Chitosan nanogel aqueous treatment improved blood biochemicals, antioxidant capacity, immune response, immune-related gene expression and infection resistance of Nile tilapia

Candida albicans is a pathogenic yeast recently associated with diverse diseases in aquaculture. The present study investigated the efficacy of chitosan nanogel (CNG) in ameliorating effects of C. albicans on Nile tilapia (Oreochromis niloticus). Fish were randomly distributed into four groups (control, waterborne CNG at 75 μg/L, intraperitoneally challenged with C. albicans (1.8 × 107 CFU/mL), and waterborne CNG at 75 μg/L + C. albicans at 1.8 × 107 CFU/mL). Results showed that C. albicans infection reduced survival rate (57.5%) and caused marked clinical symptoms in fish among all infected groups. Substantial declines in immunological (complement 3, lysozyme, and immunoglobulin M), protein (total protein and non-albumin protein), and antioxidant (catalase, glutathione peroxidase, and superoxide dismutase) biochemical endpoints were exhibited, The C. albicans infected group also showed marked down-regulation in the expression of immune-related genes, including toll-like receptor 2 (TLR-2), transforming growth factor beta2, tumor necrosis factor alpha, interleukins (IL-1β, IL-6, and IL-10), and antiapoptotic gene (B-cell lymphoma, BCL-2). The expression of the apoptotic gene (Bcl-2 associated X protein, BAX) was up-regulated in fish challenged by C. albicans. The application of waterborne CNG to fish challenged with C. albicans infection improved fish survival (79.5%) and all other measured parameters. The main finding of this work was that CNG is a nanotechnology with potential for preventing degraded health status by C. albicans infection in tilapia, and thus has promise as an intervention in aquaculture settings.

Comparison of the Morpho-Physiological and Molecular Responses to Salinity and Alkalinity Stresses in Rice

Rice is a major food crop that has a critical role in ensuring food security for the global population. However, major abiotic stresses such as salinity and alkalinity pose a major threat to rice farming worldwide. Compared with salinity stress, there is limited progress in elucidating the molecular mechanisms associated with alkalinity tolerance in rice. Since both stresses coexist in coastal and arid regions, unraveling of the underlying molecular mechanisms will help the breeding of high-yielding stress-tolerant rice varieties for these areas. This study examined the morpho-physiological and molecular response of four rice genotypes to both salinity and alkalinity stresses. Geumgangbyeo was highly tolerant and Mermentau was the least tolerant to both stresses, while Pokkali and Bengal were tolerant to only salinity and alkalinity stress, respectively. A set of salinity and alkalinity stress-responsive genes showed differential expression in the above rice genotypes under both stress conditions. The expression patterns were consistent with the observed morphological responses in these rice genotypes, suggesting the potential role of these genes in regulating tolerance to these abiotic stresses. Overall, this study suggested that divergence in response to alkalinity and salinity stresses among rice genotypes could be due to different molecular mechanisms conferring tolerance to each stress. In addition to providing a basis for further investigations into differentiating the molecular bases underlying tolerance, this study also emphasizes the possibilities of developing climate-resilient rice varieties using donors that are tolerant to both abiotic stresses.

SARS-CoV-2 virus associated angiotensin converting enzyme 2 expression modulation in colorectal cancer: Insights from mRNA and protein analysis COVID-19 associated (ACE2) expression in colorectal cancer

The SARS-CoV-2 virus gains entry into human cells by exploiting the angiotensin-converting enzyme 2 (ACE2), a key component known as the spike protein (S), as a point of entry. Initially, SARS-CoV-2 suppresses the natural function of ACE2, leading to a gradual decline in cell health. Additionally, individuals with cancer are considered more susceptible to COVID-19. This study investigates the expression patterns of ACE2 in colorectal cancer (CRC) patients with and without a history of COVID-19 infection. RT-PCR was used to analyze samples from both cancerous and adjacent non-affected colorectal tissues of 47 CRC patients, comprising two groups: 24 CRC patients with no history of COVID-19 and 23 CRC patients with a recent history of COVID-19 infection. Epithelial CR cells were isolated from both types of tissues and cultured to evaluate cell adhesion. Immunohistochemistry analyses were conducted to examine ACE2 protein expression using various ACE2 antibodies for both cell types. The study revealed ACE2 mRNA expression in all CRC tissues of patients with and without a history of COVID-19. ACE2 expression was significantly higher in CRC patients without a history of COVID-19. Notably, the non-affected colorectal cancer (NACRC) tissues of patients without a history of COVID-19 also showed ACE2 expression, whereas no ACE2 expression was detected in the biopsies of CRC patients with a positive COVID-19 history. ACE2 antibodies were employed to validate ACE2 protein expression at the mRNA level. COVID-19 appears to downregulate ACE2 expression in both CRC and NACRC tissues of CRC patients with a positive history of COVID-19 infection.

