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Background: Hypertension is a critical public health issue worldwide. The identification of specific proteomic biomarkers in the Qatari population aims to advance personalized treatment strategies., Methods: We conducted proteomic profiling on 778 Qatari individuals using an aptamer-based SOMAscan platform to analyze 1,305 biomarkers. Statistical analysis involved two-way ANOVA and association analyses with FDR correction, alongside pathway and gene-set enrichment analyses using Reactome and DisGeNET databases., Results: The study identified 26 significant protein biomarkers associated with hypertension. Notably, QORL1 and BMP1 were identified as novel protein biomarkers. Enrichment analysis linked these biomarkers to critical pathways involved in vascular biology, immune system responses, and pathologies like arteriosclerosis and coronary artery disease. Correlation analyses highlighted robust interactions, particularly between QORL1 and various Apolipoprotein E isoforms, suggesting these biomarkers play pivotal roles in the molecular mechanisms underlying hypertension., Conclusions: This research enhances our understanding of the molecular basis of hypertension in the Qatari population and supports the development of precision medicine approaches for treatment., Competing Interests: Declarations. Ethics approval and consent to participate: Ethical approval was obtained from the Institutional Review Board of the Qatar Biobank (QF-QBB-RES-ACC-00095) and carried out according to the Declaration of Helsinki. A written consent was obtained for all participants to share their data. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Background: Wheat landraces represent a reservoir of genetic diversity that can support wheat improvement through breeding. A core panel of 300 Watkins wheat landraces, as well as 16 non-Watkins landraces and elite wheat cultivars, was grown during the 2020-2021 and 2021-2022 seasons at four Agricultural Research Stations in Egypt, Gemmiza, Nubaria, Sakha, and Sids, to evaluate the core panel for agromorphological and yield-related traits. The genetic population structure within these genotypes were assessed using 35,143 single nucleotide polymorphisms (SNPs)., Results: Cluster analyses using Discriminant Analysis of Principal Components (DAPC) and k-means revealed three clusters with moderate genetic differentiation and population structure, possibly due to wheat breeding systems and geographical isolation. The best ancestry was k = 4, but k = 2 and k = 3 were also significant. A genome-wide association study (GWAS) identified clustered marker trait associations (MTAs) linked to thousand kernel weight on chromosome 5A, plant height on chromosomes 3B and 1D, days to heading on chromosomes 2A, 4B, 5B and 1D, and plant maturity on chromosomes 3A, 2B, and 6B. In the future, these MTAs can be used to accelerate the incorporation of beneficial alleles into locally adapted germplasm through marker-assisted selection. Gene enrichment analysis identified key genes within these loci, including Reduced height-1 (Rht-A1) and stress-related genes., Conclusion: These findings underscore significant genetic connections and the involvement of crucial biological pathways., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Elkot, Nassar, Elmassry, Forner-Martínez, Awal, Wingen, Griffiths, Alsamman and Kehel.)

Background: Arbuscular mycorrhiza (AM) refers to a symbiotic association between plant roots and fungi that enhances the uptake of mineral nutrients from the soil and enables the plant to tolerate abiotic and biotic stresses. Although previously reported RNA-seq analyses have identified large numbers of AM-responsive genes in model plants, such as Solanum lycopersicum L., further studies are underway to comprehensively understand the complex interactions between plant roots and AM, especially in terms of the short- and long-term responses after inoculation., Results: Herein, we used RNA-seq technology to obtain the transcriptomes of tomato roots inoculated with the fungus Rhizophagus irregularis at 7 and 30 days post inoculation (dpi). Of the 1,019 differentially expressed genes (DEGs) in tomato roots, 635 genes showed differential expressions between mycorrhizal and non-mycorrhizal associations at the two time points. The number of upregulated DEGs far exceeded the number of downregulated ones at 7 dpi, and this difference decreased at 30 dpi. Several notable genes were particularly involved in the plant defense, plant growth and development, ion transport, and biological processes, namely, GABAT , AGP , POD , NQO1 , MT4 , MTA , and AROGP3 . In addition, the Kyoto encyclopedia of genes and genomes pathway enrichment analysis revealed that some of the genes were involved in different pathways, including those of ascorbic acid ( AFRR , GME1 , and APX ), metabolism ( CYP , GAPC2 , and CAM2 ), and sterols ( CYC1 and HMGR ), as well as genes related to cell division and cell cycle ( CDKB2 and PCNA )., Conclusion: These findings provide valuable new data on AM-responsive genes in tomato roots at both short- and long-term postinoculation stages, enabling the deciphering of biological interactions between tomato roots and symbiotic fungi., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Abdelsattar, Soliman, Mohamed, Radwan, El-Mahdy, Mousa, Khalil, Osman, Alameldin, Hussein, Hassanein, Abdallah, Alsamman and Osama.)

Background: Monkeypox (Mpox) is an important human pathogen without etiological treatment. A viral-host interactome study may advance our understanding of molecular pathogenesis and lead to the discovery of suitable therapeutic targets., Methods: GEO Expression datasets characterizing mRNA profile changes in different host responses to poxviruses were analyzed for shared pathway identification, and then, the Protein-protein interaction (PPI) maps were built. The viral gene expression datasets of Monkeypox virus (MPXV) and Vaccinia virus (VACV) were used to identify the significant viral genes and further investigated for their binding to the library of targeting molecules., Results: Infection with MPXV interferes with various cellular pathways, including interleukin and MAPK signaling. While most host differentially expressed genes (DEGs) are predominantly downregulated upon infection, marked enrichments in histone modifiers and immune-related genes were observed. PPI analysis revealed a set of novel virus-specific protein interactions for the genes in the above functional clusters. The viral DEGs exhibited variable expression patterns in three studied cell types: primary human monocytes, primary human fibroblast, and HeLa, resulting in 118 commonly deregulated proteins. Poxvirus proteins C6R derived protein K7 and K7R of MPXV and VACV were prioritized as targets for potential therapeutic interventions based on their histone-regulating and immunosuppressive properties. In the computational docking and Molecular Dynamics (MD) experiments, these proteins were shown to bind the candidate small molecule S3I-201, which was further prioritized for lead development., Results: MPXV circumvents cellular antiviral defenses by engaging histone modification and immune evasion strategies. C6R-derived protein K7 binding candidate molecule S3I-201 is a priority promising candidate for treating Mpox., (© 2024. The Author(s).)

Weeds pose a major constraint in lentil cultivation, leading to decrease farmers' revenues by reducing the yield and increasing the management costs. The development of herbicide tolerant cultivars is essential to increase lentil yield. Even though herbicide tolerant lines have been identified in lentils, breeding efforts are still limited and lack proper validation. Marker assisted selection (MAS) can increase selection accuracy at early generations. Total 292 lentil accessions were evaluated under different dosages of two herbicides, metribuzin and imazethapyr, during two seasons at Marchouch, Morocco and Terbol, Lebanon. Highly significant differences among accessions were observed for days to flowering (DF) and maturity (DM), plant height (PH), biological yield (BY), seed yield (SY), number of pods per plant (NP), as well as the reduction indices (RI) for PH, BY, SY and NP. A total of 10,271 SNPs markers uniformly distributed along the lentil genome were assayed using Multispecies Pulse SNP chip developed at Agriculture Victoria, Melbourne. Meta-GWAS analysis was used to detect marker-trait associations, which detected 125 SNPs markers associated with different traits and clustered in 85 unique quantitative trait loci. These findings provide valuable insights for initiating MAS programs aiming to enhance herbicide tolerance in lentil crop., (© 2024. The Author(s).)

