Molecular Biology Commons^™

Characterization Of The Overexpression Of The Native H+-Pumping Pyrophosphatase In The Microalga Picochlorum Soloecismus, Kimberly T. Wright

Biology ETDs

Microalgae are of interest for the creation of sustainable and cost competitive alternatives to petroleum-based fuels and chemicals. However, cultivation, extraction and processing of algal biomass requires improved yields to achieve economic feasibility. The advancement of microalgal biotechnology and various genetic engineering techniques allow the improvement of microalgae biomass for this purpose. Here, the characterization of the overexpression of the native vacuolar H+ pumping pyrophosphate (AVP1) in Picochlorum soloecismus was examined. AVP1 overexpression causes biomass increase in relevant plant crops. When overexpressed in this microalga it increases carbon storage in the form of starch in a closed laboratory photobioreactor. However, …

In Vivo Biosynthesis Of Inorganic Nanomaterials Using Eukaryotes - A Review, Ashiqur Rahman, Julia Lin, Francisco E. Jaramillo, Dennis A. Bazylinski, Clayton Jeffryes, Si Amar Dahoumane

Life Sciences Faculty Research

Bionanotechnology, the use of biological resources to produce novel, valuable nanomaterials, has witnessed tremendous developments over the past two decades. This eco-friendly and sustainable approach enables the synthesis of numerous, diverse types of useful nanomaterials for many medical, commercial, and scientific applications. Countless reviews describing the biosynthesis of nanomaterials have been published. However, to the best of our knowledge, no review has been exclusively focused on the in vivo biosynthesis of inorganic nanomaterials. Therefore, the present review is dedicated to filling this gap by describing the many different facets of the in vivo biosynthesis of nanoparticles (NPs) using living eukaryotic …

Analysis Of Biofilm Remediation Capacity For Octenyl Succinic Anhydride (Osa), A Bioactive Food Starch Modifier Compound, Matthew R. Borglin

Master's Theses

Matthew R. Borglin

This thesis demonstrates efficacy of Octenyl Succinic Anhydride (OSA), as a biofilm sanitizer. Biofilms allow bacteria to adhere to solid surfaces with the use of excreted polymeric compounds. For example, surfaces found in food production or processing facilities such as the interior of a raw milk holding tank, are some of the most susceptible to biofilm contamination. When present, biofilms can cause a variety of negative effects, which include; reduction of product shelf life, corrosion, and outbreaks of foodborne illnesses. The close association of biofilms with the majority of foodborne illness cases led the US Environmental Protection …

Short Tandem Repeats Diversity In Indian And Pakistani Population Living In United Arab Emirates, Ruksar Salim Damji

Biology Theses

Short Tandem Repeats (STRs), have become increasingly popular markers of choice due to its wide array of advantages in the sector of forensic investigation. It is necessary to expand genetic research into residing populations i.e., Indian and Pakistani, in the same geographic region such as in the United Arab Emirates (UAE). The objectives of this study were to: (1) assess the forensic efficiency parameters and population structure analysis of the autosomal STR loci for the most potent amplification kit (2) estimate the allele frequencies; and (3) determine the significance of increasing the number of STR loci used in forensic DNA …

Mutagenesis Of The Btea Gene Encoding A Bordetella Virulence Protein, Xiaolei Mao

2020 Symposium Posters

Bordetella Type III Secretion System Effector A (BteA) is a virulence protein found in members of the genus Bordetella which include important pathogens of humans and other mammals. Bordetella pertussis is a causative agent of the whooping cough, a highly contagious respiratory disease that is especially dangerous, and sometimes deadly, for infants. The BteA protein appears to be an important factor in the ability of these pathogens to cause disease, as it leads to rapid killing of a wide range of mammalian cells. The aim of this project is to determine which regions of the DNA are important for mediating …

Chemoenzymatic Study Of Coa-Linked Rna In Bacteria, Krishna Sapkota

Dissertations

The ability of RNA to store genetic information and to catalyze biochemical transformations led to the speculation of the existence of RNA world before the evolution of contemporary ribonucleoprotein (RNP) world. Recent discovery of RNA molecules containing metabolic cofactors including coenzyme A and its various thioesters at their 5’ end further supported the RNA world hypothesis as these CoA-linked RNA molecules could be the molecular fossils with very ancient origin. As both RNA and Coenzyme A are believed to have co-existed since last universal common ancestor (LUCA) or even before, the CoA-RNA conjugates in current biology may reveal fundamental molecular …

