring at 7 DPI, which did not recover until 15 DPI. Following the challenge, gastrointestinal physiology shifted toward the host defense against the Eimeria infection by upregulating mRNA expression of tight junction proteins and immune responses while downregulating the expression of key nutrient transporters on 6 and 14 DPI (P < 0.05). An interaction between the Eimeria inoculation dosage and DPI was also observed for daily HDEP (P < 0.0001). Overall, HDEP was lower in the challenged groups compared to the control. Daily HDEP in the challenged groups dropped from 8 DPI and became similar to the control birds only after 24 DPI. Egg production temporarily ceased in most of the laying hens infected with the high and medium-high dosages of Eimeria. In conclusion, Eimeria infection activated the host immune response, negatively affecting the gastrointestinal health, growth performance, and temporarily ceased the egg production of Hy-Line W-36 laying hens when infected at peak production.

Data mining and spatio-temporal characteristics of urban road traffic emissions: A case study in Shijiazhuang, China.

Accurate estimation of traffic emissions and analysis of spatio-temporal distribution on urban roads play a crucial role in the development of low-carbon transportation system. Traditionally, a region's emission characteristics have been studied using numerous emission models with GPS-based spatio-temporal data. Due to the heavy data processing needs of GPS-based data, emission characteristics for a large region have been studied by dividing the region into a limited number of smaller areas or units. Additionally, GPS data are based on a few vehicles in the traffic which does not fully reflect road conditions. This paper proposed an approach that can be used to study and calculate the spatio-temporal emission pattern of a region at a roadway section level by using Baidu's online traffic data and COPERT model. The proposed method can be used to estimate road-level emission patterns while avoiding the impact of redundant data in large datasets, making the dataset more reliable, applicable, and scalable. The proposed approach has been demonstrated through a study of spatio-temporal emission patterns in the Qiaoxi district within city of Shijiazhuang, China. Online data crawling technology was used to obtain data on urban road traffic speed and driving distance. The linear reference technology was used to construct a two-layer road network model to conduct the coupling and matching of traffic data with the road network data. The COPERT model was implemented to calculate the average traffic emissions on each road in the road network, and a traffic emission intensity index was proposed to quantify the CO, VOC, NOx and CO2 emissions on urban roads in the study area. The analysis results show that the traffic emission intensity of the expressway, trunk road, secondary road, and branch road is high during the morning peak (7 AM-9 AM) and evening peak (5 PM-7 PM). The sections with higher traffic emission intensity are mainly concentrated on the main roads and secondary roads such as Jiefang South Street, Shitong Road and Xinhua Road. Nearly one-third of 2nd Ring and 3rd Ring roads also have relatively high emission intensity. The research results provide new ideas for estimating traffic emissions in urban road networks and analyzing the spatio-temporal distribution of traffic emissions. The research results can also provide a decision-making basis for traffic management departments to formulate energy-saving and emission-reduction measures and promote the development of urban green and low-carbon transportation.

Modulation of terpenoid indole alkaloid pathway via elicitation with phytosynthesized silver nanoparticles for the enhancement of ajmalicine, a pharmaceutically important alkaloid.

MAIN CONCLUSION: The use of silver nanoparticles as elicitors in cell cultures of Rauwolfia serpentina resulted in increased levels of ajmalicine, upregulated structural and regulatory genes, elevated MDA content, and reduced activity of antioxidant enzymes. These findings hold potential for developing a cost-effective method for commercial ajmalicine production. Plants possess an intrinsic ability to detect various stress signals, prompting the activation of defense mechanisms through the reprogramming of metabolites to counter adverse conditions. The current study aims to propose an optimized bioprocess for enhancing the content of ajmalicine in Rauwolfia serpentina callus through elicitation with phytosynthesized silver nanoparticles. Initially, callus lines exhibiting elevated ajmalicine content were established. Following this, a protocol for the phytosynthesis of silver nanoparticles using seed extract from Rauwolfia serpentina was successfully standardized. The physicochemical attributes of the silver nanoparticles were identified, including their spherical shape, size ranging from 6.7 to 28.8 nm in diameter, and the presence of reducing-capping groups such as amino, carbonyl, and amide. Further, the findings indicated that the presence of 2.5 mg L-1 phytosynthesized silver nanoparticles in the culture medium increased the ajmalicine content. Concurrently, structural genes (TDC, SLS, STR, SGD, G10H) and regulatory gene (ORCA3) associated with the ajmalicine biosynthetic pathway were observed to be upregulated. A notable increase in MDA content and a decrease in the activities of antioxidant enzymes were observed. A notable increase in MDA content and a decrease in the activities of antioxidant enzymes were also observed. Our results strongly recommend the augmentation of ajmalicine content in the callus culture of R. serpentina through supplementation with silver nanoparticles, a potential avenue for developing a cost-effective process for the commercial production of ajmalicine.

