Biochemistry & Molecular Biology الكيمياء الحيوية والأحياء الجزيئية

Permanent URI for this collection

http://dspace.alquds.edu:4000/handle/20.500.12213/1087

Browse

Now showing 1 - 20 of 46

Analysis of the Secondary Structure of the Transmembrane Domain of SARS CoV E Protein using FTIR Spectroscopy
(AL-Quds University, 2007-05-10) قاسم موسى هاشم أبو رميله; Qassem Mussa Hashem Abu Rmeleh; معتز عكاوي; Mohammed Abo-Alhaj; Sameir Alnajde
One of the major obstacles facing the field of structural biology in the postgenomic era is the inherent difficulty of solving the structure of membrane proteins under native conditions. Membrane proteins share a common property; part of their structure is embedded in the lipid bilayer. This feature makes them attractive drug targets, which requires a detailed knowledge of the secondary structure of their transmembrane domain. Both crystallography and NMR still encounter difficulties in handling membrane proteins, so there is an urgent need for new biophysical methods and new insights in the biophysics of membrane proteins to solve the secondary structure of such proteins. The outbreak of the severe acute respiratory syndrome (SARS) virus, July 2003, has presented a formidable challenge for the scientific community. As part of that effort, we decided to study the high resolution backbone structure of E transmembrane proteins of the SARS coronavirus, by Attenuated Total Internal Reflection (ATR) FTIR of eighteen of isotopically labeled sites with ( 13C=18O) of the synthesized sequence for the SARS coronavirus E protein transmembrane domain. ATR-FTIR spectroscopy is a wellestablished method for generating precise structural information on isotopically labeled membrane proteins embedded in a lipid bilayer. We used the new biophysical method site specific infrared dichroism (SSID), to investigate the structure and orientation of transmembrane. α-helical bundles We postulate in this work that the E protein of SARS CoV is α-helix, and it has 26 residues embedded in the lipid bilayer, and the SARS CoV E protein is not a regular helix, but it adopts a unique transmembrane helical hairpin model, and the E protein has two possible kinks at residue No. 26 and 31 Phe and Leu respectively within the lipid bilayer, which isreported for the first time in this thesis. And it also has a possible kink in residue No 15 too. All the results were confirmed experimentally.
MOLECULAR DIAGNOSIS AND GENOTYPING OF CANINE VISCERAL LEISHMANIASIS IN THE NORTHERN PART OF THE WEST BANK, PALESTINE
(AL-Quds University, 2005-05-10) سهير ابراهيم محمدعريقات; Suhair Ibrahim Mohammed Oraiqat; زياد عابدين; Robin Abu-Ghazaleh; Moaen Kanan
Molecular Genetics Analysis Of MEFV Gene Mutations In Familial Mediterranean Fever (FMF) Among Palestinans In The West Bank
(AL-Quds University, 2001-05-01) رانية يوسف ابراهيم أبو سير; Raniah Yousef Ibrahim Abu Seir; هشام درويش; محمود ابو حديد
The Role of Human Cytomegalovirus UL16 Glycoprotein and pp65 Phosphoprotein on Tegument Site, Membrane and Raft Association in Human Fibroblast Infected Cells
(AL-Quds University, 2009-06-30) خضر محمد ابراهيم زواهرة; Khader Mohammed Ibrahim Zawahreh; ميساء العزة; Musa Hindiyeh; Zaidoun Salah
استعمال تقنية الجيل الثاني في كشف تسلسل الحمض النووي لمعرفة نوع ذبابة الرمل و طفيل الليشمانيا
