Biotechnology Commons^™

The Genomics Education Partnership: Successful Integration Of Research Into Laboratory Classes At A Diverse Group Of Undergraduate Institutions, Christopher D. Shaffer, Consuelo Alvarez, Cheryl Bailey, Daron Barnard, Satish Bhalla, Chitra Chandrasekaran, Vidya Chandrasekaran, Hui-Min Chung, Douglas R. Dorer, Chunguang Du, Todd T. Eckdahl, Jeff L. Poet, Donald Frohlich, Anya L. Goodman, Yuying Gossner, Charles Hauser, Laura L.M. Hoopes, Diana Johnson, Christopher J. Jones, Marian Kaehler, Nighat Kokan, Olga R. Kopp, Gary A. Kuleck, Gerard Mcneil, Robert Moss, Jennifer L. Myka, Alexis Nagengast, Robert Morris, Paul J. Overvoorde, Elizabeth Shoop, Susan Parrish, Kelynne Reed, E. Gloria Regisford, Dennis Revie, Anne G. Rosenwald, Ken Saville, Stephanie Schroeder, Mary Shaw, Gary Skuse, Christopher Smith, Mary Smith, Eric P. Spana, Mary Spratt, Joyce Stamm, Jeff S. Thompson, Matthew Wawersik, Barbara A. Wilson, Jim Youngblom, Wilson Leung, Jeremy Buhler, Elaine R. Mardis, David Lopatto, Sarah C.R. Elgin

Department of Biochemistry: Faculty Publications

Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than 2 …

Adventures In Nontranslational Research, Martin Chalfie

IMSA Great Minds Program ®

Over the last ten years administrators, governmental officials, and clinical researchers have increasingly called for a greater emphasis on "translational research", i.e., research that translates findings in the laboratory into new treatments for medical conditions, over basic research in the biological sciences. Although the application of biological research to human disease (as well as toward improvements in agriculture and development of biotechnology) is important, I feel that an increased emphasis is not needed and is actually detrimental. Ultimately, this emphasis is self-defeating because one needs the fruits of basic research to fuel these applications. I will give examples from my …

Consumers And Benefits Of Genetically Modified Vegetables, Megan Carter Judge

Master's Theses

With the adoption of biotechnology in many agricultural products with first-generation biotechnology traits such as increased pest resistance, greater herbicide resistance, and increased yields the growers have accepted them. The next wave of biotech crops have second-generation traits, such as improved nutrient content, extended shelf life, reduced pesticide and herbicide application (a consumer demanded trait), and better taste. Will these consumer benefits offset any concern that the consumer has regarding biotechnology? What are those benefits and how should the information be communicated to the consumer?

Three focus groups give insight to the proposed questions. The focus groups were done in …

Monopoly, Regulation, And Innovation, Matt Bogard

Economics Faculty Publications

Recently the Justice department has started investigations into alleged anti-trust violations by Monsanto. This has helped fuel a lot of already hyped discontent with one of the world’s leaders in innovative solutions for sustainable agriculture. This article discusses how the regulatory environment could possibly have contributed to more concentration and power in the biotech industry. Increasing regulation would likely have the opposite effect of creating a level playing field in the agriculture industry. From AgWeb, March 27,2010 http://www.agweb.com/blog/Economic_Sense_190/Monopoly_Regulation__and_Innovation_10771/

Electrically Mediated Delivery Of Plasmid Dna To The Skin, Using A Multielectrode Array, Richard Heller, Yolmari Criz, Loree C. Heller, Richard A. Gilbert, Mark J. Jaroszeski

Bioelectrics Publications

The easy accessibility of skin makes it an excellent target for gene transfer protocols. To take full advantage of skin as a target for gene transfer, it is important to establish an efficient and reproducible delivery system. Electroporation is a strong candidate to meet this delivery criterion. Electroporation of the skin is a simple, direct, in vivo method to deliver genes for therapy. Previously, delivery to the skin was performed by means of applicators with relatively large distances between electrodes, resulting in significant muscle stimulation and pain. These applicators also had limitations in controlling the directionality of the applied field. …

What About The Children? Benjamin And Arendt: On Education, Work, And The Political, Jules Simon

Selected Works Temporary Series

This article is a rough draft of an article that I contributed to an edited volume of articles dealing with progressive education theory. I reflect on articles that Hannah Arendt and Walter Benjamin wrote that deal with educational reform and innovation, both political in nature.