Background and Objectives : Urinary tract infections [UTIs] are considered the third most known risk of infection in human health around the world. There is increasing appreciation for the pathogenicity of Gram-positive and Gram-negative strains in UTIs, aside from fungal infection, as they have numerous virulence factors. Materials and Methods : In this study, fifty urine samples were collected from patients suffering from UTI. Among the isolates of UTI microbes, six isolates were described as MDR isolates after an antibiotic susceptibility test carried out using ten different antibiotics. An alternative treatment for microbial elimination involved the use of biosynthesized silver nanoparticles (AgNPs) derived from Solanum lycopersicum [ S. cumin ]. Results : The sizes and shapes of AgNPs were characterized through TEM imaging, which showed spherical particles in a size range of 35-80 nm, of which the average size was 53 nm. Additionally, the silver nanoparticles (AgNPs) demonstrated inhibitory activity against Staphylococcus aureus (OR648079), exhibiting a 31 mm zone of inhibition at a minimum inhibitory concentration (MIC) of 4 mg/mL and a minimum bactericidal concentration (MBC) of 8 mg/mL. This was followed by Aspergillus niger (OR648075), which showed a 30 mm inhibition zone at an MIC of 16 mg/mL and a minimum fungicidal concentration (MFC) of 32 mg/mL. Then, Enterococcus faecalis (OR648078), Klebsiella pneumoniae (OR648081), and Acinetobacter baumannii (OR648080) each displayed a 29 mm zone of inhibition at an MIC of 8 mg/mL and an MBC of 16 mg/mL. The least inhibition was observed against Candida auris (OR648076), with a 25 mm inhibition zone at an MIC of 16 mg/mL and an MFC of 32 mg/mL. Furthermore, AgNPs at different concentrations removed DPPH and H 2 O 2 at an IC50 value of 13.54 μg/mL. Also, AgNPs at 3 mg/mL showed remarkable DNA fragmentation in all bacterial strains except Enterococcus faecalis . The phytochemical analysis showed the presence of different active organic components in the plant extract, which concluded that rutin was 88.3 mg/g, garlic acid was 70.4 mg/g, and tannic acid was 23.7 mg/g. Finally, AgNPs concentrations in the range of 3-6 mg/mL showed decreased expression of two of the fundamental genes necessary for biofilm formation within Staphylococcus aureus , fnbA (6 folds), and Cna (12.5 folds) when compared with the RecA gene, which decreased by one-fold when compared with the control sample. These two genes were submitted with NCBI accession numbers [OR682119] and [OR682118], respectively. Conclusions : The findings from this study indicate that biosynthesized AgNPs from Solanum lycopersicum exhibit promising antimicrobial and antioxidant properties against UTI pathogens, including strains resistant to multiple antibiotics. This suggests their potential as an effective alternative treatment for UTIs. Further research is warranted to fully understand the mechanisms of action and to explore the therapeutic applications of these nanoparticles in combating UTIs.

Chickpea, renowned for its exceptional nutritional value, stands as a crucial crop, serving as a dietary staple in various parts of the world. However, its productivity faces a significant challenge in the form of drought stress. This challenge highlights the urgent need to find genetic markers linked to drought tolerance for effective breeding programs. The primary objective of this study is to identify genetic markers associated with drought tolerance to facilitate effective breeding programs. To address this, we cultivated 185 chickpea accessions in two distinct locations in Lebanon over a two-year period, subjecting them to both irrigated and rain-fed environments. We assessed 11 drought-linked traits, including morphology, growth, yield, and tolerance score. SNP genotyping revealed 1344 variable SNP markers distributed across the chickpea genome. Genetic diversity across populations originating from diverse geographic locations was unveiled by the PCA, clustering, and structure analysis indicating that these genotypes have descend from five or four distinct ancestors. A genome-wide association study (GWAS) revealed several marker trait associations (MTAs) associated with the traits evaluated. Within the rainfed conditions, 11 significant markers were identified, each associated with distinct chickpea traits. Another set of 11 markers exhibited associations in both rainfed and irrigated environments, reflecting shared genetic determinants across these conditions for the same trait. The analysis of linkage disequilibrium (LD) highlighted two genomic regions with notably strong LD, suggesting significant interconnections among several investigated traits. This was further investigated by the correlation between major markers associated with these traits. Gene annotation of the identified markers has unveiled insights into 28 potential genes that play a role in influencing various chickpea drought-linked traits. These traits encompass crucial aspects such as blooming organ development, plant growth, seed weight, starch metabolism, drought regulation, and height index. Among the identified genes are CPN60-2 , hsp70 , GDSL(GELP) , AHL16 , NAT3 , FAB1B , bZIP , and GL21 . These genes collectively contribute to the multifaceted response of chickpea plants to drought stress. Our identified genetic factors exert their influence in both irrigated and rainfed environments, emphasizing their importance in shaping chickpea characteristics., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Istanbuli, Nassar, Abd El-Maksoud, Tawkaz, Alsamman and Hamwieh.)

Introduction: Chickpea is a legume crop that thrives in regions with semi-arid or temperate climates. Its seeds are an excellent source of proteins, carbohydrates, and minerals, especially high-quality proteins. Chickpea cultivation faces several challenges including Fusarium wilt (FW), a major fungal disease that significantly reduces productivity. Methods: In this study, a Genome-wide Association Analysis (GWAS) was conducted to identify multiple genomic loci associated with FW resistance in chickpea. We conducted a comprehensive evaluation of 180 chickpea genotypes for FW resistance across three distinct locations (Ethiopia, Tunisia, and Lebanon) during the 2-year span from 2015 to 2016. Disease infection measurements were recorded, and the wilt incidence of each genotype was calculated. We employed a set of 11,979 single nucleotide polymorphisms (SNPs) markers distributed across the entire chickpea genome for SNP genotyping. Population structure analysis was conducted to determine the genetic structure of the genotypes. Results and Discussion: The population structure unveiled that the analyzed chickpea germplasm could be categorized into four sub-populations. Notably, these sub-populations displayed diverse geographic origins. The GWAS identified 11 SNPs associated with FW resistance, dispersed across the genome. Certain SNPs were consistent across trials, while others were specific to particular environments. Chromosome CA2 harbored five SNP markers, CA5 featured two, and CA4, CA6, CA7, and CA8 each had one representative marker. Four SNPs demonstrated an association with FW resistance, consistently observed across a minimum of three distinct environments. These SNPs included SNP5826041, SNP5825086, SNP11063413, SNP5825195, which located in CaFeSOD, CaS13like, CaNTAQ1, and CaAARS genes, respectively. Further investigations were conducted to gain insights into the functions of these genes and their role in FW resistance. This progress holds promise for reducing the negative impact of the disease on chickpea production., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Alsamman, H. Mousa, Istanbuli, Abd El-Maksoud, Tawkaz and Hamwieh.)