FGFR3 and FGFR4 overexpression in juvenile nasopharyngeal angiofibroma: impact of smoking history and implications for personalized management

Lifestyle factors, including smoking, have been linked to neoplastic diseases, and reports suggest an association between smoking and overexpression of FGFR (fibroblast growth factor receptor) in certain neoplasms. This study aims to assess the expression of FGFR3 and FGFR4 genes in patients with and without a history of smoking.A total of 118 participants were recruited, including 83 Juvenile Nasopharyngeal Angiofibroma (JNA) patients and 35 healthy participants, the JNA patients were further stratified as smokers and nonsmokers. Total RNA was extracted from the blood & saliva sample by using TRIzol reagent, and quantified using a Nanodrop, and then subjected to gene expression analysis of FGFR3/4 using RT-PCR. Immunohistochemistry analysis was employed using fresh biopsies of JNA to validate the findings. All experiments were performed in triplicates and analysed using the Chi-Square test (P < 0.05). Smokers exhibited significantly lower total RNA concentrations across all sample types (P < 0.001). The study revealed significant upregulation of both FGFR3/4 genes in JNA patients (P < 0.05). Moreover, FGFR3 expression was significantly higher among smokers 66% (95% CI: 53-79%) compared to non-smokers 22% (95% CI: 18-26%). Immunohistochemistry analysis demonstrated moderate to strong staining intensity for FGFR3 among smokers. The study highlights the overexpression of FGFR3/4 genes in JNA patients, with a stronger association observed among smokers. Furthermore, medical reports indicated higher rates of recurrence and bleeding intensity among smokers. These findings emphasize the potential role of FGFR3 as a key molecular factor in JNA, particularly in the context of smoking.

Impact of iodine supplementation and mtDNA mutations on papillary thyroid cancer in saudi women following a vegetarian diet

This study examined the influence of iodine supplementation and mitochondrial DNA (mtDNA)  mutations in Saudi vegetarian women with papillary thyroid cancer (PTC). Blood and tissue samples from PTC-diagnosed women were analyzed for thyroid function, mtDNA mutations, and immunohistological features. Statistical analysis using Sigmastat was employed to compare thyroid hormone levels and mtDNA mutations between groups. Serum total levels of tri-iodothyronine and thyroid-stimulating hormone were significantly different in patients following a vegetarian diet (P<0.05). Patients with PTC showed an increased frequency of mtDNA mutations in the D-loop region, with significantly higher mutation rates observed in patients following a vegetarian diet compared to other PTC patient groups (P<0.001) and controls (P<0.01). Notably, the mutations were predominantly somatic in Group 3 and germline in Groups 1 and 2. The findings suggest a possible link between iodine deficiency and accelerated PTC tumorigenesis. Furthermore, mtDNA mutations may serve as potential biomarkers for the diagnosis and prognosis of PTC.

Evolutionary insights and expression dynamics of the CaNFYB transcription factor gene family in pepper (Capsicum annuum) under salinity stress

Introduction: The Capsicum annuum nuclear factor Y subunit B (CaNFYB) gene family plays a significant role in diverse biological processes, including plant responses to abiotic stressors such as salinity. Methods: In this study, we provide a comprehensive analysis of the CaNFYB gene family in pepper, encompassing their identification, structural details, evolutionary relationships, regulatory elements in promoter regions, and expression profiles under salinity stress. Results and discussion: A total of 19 CaNFYB genes were identified and subsequently characterized based on their secondary protein structures, revealing conserved domains essential for their functionality. Chromosomal distribution showed a non-random localization of these genes, suggesting potential clusters or hotspots for NFYB genes on specific chromosomes. The evolutionary analysis focused on pepper and comparison with other plant species indicated a complex tapestry of relationships with distinct evolutionary events, including gene duplication. Moreover, promoter cis-element analysis highlighted potential regulatory intricacies, with notable occurrences of light-responsive and stress-responsive binding sites. In response to salinity stress, several CaNFYB genes demonstrated significant temporal expression variations, particularly in the roots, elucidating their role in stress adaptation. Particularly CaNFYB01, CaNFYB18, and CaNFYB19, play a pivotal role in early salinity stress response, potentially through specific regulatory mechanisms elucidated by their cis-elements. Their evolutionary clustering with other Solanaceae family members suggests conserved ancestral functions vital for the family's survival under stress. This study provides foundational knowledge on the CaNFYB gene family in C. annuum, paving the way for further research to understand their functional implications in pepper plants and relative species and their potential utilization in breeding programs to enhance salinity tolerance.

Partnering essential oils with antibiotics: proven therapies against bovine Staphylococcus aureus mastitis

Introduction

There is an urgent need to develop therapeutic options for biofilm-producing Staphylococcus aureus (S. aureus). Therefore, the renewed interest in essential oils (EOs), especially carvacrol, linalool and eugenol, has attracted the attention of our research group.

Methods

Multidrug resistance and multivirulence profiles in addition to biofilm production of S. aureus strains isolated from cows with mastitis were evaluated using both phenotypic and genotypic methods. The antimicrobial and antibiofilm activities of EOs were tested using both in vitro and molecular docking studies. Moreover, the interactions between commonly used antibiotics and the tested EOs were detected using the checkerboard method.

Results

We found that all our isolates (n= 37) were biofilm methicillin resistant S. aureus (MRSA) producers and 40.5% were vancomycin resistant S. aureus (VRSA). Unfortunately, 73 and 43.2% of the recovered MRSA isolates showed multidrug resistant (MDR) and multivirulence patterns, respectively. The antimicrobial activities of the tested EOs matched with the phenotypic evaluation of the antibiofilm activities and molecular docking studies. Linalool showed the highest antimicrobial and antibiofilm activities, followed by carvacrol and eugenol EOs. Fortunately, synergistic interactions between the investigated EOs and methicillin or vancomycin were detected with fractional inhibitory concentration index (FICI) values ≤ 0.5. Moreover, the antimicrobial resistance patterns of 13 isolates changed to sensitive phenotypes after treatment with any of the investigated EOs. Treatment failure of bovine mastitis with resistant S. aureus can be avoided by combining the investigated EOs with available antimicrobial drugs.