What About The Children? Benjamin And Arendt: On Education, Work, And The Political, Jules Simon

Departmental Papers (Philosophy)

This article is a rough draft of an article that I contributed to an edited volume of articles dealing with progressive education theory. I reflect on articles that Hannah Arendt and Walter Benjamin wrote that deal with educational reform and innovation, both political in nature.

Diversity Of Protein And Mrna Forms Of Mammalian Methionine Sulfoxide Reductase B1 Due To Intronization And Protein Processing, Xinwen Liang, Dmitri E. Fomenko, Deame Hua, Alaattin Kaya, Vadim N. Gladyshev

Department of Biochemistry: Faculty Publications

Background: Methionine sulfoxide reductases (Msrs) are repair enzymes that protect proteins from oxidative stress by catalyzing stereospecific reduction of oxidized methionine residues. MsrB1 is a selenocysteine-containing cytosolic/nuclear Msr with high expression in liver and kidney.

Principal Findings: Here, we identified differences in MsrB1 gene structure among mammals. Human MsrB1 gene consists of four, whereas the corresponding mouse gene of five exons, due to occurrence of an additional intron that flanks the stop signal and covers a large part of the 39-UTR. This intron evolved in a subset of rodents through intronization of exonic sequences, whereas the human gene structure represents …

Incorporating Genomics And Bioinformatics Across The Life Sciences Curriculum, Jayna L. Ditty, Christopher A. Kvaal, Brad Goodner, Sharyn K. Freyermuth, Cheryl Bailey, Robert A. Britton, Stuart G. Gordon, Sabine Heinhorst, Kelynne Reed, Zhaohui Xu, Erin R. Sanders-Lorenz, Seth Axen, Edwin Kim, Mitrick Johns, Kathleen Scott, Cheryl A. Kerfeld

Department of Biochemistry: Faculty Publications

Undergraduate life sciences education needs an overhaul, as clearly described in the National Research Council of the National Academies’ publication BIO 2010: Transforming Undergraduate Education for Future Research Biologists. Among BIO 2010’s top recommendations is the need to involve students in working with real data and tools that reflect the nature of life sciences research in the 21st century [1]. Education research studies support the importance of utilizing primary literature, designing and implementing experiments, and analyzing results in the context of a bona fide scientific question [1–12] in cultivating the analytical skills necessary to become a scientist. Incorporating these …

Structural Basis For Feedback And Pharmacological Inhibition Of Saccharomyces Cerevisiae Glutamate Cysteine Ligase, Ekaterina I Biterova, Joseph J. Barycki

Department of Biochemistry: Faculty Publications

Structural characterization of glutamate cysteine ligase (GCL), the enzyme that catalyzes the initial, rate-limiting step in glutathione biosynthesis, has revealed many of the molecular details of substrate recognition. To further delineate the mechanistic details of this critical enzyme, we have determined the structures of two inhibited forms of Saccharomyces cerevisiae GCL (ScGCL), which shares significant sequence identity with the human enzyme. In vivo, GCL activity is feedback regulated by glutathione. Examination of the structure of ScGCL-glutathione complex (2.5 A ; R = 19.9%, R_free = 25.1%) indicates that the inhibitor occupies both the glutamate- and the presumed cysteine- …

Cug Start Codon Generates Thioredoxin/Glutathione Reductase Isoforms In Mouse Testes, Maxim Gerashchenko, Dan Su, Vadim Gladyshev

Department of Biochemistry: Faculty Publications

Mammalian cytosolic and mitochondrial thioredoxin reductases are essential selenocysteine-containing enzymes that control thioredoxin functions. Thioredoxin/glutathione reductase (TGR) is a third member of this enzyme family. It has an additional glutaredoxin domain and shows highest expression in testes. Herein, we found that human and several other mammalian TGR genes lack any AUG codons that could function in translation initiation. Although mouse and rat TGRs have such codons, we detected protein sequences upstream of them by immunoblot assays and direct proteomic analyses. Further gene engineering and expression analyses demonstrated that a CUG codon, located upstream of the sequences previously thought to initiate …

