Biotechnology Commons^™

Development Of Wiskott-Aldrich Syndrome Knock Out Protocol For Drug Substance Assay Development, Julia C. Hanna

Master's Theses

Wiskott-Aldrich Syndrome (WAS) is a rare X-linked primary immunodeficiency affecting approximately 1 in 100,000 live XY births in North America and is caused by a mutation to the WAS gene which is expressed across hematopoietic lineages. The WAS protein (WASp) plays a role in regulating actin polymerization. On a cellular level, there are a variety of effects of a lack of WASp or expression of a dysfunctional WASp protein for patients including issues with migration, adhesion, chemotactic response, phagocytosis, activation, and proliferation across different cell types in addition to reduced platelet size and output. This can lead to several systematic …

Bola3 And Nfu1 Link Mitoribosome Iron-Sulfur Cluster Assembly To Multiple Mitochondrial Dysfunctions Syndrome, Hui Zhong, Alexandre Janer, Oleh Khalimonchuk, Hana Antonicka, Eric Shoubridge, Antoni Barrientos

Department of Biochemistry: Faculty Publications

The human mitochondrial ribosome contains three [2Fe-2S] clusters whose assembly pathway, role, and implications for mitochondrial and metabolic diseases are unknown. Here, structure-function correlation studies show that the clusters play a structural role during mitoribosome assembly. To uncover the assembly pathway, we have examined the effect of silencing the expression of Fe-S cluster biosynthetic and delivery factors on mitoribosome stability. We find that the mitoribosome receives its [2Fe-2S] clusters from the GLRX5-BOLA3 node. Additionally, the assembly of the small subunit depends on the mitoribosome biogenesis factor METTL17, recently reported containing a [4Fe-4S] cluster, which we propose is inserted via the …

The Development Of A Primer Payload With Microparticles For Uti Pathogen Identification Using Polythymidine- Modified Lamp Primers In Droplet Lamp, Jonas Otoo

KGI Theses and Dissertations

Nucleic acid amplification tests (NAATs) are among the diagnostic tests with the highest sensitivity and specificity. However, they are more complex to develop than other diagnostic tests such as biochemical tests and lateral flow immunoassay tests. Polymerase chain reaction (PCR) is the gold standard for NAATs. PCR requires thermal cycling to achieve clonal amplification of the target pathogen DNA for diagnosis. Thermal cycling poses a challenge in the development of PCR diagnostics for point-of-care (POC) settings. Loop-mediated isothermal amplification (LAMP) offers an isothermal method for NAATs diagnostics. The advancement of the microfluidics field significantly enhances the development of LAMP diagnostics …

Dietary Marine-Derived Ingredients For Stimulating Hair Cell Cycle, Aleksandra Augustyniak, Helena Mcmahon

Publications

In normal condition human hair growth occurs through three phases, anagen (growth phase included about 85 % of hairs, last from 2 to 6 years), catagen (transitional phase lasting up to 2 weeks) and telogen (resting phase which last from 1 to 4 months). Natural dynamics of the hair growth process can be impaired by several factors, such as genetic predisposition, hormonal disorders, aging, poor nutrition or stress, which can lead to the slowdown in the growth of hair or even hair loss. The aim of the study was to assess the hair growth promotion effect of marine-derived ingredients, hair …

On The Resurrection Of Microbes: An Eco-Christological Approach To The Resurrection, Denys Janiga Osb

Obsculta

This article attempts to bring ecology and Christology into conversation through a transdisciplinary approach. It looks at the pastoral implications of eco-anxiety, resurrection ecology in the field of biotechnology, Church teaching on the Resurrection, and concludes by initiating an interpretation of the resurrection appearances in the Gospel of Luke through the lens of the microbiome.

Extravasated Brain-Reactive Autoantibodies Perturb Neuronal Surface Protein Expression In Alzheimer's Pathology, Wardah Bajwa, Mary Kosciuk, Randel L. Swanson, Anuradha Krishnan, Venkat Venkataraman, Robert Nagele, Nimish Acharya

Rowan-Virtua Research Day

Background: Increased blood-brain barrier (BBB) permeability is reported in both the neuropathological and in vivo studies in both Alzheimer’s Disease (AD) and age matched cognitively normal, no cognitive impairment (NCI), subjects. Impaired BBB allows various vascular components such as immunoglobulin G (IgG) to extravasate into the brain and specifically bind to various neuronal surface proteins (NSP), also known as brain reactive autoantibodies (BrABs). This interaction is predicted to further enhance deposition of amyloid plaques.

Hypothesis: Interaction between extravasated BrABs and its cognate NSPs lower the expression of that NSPs in AD patients.