Cloning And Expression Of Hydra Innexin 2, A Gap Junction Protein Required For Coordinated Contraction Of The Body Column, Ashley O'Brien

Biology Theses

In invertebrates gap junctions are formed by the innexin family of proteins. Remarkably, the genome of Hydra magnipapillata contains 17 innexin genes. This study focused on Hydra innexin-2 (h-Inx2) which is expressed in nerve cells and plays a role in contraction of the body column. The gene sequence of H-Inx2 was obtained from the National Center for Biotechnology Information (NCBI), the gene was synthesized externally and transferred to a vector suitable for expression in Xenopus oocytes (pcDNA3.1 CT-GFP TOPO). The TOPO CT-GFP vector includes a priming site for RNA polymerase which allows in vitro preparation of RNA. Another advantage is …

An Analysis Of Crispr-Cas Gene Editing In Agriculture, Ashley Laliberte

Honors Scholar Theses

The CRISPR-Cas system is a promising form of gene editing, especially for the agriculture industry. The ability to make single-nucleotide edits within a gene of interest, without the need to introduce foreign DNA, is a powerful tool for designing healthier and more efficient crops and food animals. This system provides opportunity for increased nutritional value, decreased food waste, and more economically and environmentally sustainable food production. Though this biotechnology is facing mechanistic limitations due to off-target effects and inefficient homology-directed repair, vast improvements have already been made to improve its efficacy. The CRISPR-Cas system is already the most advanced form …

Molecular Differentiation Of Astragalus Species And Varieties From The Western United States: The Chloroplast Dna Bridge Between Evolution And Molecular Systematics, Marwa Neyaz, Daniel Cook, Rebecca Creamer

Poisonous Plant Research (PPR)

Locoweeds are the most widespread poisonous plant problem in the world and have been reported in the Western United States since the 1800s, causing tremendous losses in livestock. Consumption of locoweeds by grazing animals stimulates the neurological disease, locoism, characterized by weight loss, ataxia, and lack of muscular coordination. The name locoweed is used for Astragalus and Oxytropis species known to contain swainsonine, the toxic principle produced by the plant endophytic fungus Undifilum. Astragalus includes 2,500-3,000 species and many varieties that have almost identical morphological characteristics that overlap among species, leading to improper identification. Therefore, the aim of this study …

Hur Ubiquitination By Brca1/Bard1 And Its Role In Controlling Gene Expression During Dna Damage Response, Gamage M. Aruggoda

Dissertations, Theses, and Capstone Projects

Despite our understanding of the biochemistry of the BRCA1/BARD1 E3 ligase, we know very little of the mechanism by which its cellular substrates, how they are chosen, how its E3 Ub ligase activity is regulated, which are the cofactors involved in this regulation, and how the substrates are modified during DDR. In this dissertation, I further evaluate BRCA1/BARD1-mediated E3 ligase activity and how CstF-50 and p97 regulate this reaction working as cofactors. My data show that BRCA1/BARD1 is an E3 ligase that ubiquitinates the RNA binding protein Human antigen R(HuR).

HuR is abundant in the nucleus and is transported to …

Synthesis And The Genetic Encoding Of Novel Lysine Post-Translational Modifications, Sahan A. Galbada Liyanage

Theses and Dissertations

Post-translational modifications (PTMs) play a significant role in regulating cell signaling and regulating the inner cellular environment. The study of PTMs and their primary biological functions is critical for the development of new medicines targeting the pathways and biomolecules responsible for the PTMs.

Previous studies revealed the direct coupling of the β -hydroxybutyryl lysine (K_BHB) modification with the gene expression. K_BHB in histone proteins links metabolism to epigenetics and gene expression and enables to study in-depth, how cell metabolism controls the gene expression and vice versa. Similar novel histone modification, K_Lac, attracts a special interest …

The Balancing Act Of Cytokinin In Environmental Stress Tolerance, Sumudu Sandeepani Karunadasa

Theses and Dissertations--Plant and Soil Sciences

Cytokinin, long known as a phytohormone that regulates plant growth and development, has been recently recognized as an important regulator of stress responses. However, our current knowledge about the mechanisms by which cytokinin regulates stress responses is fragmentary, as many of the studies in this field yielded conflicting results. Most of the work described here has focused on analyses of the molecular mechanisms of cytokinin-dependent regulation of growth and development under stress conditions, with an emphasis on the role of cytokinin-dependent regulation of protein synthesis in development and stress tolerance.

