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University of Nebraska - Lincoln

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Articles 331 - 360 of 1329

Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

Downregulation Of A Cyp74 Rubber Particle Protein Increases Natural Rubber Production In Parthenium Argentatum, Dante F. Placido, Niu Dong, Chen Dong, Von Mark V. Cruz, David A. Dierig, Rebecca E. Cahoon, Byung-Guk Kang, Trinh Huynh, Maureen Whalen, Grisel Ponciano, Colleen Mcmahan Jan 2019

Downregulation Of A Cyp74 Rubber Particle Protein Increases Natural Rubber Production In Parthenium Argentatum, Dante F. Placido, Niu Dong, Chen Dong, Von Mark V. Cruz, David A. Dierig, Rebecca E. Cahoon, Byung-Guk Kang, Trinh Huynh, Maureen Whalen, Grisel Ponciano, Colleen Mcmahan

Department of Biochemistry: Faculty Publications

We report functional genomics studies of a CYP74 rubber particle protein from Parthenium argentatum, commonly called guayule. Previously identified as an allene oxide synthase (AOS), this CYP74 constitutes the most abundant protein found in guayule rubber particles. Transgenic guayule lines with AOS gene expression down-regulated by RNAi (AOSi) exhibited strong phenotypes that included agricultural traits conducive to enhancing rubber yield. AOSi lines had higher leaf and stem biomass, thicker stembark tissues, increased stem branching and improved net photosynthetic rate. Importantly, the rubber content was significantly increased in AOSi lines compared to the wild-type (WT), vector control and …

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Novel Amphiphilic Cyclobutene And Cyclobutane Cis-C18 Fatty Acid Derivatives Inhibit Mycobacterium Avium Subsp. Paratuberculosis Growth, Denise K. Zinniel, Wantanee Sittiwong, Darrell D. Marshall, Govardhan Rathnaiah, Isin T. Sakallioglu, Robert Powers, Patrick H. Dussault, Raul G. Barletta Jan 2019

Novel Amphiphilic Cyclobutene And Cyclobutane Cis-C18 Fatty Acid Derivatives Inhibit Mycobacterium Avium Subsp. Paratuberculosis Growth, Denise K. Zinniel, Wantanee Sittiwong, Darrell D. Marshall, Govardhan Rathnaiah, Isin T. Sakallioglu, Robert Powers, Patrick H. Dussault, Raul G. Barletta

School of Veterinary and Biomedical Sciences: Faculty Publications

Mycobacterium avium subspecies paratuberculosis (Map) is the etiologic agent of Johne’s disease in ruminants and has been associated with Crohn’s disease in humans. An effective control of Map by either vaccines or chemoprophylaxis is a paramount need for veterinary and possibly human medicine. Given the importance of fatty acids in the biosynthesis of mycolic acids and the mycobacterial cell wall, we tested novel amphiphilic C10 and C18 cyclobutene and cyclobutane fatty acid derivatives for Map inhibition. Microdilution minimal inhibitory concentrations (MIC) with 5 or 7 week endpoints were measured in Middlebrook 7H9 base broth media. We compared the …

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Investigation Of Congestive Heart Failure In Beef Cattle In A Feedyard At A Moderate Altitude In Western Nebraska, Rodney A. Moxley, David R. Smith, Dale M. Grotelueschen, Tom Edwards, David Steffen Jan 2019

Investigation Of Congestive Heart Failure In Beef Cattle In A Feedyard At A Moderate Altitude In Western Nebraska, Rodney A. Moxley, David R. Smith, Dale M. Grotelueschen, Tom Edwards, David Steffen

School of Veterinary and Biomedical Sciences: Faculty Publications

Right-sided congestive heart failure (brisket disease) commonly occurs in cattle raised at elevations >2,500– 3,500 m. We investigated clinical cases resembling brisket disease at a western Nebraska feedyard at a moderate altitude (1,369 m). Over a 15-mo period (2009–2010), we examined 17 cases (16 steers and 1 heifer), all purebred Angus. All animals had clinical right-sided heart failure: brisket and ventral abdominal edema, and severe chronic passive congestion of the liver. Gross examination confirmed right ventricular hypertrophy (left ventricle plus septum: right ventricle weight ratio mean: 1.33 vs. 2.8–4.0 reference interval). Microscopically, all 17 cases had interstitial fibrosis (mean score: …

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Changes On Movement Control Of Dart Throwing Under Distance And Target Weight Constraints, Carlos E. Campos, Guilherme M. Lage, Andre G.P. Andrade, Crislaine R. Couto, Suziane P. Santos, Vitor L.S. Profeta, Herbert Ugrinowitsch Jan 2019