(AL-Quds University, 2019-05-18) محمد هاشم حسين الطرده; Mohammad hashem hosen altarade; زياد عابدين; Abed Nasereddin; Ibrahim Abbasi; Robin Abu Ghazaleh
الارتباط بين الأشكال المتعددة الوراثية في أنماط إيبوكسايد إيبوكسيد فيتامين ك و GAS6 مع فقد الحمل المتكرر بين النساء الفلسطينيات
(AL-Quds University, 2010-08-08) أنظار صقر محمد درويش; Anthar saqer Mohammed Darwish; هشام درويش; عماد معتوق; مي مغاثي
التحقق من العلاقة في التغيرات المحذثة في جيني PPAR? و PGC-1? ومرضى السكري من النوع الثان للمرضى الفلسطينيين
(AL-Quds University, 2010-06-10) انمار مصطفى توفيق ابوزهره; Anmar Mustafa Tawfeeq Abuzahrah; هشام درويش; اكرم خروبي; Ahed Abdulkhaliq
التحليل الجزيئي والتعريف لفصائل بكتيريا البارتونيلا من براغيث تم جمعها من حيوانات حاضنه من مدن فلسطينية
(AL-Quds University, 2015-05-06) احمد 'محمد رشيد' سعدي رشق; Ahmed (Mohd Rasheed) Sadi Rishiq; زياد عابدين; ابراهيم عبسي; امير الجواربة
For an extended period of time, researchers have considered small ectoparasite insects that belong to Siphonaptera order as vectors for many microorganisms as Bartonella and Yersinia bacteria. Bacteria from genus Bartonella are gram-negative, haemotrophic and fastidious were suspected to be transmitted through fleas. However, Bartonella can cause a wide range of diseases according to their species type. No data on Bartonella were ever recorded in Palestine before. This study investigated the prevalence of Bartonella organisms in fleas from cats, dogs, rats, and hyraxes in Palestine and characterized their genetic composition. Collected fleas from different districts in Palestine were characterized. The identified species were subjected to traditional molecular methods (DNA extraction, PCR and RFLP) followed by DNA sequencing for the aim of Bartonella spp identification. Based on the previous steps, dendrogram trees have been constructed using three different genetic loci. Fleas (n=289) were collected from cats (121), dogs (135), hyraxes (26) and rats (7) from northern (n=165), central (n=113), and southern (n=11) regions of Palestine. The prevalent flea species were: Ctenocephalides felis (n=119/289; 41.2%), Ctenocephalides canis (n=159/289; 55%), and Xenopsylla spp. (n=7/289; 2.4%). Targeting the Intergenic Transcribed Spacer (ITS) locus, DNA of Bartonella was detected in 22% (64/289) of all fleas. Fifty percent of the C. felis and 57% of the Xenopsylla spp. contained Bartonella DNA. DNA sequencing showed the presence of Bartonella clarridgeiae (46.7%), Bartonella henselae (25%), and Bartonella koehlerae (3.1%) in C. felis. Xenopsylla spp. collected from Rattus rattus were infected with Bartonella tribocorum, Bartonella elizabethae, and Bartonella rochalimae. By using the 16S-23S ribosomal RNA gene (ITS) for constructing the phylogenetic tree; ITS DNA sequence analysis showed four genetic clusters with unique sublcusters: cluster 1 includes B. henselae and B. koehlerae as its two subclusters, cluster 2 includes B. clarridgeiae. However, B. tribocorum and B. elizabethae formed two more out-group clusters. On the other hand, citrate synthase (gltA) showed two main clusters and RNA polymerase. β subunit (rpoβ) genes displayed two main clusters All confirms the effectiveness of the ITS gene in discriminating between Bartonella spp. These findings showed the important role of cat and rat fleas as vectors of zoonotic Bartonella species in our region. It is anticipated that this study will raise awareness among Palestinian physicians, veterinarians, and other health workers of the highprevalence of Bartonella spp. in fleas and the potential risk of these pathogens to humans and animals in this region. This work has been published in a peer reviewed journal: Journal of Vector Ecology; 2014; 39 (2): 261-270