Molecular dynamics simulations assisted investigation of phytochemicals as potential lead candidates against anti-apoptotic Bcl-B protein.

Due to the multifarious nature of cancer, finding a single definitive cure for this dreadful disease remains an elusive challenge. The dysregulation of the apoptotic pathway or programmed cell death, governed by the Bcl-2 family of proteins plays a crucial role in cancer development and progression. Bcl-B stands out as a unique anti-apoptotic protein from the Bcl-2 family that selectively binds to Bax which inhibits its pro-apoptotic function. Although several inhibitors are reported for Bcl-2 family proteins, no specific inhibitors are available against the anti-apoptotic Bcl-B protein. This study aims to address this research gap by using virtual screening of an in-house library of phytochemicals from seven anti-cancer medicinal plants to identify lead molecules against Bcl-B protein. Through pharmacokinetic analysis and molecular docking studies, we identified three lead candidates (Enterolactone, Piperine, and Protopine) based on appreciable drug-likeliness, ADME properties, and binding affinity values. The identified molecules also exhibited specific interactions with critical amino acid residues of the binding cleft, highlighting their potential as lead candidates. Finally, molecular dynamics simulations and MM/PBSA based binding free energy analysis revealed that Enterolactone (CID_114739) and Piperine (CID_638024) molecules were on par with Obatoclax (CID_11404337), which is a known inhibitor of the Bcl-2 family proteins.Communicated by Ramaswamy H. Sarma.

Meta-QTL analysis in wheat: progress, challenges and opportunities.

Wheat, an important cereal crop globally, faces major challenges due to increasing global population and changing climates. The production and productivity are challenged by several biotic and abiotic stresses. There is also a pressing demand to enhance grain yield and quality/nutrition to ensure global food and nutritional security. To address these multifaceted concerns, researchers have conducted numerous meta-QTL (MQTL) studies in wheat, resulting in the identification of candidate genes that govern these complex quantitative traits. MQTL analysis has successfully unraveled the complex genetic architecture of polygenic quantitative traits in wheat. Candidate genes associated with stress adaptation have been pinpointed for abiotic and biotic traits, facilitating targeted breeding efforts to enhance stress tolerance. Furthermore, high-confidence candidate genes (CGs) and flanking markers to MQTLs will help in marker-assisted breeding programs aimed at enhancing stress tolerance, yield, quality and nutrition. Functional analysis of these CGs can enhance our understanding of intricate trait-related genetics. The discovery of orthologous MQTLs shared between wheat and other crops sheds light on common evolutionary pathways governing these traits. Breeders can leverage the most promising MQTLs and CGs associated with multiple traits to develop superior next-generation wheat cultivars with improved trait performance. This review provides a comprehensive overview of MQTL analysis in wheat, highlighting progress, challenges, validation methods and future opportunities in wheat genetics and breeding, contributing to global food security and sustainable agriculture.

Activation-induced cytidine deaminase an antibody diversification enzyme interacts with chromatin modifier UBN1 in B-cells.

Activation-induced cytidine deaminase (AID) is the key mediator of antibody diversification in activated B-cells by the process of somatic hypermutation (SHM) and class switch recombination (CSR). Targeting AID to the Ig genes requires transcription (initiation and elongation), enhancers, and its interaction with numerous factors. Furthermore, the HIRA chaperon complex, a regulator of chromatin architecture, is indispensable for SHM. The HIRA chaperon complex consists of UBN1, ASF1a, HIRA, and CABIN1 that deposit H3.3 onto the DNA, the SHM hallmark. We explored whether UBN1 interacts with AID using computational and in-vitro experiments. Interestingly, our in-silico studies, such as molecular docking and molecular dynamics simulation results, predict that AID interacts with UBN1. Subsequently, co-immunoprecipitation and pull-down experiments established interactions between UBN1 and AID inside B-cells. Additionally, a double immunofluorescence assay confirmed that AID and UBN1 were co-localized in the human and chicken B-cell lines. Moreover, proximity ligation assay studies validated that AID interacts with UBN1. Ours is the first report on the interaction of genome mutator enzyme AID with UBN1. Nevertheless, the fate of interaction between UBN1 and AID is yet to be explored in the context of SHM or CSR.