Biotechnology Commons^™

Integrative Genomic Insights Into Coral Resilience: Adaptive And Acclimatory Responses To Seasonal Environmental Shifts, Tasnim Ghanim

Theses and Dissertations

Coral reefs, critical to marine biodiversity and coastal protection, face escalating threats from climate change-related phenomena such as ocean warming. This warming is leading to widespread thermal stress that contributes to coral bleaching and infectious disease in corals, leading to the disruption of marine ecosystems and the economies that depend on them. Focusing on the brain coral Platygyra daedalea, known for its thermal resilience in the Persian Arabian Gulf—a region that exemplifies the extreme stressors of climate change—our study aims to dissect the genetic, transcriptomic, and microbiological underpinnings of coral survival in high-temperature environments predicted for the end of …

Cytotoxic Activity Of Salvia Officinalis Extract Mediated By The Inhibition Of Jak2 In Breast Cancer, Salma Alawadi Dawood

Theses and Dissertations

Background: Breast cancer is the most common type of invasive cancer in women in their forties and fifties. Recent evidence suggests that JAK2/STAT3 signaling is constitutively active in breast cancer. Previous studies suggest that plant extracts, including Salvia Officinalis, have strong cytotoxic effects on breast cancer cells. The differential expression of miRNAs is also strongly linked to cancer development.

Aim: In the current study, we hypothesize that S. Officinalis extract suppresses JAK2 expression and has strong anticancer potential in MCF7 breast cancer cell lines.

Methods: GC-MS analysis showed the presence of flavonoids in dried leaf of …

Association Of Gut Microbiota Composition With Alzheimer’S-Like Disease In A Rat Model, Hana Heiba

Theses and Dissertations

With many countries turning ‘grey’ and facing an issue with aging populations, the risk of developing one form of neurodegenerative disease is increasing. Dementia, being the most common syndrome resulting from neurodegeneration, severely affects memory and cognitive functions. Alzheimer’s disease (AD) is the most common neurodegenerative disorder, with an estimated 615,000 new cases will be added to the existing 5.7 million by 2030 (Alkasir et al., 2017).

In the current study, we establish a sporadic AD-like rat model by injecting STZ intracerebrally. Stool samples were collected at two time points; after three weeks for the acute stage, and 3 months …

Characterization Of Testis-Derived Mesenchymal Cells And The Hunt For Universal Stemness Markers, Myret Ghabriel

Theses and Dissertations

Mesenchymal stromal/stem cells (MSCs) are multipotent cells residing in multiple tissues with the capacity for self-renewal and differentiation into various cell types. Due to the myriad sources of MSCs the International Society for Cellular Therapy (ISCT) proposed certain criteria for their characterization. Here, we isolate adult MSCs from mouse testes and demonstrate that these testis-derived MSCs (tMSCs) follow some of the ISCT’s criteria. tMSCs expressed the MSCs surface markers CD44, CD73, and CD29 and lacked the expression of the hematopoietic cell marker CD45. Moreover, the cells displayed the capacity for self-renewal and in vitro differentiation into adipocytes. Since the isolation …

Selective Gsk3Β Inhibition Mediates An Nrf2-Independent Anti-Inflammatory Microglial Response, Mohamed H. Yousef

Theses and Dissertations

Glycogen Synthase Kinase 3 (GSK3) is associated with the proinflammatory phenotype of microglia and has been shown to act in concert with Nuclear factor kappa B (NF-κB). . GSK3 is also a suppressor of Nuclear factor erythroid 2-related factor 2 (Nrf2), the principal regulator of redox homeostasis. Agreeing with the oxidative paradigm of aging, Nrf2 is often deregulated in parainflammatory and neurodegenerative diseases. In this study, we aimed to explore a multimodal disease-modifying utility of GSK3 inhibition, beyond neuronal proteopathologies, Furthermore, we aimed to underscore the difference in therapeutic value between the two GSK3 paralogs by isoform-selective chemical inhibition.