التشخيص الجزيئي لطفيل اللشمانيا
(AL-Quds University, 2011-07-20) صفاء محمد عبد الدمج; SAFAA MOHAMMED ABED AL-DAMAJ; عمر حارشة; Sameer Barghouthi; Emilia Rappocciolo
التشخيص الجزئي للمرضى المشتبه باصابتهم بمرض البورفيريافي منطقة الخليل ,فلسطين
(AL-Quds University, 2018-12-22) نورس زيدان حسن فاتوني; Nawras Zeidan Hassan Fatouni; زياد عابدين; Abed El majeed Nasereddin; Marwan Qubaja; Asad Ramlawi
التعرف على الفصائل والشجرة الوراثية للقراد الصلب (Rhipicephalus) بواسطة التحليل الجيني الجزيئي من عدة محافظات فلسطينية مختلفة
(AL-Quds University, 2016-05-10) رائدة سالم احميدان طقاطقة; Raida Salim Ihmeidan Taqatqa; سهير عريقات; عبد المجيد ناصر الدين; سمير البرغوثي; بسمة الضميري
Ticks are obligate blood-sucking hematophagous ectoparasites of terrestrial vertebrates, including amphibians, reptiles, birds, and mammals. Two general families of ticks are recognized: Argasid (soft ticks) and Ixodid (hard ticks).The family Ixodidae of hard ticks is divided into two groups based on morphological features: the Metastriata and the Prostriata. In the Ixodidae family the genera Ixodes, Amblyomma, Dermacentor, and Rhipicephalus are considered medically important. Among Rhipicephalus ticks, R. sanguineus, R. turanicus and R. bursa, are the most common species in Palestine. All three Rhipicephalus species are medically important vectors; therefore their accurate identification is necessary. Morphological identification of these species is difficult, especially when the specimens are damaged or engorged with blood or in on immature stage. The objectives of this study are to identify the most common hard-ticks species in Palestine, to establish a molecular approach for discrimination between hard ticks species that infest sheep, and dogs and to study the genetic variation within each species in comparison to local and foreign hard ticks species. By identification of hard tick species, the potential risk to animals as well as humans may be evaluated and thus more adequately controlled. A total of 351 hard ticks (Ixodidae) were collected from sheep, goats and dogs during March to October 2014. Ticks were identified based on morphological features into two main genus; Rhipicephalus (97.4%) and Haemaphysalis (2.6%). The ticks were further identified down to the species level as following: R. sanguineus (79.2%), R. turanicus (9.7%), R. bursa (3.4%), H. alderi (0.9%) and H. parva (1.6%). All tick samples were identified by polymerase chain reaction (PCR) targeting the COX-1 gene followed by RFLP using AluI restriction enzyme. A highly significant correlation was observed between RFLP and microscopy identification (p= 0.01). Phylogenetic analysis based onCOX-1 genetic sequences showed four main clusters, R. sanguineus-like cluster, R. turanicus -like cluster G1 and G2, and R. bursa-like cluster. This study is the first of its kind to identify the hard tick species, using COX-1 gene followed by RFLP as genetic marker. Distinction between the closely related Rhipicephalus species: R. bursa, R. turanicus and R. sanguineus was successfully accomplished.
