Biotechnology Commons^™

Observing The Effects Of Antimalarial Drug Availability On Women’S Work Absenteeism, Rei Imada

CMC Senior Theses

This study aims to provide insight on how availability of antimalarial drugs can help alleviate the economic burden of malaria. Much of the existing literature that looks into the effects of antimalarial drug availability focuses on the associated health benefits, but fails to draw a link to the economic benefits that may also be incurred. Using data from the 2015-2016 Tanzania Demographic and Health Survey and Malaria Indicator Survey, this study performs a series of multiple regressions to observe how increased availability of artemisinin-based combination therapies (ACTs), a front-line antimalarial drug in most African countries, affects likelihood of work absenteeism …

Characterisation Of Carbapenem-Resistant Gram-Negative Organisms From Clinical Specimens In Yola, Nigeria, Shuwaram A. Shettima, Isabella A. Tickler, Caitlin M. Dela Cruz, Fred C. Tenover

Biology Faculty Publications

Objectives: This study aimed to identify carbapenem-resistant Gram-negative bacteria from clinical specimens of patients in Yola, Nigeria.

Methods: Routine clinical specimens were screened for the presence of carbapenem-resistant Gramnegative bacteria using chromogenic agar plates. Susceptibility of all presumptive isolates to carbapenems was tested by MIC and disk diffusion methods. Real-time PCR was used to test for the presence of carbapenemase genes.

Results: Screening of 1741 clinical specimens yielded 119 (6.8%) presumptive carbapenem-resistant Gram-negative bacteria. Antimicrobial susceptibility testing confirmed carbapenem resistance in 105 of these isolates. New Delhi metallo-β-lactamase (blaNDM) gene was detected in 26 isolates and Verona integron-encoded metallo-β-lactamase (bla …

Higher Tensile Forces Across Cellular Junctions And An Intact Nuclear Linc Complex Is Required For Epithelial Function And Stability, Fnu Vani Narayanan

Theses and Dissertations

Recent advances in three-dimensional (3D) cell culture systems have provided key insights into the understanding of biochemical and physiological states of native tissue. A significant progress in the field of mechanobiology involves measuring cellular traction forces in a more native 3D environment. However, the effects of mechanical forces exerted across cellular junctions and the nuclear LINC complex, in an organized 3D system has not been investigated thus far. Epithelial cells spontaneously form acini (also known as cysts or spheroids) with a single, fluid-filled central lumen, when grown in 3D matrices. The size of the lumen is dependent on apical secretion …

Spatial And Temporal Genetic Structure Of Winter-Run Steelhead (Oncorhynchus Mykiss) Returning To The Mad River, California, Steven R. Fong

Cal Poly Humboldt theses and projects

Distinct populations of steelhead in the wild are in decline. The propagation of steelhead in hatcheries has been used to boost population numbers for recreational fisheries and for use in conservation. However, hatchery breeding practices of steelhead can result in changes in genetic structure. I investigated the genetic structure of winter-run steelhead (Oncorhynchus mykiss) returning to the Mad River, California, where a hatchery has been used enhance production for recreational fisheries since 1971. Genetic variability in Mad River steelhead was evaluated using 96 single nucleotide polymorphisms (SNPs) among 4203 individuals, including the Mad River and nearby locations, and …

Identification Of Novel Antimalarials From Natural Product Inspired Libraries, David Perry

Electronic Theses and Dissertations, 2020-2023

To identify novel antimalarials from unexplored areas of chemical space, we have utilized two approaches: (a) using Torrey Pines Institute for Molecular Studies (TPIMS) proprietary high-density combinatorial libraries containing a large number of small molecule compounds residing largely in the underexplored areas of chemical space; and, (b) using novel, complexity-to-diversity/ring distortion of available natural products. The first approach involved the screening of more than 30 million compounds derived from 81 small molecule libraries, built on 81 distinct scaffolds. From this, we identified the pyrrolidine bis-cyclic guanidine library (TPI-1955) to be one of the most active and selective for antiplasmodial activity. …