Changes On Movement Control Of Dart Throwing Under Distance And Target Weight Constraints, Carlos E. Campos, Guilherme M. Lage, Andre G.P. Andrade, Crislaine R. Couto, Suziane P. Santos, Vitor L.S. Profeta, Herbert Ugrinowitsch

Athletic Performance Research

The aim of the study was to verify the effects of dart weight and target distance on kinematic variables of the movement control of the underarm dart throwing task. Four women and one man performed the task of throwing a dart at two horizontal circular targets located at 2m (Nt) and 3m (Ft) away, with two different weights, 22g (Ld) and 44g (Hd). On the first phase of the experiment, the human volunteers performed 200 trials per day during four sessions. On the fifth day, it had 40 more trials in a pseudo random order that were recorded and analysed. …

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Biomass Yield In A Genetically Diverse Miscanthus Sinensis Germplasm Panel Evaluated At Five Locations Revealed Individuals With Exceptional Potential, Lindsay V. Clark, Maria S. Dwiyanti, Kossonou G. Anzoua, Joe E. Brummer, Bimal Kumar Ghimire, Katarzyna Glowacka, Megan Hall, Kweon Heo, Xiaoli Jin, Alexander E. Lipka, Junhua Peng, Toshihiko Yamada, Ji Hye Yoo, Chang Yeon Yu, Hua Zhao, Stephen P. Long, Erik J. Sacks Jan 2019

Biomass Yield In A Genetically Diverse Miscanthus Sinensis Germplasm Panel Evaluated At Five Locations Revealed Individuals With Exceptional Potential, Lindsay V. Clark, Maria S. Dwiyanti, Kossonou G. Anzoua, Joe E. Brummer, Bimal Kumar Ghimire, Katarzyna Glowacka, Megan Hall, Kweon Heo, Xiaoli Jin, Alexander E. Lipka, Junhua Peng, Toshihiko Yamada, Ji Hye Yoo, Chang Yeon Yu, Hua Zhao, Stephen P. Long, Erik J. Sacks

Department of Biochemistry: Faculty Publications

To breed improved biomass cultivars of Miscanthus ×giganteus, it will be necessary to select the highest‐yielding and best‐adapted genotypes of its parental species, Miscanthus sinensis and Miscanthus sacchariflorus. We phenotyped a diverse clonally propagated panel of 569 M. sinensis and nine natural diploid M. ×giganteus at one subtropical (Zhuji, China) and five temperate locations (Sapporo, Japan; Leamington, Ontario, Canada; Fort Collins, CO; Urbana, IL; and Chuncheon, Korea) for dry biomass yield and 14 yield‐component traits, in trials grown for 3 years. Notably, dry biomass yield of four Miscanthus accessions exceeded 80 Mg/ha in Zhuji, China, approaching …

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An Arabidopsis Protoplast Isolation Method Reduces Cytosolic Acidification And Activation Of The Chloroplast Stress Sensor Sensitive To Freezing 2, Allison C. Barnes, Christian G. Elowsky, Rebecca Roston Jan 2019

An Arabidopsis Protoplast Isolation Method Reduces Cytosolic Acidification And Activation Of The Chloroplast Stress Sensor Sensitive To Freezing 2, Allison C. Barnes, Christian G. Elowsky, Rebecca Roston

Department of Biochemistry: Faculty Publications

Chloroplasts adapt to freezing and other abiotic stresses in part by modifying their membranes. One key-remodeling enzyme is SENSITIVE TO FREEZING2 (SFR2). SFR2 is unusual because it does not respond to initial cold stress or cold acclimation, instead it responds during freezing conditions in Arabidopsis. This response has been shown to be sensitive to cytosolic acidification. The unique lipid products of SFR2 have also been detected in response to non-freezing stresses, but what causes SFR2 to respond in these stresses is unknown. Here, we investigate protoplast isolation as a representative of wounding stress. We show that SFR2 oligogalactolipid products accumulate …

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Ehdv-2 Infection Prevalence Varies In Culicoides Sonorensis After Feeding On Infected White-Tailed Deer Over The Course Of Viremia, Sandra Y. Mendiola, Mary K. Mills, Elin Maki, Barbara S. Drolet, William C. Wilson, Roy D. Berghaus, David E. Stallknecht, Jonathan Breitenbach, D. Scott Mcvey, Mark G. Ruder Jan 2019

Ehdv-2 Infection Prevalence Varies In Culicoides Sonorensis After Feeding On Infected White-Tailed Deer Over The Course Of Viremia, Sandra Y. Mendiola, Mary K. Mills, Elin Maki, Barbara S. Drolet, William C. Wilson, Roy D. Berghaus, David E. Stallknecht, Jonathan Breitenbach, D. Scott Mcvey, Mark G. Ruder

