Biotechnology Commons^™

Improving Photosynthetic Efficiency In Microalgae Through The Genetic Engineering Of Energy Sensors And Photoreceptors, Taylor L. Britton

Biology ETDs

Through photosynthesis microalgae can convert sunlight, water, and CO₂ into chemical energy that can be used to generate carbon neutral biofuels and biomass. With an ever-increasing demand and need for petroleum substitutes it is imperative that we improve the output of industrial-relevant crops such as microalgae. One important way of improving output in algae is by understanding the roles that stress and energy conversion is regulated in these organisms. Photosynthetic organisms fundamentally depend on light- and sugar-driven metabolic and signaling networks, which integrate environmental cues to govern and sustain growth and survival. SnRKs (SNF1-related protein kinases) and the photoreceptor …

Developing An Electroporation Method For Transforming Streptomyces Nymphaeiformis, Heather Knott, Stephen Baron

Honors Projects

Streptomyces species are notoriously difficult to transform. Streptomyces nymphaeiformis is no different, so a method of electroporation was used to attempt to transform the cells. Multiple growth stages were used in order to alter the degree of development of the cell wall. The procedure did not kill the cells, but the cells were not transformed. Due to the lack of transformation with S. nymphaeiformis, transformation was attempted on two other Streptomyces strains, S. lividans and S. coelicolor. Neither was successfully transformed to thiostrepton (tsr) resistance, nor did they grow on a plate lacking thiostrepton. One possibility for the …

A Computational Assessment Of The Allosteric Modulation Of Gabaa Receptor, Abdel Rahman Atef Aly

Theses

γ-aminobutyric acid (GABA) type A receptor (GABA_AR) is a pentameric ligand gated ion channel and a member of the Cys-loop superfamily. It is targeted by several clinically significant allosteric modulators. The role of individual subunits of the receptor has been very extensively studied. However, the exact molecular pathway upon which the receptor is activated remains elusive. The main objective of this study was to probe the molecular activation pathway for the orthosteric GABA and to understand how two of the most well-established positive (PAM) and negative (NAM) allosteric modulators tend to modulate the receptor. Three independent long scale …

Characterization Of SccMec Instability In Methicillin-Resistant Staphylococcus Aureus Affecting Adjacent Chromosomal Regions, Including The Gene For Staphylococcal Protein A (Spa), Isabella A. Tickler, Fred C. Tenover, C. R. Scharn, R. V. Goering

Biology Faculty Publications

Staphylococcal cassette chromosome mec (SCCmec) represents a sequence of clear clinical and diagnostic importance in staphylococci. At a minimum the chromosomal cassette contains the mecA gene encoding PBP2a but frequently also includes additional antibiotic resistance genes (e.g., ermA and aadC; macrolide and aminoglycoside resistance, respectively). Certain regions within SCCmec elements are hot spots for sequence instability due to cassette-specific recombinases and a variety of internal mobile elements. SCCmec changes may affect not only cassette stability but the integrity of adjacent chromosomal sequences (e.g., the staphylococcal protein A gene; spa). We investigated SCCmec stability …

Carbapenemase-Producing Pseudomonas Aeruginosa – An Emerging Challenge, Fred C. Tenover, David P. Nicolau, Christian M. Gill

Biology Faculty Publications

Carbapenem-resistant Pseudomonas aeruginosa (CR-PA) is a major healthcare-associated pathogen worldwide. In the United States, 10–30% of P. aeruginosa isolates are carbapenem-resistant, while globally the percentage varies considerably. A subset of carbapenem-resistant P. aeruginosa isolates harbour carbapenemases, although due in part to limited screening for these enzymes in clinical laboratories, the actual percentage is unknown. Carbapenemase-mediated carbapenem resistance in P. aeruginosa is a significant concern as it greatly limits the choice of anti-infective strategies, although detecting carbapenemase-producing P. aeruginosa in the clinical laboratory can be challenging. Such organisms also have been associated with nosocomial spread requiring infection prevention interventions. The carbapenemases …

Detection Of Methicillin-Resistant Staphylococcus Aureus Infections Using Molecular Methods, Fred C. Tenover, Isabella A. Tickler

Biology Faculty Publications

The application of molecular detection methods for bacterial pathogens has dramatically improved the outcomes of septic patients, including those with methicillin-resistant Staphylococcus aureus (MRSA) infections. Molecular methods can be applied to a variety of clinical specimens including nasal swabs, growth in blood culture bottles, and wounds. While data show that the overall accuracy of molecular tests for MRSA is high, results can be confounded by the presence of multiple staphylococcal species in a specimen, insertions and deletions of DNA in and around the Staphylococcal Cassette Chromosome mec (SCCmec) element, and point mutations in mecA. Herein, we explore the complexities of …

Clinical Performance Of The Xpert® Ct/Ng Test For Detection Of Chlamydia Trachomatis And Neisseria Gonorrhoeae: A Multicenter Evaluation In Chinese Urban Hospitals, Fred C. Tenover, Yan Han, Mei-Qin Shi, Qing-Ping Jiang, Wen-Jing Le, Xiao-Lin Qin, Han-Zhen Xiong, He-Ping Zheng, Yi-Wei Tang, Yue-Ping Yin

Biology Faculty Publications

Background: We aimed to evaluate the clinical performance of the GeneXpert® (Xpert) CT/NG assay for the detection of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) using urine and cervical swabs collected from patients in China.

Methods: This study was conducted from September 2016 to September 2018 in three Chinese urban hospitals. The results from the Xpert CT/NG test were compared to those from the Roche cobas® 4800 CT/NG test. Discordant results were confirmed by DNA sequence analysis.