การพัฒนาหัวเชื้อราเอ็กโทไมคอร์ไรซาเห็ดเผาะหนัง Astraeus Odoratus โดยการดักจับเซลล์ด้วยแคลเซียมอัลจิเนต, ณิชา มณีศิลาสันต์

Chulalongkorn University Theses and Dissertations (Chula ETD)

เห็ดเผาะหนัง Astraeus odoratus เป็นราเอ็กโทไมคอร์ไรซาที่มีความสัมพันธ์แบบพึ่งพาอาศัยกันกับไม้วงศ์ไม้ยาง ซึ่งเป็นไม้พื้นถิ่นที่มีความสำคัญทางเศรษฐกิจอย่างมากของประเทศไทย ในปัจจุบันการปลูกไม้วงศ์ไม้ยางได้รับความสนใจเป็นอย่างมาก เนื่องจากเป็นไม้เนื้อแข็งที่มีคุณค่าทางการค้า และเกิดดอกเห็ดของราเอ็กโทไมคอร์ไรซาที่สามารถรับประทานได้อีกด้วย อย่างไรก็ตามความสำเร็จในการปลูกไม้วงศ์ไม้ยางและการปลูกป่าต้องการหัวเชื้อราเอ็กโทไมคอร์ไรซาเพื่อเพิ่มการเจริญเติบโตของพืช อัตราการอยู่รอดหลังการย้ายปลูก และความทนต่อสภาพแวดล้อมที่ไม่เหมาะสม ดังนั้นการพัฒนาหัวเชื้อราเอ็กโทไมคอร์ไรซาเพื่อให้ได้หัวเชื้อที่มีประสิทธิภาพจึงเป็นเรื่องสำคัญอย่างยิ่ง ในการศึกษานี้ เส้นใยของเห็ดเผาะหนังจะถูกดักจับเซลล์ด้วยแคลเซียมอัลจิเนตเพื่อให้ได้เป็นหัวเชื้อที่มีประสิทธิภาพ สายพันธุ์เห็ดเผาะ 9 สายพันธุ์ได้มาจาก 3 แหล่ง ได้แก่ จังหวัดน่าน กาญจนบุรี และสระบุรี โดยเห็ดเผาะสายพันธุ์ K-1 เป็นสายพันธุ์ที่ถูกคัดเลือกมาใช้ในการดักจับเซลล์ด้วยแคลเซียมอัลจิเนต เนื่องจากมีอัตราการเจริญของเส้นใยบนอาหารแข็ง PDA ภายใน 14 วัน มากที่สุด และได้มีการศึกษาผลของอาหารเลี้ยงเชื้อ 6 ชนิด ได้แก่ PDB, PG, MMN, MEB, Ohta และ Czapek ต่อการเจริญของเส้นใยเห็ดเผาะหนังสายพันธุ์ K-1 และ S-24 พบว่า PDB และ PG ส่งผลให้เส้นใยมีน้ำหนักแห้งมากที่สุดหลังการเลี้ยงเชื้อ 30 วัน ผลของสารเติมแต่งต่อการงอกของเส้นใยจากเม็ดแคลเซียมอัลจิเนต พบว่าน้ำตาลกลูโคสความเข้มข้น 0.5 ถึง 2 เปอร์เซ็นต์ และซอร์บิทอลความเข้มข้น 5 เปอร์เซ็นต์ สามารถรักษาอัตราการงอกของเม็ดแคลเซียมอัลจิเนตได้มากที่สุดเท่ากับ 100 และ 96 เปอร์เซ็นต์ ตามลำดับ เม็ดแคลเซียมอัลจิเนตคงเหลืออัตราการงอกของเส้นใย 55 เปอร์เซ็นต์ หลังจากการเก็บรักษา 90 วัน ในน้ำกลั่นที่อุณหภูมิ 25 องศาเซลเซียส โดยอัตราการงอกของเส้นใยจากชิ้นวุ้นที่ถูกเก็บในภาวะเดียวกันมีการลดลงอย่างรวดเร็วหลังการเก็บรักษาเพียง 5 วัน และไม่พบอัตราการงอกของเส้นใยหลังการเก็บรักษา 75 วัน หลังการเก็บรักษาเป็นเวลา 3 เดือน เส้นใยของเห็ดเผาะหนังสายพันธุ์ K-1 ในรูปเม็ดแคลเซียมอัลจิเนตสามารถเข้าติดเชื้อต้นกล้าตะเคียนทอง Hopea odorata ได้ด้วยอัตราการติดเชื้อ 46 เปอร์เซ็นต์ จากการทดลองนี้แสดงให้เห็นว่าเส้นใยของเห็ดเผาะหนังที่ถูกดักจับในเม็ดแคลเซียมอัลจิเนตสามารถนำมาใช้เป็นหัวเชื้อสำหรับการผลิตทางการค้าและใช้ในการอนุบาลกล้าไม้ป่าได้

