Natural sciences

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    Searching for potential novel Orf virus epitopes using reverse vaccinology
    (Al-Quds University, Deanship of Scientific Research, 2020-12-22) AL-Shareef, Aseel ; Al-Natsheh, Raghad ; Abu Omar, Zainab ; Abu Ghazaleh, Robin
    Orf virus is a zoonotic virus that mainly affects sheep and goats and causes skin lesions, which reduce the feeding process among their lambs and kids. An Orf virus vaccine is available, however, the immunity it induces doesn’t last for more than one year, making the reinfection of the virus very common. This research aims to find epitopes that could be a good target for a long-term protein-based vaccine. Using reverse vaccinology, all proteins of the three Orf virus strains (ORFV-SA00, ORFV-NZ2 & ORFV-SY17) were studied by searching for proteins that could have good subcellular localization, antigenicity, as well as being conserved among the three genomes. After selecting proteins with these properties, linear B-cell and T-cell epitopes were detected. The last step was to test the stability of these chosen epitopes by searching for potential proteasomal cleavage sites. This final step in the bioinformatics discovery pipeline left a single stable epitope candidate (DRRPCGVQD). This protein (epitope) is recommended to be tested experimentally to ensure its effectiveness as a vaccine target protein.
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    Microbiological Quality of Fermented Homemade Green Olive
    (Al-Quds University, Deanship of Scientific Research, 2020-12-22) Ayyad, Jamila Ismail ; Khalid, Mahmoud
    Background: Table olive is one of the most popular fermented vegetables in the Mediterranean Basin and has great importance as a food source. Traditionally, table olive fermentation proceeds spontaneously by soaking olives in a brine solution containing water and certain concentrations of table salt (NaCl). In fact, some bacterial types can grow and multiply in salty environments and high acidity conditions of fermented olives, which can be pathogenic and can increase the risk of food poisoning. Objective: This study was done to investigate the microbial quality of fermented homemade green olives at three different salt concentrations. Methods: Fresh green olives were processed using the traditional method, they were directly soaked in brine solutions with three different concentrations 5%, 10%, and 15% of NaCl and the fermentation process took place spontaneously. The microbial analysis was done on the olive pulp and the brine solution using the traditional producer. Results: Lactic acid bacteria were the predominant bacterial type, the growth of lactic acid bacteria was observed in almost all samples. Fermented olives with lower concentrations of NaCl yielded higher bacterial counts. However, the bacterial counts did not show significant differences between the three levels of salt concentration with increasing the fermentation time. Total viable counts of bacteria had an average of 4.2 log CFU/mL. Conclusion: The harsh environmental conditions of fermented olive are not suitable for the existence of pathogenic microorganisms, resulting in a safe product with good quality. The predominant bacterial types present in fermented table olives were mainly lactic acid bacteria, and the presence of pathogenic bacteria was only detected at the beginning of the fermentation process with low salt concentrations.
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    Isolation of bacteria that are able to digest keratin as an alternative to harmful chemicals used in tanning industries
    (Al-Quds University, Deanship of Scientific Research, 2020-12-22) Bheis, Dalia ; Abu Sbaih, Naheda ; Najjar, Nedaa ; Harahshe, Ienas ; Al-Razem, Fawzi ; Ishnaiwer, Murad
    Abstract:Macroccocus is a bacteria that was isolated from a soil sample containing decaying hair and It was found to contain keratinase enzyme due to its high ability to digest keratin protein. The isolated bacteria by this study can be used as an alternative to harmful chemicals tanning processes represents a safe and, clean technology that achieves economic feasibility in the process of skin soaking and hair removal. Background: Leather tanning is considered one of the ancient professions that Hebron has been known for hundreds of years which is the only source of raw materials for Palestinian factories thatdepends on this commodity. In the past, the industry relied on environmentally friendly natural materials in tanning, but today they have become a source of pollution of soil and groundwater, especially after the entry of chemicals in this craft, such as chromium and some acids that infect humans and destroy the Palestinian environment because of the toxic gases that result from the process of soaking and hair removal. Objectives: 1. To Isolate keratinolytic bacteria from soil sample 2. To test the bacterial effectiveness for hair degradation 3. To identify and characterize of bacteria by sequencing tool. Methods: Soil sample containing decaying hair was collected from the industrial area in Hebron city and processed in the lab, bacteria were isolated by using spreading and streaking plate technique, their ability for hair degradation was tested by incubating bacterial colony, hair and water for several days, after the bacterial ability for hair degradation appeared bacterial isolate was identified