School of Veterinary and Biomedical Sciences: Faculty Publications

Epizootic hemorrhagic disease viruses (EHDVs) are arboviral pathogens of white-tailed deer and other wild and domestic ruminants in North America. Transmitted by various species of Culicoides, EHDVs circulate wherever competent vectors and susceptible ruminant host populations co-exist. The impact of variation in the level and duration of EHDV viremia in white-tailed deer (Odocoileus virginianus) on Culicoides infection prevalence is not well characterized. Here we examined how infection prevalence in a confirmed North American vector of EHDV-2 (Culicoides sonorensis) varies in response to fluctuations in deer viremia. To accomplish this, five white-tailed deer were experimentally infected with EHDV-2 and colonized C. …

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Treatment Of Plastic Wastes Using Plasma Gasification Technology, Zachary Homolka Jan 2019

Treatment Of Plastic Wastes Using Plasma Gasification Technology, Zachary Homolka

Honors Program: Senior Projects (Public)

Plasma gasification (PG) complements traditional recycling when applied to contaminated or mixed plastics. Without PG these plastics cost recyclers more to process than they are worth on the market, and sometimes they are landfilled or incinerated instead of being recycled. Plasma gasification can take plastic not suitable for traditional recycling and break it down into high-quality syngas for use in electricity generation, chemical manufacturing, or hydrogen production. The technology can be implemented without changing the behavior of consumers, which is a major advantage over attempting to decrease contamination or reduce use of low-value plastic. Due to high capital requirements and …

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Pancreas Of Coxsackievirus-Infected Dams And Their Challenged Pups: A Complex Issue, Sona Sarmirova, Maria Borsanyiova, Brigita Benkoova, Michaela Pospisilova, Rajkumar Rajasekaran, Katarina Berakova, Pavol Gomolcak, Jay Reddy, Shubhada Bopegamage Jan 2019

Pancreas Of Coxsackievirus-Infected Dams And Their Challenged Pups: A Complex Issue, Sona Sarmirova, Maria Borsanyiova, Brigita Benkoova, Michaela Pospisilova, Rajkumar Rajasekaran, Katarina Berakova, Pavol Gomolcak, Jay Reddy, Shubhada Bopegamage

School of Veterinary and Biomedical Sciences: Faculty Publications

Enteroviral infections are frequent, often asymptomatic in humans and during gravidity. The present study is an extension of our previous investigations where we had shown pancreatitis in challenged pups of CVB4-E2-infected dams. Present investigation describes the effect of gestational infection with this virus on the pancreas of both dams and their challenged pups. Gravid CD1 outbred mice were orally infected with CVB4-E2 virus at different gestation times. Pups were challenged orally with the same virus after 25 days of birth. Organs were collected at selected intervals postinfection (p.i.), and replicating virus and viral-RNA copies were analyzed. Additional readouts included histopathology …

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The Role Of Isothiocyanates As Cancer Chemo‐Preventive, Chemo‐Therapeutic And Anti‐Melanoma Agents, Melina Mitsiogianni, Georgios Koutsidis, Nikos Mavroudis, Dimitrios T. Trafalis, Sotiris Botaitis, Rodrigo Franco, Vasilis Zoumpourlis, Tom Amery, Alex Galanis, Aglaia Pappa, Mihalis I. Panayiotidis Jan 2019

The Role Of Isothiocyanates As Cancer Chemo‐Preventive, Chemo‐Therapeutic And Anti‐Melanoma Agents, Melina Mitsiogianni, Georgios Koutsidis, Nikos Mavroudis, Dimitrios T. Trafalis, Sotiris Botaitis, Rodrigo Franco, Vasilis Zoumpourlis, Tom Amery, Alex Galanis, Aglaia Pappa, Mihalis I. Panayiotidis

School of Veterinary and Biomedical Sciences: Faculty Publications

Many studies have shown evidence in support of the beneficial effects of phytochemicals in preventing chronic diseases, including cancer. Among such phytochemicals, sulphur‐containing compounds (e.g., isothiocyanates (ITCs)) have raised scientific interest by exerting unique chemopreventive properties against cancer pathogenesis. ITCs are the major biologically active compounds capable of mediating the anticancer effect of cruciferous vegetables. Recently, many studies have shown that a higher intake of cruciferous vegetables is associated with reduced risk of developing various forms of cancers primarily due to a plurality of effects, including (i) metabolic activation and detoxification, (ii) inflammation, (iii) angiogenesis, (iv) metastasis and (v) regulation …

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Viral Emergence In Marine Mammals In The North Pacific May Be Linked To Arctic Sea Ice Reduction, Elizabeth Vanwormer, J. A.K. Mazet, A. Hall, V. A. Gill, P. L. Boveng, J. M. London, T. Gelatt, B. S. Fadely, M. E. Lander, J. Sterling, V. N. Burkanov, R. R. Ream, P. M. Brock, L. D. Rea, B. R. Smith, A. Jeffers, M. Henstock, M. J. Rehberg, K. A. Burek-Huntington, S. L. Crosby, J. A, Hammond, T. Goldstein Jan 2019