Innovation In Meat Production: A Problem And An Opportunity, Christopher J. Bryant

Animal Sentience

Innovation in meat production has enabled modern humans to inflict far greater harm on animals, the environment, and public health than was possible just a few decades ago. Wiebers & Feigin aptly express the urgency with which these issues must be addressed. Those advocating for animals on moral grounds face resistance from omnivores citing taste, price and convenience. Further innovation in meat production (plant-based and cultured meat) will enable us to preserve the experience of eating meat whilst phasing out the many problems caused by industrial animal farming.

Optimization And Validation Of The Neurolux Wireless Optoelectronics System For Optogenetics, Karis Courey, Su Hyun Lee Ph.D., Adam Smith Ph.D., Nicholas Cilz Ph.D., Sarah K. Williams Avram Ph.D., Adi Cymerblit-Sabba Ph.D., June Song, Nicholas Leipzig Ph.D., W. Scott Young M.D., Ph.D.

Williams Honors College, Honors Research Projects

Utilizing light and genetic engineering, optogenetics permits the manipulation of events within cells via light using the light-sensitive properties of single-component microbial opsins. Microbial opsins are activated by a light source, such as lasers, light-emitting diodes, and incandescent sources that deliver light to the region of interest either directly or indirectly, such as through fiberoptics. In classical in vivo optogenetics, the wiring of optic fibers necessitates tethering of animals by the optic fiber to the light source. The novel NeuroLux wireless optoelectronic system for optogenetics circumvents issues pertaining to classical optogenetics by utilizing near-field power transfer via magnetic coil antennae …

Advancing Knowledge Management (Km) As An Ich Q10 Enabler In The Biopharmaceutical Industry, Paige Kane, Martin Lipa, Anne Greene (Editor), Nuala Calnan (Editor), Anne Murphy (Editor)

Books

A monograph based on doctoral research by the authors through the School of Chemistry & Pharmaceutical Science, Technological University Dublin, Ireland

Genome Biology Of The Paleotetraploid Perennial Biomass Crop Miscanthus, Therese Mitros, Adam M. Session, Brandon T. James, Guohong Albert Wu, Katarzyna Glowacka, Kankshita Swaminathan, Daniel S. Rokhsar, 35 Additional Co-Authors

Department of Biochemistry: Faculty Publications

Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. …

The Genome Evolution And Domestication Of Tropical Fruit Mango, Peng Wang, Yingfeng Luo, Jianfeng Huang, Shenghan Gao, Guopeng Zhu, Zhiguo Dang, Jiangtao Gai, Meng Yang, Min Zhu, Huangkai Zhang, Xiuxu Ye, Aiping Gao, Xinyu Tan, Sen Wang, Shuangyang Wu, Edgar B. Cahoon, Beibei Bai, Zhichang Zhao, Qian Li, Junya Wei, Huarui Chen, Ruixiong Luo, Deyong Gong, Kexuan Tang, Bing Zhang, Zhangguang Ni, Guodi Huang, Songnian Hu, Yeyuan Chen

Department of Biochemistry: Faculty Publications

Background: Mango is one of the world’s most important tropical fruits. It belongs to the family Anacardiaceae, which includes several other economically important species, notably cashew, sumac and pistachio from other genera. Many species in this family produce family-specific urushiols and related phenols, which can induce contact dermatitis.

