Biotechnology Commons^™

Effects Of Articular Knee Injections On Cartilage Of Knee Osteoarthritis Patients And Development Of Rapid Decalcification Method For Articular Cartilage And Subchondral Bone, Pattaranatcha Charnwichai

Chulalongkorn University Theses and Dissertations (Chula ETD)

Osteoarthritis (OA) is the most common degenerative joint disease that affects articular cartilage. Intra-articular injection (IA) is one of the treatments that is used to reduce pain and relieve symptoms. Triamcinolone acetonide (TA) and hyaluronic acid (HA) are frequently used in IA injections for OA treatment. Several publications have reported effects of TA, but some of HA, on articular cartilage. Moreover, for histopathological studies, articular cartilage and subchondral bones are commonly used as samples, but the decalcification process is time consuming. Thus, this study aims to compare effects of drugs used in IA injections on cartilage and chondrocytes of osteoarthritis …

An Exploration On Apts In Biocybersecurity And Cyberbiosecurity, Xavier-Lewis Palmer, Lucas Potter, Saltuk Karahan

School of Cybersecurity Faculty Publications

Novel and complex digital threats that are increasingly interwoven with means and products of biology that can affect society. Much work in Biocybersecurity/Cyberbiosecurity (BCS/CBS) discuss vulnerabilities, but few deeply address malicious actor varieties as attacks at this intersection are new. The path to those attacks remains mostly theoretical, presenting considerable difficulty to accomplish in practical scenarios. In terms of advanced persistent threats (APTs) this of course needs to change as biomanufacturing facilities are at risk, considering Covid-19 and other potential pandemics. Further attacks are not out of reach and thus we must start to imagine how BCS APTs may appear. …

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.

Building Digital Twins Of The Human Immune System: Toward A Roadmap, Reinhard Laubenbacher, Anna Niarakis, Tomas Helikar, G. An, B. Shapiro, R. S. Malik-Sheriff, T. J. Sego, P. Macklin, J. A. Glazier

Department of Biochemistry: Faculty Publications

Digital twins, customized simulation models pioneered in industry, are beginning to be deployed in medicine and healthcare, with some major successes, for instance in cardiovascular diagnostics and in insulin pump control. Personalized computational models are also assisting in applications ranging from drug development to treatment optimization. More advanced medical digital twins will be essential to making precision medicine a reality. Because the immune system plays an important role in such a wide range of diseases and health conditions, from fighting pathogens to autoimmune disorders, digital twins of the immune system will have an especially high impact. However, their development presents …

Addressing Barriers In Comprehensiveness, Accessibility, Reusability, Interoperability And Reproducibility Of Computational Models In Systems Biology, Anna Niarakis, Dagmar Waltemath, James Glazier, Falk Schreiber, Sarah M. Keating, David Nickerson, Claudine Chaouiya, Anne Siegel, Vincent Noël, Henning Hermjakob, Tomáš Helikar, Sylvain Soliman, Laurence Calzone

Department of Biochemistry: Faculty Publications

Computational models are often employed in systems biology to study the dynamic behaviours of complex systems. With the rise in the number of computational models, finding ways to improve the reusability of these models and their ability to reproduce virtual experiments becomes critical. Correct and effective model annotation in community-supported and standardised formats is necessary for this improvement. Here,we present recent efforts toward a common framework for annotated, accessible, reproducible and interoperable computational models in biology, and discuss key challenges of the field.

Scientists from different systems biology fields have long been developing community-driven guidelines and best practices for annotation, …

Development, Structure, And Mechanism Of Synthetic Antibodies That Target Claudin And Clostridium Perfringens Enterotoxin Complexes, Benjamin J. Orlando, Pawel K. Dominik, Sourav Roy, Chinemerem P. Ogbu, Satchal K. Erramilli, Anthony A. Kossiakoff, Alex J. Vecchio

Department of Biochemistry: Faculty Publications

Strains of Clostridium perfringens produce a two-domain enterotoxin (CpE) that afflicts humans and domesticated animals, causing prevalent gastrointestinal illnesses. CpE’s C-terminal domain (cCpE) binds cell surface receptors, followed by a restructuring of its N-terminal domain to form a membranepenetrating β-barrel pore, which is toxic to epithelial cells of the gut. The claudin family of membrane proteins are known receptors for CpE and also control the architecture and function of cell-cell contacts (tight junctions) that create barriers to intercellular molecular transport. CpE binding and assembly disables claudin barrier function and induces cytotoxicity via β-pore formation, disrupting gut homeostasis; however, a structural …

