Biochemistry & Molecular Biology الكيمياء الحيوية والأحياء الجزيئية
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- ItemEstablishment of Vitamin D Reference Values in the Palestinian Society And Investigation of Cultural, Behavioral, and Socioeconomic Effects(Al-Quds Univeersity, 2022-08-21) Mohammed Ibrahim Issa Al-mahariq; محمد ابراهيم عيسى المحاريقThis thesis documents several key contributions made to the vitamin D field. Vitamin D is recognized as a sunshine vitamin with regular sun exposure conditions. Unsurprisingly, vitamin D dietary intake is considered of minor importance in science. However, sun exposure reveals about 90% of vitamin D. In the last decade, vitamin D testing and the use of vitamin D supplements have increased significantly with neither clear nor agreement on blood level recommendation of vitamin D in healthy individuals. The recommended sufficient level of serum vitamin D is ≥30 ng/mL (≥75 nmol/L). In contrast, vitamin D deficiency is defined as 25(OH)D levels ≤ 20 ng/ml (≤ 50 nmol/L), and the serum level between 20 and 30 ng/ml (50-75 nmol/L) indicates insufficiency. The main objective of this study is to establish a population-based reference range of vitamin D in Palestinian society and investigate its associated cultural, socioeconomic, and human behavioural factors. We adopted a cross-sectional study that was conducted on 300 healthy Palestinian individuals from different cities and villages in the West Bank. Those individuals did not report a history of kidney, liver, or malabsorption disorders. The sample consisted of 123 males and 177 female adults aged between 19 and 65 years old. We used a structured questionnaire to obtain demographic and socioeconomic data, and information about health status and risk factors related to vitamin D insufficiency. Moreover, serum 25(OH)D was measured by the Abbott chemiluminescence immunoassay analyzer (ARCHITECT i1000SR) to establish and provide reference values. The mean 25(OH)D serum level was 13.4 ng/ml (5th; 95th percentile, 12.34; 14.5). Notably, 92% of the studied sample had 25(OH)D serum levels below 30 ng/mL, 79.3% below 20 ng/mL and 61% below 12 ng/ml. The younger group (18-28) years of age was reported to have a significantly lower serum 25(OH)D level compared to the other three different age groups (29-40),(41-50),(51-65) years old. Our results also showed that serum 25(OH)D level was not significantly associated with gender, obesity (BMI), sun cream use, sun exposure, and wearing a hijab (head cover). However, no significant differences of serum 25(OH)D level were reported among individuals consuming cheese, yoghurt, egg, fish, milk, bread, and nuts meals intake. In conclusion, according to the lack of correlated evidence of major skeletal and non-skeletal disease conditions with vitamin D levels that are recommended as optimal (≥20 ng/mL, or even ≥30 ng/mL), and in light of our study to establish vitamin D reference level in healthy adults, we recommend to consider levels below 20ng/ml and close to 14 ng/ml as sufficient serum 25(OH)D level for the general population in the West Bank society. However, our study sample is limited with the small number of participants, hence further investigation and research are needed to establish more comprehensive and inclusive conclusions regarding reference levels and related factors.
- ItemAssociation of Vitamin D Receptor Gene Polymorphisms with Type 2 Diabetes Mellitus in Hebron, Palestine(Al-Quds Unversity, 2026-01-10) Marah Imad Ali Al-Atrash; مرح عماد علي الأطرشType 2 diabetes mellitus (T2DM) is a chronic metabolic disorder characterized by hyperglycemia resulting from insulin resistance and decreased insulin secretion. Vitamin D receptor (VDR) mediates the actions of vitamin D, whichisnecessary for glucose metabolism, insulin secretion, and modulation of inflammation. Variations in the VDR gene, including FokI polymorphism which may alter the VDR protein structure, and the non-functional ApaI, TaqI, and BsmI polymorphisms, which may influence VDR activity or expression and thereby affect susceptibility to T2DM. However, data on the relationship between these VDR variants and T2DM in the Palestinian population are limited. This study aimed to examine the relationship of four VDR polymorphisms and the risk of developing T2DM in the West Bank, Palestine specifically in Hebron. In this case-control study, a total of 300 participants, including 200 T2DM patients and 100 non-diabetic controls aged 40 years and above, were recruited from Alia Governmental Hospital and the Palestinian Diabetes Institute in Hebron between January and April 2025. Demographic, clinical, and biochemical data were collected from medical records. Blood samples were used for DNA extraction, PCR amplification, and genotyping of FokI (rs2228570), TaqI (rs731236), BsmI (rs1544410), andApaI (rs7975232) polymorphisms using next-generation sequencing. Diabetic patients had significantly higher age, BMI, weight, HbA1c, fasting blood glucose, and triglycerides, and lower HDL cholesterol compared to controls. In diabetic patients, the minor allele frequencies were 45.7% for rs7975232 (C), 41.1% for rs731236 (G), 58.6% for rs1544410 (C), and 73.5% for rs2228570 (C). Among these, only TaqI (rs731236) showed a statisticallysignificant association with type 2 diabetes (p = 0.030), while the other polymorphisms were not significantlyassociated.Logistic Regression showed asignificant association between rs731236 (TaqI) and T2DM under the recessive model (GG genotype: OR = 1.5, p = 0.016), with GG carriers exhibiting higher HbA1c in diabetic participants and elevated triglycerides in non-diabetics. Haplotype analysis showed no significant correlations with T2DM risk. These findings suggest that the TaqI (rs731236) variant may serve as a genetic marker for T2DM susceptibility in Palestinian population and highlight the potential role of vitamin D signaling in the disease development. In Conclusion, among the four VDR polymorphisms investigated, only rs731236 (TaqI) showed a statistic significant association with T2DM in the study population from Hebron West Bank, Palestine,indicating its potential utility as a genetic marker and supporting a role for vitamin D signaling in T2DM development in our population. Further studies with larger sample size are needed to confirm these findings and explore additional VDR-related variants
- ItemDetection of Class I Integrons and Insertion Sites in Bacteriophage Genomes: Evidence of Shared Genetic Material with Multidrug-Resistant Klebsiella pneumoniae and Acinetobacter species(Al-Quds University, 2025-08-23) Qais Mohammed Saif El Din AmAli; قيس محمد سيف الدين عم عليEver since the emergence of antibiotic resistance, it has introduced a significant inevitable challenge in clinical administration and treatment of bacterial infections. During the year of 2021, health records have demonstrated a total of 4.71 million deaths due to antimicrobial resistance health consequences, with nearly 25% of them being directly attributable to resistant pathogenic bacteria. Data-based projections estimate the annual death toll to reach 8.2 million within 2025 2050. These concerning clinical records illustrate the necessity for continuous research efforts for developing approaches towards allocating this topic and limiting its health consequences. Ascribed to the latter, we introduce this innovative research, inspired by worldwide publications and implemented here in Palestine to address the yet to be allocated research gap. We designed a study approach that aims to investigate the significant incorporation of bacteriophages in mediating the transfer of antimicrobial resistance-related genetic material across different bacterial species. Furthermore, we focused on unravelling the molecular entities and constitutes involved in this integrational process characterized by Integrons, specific insertion sites and resistance-acquiring genes. In order to achieve this, we retrieved samples from clinically-relevant environments that represent a reservoir for such bacteriophages, samples were taken from both a sewage-water treating facility based in Al-Tireh, Ramallah & an oil mill located in Aroura village where the liquid by-product was collected. These samples exhibited a thorough well-structured process of laboratory work to eventually retrieve the extracted DNA material, two different specific primer sets were designed for an accurate investigation approach. The 1st pair being intCiF3a & intCiiiR3a which were utilized for the purpose of amplifying Class I Integrons that have been documented to harbor MDR genes, while the 2nd pair was designed for amplification of specific insertion sites where integration of resistance-affiliated genetic material takes place IS-F & IS-R. Eventually, we successfully managed to confirm and validate the presence of both Class I Integrons and insertion sites in our phage samples. Moreover, we further investigated the clinical relevance of our findings as we aligned them against already annotated genomes where we discovered a 100% similarity of a 200bp insertion site with MDR-resistant pathogenic Klebseilla pneumoniae. We also discovered another identical alignment of a 240bp sequence representing a Class I Integron with pathogen inducing Acinetobacter harboring antibiotic-resistant characteristics. Finally, a 40bp identical alignment of few of our amplicons with E. coli plasmid “pV139-a” was highlighted. This highlights the incorporation of Class I Integrons, insertion sites and mobility-facilitating constituents taking part in transfer of MDR genes and the corresponding health consequences.
