Spectrum of Diarrheagenic Escherichia coli in Drinking and Wastewater in Rafha City of Saudi Arabia

Introduction: E coli is one of the most important etiologic agent of diarrhea in children and adults. Based on the clinical features and virulence determinants, there are five major E. coli strains which cause diarrhea; Enterohemorrhagic E. coli (EHEC), Enteropathogenic E. coli (EPEC), Enterotoxigenic E. coli (ETEC), Enteroinvasive E. coli (EIEC) and Enteroaggregative E. coli (EAEC). The PCR based identification proves to be a better choice as it can differentiate between different strains on the basis of genetic difference. Aim: The purpose of the current study was to isolate diarrheagenic E. coli from the drinking and wastewater from Rafha city of Saudi Arabia. Methodology: One 100 drinking and wastewater samples (50 each) were included in the study. The samples were cultured on MacConkey agar plates at 37 oC for 24 hours. Pink colonies were carefully picked and subjected to DNA isolation and PCR detection and identification of E. coli and Diarrheagenic E. coli. The detected PCR products were sequenced for the confirmation. Results: We identified 5 isolates out of 50 wastewater samples (10%) which were further categorized into 3 different DEC pathotypes. They included ETEC (2 out of 5), atypical EPEC (1 out of 5), and EAEC (1 out of 5); EIEC and EHEC were not detected. Discussion and Conclusion: The prevalence of DEC strains is different across different studies which depends on different factors such as geographical location, number of samples taken, and the number and type of the target genes selected. The prevalence of DEC in the current study was much lower than other reported studies. Although the percentage of DEC strains in the wastewater samples from WWTP of Rafha was moderate to low, it can be a considerable risk factor for the people using ground water for drinking.

Genetic (SSRs) versus morphological differentiation of date palm cultivars: Fst versus Pst estimates

Date Palm (Phoenix dactylifera L.) is one of the oldest domesticated fruit trees. For future breeding program, knowledge on genetic structure of cultivars is necessary. Therefore, the present study was performed with the following aims: 1- To provide data on genetic diversity and genetic structure of 36 date palm cultivars, 2- To provide data on the association between fruit characteristics and the genetic features of the cultivars. We used nine SSRs and EST-SSR loci for our genetic investigation. The most of SSR loci obtained have a high Gst value (0.70), and therefore have a good discrimination power for date palm cultivar differentiation task. K-Means clustering grouped date palm cultivars either in two broad clusters, or in 16 smaller genetic groups. This was supported by delta K = 2 of the STRUCTURE analysis. AMOVA produced significant genetic difference among date palm cultivars (PhiPT = 0.70, P = 0.001). New genetic differentiation parameters estimated also produced significant difference among date palm cultivars (G’st(Nei) = 0.673, P =0.001; G’st(Hed) = 0.738, P = 0.001). Test of assignment revealed that some of the cultivars have 33-66% misassignment, probably due to genetic admixture. Heatmaps of genetic versus morphological/or agronomical characters in date palm cultivars differed from each other showing the cultivars morphological changes is not merely related to their genetic content. It points toward the potential role played either by environmental conditions or local selection practice. The new findings can be utilized in future conservation and breeding of date palms in the country.

Application of Data Science Approaches to Investigate Autoimmune Thyroid Disease in Precision Medicine

In recent times, the application of artificial intelligence in facilitating, capturing, and restructuring Big data has transformed the accuracy of diagnosis and treatment of diseases, a field known as precision medicine. Big data has been established in various domains of medicine for example, artificial intelligence has found its way into immunology termed as immunoinformatics. There is evidence that precision medicine tools have made an effort to accurately detect, profile, and suggest treatment regimens for thyroid dysfunction using Big data such as imaging and genetic sequences. In addition, the accumulation of data on polymorphisms, autoimmune thyroid disease, and genetic data related to environmental factors has occurred over time resulting in drastic development of clinical autoimmune thyroid disease study. This review emphasized how genetic data plays a vital role in diagnosing and treating diseases related to autoimmune thyroid disease like Graves’ disease, subtle subclinical thyroid dysfunctions, Hashimoto’s thyroiditis, and hypothyroid autoimmune thyroiditis. Furthermore, connotation between environmental and endocrine risk factors in the etiology of the disease in genetically susceptible individuals were discussed. Thus, endocrinologists’ potential hurdles in cancer and thyroid nodules field include unreliable biomarkers, lack of distinct therapeutic alternatives due to genetic difference. Precision medicine data may improve their diagnostic and therapeutic capabilities using artificial intelligence.