Viral Emergence In Marine Mammals In The North Pacific May Be Linked To Arctic Sea Ice Reduction, Elizabeth Vanwormer, J. A.K. Mazet, A. Hall, V. A. Gill, P. L. Boveng, J. M. London, T. Gelatt, B. S. Fadely, M. E. Lander, J. Sterling, V. N. Burkanov, R. R. Ream, P. M. Brock, L. D. Rea, B. R. Smith, A. Jeffers, M. Henstock, M. J. Rehberg, K. A. Burek-Huntington, S. L. Crosby, J. A, Hammond, T. Goldstein

School of Veterinary and Biomedical Sciences: Faculty Publications

Climate change-driven alterations in Arctic environments can influence habitat availability, species distributions and interactions, and the breeding, foraging, and health of marine mammals. Phocine distemper virus (PDV), which has caused extensive mortality in Atlantic seals, was confirmed in sea otters in the North Pacific Ocean in 2004, raising the question of whether reductions in sea ice could increase contact between Arctic and sub-Arctic marine mammals and lead to viral transmission across the Arctic Ocean. Using data on PDV exposure and infection and animal movement in sympatric seal, sea lion, and sea otter species sampled in the North Pacific Ocean from …

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Visualizing The Invisible: A Guide To Designing, Printing, And Incorporating Dynamic 3d Molecular Models To Teach Structure–Function Relationships, Michelle Howell, Karin Van Dijk, Christine S. Booth, Tomáš Helikar, Brain A. Couch, Rebecca Roston Jan 2019

Visualizing The Invisible: A Guide To Designing, Printing, And Incorporating Dynamic 3d Molecular Models To Teach Structure–Function Relationships, Michelle Howell, Karin Van Dijk, Christine S. Booth, Tomáš Helikar, Brain A. Couch, Rebecca Roston

Department of Biochemistry: Faculty Publications

Understanding the intricate relationship between macromolecular structure and function represents a central goal of undergraduate biology education (1–3). In teaching complex three-dimensional (3D) concepts, instructors typically depend on static two-dimensional (2D) textbook images or computer-based visualization software, which can lead to unintended misconceptions (4–6). While chemical and molecular kits exist, these models cannot handle the size and detail of macromolecules. Consequently, students may graduate in the life sciences without understanding how structure underlies function or acquiring skills to translate between 2D and 3D molecular models (5, 7). Building on recent technological advances, 3D printing (3DP) potentiates an era in which …

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Autophagy In Adipocyte Browning: Emerging Drug Target For Intervention In Obesity, Seung-Hyun Ro, Yura Jang, Jiyoung Bae, Isaac M. Kim, Cameron Schaecher, Zachery D. Shomo Jan 2019

Autophagy In Adipocyte Browning: Emerging Drug Target For Intervention In Obesity, Seung-Hyun Ro, Yura Jang, Jiyoung Bae, Isaac M. Kim, Cameron Schaecher, Zachery D. Shomo

Department of Biochemistry: Faculty Publications

Autophagy, lipophagy, and mitophagy are considered to be the major recycling processes for protein aggregates, excess fat, and damaged mitochondria in adipose tissues in response to nutrient status-associated stress, oxidative stress, and genotoxic stress in the human body. Obesity with increased body weight is often associated with white adipose tissue (WAT) hypertrophy and hyperplasia and/or beige/brown adipose tissue atrophy and aplasia, which significantly contribute to the imbalance in lipid metabolism, adipocytokine secretion, free fatty acid release, and mitochondria function. In recent studies, hyperactive autophagy in WAT was observed in obese and diabetic patients, and inhibition of adipose autophagy through targeted …

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Dna Uptake By Type Iv Filaments, Kurt H. Piepenbrink Jan 2019

Dna Uptake By Type Iv Filaments, Kurt H. Piepenbrink

Department of Biochemistry: Faculty Publications

Bacterial uptake of DNA through type IV filaments is an essential component of natural competence in numerous gram-positive and gram-negative species. Recent advances in the field have broadened our understanding of the structures used to take up extracellular DNA. Here, we review seminal experiments in the literature describing DNA binding by type IV pili, competence pili and the flp pili of Micrococcus luteus; collectively referred to here as type IV filaments. We compare the current state of the field on mechanisms of DNA uptake for these three appendage systems and describe the current mechanistic understanding of both DNA-binding and …