The …

A Predictive Model For Geographical Location Using Microbiome Composition And Covid-19 Based Analysis, Ahmed Adel Aboushanab

Theses and Dissertations

The human microbiome is a main contributor for the health and welfare of the human body. It is affected by many factors like diet and hygiene. These factors differ between different populations. Testing the population-microbiome differences using healthy samples from different countries is the first objective of this study. This data was then used in training and testing machine learning models (Random Forest and L2-logistic Regression Classifiers) for the prediction of the geographical location based on the microbiome data. Random Forest Classifier had the highest accuracy. Feature importance analysis showed that the data for Proteobacteria, Actinobacteria, and Bacteroidetes improved the …

Optimization Of In-Vitro Tissue Culture And Transformation System For Sweet Sorghum Cultivars Using Immature Inflorescence, Logayn Abushal

Theses and Dissertations

Background: Sweet sorghum is a multi-purpose crop that can be used for human food, animal feed, and bio-fuel production. This crop is drought-tolerant and can therefore be grown in arid and semi-arid regions especially in marginal areas in Egypt. Nevertheless, production of Sweet sorghum cannot coup with the increasing demand in consumption as a food, and fuel due to a lag in scientific research regarding its genetic improvement. Therefore, genetic improvement of Sweet sorghum is innately required so that new traits of economic importance could be introduced; however, this can only be achieved through the establishment of a robust in-vitro …

Identifying Micrornas Panel Associated With Hepatocellular Carcinoma In Serum Of Chronic Hepatitis C Patients, Areeg Dabbish

Theses and Dissertations

Introduction: early detection of hepatocellular carcinoma (HCC) will reduce morbidity and mortality rates of this poorly diagnosed widely-spread disease. Dysregulation in microRNA (miRNAs) expression is associated with HCC progression. Objective: Is to identify a panel of differentially expressed miRNAs (DE-miRNAs) to enhance HCC early prediction in hepatitis C virus (HCV) infected patients. Methodology: Candidate miRNAs were selected using bioinformatic analysis of microarray and RNA-sequencing datasets, resulting in nine DE- miRNAs (miR-142, miR-150, miR-183, miR-199a, miR-215, miR-217, miR-224, miR-424 and miR-3607). Their expressions were validated in the serum of 44 healthy individuals, 62 non-cirrhotic HCV patients, 67 cirrhotic-HCV and 72 HCV-associated …

Self-Extending Symbiosis In Symbiodinium Microadriaticum And The Effect Of Endosymbiotic / Horizontal Gene Transfer On Dinoflagellates And The Tree Of Life, Maha Kadry Ahmed Fathy

Archived Theses and Dissertations

Symbiodinium microadriaticum is a dinoflagellate that lives in a mutualistic relationship with the coral Stylophora pistillata in the Red Sea. Symbiodinium microadriaticum is divided into several clades and the A1 clade of Symbiodinium microadriaticum lives in shallow waters and is resilient to thermal stress. The association between Symbiodinium microadriaticum A1 and Stylophora pistillata enables Stylophora pistillata to tolerate the rise in the sea surface temperature caused by global warming and climate change. Here, the first completely sequenced dinoflagellate genome is explored to answer two questions: The first question is whether self-extending symbiosis has a role in the ability of Symbiodinium …

Enrichment Of Extremophilic Bacteria From Atlantis Ii Deep Brine Sediments Using Various Electron Donors & Acceptors, Nelly Abu Alkheir

Archived Theses and Dissertations

The Atlantis II Deep is the most studied and largest brine pool in the Red Sea. It is an active hydrothermal habitat with unique physical conditions. Its unique characteristics (70°C temperature, 26% salinity, pH 5.2) caused it to be a very attractive marine ecosystem for microbiological and metagenomics studies. Sediments of the Atlantis II Deep brine were investigated for the presence of extremophilic bacteria using a cultivation approach combined with phylogenetic analysis. Two different cultivation methods were utilized: substrate gradient cultures and minimal salts medium supplemented with various combinations of electron donors and acceptors. A bacterial culture enriched from the …

Metagenomic Assessment Of The Mobilomes Of Red Sea's Atlantis Ii, Discovery And Kebrit Deeps, Mohamed Mohamed El Rifai

Archived Theses and Dissertations

Mobile genetic elements in microbial communities are mainly composed of plasmids, transposons and viruses. They are collectively referred to as the mobilome and serve as agents that facilitate horizontal gene transfer, which plays an important role in evolution and adaptation of microorganisms. In order to study the abundance and distribution of mobile genetic elements in different marine environments and to clarify whether certain environmental conditions could explain such distribution, sequence similarity searches using protein family signatures against diverse marine metagenomic datasets were used to determine the relative frequency of coding sequences associated with transposases, integrases, plasmids and viruses, or phages. …