The Follicular Lymphoma Epigenome Regulates Its Microenvironment, Rada Amin, Mounia S. Braza

Department of Biochemistry: Faculty Publications

Follicular lymphoma (FL) is a B-cell non-Hodgkin lymphoma of germinal center (GC) origin with a distinctive tumor microenvironment (TME) and a unique spectrum of mutations. Despite the important therapeutic advances, FL is still incurable. During B-cell development, the GC reaction is a complex multistep process in which epigenetic regulators dynamically induce or suppress transcriptional programs. In FL, epigenetic gene mutations perturb the regulation of these programs, changing GC B-cell function and skewing differentiation towards tumor cells and altering the microenvironment interactions. FL pathogenesis and malignant transformation are promoted by epigenetic reprogramming of GC B cells that alters the immunological synapse …

Feedlot Diets Containing Different Starch Levels And Additives Change The Cecal Proteome Involved In Cattle’S Energy Metabolism And Inflammatory Response, Leone Campos Rocha, Andrey Sávio De Almeida Assunção, Renata Aparecida Martins, Victor Valério De Carvalho, Alexandre Perdigão2, Marília Afonso Rabelo Buzalaf, Jiri Adamec, Camila Pereira Braga, Danilo Domingues Millen, José Cavalcante Souza Vieira, Pedro De Magalhães Padilha

Department of Biochemistry: Faculty Publications

Diets for feedlot cattle must be a higher energy density, entailing high fermentable carbohydrate content. Feed additives are needed to reduce possible metabolic disorders. This study aimed to analyze the post-rumen effects of different levels of starch (25%, 35%, and 45%) and additives (monensin or a blend of essential oils and exogenous α-amylase) in diets for Nellore feedlot cattle. The cecum tissue proteome was analyzed via two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and then differentially expressed protein spots were identified with liquid chromatography–tandem mass spectrometry (LC–MS/MS). The use of blends of essential oils associated with α-amylase as a feed additive promoted …

Endothelial Cell-Specific Deletion Of A Microrna Accelerates Atherosclerosis, Dafeng Yang, Stefan Haemmig, Jingshu Chen, Michael Mccoy, Henry S. Cheng, Haoyang Zhou, Daniel Pérez-Cremades, Xiao Cheng, Xinghui Sun, Jorge Haneo-Mejia, Shamsudheen K. Vellarikkal, Rajat M. Gupta, Victor Barrera, Mark W. Feinberg

Department of Biochemistry: Faculty Publications

Background and aims: Chronic vascular endothelial inflammation predisposes to atherosclerosis; however, the cell-autonomous roles for endothelial-expressing microRNAs (miRNAs) are poorly understood in this process. MiR-181b is expressed in several cellular constituents relevant to lesion formation. The aim of this study is to examine the role of genetic deficiency of the miR-181b locus in endothelial cells during atherogenesis.

Methods and Results: Using a proprotein convertase subtilisin/kexin type 9 (PCSK9)-induced atherosclerosis mouse model, we demonstrated that endothelial cell (EC)-specific deletion of miR-181a2b2 significantly promoted atherosclerotic lesion formation, cell adhesion molecule expression, and the influx of lesional macrophages in the vessel wall. Yet, …

The Third International Hackathon For Applying Insights Into Large-Scale Genomic Composition To Use Cases In A Wide Range Of Organisms, Kimberly Walker, Divya Kalra, Rebecca Lowdon, Guangyi Chen, Fritz J. Sedlazeck, Ben Busby, Chia-Sin Liew, Et Al.

Nebraska Center for Biotechnology: Faculty and Staff Publications

In October 2021, 59 scientists from 14 countries and 13 U.S. states collaborated virtually in the Third Annual Baylor College of Medicine & DNANexus Structural Variation hackathon. The goal of the hackathon was to advance research on structural variants (SVs) by prototyping and iterating on open-source software. This led to nine hackathon projects focused on diverse genomics research interests, including various SV discovery and genotyping methods, SV sequence reconstruction, and clinically relevant structural variation, including SARS-CoV-2 variants. Repositories for the projects that participated in the hackathon are available at https://github.com/collaborativebioinformatics.