Autism Spectrum Disorder (ASD) is a complex neurodevelopmental condition characterized by altered brain connectivity and function. In this study, we employed advanced bioinformatics and explainable AI to analyze gene expression associated with ASD, using data from five GEO datasets. Among 351 neurotypical controls and 358 individuals with autism, we identified 3,339 Differentially Expressed Genes (DEGs) with an adjusted p-value (≤ 0.05). A subsequent meta-analysis pinpointed 342 DEGs (adjusted p-value ≤ 0.001), including 19 upregulated and 10 down-regulated genes across all datasets. Shared genes, pathogenic single nucleotide polymorphisms (SNPs), chromosomal positions, and their impact on biological pathways were examined. We identified potential biomarkers (HOXB3, NR2F2, MAPK8IP3, PIGT, SEMA4D, and SSH1) through text mining, meriting further investigation. Additionally, ‎we shed light on the roles of RPS4Y1 and KDM5D genes in neurogenesis and neurodevelopment. Our analysis detected 1,286 SNPs linked to ASD-related conditions, of which 14 high-risk SNPs were located on chromosomes 10 and X. We highlighted potential missense SNPs associated with FGFR inhibitors, suggesting that it may serve as a promising biomarker for responsiveness to targeted therapies. Our explainable AI model identified the MID2 gene as a potential ASD biomarker. This research unveils vital genes and potential biomarkers, providing a foundation for novel gene discovery in complex diseases., (© 2023. The Author(s).)

Next-generation sequencing technologies have opened new avenues for using genomic data to study and develop molecular markers and improve genetic resources. Simple Sequence Repeats (SSRs) as genetic markers are increasingly used in molecular diversity and molecular breeding programs that require bioinformatics pipelines to analyze the large amounts of data. Therefore, there is an ongoing need for online tools that provide computational resources with minimal effort and maximum efficiency, including automated development of SSR markers. These tools should be flexible, customizable, and able to handle the ever-increasing amount of genomic data. Here we introduce MegaSSR (https://bioinformatics.um6p.ma/MegaSSR), a web server and a standalone pipeline that enables the design of SSR markers in any target genome. MegaSSR allows users to design targeted PCR-based primers for their selected SSR repeats and includes multiple tools that initiate computational pipelines for SSR mining, classification, comparisons, PCR primer design, in silico PCR validation, and statistical visualization. MegaSSR results can be accessed, searched, downloaded, and visualized with user-friendly web-based tools. These tools provide graphs and tables showing various aspects of SSR markers and corresponding PCR primers. MegaSSR will accelerate ongoing research in plant species and assist breeding programs in their efforts to improve current genomic resources., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Mokhtar, Alsamman and El Allali.)

Multiple sequence alignment (MSA) is essential for understanding genetic variations controlling phenotypic traits in all living organisms. The post-analysis of MSA results is a difficult step for researchers who do not have programming skills. Especially those working with large scale data and looking for potential variations or variable sample groups. Generating bi-allelic data and the comparison of wild and alternative gene forms are important steps in population genetics. Customising MSA visualisation for a single page view is difficult, making viewing potential indels and variations challenging. There are currently no bioinformatics tools that permit post-MSA analysis, in which data on gene and single nucleotide scales could be combined with gene annotations and used for cluster analysis. We introduce "AlignStatPlot," a new R package and online tool that is well-documented and easy-to use for MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analyses on sequencing data and generates new visualisation methods for MSA results. When compared to currently available tools, AlignStatPlot provides a robust ability to handle and visualise diversity data, while the online version will save time and encourage researchers to focus on explaining their findings. It is a simple tool that can be used in conjunction with population genetics software., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Alsamman et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

New evidence strongly discloses the pathogenesis of host-associated microbiomes in respiratory diseases. The microbiome dysbiosis modulates the lung's behavior and deteriorates the respiratory system's effective functioning. Several exogenous and environmental factors influence the development of asthma and chronic lung disease. The relationship between asthma and microbes is reasonably understood and yet to be investigated for more substantiation. The comorbidities such as SARS-CoV-2 further exacerbate the health condition of the asthma-affected individuals. This study examines the raw 16S rRNA sequencing data collected from the saliva and nasopharyngeal regions of pre-existing asthma (23) and non-asthma patients (82) infected by SARS-CoV-2 acquired from the public database. The experiment is designed in a two-fold pattern, analyzing the associativity between the samples collected from the saliva and nasopharyngeal regions. Later, investigates the microbial pathogenesis, its role in exacerbations of respiratory disease, and deciphering the diagnostic biomarkers of the target condition. LEfSE analysis identified that Actinobacteriota and Pseudomonadota are enriched in the SARS-CoV-2-non-asthma group and SARS-CoV-2 asthma group of the salivary microbiome, respectively. Random forest algorithm is trained with amplicon sequence variants (ASVs) attained better classification accuracy, ROC scores on nasal (84% and 87%) and saliva datasets (93% and 97.5%). Rothia mucilaginosa is less abundant, and Corynebacterium tuberculostearicum showed higher abundance in the SARS-CoV-2 asthma group. The increase in Streptococcus at the genus level in the SARS-CoV-2-asthma group is evidence of discriminating the subgroups., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Sekaran et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Several proteins and peptides have therapeutic potential and can be used for cancer therapy. By binding to cell surface receptors and other indicators uniquely linked with or overexpressed on tumors compared to healthy tissue, protein biologics enhance the active targeting of cancer cells, as opposed to the passive targeting of cells by conventional small-molecule chemotherapeutics. This study focuses on peptide medications that exist to slow or stop tumor growth and the spread of cancer, demonstrating the therapeutic potential of peptides in cancer treatment. As an alternative to standard chemotherapy, peptides that selectively kill cancer cells while sparing healthy tissue are developing. A mountain of clinical evidence supports the efficacy of peptide-based cancer vaccines. Since a single treatment technique may not be sufficient to produce favourable results in the fight against cancer, combination therapy is emerging as an effective option to generate synergistic benefits. One example of this new area is the use of anticancer peptides in combination with nonpeptidic cytotoxic drugs or the combination of immunotherapy with conventional therapies like radiation and chemotherapy. This review focuses on the different natural and synthetic peptides obtained and researched. Discoveries, manufacture, and modifications of peptide drugs, as well as their contemporary applications, are summarized in this review. We also discuss the benefits and difficulties of potential advances in therapeutic peptides., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier Masson SAS.. All rights reserved.)

Grass pea is a promising crop with the potential to provide food and fodder, but its genomics has not been adequately explored. Identifying genes for desirable traits, such as drought tolerance and disease resistance, is critical for improving the plant. Grass pea currently lacks known R-genes, including the nucleotide-binding site-leucine-rich repeat (NBS-LRR) gene family, which plays a key role in protecting the plant from biotic and abiotic stresses. In our study, we used the recently published grass pea genome and available transcriptomic data to identify 274 NBS-LRR genes. The evolutionary relationships between the classified genes on the reported plants and LsNBS revealed that 124 genes have TNL domains, while 150 genes have CNL domains. All genes contained exons, ranging from 1 to 7. Ten conserved motifs with lengths ranging from 16 to 30 amino acids were identified. We found TIR-domain-containing genes in 132 LsNBSs, with 63 TIR-1 and 69 TIR-2, and RX-CCLike in 84 LsNBSs. We also identified several popular motifs, including P-loop, Uup, kinase-GTPase, ABC, ChvD, CDC6, Rnase_H, Smc, CDC48, and SpoVK. According to the gene enrichment analysis, the identified genes undergo several biological processes such as plant defense, innate immunity, hydrolase activity, and DNA binding. In the upstream regions, 103 transcription factors were identified that govern the transcription of nearby genes affecting the plant excretion of salicylic acid, methyl jasmonate, ethylene, and abscisic acid. According to RNA-Seq expression analysis, 85% of the encoded genes have high expression levels. Nine LsNBS genes were selected for qPCR under salt stress conditions. The majority of the genes showed upregulation at 50 and 200  μ M NaCl. However, LsNBS-D18 , LsNBS-D204 , and LsNBS-D180 showed reduced or drastic downregulation compared to their respective expression levels, providing further insights into the potential functions of LsNBSs under salt stress conditions. They provide valuable insights into the potential functions of LsNBSs under salt stress conditions. Our findings also shed light on the evolution and classification of NBS-LRR genes in legumes, highlighting the potential of grass pea. Further research could focus on the functional analysis of these genes, and their potential use in breeding programs to improve the salinity, drought, and disease resistance of this important crop., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Alsamman, Mousa, Nassar, Faheem, Radwan, Adly, Hussein, Istanbuli, Mokhtar, Elakkad, Kehel, Hamwieh, Abdelsattar and El Allali.)