Lack of Association between Chlamydophila psittaci and Ocular Adnexal MALT Lymphoma in Korean Patients—Is the Geographic or Genetic Difference Significant?

Clamydophila psittaci (C. psittaci) has been proposed to be an etiologic factor in extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue (MALT lymphoma) in the ocular adnexa. However, the pathogenetical significance of the infection has not been fully elucidated. Many previous studies have shown controversial results regarding C. psittaci detection rates in said patients, ranging from 0 to 87%. We investigated the presence of C. psittaci in a single institutional cohort (n = 150) of ocular adnexal MALT lymphoma (OAML) patients in Korea. We tried to exclude the methodological biases derived from the different primer sets in polymerase chain reaction-based studies. For that reason, we applied five sets of primers, including four previously reported and one newly designed primer set. There was no case of C. psittaci-positive OAML in repeated trials validated with appropriate positive and negative controls. All 150 cases showed negative results with five primer sets. These results suggest that the pathogenetic role of C. psittaci in ocular adnexal MALT lymphoma might have been overestimated to date, at least in the Korean population. Therefore, the molecular diagnosis of C. psittaci is considered a very low priority.

Albino mice with the point mutation at the tyrosinase locus show high cholesterol diet-induced NASH susceptibility

Non-alcoholic fatty liver disease (NAFLD) constitutes a metabolic disorder with high worldwide prevalence and increasing incidence. The inflammatory progressive state, non-alcoholic steatohepatitis (NASH), leads to liver fibrosis and carcinogenesis. Here, we evaluated whether tyrosinase mutation underlies NASH pathophysiology. Tyrosinase point-mutated B6 (Cg)-Tyrc-2J/J mice (B6 albino) and C57BL/6J black mice (B6 black) were fed with high cholesterol diet (HCD) for 10 weeks. Normal diet-fed mice served as controls. HCD-fed B6 albino exhibited high NASH susceptibility compared to B6 black, a phenotype not previously reported. Liver injury occurred in approximately 50% of B6 albino from one post HCD feeding, with elevated serum alanine aminotransferase and aspartate aminotransferase levels. NASH was induced following 2 weeks in severe-phenotypic B6 albino (sB6), but B6 black exhibited no symptoms, even after 10 weeks. HCD-fed sB6 albino showed significantly higher mortality rate. Histological analysis of the liver revealed significant inflammatory cell and lipid infiltration and severe fibrosis. Serum lipoprotein analysis revealed significantly higher chylomicron and very low-density lipoprotein levels in sB6 albino. Moreover, significantly higher small intestinal lipid absorption and lower fecal lipid excretion occurred together with elevated intestinal NPC1L1 expression. As the tyrosinase point mutation represents the only genetic difference between B6 albino and B6 black, our work will facilitate the identification of susceptible genetic factors for NASH development and expand the understanding of NASH pathophysiology.

Determine The Genetic Variation of Phenotypic Groups of Quail (Different With Feathers Color ) Using The Chain Polymerase Reaction Technique (PCR)

The main objective of this research was to specify the hereditary variation associated with the plumage color in three local genotypes of Japanese quail which bred in two geographical locations. The birds distributed on six treatments with five birds for each depending on the feather's color and geographical locations. DNA extraction was executed from the blood samples of each treatment and amplified by thermo cycler apparatus and the electrophoresis was done using 1.5% agarose gel for DNA bands exhibiting. Genotype influence has been shown that the black color quail B1 of the agricultural research station in the city of Mosul showed maximum genetic similarity with the Black quail B2 of Tikrit University with a value of 0.9549, the highest genetic similarity between different colors found between B1 and W2 that amounted to 0.9391 based on the similarity index (band sharing). While, the least genetic similarity observed between B2 and W1, which went down to 0.8468. Genetic difference values among studied quail groups showed that the groups B2 and W1 in the higher genetic variation, whereas the least genetic difference found between B1 and B2 groups. The average of dissimilarities for each group with all others varied between the values 0.1203 - 0.0851. The present work prove that the effectiveness of RAPD markers in knowing the similarity and specify the inherited relationship within the quail varieties.