التعرف على مجتمع الميكروبات في الوبر الصخري المستودع المشتيه به لداء الليشمانيات في فلسطين تحليل الميتاجينوم
(AL-Quds University, 2020-01-11) رنا نايف مصلح عوايصة; Rana Nayef Mesleh Awaysa; سهير عريقات; Omar Hamarsheh; Amer Al-jawabreh
التفاعل بين جينات السيروتونين و الساعة البيولوجية و تواسطها في التفاعل بين الإكتئاب السريري و الأنماط الزمنية
(AL-Quds University, 2019-08-05) عبد الرحمن صلاح جبر سوالمه; Abdelrahman Salah Jabr Sawalma; محمد حرزالله; Dr. Jürgen Dammers; فواز عواد; هشام درويش
التوصيف الوراثي للبكتيريا من الجنسين والحيوانات العائلة لها في فلسطين: التوزيع المكاني
(AL-Quds University, 2017-05-16) طاهر محمد طاهر زيد; Taher Mohammad Taher Zaid; سهير عريقات; Dr. Abedelmajeed Nasereddin; Dr.Sameer A.Barghouthi; Dr. Amer Al-Jawabreh
العلاقة بين المتغير الجيني FTO (rs9939609) مع مضاعفات الاوعية الدموية Macrovascular Complications في النوع الثاني من مرض السكري Type 2 diabetes mellitus بين السكان الفلسطينيين
(AL-Quds University, 2018-05-05) انس رزق حسن صبارنه; anas riziq hassan sabarna; سهير عريقات; marwan Qubajeh; amjad Hussein
Type 2 diabetes mellitus (T2DM) is the most common form of diabetes and accounts for over 90 % of all diabetes cases worldwide. Type 2 diabetes is characterized by insulin resistance and relative insulin deficiency, either of which may be present at the time that diabetes becomes clinically manifest. Genetic background was perceived to be linked with the development of T2DM and its related complications including retinopathy, nephropathy, diabetic foot and cardiovascular disease. Several variants in the FTO gene were analyzed and found to be associated with T2DM and obesity in different population. Therefore, our study was designed to investigate the association of FTO (rs9939609) gene polymorphisms with T2DM and its related complications. A case-control study was conducted during the period of 2016-2017. A total of 281 diabetic patients (181 obese and 15 non-obese) and 118 controls (52 obese and 39 non-obese) were recruited. All of them were unrelated and aged ≥40 years. The anthropometric, clinical and biochemical data was collected on a structured questionnaire. The single nucleotide polymorphism (SNP) in the FTO gene was identified by PCR-RFLP. Comparison of allele frequencies and genotype distributions between the diabetic and non-diabetic groups were done using the Pearson‟s Chi-square test. R statistics (v2.8.0). software was used to measure OR for T2DM adjusted for age, gender and BMI. Our results showed a strong association between the minor allele A at rs9939609 of the FTOand increase T2DM risk with an allelic odd ratio (OR) of 1.84, (95%CI [1.04-3.05], P=0.034) after adjustment by age, gender and BMI. Stratified data by glycemic status and across FTO genotype, revealed a marginally association between the FTO A variant and body mass index (BMI) in the diabetic group (P=0.057), while no association was found in non-diabetic control group (P=0.688). Furthermore, no significant association was observed between FTO genotypes and covariates of age, gender, T2DM complications or any tested metabolic trait in both diabetic and non-diabetic individuals (P>0.05). In conclusion, our results demonstrated FTO rs9939609 variant was associated with T2DM. However, further large-scale study is required to elucidate the role of this variant on the predisposition of increased BMI in Palestinian population.
العلاقة بين المتغيرين الجينين (rs7794745rs2710102) في حين الCNTNAP2 مع مرضى التوحد الفلسطينين
(AL-Quds University, 2018-10-26) مهند سعيد سليمان القيق; Mohannad said suleiman qeeq; هشام درويش; Kifaya Azmi; Muhanad Khdeir
الكشف الجزيئي Molecular Identification والتصنيف القائم على التسلسل الجيني Sequence Based Typing لبكتيريا الليجيونيلا نيوموفيلا Legionella pneumophila في العينات البيئية والسريرية في فلسطين
(AL-Quds University, 2017-05-08) محمود جميل اسحق عمرو; mahmod jameel ishaq amro; دينا البيطار; د. سهير عريقات; د. كامل عدوان
