Biotechnology Commons^™

Functionalization Of Chitosan Based Microparticles For In Vitro 3d Culture Of Human Liver Cells, William Imes

Williams Honors College, Honors Research Projects

Previous work involving 3D culture of human liver cells with fluorinated chitosan based microparticles has shown that their incorporation provides needed structural cues that the culture of cells alone does not provide, such as increased gas transport. However, using bare microparticles to grow large 3D cellular structures is not practical as they tend to collapse before any meaningful research can be done on them. It is proposed that this is because of the lack of extracellular matrix (ECM)components within pure cell culture in vitro, which in their absence cannot adequately facilitate biochemical communication and adhesion between cells. It is …

Functional Foods: Promising Therapeutics For Nigerian Children With Sickle Cell Diseases, Oladeji John Alabi, Fikayo Noah Adegboyega, Dolapo Samuel Olawoyin, Oluwakemi Arinola Babatunde

Department of Biochemistry: Faculty Publications

Sickle cell disease (SCD), also known as sickle cell anemia (SCA) is one of the structural hemoglobinopathies that occurs due to a single nucleotide mutation from GAG to GTG, which changes the amino acid of a β-globin chain of hemoglobin (Hb) from glutamate to valine. This singular mutation results to disorderliness in red blood cells (RBCs) with advent of changes in RBC morphology and other pathological conditions. In the 1980s, intermittent red blood cell transfusions, opioids, and penicillin prophylaxis were the only available therapy for SCA and were commonly reserved for acute, life threatening complications. So far, the US Food …

Fish Oil Intake During Gestation And Lactation Attenuated Stz-Induced Diabetes Inmale Offspring Via Activation Of Brown Fat And Modulating Oxylipin Profile, Rong Fan, Shalom Thomas, Mikyoung You, Zhuoheng Li, Brandt Bessell, Bhanwar Lal Puniya, Tomáš Helikar, Zhenhua Liu, Soonkyu Chung

Department of Biochemistry: Faculty Publications

Fish oil (FO) has been demonstrated to activate brown thermogenesis and attenuate inflammation in the brown adipose tissue (BAT). Previously, we have reported thatmaternal FO supplementation promotes BAT activity of the weaned mice pups. However, whether maternal FO intake could confer sustainable metabolic benefits to offspring remains uncovered. Therefore, this study aimed to determine the differential impact of maternal FO during pregnancy versus lactation on BAT transcriptome and evaluate the role of bioactive lipid metabolites derived from maternal FO supplementation on the extended metabolic benefits of older pups in the context of type 1 diabetes (T1D).

Conclusions: Our results suggested …

Recognition Of Extracellular Dna By Type Iv Pili Promotes Biofilm Formation By Clostridioides Difficile, Leslie A. Ronish, Ben Sidner, Yafan Yu, Kurt H. Piepenbrink

Department of Biochemistry: Faculty Publications

Clostridioides difficile is a Gram-positive bacillus, which is a frequent cause of gastrointestinal infections triggered by the depletion of the gut microbiome. Because of the frequent recurrence of these infections after antibiotic treatment, mechanisms of C. difficile persistence and recurrence, including biofilm formation, are of increasing interest. Previously, our group and others found that type IV pili, filamentous helical appendages polymerized from protein subunits, promoted microcolony and biofilm formation in C. difficile. In Gram-negative bacteria, the ability of type IV pili to mediate bacterial self-association has been explained through interactions between the pili of adjacent cells, but type …

Coordination Of Metal Center Biogenesis In Human Cytochrome C Oxidase, Eva Nývltová, Jonathan Dietz, Javier Seravalli, Oleh Khalimonchuk, Antoni Barrientos

Department of Biochemistry: Faculty Publications

Mitochondrial cytochrome c oxidase (CcO) or respiratory chain complex IV is a heme aa3- copper oxygen reductase containing metal centers essential for holo-complex biogenesis and enzymatic function that are assembled by subunit-specific metallochaperones. The enzyme has two copper sites located in the catalytic core subunits. The COX1 subunit harbors the CuB site that tightly associates with heme a3 while the COX2 subunit contains the binuclear CuA site. Here, we report that in human cells the CcO copper chaperones form macromolecular assemblies and cooperate with several twin CX9C proteins to control heme a biosynthesis and coordinate copper transfer sequentially to the …