E2 Evolutionary Motif Prediction And Identification Of Drug Candidates To Prevent Hepatitis C Virus Cellular Entry, Shairy Azmy Danial

Archived Theses and Dissertations

Hepatitis C Virus (HCV) infection causes around three quarters of worldwide chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Interferon and ribavirin combination therapy is not effective with all HCV genotypes, and has serious side effects that may result in discontinuation of treatment. The aim of our work is to design inhibitors against HCV envelope glycoprotein E2 to prevent its binding to CD81 surface receptor and the consequent viral entry into hepatocytes. Currently, no crystal structure is constructed for E2. However, a model of E2 is available, Yagnik et al. model, which served as the starting point for the structure-based inhibitor …

Exploring The Aerobic Methanotrophs Community In The Red Sea Atlantis Ii Deep Brine Area, Rehab Abdallah

Archived Theses and Dissertations

Methane represents one of the most abundant hydrocarbons on earth and a powerful greenhouse gas. Methane oxidation by microbial consortia contributes positively to the environment by decreasing methane emission to the atmosphere from different ecosystems. Aerobic methanotrophic bacteria are considered one of the main groups involved in methane oxidation. Brine pools are dynamic habitats for microbial cycling of carbon. Atlantis II Deep is the largest brine pool in the Red Sea. The pool is well known for its elevated temperature, salinity and methane concentration. Methane seeps from the deep brine to the overlying brine seawater interface layer, providing a suitable …

Unique Biodiversity Of The Red Sea Brine Floor Revealed By Comparative Taxonomic Analysis Of Atlantis Ii And Discovery Deep Brine Sediments, Ghada Alaa El-Din Mustafa

Archived Theses and Dissertations

The sea floor is a unique and diverse ecosystem to investigate how geochemical processes affect the diversity of biological life. Red Sea brine pools are water bodies characterized by a unique multitude of extreme conditions, including high temperature, high salinity, and unusual high concentration of heavy metals. We performed a comparative metagenomic analysis of the microbial communities in the sea floor of the Atlantis II (2168 m; 68oC), Discovery Deep (2166 m; 48oC) brine pools and two non-brinesites (1,856 m; 21.93°C and 1,937 m; 31.87°C) in the Red Sea. Each brine core wasvertically dissected into seven distinct subsections. CHN&S profiles …

Bacterial Production Of Human Discoidin Domain Receptor 2 (Ddr2) Kinase And Its Gatekeeper Mutants To Assess Activation By Phosphorylation, Dina Allam Abdel Azeem

Archived Theses and Dissertations

Discoidin domain receptor 2 (DDR2) belongs to a subfamily of receptor tyrosine kinases (RTKs) known as discoidin domain receptors (DDRs). DDRs are characterized by an extracellular discoidin homology domain and being activated by collagen resulting in a delayed but sustained activation. DDR2 overexpression was reported in some tumors, atherosclerosis as well as a number of inflammatory and fibrotic conditions. Recently 3 kinase inhibitor drugs (imatinib, nilotinib and dasatinib) were reported to inhibit DDR2 kinase activity suggesting it might have a role in their therapeutic effect. However minimal information is available on DDR2 downstream signaling. Identification of DDR2 substrates is essential …

Isolation And Characterization Of A Novel Thermostable, Halotolerant L-Asparaginase Ii From The Metagenome Of The Red Sea; Atlantis Ii Brine Pool, Aya Medhat Saleh

Archived Theses and Dissertations

L-Asparaginases (E.C. 3.5.1.1) are group of enzymes which catalyze the hydrolysis of L-asparagine to L-aspartic acid and ammonia. Many microorganisms are known to produce two types of L-asparaginase. Considerable attention has been specifically drawn to type II L-asparaginases due to their potent tumor-inhibitory activity. Various limitations, such as high toxicity, poor stability and short half-life, are associated with the commercially available L-asparaginases used in cancer therapy. Additionally, L-asparaginases have a significant role in food industry owing to their ability to reduce the levels of acrylamide, which is a known neurotoxin and a potential carcinogen, in various food products. Knowing that …

Crispr Diversity In Brine Pools Of The Red Sea: A Comparative Study Of Clustered Regularly Interspaced Short Palindromic Repeats From The Red Sea Metagenomes, Mohamed Mohamed Lotaief