One of the important contributions of this study is the …

Deepep: A Deep Learning Framework For Identifying Essential Proteins, Min Zeng, Min Li, Fang-Xiang Wu, Yaohang Li, Yi Pan

Computer Science Faculty Publications

Background: Essential proteins are crucial for cellular life and thus, identification of essential proteins is an important topic and a challenging problem for researchers. Recently lots of computational approaches have been proposed to handle this problem. However, traditional centrality methods cannot fully represent the topological features of biological networks. In addition, identifying essential proteins is an imbalanced learning problem; but few current shallow machine learning-based methods are designed to handle the imbalanced characteristics. Results: We develop DeepEP based on a deep learning framework that uses the node2vec technique, multi-scale convolutional neural networks and a sampling technique to identify essential proteins. …

The Democratization And Development Of Cell-Free Protein Synthesis, Max Z. Levine

Master's Theses

Cell-free protein synthesis (CFPS) using crude lysates has developed into a robust platform technology over the last 60 years to express numerous types of recombinant proteins. The open-nature, elimination of reliance on cell viability, and focus of all energy towards production of the protein of interest represent substantial advantages of CFPS over in vivo protein expression methods. CFPS has provided new opportunities across a series of research fields that include metabolic engineering, therapeutic and vaccine development, education, biosensors, and many more. In recent years, optimizations of CFPS have even allowed the platform to reach the industrial level of protein production. …

Label-Free Microrna Optical Biosensors, Meimei Lai, Gymama Slaughter

Bioelectrics Publications

MicroRNAs (miRNAs) play crucial roles in regulating gene expression. Many studies show that miRNAs have been linked to almost all kinds of disease. In addition, miRNAs are well preserved in a variety of specimens, thereby making them ideal biomarkers for biosensing applications when compared to traditional protein biomarkers. Conventional biosensors for miRNA require fluorescent labeling, which is complicated, time-consuming, laborious, costly, and exhibits low sensitivity. The detection of miRNA remains a big challenge due to their intrinsic properties such as small sizes, low abundance, and high sequence similarity. A label-free biosensor can simplify the assay and enable the direct detection …

The Association Of Dna And Histone Methyltransferase Genes With Different Methylation Levels In Fragile X Syndrome Individuals, Sara Humaid Sembaij

Theses

Fragile X Mental Retardation 1 (FMR1) gene produces an FMR protein (FMRP) which is known to regulate the translation process in various organs. It has a significant role in neurons function, maturation, and synaptic plasticity. FMR1 gene encompasses 5 - 30 CGG repeats and the greater number of repeats has the potential to expand during gametogenesis. The expansion depending on the number of CGG repeat undergoes hyper-methylation and is considered as a dynamic mutation in which the expansion increases through generation. Methylation of expanded CGG repeats results in inhibiting the transcription and silencing the gene. There are two types of …

In Vitro Investigation Of The Effect Of Camel Milkproteins And Its Fractions On Insulin Receptor Function, Arshida Ashraf

Biology Theses

Camel milk (CM) has been reported to have anti-diabetic properties in many in vitro and in vivo studies but the molecular basis of such beneficial properties are still elusive. Recently, camel milk whey proteins (CWPs) have been shown to positively affect the activity of the human insulin receptor (hIR) in cell lines. In this study, we profiled crude CWPs and their hydrolysates as well as camel milk lactoferrin (CMLF) for their pharmacological and functional effects on hIR activity and its downstream signaling in both human embryonic kidney (HEK293) and hepatocarcinoma (HepG2) cell lines. For this, bioluminescence resonance energy transfer (BRET) …

Forensic Evaluation Of 6-Dye Chemistry Kit Composed Of 23 Loi With Casework Samples, Naeema Saleh Al Janaahi

Biology Theses

Short Tandem Repeats (STRs) are short nucleotide sequence repeats consisting of 2-8 base pairs (bp), representing approximately 3% of human DNA. Markers of STRs have been widely used as genetic markers in forensic DNA analysis and have proven to be an extremely discriminating method for human identification in forensics. The main objective of this research was to evaluate a six-dye STR multiplex assay (Virifiler™ Plus) composed of 23 autosomal STR loci, one insertion/deletion polymorphic marker on the Y chromosome, Amelogenin and two internal quality control markers (IQCS and IQCL) using biological stains found in different crime scenes. The study investigated …

Developing A Dissociative Nanocontainer For Peptide Drug Delivery, Michael Patrick Kelly