Beta-hemolytic multidrug-resistant bacteria (MDR) are highly regarded as a major public health risk because they are resistant to at least 10 antibiotics in different groups with different mechanisms of action. The present study shows that among 98 bacterial isolates collected from laboratory fecal samples: 15 were beta-hemolytic and tested against 10 different antibiotics. 15 beta-hemolytic; 5 isolates exhibit strong multidrug resistance traits. Isolate 5 Escherichia coli (E. coli), Isolate 7 (E. coli), Isolate 21 (Enterococcus faecium), Isolate 27 (Staphylococcus sciuri), and isolate 36 (E. coli) are largely untested antibiotics. Substances (clear zone >10 mm) Its growth sensitivity to different types of nanoparticles was further evaluated by the agar well diffusion method. AgO, TiO2, ZnO, and Fe3O4 nanoparticles have been separately synthesized by microbial and plant-mediated biosynthesis. By evaluating the antibacterial activity of different nanoparticle types against selected MDR isolates, the results showed that global MDR bacterial growth was inhibited differently depending on the nanoparticle type. TiO 2 was the most potent antibacterial nanoparticle type, followed by AgO, while Fe3O4 showed the least efficacy against selected isolates. The MICs of microbially synthesized AgO and TiO 2 nanoparticles were 3 μg (67.2 μg/mL) and 9 μg (180 μg/mL) for isolates 5 and 27, respectively, indicating that biosynthetic nanoparticles via pomegranate of antibacterial activity at a higher MIC than microbial-mediated ones, it recorded (300 and 375 μg/ml, respectively) of AgO and TiO 2 nanoparticles for isolates 5 and 27. Biosynthesized nanoparticles were examined by TEM, the average sizes of microbial AgO and TiO 2 nanoparticles were 30 nm and 70 nm, respectively, and the average sizes of plant mediated AgO and TiO 2 NPs were 52 nm and 82 nm respectively. Two most potent extensive MDR isolates (5 and 27) were identified as E. coli and Staphylococcus sciuri by 16s rDNA technology, and the sequencing results of the isolates were deposited with NCBI GenBank under accession numbers ON739202 and ON739204, respectively., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Microbial Dysbiosis is associated with the etiology and pathogenesis of diseases. The studies on the vaginal microbiome in cervical cancer are essential to discern the cause and effect of the condition. The present study characterizes the microbial pathogenesis involved in developing cervical cancer. Relative species abundance assessment identified Firmicutes , Actinobacteria , and Proteobacteria dominating the phylum level. A significant increase in Lactobacillus iners and Prevotella timonensis at the species level revealed its pathogenic influence on cervical cancer progression. The diversity, richness, and dominance analysis divulges a substantial decline in cervical cancer compared to control samples. The β diversity index proves the homogeneity in the subgroups' microbial composition. The association between enriched Lactobacillus iners at the species level, Lactobacillus , Pseudomonas , and Enterococcus genera with cervical cancer is identified by Linear discriminant analysis Effect Size (LEfSe) prediction. The functional enrichment corroborates the microbial disease association with pathogenic infections such as aerobic vaginitis, bacterial vaginosis, and chlamydia. The dataset is trained and validated with repeated k-fold cross-validation technique using a random forest algorithm to determine the discriminative pattern from the samples. SHapley Additive exPlanations (SHAP), a game theoretic approach, is employed to analyze the results predicted by the model. Interestingly, SHAP identified that the increase in Ralstonia has a higher probability of predicting the sample as cervical cancer. New evidential microbiomes identified in the experiment confirm the presence of pathogenic microbiomes in cervical cancer vaginal samples and their mutuality with microbial imbalance.

Introduction: Osteosarcoma is a rare disorder among cancer, but the most frequently occurring among sarcomas in children and adolescents. It has been reported to possess the relapsing capability as well as accompanying collateral adverse effects which hinder the development process of an effective treatment plan. Using networks of omics data to identify cancer biomarkers could revolutionize the field in understanding the cancer. Cancer biomarkers and the molecular mechanisms behind it can both be understood by studying the biological networks underpinning the etiology of the disease., Methods: In our study, we aimed to highlight the hub genes involved in gene-gene interaction network to understand their interaction and how they affect the various biological processes and signaling pathways involved in Osteosarcoma. Gene interaction network provides a comprehensive overview of functional gene analysis by providing insight into how genes cooperatively interact to elicit a response. Because gene interaction networks serve as a nexus to many biological problems, their employment of it to identify the hub genes that can serve as potential biomarkers remain widely unexplored. A dynamic framework provides a clear understanding of biological complexity and a pathway from the gene level to interaction networks., Results: Our study revealed various hub genes viz. TP53, CCND1, CDK4, STAT3, and VEGFA by analyzing various topological parameters of the network, such as highest number of interactions, average shortest path length, high cluster density, etc. Their involvement in key signaling pathways, such as the FOXM1 transcription factor network, FAK-mediated signaling events, and the ATM pathway, makes them significant candidates for studying the disease. The study also highlighted significant enrichment in GO terms (Biological Processes, Molecular Function, and Cellular Processes), such as cell cycle signal transduction, cell communication, kinase binding, transcription factor activity, nucleoplasm, PML body, nuclear body, etc., Conclusion: To develop better therapeutics, a specific approach toward the disease targeting the hub genes involved in various signaling pathways must have opted to unravel the complexity of the disease. Our study has highlighted the candidate hub genes viz. TP53, CCND1 CDK4, STAT3, VEGFA. Their involvement in the major signaling pathways of Osteosarcoma makes them potential candidates to be targeted for drug development. The highly enriched signaling pathways include FOXM1 transcription pathway, ATM signal-ling pathway, FAK mediated signaling events, Arf6 signaling events, mTOR signaling pathway, and Integrin family cell surface interactions. Targeting the hub genes and their associated functional partners which we have reported in our studies may be efficacious in developing novel therapeutic targets., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Dey, Vasudevan, Doss C., Kumar, El Allali, Alsamman and Zayed.)