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Student Understanding Of Dna Structure–Function Relationships Improves From Using 3d Learning Modules With Dynamic 3d Printed Models, Michelle E. Howell, Christine S. Booth, Sharmin M. Sikich, Tomáš Helikar, Rebecca Roston, Brain A. Couch, Karin Van Dijk Jan 2019

Student Understanding Of Dna Structure–Function Relationships Improves From Using 3d Learning Modules With Dynamic 3d Printed Models, Michelle E. Howell, Christine S. Booth, Sharmin M. Sikich, Tomáš Helikar, Rebecca Roston, Brain A. Couch, Karin Van Dijk

Department of Biochemistry: Faculty Publications

Understanding the relationship between molecular structure and function represents an important goal of undergraduate life sciences. Although evidence suggests that handling physical models supports gains in student understanding of structure–function relationships, such models have not been widely implemented in biochemistry classrooms. Three-dimensional (3D) printing represents an emerging cost-effective means of producing molecular models to help students investigate structure–function concepts. We developed three interactive learning modules with dynamic 3D printed models to help biochemistry students visualize biomolecular structures and address particular misconceptions. These modules targeted specific learning objectives related to DNA and RNA structure, transcription factor-DNA interactions, and DNA supercoiling dynamics. …

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Winter Hardiness Of Miscanthus (Iii): Genome‐Wide Association And Genomic Prediction For Overwintering Ability In Miscanthus Sinensis, Hongxu Dong, Lindsay V. Clark, Alexander E. Lipka, Joe E. Brummer, Katarzyna Glowacka, Megan C. Hall, Kweon Heo, Xiaoli Jin, Junhua Peng, Toshihiko Yamada, Bimal Kumar Ghimire, Ji Hye Yoo, Chang Yeon Yu, Hua Zhao, Stephen P. Long, Erik J. Sacks Jan 2019

Winter Hardiness Of Miscanthus (Iii): Genome‐Wide Association And Genomic Prediction For Overwintering Ability In Miscanthus Sinensis, Hongxu Dong, Lindsay V. Clark, Alexander E. Lipka, Joe E. Brummer, Katarzyna Glowacka, Megan C. Hall, Kweon Heo, Xiaoli Jin, Junhua Peng, Toshihiko Yamada, Bimal Kumar Ghimire, Ji Hye Yoo, Chang Yeon Yu, Hua Zhao, Stephen P. Long, Erik J. Sacks

Department of Biochemistry: Faculty Publications

Overwintering ability is an important selection criterion for Miscanthus breeding in temperate regions. Insufficient overwintering ability of the currently leading Miscanthus biomass cultivar, M. ×giganteus (M×g) ‘1993–1780’, in regions where average annual minimum temperatures are −26.1°C (USDA hardiness zone 5) or lower poses a pressing need to develop new cultivars with superior cold tolerance. To facilitate breeding of Miscanthus, this study characterized phenotypic and genetic variation of overwintering ability in an M. sinensis germplasm panel consisting of 564 accessions, evaluated in field trials at three locations in North America and two in Asia. Genome‐wide association (GWA) and genomic …

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Chronic Alcohol Exposure Alters Circulating Insulin And Ghrelin Levels: Role Of Ghrelin In Hepatic Steatosis, Karuna Rasineni, Paul G. Thomes, Jacy L. Kubik, Edward N. Harris, Kusum K. Kharbanda, Carol A. Casey Jan 2019

Chronic Alcohol Exposure Alters Circulating Insulin And Ghrelin Levels: Role Of Ghrelin In Hepatic Steatosis, Karuna Rasineni, Paul G. Thomes, Jacy L. Kubik, Edward N. Harris, Kusum K. Kharbanda, Carol A. Casey

Department of Biochemistry: Faculty Publications

Fatty liver is the earliest response of the liver to excessive ethanol consumption. Central in the development of alcoholic steatosis is increased mobilization of nonesterified free fatty acids (NEFAs) to the liver from the adipose tissue. In this study, we hypothesized that ethanol-induced increase in ghrelin by impairing insulin secretion, could be responsible for the altered lipid metabolism observed in adipose and liver tissue. Male Wistar rats were fed for 5–8 wk with control or ethanol Lieber-DeCarli diet, followed by biochemical analyses in serum and liver tissues. In addition, in vitro studies were conducted on pancreatic islets isolated from experimental …

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The Mitochondrial Nad+ Transporter (Ndt1) Plays Important Roles In Cellular Nad+ Homeostasis In Arabidopsis Thaliana, Izabel De Souza Chaves, Elias Feitosa-Araujo, Alexandra Florian, David B. Medeiros, Paula Da Fonseca-Pereira, Lennart Charton, Elmien Heyneke, Jorge A. C. Apfata, Marcel V. Pires, Tabea Mettler-Altmann, Wagner L. Arajuo, H. Ekkehard Neuhaus, Ferdinando Palmieri, Toshihiro Obata, Andreas P. M. Weber, Nicole Linka, Alisdair R. Femie, Adriano Nunes-Nesi Jan 2019