- ItemMolecular Detection and Genotyping of Hydatid Cysts in Slaughtered Livestock in the West Bank, Palestine(Al-Quds University, 2025-01-08) Walaa Habes Mohammad Yones; ولاء حابس محمد يونسDespite the widespread occurrence of CE, there is a significant gap in understanding the specific Echinococcus genotypes present in various regions, including the West Bank of Palestine. This lack of knowledge hampers effective disease management and control strategies. Identifying and genotyping the parasites affecting the intermediate hosts is crucial for epidemiological surveillance, Public Health Implications by informing health authorities and policymakers to implement effective control measures based on local epidemiological data. This study aimed to identify and genotype the Echinococcus parasite genotypes causing CE in the West Bank of Palestine, specifically targeting the intermediate hosts (IMHs) such as sheep and goats. Materials and Methods: A total of 54 cyst tissue samples were collected from livestock in the West Bank, 52 sheep samples from different slaughterhouses from areas known for high CE incidence in the West Bank consisting of hydatid cyst tissues were isolated from infected organs during examinations of the intermediate host, and two are human cysts tissue collected from hospitals after surgery as accidental intermediate hosts. DNA was extracted and amplified by PCR to ensure high-quality genomic DNA for sequencing using the EgG1 Hae III sequence (266 bp). The extracted DNA was subjected to NGS using two primers pools, allowing for comprehensive genetic analysis. Targeting all SNPs of both mitochondrial genes at once: COX-1 (Cytochrome c oxidase subunit 1) and NAD-1 (NADH dehydrogenase subunit 1) for the first time in the present study, which were selected for their variability and are useful for distinguishing between different Echinococcus species and genotypes. Finally, using the Variant Call Analysis platform for identifying and genotyping of Echinococcus specific sequences among thousands of sequences through online bioinformatics software Galaxy/Europe. Results: An EgG1 Hae III sequence of 266 bp was identified in 98% of samples. NAD1 and COX-1 specific fragments were successfully amplified and sequenced through NGS platform from 53 cyst tissue samples. Genotyping analysis was successfully performed in 84% of sequenced samples, revealing that 58% were the G1 genotype and 42% were for the G3 genotype. Conclusion: This study was to distinguish between s.s genotypes G1 and G3 in our isolates based on seven different informative regions together for the first time using NGS with high-quality outputs confirmed the predominance of the G1 genotype while also indicating a significant presence of the G3 genotype among the intermediate hosts in endemic areas of Palestine. While the sensitivity of NGS is widely acknowledged in the scientific community, our findings emphasize the importance of understanding the local epidemiology of CE. The identification of both G1 and G3 genotypes in this region provides crucial data that can inform future public health strategies and control measures.
- ItemScreening of mutations in Polynucleotide Kinase 3' - Phosphatase gene causing Microcephaly, Seizures, and Developmental Delay in Palestine(Al-Quds University, 2025-01-05) Maysa "Mohammad Amer" Kamal Natsheh; ميساء "محمد عامر" كمال نتشةMicrocephaly, Seizures, and Developmental Delay (MCSZ) is an uncommon genetic disorder with an undetermined prevalence. It is inherited in an autosomal recessive pattern associated with either a homozygous or compound heterozygous mutation in the PNKP gene. This gene plays a crucial role in various DNA repair mechanisms, and its mutation leads to the continuous activation of the DNA damage response. This persistent activation is a consequence of the accumulation of double-strand breaks within the affected cells, which may result in the death of sensitive neuronal cells, potentially contributing to the pathogenesis of MCSZ. The disorder is primarily characterized by microcephaly, or an unusually small head size, along with a range of neurological impairments. Purpose: This research aims toscreen PNKP mutations in several Microcephaly, Seizure and Developmental Delay (MCSZ) disorder patients from Palestine. Methods: Three patients from different families were studied, who fulfilled our inclusion criteria: (1) Patients (males and females of different ages) having the general characteristics of MCSZ. (2) Their parents, especially if they are consanguineous in marriage determine if they are carriers for PNKP mutation, and/or family members. Genomic DNA was extracted after obtaining a blood samples which drawn for PNKP gene detection using PCR and Sanger sequencing. PNKP mutations were screenedand targeted the most common published exons (Exon 11, 14 and 15). Results:In this research, we identified a female patient exhibiting microcephaly, significant developmental delays, and early-onset refractory seizures, attributed to a homozygous mutation in the PNKP gene. This mutation, classified as likely pathogenic, is a missense variant denoted as NM_007254.4: c.968 C > T: p. (Thr323Met),located in exon 11 of thePNKP genes. The screening of first-degree relatives revealed that this genetic variant was inherited from both the father and mother who were identified as heterozygous for the MCSZ variant (GA). A pedigree was constructed following the screening of the affected individuals’ first-degree relatives. In contrast, samples from the other two patients did not exhibit any mutations in the PNKP gene. These samples were subsequently subjected to Whole Exome Sequencing, which confirmed the absence of mutations in the PNKP gene for both patients. Conclusion: Microcephaly, Seizures, and Developmental Delay (MCSZ) is underdiagnosed and undertreated in our population. Even simple knowledge among families toward consanguineous marriages, genetic counseling and cascade screening are essentialfor the diagnosis and prevention of MCSZ early in life. The results in this research will be considered as preliminary results on that disease among our population and more cohorts studiesand advanced genetic analysis are still needed.