Potential Of Oleaginous Yeast Isolated From Natural Sources In Thailand For Biodiesel Production, Nuttha Chuengcharoenphanich

Chulalongkorn University Theses and Dissertations (Chula ETD)

Oleaginous yeast is described as yeast that can accumulate lipid more than 20% of cell dry weight (CDW) and can be used to produce biodiesel as an alternate source. Hence, the goals of this study have three main objectives, including (i) to isolate and identify effective oleaginous yeast strains from natural and industrial sources in Thailand, (ii) to select cellulolytic oleaginous yeast and evaluate the possibility of lipid production, and (iii) to evaluate the potential of using oleaginous yeast for biodiesel production from various agricultural residual waste and grasses as carbon sources. In this study, a newly isolated cellulolytic oleaginous …

Anti-Melanogenic Compounds From Litchi Chinensis Sonn. And Nephelium Lappaceum L. For Cosmeceutical Applications, Junsuda Pimpa

Chulalongkorn University Theses and Dissertations (Chula ETD)

Melanogenesis is a biosynthetic process that produces the melanin pigment in human skin. Therefore, inhibition of melanin production is crucial for the development of whitening products. Thailand has many fruits processing industry, leading to big amounts of waste from inedible parts such as seeds, peels, and branches. To add value to these waste, this research study aims to investigate their inhibitory effects on melanin in B16F10 melanoma cells and cytotoxicity of eight compounds, shikimic acid (1), proanthocyanidin A-2 (2), δ-tocotrienol (3), and walsurol (4) isolated from Litchi chinensis Sonn and quercetin-3-O-rhamnoside (5), kaempferol-3-O-rhamnoside (6), kaempferol 7-O-α-L-rhamnopyranoside (7), and kaempferol-3-O-β-D-glucopyranosyl-7-O-α-L-rhamnopyranoside (8) …

Discovery Of Pharmaceutical Agents Towards The Inhibition Of P38 Mitogen- Activated Protein Kinase (Mapk): In Silico And In Vitro Studies, Utid Suriya

Chulalongkorn University Theses and Dissertations (Chula ETD)

In this research, we combined the accelerated in silico screening methods alongside experimental evaluations to search for novel anti-non-small cell lung cancer (NSCLC) drug candidates specifically targeting the up-regulated kinases including epidermal growth factor receptor tyrosine kinase (EGFR TK), p38 mitogen-activated protein kinase (p38 MAPK) and Janus kinase 2 (JAK2). A novel compound scaffold, quinoxalinones including CPD4, CPD15, CPD16, and CPD21 was identified to inhibit the EGFR (L858R/T790M/C797S) TK with an IC50 value down to a nanomolar scale as well as showing a cytotoxic effect against NSCLC cell lines. Apart from that, we employed a drug repositioning platform to elucidate …

Development Of Advanced Lateral Flow Immunoassay For Leptospirosis, Covid-19 And Delta-9-Tetrahydrocannabinol Detection, Wanwisa Deenin

Chulalongkorn University Theses and Dissertations (Chula ETD)

This dissertation focuses on the development of advanced lateral flow immunoassays (LFIA) for the detection of infectious diseases and pharmacologically active phytochemicals. The research is divided into two parts. The first part involves the development of electrochemical LFIA (eLFIA) for the diagnosis of infectious diseases (Leptospirosis and COVID-19) and the detection of Delta-9-Tetrahydrocannabinol (THC). In this approach, ferrocene carboxylic acid (Fc) is utilized as a redox species labeled on a specific antibody targeting the analyte of interest, enabling enhanced electrochemical signal detection. A disposable SPCE is integrated into the LFIA, and a bioreceptor specific to the target analyte is immobilized …

Metabolic Engineering Of Saccharomyces Cerevisiae For 3-Hydroxypropionic Acid Production, Supattra Lertsriwong

Chulalongkorn University Theses and Dissertations (Chula ETD)