The Mitochondrial Nad+ Transporter (Ndt1) Plays Important Roles In Cellular Nad+ Homeostasis In Arabidopsis Thaliana, Izabel De Souza Chaves, Elias Feitosa-Araujo, Alexandra Florian, David B. Medeiros, Paula Da Fonseca-Pereira, Lennart Charton, Elmien Heyneke, Jorge A. C. Apfata, Marcel V. Pires, Tabea Mettler-Altmann, Wagner L. Arajuo, H. Ekkehard Neuhaus, Ferdinando Palmieri, Toshihiro Obata, Andreas P. M. Weber, Nicole Linka, Alisdair R. Femie, Adriano Nunes-Nesi

Department of Biochemistry: Faculty Publications

Nicotinamide adenine dinucleotide (NAD+) is an essential coenzyme required for all living organisms. In eukaryotic cells, the final step of NAD+ biosynthesis is exclusively cytosolic. Hence, NAD+ must be imported into organelles to support their metabolic functions. Three NAD+ transporters belonging to the mitochondrial carrier family (MCF) have been biochemically characterized in plants. AtNDT1 (At2g47490), focus of the current study, AtNDT2 (At1g25380), targeted to the inner mitochondrial membrane, and AtPXN (At2g39970), located in the peroxisomal membrane. Although AtNDT1 was presumed to reside in the chloroplast …

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Acyltransferases And Methods Of Using, Edgar Cahoon, Umidjon Iskandarov, Hae Jin Kim, Jillian Collins-Silva Jan 2019

Acyltransferases And Methods Of Using, Edgar Cahoon, Umidjon Iskandarov, Hae Jin Kim, Jillian Collins-Silva

Department of Biochemistry: Faculty Publications

Provided herein are novel acyltransferases and methods of using such novel acyltransferases in making medium - chain fatty acids.

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Charting A New Frontier Of Science By Integrating Mathematical Modeling To Understand And Predict Complex Biological Systems, Katharine White, Kira Mcentire, Nicole R. Buan, Kingshuk Ghosh, Lecia Robinson, Elisar Barbar Jan 2019

Charting A New Frontier Of Science By Integrating Mathematical Modeling To Understand And Predict Complex Biological Systems, Katharine White, Kira Mcentire, Nicole R. Buan, Kingshuk Ghosh, Lecia Robinson, Elisar Barbar

Department of Biochemistry: Faculty Publications

Biological systems are staggeringly complex. To untangle this complexity and make predictions about biological systems is a continuous goal of biological research. One approach to achieve these goals is to emphasize the use of quantitative measures of biological processes. Advances in quantitative biology data collection and analysis across scales (molecular, cellular, organismal, ecological) has transformed how we understand, categorize, and predict complex biological systems. Simultaneously, thanks to increased computational power, mathematicians, engineers and physical scientists -- collectively termed theoreticians -- have developed sophisticated models of biological systems at different scales. But there is still a disconnect between the two fields. …

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Fatty Acid Transporter 2 Reprograms Neutrophils In Cancer, Filippo Veglia, Vladimir A. Tyurin, Maria Blasi, Alessandra De Leo, Andrew Kossenkov, Laxminarasimha Donthireddy, To Tsun Ki Jerrick, Zach Schug, Subhasree Basu, Fang Wang, Emanuela Ricciotti, Concetta C. Dirusso, Maureen E. Murphy, Robert H. Vonderheide, Paul M. Lieberman, Charles Mulligan, Brian Nam, Neil Hockstein, Gregory Masters, Michael Guarino, Cindy Lin, Yulia Nefedova, Paul N. Black, Valerian E, Kagan, Dmitry Gabrilovich Jan 2019

Fatty Acid Transporter 2 Reprograms Neutrophils In Cancer, Filippo Veglia, Vladimir A. Tyurin, Maria Blasi, Alessandra De Leo, Andrew Kossenkov, Laxminarasimha Donthireddy, To Tsun Ki Jerrick, Zach Schug, Subhasree Basu, Fang Wang, Emanuela Ricciotti, Concetta C. Dirusso, Maureen E. Murphy, Robert H. Vonderheide, Paul M. Lieberman, Charles Mulligan, Brian Nam, Neil Hockstein, Gregory Masters, Michael Guarino, Cindy Lin, Yulia Nefedova, Paul N. Black, Valerian E, Kagan, Dmitry Gabrilovich