Archived Theses and Dissertations

Exploration of CRISPR/Cas systems in the unique Red sea Brine pools can provide insights into host-viral interactions in highly extremophile environments. 454 Metagenomic datasets from different strata of Atlantis II, Discovery deep and Kebrit deep brine pools were mined for CRISPR arrays, and Cas proteins and compared to one another. Overall composition of CRISPR types was inferred by Cas protein HMM data, together with Cas1 phylogenetic placement using RaxML and direct repeat typing. Spacerâ viral interaction was explored using local alignments of mined spacer data to local metagenomic prophage sequences, showing and comparing specific sample CRISPR affected viral occurrences as …

Mining And Identification Of A Potential Subtilisin-Like Serine Protease From The Lower Convective Layer Of The Atlantis Ii Brine Pool In The Red Sea, Ahmed Shibl

Archived Theses and Dissertations

The Red Sea harbors a number of deep-sea brine pools with diverse chemical, physical, and geological conditions. One of the environments, the Atlantis II Brine Pool, is unique to the Red Sea. The deepest part of Atlantis II Brine Pool â the Lower Convective Layer (LCL) â is 2060 meters below the sea surface water, with 26% salinity, and a temperature of about 68 °C. Moreover, it is almost anoxic, and contains a very high concentration of heavy metals. We are interested in identifying subtilisin-like serine proteases, which are an important group of proteolytic enzymes with a broad range of …

Potential Endoglucanase Genes From The Red Sea Atlantis Ii Brine Pool: Structure, Organization And Halophilic Signature, Mohamad Maged Galal

Archived Theses and Dissertations

Cellulolytic enzymes have many industrial applications and play a major role in the process of biofuel production. Bioethanol is a cheap and clean alternative to non-renewable, polluting and expensive fossil fuel. Cellulases and hemicellulases act synergistically to degrade the cellulose polymer into glucose which can then be fermented by specific anaerobic organisms into ethanol. The overall manufacturing process occurs under harsh conditions such as low pH, high temperature and in the presence of elevated salt concentrations. The Atlantis II brine pool in the Red Sea is a unique habitat in terms of its diverse microbial community and physical conditions; high …

Triple Trouble: Examining The Effect Of Combining Mechanical Stress, Pbmcs And Cisplatin On Hepg2 Cell Death, Lalia Ziko

Archived Theses and Dissertations

In an attempt to find better cancer treatments, a new mathematical model proposed by Klika & Marsik (2009) suggests that more cancer cells could possibly be killed by applying several stress factors to tumour cells, however only as a simulation in silico. The proposed stresses include healthy cell anti-tumour effect, the biochemical effect exerted by a cytotoxic drug and a newly introduced mechanical stress. The hypothesis entails that upon applying these three stress factors together simultaneously to tumour cells, the concentration of the tumour cells decreases more than if a stress factor was applied alone. The two main objectives in …

Identification Of Potential Subtilisin-Like Serine Proteases From The Microbial Community Of The Red Sea Atlantis-Ii Brine Pool Using A Metagenomic Approach, Nadine Hosny El-Said

Archived Theses and Dissertations

The Atlantis II deep is the largest brine pool in the Red Sea of around 60 km2. It is located in the central Red Sea (21° 21' N., 38° 04' E.) at a depth of 2200 meters from the sea surface. The lower part of this pool, the lower convective layer (LCL), has extremely harsh environmental conditions characterized by a temperature of up to 68°C, pH 5.3, saturated salt (252 psu), anoxic condition, and high concentration of heavy metals. These harsh abiotic factors exert strong selective pressure in favor of microbial communities adapted to survive in such environment. Therefore, proteins …

Molecular Characterization Of Neuraminidase Surface Proteins Of Influenzavirus B Isolates From Egypt, 1999-2008, Nadean Safwan Khedr

Archived Theses and Dissertations

No abstract provided.

Deciphering The Unique Microrna Signature In Human Esophageal Adenocarcinoma: Dissecting Esophageal Adenocarcinoma Progressive Profile And Its Distinctions From Gastric Cancer, Rama Ahmed Saad Ahmed Ali

Archived Theses and Dissertations

No abstract provided.

Microbial And Chemical Profiles Of Sediments Isolated From Atlantis Ii And Discovery Deep Brine Pools In The Red Sea., Nardine G. Rasmy Marsis

Archived Theses and Dissertations

No abstract provided.