Results: We generate a chromosome-scale genome assembly of mango, providing a reference genome for the Anacardiaceae family. Our results indicate the occurrence of a recent whole-genome duplication (WGD) event in mango. Duplicated genes preferentially retained include photosynthetic, photorespiration, and lipid metabolic genes that may have provided adaptive advantages to sharp historical decreases …

From Synthesis To Utilization: The Ins And Outs Of Mitochondrial Heme, Samantha A. Swenson, Courtney M. Moore, Jason R. Marcero, Amy E. Medlock, Amit R. Reddi, Oleh Khalimonchuk

Department of Biochemistry: Faculty Publications

Heme is a ubiquitous and essential iron containing metallo-organic cofactor required for virtually all aerobic life. Heme synthesis is initiated and completed in mitochondria, followed by certain covalent modifications and/or its delivery to apo-hemoproteins residing throughout the cell. While the biochemical aspects of heme biosynthetic reactions are well understood, the trafficking of newly synthesized heme—a highly reactive and inherently toxic compound—and its subsequent delivery to target proteins remain far from clear. In this review, we summarize current knowledge about heme biosynthesis and trafficking within and outside of the mitochondria.

Connecting Theory To Practice: Using Self-Determination Theory To Better Understand Inclusion In Stem, Michael E. Moore, Dulce M. Vega, Katie M. Wiens, Natalia Caporale

Department of Biochemistry: Faculty Publications

In the United States, persistence for women and ethnic minorities in science, technology, engineering, and math (STEM) careers is strongly impacted by affective factors such as science identity, agency, and sense of belonging. Policies aimed at increasing the diversity of the national STEM student population and workforce have recently focused on fostering inclusive learning environments that can positively impact the experi-ences of underrepresented minorities (URMs) in STEM, thus increasing their retention. While research on inclusion in STEM in higher education is relatively new, inclusion research has a rich history in several other disciplines. These fields have developed theoretical frameworks and …

Systematic Age-, Organ-, And Diet-Associated Ionome Remodeling And The Development Of Ionomic Aging Clocks, Bohan Zhang, Dmitriy I. Podolskiy, Marco Mariotti, Javier Seravalli, Vadim N. Gladyshev

Department of Biochemistry: Faculty Publications

Aging involves coordinated yet distinct changes in organs and systems throughout life, including changes in essential trace elements. However, how aging affects tissue element composition (ionome) and how these changes lead to dysfunction and dis-ease remain unclear. Here, we quantified changes in the ionome across eight organs and 16 age groups of mice. This global profiling revealed novel interactions between elements at the level of tissue, age, and diet, and allowed us to achieve a broader, organismal view of the aging process. We found that while the entire ionome stead-ily transitions along the young-to-old trajectory, individual organs are characterized by …

Training Population Optimization For Genomic Selection In Miscanthus, Marcus O. Olatoye, Lindsay V. Clark, Nicholas R. Labonte, Hongxu Dong, Maria S. Dwiyanti, Kossonou G. Anzoua, Joe E. Brummer, Bimal K. Ghimire, Elena Dzyubenko, Nikolay Dzyubenko, Larisa Bagmet, Andrey Sabitov, Pavel Chebukin, Katarzyna Głowacka, Kweon Heo, Xiaoli Jin, Hironori Nagano, Junhua Peng, Chang Y. Yu, Ji H. Yoo, Hua Zhao, Stephen P. Long, Toshihiko Yamada, Erik J. Sacks, Alexander E. Lipka

Department of Biochemistry: Faculty Publications

Miscanthus is a perennial grass with potential for lignocellulosic ethanol production. To ensure its utility for this purpose, breeding efforts should focus on increasing genetic diversity of the nothospecies Miscanthus x giganteus (M·g) beyond the single clone used in many programs. Germplasm from the corresponding parental speciesM. sinensis (Msi) and M. sacchariflorus (Msa) could theoretically be used as training sets for genomic prediction of M·g clones with optimal genomic estimated breeding values for biofuel traits. To this end, we first showed that subpopulation structure makes a substantial contribution to the genomic selection (GS) prediction accuracies within a 538-member diversity panel …

Differences In Blood-Derived Francisella Tularensis Type B Strains From Clinical Cases Of Tularemia, Marilyn A. Larson, Baha Abdalhamid, Bhanwar Lal Puniya, Tomáš Helikar, David W. Kelley, Peter C. Iwen