Conclusion

We hope that our findings can be translated into a formulation of new pharmaceutical dosage forms against biofilm-producing S. aureus pathogens.

Identification, forensic evidences and effect of the most used lip cosmetics on the human STR profiling at Kingdom of Saudi Arabia

This study aimed to identify the DNA STR profiles that were obtained from the lips with various lip cosmetics involved in lip pencil, lipsticks and lip gloss for a brand - Makeup Forever and lip balms (Labello brand) - have been popularly used by Saudi women at KSA. The study was involved 35 unrelated participants (healthy female donors) aged between 26 and 32. The swabbing of lip cosmetics was done prior to using them as negative control samples, other sterilized swabs were collected from the used lip cosmetics which contained the lip cells for each participant as a study sample. Moreover, the buccal swabs were firmly collected from the cleaned oral cavities for the same donors as reference samples. The air-drying of the collected swabs was done for ten minutes at room temperature and then stored them at - 20 °C before the DNA analysis. The 7500 Real-Time PCR (qRT-PCR) was quantified the extracted DNA. The amplification of 16 STR loci was done using the AmpFlSTR® Identifiler® PCR amplification kit using the Thermocycler ABI 9700 to amplify the extracted DNA. The Applied Bio-systems 3130™ Genetic Analyzer with Gene Mapper® ID-X Software v3.5 was used to analyze the PCR products. The data for quantifying DNA recorded significant decrease in the concentrations of DNA samples ranged from 0.15 to 0.55 ng/µL in comparison to the reference samples, while DNA was not detected in all the negative control samples. Some STR loci showed considerably high inhibition and low heterozygosity loss in the study samples compared to the reference and negative samples. The possibility of extracting DNA samples from lip cosmetics were used in the present study could be useful and successful in some cases due to the effect of the chemical compositions such as heavy pigments, organic components, and aromatic wax on the STR profiles in the lip cosmetics, especially in the lipsticks, lip glosses and lip pencils.

The function of long non-coding RNA SNHG11 and its working mechanism in triple-negative breast cancer

Triple-negative breast cancer (TNBC) seriously affects woman's health. The present work is to study the working mechanism of lncRNA SNHG11 in TNBC. The expressions of SNHG11, microRNA (miR)- 7-5p, specificity protein 2 (SP2) and mucin 1 (MUC-1) in TNBC tissues and cells were detected. SNHG11, miR-7-5p and SP2 expressions were then evaluated for TNBC cell malignant behaviors. The relationships among SNHG11, miR-7-5p and SP2 were predicted and verified. Finally, the binding of the transcription factor SP2 to MUC-1 promoter was detected. Abnormally elevated SNHG11, SP2 and MUC-1 expressions were observed in cultured TNBC cells and tumor tissues. SNHG11 knockdown in TNBC cells. Silencing SP2 weakened the promoting effect of SNHG11 on TNBC progression. SNHG11 negatively regulated miR-7-5p expression and positively regulated SP2 expression. SP2 bound to the P2 site of MUC-1 promoter, and SP2 knockdown suppressed MUC-1 expression. It was demonstrated that lncRNA SNHG11 promoted TNBC cell malignant behaviors to facilitate TNBC progression. The study is first of its kinds to unravel the potential of lncRNA SNHG11 in relation to TNBC.

Patterns of mutations in nine cancer-related genes and PAF development among smoking male patients diagnosed with bladder cancer

BACKGROUND

Smoking is one of the most popular risk factors provoking bladder cancer (BC). This research intended to estimate cigarette smoking effect involving PAF signs between smoking patients with BC and non-smoking patients with same diagnosis to define relations with pathological characteristics and their prognosis on zero-relapse and disease-associated recovery.

METHODS

Two groups of smokers (n = 54) and non-smokers (n = 62) were selected. Both cohorts of patients had BC. They were evaluated utilizing NGS on 9 cancer-related genes and confirmed through the Sanger DNA sequencing and histopathological tests based on H&E staining. The factor of smoking and impact of PAF development by ELISA assay and PAF-R manifestation in terms of immunochemical evaluation on BC areas comparing to a control group (n = 30) was examined involving healthy contributors, including the use of well-designed statistical trials.

RESULTS

The multivariate evaluation showed considerable rise in mutation patterns related to smoking among BC patients (group 3), increase in PAF development (***P<0.001) and vivid signs of PAF-R contrasted to non-smokers with BC (group 2) and control group (group 1). All the identified biological changes (gains/losses) were recorded at the same locations in both groups. Patients from group 3 held 3-4 various mutations, while patients from group 2 held 1-3 various mutations. Mutations were not identified in 30 respondents from control group. The most repeated mutations were identified in 3 of 9 examined genes, namely TP53, PIK3CA and PTEN, with highest rates of increase in Group 3. Moreover, histopathological tests revealed barely identifiable and abnormal traits in BC tissues, i.e. were without essential histopathological changes between groups 2 and 3.

CONCLUSION

Smoking of cigarettes provokes PAF development due to urothelial inflammation and rise of mutations in 9 cancer-related genes. These are indicative factors of inducing BC.