Department of Biochemistry: Faculty Publications

Polymorphonuclear myeloid derived suppressor cells (PMN-MDSC) are pathologically activated neutrophils that are critically important for the regulation of immune responses in cancer. They contribute to the failure of cancer therapies and are associated with poor clinical outcomes. Despite the recent advances in understanding of the PMN-MDSC biology, the mechanisms responsible for pathological activation of neutrophils are not well defined, which limits selective targeting of these cells. Here, we report that mouse and human PMN-MDSC exclusively up-regulate fatty acid transporter protein 2 (FATP2). Over-expression of FATP2 in PMN-MDSC was controlled by GM-CSF, through the activation of STAT5 transcription factor. Deletion of …

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Arsenite Exposure Suppresses Adipogenesis, Mitochondrial Biogenesis And Thermogenesis Via Autophagy Inhibition In Brown Adipose Tissue, Jiyoung Bae, Yura Jang, Heejeong Kim, Kalika Mahato, Cameron Schaecher, Issac M. Kim, Eunju Kim, Seung-Hyun Ro Jan 2019

Arsenite Exposure Suppresses Adipogenesis, Mitochondrial Biogenesis And Thermogenesis Via Autophagy Inhibition In Brown Adipose Tissue, Jiyoung Bae, Yura Jang, Heejeong Kim, Kalika Mahato, Cameron Schaecher, Issac M. Kim, Eunju Kim, Seung-Hyun Ro

Department of Biochemistry: Faculty Publications

Arsenite, a trivalent form of arsenic, is an element that occurs naturally in the environment. Humans are exposed to high dose of arsenite through consuming arsenite-contaminated drinking water and food, and the arsenite can accumulate in the human tissues. Arsenite induces oxidative stress, which is linked to metabolic disorders such as obesity and diabetes. Brown adipocytes dissipating energy as heat have emerging roles for obesity treatment and prevention. therefore, understanding the pathophysiological role of brown adipocytes can provide effective strategies delineating the link between arsenite exposure and metabolic disorders. Our study revealed that arsenite significantly reduced differentiation of murine brown …

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The Structure Of Pila From Acinetobacter Baumannii Ab5075 Suggests A Mechanism For Functional Specialization In Acinetobacter Type Iv Pili, Leslie A. Ronish, Erik Lillehoj, James K. Fields, Eric J. Sundberg, Kurt Piepenbrink Jan 2019

The Structure Of Pila From Acinetobacter Baumannii Ab5075 Suggests A Mechanism For Functional Specialization In Acinetobacter Type Iv Pili, Leslie A. Ronish, Erik Lillehoj, James K. Fields, Eric J. Sundberg, Kurt Piepenbrink

Department of Biochemistry: Faculty Publications

Type IV pili (T4P) are bacterial appendages composed of protein subunits, called pilins, noncovalently assembled into helical fibers. T4P are essential, in many bacterial species, for processes as diverse as twitching motility, natural competence, biofilm or microcolony formation, and host cell adhesion. The genes encoding type IV pili are found universally in the Gram-negative, aerobic, nonflagellated, and pathogenic coccobacillus Acinetobacter baumannii, but there is considerable variation in PilA, the major protein subunit, both in amino acid sequence and in glycosylation patterns. Here we report the X-ray crystal structure of PilA from AB5075, a recently characterized, highly virulent isolate, at …

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Methanogens: Pushing The Boundaries Of Biology, Nicole R. Buan Dec 2018

Methanogens: Pushing The Boundaries Of Biology, Nicole R. Buan

Department of Biochemistry: Faculty Publications

Methanogens are anaerobic archaea that grow by producing methane gas. These microbes and their exotic metabolism have inspired decades of microbial physiology research that continues to push the boundary of what we know about how microbes conserve energy to grow. The study of methanogens has helped to elucidate the thermodynamic and bioenergetics basis of life, contributed our understanding of evolution and biodiversity, and has garnered an appreciation for the societal utility of studying trophic interactions between environmental microbes, as methanogens are important in microbial conversion of biogenic carbon into methane, a high-energy fuel. This review discusses the theoretical basis for …

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Methanogens: Pushing The Boundaries Of Biology, Nicole R. Buan Dec 2018

Methanogens: Pushing The Boundaries Of Biology, Nicole R. Buan

Department of Biochemistry: Faculty Publications

Methanogens are anaerobic archaea that grow by producing methane gas. These microbes and their exotic metabolism have inspired decades of microbial physiology research that continues to push the boundary of what we know about how microbes conserve energy to grow. The study of methanogens has helped to elucidate the thermodynamic and bioenergetics basis of life, contributed our understanding of evolution and biodiversity, and has garnered an appreciation for the societal utility of studying trophic interactions between environmental microbes, as methanogens are important in microbial conversion of biogenic carbon into methane, a high-energy fuel. This review discusses the theoretical basis for …

