Biochemistry & Molecular Biology الكيمياء الحيوية والأحياء الجزيئية
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- ItemFollow-up of Tobamovirus infection in cultivated tomato crop using NGS analysis(Al-Quds University, 2024-05-18) Maram Hatem Adel Jaafreh; مرام حاتم عادل جعافرهThe Tomato vegetable plant (Solanum lycopersicum), which bears edible fruit, is a common component of the diet, and it is economically importance across the world. Tobamovirus group (family: Virgaviridae) are destructive agricultural diseases that infect plants. The main goal of the current research is to identify the most tomato cultivars that show the best resistance to viral infections. This outcome could help farmers to avoid many financial losses by choosing specific disease tomato resistance varieties. This study is designed to detect the presence of Tobamovirus relied on next generation sequencing (NGS) technology. The study was performed after collection of leaves, fruit tomato plants and soil samples from 4 different greenhouses located in Jericho district over a period of four months starting from February to May 2023 till the end of the samples collection period, a total of 155 of soil and plant samples were collected. For each collected sample total nucleic acid extraction was done, and processed for genetic analysis. First single stranded cDNA was synthesized from the produced total nucleic acid, followed by amplification via polymerase chain reaction. For each sample two PCR systems were applied for the viral detection and later its DNA sequence analysis was performed by NGS method. All files were uploaded on Galaxy platform program (usegalaxy.org), quality filtered, and analysis were achieved. Among the 155 PCR-tested samples using PCR system 1 and system 2; there was consistency in the PCR results of the two systems. Samples that were seen to have faint or weak amplification were different among the two used PCR systems. It was clear more positive results were seen among the tested samples using PCR system 1 compared to PCR systems 2. From the total tested samples using PCR system 1, 86 samples revealed to have moderate strong PCR results reflected by showing strong PCR bands on agarose gel electrophoresis of Tobamovirus compared to about 46 samples of the same criteria were obtained by PCR system 2. On the other hand, the samples that showed a faint or weak amplification were calculated to be 45 samples applying PCR system 1 and 86 samples applying PCR system 2. All other samples were revealed to be negative by the two used PCR systems. IV Using NGS analysis, the sequences showed 99% similarity to different isolates of Tomato brown rugose fruit virus including the Jordanian tomato Tobamovirus isolate (TBRFV-Jo), (GenBank accession no. KT383474.1).
- ItemDetection of Familial Hypercholesterolemia Variants in Selected Patients with Premature Coronary Artery Disease from Hebron Region(Al-Quds University, 2024-05-15) Enas Yousef Mustafa Sarahna; ايناس يوسف مصطفى سراحنهBackground: The Familial hypercholesterolemia disorder is prevalent but varies across ethnicities. Familial hypercholesterolemia is an autosomal dominant disease with 87% penetrance caused by pathogenic variants in the genes involved in cholesterol metabolism: LDL Receptor, apolipoprotein B or Proprotein Convertase Subtilisin/ Kexin 9 genes, resulting in impaired clearance of circulating Low Density Lipoprotein cholesterol, given that up to 90% of genetically confirmed familial hypercholesterolemia have LDL Receptor variants. It is a highly atherogenic metabolic disorder characterized by lifelong vascular exposure to LDL-C, leading to premature coronary artery disease. Purpose: This work aims to identify the pathogenic variant that cause this disease and verify cascade screening among the studied family. Methods: We selected a patient who fulfilled our inclusion criteria: (1) fasting plasma LDL-C level >190 mg/dL and triglycerides < 220 mg/dL; (2) presence of tendon xanthomata/xanthelasma/corneal arcus or premature coronary artery disease or a first degree relative, or a family history of hypercholesterolemia. The proband’s whole blood sample was sent to Whole Exome Sequencing. Then, blood samples were drawn for PCR and Sanger sequencing from his first-degree relatives. Any newfound case was treated as a new index, and his/her first-degree relatives were screened for that variant. Results: Findings showed that our proband has a heterozygous likely pathogenic missense NM_000527.2: c.1210A>G p. (Thr404Ala) variant in exon 9 of LDL Receptor gene. This variant has not yet been submitted to the Clinvar database. Screening results of his first-degree relatives showed that this variant was transmitted from his father (homozygous familial hypercholesterolemia: GG) to all of his brothers (heterozygous familial hypercholesterolemia: AG). First-degree relatives of affected individuals were screened; a pedigree was drawn. Sequence result and LDL-C level was significantly correlated. Conclusion: Familial hypercholesterolemia is underdiagnosed and undertreated in our population, and this increased the number of premature Atherosclerotic cardiovascular disease cases. Cascade screening is a beneficial and cost-effective process for the diagnosis and treatment of familial hypercholesterolemia early in life using lipid-lowering agents in order to decrease the burden of Atherosclerotic cardiovascular disease and prevent premature cardiovascular death among our population. The variant NM_000527.2: c.1210A>G p. (Thr404Ala) is highly suspected to be FH-causing as A>G substitution has a significant correlation with LDL-C mean level.