Legionellae are gram-negative bacteria, rod shaped, strictly aerobic and nutritionally fastidious. Legionella species are implicated in two clinical syndromes: Legionnaires’ Disease (LD), and Pontiac fever, which are collectively known as legionellosis. Among the 56 species and 70 serogroups of Legionella species, Legionella pneumophila is the major cause of sporadic and outbreak legionellosis (91.5%), and serogroup 1 is the predominant serotype (84.2%). Many studies have demonstrated that the main source for LD is the potable water systems in large buildings like hospitals and hotels. The contamination of hospitals' water systems with Legionella is high risk for patients with various diseases, especially immunocompromised and those who may stay hospitalized for long period of time. LD is acquired by inhalation of aerosols contaminated with Legionella spp. or less commonly by aspiration of contaminated drinking water. Previous work in the Microbiology Research Laboratory at AQU has shown high prevalence of Legionella spp. in the water and biofilm samples collected from eight hospitals in the West Bank over a two-year period December 2012- December 2014, by using culture method and 16S rRNA-based PCR. Moreover study of the prevalence of L. pneumophila in 195 respiratory samples (sputum or Broncho alveolar lavage (BAL)) by culture yielded only one positive. However, by PCR, 23% (44/195) of the respiratory samples were positive for L. pneumophila. BAL presented a higher percentage 35% (26/74) than sputum 15% (18 /121). Molecular diagnosis of L. pneumophila is well established and adopted worldwide especiallythat culture methods are time consuming and less efficient. Furthermore, genotyping of L. pneumophila is important for epidemiological investigation and control of legionellosisoutbreaks. The current gold standard for L. pneumophila genotyping is Nested PCR Sequence Based Typing (NPSBT), based on the sequence of seven loci (flaA, pilE, asd, mip, mompS, proA and neuA). NPSBT allows the Sequence Typing (ST) of L. pneumophila in the absence of isolates. This high-resolution molecular typing tool is recommended by the European Working Group for Legionella Infections (EWGLI). The previous results in the Microbiology Research Laboratory entitled the use of NPSBT to be able to do epidemiological typing of the respiratory samples in the absence of isolates and to relate the ST’s of environmental samples previously collected from the same hospital with the ST of the respiratory samples to evaluate possible nosocomial infection. The overall goal of this study was to determine the Sequence types (ST’s) of the PCR positive respiratory samples by NPSBT method. Also to determine the ST’s of the environmental samples obtained from the same hospital ward. Our sample study included a subset (34 samples) out of the 44 respiratory samples previously tested positive by PCR targeting 16S rRNA for L. pneumophila. These thirty-four positive samples were further subtyped by NPSBT method. Also DNA previously extracted from 15 biofilm samples previously collected from Makassed hospital wards and tested positive for L. pneumophila was also analyzed by NPSBT. Analysis of the seven allele profiles for the NPSBT of the 34 selected respiratory samples showed a full 7-allele profile for 3 /34 (8.8 %) specimens, a further 18/34 (52.9%) gave 5- or6-allele profiles (sufficient to identify the strain as one or two sequence types (ST’s), 6/34 (17.6%) gave 3- or 4-allele profiles (usually enough to differentiate different profiles), and 5 /34 (14.7%) gave 1- or 2-allele profiles (sufficient to distinguish strains). Overall, 24/34 (70%) samples gave ≥ 4 alleles profiles (4, 5, 6 and 7 alleles). However, 10 samples gave < 4 alleles profiles, these samples were excluded from sequencing in order to identify the ST. Analysis of the seven alleles’ products of the selected fifteen environmental samples revealed fourteen samples positive for six to seven alleles and one sample was positive for one allele, this sample was excluded from sequencing in order to identify the ST Sequence analysis showed the following ST’s in the 24 respiratory samples: ST1 (29.1%, 7/24On the other hand, 14 environmental samples typing showed: ST 1(28.6%, 4/14), ST 187 (21.4%, 3/14), one sample of each ST 2070, ST 461 and ST 187 (7.1 %, 1/14), while the rest of samples (28.5%, 4/14) were unspecified Sequence Types. Thus ST1 is the most prevalent sequence type in both the respiratory samples and the environmental samples representing 29.1% and 28.5% respectively. The other ST’s were unique to each type of sample. ST1 is also the most prevalent ST worldwide in clinical and environmental samplesST 461 (25%, 6/24), ST 1037 (4%, 1/24), and (41.9%, 10/24) gave incomplete profile.