Heterosis and Genetic Diversity of Yield and Its Some Components in F1 of Sunflower Inbred Lines

Fall season 2020, six inbred lines of sunflower were crossed by half-diallel crosses to obtain 15 single hybrids. The genotypes (parents and first-generation hybrids -F1) were planted in randomized comlete block design (RCBD) with three replications in a field/Babylon Governorate during the spring season 2021. The study aimed to estimate Heterosis of the first generation hybrids from the mean of the parents for the traits; stem diameter, head diameter, number of seeds per head, weight of 100 seeds, seed yield and oil yield per plant. Furthermore, estimation of genetic distance among genotypes using cluster analysis. The results of the analysis of variance showed that there were significant differences at the probability level (0.01) for all the studied traits of the parents and the first generation hybrids. The two hybrids (I×Q) and (Q×C) were distinguished a high significant positive heterosis for most of the traits measured. The cluster analysis showed that the two genotypes that include hybrids (Q×C) and (Q×F) had the highest Euclidean distance (175.92 and 183.66) respectively. This indicated to high degree of genetic diversity between the two hybrids and the rest of the studied hybrids, which it positively reflected on the performance of the hybrids for the studied traits. The results of Principal Component Analysis (PCA) and Dendrogram showed that (Q) genotype was far from the rest of the genotypes and isolated to a single group, whereas the remaining genotypes separated into groups to two separed branches, especially the two genotypes (C( and )Q). The reason may be due to the distinguish genetic difference of these interested genotypes which have the ablility to transfer from parents to the its progenies, which resulted from a presence of the clear genetic distance between them, while, other genotypes lacks the of this genetic variation case.

A morphological, phylogenetic and phylogeographic reappraisal of the land crabs Gecarcinus quadratus De Saussure, 1853, and G. lateralis Fréminville in Guérin, 1832 (Decapoda: Gecarcinidae). Are they different species?

Land crabs of the genus Gecarcinus are distributed along both versants of the American continent. At some point four species were recognized: G. lateralis, G. nobilii, G. quadratus, and G. ruricola. Taxonomically, several authors have tried to differentiate Gecarcinus lateralis from the Atlantic coast and G. quadratus from the Pacific coast. Because morphologic characters used showed high intra-population variability, identification were very difficult. Consequently, these two species have occasionally been considered synonyms. To establish the degree of genetic difference between them a molecular analysis was performed with both species, G. lateralis and G. quadratus, including Mexican Pacific and Atlantic specimens, using the mitochondrial COI and 16S genes. The maximum clade credibility and maximum likelihood trees showed two clades with high support values, one corresponding to the Gulf of Mexico population and the other one to the Pacific coast population, with a genetic distance of 6.1%. The within-clade average distance for the Atlantic populations (G. lateralis) was 1.1% and 0.2% for those of the Pacific coast (G. quadratus). This supports the status of G. quadratus as a valid species, not as a synonym of G. lateralis. The estimated time of divergence between both species ranged between 2.3 to 4.3 million years, coinciding with the proposed closure of the Isthmus of Panama. Morphologically, some populations show high variability in somatic characters, whereas sexual appendices of males of both species showed very little variation. Color in life, shape of sternite 3, and shape and degree of coverage of the abdomen of thoracic sternites, in both sexes, are traits that can be used to differentiate both species.

Application of Biomarkers and Oil Fingerprinting for Genetic Classification of Oil and Prediction of Petroleum Migration Pathways of Aryskum Downfold of South-Torgay Depression