Anti-Angiogenic Effects Of Chemotherapeutic Agents And Their Enhancement With Ot-515 And S-Nach, Shimaa Adel Heikal

Theses and Dissertations

Chemotherapeutic agents have been used for the treatment of numerous types of tumors with great success. Cisplatin and Doxorubicin are among the well-known chemotherapeutic drugs that showed efficacy against various types of cancers. However, cell resistance and major side effects like chemotherapy-induced peripheral neuropathy (CIPN) are limiting factors in using these compounds. Using a combination or adjuvant compounds with anti-angiogenic effects is one of the strategies suggested to decrease resistance or ameliorate chemotherapeutic toxicity. The present study investigated the anti-angiogenic effects of Cisplatin and Doxorubicin alone and combined with Sulfated non-anticoagulant heparin (S-NACH), a low molecular weight heparin LMWH that …

Insights Into Halophilic Microbial Adaptation: Analysis Of Integrons And Associated Genomic Structures And Characterization Of A Nitrilase In Hypersaline Environments, Sarah Sonbol

Theses and Dissertations

Hypersaline environments are extreme habitats that can be exploited as biotechnological resources. Here, we characterized a nitrilase (NitraS-ATII) isolated from Atlantis II Deep brine pool. It showed higher thermal stability and heavy metal tolerance compared to a closely related nitrilase.

We also studied integrons in halophiles and hypersaline environments. Integrons are genetic platforms in which an integron integrase (IntI) mediates the excision and integration of gene cassettes at specific recombination sites. In order to search for integrons in halophiles and hypersaline metagenomes, we used a PCR-based approach, in addition to different bioinformatics tools, mainly IntegronFinder.

We found that integrons and …

Herbal Extracts As Neuroprotective Agents In An In-Vitro Model Of Aluminum Neurotoxicity, Nada Ezzelarab

Theses and Dissertations

Background: Aluminum toxicity due to environmental or industrial exposure, medical applications, or from cooking utensils is a serious medical problem. The current study aims to investigate three herbal extracts: pomegranate peel extract, Achillea fragrantissima extract, and papaya fruit extract to combat this neurotoxicity.

Methods: Chemical characterization of the three extracts were evaluated using HPLC MS while their neuroprotective activity was assayed using MTT assay on SHSY5Y cells and nitric oxide levels.

Results: Using HPLC-MS chromatography, we have identified twenty-one compounds in the hydro-alcoholic Achillea fragrantissima, seventeen were determined in the pomegranate peel, eleven were assessed in the Carica papaya …

Evaluation Of The Anticancer Potential Of Alchemilla Vulgaris Extract Against Human Neuroblastoma Cells, Yomna Moqidem

Theses and Dissertations

Neuroblastoma is one of the most challenging pediatric tumors that present heterogeneity in prognosis and survival despite intensive treatment protocols. Therefore, there is an urge to develop novel and more potent anticancer drugs. Medicinal plants have recently gained worldwide attention due to their variable activities, wide availability, and cost-efficiency. Accordingly, this study attempted to identify novel plant extracts that could show potential anticancer properties against neuroblastoma. In this study, Alchemilla vulgaris (A.vulgaris) ethyl acetate extract was prepared and evaluated for its anticancer potential against SH-SY5Y Human neuroblastoma cell line. The Phenolic content of the prepared extract was characterized …

Mining Selected Metagenomes/Metatranscriptomes For Biosynthetic Gene Clusters And Antimicrobial Resistance Genes, Ahmed Yamany

Theses and Dissertations

Antimicrobial resistance is one of the serious global challenges in the current century. The fact that resistance genes transfer between bacteria, coupled with the fact that the world is connected through complex dynamics. Studying microbial behavior and understanding the different factors coffering microbial resistance to a broad spectrum of the available drug classes, parallel with a comprehensive analysis of the natural microbial products as the primary source of the novel antibiotics, might shed some light on solutions for this problem. Microbial environments harbor a wide range of secondary metabolites (SM) with different functional groups. SMs are not directly involved in …

Assessment Of The Potential Anti-Tumour Effect Of Salvia Triloba And The Combination Of Salvia Triloba And Paclitaxel On Ovarian Cancer: Skov3 Cell Line, Naela Adel Mohammed

Archived Theses and Dissertations

No abstract provided.