DNA Barcoding of Wild Plants with Potential Medicinal Properties from Faifa Mountains in Saudi Arabia

Wild medicinal plants are the main source of active ingredients and provide a continuous natural source for many folk medicinal products, a role that is important for society's health with an impressive record of utilization. Thus, surveying, conserving, and precisely identifying wild medicinal plants is required. The current study aimed to precisely identify fourteen wild-sourced medicinal plants from southwest Saudi Arabia, within the Fifa mountains area located in Jazan province, using the DNA barcoding technique. Two DNA regions (nuclear ITS and chloroplast rbcL) were sequenced and analyzed for the collected species using BLAST-based and phylogeny-based identification methods. Based on our analysis, ten of the fourteen species were successfully identified by DNA barcoding, five were identified as morphologically inspected, and three were morphologically indifferent. The study was able to distinguish some key medicinal species and highlight the importance of combining morphological observation with DNA barcoding to ensure the precise identification of wild plants, especially if they are medicinally relevant and associated with public health and safety usage.

Detecting STR profiles from degrading menstrual blood samples and their use as possible evidence in forensic investigations

This research explores DNA consistency and attempts to detect STR profiles from the degrading menstrual blood samples (MBS) as reliable forensic evidence. Peripheral (PBS) and MBS of 30 healthy fertile females were taken on the menstrual cycle's second day. They were obtained at different time periods (0, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 24, and 48 h) at 25 °C. DNA evaluation was fulfilled to analyze DNA profiles. A considerable elevation in the median concentrations of DNA between 0 and 14-h intervals were documented, whereas decreased extents were registered between 16 and 48 h. Moreover, complete STR profiles (24/24) for DNA were discovered in all the intervals (0, 2, and 48 h). Periods of 0-8 h demonstrated the maximum extents of DNA materials. Full STR were discovered in all the intervals (0, 2, and 48 h). Eventually, MBS can be utilized as forensic evidence.

Antibacterial, Antioxidant Activities, GC-Mass Characterization, and Cyto/Genotoxicity Effect of Green Synthesis of Silver Nanoparticles Using Latex of Cynanchum acutum L

Green synthesis of nanoparticles is receiving more attention these days since it is simple to use and prepare, uses fewer harsh chemicals and chemical reactions, and is environmentally benign. A novel strategy aims to recycle poisonous plant chemicals and use them as natural stabilizing capping agents for nanoparticles. In this investigation, silver nanoparticles loaded with latex from Cynanchum acutum L. (Cy-AgNPs) were examined using a transmission electron microscope, FT-IR spectroscopy, and UV-visible spectroscopy. Additionally, using Vicia faba as a model test plant, the genotoxicity and cytotoxicity effects of crude latex and various concentrations of Cy-AgNPs were studied. The majority of the particles were spherical in shape. The highest antioxidant activity using DPPH was illustrated for CAgNPs (25 mg/L) (70.26 ± 1.32%) and decreased with increased concentrations of Cy-AGNPs. Antibacterial activity for all treatments was determined showing that the highest antibacterial activity was for Cy-AgNPs (50 mg/L) with inhibition zone 24 ± 0.014 mm against Bacillus subtilis, 19 ± 0.12 mm against Escherichia coli, and 23 ± 0.015 against Staphylococcus aureus. For phytochemical analysis, the highest levels of secondary metabolites from phenolic content, flavonoids, tannins, and alkaloids, were found in Cy-AgNPs (25 mg/L). Vicia faba treated with Cy-AgNPs- (25 mg/L) displayed the highest mitotic index (MI%) value of 9.08% compared to other Cy-AgNP concentrations (50-100 mg/L) and C. acutum crude latex concentrations (3%). To detect cytotoxicity, a variety of chromosomal abnormalities were used, including micronuclei at interphase, disturbed at metaphase and anaphase, chromosomal stickiness, bridges, and laggards. The concentration of Cy-AgNPs (25 mg/L) had the lowest level of chromosomal aberrations, with a value of 23.41% versus 20.81% for the control. Proteins from seeds treated with V. faba produced sixteen bands on SDS-PAGE, comprising ten monomorphic bands and six polymorphic bands, for a total percentage of polymorphism of 37.5%. Eight ISSR primers were employed to generate a total of 79 bands, 56 of which were polymorphic and 23 of which were common. Primer ISSR 14 has the highest level of polymorphism (92.86%), according to the data. Using biochemical SDS-PAGE and ISSR molecular markers, Cy-AgNPs (25 mg/L) showed the highest percentage of genomic template stability (GTS%), with values of 80% and 51.28%, respectively. The findings of this work suggest employing CyAgNPs (25 mg/L) in pharmaceutical purposes due to its highest content of bioactive compounds and lowest concentration of chromosomal abnormalities.

Genetic diversity and forensic application of Y-filer STRs in four major ethnic groups of Pakistan

17 Y-chromosomal STRs which are part of the Yfiler Amplification Kit were investigated in 493 unrelated Pakistani individuals belonging to the Punjabi, Sindhi, Baloch, and Pathan ethnic groups. We have assessed the forensic parameters and population genetic structure for each group. Among the 493 unrelated individuals from four ethnic groups (128 Baloch, 122 Pathan, 108 Punjabi, and 135 Sindhi), 82 haplotypes were observed with haplotype diversity (HD) of 0.9906 in Baloch, 102 haplotypes with HD value of 0.9957 in Pathans, 80 haplotypes with HD value of 0.9924 in Punjabi, and 105 haplotypes with HD value of 0.9945 in the Sindhi population. The overall gene diversity for Baloch, Pathan, Punjabi, and Sindhi populations was 0.6367, 0.6479, 0.6657, and 0.6112, respectively. The results had shown us that Pakistani populations do not have a unique set of genes but share the genetic affinity with regional (Central Asia and Northern India) populations. The observed low gene diversity (heterozygosity) values may be because of endogamy trends and this observation is equally supported by the results of forensic parameters which are mostly static across 4 combinations (minimal STRs, extended 11 Y-STRs, Powerplex 12 Y System, and Yfiler 17 Y-STRs) of STRs in these four populations.