Methods: We selected Western blotting technique to study …

Green Biorefinery Systems For The Production Of Climate-Smart Sustainable Products From Grasses, Legumes And Green Crop Residues, James Gaffey, Gaurav Rajuaria, Helena Mcmahon, Rajeev Ravindran, Carmen Dominguez, Morten Ambye Jensen, Macella F. Souza, Erik Meers, Marta Macias Aragonés, Dubravka Skunka, Johan P. M. Sanders

Publications

Grasses, legumes and green plant wastes represent a ubiquitous feedstock for developing a bioeconomy in regions across Europe. These feedstocks are often an important source of ruminant feed, although much remains unused or underutilised. In addition to proteins, these materials are rich in fibres, sugars, minerals and other components that could also be used as inputs for bio-based product development. Green Biorefinery processes and initiatives are being developed to better capitalise on the potential of these feedstocks to produce sustainable food, feed, materials and energy in an integrated way. Such systems may support a more sustainable primary production sector, enable …

Assesment Of Structure, Function, And Microevolutionary Dynamics Of Extrachromosomal Circular Dna In Chinese Hamster Ovary Cells, Dylan Chitwood

All Dissertations

Chinese hamster ovary (CHO) cell lines are among the most popular expression hosts used in biopharmaceutical manufacturing due to relative ease of culture, capacity to perform human-like post-translational modifications, and non-susceptibility to viruses. However, the intrinsic plasticity of the CHO genome can lead to undesired genetic rearrangements, phenotypic shifts, reduced product quality, and early culture termination that prevents continuous biomanufacturing. A characteristic of plastic and unstable genomes that is poorly understood in CHO cells is extrachromosomal circular DNA (eccDNA). EccDNAs are focal amplifications of the genome that reside in the extranuclear space. These plasmid-like entities are structurally complex and are …

Rapid & Sensitive Detection Of Antibiotic Resistance Genes By Utilizing New Diagnostic Probe Tales With 2d-Nanosheet Graphene Oxide, Jihye Kang

Masters Theses & Specialist Projects

As antibiotic resistance is one of the major health concerns in infectious diseases because of reducing the efficacy of antibiotics, rapid and sensitive detection of antibiotic resistance genes is critical for the effective treatment of infectious diseases. Polymerase chain reaction (PCR) is widely used to detect nucleic acids, but it requires additional steps involved in DNA denaturation and subsequent hybridization. A new class of DNA-binding domains called transcriptional activator-like effectors (TALEs) provide a novel scaffold for designing versatile DNA-binding proteins due to their modularity and predictability. Here, we developed a simple, rapid, and sensitive system for detecting antibiotic resistance genes …

Review Of Biomedical Applications Of Cardiovascular Tissue Engineering, Natalie M. Howard

Honors College Theses

Tissue engineering can be defined as processes that aim to generate three-dimensional functional tissues in vitrothat have been favorably altered according to the structural, biochemical, electrophysiological, and biomechanical properties of the desired tissue before implantation into the human body. In relation to cardiac tissues, these properties would include the ability to conduct action potentials, withstand systolic pressure, permit sufficient O₂ and CO₂penetration, sufficient vascularization to supply nutrients for cellular activity, surface topology that enables cellular communication, and more. As heart diseases and instances of myocardial infarction continue to rise worldwide, there is an increasing need for …

Laser Inscribed Graphene Aptasensor For Detection Of Apple Stem Pitting Virus, Yifan Tang

All Theses

Apple stem pitting virus (ASPV) is a latent RNA virus that could cause significant loss to apple production; early-stage field diagnosis could reduce the economic loss caused by ASPV infection. Biosensor is a promising user-friendly detection tool that could transduce biological or chemical interactions into electric signals. Among various types of biosensors, aptasensor, which use aptamers as recognition elements show potential as a high throughput, in-field test. The goal of this thesis is to develop an electrochemical aptasensor testing system for ASPV detection. The quality control study of laser inscribed graphene (LIG) based working electrode of the biosensor was conducted …

Impact Of Lyophilization On Porcine Hemoglobin Properties., Mustafa Almosawi

College of Arts & Sciences Senior Theses

Blood transfusion is the single most often performed lifesaving procedure in hospitals worldwide. Unfortunately, packed red blood cells (RBCs) used for transfusion can only be stored for 42 days at 4 °C before being discarded due to irreversible damage that occurs during storage. Any reduction in available RBCs for an extended period can lead to blood shortages. To increase the shelf-life of RBCs, we investigated freeze-drying (lyophilizing) in the presence of the non-toxic sugar trehalose as a method for long-term preservation. However, the oxidative stress of the lyophilization and storage processes can compromise the functionality of these cells, and the …

Investigation The Plugging Behavior Of Virus Filters, Iman Abdulqader Saab

Graduate Theses and Dissertations

A virus filtration step is integral to the manufacturing of biopharmaceuticals to ensure viral safety. A virus filter is a single-use device that uses a size-based separation process and has a unique structure with minimal defects, so that contaminating virus particles cannot pass through the membrane pores, while therapeutic molecules can. The development of novel antibodies (Abs), including significant increases in product titers, is frequently challenged by virus filter fouling, making a better understanding of the underlying mechanisms essential. This thesis focused investigating of the effect of prefilter types, buffer type and salt content on virus filtration performance. The impact …