3-Hydroxypropionic acid (3-HP) is an important building block chemical that can be produced from renewable resources through the malonyl-CoA pathway. This route is the best candidate for 3-HP biosynthesis through the expression of the malonyl-CoA reductase (MCR). However, the problem of the imbalance between MCR-C and MCR-N proteins causes a low conversion rate of malonyl-CoA to 3-HP. Therefore, this study aimed to balance the bi-functional MCR enzyme by dissecting MCR into two fragments and enhancing the supply of intermediates to increase the production of 3-HP. It was found that the recombinant harboring dissected MCR produced 1.26 g/L of 3-HP, which …

Intrahost Diversity Of Staphylococcus Aureus In Carriage Among Native Americans, Julia Webb

Electronic Theses and Dissertations, 2020-2023

Staphylococcus aureus (SA) is an opportunistic pathogen and a commensal member of the human microbiota that frequently colonizes the upper respiratory tract and skin. While SA can cause disease ranging from minor skin infections to life-threatening septicemia, it can also be carried asymptomatically. As carriage is the most significant risk factor for SA disease, surveillance is important for the prevention of outbreaks in vulnerable communities. Native Americans have a greater risk of infectious disease than the general US population, and Native Americans in the Southwestern United States have been shown to experience high rates of invasive SA disease. Here we …

Building Tools For Improved Modulation Of The Human Gabaa Receptor, A Central Nervous System Target For The Treatment Of Anxiety, Garrett Edward Zinck

Theses and Dissertations--Pharmacy

In the U.S., anxiety is recognized as an increasing range of mentally and physically debilitating psychiatric health disorders with significant economic repercussions. Over the last 20 years, several novel anti-anxiety therapies have entered the drug development pipeline, but none have made it to market.

The work in this dissertation focused on structurally modifying valerenic acid (VA), a structurally unique carboxylated sesquiterpene acid found in Valeriana officinalis. VA is putatively reported to have allosteric modulatory activity of the human GABA_A receptor, a ligand-gated ion channel responsible for attenuating neurotransmissions. Structural modeling of VA’s GABA_A receptor interaction suggests that …

Rna Interference For Emerald Ash Borer Suppression: Ecotoxicological Assessment And Delivery Methods, Flavia Pampolini

Theses and Dissertations--Entomology

The emerald ash borer (EAB), Agrilus planipennis (Coleoptera: Buprestidae), is a highly invasive phloem-feeding insect native to Asia. It has killed millions of ash trees (Fraxinus spp.) since its accidental introduction into North America, causing profound economic and ecological impacts. RNA interference (RNAi) or double-stranded RNA (dsRNA)-mediated gene silencing is an emerging biotechnology that is developing as an innovative tool for pest management. Exogenous dsRNA triggers the RNAi pathway, silences genes, and disrupts protein function, causing insect mortality. RNAi has proven effective in reducing target gene expression and causing mortality in EAB; however, two aspects stand as barriers …

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 …

Bioactivities Of Extracts And Pure Compound From Monofloral Bee Pollen Of Western Honeybee Apis Mellifera, Phanthiwa Khongkarat

Chulalongkorn University Theses and Dissertations (Chula ETD)

Bee pollen is one of interesting bee products which contain many bioactive compounds. However, its constituents depend on habitats and species of food plants. That results in a variety of bioactivities. In Thailand, there are many types of bee pollen, but there are few reports on their biological activities. In this study, bee pollen of A. mellifera was focused. Six types of monofloral bee pollen were harvested and identified as floral pollen of tea (Camellia sinensis L.), sunflower (Helianthus annuus L.), giant sensitive plant (Mimosa diplotricha), lotus (Nelumbo nucifera), leuuang tipwan (Xyris complanata), and sap raeng sap ka (Ageratum conyzoides) …

Hydrolysis Of Grass Xylan By Xylanases From Aureobasidium Pullulans For Xylooligosaccharide And Xylitol Productions, Sorawit Na Nongkhai

Chulalongkorn University Theses and Dissertations (Chula ETD)