Utilization of Genetic Resources, Genetic Diversity and Genetic Variability for Selecting New Restorer Lines of Rice (Oryza sativa L.)

Exploration of and understanding diversity and variability in genotypes of germplasm determines the success of rice improvement programs. One of the most important determinants of the success of breeding programs is genetic diversity and inheritance of traits. Genetic variability analysis helps breeders to determine the appropriate selection method and standards to be used to improve the preferred trait. The aim of this study was to estimate genetic components, heritability and to obtain information about genetic diversity using cluster analysis and principal component analysis. Twenty rice genotypes with three replicates in a randomized complete block design were analyzed at the Experimental Farm at Sakha Agricultural Research Station, Sakha, Kafr El-Sheikh, Egypt, during the period from 2017 to 2020. The results of the analysis of variance showed that highly significant variations were recorded between the studied genotypes for all traits. The genotypic coefficient of variation (GCV%) and phenotypic (PCV%) coefficient of variation were moderate for plant height, panicles/plant, panicle weight, spikelets/panicle, filled grains/panicle, grain yield/plant and amylose content percentage for the first-year, second-year and combined data. This indicates the existence of beneficial genetic variability that can be exploited to improve these traits. The broad-sense estimates of heritability were high and recorded values higher than 60% for all the studied traits for the two-year and combined data, except for hulling percentage. This indicates that the selection of traits that have high heritability and are less affected by the environment leads to an acceleration of the improvement of these traits. The results from the cluster analysis and principal component analysis revealed a high level of genotypic variation among the studied genotypes and genetic diversity between them. One of the most important outcomes of this study is the successful utilization of genetic resources (germplasm) from ancient varieties and lines of rice in selecting and identifying 17 new restoration lines of rice, which have various improvement purposes in rice and hybrid rice breeding programs.

DNA Barcoding of Endangered and Rarely Occurring Plants in Faifa Mountains (Jazan, Saudi Arabia)

Conservation of plant genetic resources, especially threatened species, is an important topic in biodiversity. It is a field that requires prior knowledge of the target species, in addition to correct identification and taxonomic description. In botany, the identification of plant species traditionally relies on key morphological descriptions and anatomical features. However, in complex species and tree plants, molecular identification can facilitate identification and increase species delimitation accuracy. In the Faifa mountains of Jazan province in Saudi Arabia, 12 rarely occurring plants were recorded and identified using two DNA barcoding regions (i.e., rbcL and ITS). All the samples were successfully amplified, sequenced, and analyzed using the standard DNA barcode protocol, and this resulted in the clear and accurate identification of 11 out of the 12 sampled species. A total of five species were in agreement in terms of both morpho- and molecular-based identification. Four and two species were identified based solely on ITS and rbcL phylogenetics, respectively. The geographic distribution records of the identified species showed that some species were distributed at a distance far from their usual region, while others were reported in proximate regions and localities. Some species were found to be medicinally important and required additional conservation plans.

Genetic Characterization of Some Saudi Arabia's Accessions from Commiphora gileadensis Using Physio-Biochemical Parameters, Molecular Markers, DNA Barcoding Analysis and Relative Gene Expression

Commiphora gileadensis L. is a medicinal plant, known as balsam, with pharmaceutical potential for its phytochemical activities and chemical constituents. Genetic diversity is a genetic tool used in medicinal plant evolution and conservation. Three accessions from C. gileadensis were collected from three localities in Saudi Arabia (Jeddah, Jizan and Riyadh). Genetic characterization was carried out using physio-biochemical parameters, molecular markers (inter-simple sequence repeat (ISSR) and start codon targeted (SCoT)), DNA barcoding (18 S rRNA and ITS rDNA regions), relative gene expressions (phenylalanine ammonia-lyase 1 (PAL1), defensin (PR-12)) and pathogenesis-related protein (AFPRT). The results of this study showed that C. gileadensis accession C3, collected from Riyadh, had the highest content from the physio-biochemical parameters perspective, with values of 92.54 mg/g and 77.13 mg/g for total phenolic content (TPC) and total flavonoid content (TFC), respectively. Furthermore, the highest content of antioxidant enzyme activity was present in accession C3 with values of 16.87, 60.87, 35.76 and 27.98 U mg-1 for superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) (mol/min/mg FW) and ascorbate peroxidase (APX) (U mg-1 protein), respectively. The highest total number of bands and number of unique bands were 138 and 59, respectively, for the SCoT marker. The SCoT marker was the most efficient for the genetic diversity of C. gileadensis by producing the highest polymorphism (75.63%). DNA barcoding using 18 S and ITS showed the nearby Commiphora genus and clustered C. gileadensis accessions from Jeddah and Jizan in one clade and the C. gileadensis accession from Ryiadh in a separate cluster. Moreover, relative gene expression of the PAL1, defensin (PR-12) and AFPRT (PR1) genes was upregulated in the C. gileadensis accession from Ryiadh. In conclusion, ecological and environmental conditions in each locality affect the genomic expression and genetic diversity, which can help the evolution of important medicinal plants and improve breeding and conservation systems.