The progressive, chronic nature of Alzheimer's disease (AD), a form of dementia, defaces the adulthood of elderly individuals. The pathogenesis of the condition is primarily unascertained, turning the treatment efficacy more arduous. Therefore, understanding the genetic etiology of AD is essential to identifying targeted therapeutics. This study aimed to use machine-learning techniques of expressed genes in patients with AD to identify potential biomarkers that can be used for future therapy. The dataset is accessed from the Gene Expression Omnibus (GEO) database (Accession Number: GSE36980). The subgroups (AD blood samples from frontal, hippocampal, and temporal regions) are individually investigated against non-AD models. Prioritized gene cluster analyses are conducted with the STRING database. The candidate gene biomarkers were trained with various supervised machine-learning (ML) classification algorithms. The interpretation of the model prediction is perpetrated with explainable artificial intelligence (AI) techniques. This experiment revealed 34, 60, and 28 genes as target biomarkers of AD mapped from the frontal, hippocampal, and temporal regions. It is identified ORAI2 as a shared biomarker in all three areas strongly associated with AD's progression. The pathway analysis showed that STIM1 and TRPC3 are strongly associated with ORAI2. We found three hub genes, TPI1, STIM1, and TRPC3, in the network of the ORAI2 gene that might be involved in the molecular pathogenesis of AD. Naive Bayes classified the samples of different groups by fivefold cross-validation with 100% accuracy. AI and ML are promising tools in identifying disease-associated genes that will advance the field of targeted therapeutics against genetic diseases., (© 2023. The Author(s).)

Background: The basic helix-loop-helix (bHLH) transcription factor is a vital component in plant biology, with a significant impact on various aspects of plant growth, cell development, and physiological processes. Grass pea is a vital agricultural crop that plays a crucial role in food security. However, the lack of genomic information presents a major challenge to its improvement and development. This highlights the urgency for deeper investigation into the function of bHLH genes in grass pea to improve our understanding of this important crop. Results: The identification of bHLH genes in grass pea was performed on a genome-wide scale using genomic and transcriptomic screening. A total of 122 genes were identified as having conserved bHLH domains and were functionally and fully annotated. The LsbHLH proteins could be classified into 18 subfamilies. There were variations in intron-exon distribution, with some genes lacking introns. The cis-element and gene enrichment analyses showed that the LsbHLHs were involved in various plant functions, including response to phytohormones, flower and fruit development, and anthocyanin synthesis. A total of 28 LsbHLHs were found to have cis-elements associated with light response and endosperm expression biosynthesis. Ten conserved motifs were identified across the LsbHLH proteins. The protein-protein interaction analysis showed that all LsbHLH proteins interacted with each other, and nine of them displayed high levels of interaction. RNA-seq analysis of four Sequence Read Archive (SRA) experiments showed high expression levels of LsbHLHs across a range of environmental conditions. Seven highly expressed genes were selected for qPCR validation, and their expression patterns in response to salt stress showed that LsbHLHD4, LsbHLHD5, LsbHLHR6, LsbHLHD8, LsbHLHR14, LsbHLHR68 , and LsbHLHR86 were all expressed in response to salt stress. Conclusion: The study provides an overview of the bHLH family in the grass pea genome and sheds light on the molecular mechanisms underlying the growth and evolution of this crop. The report covers the diversity in gene structure, expression patterns, and potential roles in regulating plant growth and response to environmental stress factors in grass pea. The identified candidate LsbHLHs could be utilized as a tool to enhance the resilience and adaptation of grass pea to environmental stress., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Alsamman, Abdelsattar, El Allali, Radwan, Nassar, Mousa, Hussein, Mokhtar, Abd El-Maksoud, Istanbuli, Kehel and Hamwieh.)

Pomegranate has a unique evolutionary history given that different cultivars have eight or nine bivalent chromosomes with possible crossability between the two classes. Therefore, it is important to study chromosome evolution in pomegranate to understand the dynamics of its population. Here, we de novo assembled the Azerbaijani cultivar "Azerbaijan guloyshasi" (AG2017; 2n = 16) and re-sequenced six cultivars to track the evolution of pomegranate and to compare it with previously published de novo assembled and re-sequenced cultivars. High synteny was observed between AG2017, Bhagawa (2n = 16), Tunisia (2n = 16), and Dabenzi (2n = 18), but these four cultivars diverged from the cultivar Taishanhong (2n = 18) with several rearrangements indicating the presence of two major chromosome evolution events. Major presence/absence variations were not observed as >99% of the five genomes aligned across the cultivars, while >99% of the pan-genic content was represented by Tunisia and Taishanhong only. We also revisited the divergence between soft- and hard-seeded cultivars with less structured population genomic data, compared to previous studies, to refine the selected genomic regions and detect global migration routes for pomegranate. We reported a unique admixture between soft- and hard-seeded cultivars that can be exploited to improve the diversity, quality, and adaptability of local pomegranate varieties around the world. Our study adds body knowledge to understanding the evolution of the pomegranate genome and its implications for the population structure of global pomegranate diversity, as well as planning breeding programs aiming to develop improved cultivars., Competing Interests: Authors PK and VS were employed by Softberry Inc. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Akparov, Hajiyeva, Abbasov, Kaur, Hamwieh, Alsamman, Hajiyev, Babayeva, Izzatullayeva, Mustafayeva, Mehdiyeva, Mustafayev, Shahmuradov, Kosarev, Solovyev, Salamov and Jighly.)

LTR-retrotransposons (LTR-RTs) are a large group of transposable elements that replicate through an RNA intermediate and alter genome structure. The activities of LTR-RTs in plant genomes provide helpful information about genome evolution and gene function. LTR-RTs near or within genes can directly alter gene function. This work introduces PlantLTRdb, an intact LTR-RT database for 195 plant species. Using homology- and de novo structure-based methods, a total of 150.18 Gbp representing 3,079,469 pseudomolecules/scaffolds were analyzed to identify, characterize, annotate LTR-RTs, estimate insertion ages, detect LTR-RT-gene chimeras, and determine nearby genes. Accordingly, 520,194 intact LTR-RTs were discovered, including 29,462 autonomous and 490,732 nonautonomous LTR-RTs. The autonomous LTR-RTs included 10,286 Gypsy and 19,176 Copia , while the nonautonomous were divided into 224,906 Gypsy , 218,414 Copia , 1,768 BARE-2, 3,147 TR-GAG and 4,2497 unknown. Analysis of the identified LTR-RTs located within genes showed that a total of 36,236 LTR-RTs were LTR-RT-gene chimeras and 11,619 LTR-RTs were within pseudo-genes. In addition, 50,026 genes are within 1 kbp of LTR-RTs, and 250,587 had a distance of 1 to 10 kbp from LTR-RTs. PlantLTRdb allows researchers to search, visualize, BLAST and analyze plant LTR-RTs. PlantLTRdb can contribute to the understanding of structural variations, genome organization, functional genomics, and the development of LTR-RT target markers for molecular plant breeding. PlantLTRdb is available at https://bioinformatics.um6p.ma/PlantLTRdb., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Mokhtar, Alsamman and El Allali.)