Ten grass samples were screened for potential as a xylan source and five including sugarcane leaf, purple guinea grass, Napier grass, sabi grass and vetiver grass were selected for optimization of xylan extraction. After optimization, sugarcane leaf gave the highest xylan recovery at 99.42% when it was extracted by 14.32% (w/v) NaOH at 13.25:1 liquid: solid ratio with 32.36-min steaming time. From the xylan structural and sugar composition analyses, the major xylan from sugarcane leaf was arabinoxylan whereas those from the other grass samples were (glucurono)arabinoxylan. Xylans from sugarcane leaf, purple guinea grass and Napier grass were selected for further …

Foam-Mat-Freeze Dried Clove Essential Oil Nanoemulsion For Inhibition Of Spoilage Microorganisms In Whiteleg Shrimp Litopenaeus Vannamei, Puncharat Pilong

Chulalongkorn University Theses and Dissertations (Chula ETD)

This research developed foam-mat freeze-dried clove essential oil nanoemulsion (FFD-CN) for inhibiting food spoilage microorganisms. This research comprised three parts. Firstly, the fabrication of clove essential oil nanoemulsion (CN) was optimized. The characteristics including particle size, polydispersity index (PDI), Zeta-potential, and viscosity of the fabricated nanoemulsions were observed. The optimal CN having a droplet size of 30.76 nm, PDI of 0.179, Zeta-potential of -50.01 mV, and viscosity of 7.81 cP was achieved at 1% v/v clove oil and 3% v/v Tween® 80 concentration and 10,000 psi operating pressure. The CN exhibited stability against particle aggregation and phase separation throughout storage. …

Gamma-Aminobutyric Acid Contents And Glutamate Decarboxylase Activity In Local Thai Rice And Transgenic Rice Overexpressing Oscam1-1 Gene, Potitorn Kanchitanurak

Chulalongkorn University Theses and Dissertations (Chula ETD)

In rice grain, many considerable nutrients are shown to have potential functional food benefits. GABA is a metabolic product that is primarily produced by the decarboxylation of L-glutamic acid (L-Glu), catalyzed by glutamate decarboxylase (GAD), which is a cytosolic enzyme regulated by Ca2+-calmodulin (CaM) complex. The accumulation of GABA is related to the activity of GAD and substrate concentration of L-Glu. In this study, analysis of GABA contents in local Thai rice (Oryza sativa L.) during 0-72 h of germination revealed that GABA concentrations rapidly increased and the pattern of increment varied among different rice varieties. Genome-wide association mapping using …

Metabolic Alterations For Increased Glycogen And Poly(3-Hydroxybutyrate) Production In Cyanobacterium Synechocystis Sp. Pcc 6803, Nannaphat Sukkasam

Chulalongkorn University Theses and Dissertations (Chula ETD)

Cyanobacteria are a potential biofactory for biopolymer production because they can convert greenhouse gas carbon dioxide and light to useful biopolymers. Synechocystis sp. PCC 6803 is a widely used model cyanobacterium due to its simple genetic information and known biochemistry metabolism. This research aims to develop strategies to increase the accumulation and productivity of biopolymers, poly(3-hydroxybutyrate) (PHB) and glycogen, which are required in current and future industries. Three strategies, namely genetic engineering, metabolic inhibition using chemical treatment, and culture media optimization (regarding nitrogen supply), were studied, as well as their combination to increase the PHB and/or glycogen production. Genetic engineering …

Anti-Melanogenic Compounds From Artocarpus Lakoocha, Patsarunnut Dachma

Chulalongkorn University Theses and Dissertations (Chula ETD)

In this study, a purification of the methanol crude extract of A. lakoocha twigs resulted in the isolation of eight compounds (1–8). These compounds were identified as ß-amyrin acetate (1), lupeol (2), cudraflavone A (3), cycloartocarpin (4), brosimone I (5), artocarpin (6), oxyresveratrol (7), and hopeafuran (8). Their structures were elucidated through the interpretation of spectroscopic data and comparison with those previously reported. Subsequently, all the isolated compounds were evaluated for their anti-melanogenic activity. The results showed that fraction D (IC50: 12.04 ± 0.02 µg/mL) displayed potent inhibitory melanogenic activity in B16F10 melanoma cells, compared to positive control, arbutin (IC50: …

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.