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Combining Mass Spectrometry And Nmr Improves Metabolite Detection And Annotation, Fatema Bhinderwala, Nishikant Wase, Concetta Dirusso, Robert Powers Nov 2018

Combining Mass Spectrometry And Nmr Improves Metabolite Detection And Annotation, Fatema Bhinderwala, Nishikant Wase, Concetta Dirusso, Robert Powers

Department of Biochemistry: Faculty Publications

Despite inherent complementarity, nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS) are routinely separately employed to characterize metabolomics samples. More troubling is the erroneous view that metabolomics is better served by exclusively utilizing MS. Instead, we demonstrate the importance of combining NMR and MS for metabolomics by using small chemical compound-treatments of Chlamydomonas reinhardtii as an illustrative example. A total of 102 metabolites were detected (82 by GC-MS, 20 by NMR and 22 by both techniques). Out of these 47 metabolites of interest were identified, where 14 metabolites were uniquely identified by NMR and 16 metabolites were uniquely identified …

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Mouse Genome-Wide Association Studies And Systems Genetics Uncover The Genetic Architecture Associated With Hepatic Pharmacokinetic And Pharmacodynamic Properties Of A Constrained Ethyl Antisense Oligonucleotide Targeting Malat1, Elaine Pirie, Shayoni Ray, Calvin Pan, Wuxia Fu, Andrew F. Powers, Danielle Polikoff, Colton M. Miller, Katrina M. Kudrna, Edward N. Harris, Aldons J. Lusis, Rosanne M. Crooke, Richard G. Lee Oct 2018

Mouse Genome-Wide Association Studies And Systems Genetics Uncover The Genetic Architecture Associated With Hepatic Pharmacokinetic And Pharmacodynamic Properties Of A Constrained Ethyl Antisense Oligonucleotide Targeting Malat1, Elaine Pirie, Shayoni Ray, Calvin Pan, Wuxia Fu, Andrew F. Powers, Danielle Polikoff, Colton M. Miller, Katrina M. Kudrna, Edward N. Harris, Aldons J. Lusis, Rosanne M. Crooke, Richard G. Lee

Department of Biochemistry: Faculty Publications

Antisense oligonucleotides (ASOs) have demonstrated variation of efficacy in patient populations. This has prompted our investigation into the contribution of genetic architecture to ASO pharmacokinetics (PK) and pharmacodynamics (PD). Genome wide association (GWA) and transcriptomic analysis in a hybrid mouse diversity panel (HMDP) were used to identify and validate novel genes involved in the uptake and efficacy of a single dose of a Malat1 constrained ethyl (cEt) modified ASO. The GWA of the HMDP identified two significant associations on chromosomes 4 and 10 with hepatic Malat1 ASO concentrations. Stabilin 2 (Stab2) and vesicle associated membrane protein 3 ( …

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Amino Acid Pop-Set: Model File Name: Amino-Acid-Wgrp-Pop_Sc3.Stl, Michelle Howell, Rebecca Roston Oct 2018

Amino Acid Pop-Set: Model File Name: Amino-Acid-Wgrp-Pop_Sc3.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model for protein primary structure. It consists of four amino acids (tryptophan, proline, arginine, and glycine) depicted in stick and space-fill representations, five peptide bonds depicted in space-fill, and an N-terminus and a C-terminus depicted in space-fill. It is designed so that students can make various peptides to explore the amount of space of the electron clouds of the amino acids and bonds, and explore the psi and phi angles for the peptides. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Amino acid pop-set”. This model has …

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Lipoprotein Signal Peptidase Ii: Model File Name: 5dir-Lipoii-Reps_Sc1-5.Stl, Michelle Howell, Rebecca Roston Oct 2018

Lipoprotein Signal Peptidase Ii: Model File Name: 5dir-Lipoii-Reps_Sc1-5.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model of lipoprotein signal peptidase II (PDB: 5DIR). It is designed with different regions of the protein depicted in space-filling, ribbon, stick, and backbone-only representations to explore protein secondary structure and illustrate how much space the protein takes up. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Lipoprotein signal peptidase II” and is intended to accompany the “Crambin”, “Cytochrome c” and “3 water molecules” models. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in …

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3 Water Molecules: Model File Name: 3hoh-Final.Stl, Michelle Howell, Rebecca Roston Oct 2018

3 Water Molecules: Model File Name: 3hoh-Final.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model of 3 water molecules depicted in space-fill. It is designed to the same scale as the “Lipoprotein signal peptidase II”, “Crambin”, and “Cytochrome c” models to illustrate the amount of space taken up by proteins. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “3 water molecules” and is intended to accompany the “Lipoprotein signal peptidase II”, “Crambin”, and “Cytochrome c” models. This model has been printed successfully using these parameters on Shapeways’ laser sintering …

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