As a complex endocrine and metabolic condition, polycystic ovarian syndrome (PCOS) affects women's reproductive health. These common symptoms include hirsutism, hyperandrogenism, ovulatory dysfunction, irregular menstruation, and infertility. No one knows what causes it or how to stop it yet. Alterations in gut microbiota composition and disruptions in secondary bile acid production appear to play a causative role in developing PCOS. PCOS pathophysiology and phenotypes are tightly related to both enteric and vaginal bacteria. Patients with PCOS exhibit changed microbiome compositions and decreased microbial diversity. Intestinal microorganisms also alter PCOS patient phenotypes by upregulating or downregulating hormone release, gut-brain mediators, and metabolite synthesis. The human body's gut microbiota, also known as the "second genome," can interact with the environment to improve metabolic and immunological function. Inflammation is connected to PCOS and may be caused by dysbiosis in the gut microbiome. This review sheds light on the recently discovered connections between gut microbiota and insulin resistance (IR) and the potential mechanisms of PCOS. This study also describes metabolomic studies to obtain a clear view of PCOS and ways to tackle it.

Environmental stresses, particularly drought, limit symbiotic nitrogen fixation in legumes, resulting in decreased yielding capacity. Drought is one of the most important constraints limiting yield potential in crops and it is the major abiotic stress that can cause more than 70% yield loss in chickpea. In this study, a total of two hundred four chickpea (Cicer arietinum L.) genotypes were selected to study the interaction between drought stress and nodule formation. This interaction was assessed by using morphological, yield and yield components. The field experiments were laid out in two locations (Terbol and Kfardan stations, Bekaa valley, Lebanon) using Alpha lattice design with two replications and two watering treatments (irrigation and rainfed) during 2016 and 2017 seasons. Parameters that were measured include days to 50% flowering (DFL), day to maturity (DM), plant height (PLH), nodule biomass (NB), nodule fresh weight (NFW), nodule dry weight (NDW), grain yield (GY), Biological yield (BY), 100 seed weight (100SW) and drought tolerance stress (DTS). The results indicated a significant variation between genotypes, environments and other morphological, yield and yield components traits. Drought stress reduced significantly the yield and the nodule's characteristics, biological and grain yield. The genotypes with the highest levels of drought tolerance, such as IG70399, IG8256, IG71832, IG70270, and IG70272, showed a minimal decrease in yield and nodule biomass. Nodule observations significantly and positively correlated with GY (0.36-0.38) under drought stress treatment. The correlation values for nodule characteristics with DFL and DM were higher under drought stress compared to irrigated conditions. This is a comparative study between drought stress and nodule formation traits associated with morphological, yield and yield components traits., Competing Interests: The authors have declared that no competing interests exist.

The molecular basis of diabetes mellitus is yet to be fully elucidated. We aimed to identify the most frequently reported and differential expressed genes (DEGs) in diabetes by using bioinformatics approaches. Text mining was used to screen 40,225 article abstracts from diabetes literature. These studies highlighted 5939 diabetes-related genes spread across 22 human chromosomes, with 112 genes mentioned in more than 50 studies. Among these genes, HNF4A , PPARA , VEGFA , TCF7L2 , HLA-DRB1 , PPARG , NOS3 , KCNJ11 , PRKAA2 , and HNF1A were mentioned in more than 200 articles. These genes are correlated with the regulation of glycogen and polysaccharide, adipogenesis, AGE/RAGE, and macrophage differentiation. Three datasets (44 patients and 57 controls) were subjected to gene expression analysis. The analysis revealed 135 significant DEGs, of which CEACAM6 , ENPP4 , HDAC5 , HPCAL1 , PARVG , STYXL1 , VPS28 , ZBTB33 , ZFP37 and CCDC58 were the top 10 DEGs. These genes were enriched in aerobic respiration, T-cell antigen receptor pathway, tricarboxylic acid metabolic process, vitamin D receptor pathway, toll-like receptor signaling, and endoplasmic reticulum (ER) unfolded protein response. The results of text mining and gene expression analyses used as attribute values for machine learning (ML) analysis. The decision tree, extra-tree regressor and random forest algorithms were used in ML analysis to identify unique markers that could be used as diabetes diagnosis tools. These algorithms produced prediction models with accuracy ranges from 0.6364 to 0.88 and overall confidence interval (CI) of 95%. There were 39 biomarkers that could distinguish diabetic and non-diabetic patients, 12 of which were repeated multiple times. The majority of these genes are associated with stress response, signalling regulation, locomotion, cell motility, growth, and muscle adaptation. Machine learning algorithms highlighted the use of the HLA-DQB1 gene as a biomarker for diabetes early detection. Our data mining and gene expression analysis have provided useful information about potential biomarkers in diabetes.

Heat stress caused by climatic changes is one of the most significant stresses on livestock in hot and dry areas. It has particularly adverse effects on the ability of the breed to maintain homeothermy. Developing countries are advised to protect and prepare their animal resources in the face of potential threats such as climate change. The current study was conducted in Egypt's three hot and dry agro-ecological zones. Three local sheep breeds (Saidi, Wahati, and Barki) were studied with a total of 206 ewes. The animals were exercised under natural heat stress. The heat tolerance index of the animals was calculated to identify animals with high and low heat tolerance based on their response to meteorological and physiological parameters. Genomic variation in these breeds was assessed using 64,756 single nucleotide polymorphic markers (SNPs). From the perspective of comparative adaptability to harsh conditions, our objective was to investigate the genomic structure that might control the adaptability of local sheep breeds to environmental stress under hot and dry conditions. In addition, indices of population structure and diversity of local breeds were examined. Measures of genetic diversity showed a significant influence of breed and location on populations. The standardized index of association (rbarD) ranged from 0.0012 (Dakhla) to 0.026 (Assuit), while for the breed, they ranged from 0.004 (Wahati) to 0.0103 (Saidi). The index of association analysis (I a ) ranged from 1.42 (Dakhla) to 35.88 (Assuit) by location and from 6.58 (Wahati) to 15.36 (Saidi) by breed. The most significant SNPs associated with heat tolerance were found in the MYO5A, PRKG1, GSTCD, and RTN1 genes ( p ≤ 0.0001). MYO5A produces a protein widely distributed in the melanin-producing neural crest of the skin. Genetic association between genetic and phenotypic variations showed that OAR1_18300122.1, located in ST3GAL3 , had the greatest positive effect on heat tolerance. Genome-wide association analysis identified SNPs associated with heat tolerance in the PLCB1, STEAP3, KSR2, UNC13C, PEBP4 , and GPAT2 genes., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Aboul-Naga, Alsamman, El Allali, Elshafie, Abdelal, Abdelkhalek, Abdelsabour, Mohamed and Hamwieh.)

Essential hypertension (EH) is a leading risk condition for cardiovascular and renal complications. While multiple genes are associated with EH, little is known about its genetic etiology. Therefore, this study aimed to screen for variants that are associated with EH in 100 hypertensive/100 control patients comprising Qatari individuals using GWASs of whole-genome sequencing and compare these findings with genetic data obtained from more than 10,000 published peer-reviewed studies on EH. The GWAS analysis performed with 21,096 SNPs revealed 38 SNPs with a significant ≥4 log- p value association with EH. The two highest EH-associated SNPs (rs921932379 and rs113688672) revealed a significance score of ≥5 log- p value. These SNPs are located within the inter-genic region of GMPS-SETP14 and ISCA1P6-AC012451.1 , respectively. Text mining yielded 3748 genes and 3078 SNPs, where 51 genes and 24 SNPs were mentioned in more than 30 and 10 different articles, respectively. Comparing our GWAS results to previously published articles revealed 194 that are unique to our patient cohort; of these, 13 genes that have 26 SNPs are the most significant with ≥4 log- p value. Of these genes, C2orf47-SPATS2L contains nine EH-associated SNPs. Most of EH-associated genes are related to ion gate channel activity and cardiac conduction. The disease-gene analysis revealed that a large number of EH-associated genes are associated with a variety of cardiovascular disorders. The clustering analysis using EH-associated SNPs across different ethnic groups showed high frequency for the minor allele in different ethnic groups, including Africans, East Asians, and South Asians. The combination of GWAS and text mining helped in identifying the unique genetic susceptibility profile of Qatari patients with EH. To our knowledge, this is the first small study that searched for genetic factors associated with EH in Qatari patients.