Results: In this study, 619 first void urine (FVU) specimens and 1,042 cervical swab specimens were included in the final dataset. There were …

Editing Genes In Baker’S Yeast To Model Rare Mitochondrial Diseases, Alyssa Dekker, Amy Wilstermann, Rachael Baker

Summer Research

BCS1L is a nuclear-encoded mitochondrial member of the AAA+ (ATPases associated with various cellular activities) family of proteins. BCS1L functions as a translocase in the integration of the Rieske Fe/S protein into respiratory chain complex III during assembly. BCS1L may also play a role in mitochondrial morphology

Cpf1-Based Crispr Genome Editing In The Cyanobacterium N. Punctiforme, Soohan Woo

University of the Pacific Theses and Dissertations

CRISPR systems have been growing in their utility and their application throughout the biological field as researchers continue to grow in their understanding of the relatively novel genome editing technology. However, despite the potential of CRISPR as a genome editing tool, the complexity of applying this technology to a specific organism calls for custom modifications to the system to improve its success rate. In this project, a CRISPR-Cpf1 system that can be effectively employed in the cyanobacterium Nostoc punctiforme was designed, with a focus on the hormogonium development of this species. Multiple plasmids containing the CRISPR system and targeting different …

Chemogenetic Induced Tinnitus Model, Cara Bunner

Williams Honors College, Honors Research Projects

This project will use chemogenetic drug activation in the inferior colliculus (IC) to formulate a new tinnitus model in animals. Gq-signaling DREADD [AAV8-CaMIIKa-HDM2(Gq)-mCherry] will be used to selectively activate glutamatergic neurons in the mouse, then the brain will be dissected to obtain the IC. The IC will be immunohistochemically stained to visualize the AAV mCherry, the glutamatergic neuron distribution, and the GABAergic neuron distribution within the IC. Thus, the findings of this study will better our understandings of the pathological mechanisms of tinnitus.

Monitoring And Modelling The Dynamics Of The Cellular Glycolysis Pathway: A Review And Future Perspectives, Nitin Patil, Hugh Byrne, Orla L. Howe, Paul A. Cahill

Articles

Background

The dynamics of the cellular glycolysis pathway underpin cellular function and dysfunction, and therefore ultimately health, disease, diagnostic and therapeutic strategies. Evolving our understanding of this fundamental process and its dynamics remains critical.

Scope of review

This paper reviews the medical relevance of glycolytic pathway in depth and explores the current state of the art for monitoring and modelling the dynamics of the process. The future perspectives of label free, vibrational microspectroscopic techniques to overcome the limitations of the current approaches are considered.

Major conclusions

Vibrational microspectroscopic techniques can potentially operate in the niche area of limitations of other …

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 …

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 …

Prospecting For And Isolation Of Microalgae In South Texas, Mauricio Alejandro Peña

Theses and Dissertations

Microalgae is a very important microorganism that can be used for beneficial purposes for humans. One way to show the importance of algae in this planet is the contribution of Oxygen it provides to the atmosphere, which many organisms rely on (Medeiros et al., 2015). Carbon footprint has been one of the greatest causes for global warming and it is due to the use of fossils to create diesel. One of the ways to avoid contamination is to replace those fuels that are used on daily basis, such as for transportation. The microalgae are able to produce lipids that can …

Reintegrating Biology Through The Nexus Of Energy, Information, And Matter, Kim L. Hoke, Sara L. Zimmer, Adam B. Roddy, Mary Jo Ondrechen, Craig E. Williamson, Nicole R. Buan

Department of Biochemistry: Faculty Publications

Information, energy, and matter are fundamental properties of all levels of biological organization, and life emerges from the continuous flux of matter, energy, and information. This perspective piece defines and explains each of the three pillars of this nexus. We propose that a quantitative characterization of the complex interconversions between matter, energy, and information that compose this nexus will help us derive biological insights that connect phenomena across different levels of biological organization. We articulate examples from multiple biological scales that highlight how this nexus approach leads to a more complete understanding of the biological system. Metrics of energy, information, …

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.

Simplifying The Development Of Portable, Scalable, And Reproducible Workflows, Stephen Piccolo, Zachary E. Ence, Elizabeth C. Anderson, Jeffrey T. Chang, Andrea H. Bild

Faculty Publications

Command-line software plays a critical role in biology research. However, processes for installing and executing software differ widely. The Common Workflow Language (CWL) is a community standard that addresses this problem. Using CWL, tool developers can formally describe a tool’s inputs, outputs, and other execution details. CWL documents can include instructions for executing tools inside software containers. Accordingly, CWL tools are portable—they can be executed on diverse computers—including personal workstations, high-performance clusters, or the cloud. CWL also supports workflows, which describe dependencies among tools and using outputs from one tool as inputs to others. To date, CWL has been used …

Using Molecular Diagnostics To Develop Therapeutic Strategies For Carbapenem-Resistant Gram-Negative Infections, Fred C. Tenover

Biology Faculty Publications

Infections caused by multidrug-resistant Gram-negative organisms have become a global threat. Such infections can be very difficult to treat, especially when they are caused by carbapenemase-producing organisms (CPO). Since infections caused by CPO tend to have worse outcomes than non-CPO infections, it is important to identify the type of carbapenemase present in the isolate or at least the Ambler Class (i.e., A, B, or D), to optimize therapy. Many of the newer beta-lactam/beta-lactamase inhibitor combinations are not active against organisms carrying Class B metallo-enzymes, so differentiating organisms with Class A or D carbapenemases from those with Class B enzymes rapidly …