Comprehensive Long- And Short- Read Sequencing Approaches To Screen The Mutational Landscape After Therapeutic Crispr-Editing For Duchenne Muscular Dystrophy, Mary Jia, Made Harumi Padmaswari, Landon Burcham, Shilpi Agrawal, Alexis Ivy, Abbey Bryan, Christopher E. Nelson

Biomedical Engineering Undergraduate Honors Theses

Duchenne muscular dystrophy (DMD) is an X-linked muscle wasting disease caused by mutations in the Dmd gene resulting in non-functional dystrophin. Adeno-associated virus (AAV)-mediated delivery of classical CRISPR systems resulting in double-stranded breaks (DSBs) has yielded promise as a curative DMD therapeutic. However, the consequences of AAV-CRISPR require more thorough characterization. PCR-enriched short-read amplicon sequencing at cut sites is the most common method of sequencing CRISPR editing, but PCR bias results in unreliable quantification of on-target edits. We analyze orthogonal long- and short-read sequencing approaches to screen the outcomes of CRISPR technologies at the DNA and RNA-level for DMD. We …

Exploration Of Spider Silk Assembly, Natalie Naseib, Joshua Navarro, Nadia Duong, Seohyun Lee, Daniel Kim, Danbir Somal, Sevak Manucharyan, Josephine Kim, Seha Park, Alice Lan, Karen Kwong, Mason Tri

Pacific Undergraduate Research and Creativity Conference (PURCC)

No abstract provided.

Study Of The Assembly Trigger For Spider Silk Proteins, Katina Zhu, Amanda Lee, Megan Lau, Sungkyung Lee, Kaden Chen, Katherine Yoo, David Eum, Daniel Eum, Austin Cho, Jiho Choi

Pacific Undergraduate Research and Creativity Conference (PURCC)

No abstract provided.

Potential Use Of The Gel Extract Of Butterfly Pea Flower As Topical Therapy To Prevent Photodamage By Downregulating Tnf-Α And Caspase-3 Expression Levels In Uvb-Exposed Rats, Elvana Cahyani, Agung Putra, Prasetyowati Subchan

Makara Journal of Health Research

Background: Prolonged exposure to UVB radiation causes DNA damage in skin cells by raising the levels of reactive oxygen species, resulting in the production of inflammatory factors and skin issues. Plant extracts are frequently used to counteract photodamage due to their antioxidant properties. One example is the floral extract of the butterfly pea plant, which contains flavonoid antioxidants. However, the effect of the extract on inflammatory factors is unknown. This study investigated how tumor necrosis factor-alpha (TNF-α) and caspase-3 expression changed when a butterfly pea flower extract gel was applied topically to UVB-exposed animals.

Methods: Experimental and control …

Electrochemical Reduction Of Carbon Dioxide Using Ruthenium And Amines, Sydney Moise

Honors Theses

With an increased concern for climate change in the recent years, a significant area of research has been devoted to the reduction of greenhouse gases. Carbon dioxide (CO2) resides in the atmosphere between 300 – 1000 years, making the reduction of the molecule a substantial field of study.1 Amines have been used as CO2 scrubbing agents in literature historically, due to their ability to form bonds to carbon.2 Although studies involving metal catalysts and amines have been reported numerous times, research involving chemical reduction of CO2 using purely amines is scarce. In this paper, amines, in addition to hydride donors …

Pyrus Calleryana Extracts Reduce Germination Of Native Grassland Species, Suggesting The Potential For Allelopathic Effects During Ecological Invasion, Michaela J. Woods, Jonathan T. Bauer, Dena Schaeffer, Ryan W. Mcewan

Biology Faculty Publications

Invasive plant species’ success may be a result of allelopathy, or the release of secondary metabolites that are harmful for surrounding plant species. Allelopathy can be mediated through the abiotic environment by chemical sorption or transformation, so the substrate on which interactions occur can lead to differential outcomes in allelopathic potential. One aggressive invader, Pyrus calleryana, has become dominant in many ecosystems throughout Eastern US, and has reduced the abundance of native species where it invades. Thus, our goal was to identify if P. calleryana had allelopathic potential by testing the impact of leaf and flower leachate on gemination …

From Deep Mutational Mapping Of Allosteric Protein Landscapes To Deep Learning Of Allostery And Hidden Allosteric Sites: Zooming In On “Allosteric Intersection” Of Biochemical And Big Data Approaches, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao

Mathematics, Physics, and Computer Science Faculty Articles and Research

The recent advances in artificial intelligence (AI) and machine learning have driven the design of new expert systems and automated workflows that are able to model complex chemical and biological phenomena. In recent years, machine learning approaches have been developed and actively deployed to facilitate computational and experimental studies of protein dynamics and allosteric mechanisms. In this review, we discuss in detail new developments along two major directions of allosteric research through the lens of data-intensive biochemical approaches and AI-based computational methods. Despite considerable progress in applications of AI methods for protein structure and dynamics studies, the intersection between allosteric …