Identification And Characterization Of Oxalate Oxidoreductase, A Novel Thiamine Pyrophosphate-Dependent 2-Oxoacid Oxidoreductase That Enables Anaerobic Growth On Oxalate, Elizabeth Pierce, Donald F. Becker, Stephen W. Ragsdale

Department of Biochemistry: Faculty Publications

Moorella thermoacetica is an anaerobic acetogen, a class of bacteria that is found in the soil, the animal gastrointestinal tract, and the rumen. This organism engages the Wood-Ljungdahl pathway of anaerobic CO₂ fixation for heterotrophic or autotrophic growth. This paper describes a novel enzyme, oxalate oxidoreductase (OOR), that enables M. thermoacetica to grow on oxalate, which is produced in soil and is a common component of kidney stones. Exposure to oxalate leads to the induction of three proteins that are subunits of OOR, which oxidizes oxalate coupled to the production of two electrons and CO₂ or bicarbonate. Like …

Structure Of The Proline Utilization A Proline Dehydrogenase Domain Inactivated By N-Propargylglycine Provides Insight Into Conformational Changes Induced By Substrate Binding And Flavin Reduction, Dhiraj Srivastava, Weidong Zhu, William H. Johnson Jr., Christian P. Whitman, Donald F. Becker, John J. Tanner

Department of Biochemistry: Faculty Publications

Proline utilization A (PutA) from Escherichia coli is a flavoprotein that has mutually exclusive roles as a transcriptional repressor of the put regulon and a membrane-associated enzyme that catalyzes the oxidation of proline to glutamate. Previous studies have shown that the binding of proline in the proline dehydrogenase (PRODH) active site and subsequent reduction of the FAD trigger global conformational changes that enhance PutA-membrane affinity. These events cause PutA to switch from its repressor to enzymatic role, but the mechanism by which this signal is propagated from the active site to the distal membrane-binding domain is largely unknown. Here, it …

Identification And Characterization Of Small Compound Inhibitors Of Human Fatp2, Angel Sandoval, Aalap Chokshi, Elliot D. Jesch, Paul N. Black, Concetta C. Dirusso

Department of Biochemistry: Faculty Publications

Fatty acid transport proteins (FATPs) are bifunctional proteins, which transport long chain fatty acids into cells and activate very long chain fatty acids by esterification with coenzyme A. In an effort to understand the linkage between cellular fatty acid transport and the pathology associated with excessive accumulation of exogenous fatty acids, we targeted FATP-mediated fatty acid transport in a high throughput screen of more than 100,000 small diverse chemical compounds in yeast expressing human FATP2 (hsFATP2). Compounds were selected for their ability to depress the transport of the fluorescent long chain fatty acid analogue, C₁-BODIPY-C₁₂. Among …

Quantitative Nuclear Proteomics Identifies Mtor Regulation Of Dna Damage Response, Sricharan Bandhakavi, Young-Mi Kim, Seung-Hyun Ro, Hongwei Xie, Getiria Onsongo, Chang-Bong Jun, Do-Hyung Kim, Timothy J. Griffin

Department of Biochemistry: Faculty Publications

Cellular nutritional and energy status regulates a wide range of nuclear processes important for cell growth, survival, and metabolic homeostasis. Mammalian target of rapamycin (mTOR) plays a key role in the cellular responses to nutrients. However, the nuclear processes governed by mTOR have not been clearly defined. Using isobaric peptide tagging coupled with linear ion trap mass spectrometry, we performed quantitative proteomics analysis to identify nuclear processes in human cells under control of mTOR. Within 3 h of inhibiting mTOR with rapamycin in HeLa cells, we observed downregulation of nuclear abundance of many proteins involved in translation and RNA modification. …

Methanogenesis By Methanosarcina Acetivorans Involves Two Structurally And Functionally Distinct Classes Of Heterodisulfide Reductase, Nicole R. Buan, William W. Metcalf