Dissertations, Theses, and Capstone Projects

The potency and specificity of bioactive peptides have propelled these agents to the forefront of pharmacological research. However, delivery of peptides to their molecular target in cells is a major obstacle to their widespread application. A Trojan Horse strategy of packaging a bioactive peptide within a modified protein cage to protect it during transport, and releasing it at the target site, is a promising delivery method. Recent work has demonstrated that the viral capsid of the P22 bacteriophage can be loaded with an arbitrary, genetically-encoded peptide, and externally decorated with a cell-penetrating peptide, such as HIV-Tat, to translocate across in …

Ipsc Based Gene Correction And Disease Model Of A New Class Of Lgmd Due To Poglut1 Mutation, Jose Ortiz-Vitali

Dissertations and Theses (Open Access)

Recently, a novel class of muscular dystrophy has been discovered in a family due to autosomal recessive missense mutation in POGLUT1. Mutation of this enzyme leads to decreased O-glucosyltransferase activity and impaired Notch signaling, the pathways important for skeletal muscle stem cell (satellite cells) quiescence and activation. We hypothesize that reduced POGLUT1 activity and impaired Notch signaling is causative of this limb girdle muscular dystrophy through dysfunction of muscle stem cells and myogenic progenitors.

To test this, we have used iPSCs for disease modeling and rescue experiments. Using a CRISPR based gene targeting method, we aimed to correct the point …

Genetic Variation Of Human Leukocyte Antigen (Hla) Alleles Among Rheumatiod Arthritis Patients In Fujairah, Amna Abdulla Harib Al-Dhmanie

Biology Theses

Rheumatoid arthritis (RA) is an autoimmune disease characterized by chronic inflammation that affects the joints. It occurs when the immune system attacks the body's own tissues and organs. The precise cause of RA is not fully understood but evidence suggests that genes, hormones and environmental factors could be involved. It has been established that human leukocyte antigen (HLA) loci is a strong risk factor of RA. Specifically, the shared epitope (SE) region of HLA-DRB1 and variations at position 11 and 13 of HLA-DRB1 and position 77 of HLA-A have shown strong association with RA. The hypothesis of this study was …

Microrna Profiling And Engineering Of Cho Cell Lines Stably Expressing Difficult-To-Express Lysosomal Protein, Ifeanyi Amadi

KGI Theses and Dissertations

Difficult-to-express (DTE) recombinant proteins like multi-specific proteins, DTE monoclonal antibodies and lysosomal enzymes, have seen difficulties in manufacturability using Chinese hamster ovary (CHO) cells and other mammalian cells as production platforms. CHO cells are preferably used for protein production because of their innate ability to secrete human-like recombinant proteins with post-translational modification, resistance to viral infection and familiarity with drug regulators. However, despite huge progress made in engineering CHO cells for high volumetric productivity, expression of DTE proteins like recombinant lysosomal sulfatase represent one of the poorly understood proteins. Furthermore, there are growing interest in the use of microRNAs (miRNAs) …

Development Of A Sonically Powered Biodegradable Nanogenerator For Bone Regeneration, Avi S. Patel

University Scholar Projects

Background: Reconstruction of bone fractures and defects remains a big challenge in orthopedic surgery. While regenerative engineering has advanced the field greatly using a combination of biomaterial scaffolds and stem cells, one matter of difficulty is inducing osteogenesis in these cells. Recent works have shown electricity’s ability to promote osteogenesis in stem cell lines when seeded in bone scaffolds; however, typical electrical stimulators are either (a) externally housed and require overcomplex percutaneous wires be connected to the implanted scaffold or (b) implanted non-degradable devices which contain toxic batteries and require invasive removal surgeries.

Objective: Here, we establish a biodegradable, piezoelectric …

Development Of A Lectin-Fc Fusion Protein With Antiviral And Anti-Cancer Activity., Matthew William Dent

Electronic Theses and Dissertations

This thesis describes the development of a novel lectin-Fc fusion protein and its antiviral and anti-cancer activity. The molecule, Avaren-Fc (AvFc), is a fusion of a variant of the actinomycete lectin actinohivin (Avaren) and the Fc region of human IgG1, and is selective for the terminal α1,2-mannose residues found at the ends of high-mannose-type glycans that can be found on the surface of certain heavily glycosylated viruses and cancer cells. Here, AvFc was found to be able to neutralize simian immunodeficiency virus as well as Hepatitis C virus with nanomolar IC₅₀ values. Furthermore, AvFc recognizes a number of cell …

The Role Of Parathyroid Hormone 1 Receptor (Pth1r) Signaling In Gastric Epithelial Homeostasis, Maram Maher Al-Hasan

Theses

In the stomach, the epithelial stem cells are responsible for glandular homeostasis. These stem cells continuously undergo cellular proliferation and differentiation to balance the death of senescent cells. Studies conducted on gastric cancers showed a significant increase in parathyroid hormone-like hormone (PTHLH). Moreover, both PTHLH along with parathyroid hormone (PTH) act as endogenous ligands for parathyroid hormone 1 receptor (PTH1R) which belongs to family B of G- protein-coupled receptors (GPCRs). This receptor functions by mediating many different signaling pathways and the most studied pathway is the stimulation of cyclic adenosine monophosphate (cAMP) as a second messenger.

