Biotechnology Commons^™

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 …

Two Heads Are Better Than One: Current Landscape Of Integrating Qsp And Machine Learning, Tongli Zhang, Ioannis P. Androulakis, Peter Bonate, Limei Cheng, Tomáš Helikar, Jaimit Parikh, Christopher Rackauckas, Kalyanasundaram Subramanian, Carolyn R. Cho

Department of Biochemistry: Faculty Publications

Quantitative systems pharmacology (QSP) modeling is applied to address essential questions in drug development, such as the mechanism of action of a therapeutic agent and the progression of disease. Meanwhile, machine learning (ML) approaches also contribute to answering these questions via the analysis of multi-layer ‘omics’ data such as gene expression, proteomics, metabolomics, and high-throughput imaging. Furthermore, ML approaches can also be applied to aspects of QSP modeling. Both approaches are powerful tools and there is considerable interest in integrating QSP modeling and ML. So far, a few successful implementations have been carried out from which we have learned about …

Role Of Simulation In Open Varicose Veins Surgery: A Systematic Review, Muhammad Ammar Pirzada, Fareed Ahmed Shaikh, Shoaib Badini, Nadeem Ahmed Siddiqui

Department of Surgery Docs

Objective: To assess the types and effectiveness of simulators present for open varicose vein surgery.
Methods: The systematic review was conducted at The Aga Khan University Hospital Karachi and comprised studies published from 1st January 2000 to 30th June 2020 related to open varicose vein surgical procedures done on simulators. Databases searched were PubMed, Medline, Google Scholar, Cochrane and Scopus using appropriate key words. The primary outcome of the review was to assess the effectiveness of different types of simulators used for varicose vein surgery.
Results: Of the 286 articles found, 6(2%) were included. A variety of simulators ranging from …

Innovations In Surgery Between The Past And Future: A Narrative Review Of Targeted Literature, Obada Hasan, Ahmed Ayaz, Laiba Masood, Abdul Mannan Baig, Naveed Baloch

Medical College Documents

Innovation is the introduction of a new method or technology designed to change the way things are done. History is full of remarkable innovations in surgery over the years as surgeons have always been innovating and pioneering latest techniques and equipment that can benefit the mankind. Though persistent, progress has been far from uniform. Despite all the bells and whistles that these innovations bring to the table, the little acknowledged fact is that they are only accessible to a very small proportion of the global population. Five billion people on this planet do not even have access to an operating …

A Predictive Model For Geographical Location Using Microbiome Composition And Covid-19 Based Analysis, Ahmed Adel Aboushanab

Theses and Dissertations

The human microbiome is a main contributor for the health and welfare of the human body. It is affected by many factors like diet and hygiene. These factors differ between different populations. Testing the population-microbiome differences using healthy samples from different countries is the first objective of this study. This data was then used in training and testing machine learning models (Random Forest and L2-logistic Regression Classifiers) for the prediction of the geographical location based on the microbiome data. Random Forest Classifier had the highest accuracy. Feature importance analysis showed that the data for Proteobacteria, Actinobacteria, and Bacteroidetes improved the …

Selective Gsk3Β Inhibition Mediates An Nrf2-Independent Anti-Inflammatory Microglial Response, Mohamed H. Yousef

Theses and Dissertations

Glycogen Synthase Kinase 3 (GSK3) is associated with the proinflammatory phenotype of microglia and has been shown to act in concert with Nuclear factor kappa B (NF-κB). . GSK3 is also a suppressor of Nuclear factor erythroid 2-related factor 2 (Nrf2), the principal regulator of redox homeostasis. Agreeing with the oxidative paradigm of aging, Nrf2 is often deregulated in parainflammatory and neurodegenerative diseases. In this study, we aimed to explore a multimodal disease-modifying utility of GSK3 inhibition, beyond neuronal proteopathologies, Furthermore, we aimed to underscore the difference in therapeutic value between the two GSK3 paralogs by isoform-selective chemical inhibition.

The …

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 …

Genome Structure And Evolutionary History Of Frankincense Producing Boswellia Sacra, Abdul Latif Khan, Ahmed Al-Harrasi, Jin-Peng Wang, Sajjad Asaf, Jean-Jack Riethoven, Tariq Shehzad, Chia-Sin Liew, Xiao-Ming Song, Daniel P. Schachtman, Chao Liu, Ji-Gao Yu, Zhi-Kang Zhang, Fan-Bo Meng, Jia-Qing Yuan, Chen-Dan Wei, He Guo, Xuewen Wang, Ahmed Al-Rawahi, In-Jung Lee, Jeffrey L. Bennetzen, Xi-Yin Wang

Nebraska Center for Biotechnology: Faculty and Staff Publications

Boswellia sacra Flueck (family Burseraceae) tree is wounded to produce frankincense. We report its de novo assembled genome (667.8 Mb) comprising 18,564 high-confidence protein-encoding genes. Comparing conserved single-copy genes across eudicots suggest >97% gene space assembly of B. sacra genome. Evolutionary history shows B. sacra gene-duplications derived from recent paralogous events and retained from ancient hexaploidy shared with other eudicots. The genome indicated a major expansion of Gypsy retroelements in last 2 million years. The B. sacra genetic diversity showed four clades intermixed with a primary genotype—dominating most resin-productive trees. Further, the stemtranscriptome revealed that wounding concurrently activates phytohormones signaling, …

Characterizing Isoform Switching Events In Esophageal Adenocarcinoma, Yun Zhang, Katherine M. Weh, Connor L. Howard, Jean-Jack Riethoven, Jennifer L. Clarke, Kiran H. Lagisetty, Jules Lin, Rishindra M. Reddy, Andrew C. Chang, David G. Beer, Laura A. Kresty