الكشف عن وجود الحمض النوووي للحلم و آفات الحشرات في عينات من الحبوب المخزنة منزليا بواسطة طرق البيولوجيا الجزيئية
(AL-Quds University, 2013-05-25) لمياء يوسف أحمد الهلسه; lamia yousef ahmad alhalaseh; هشام درويش; ابراهيم العباسي; سمير البرغوثي; خلدون نجم
Home stored grains such as wheat, rice, lentils, corn...etc, are usually exposed to contamination with insect pests. Over 60 species of insects infest stored grains where Indian meal moth, flour beetles, saw-toothed grain beetles and granary weevil are the most common. These pests are economically important and are responsible of millions of dollars loss because contamination by these pests reduces grains quality and therefore discarding them. They may also cause several health problems including allergies and gastrointestinal disorders. Insect pests are classified as primary and secondary pests. The primary pests present a bigger problem than secondary pests because they infest grain kernel; feed upon them and reproduce on it leading to major damage of the whole sound grain, while secondary pests feed on grains damaged by primary pests because they are not capable to penetrate grain kernel. The global spreading of these insects occurs as a result of word wide cereal distribution. Infestation might occur during storage, shipping and transportation. Control managements of these insect infestations can be achieved either by chemical (fumigation), physical (thermal control, inert dust, ionizing radiation, light and sound control) or biological treatments (pheromones, growth regulators, microbial control and plant extracts). There are several methods for detection of insect pests in grains. Traditional detection techniques include staining kernels, density separation, uric acid analysis, acoustical sensors, x-ray, near infrared spectroscopy (NIR) and enzyme linked immune-sorbent assay (ELISA). Problems encountered with these methods are that they are laborious, expensive and not sensitive to detect insect contamination at the egg and larvae stages. Therefore, newer methods are needed forrapid and sensitive detection. One obvious approach is to develop a molecular biology technique that utilizing genetic information of the different insects for amplification of specific target gene sequences by polymerase chain reaction [PCR] and real time PCR for that purpose. In this study, used a number of infested grain samples were used to isolate larvae and adult insects from them which serve as positive controls in our work. The isolated insects were subjected to DNA extraction, PCR amplification of defined regions in the cytochrome oxidase gene followed by sequencing to identify each pest species. The sequences were identified according using BLAST generated comparison to the original gene sequence obtained from GeneBank. The sequences of the gene from the differentinsects were aligned to design three sets of primers specific for insect mitochondrial cytochrome oxidase subunit I gene. Two primer sets, COI-long1 and COI-long2 for general pest species and COI-mite for the detection of mites. The designed primers were tested for their specificity and sensitivity. A problem was encountered with grain swelling after they were mixed with the aqueous solutions to collect the contaminating insects. This problem was solved by developing and adapting two different methods for grain treatment before DNA extraction using a centrifugation washing method or filtration washing method with the different sample size including either 10 or 50 grams respectively. For PCR optimization, the original DNA sample, 1:10 and 1:100 sample dilution were tested which indicated the best and sample dilution to use was 1:10.. The suitability of PCR primers and DNA extraction methods was evaluated on eleven samples of commercial grains in six separate PCR reactions utilizing each primer set with the two extraction methods. The detection sensitivity varied between the different primers used and extraction method where superiority with COI-long1 primer compared to the COIlong2 primer and the filtration washing method was more efficient over centrifugation washing method giving the pest combination is COI-long1 with filtration washing method.
اللشمانيا الجلدية
(AL-Quds University, 2001-11-10) كفاية عزمي محمد سليمان; Kifaiah Azmi Mohammad Suliman; هارون خنفر; Dr. Ziad Abdeen; د زياد عابدين
النشاط ماسخ من الفثالات على تطوير الفراخ وخصوبة فئران الإناث
(AL-Quds University, 2010-05-24) صفاء عبد السلام سامي عبد الغني; safa Abdul Salam Sami Abdul Ghani; زياد عابدين; منير قزاز; معتز عكاوي

Browse

Browsing Biochemistry & Molecular Biology الكيمياء الحيوية والأحياء الجزيئية by Subject "Biochemistry & Molecular Biology"

Results Per Page

Sort Options