Genetic admixture history and forensic characteristics of Tibeto-Burman-speaking Qiang people explored via the newly developed Y-STR panel and genome-wide SNP data

Fine-scale patterns of population genetic structure and diversity of ethnolinguistically diverse populations are important for biogeographical ancestry inference, kinship testing, and development and validation of new kits focused on forensic personal identification. Analyses focused on forensic markers and genome-wide single nucleotide polymorphism (SNP) data can provide new insights into the origin, admixture processes, and forensic characteristics of targeted populations. Qiang people had a large sample size among Tibeto-Burmanspeaking populations, which widely resided in the middle latitude of the Tibetan Plateau. However, their genetic structure and forensic features have remained uncharacterized because of the paucity of comprehensive genetic analyses. Here, we first developed and validated the forensic performance of the AGCU-Y30 Y-short tandem repeats (STR) panel, which contains slowly and moderately mutating Y-STRs, and then we conducted comprehensive population genetic analyses based on Y-STRs and genome-wide SNPs to explore the admixture history of Qiang people and their neighbors. The validated results of this panel showed that the new Y-STR kit was sensitive and robust enough for forensic applications. Haplotype diversity (HD) ranging from 0.9932 to 0.9996 and allelic frequencies ranging from 0.001946 to 0.8326 in 514 Qiang people demonstrated that all included markers were highly polymorphic in Tibeto-Burman people. Population genetic analyses based on Y-STRs [RST, FST, multidimensional scaling (MDS) analysis, neighboring-joining (NJ) tree, principal component analysis (PCA), and median-joining network (MJN)] revealed that the Qiang people harbored a paternally close relationship with lowland Tibetan-Yi corridor populations. Furthermore, we conducted a comprehensive population admixture analysis among modern and ancient Eurasian populations based on genome-wide shared SNPs. We found that the Qiang people were a genetically admixed population and showed closest relationship with Tibetan and Neolithic Yellow River farmers. Admixture modeling showed that Qiang people shared the primary ancestry related to Tibetan, supporting the hypothesis of common origin between Tibetan and Qiang people from North China.

Genetic diversity using biochemical, physiological, karyological and molecular markers of Sesamum indicum L

The genetic diversity and the relationships among sesame cultivars were investigated using physiological and cyto/molecular analysis. To our information, no studies have yet been conducted on the genetic evaluation of sesame genotypes based on cyto/molecular analysis in Saudi Arabia. This study showed that genotype Bah-312 had the highest values from physiological and biochemical traits (plant height, harvest index, total plant dry matter, seed yield, oil content, and fatty acids content). Using 20 ISSR and 25 SCoT primers, the studied genotypes amplified 233 and 275 alleles, while the average polymorphism percentage (P%) was 65.32% (ISSR) and 77.8% (SCoT) across all the studied genotypes, respectively. To assess the markers efficiency analysis the polymorphism information contents (PIC), Marker Index (MI), Effective Multiplex Ratio (EMR), Resolving Power (Rp) were estimated. In general, primers (ISSR 2 & SCoT 21) and (ISSR 4 & SCoT 3) revealed the highest and lowest values for P %, PIC, MI, and EMR%. Furthermore, 188 positive and negative unique bands were detected, out of which ISSR generated 84, while 104 were amplified by SCoT analysis. In this regard, genotype Bah-312 generated 41 unique amplicons, and Jiz-511 genotype 23 unique amplicons. In the same context, the population genetics parameters, number of different alleles (Na), number of effective alleles (Ne), Shannon’s index (I), expected heterozygosity (He), and Unbiased Expected Heterozygosity (uHe), were calculated. ISSR marker showed the highest values for all the estimated parameters. In this regard, genotype Bah-312 exhibited the highest values (1.35, 1.37, 0.31, 0.21, 0.29) & (1.31, 1.35, 0.30, 0.20, 0.27) while, genotype Ahs-670 revealed the least values (1.29, 1.31, 0.26, 0.16, 0.23) &(1.14, 1.26, 0.22, 0.15, 0.20) for ISSR and SCoT markers respectively. For cytological data, according to the highest asymmetry index (AsK%) and lowest total form percentage (TF%) values, genotype Ahs-670 was the most advanced cultivar, and genotype Bah-312 was the most primitive one. According to the degree of asymmetry of karyotype (A) and intrachromosomal asymmetry index (A1), sesame genotype Ahs-670 was the most asymmetrical, and Bah-312 was the most symmetrical genotype. This study gives some helpful information about the genetic diversity of six sesame landraces. The variation harbored by these landraces could be used in sesame breeding programs.