Department of Biochemistry: Faculty Publications

Biochemical studies have revealed two distinct classes of Coenzyme B-Coenzyme M heterodisulfide (CoB-S-S-CoM) reductase (Hdr), a key enzyme required for anaerobic respiration in methaneproducing archaea. A cytoplasmic HdrABC enzyme complex is found in most methanogens, whereas a membrane-bound HdrED complex is found exclusively in members of the order Methanosarcinales. Unexpectedly, genomic data indicate that multiple copies of both Hdr classes are found in all sequenced Methanosarcinales genomes. The Methanosarcina acetivorans hdrED1 operon is constitutively expressed and required for viability under all growth conditions examined, consistent with HdrED being the primary Hdr. HdrABC appears to be specifically involved in methylotrophic …

Analysis Of Leigh Syndrome Mutations In The Yeast Surf1 Homolog Reveals A New Member Of The Cytochrome Oxidase Assembly Factor Family, Megan Bestwick, Mi-Young Jeong, Oleh Khalimonchuk, Hyung Kim, Dennis R. Winge

Department of Biochemistry: Faculty Publications

Three missense SURF1 mutations identified in patients with Leigh syndrome (LS) were evaluated in the yeast homolog Shy1 protein. Introduction of two of the Leigh mutations, F²⁴⁹T and Y³⁴⁴D, in Shy1 failed to significantly attenuate the function of Shy1 in cytochrome c oxidase (CcO) biogenesis as seen with the human mutations. In contrast, a G¹³⁷E substitution in Shy1 results in a nonfunctional protein conferring a CcO deficiency. The G¹³⁷E Shy1 mutant phenocopied shy1 Δ cells in impaired Cox1 hemylation and low mitochondrial copper. A genetic screen for allele-specific suppressors of the G137E …

The Role Of Coa2 In Hemylation Of Yeast Cox1 Revealed By Its Genetic Interaction With Cox10, Megan Bestwick, Oleh Khalimonchuk, Fabien Pierrel, Dennis R. Winge

Department of Biochemistry: Faculty Publications

Saccharomyces cerevisiae cells lacking the cytochrome c oxidase (CcO) assembly factor Coa2 are impaired in Cox1 maturation and exhibit a rapid degradation of newly synthesized Cox1. The respiratory deficiency of coa2 Δ cells is suppressed either by the presence of a mutant allele of the Cox10 farnesyl transferase involved in heme a biosynthesis or through impaired proteolysis by the disruption of the mitochondrial Oma1 protease. Cox10 with an N196K substitution functions as a robust gain-of-function suppressor of the respiratory deficiency of coa2 Δ cells but lacks suppressor activity for two other CcO assembly mutant strains, the coa1 Δ and shy1 …

Transgenic Rat Model Of Neurodegeneration Caused By Mutation In The Tdp Gene, Hongxia Zhou, Cao Huang, Han Chen, Dian Wang, Carlisle P. Landel, Pedro Yuxing Xia, Robert Bowser, Yong-Jian Liu, Xu Gang Xia

Nebraska Center for Biotechnology: Faculty and Staff Publications

TDP-43 proteinopathies have been observed in a wide range of neurodegenerative diseases. Mutations in the gene encoding TDP-43 (i.e., TDP) have been identified in amyotrophic lateral sclerosis (ALS) and in frontotemporal lobe degeneration associated with motor neuron disease. To study the consequences of TDP mutation in an intact system, we created transgenic rats expressing normal human TDP or a mutant form of human TDP with a M337V substitution. Overexpression of mutant, but not normal, TDP caused widespread neurodegeneration that predominantly affected the motor system. TDP mutation reproduced ALS phenotypes in transgenic rats, as seen by progressive degeneration of motor neurons …

A Study On Cell Suspension Cultures For Micropropagation And The Production Of Carpaine From Papaya (Carica Papaya L. Var. Eksotika)., Mohamad Fhaizal Mohamad Bukhori

Student Works (2010-2019)

Carica papaya L. is a member of Caricaceae family with four native genera. This fruit is economically important as in multi-purpose fruit produced for dessert and vegetable and is highly in demand for pharmaconomical trade particularly the plant compound as source of medicine. This species is a popular fruit crop in the tropical and sub-tropical regions of Malaysia, Thailand, Indonesia and the Philippines. It is also one of the most widely grown fruits in Malaysia and is mainly cultivated in Johor, Perak and Selangor. The Eksotika papaya variety was introduced to the farmers in the late eighties and this resulted …