This article presents the results of fingerprinting and biomarker analysis of 254 oil samples derived from 11 different fields and structures in Aryskum downfold of the South-Torgay depression for genetic classification of oils and prediction of petroleum migration pathways. According to the oil fingerprinting results based on patented Shell technology, 12 groups of oils were found: oils in reservoirs of central part of Nuraly field form the first group, while oils in the producing horizons of Western Nuraly, Southern Khayrgeldy, Akshabulak East and fluvial beds of Central Akshabulak fields form the second group. The oils related to the third group were found in the wells exploiting producing horizon I in the north dome of Central Akshabulak, while the oils from wells penetrating lower producing horizons(III-IV-V) of Central Akshabulak, upper producing horizons in South dome of Central Akshabulak and of all producing horizons of the north dome of Akshabulak South constitute the fourth group. The fifth group includes only one oil sample of different genesis from well № 37, which penetrates the paleo-channel №13 at South Akshabulak. The genetic difference of this oil from other oils was also confirmed by its biomarker composition. Most of oil fingerprinting star plots in Aksay field are identical and form the sixth group, although the seventh group comprises only one oil № 47 in Aksay. Sample set with №8 was discovered in the pay zones of Taur field and well № 75, exploiting the same horizon in the northern part of Aksay. The ninth oil group was identified in cretaceous producing layers of the Khairgeldy South-West field and Jurassic beds of the Khargeldy North field, while the identical composition of the cretaceous oil from the Khairgeldy North and Khairgeldy fields forms the tenth group. The last eleventh group includes oil from well №. 12 on South-west Khairgeldy, although it has some similarities with Taur oils. For 20 oil samples was carried out biomarker analysis, according to the results of which all studied oils were formed in terrigenous (shaly) OM, deposited in lacustrine environment. Oils from central Nuraly are more thermally mature and lighter in density than those from western Nuraly. Oils of Akshabulak East are thermally less mature than oils of Central Akshabulak and Akshabulak South despite its deeper deposition. Based on the performed analysis, in the conclusion were presented 5 prospective hydrocarbon accumulation zones for increasing hydrocarbon reserves in the future. But the results of the performed studies provide valuable information only when integrated with confirmed geological and seismic data.

Based on network pharmacology, using methods such as molecular docking and gene difference analysis, small molecule compounds for the treatment of lung adenocarcinoma and lung squamous cell carcinoma were screened in saussurea involucrata, and new therapeutic targets were discovered

Purpose: Based on systemic pharmacology and network pharmacology, to evaluate the therapeutic effect of saussurea involucrata (SAIN) on lung adenocarcinoma and lung squamous cell carcinoma (LUAD&LUSC) through clinical sample genetic difference analysis and compound-target molecular docking, and discover new The target of prevention or treatment of LUAD&LUSC. Materials and methods: Using the TCM System Pharmacology Database (TCMSP) as the starting point for preliminary selection of ingredients and targets (OB≥30%, DL≥0.18, n=9), with the GDC database as the end point, using Cytoscape 3.8, TBtools 1.082, AutoDock 4.2.6, R 4.0.4, PyMol and other tools have conducted a preliminary screening of the ingredients and targets of SAIN. In order to further screen the effective ingredients and targets, we used clinical samples from LUAD and LUSC from TCGA and GEPIA to perform genetic difference analysis (n=6), and perform biological process (BP) analysis (FDR) on these targets. ≤0.05, n=6), KEGG pathway analysis (FDR≤0.05, n=6), protein interaction network (PPI) analysis (n=6) and compounds-targets-pathways network analysis (n=6), obtain biological processes, disease pathways and various compounds regulated by targets-the relationship between targets and pathways. Through the precise molecular docking of ingredients and targets, we further screened the targets of the effective ingredients of SAIN (affinity≤-7.0 kcal/mol, H-Bond dist≤3.0, n=6) and visualized the data, Then these targets were verified by using PSORTⅡ, CELLO and BUSCA databases for subcellular localization prediction (n=6). Finally, use the large amount of TCGA clinical data provided by Cbiportal for the prognostic survival analysis of LUAD and LUSC for the genes obtained through the screening. , And consult a large number of documents to verify the results.Results: After screening, comparing, analyzing and verifying a series of data, it is finally confirmed that there are three main active ingredients in SAIN. They are Quercetin, Luteolin and Kaempferol, which mainly act on 6 protein targets. The target mainly regulates 20 signal pathways including Pathways in cancer, Transcriptional misregulation in cancer, EGFR tyrosine kinase inhibitor resistance, Adherens junction, IL-17 signaling pathway, Melanoma, Non-small cell lung cancer and MicroRNAs in cancer. The preventive or therapeutic effects of LUSC. Conclusion: There are three active compounds of Q, L and K in SAIN, which play a role in the treatment and prevention of NSCLC by directly or indirectly regulating the expression of genes such as MMP1, MMP3 and EGFR.