Genetic Diversity, Analysis of Some Agro-Morphological and Quality Traits and Utilization of Plant Resources of Alfalfa

Alfalfa (Medicago sativa L.) is one of the most important perennial forage crops to build effective diets for livestock producers. Forage crop improvement depends largely on the availability of diverse germplasms and their efficient utilization. The present investigation was conducted at Ismailia Agricultural Research Station to assess twenty-one alfalfa genotypes for yield components, forage yield and quality traits during 2019/2020 and 2020/2021. The genotypes were evaluated in field experiments with three replicates and a randomized complete block design, using analysis of variance, estimate of genetic variability, estimate of broad sense heritability (hb2) and cluster analysis to identify the inter relationships among the studied genotypes as well as principal component analysis (PCA) to explain the majority of the total variation. Significant differences were found among genotypes for all studied traits. The general mean of the studied traits was higher in the second year than the first year. Moreover, the combined analysis showed highly significant differences between the two years, genotypes and the year × gen. interaction for the traits studied. The genotype F18 recorded the highest values for plant height, number of tiller/m2, total fresh yield and total dry yield, while, the genotype F49 ranked first for leaf/stem ratio. The results showed highly significant variation among the studied genotypes for crude protein %, crude fiber % and ash %. Data revealed that the genotypes P13 and P5 showed the highest values for crude protein %, whereas, the genotype F18 recorded the highest values for crude fiber % and ash content. The results revealed high estimates of genotypic coefficient and phenotypic coefficient of variation (GCV% and PCV%) with high hb2, indicating the presence of genetic variability and effective potential selection for these traits. The cluster analysis exhibited considerable genetic diversity among the genotypes, which classified the twenty one genotypes of alfalfa into five sub-clusters. The genotypes F18, F49, K75, S35, P20, P5 and P13 recorded the highest values for all studied traits compared with other clusters. Furthermore, the PC analysis grouped the studied genotypes into groups and remained scattered in all four quadrants based on all studied traits. Ultimately, superior genotypes were identified can be utilized for crop improvement in future breeding schemes.

Mutation Rate Analysis of RM Y-STRs in Deep-Rooted Multi-Generational Punjabi Pedigrees from Pakistan

Y chromosome short tandem repeat polymorphisms (Y-STRs) are important in many areas of human genetics. Y chromosomal STRs, being normally utilized in the field of forensics, exhibit low haplotype diversity in consanguineous populations and fail to discriminate among male relatives from the same pedigree. Rapidly mutating Y-STRs (RM Y-STRs) have received much attention in the past decade. These 13 RM Y-STRs have high mutation rates (>10−2) and have considerably higher haplotype diversity and discrimination capacity than conventionally used Y-STRs, showing remarkable power when it comes to differentiation in paternal lineages in endogamous populations. Previously, we analyzed two to four generations of 99 pedigrees with 1568 pairs of men covering one to six meioses from all over Pakistan and 216 male relatives from 18 deep-rooted endogamous Sindhi pedigrees covering one to seven meioses. Here, we present 861 pairs of men from 62 endogamous pedigrees covering one to six meioses from the Punjabi population of Punjab, Pakistan. Mutations were frequently observed at DYF399 and DYF403, while no mutation was observed at DYS526a/b. The rate of differentiation ranged from 29.70% (first meiosis) to 80.95% (fifth meiosis), while overall (first to sixth meiosis) differentiation was 59.46%. Combining previously published data with newly generated data, the overall differentiation rate was 38.79% based on 5176 pairs of men related by 1−20 meioses, while Yfiler differentiation was 9.24% based on 3864 pairs. Using father−son pair data from the present and previous studies, we also provide updated RM Y-STR mutation rates.

Genetic characteristics and forensic features of Xibe ethnic group revealed via extended set of Y-STRs

BACKGROUND

Xibe is the fifth largest minority population of Liaoning province. Predominately they live in Liaoning province (69.52%), followed by Xinjiang (18.06%), Heilongjiang (3.99%), Jilin (1.63%) and Inner Mongolia provinces (1.57%).

AIM

To provide an updated and precise population database on an extended set of Y STRs not available before and explore the forensic characteristics of 26 Y chromosomal STRs.

SUBJECTS & METHODS

In this study, we genotyped 406 unrelated Xibe male individuals from Liaoning province using Goldeneye® 26Y System kit and calculated the forensic parameters of these 26 Y STRs loci.

RESULTS

All haplotypes generated for 406 Xibe samples using Goldeneye^® 26Y kit were unique with a discrimination capacity (DC) of 1. On restricting the haplotypes to the Y-filer® set of 17 Y-STRs, we observed 392 haplotypes. Among them 93.53% (380) were unique with a DC of 0.9655 and haplotype diversity (HD) of 0.9998, showing high discrimination power of the extended set of markers in this population. Allelic frequencies ranged from 0.0024 to 0.7684 across 26 Y STRs loci. DYS385 showed the highest gene diversity (0.9691) among all markers.

CONCLUSION

According to pairwise R_ST genetic distances among Xibe populations from China, the Liaoning Xibe population showed the closest genetic distance (0.0035) followed by Xinjiang Xibe population (0.0218). Multidimensional scaling (MDS) analysis among Xibe and 29 other Chinese populations showed that local populations such as Manchu from Liaoning and Han from Beijing had a close affinity while Tibetans from Aba, China, were most distant from Xibe populations. Moreover, 12 individuals showed a null allele at DYS448 in Xibe population samples. We submitted Y-STRs data in the Y-Chromosome Haplotype Reference Database (YHRD) for future forensic and other usage.