Regulatory Mechanisms In Arabidopsis Embryogenesis, Sanjay Joshi

Theses and Dissertations--Plant and Soil Sciences

Plants have amazing regeneration properties with single somatic cells, or groups of cells able to give rise to fully formed plants. One means of regeneration is Somatic Embryogenesis (SE), by which an embryonic structure is formed that “converts” into a plantlet. Somatic embryogenesis has been used as a model for zygotic processes that are buried within layers of maternal tissues. Understanding mechanisms of somatic embryo induction and development are important as a more accessible model for seed development. We rely on seed development not only for most of our caloric intake, but also as a delivery system for engineered crops …

การคัดแยกและลักษณะสมบัติของแบคทีเรียที่มีความสามารถในการผลิตดีเอชเอจากกุ้งเคยและกะปิของไทย, ณิชาภัทร วิเศษชลธาร

Chulalongkorn University Theses and Dissertations (Chula ETD)

กรดไขมันไม่อิ่มตัวที่มีพันธะคู่หลายตำแหน่งในกลุ่มของโอเมก้า-3 เช่น ดีเอชเอ และอีพีเอ เป็นกรดอะมิโนจำเป็นต่อร่างกาย (essential amino acid) เนื่องจากในร่างกายมนุษย์ไม่มีเอนไซม์ที่สามารถสร้างพันธะคู่ตำแหน่ง ω-3 ได้ มีรายงานว่าเส้นทางการสังเคราะห์กรดไขมันผ่านวิถีทางชีวภาพ (FAS pathway) พบในแบคทีเรียจากทะเลบางสายพันธุ์เท่านั้น ในงานวิจัยนี้ทำการคักแยกแบคทีเรียทางทะเลจากตัวอย่างกะปิซึ่งมีการตรวจสอบจากงานวิจัยก่อนหน้าว่ามีกลุ่มของกรดไขมันโอเมก้า-3, 6 และ 9 ผลการศึกษาสามารถคัดแยกแบคทีเรียสะสมไขมันสูง (oleaginous bacteria) ได้ 6 ไอโซเลต โดยเฉพาะ Bacillus amyloliquefaciens SR121 เมื่อทำการวิเคราะห์ whole genome พบยีน FabF (β-ketoacyl-ACP reductase), FabG (Ketoreductase), FabZ (Dehydratase) และ FabI (Enoyl reduction) ซึ่งเกี่ยวข้องกับ 4 กระบวนการสำคัญ ใน FAS pathway นอกจากนี้ B. amyloliquefaciens SR121 มีการผลิตกรดไขมันมากที่สุดร้อยละ 75.06 ± 2.05 ของน้ำหนักเซลล์แห้ง และเมื่อใช้อาหารสำหรับการเพาะเลี้ยงที่มี pH5 พบปริมาณการผลิตไขมันเพิ่มขึ้นถึงร้อยละ 89.46 ± 3.79 ของน้ำหนักเซลล์ สำหรับการปรับภาวะเพื่อผลิตกรดไขมันกลุ่มโอเมก้า-3 พบที่ 35 องศาเซลเซียส มีการผลิตมากสุดถึง 19.73% ของปริมาณกรดไขมันทั้งหมด หรือคิดเป็นกรดไขมันไม่อิ่มตัว 92.97 มิลลิกรัม และมีการผลิตกรดไขมันกลุ่มโอเมก้า-3 มากที่สุดโดยปริมาณ 72 มิลลิกรัม ต่อน้ำหนักเซลล์ 1 กรัม

Development Of Chromatographic Methods For Geographical Indication In Thai Pineapples, Worakan Chutakool

Chulalongkorn University Theses and Dissertations (Chula ETD)

Geographical indication (GI), or its equivalent intellectual property tools, is widely used in many countries, including Thailand, to identify specific properties and uniqueness of a product that are related to its production origin. In the case of agricultural products, geographical location, weather, and soil nutrients affect their properties such as flavor and texture. In this study, a chemical method was conducted to attempt to distinguish pineapples based on their origins. This was done by collecting chemical profiles from carotenoids by high-performance liquid chromatography with diode array detector (HPLC-DAD). Thereafter, these chemical data were later processed by chemometric analysis to classify …

Designing Virtual Reality Headsets To Prevent Myopia, Kyril Van Schendel

CMC Senior Theses

Virtual reality (VR) headsets are currently being designed and developed for consumer use. Simultaneously, the rate of myopic development is increasing around the world. Little is known about the connection between the proximity viewing in VR headsets and myopic development. The past three decades of research have indicated a probable relationship between near-work activities and the development of myopia. Based on the current research, VR headsets do not appear to induce a strong myopiagenic stimulus on axial elongation. This paper offers a potential explanation and proposes a set of design recommendations for designing future VR headsets that prevent myopia.