There are very few …

Evaluating The Therapeutic Potential Of Crocin Against Diethylnitrosamine Induced Experimental Hepatocellular Carcinoma In Rats, Basma Ali Mustafa Awad

Theses

Hepatocellular carcinoma (HCC) is the fifth most common type of cancer and the third cause of cancer-related death worldwide. Liver cancer is the result of repeated injuries to the liver triggered by different causes. Currently, sorafenib is the only drug U.S. Food and Drug Administration approved targeted therapy. Sorafenib, an oral multikinase inhibitor, which inhibits the proliferation of tumor cells and blocks angiogenesis. Sorafenib has been shown to treat early and mild HCC lesions and it helped increase the survival rates at one year, but for only 44% of patients. Chemotherapies are an important line of defense when it comes …

A Study On Vitamin D Metabolic Genes Single Nucleotide Polymorphisms And Their Linkage In Adult Asthmatic Emiratis, Amneh Mohammad Al Mousa

Biology Theses

Vitamin D normal levels are vital to many biological processes including its classical role in calcium and phosphate homeostasis, and regulation of immune and non-immune cells. Vitamin D mediates its actions via the vitamin D receptor (VDR) which is expressed in most tissues of the body including the airway smooth muscle. Asthma is a syndrome of chronic inflammatory airway disease. There is a genetic and immunological link between vitamin D and asthma. In this study, we aim to investigate whether asthma and its severity were associated with single nucleotide polymorphisms (SNPs) in vitamin D metabolic genes as well as vitamin …

Study Of Insertion-Deletion Polymorphisms (Indels) In The Uae Population, Maryam M. Matar Almheiri

Biology Theses

Insertion-deletion polymorphisms (indels) have been used less in forensic identification of individuals in comparison to short tandem repeat (STR) and single nucleotide polymorphism (SNP) systems. The use of indels has many advantages including low costs, simple typing methods as well as a small amplicon size of under 160 bp making them suitable for genotyping highly degraded DNA. They can also be valuable as a complementary tool to help resolve kinship cases, with the advantage of lower mutation rates when compared to STRs.

The main objective of this study was to investigate the polymorphism of 30 indel loci in the UAE …

Method Development For Structural Assessment Of Nanolipoprotein Particles With And Without Cross-Linked Lipids, Emma J. Mullen, Wei He, Sean Gilmore, Matthias Frank, Matthew Coleman, Megan Shelby

STAR Program Research Presentations

Membrane proteins make up approximately 30% of the cellular proteome and account for over 60% of pharmaceutical targets.1 Determining the structures of this class of proteins is critical to our understanding of disease states and will advance rational drug design. But membrane proteins have limited solubility, rarely form large crystals that diffract well, and often misfold outside of a bilayer, hindering crystallographic studies.1 Nanolipoprotein particles (NLPs) have arisen as a platform to readily solubilize membrane proteins while mimicking a native lipid environment. NLPs consist of a discoidal phospholipid bilayer encircled by an apolipoprotein belt. In an effort to optimize and …

Investigation Of Transient Expression System In Nicotiana Bethamiana To Produce Novel Tales And The Development Of (Ds)Dna Detection With Quantum Dot-Labeled Proteins In Graphene Oxide Quenching Arrays, Colleen Jackson

Mahurin Honors College Capstone Experience/Thesis Projects

Our objective was to develop a faster method of quantitively detecting double stranded (ds)DNA of pathogenic bacteria such as the Shiga Toxin 2 gene present in E. coli O157. Transcription Activator-Like Effectors (TALEs) are a new class of DNA-binding proteins which selectively bind to dsDNA with the 12th and 13th amino acids of each repeat, called repeat variable diresidues (RVDs). Novel TALE proteins were designed to target the stx2 gene and were cloned into existing AvrBs3 TALE protein in the pMAL c2x vector system for bacterial BL-21 E. Coli expression. The protein’s DNA-binding region was then subcloned pEAQ vectors for …