Genetic Potential and Inheritance Patterns of Physiological, Agronomic and Quality Traits in Bread Wheat under Normal and Water Deficit Conditions

Water scarcity is a major environmental stress that adversatively impacts wheat growth, production, and quality. Furthermore, drought is predicted to be more frequent and severe as a result of climate change, particularly in arid regions. Hence, breeding for drought-tolerant and high-yielding wheat genotypes has become more decisive to sustain its production and ensure global food security with continuing population growth. The present study aimed at evaluating different parental bread wheat genotypes (exotic and local) and their hybrids under normal and drought stress conditions. Gene action controlling physiological, agronomic, and quality traits through half-diallel analysis was applied. The results showed that water-deficit stress substantially decreased chlorophyll content, photosynthetic efficiency (FV/Fm), relative water content, grain yield, and yield attributes. On the other hand, proline content, antioxidant enzyme activities (CAT, POD, and SOD), grain protein content, wet gluten content, and dry gluten content were significantly increased compared to well-watered conditions. The 36 evaluated genotypes were classified based on drought tolerance indices into 5 groups varying from highly drought-tolerant (group A) to highly drought-sensitive genotypes (group E). The parental genotypes P₃ and P₈ were identified as good combiners to increase chlorophyll b, total chlorophyll content, relative water content, grain yield, and yield components under water deficit conditions. Additionally, the cross combinations P₂ × P₄, P₃ × P₅, P₃ × P₈, and P₆ × P₇ were the most promising combinations to increase yield traits and multiple physiological parameters under water deficit conditions. Furthermore, P₁, P₂, and P₅ were recognized as promising parents to improve grain protein content and wet and dry gluten contents under drought stress. In addition, the crosses P₁ × P₄, P₂ × P₃, P₂ × P₅, P₂ × P₆, P₄ × P₇, P₅ × P₇, P₅ × P₈, P₆ × P₈, and P₇ × P₈ were the best combinations to improve grain protein content under water-stressed and non-stressed conditions. Certain physiological traits displayed highly positive associations with grain yield and its contributing traits under drought stress such as chlorophyll a, chlorophyll b, total chlorophyll content, photosynthetic efficiency (Fv/Fm), proline content, and relative water content, which suggest their importance for indirect selection under water deficit conditions. Otherwise, grain protein content was negatively correlated with grain yield, indicating that selection for higher grain yield could reduce grain protein content under drought stress conditions.

Oral cancer among Khat users: finding evidence from DNA analysis of nine cancer-related gene mutations

BACKGROUND

Khat leaves contain the alkaloid cathinone. Research shows that khat might provoke toxicity, mutagenicity, as well as carcinogenicity.

METHODS

Two groups were identified as khat abusers and were categorized by abuse time and diagnosis of oral squamous cell carcinoma (OSCC). Here, 41 participants from Group 2 were short-term khat users, and 42 participants were long-term khat users. The control group included 30 healthy individuals. The coding exons included nine cancer-related genes and were analysed. The histopathological research was conducted with H&E staining along with the TP53 protein expression by implementing immunohistochemical analyses.

RESULTS

Here, 41 short-term khat users carried seven somatic mutations in four out of nine cancer-related genes: 29/41(70.73%) ARID1A, 24/41(58.53%) MLH1, 34/41(82.92%) PIK3CA and 36/41(87.80%) TP53. The 42 long-term khat users incorporated nine somatic mutations in five out of nin ecancer-related genes: 40/42(95.23%) ARID1A, 36/42(85.71%) ARID2, 29/42(69.04%) PIK3CA, 27/42(64.28%) MLH1, and 35/42(83.33%) TP53. Every khat user had somatic mutations related to OSCC affecting the gingiva and the lower lip. TP53 protein expression was confirmed in all immunohistochemical oral tests. Carcinoma was also positive in the histopathological analysis.

CONCLUSIONS

Khat is a mutagenic and carcinogenic plant that provoked OSCC among short-term khat users (<15 years of use) and long-term users (>15 years of use).

Assessment of Metastatic Colorectal Cancer (CRC) Tissues for Interpreting Genetic Data in Forensic Science by Applying 16 STR Loci among Saudi Patients

Background:

In forensic science, there are cases when the only available provider of biological data is samples of malignant tissues. It can be useful in identification and/or paternity tests. Still, such samples have ambiguities because of microsatellite instability (MSI) and loss of heterozygosity (LOH) effects, being often related to neoplasia.

Methods:

This research evaluates 16 autosomal short tandem repeat (STR) loci (traditional in forensic investigations) to get genetic data. MSI and LOH were estimated in DNA patterns derived from 73 Saudi respondents (30 healthy individuals and 43 persons with diagnosed colorectal cancer (CRC). Upon deriving DNA from blood, CRC specimens were obtained in both groups, along with the adjoining normal non-cancerous tissues (N-CRC). All specimens and 16 loci (15 STR loci and Amelogenin) were evaluated. Moreover, both colorectal samples were histologically analyzed utilizing HandE staining.

Results:

Findings revealed non-essential variability in genetic information because of MSI and/or LOH. In CRC, mutations rates were 0.42% (MSI) and 1.62% (LOH). In N-CRC, mutation rates were 0.00% (MSI) and 0.59% (LOH). Further, LOH-related deviations were recorded in 5 loci out of 16. MSI-related deviations were recorded in 4 out of 16 loci, being present in CRC samples only. Genetic deviations within the marker loci might inform about false homozygosity/heterozygosity. Similarly, false gender might come from improper interpretation of DNA profiles. Finally, histopathological trials showed considerable histopathological alterations contrasted to N-CRC.

Conclusion:

This study is unique in demonstrating the application of 16 autosomal STRs from CRC samples and their comparison with the adjoining N-CRCs in Saudi participants, contributing to the field of forensic science. The experiment revealed no considerable distinctions, while showing that cancer tissues might display MSI and LOH effects that might challenge data interpretation, if STRs are to be applied in the forensic investigation.