Nebraska Center for Biotechnology: Faculty and Staff Publications

Isoform switching events with predicted functional consequences are common in many cancers, but characterization of switching events in esophageal adenocarcinoma (EAC) is lacking. Next-generation sequencing was used to detect levels of RNA transcripts and identify specific isoforms in treatment- naïve esophageal tissues ranging from premalignant Barrett’s esophagus (BE), BE with low- or high-grade dysplasia (BE.LGD, BE.HGD), and EAC. Samples were stratified by histopathology and TP53 mutation status, identifying significant isoform switching events with predicted functional consequences. Comparing BE.LGD with BE.HGD, a histopathology linked to cancer progression, isoform switching events were identified in 75 genes including KRAS, RNF128, and WRAP53. Stratification …

Spatially Controlled Monolayers For Electrically Switchable Biomolecule Detection, Eduard Lukhmanov

Theses, Dissertations and Capstones

The development of biosensors that are low-waste, highly stable, and possess an ability to be interchanged between capturing and non-capturing configurations is promising for the biodetector field. Stable packing and attachment of the sensor, the ability to create an interchangeable detecting probe of interest relatively easily, and dynamic control of the probe via a reversible bias can provide for that. With the set goals to control all those properties, DNA-dendron conjugate molecules were designed, synthesized in solution, purified, and utilized to make self-assembled monolayers of single-stranded DNA on gold. To be able to manipulate the conjugates’ sensing qualities in the …

Hydroponic Lab Growing Guide Bell Peppers, Zachary N. Russell

Hydroponic Center

This is a guide for growing Bell Peppers in the Hydroponic Lab. It states how the plant was grown from propagation, which system the plant was grown in, the plants optimal conditions (PPM, pH), and time frame until fully grown.

Sugar Snap Organic Pea Hydroponic Grow Guide, Levi Mitchell

Hydroponic Center

Hydroponic Grow Guide for Sugar Snap Organic Peas in a MGS hydroponic system. Hydroponically grown Sugar Snap Peas are a vine-structured plant which require over five feet of overhead height for the vines to grow their structure before fruiting peas. This grow guide covers the optimal nutrient range, optimal pH range, propagation and growing techniques, as well as special considerations for future projects involved with growing sugar snap peas.

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

The Covid-19 Pandemic And The Importance Of Financing The Biotechnology Industry In South Africa, Ramazan Uctu, Karen Eksteen

The Journal of Entrepreneurial Finance

Whether it is a government research institution, a public-private partnership, or a private enterprise, the South African biotechnology industry requires funding for the biotechnology industry. Our goal with this research is to look into the role of venture capital (VC) in financing biotech enterprises and demonstrate how VC finance could aid in the development of diagnostic kits and vaccines for Covid-19 or future pandemics in South Africa.

The study aims to provide policymakers with a clear image of the importance of funding the biotechnology sector, notably during the Covid-19 period, as recognized by the industry's key players. We employed a …

Metabolic Synergy Between Human Symbionts Bacteroides And Methanobrevibacter, Jennie L. Catlett, Sean Carr, Mikaela Cashman, Megan D. Smith, Mary Walter, Zahmeeth Sakkaff, Christine A. Kelley, Massimiliano Pierobon, Myra B. Cohen, Nicole R. Buan

Department of Biochemistry: Faculty Publications

ABSTRACT Trophic interactions between microbes are postulated to determine whether a host microbiome is healthy or causes predisposition to disease. Two abundant taxa, the Gram-negative heterotrophic bacterium Bacteroides thetaiotaomicron and the methanogenic archaeon Methanobrevibacter smithii, are proposed to have a synergistic metabolic relationship. Both organisms play vital roles in human gut health; B. thetaiotaomicron assists the host by fermenting dietary polysaccharides, whereas M. smithii consumes end-stage fermentation products and is hypothesized to relieve feedback inhibition of upstream microbes such as B. thetaiotaomicron. To study their metabolic interactions, we defined and optimized a coculture system and used software testing …

Arginine Catabolism And Polyamine Biosynthesis Pathway Disparities Within Francisella Tularensis Subpopulations, Yinshi Yue, Bhanwar Lal Puniya, Tomáš Helikar, Benjamin Girardo, Steven H. Hinrichs, Marilyn A. Larson

Department of Biochemistry: Faculty Publications

Francisella tularensis is a highly infectious zoonotic pathogen with as few as 10 organisms causing tularemia, a disease that is fatal if untreated. Although F. tularensis subspecies tularensis (type A) and subspecies holarctica (type B) share over 99.5% average nucleotide identity, notable differences exist in genomic organization and pathogenicity. The type A clade has been further divided into subtypes A.I and A.II, with A.I strains being recognized as some of the most virulent bacterial pathogens known. In this study, we report on major disparities that exist between the F. tularensis subpopulations in arginine catabolism and subsequent polyamine biosynthesis. The genes …

Design And Development Of Medical Devices For Multifaceted Applications, Madisyn Messmore

Honors Undergraduate Theses

The fields of biotechnology and biomedical sciences are rapidly evolving and involve the constant growth of knowledge. As a consequence, engineering design has to also remain at the cutting edge in order to not inhibit the growth of these fields. This study focuses on engineering design and analysis as it pertains to the field of biotechnology, at every step of the engineering process. More specifically, how the engineering design and analysis approach can assist in solving medical problems relating to bone diseases and biomaterials. The first part of the study focuses on a project to design and manufacture a novel …

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 …