Advancing Competency In Managing Risk And Knowledge: Steps Toward Operationalisation Of The Risk-Knowledge Infinity Cycle (Rki Cycle) - Part 1: Improving Effectiveness Of Risk-Based Decision Making (Rbdm), Martin Lipa, Paige Kane, Anne Greene

Articles

To date, literature on the Risk-Knowledge Infinity Cycle (RKI Cycle) has mainly been theoretical. This paper series intent is to focus on the operationalisation of the RKI Cycle by describing a series of steps – the “How to” – for RKI Cycle deployment, to help move the RKI Cycle from theory to practice. The first paper in this series focuses on how the RKI Cycle can support effective Risk-Based Decision Making (RBDM).

Investigation Of A Carbon Monoxide Dehydrogenase From An Uncultured Archaeon, Luke Moore

Dissertations, Master's Theses and Master's Reports

The Nickel based Carbon Monoxide Dehydrogenase (CODH) is an anaerobic metalloenzyme responsible for the reversible conversion of CO and water into CO2 and 2 protons and 2 electrons. This enzyme has importance in the environment as one of Earth’s first carbon fixation pathways, and for human uses as a potential source of biofuels and other commodity chemicals. CODH enzymes are present in a wide array of taxa, many of which are uncultured. In this study we express and purify the catalytic subunit (CooS) of the anaerobic CODH from an uncultured Hydrothermarchaeota JdFR-17 co-expressed with the nickel insertion accessory protein (CooC) …

Mechanism Of Antibiotic Permeability Through The Gram-Negative Bacterial Envelope, Olaniyi Alegun

Theses and Dissertations--Chemistry

The outer membrane of Gram-negative bacteria (GN) makes them distinct among superbugs that are associated with the development of antibiotic resistance. The outer membrane, and inner membrane, separated by the periplasm, form a double-membrane barrier to the entry of antibiotics into the cell. Several studies have been conducted to examine the role of outer membrane modifications such as porins, lipopolysaccharides, and efflux pumps on antibiotic resistance. However, there is a paucity of knowledge on how antibiotics behave in the periplasm, to gain access into their target region. My thesis focuses on understanding the mechanism of antibiotic permeability through the cellular …

Cell-Engineered Vesicles For Therapeutic Delivery And Immunomodulatory Applications, Khaga Neupane

Theses and Dissertations--Chemistry

Development of a new kind of drug delivery system (DDS) that could efficiently deliver therapeutics to the cell of interest would allow us to accomplish cell-specific drug delivery while eliminating systemic toxicity. Although nanocarriers including endogenously released extracellular vesicles (EEVs), liposomes, and small molecules seem to be promising drug delivery systems, biological challenges persist for their use in clinical applications. Here, we demonstrate nanovesicles engineered by fragmenting cellular membranes can be exploited as versatile DDSs for therapeutics delivery as well as immunomodulatory functions. Cell-engineered vesicles were produced by cavitating cells using nitrogen gas at high pressure followed by serial centrifugation. …

Comparison Of Free Versus Encapsulated Drugs On 3t3 Differentiation, Simon H. Friedrich, Gabriel Volpe

UROP Posters

The scope of this project was to design, synthesize and test targeted nanoparticles containing hydrophobic and hydrophilic drugs that promote browning in adipose tissue. For hydrophilic drugs the use of liposomes and their hydrophilic core is more useful than the PLGA nanoparticles which have hydrophobic cores. The inhibition of the FOXO1 pathway and modulation of autophagy in adipose tissue can promote browning of white adipose tissue, or an energy burning state where excess energy is burned as heat instead of stored in the cell. If successful, these drugs would offer an alternative treatment for obesity where changes to the patient's …

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 …