Ascochyta blight (AB), caused by the fungal pathogen Ascochyta rabiei , is a devastating foliar disease of chickpea ( Cicer arietinum L.). The genotyping-by-sequencing (GBS)-based approach was deployed for mapping QTLs associated with AB resistance in chickpea in two recombinant inbred line populations derived from two crosses (AB 3279 derived from ILC 1929 × ILC 3279 and AB 482 derived from ILC 1929 × ILC 482) and tested in six different environments. Twenty-one different genomic regions linked to AB resistance were identified in regions CalG02 and CalG04 in both populations AB 3279 and AB 482 . These regions contain 1,118 SNPs significantly associated with AB resistance ( p ≤ 0.001), which explained 11.2-39.3% of the phenotypic variation (PVE). Nine of the AB resistance-associated genomic regions were newly detected in this study, while twelve regions were known from previous AB studies. The proposed physical map narrows down AB resistance to consistent genomic regions identified across different environments. Gene ontology (GO) assigned these QTLs to 319 genes, many of which were associated with stress and disease resistance, and with most important genes belonging to resistance gene families such as leucine-rich repeat (LRR) and transcription factor families. Our results indicate that the flowering-associated gene GIGANTEA is a possible key factor in AB resistance in chickpea. The results have identified AB resistance-associated regions on the physical genetic map of chickpea and allowed for the identification of associated markers that will help in breeding of AB-resistant varieties., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Alo, Rani, Baum, Singh, Kehel, Rani, Udupa, Al-Sham’aa, Alsamman, Istanbuli, Attar, Hamwieh and Amri.)

Heat waves are expected to become more frequent and intense, which will impact faba bean cultivation globally. Conventional breeding methods are effective but take considerable time to achieve breeding goals, and, therefore, the identification of molecular markers associated with key genes controlling heat tolerance can facilitate and accelerate efficient variety development. We phenotyped 134 accessions in six open field experiments during summer seasons at Terbol, Lebanon, at Hudeiba, Sudan, and at Central Ferry, WA, USA from 2015 to 2018. These accessions were genotyped using genotyping by sequencing (GBS), and 10,794 high quality single nucleotide polymorphisms (SNPs) were discovered. These accessions were clustered in one diverse large group, although several discrete groups may exist surrounding it. Fifteen lines belonging to different botanical groups were identified as tolerant to heat. SNPs associated with heat tolerance using single-trait (ST) and multi-trait (MT) genome-wide association studies (GWASs) showed 9 and 11 significant associations, respectively. Through the annotation of the discovered significant SNPs, we found that SNPs from transcription factor helix-loop-helix bHLH143-like S-adenosylmethionine carrier, putative pentatricopeptide repeat-containing protein At5g08310, protein NLP8-like, and photosystem II reaction center PSB28 proteins are associated with heat tolerance.

The burden of diabetes mellitus (DM) and associated complications is increasing worldwide, affecting many organ functionalities including submandibular glands (SMG). The present study aims to investigate the potential ameliorative effect of glycyrrhizic acid (GA) on diabetes-induced SMG damage. Experimental evaluation of GA treatment was conducted on a rat model of type I diabetes. Animals were assigned to three groups; control, diabetic and GA treated diabetic groups. After 8 weeks, the SMG was processed for assessment of oxidative stress markers, autophagy related proteins; LC3, Beclin-1 and P62, vascular regulator ET-1, aquaporins (AQPs 1.4 and 5), SIRT1 protein expressions in addition to LC3 and AQP5 mRNA expressions. Also, parenchymal structures of the SMG were examined. GA alleviated the diabetes-induced SMG damage via restoring the SMG levels of oxidative stress markers and ET-1 almost near to the normal levels most probably via regulation of SIRT1, AQPs and accordingly LC-3, P62 and Beclin-1levels. GA could be a promising candidate for the treatment of diabetes-induced SMG damage via regulating oxidative stress, autophagy and angiogenesis., (© 2022. The Author(s).)

Weeds represent one of the major constraints for faba bean crop. The identification of molecular markers associated with key genes imparting tolerance to herbicides can facilitate and fasten the efficient and effective development of herbicide tolerant cultivars. We phenotyped 140 faba bean genotypes in three open field experiments at two locations in Lebanon and Morocco against three herbicide treatments (T1 metribuzin 250 g ai/ha; T2 imazethapyr 75 g ai/ha; T3 untreated) and one in greenhouse where T1 and T3 were applied. The same set was genotyped using genotyping by sequencing (GBS) which yield 10,794 high quality single nucleotide polymorphisms (SNPs). ADMIXTURE software was used to infer the population structure which revealed two ancestral subpopulations. To identify SNPs associated with phenological and yield related traits under herbicide treatments, Single-trait (ST) and Multi-trait (MT) Genome Wide Association Studies (GWAS) were fitted using GEMMA software, showing 10 and 14 highly significant associations, respectively. Genomic sequences containing herbicide tolerance associated SNPs were aligned against the NCBI database using BLASTX tool using default parameters to annotate candidate genes underlying the causal variants. SNPs from acidic endochitinase, LRR receptor-like serine/threonine-protein kinase RCH1, probable serine/threonine-protein kinase NAK, malate dehydrogenase, photosystem I core protein PsaA and MYB-related protein P-like were significantly associated with herbicide tolerance traits., (© 2022. The Author(s).)

Soil salinity is significant abiotic stress that severely limits global crop production. Chickpea (Cicer arietinum L.) is an important grain legume that plays a substantial role in nutritional food security, especially in the developing world. This study used a chickpea population collected from the International Center for Agricultural Research in the Dry Area (ICARDA) genebank using the focused identification of germplasm strategy. The germplasm included 186 genotypes with broad Asian and African origins and genotyped with 1856 DArTseq markers. We conducted phenotyping for salinity in the field (Arish, Sinai, Egypt) and greenhouse hydroponic experiments at 100 mM NaCl concentration. Based on the performance in both hydroponic and field experiments, we identified seven genotypes from Azerbaijan and Pakistan (IGs: 70782, 70430, 70764, 117703, 6057, 8447, and 70249) as potential sources for high salinity tolerance. Multi-trait genome-wide association analysis (mtGWAS) detected one locus on chromosome Ca4 at 10618070 bp associated with salinity tolerance under hydroponic and field conditions. In addition, we located another locus specific to the hydroponic system on chromosome Ca2 at 30537619 bp. Gene annotation analysis revealed the location of rs5825813 within the Embryogenesis-associated protein (EMB8-like), while the location of rs5825939 is within the Ribosomal Protein Large P0 (RPLP0). Utilizing such markers in practical breeding programs can effectively improve the adaptability of current chickpea cultivars in saline soil. Moreover, researchers can use our markers to facilitate the incorporation of new genes into commercial cultivars., Competing Interests: NO authors have competing interests.