- ItemDesign, Synthesis and In Vitro Studies of Lipophilic Mixed Aliphatic/Aromatic Platinum(II/IV) Derivatives that are Encapsulated in Novel Drug Delivery Systems(Al-Quds University, 2024-05-11) Hebah Ibrahim Ali Damdoum; هبه ابراهيم علي دمدومResearch on synthesizing new anticancer compounds with minimal side effects is ongoing, with platinum-based drugs renowned worldwide for their anti-tumor properties. The main hypothesis of our study is that the choice of suitable chelating ligands for the platinum center in both oxidation states (Pt(II) or Pt(IV)) significantly influences the processing of these molecules and the nature of the lipid-based nano-delivery system. The physicochemical properties of the ligand substituents coordinated to the Pt center also strongly affect the dispersion of Pt-based complexes in drug delivery systems, such as niosomal layers. This study focuses on the synthesis and investigation of new platinum(II/IV) derivatives with aliphatic and aromatic ligands encapsulated in niosomal vesicles. Characterization was performed using Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FTIR) spectroscopy and nuclear magnetic resonance iv (NMR). The influence of the encapsulated ligands of platinum-loaded niosomal formulations on size, polydispersity, and loading efficiency was highlighted by using various novel types of platinum ligands. In vitro, studies on liver cancer cells (HepG2 and Hep3B) and the human hepatic stellate cell line (LX2) showed promising cytotoxic effects compared to those of cisplatin, miriplatin, and oxaliplatin. The results indicated that smaller and more compact ligands, such as NBA, have better loading efficiency in the niosomal formulation compared to bulkier ligands like DACH. There were also clear connections between compounds with high lipophilicity, such as myristate, and increased potency against cancer cell lines, likely due to interactions with lipidic compounds and non-ionic surfactants in the niosomes. In conclusion, this study introduces novel platinum(II/IV) compounds that show significant cytotoxic effects in liver cancer cells, highlighting the need for further investigation. This underscores the critical role of achieving well-balanced lipophilicity in drug delivery systems to enhance anticancer activity, minimize drug resistance, and ensure efficient tumor penetration. Further research is essential to understand and optimize these promising platinum-based formulations fully.
- ItemThe Role of Angiotensin-Converting Enzyme 1 and Angiotensin-Converting Enzyme 2 Genetic Polymorphism in Severe Acute Respiratory Syndrome Coronavirus-2 in Palestinian Population(Al-Quds University, 2023-08-19) Lama Khaled Hammad Abu Saleh; لما خالد حماد ابو صالحAs a key enzyme of the renin-angiotensin system (RAS), angiotensin-converting enzyme 2 (ACE2), has been validated as a SARS-CoV-2 receptor, linking RAS to COVID-19. It is likely that functional ACE1/ACE2 gene polymorphism cause the imbalance of ACE1/ACE2 ratio, causing a RAS imbalance that may contribute to the COVID-19 infection complications by causing higher lung damage and disease with severe symptoms. Herein, we developed a new genotyping method using next generation sequencing (NGS) to study four single nucleotide polymorphisms (SNPs), three for ACE1, rs4343, rs4342, rs4341 and one for ACE 2, rs2285666 in one multiplex PCR tube. Bioinformatics analysis was done using free online galaxy program (https://usegalaxy.org.au/). The association of ACE 1 (rs4343, rs4342, rs4341) and ACE 2 (rs2285666) polymorphisms with COVID-19 infection in Palestine were investigated. A total of 130 samples were collected, including 50 negative controls without COVID-19 infection, 50 positive controls with COVID-19 infection but not hospitalized, and 30 patients with severe COVID-19 infection in the intensive care unit. Results showed that the genotype distribution of ACE2 (rs2285666) polymorphism was significantly different between COVID 19 patients and the control group (P-value = 0.049, X2), while no statistical differences were observed between the ACE1 mutations (rs4341, rs4342, rs4343) and the control group (P-value > 0.05, X2). Individuals with ACE2 rs2285666 GG genotype were more prevalent in COVID-19 patients compared to control group (P-value = 0.049, X2). Age and comorbidities such as hypertension and coronary artery disease were independent risk factors for COVID-19 disease (P-value < 0.05, X2). Symptoms of COVID-19 patients such as fatigue, headaches, runny noses, and loss of smell were significantly higher in the positive cases COVID-19 (P-value < 0.05, X2), while dyspnea was more frequent in the ICU patients (P-value < 0.05, X2), In this study, we support the hypothesis that wild genotypes of ACE2 rs2285666 GG are associated with COVID-19 infection
- ItemZeta potential of electric double layer for dendrimers: Monte Carlo simulation study(Al-Quds University, 2023-11-28) Aya Ibrahim Mousa Ja'freh; اية ابراهيم موسى جعافرةIn this study, the potential of the electric double layer (EDL) of different generations of dendrimers in a spherical boundary system has been studied using Monte Carlo (MC) simulations. The effects of Changing the dielectric constant of the solvent, the charge and the radius of generations from G1 to G8, have been studied. The radial distribution function between dendrimer and counterions, running coordination number, integrated charge number, Z effective, zeta and surface potentials were plotted as results of simulation methods. Dendrimers possess a higher electrostatic potential near their surfaces, it increases with the increase of the counterions and the values of distributed ions and accumulated charge increase when the generation of Dendrimers increase. An observed correlation indicates that as generation increases, there's a simultaneous rise in the zeta potential of the electric double layer and the surface potential. This concurrent increase leads to a higher effective charge (Zeff) within the positive region, suggesting elevated charge accumulation. With the dielectric constant =10 that represents the cytoplasm, the interaction between dendrimer and counterions increases, as well as the accumulation near the surface that increases too. Moreover, the electrostatic correlation, the accumulated charge and the magnitude of the electrostatic potential increase with increasing the generation of Dendrimers. The surface potential increases as the generation of the dendrimer increase. However, the values of zeta potential decrease as generation of Dendrimers increase.