by sequencing tool and the type of bacteria was determined by bioinformatics tool. Results: Isolated a bacterial strain that is able to digest keratin and was tested on several samples and proved to be effective in degrading hair. It has been welcomed by the Modern Leather Tanning Company (MLTC-Hebron), which has cooperated with us in this project. The strain was genotyped and appeared to belong to macroccocus, this is the first report to find an industrial value for such bacteria which is also safe for human and the environment. Conclusions: Among microbial isolate screened for keratin digestion by using soil sample, a newly isolated Macroccocusequipercicuswas found with a greater ability for hair degradation, the use of such bacteria as an alternative to harmful chemicals tanning processes represents a safe and, clean technology that achieves economic feasibility in the process of skin soaking and hair removal. but in the same time, the full sequence of these strains of bacteria is unknown and not significantly studied. Therefore, additional researches have to be done for characterization of this type of bacteria
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    Development of an In-House Indirect ELISA Kit for Detection and Identification of Infectious Bronchitis Virus (IBV) Antibodies
    (Al-Quds University, Deanship of Scientific Research, 2020-12-22) Maraqa, Deema ; Abu Rmaileh, Hidaya ; Hoshiyah, Islam ; Rasheed, Ameena ; Abu Ghazaleh, Robin
    Infectious bronchitis virus is fatal and highly contagious. Despite the vaccination of industrialized poultry, it causes serious losses in commercial poultry worldwide. Several studies proved that ELISA is more accurate, sensitive, rapid and less technically demanding than Haemagglutination inhibition (HI) test when used to detect antibody titers against IBV. However, commercial ELISA kits against IBV are very expensive. The development of an in-house indirect ELISA kit will be challenging to standardized but offer the potential of providing a cost-effective tool for local vaccine efficacy testing that will be easier to use than HI testing. The setup of an in-house indirect ELISA will go through several main stages. Firstly, antigen production will rely upon obtaining the virus from a live vaccine, which will then be inoculated in eggs allantoic fluid in order to get a large amount of NDV. Secondly, purification and quantification steps will be done and verified by Haemagglutination test, spectrophotometry and SDS-PAGE. After validation of antigen preparation, ELISA plates will be coated with antigens and tested using serial diluted serum samples. In sucrose gradient purification, purified virus band is expected to form between 40%-50% sucrose gradient. According to literatures, we expect to have roughly 6 polypeptides with molecular weight ranged from 12 KDa to 160 KDaas a result of SDS-PAGE. Moreover, we predict to have a highly sensitive and specific indirect ELISA kit for the detection of IBV infection.
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    Detection of Virulence Gene Profiles of Multi-Drug Resistance (MDR) in Pseudomonas aeruginosa Bacteria in Human
    (Al-Quds University, Deanship of Scientific Research, 2020-12-22) Abu-Fanar, Aysha ; Al-Jabary, Bisan ; Hrinat, Maalem ; Ishnaiwer, Murad ; Al-Razem, Fawzi
    The spread of opportunistic bacteria Pseudomonas aeruginosa in hospitals correlated with several diseases to humans. This bacterium showed high resistance to many antibiotics due to their indiscriminate use, as well as mutations in the pathogenic genes of Pseudomonas aeruginosa, which are difficult to treat. Pseudomonas aeruginosa is transmitted to humans in hospitals as being special nosocomial bacteria through ventilators, also through food and water contaminated with these bacteria, which causes muscle fatigue, vomiting and nausea. It also weakens the immune system and is more severe in people who suffer from weak immunity, old age and children, and can lead to death. Therefore, scanning virulence genes in Pseudomonas aeruginosa helps understand pathogenesis mechanisms. The main objective of this study was to detect three pathogenic genes in these bacteria: ExoS, Apr, and Pich. Bacteriological samples were collected and detected by the Multiplex PCR mechanism. Results showed that the sizes of genes were: 444bp, 1017bp, and 608bp. The study of the reaction of multiplex polymers to detect genes (ExoS, Apr, Pich) in 32 colonies was provided by Al-Ahli Hospital in Hebron, the percentage of each gene was 95%. In addition to 12 samples provided by the Al-Istishari Hospital in the city of Ramallah, and the percentage of the presence of each gene in these samples 100%. In the antibiotic examination of Pseudomonas aeruginosa of 44 samples, the bacteria had antibiotic resistance, 43% and 31% of the bacterial strains were resistant to Gentamicin and Aztreonam, 27% of which were resistant to Meropenem, Ceftazidime and Ciprofloxacin, 18% of which were resistant to tazobactam and 22.7% of which were resistant to Amikacin. The minor objective was to identify MDR Pseudomonas aeruginosa from clinical isolates. Isolates were evaluated for their antimicrobial susceptibility to seven antibiotics, Meropenem, Ceftazidime, Amikacin, Azteronam, Ciprofloxacin, Gentamicin and Piperacillin-tazobactam. The results also provided a clear picture of bacterial resistance MDR to these antibiotics by 45.45%.