Recently, Cicer species have experienced increased research interest due to their economic importance, especially in genetics, genomics, and crop improvement. The Cicer arietinum, Cicer reticulatum, and Cicer echinospermum genomes have been sequenced and provide valuable resources for trait improvement. Since the publication of the chickpea draft genome, progress has been made in genome assembly, functional annotation, and identification of polymorphic markers. However, work is still needed to identify transposable elements (TEs) and make them available for researchers. In this paper, we present CicerSpTEdb, a comprehensive TE database for Cicer species that aims to improve our understanding of the organization and structural variations of the chickpea genome. Using structure and homology-based methods, 3942 C. echinospermum, 3579 C. reticulatum, and 2240 C. arietinum TEs were identified. Comparisons between Cicer species indicate that C. echinospermum has the highest number of LTR-RT and hAT TEs. C. reticulatum has more Mutator, PIF Harbinger, Tc1 Mariner, and CACTA TEs, while C. arietinum has the highest number of Helitron. CicerSpTEdb enables users to search and visualize TEs by location and download their results. The database will provide a powerful resource that can assist in developing TE target markers for molecular breeding and answer related biological questions. Database URL: http://cicersptedb.easyomics.org/index.php., Competing Interests: The authors have declared that no competing interests exist.

The goal of this research was to develop a new genetic database of simple sequence repetition (SSR) primers for faba and classify them according to their target genes and respective biological processes. Approximately 75,605 and 148,196 previously published genomic and transcriptomic faba sequences, respectively, have been used to detect possible SSRs. The numbers of identified SSRs from each dataset were 25,502 and 12,319, respectively. The distribution of different repeat classes indicated that trinucleotides represent the largest number of repeat counts, followed by dinucleotides. The extracted genic SSR sequences were used to design 1091 polymerase chain reaction (PCR) primers, of which only 238 (21.8%) primers target genomic sequences and the other 853 PCR primers targeted transcriptomic sequences. The annotation of gene-targeted SSRs showed that approximately 897 genes were targeted by our SSR primers. Approximately 1890 gene ontology (GO) identification codes have been obtained. The GO keywords were distributed among distinct molecular cell features. The highest redundancies involved 554 technical words, 196 domains, and 160 molecular feature phrases. These GO codes belonged to the general level of GO and included molecular function, cellular component, and biological process (544, 670, and 676 GOs, respectively). Twenty-seven SSR PCR primers were synthesized to 12 Egyptian faba bean genotypes. Approximately 11 SSR provided one to two PCR bands, whereas other SSRs provided only one sharp band with polymorphic band size. There were 13 polymorphic primers. The polymorphism information content was 0.3, which implied moderate informativeness., (© 2021. Institute of Plant Genetics, Polish Academy of Sciences, Poznan.)

The SARS-CoV-2 (COVID-19) pandemic is a global crisis that threatens our way of life. As of November 18, 2020, SARS-CoV-2 has claimed more than 1,342,709 lives, with a global mortality rate of ~2.4% and a recovery rate of ~69.6%. Understanding the interaction of cellular targets with the SARS-CoV-2 infection is crucial for therapeutic development. Therefore, the aim of this study was to perform a comparative analysis of transcriptomic signatures of infection of SARS-CoV-2 compared to other respiratory viruses (EBOV, H1N1, MERS-CoV, and SARS-CoV), to determine a unique anti-SARS-CoV-2 gene signature. We identified for the first time that molecular pathways for heparin-binding, RAGE, miRNA, and PLA2 inhibitors were associated with SARS-CoV-2 infection. The NRCAM and SAA2 genes, which are involved in severe inflammatory responses, and the FGF1 and FOXO1 genes, which are associated with immune regulation, were found to be associated with the cellular gene response to SARS-CoV-2 infection. Moreover, several cytokines, most significantly IL-8 and IL-6, demonstrated key associations with SARS-CoV-2 infection. Interestingly, the only response gene that was shared among the five viral infections was SERPINB1. The protein-protein interaction (PPI) analysis shed light on genes with high interaction activity that SARS-CoV-2 shares with other viral infections. The findings showed that the genetic pathways associated with rheumatoid arthritis, the AGE-RAGE signaling system, malaria, hepatitis B, and influenza A were of high significance. We found that the virogenomic transcriptome of infection, gene modulation of host antiviral responses, and GO terms of SARS-CoV-2 and EBOV were more similar than to SARS, H1N1, and MERS. This work compares the virogenomic signatures of highly pathogenic viruses and provides valid targets for potential therapy against SARS-CoV-2., Competing Interests: The authors have declared that no competing interests exist.

Food predilection is linked to variants in the hepatokine "Fibroblast Growth Factor-21" gene (FGF21); with rs838133 linked to the sweet tooth in Caucasians. The effect of FGF21 variants on food intake is still unclear in other populations. A cohort of 196 healthy Emirati subjects was investigated [age: 30.34 ± 9.75yrs (44.4% males)]. The FGF21 rs838133 and rs838145 were genotyped. The daily intake was calculated based on a 61-item food frequency questionnaire. Multivariate analysis was performed using in house R script that implements two-way unsupervised hierarchical clustering to detect the association of the studied single-nucleotide polymorphisms (SNPs) and related SNPs in linkage disequilibrium, using data from the 1000 genome project. Both SNPs were in Hardy-Weinberg Equilaribium (HWE). BMI positively correlated with age (p = 0.002), but not with caloric intake. Salt intake was significantly higher in subjects homozygous (A: rs838133) and (G:rs838145),(p = 0.03 and 0.01, respectively). An interaction was observed between both SNPs; significantly associated with high salt intake. Using publicly available data, both SNPs fall within a region transmitted in Iberians which has a profile closely similar to Caucasians, but far from Chinese population. In conclusion, the minor alleles of FGF21 rs838145 and rs838133 are associated with high salt intake in Emiratis and may suggest neuro-metabolic link to dietary preference across different populations., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2020 THE AUTHORS. Published by Elsevier BV on behalf of Cairo University.)

Motivation: Fine mapping becomes a routine trial following quantitative trait loci (QTL) mapping studies to shrink the size of genomic segments underlying causal variants. The availability of whole genome sequences can facilitate the development of high marker density and predict gene content in genomic segments of interest. Correlations between genetic and physical positions of these loci require handling of different experimental genetic data types, and ultimately converting them into positioning markers using a routine and efficient tool., Results: To convert classical QTL markers into KASP assay primers, KASPspoon simulates a PCR by running an approximate-match searching analysis on user-entered primer pairs against the provided sequences, and then comparing in vitro and in silico PCR results. KASPspoon reports amplimers close to or adjoining genes/SNPs/simple sequence repeats and those that are shared between in vitro and in silico PCR results to select the most appropriate amplimers for gene discovery. KASPspoon compares physical and genetic maps, and reports the primer set genome coverage for PCR-walking. KASPspoon could be used to design KASP assay primers to convert QTL acquired by classical molecular markers into high-throughput genotyping assays and to provide major SNP resource for the dissection of genotypic and phenotypic variation. In addition to human-readable output files, KASPspoon creates Circos configurations that illustrate different in silico and in vitro results., Availability and Implementation: Code available under GNU GPL at (http://www.ageri.sci.eg/index.php/facilities-services/ageri-softwares/kaspspoon)., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2019. Published by Oxford University Press.)