Department of Biochemistry: Faculty Publications

Francisella tularensis can cause the zoonotic disease tularemia and is partitioned into subspecies due to differences in chromosomal organization and virulence. The subspecies holarctica (type B) is generally considered more clonal than the other subpopulations with moderate virulence compared to the hypervirulent A.I clade. We performed whole genome sequencing (WGS) on six type B strains isolated from the blood of patients with tularemia within a one-year period from the same United States region, to better understand the associated pathogenicity. The WGS data were compared to the prototype strain for this subspecies, specifically FSC200, which was isolated from a patient with …

Metabolic Feedback Inhibition Influences Metabolite Secretion By The Human Gut Symbiont Bacteroides Thetaiotaomicron, Jennie L. Catlett, Jonathan Catazaro, Mikaela Cashman, Sean Carr, Robert Powers, Myra B. Cohen, Nicole R. Buan

Department of Biochemistry: Faculty Publications

Microbial metabolism and trophic interactions between microbes give rise to complex multispecies communities in microbe-host systems. Bacteroides thetaiotaomicron (B. theta) is a human gut symbiont thought to play an important role in maintaining host health. Untargeted nuclear magnetic resonance metabolomics revealed B. theta secretes specific organic acids and amino acids in defined minimal medium. Physiological concentrations of acetate and formate found in the human intestinal tract were shown to cause dose-dependent changes in secretion of metabolites known to play roles in host nutrition and pathogenesis. While secretion fluxes varied, biomass yield was unchanged, suggesting feedback inhibition does not affect metabolic …

Amphiphiliccyclobutenes And Cylobutanes, Wantanee Sittiwong, Patrick H. Dussault, Raul Barletta, Robert Power

Department of Biochemistry: Faculty Publications

This disclosure relates to amphiphilic compounds containing a cyclobutene or cyclobutane moiety. In some embodiments, the compounds are useful for treating infection by Mycobacterium such as Mycobacterium tuberculosis. Cyclobutene containing compounds are also useful as monomers in the preparation of amphiphilic polymers.

Reactive Oxygen Species (Ros) Mediated Degradation Of Organophosphate T Pesticides By The Green Microalgae Coccomyxa Subellipsoidea☆, Timothy J Nicodemus, Concetta C. Dirusso, Mark A. Wilson, Paul N. Black

Department of Biochemistry: Faculty Publications

The aim of this study was to define the mechanism allowing the green alga Coccomyxa subellipsoidea to break down organophosphates from agricultural run-off. This study found that metabolically active cultures of the microalga C. subellipsoidea breakdown organophosphates (paraoxon, malathion and diazinon) with differing structural conformations in freshwater through a mechanism that requires the formation of reactive oxygen species (ROS) with little to no toxic effects on the algae. Under these conditions, organophosphate levels were reduced to 0.1 mg/mL or less over the 8–10 day experimental period. These findings demonstrate a biological- based system can be tailored for the remediation of …

Sestrins Are Evolutionarily Conserved Mediators Of Exercise Benefits, Myungjin Kim, Alyson Sujkowski, Sim Namkoong, Bondong Gu, Tyler Cobb, Boyoung Kim, Allison H. Kowalsky, Chun-Seok Cho, Ian Semple, Seung-Hyun Ro, Carol Davis, Susan V. Brooks, Michael Karin, Robert J. Wessells, Jun Hee Lee

Department of Biochemistry: Faculty Publications

Exercise is among the most effective interventions for age-associated mobility decline and metabolic dysregulation. Although long-term endurance exercise promotes insulin sensitivity and expands respiratory capacity, genetic components and pathways mediating the meta- bolic benefits of exercise have remained elusive. Here, we show that Sestrins, a family of evolutionarily conserved exercise-inducible proteins, are critical mediators of exercise ben- efits. In both fly and mouse models, genetic ablation of Sestrins prevents organisms from acquiring metabolic benefits of exercise and improving their endurance through training. Conversely, Sestrin upregulation mimics both molecular and physiological effects of exercise, suggesting that it could be a major …