Digital Commons Network^™

Switchgrass For Bioethanol And Other Value-Added Applications: A Review, Deepak R. Keshwani, Jay J. Cheng

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Switchgrass is a promising feedstock for value-added applications due to its high productivity, potentially low requirements for agricultural inputs and positive environmental impacts. The objective of this paper is to review published research on the conversion of switchgrass into bioethanol and other value-added products. Environmental benefits associated with switchgrass include the potential for carbon sequestration, nutrient recovery from runoff, soil remediation and provision of habitats for grassland birds. Pretreatment of switchgrass is required to improve the yields of fermentable sugars. Based on the type of pretreatment, glucose yields range from 70% to 90%, and xylose yields range from 70% to …

Plant Sterol And Policosanol Characterization Of Hexane Extracts From Grain Sorghum, Corn, And Their Ddgs, Caolina Leguizamón, Curtis L. Weller, Vicki L. Schlegel, Timothy P. Carr

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Plant sterols (PS) and policosanols (PC) have been attributed with plasma cholesterol-lowering properties in humans. Hexane extracts from grain sorghum, corn and their distillers dried grain with solubles (DDGS), an important co-product of ethanol production, contain these health promoting compounds, which could be used to develop health promoting dietary products. However, limited information is currently available regarding optimal methods of extraction and their influence on plant sterol or PC levels and compositions. Therefore, the objective of this study was to quantify lipids, particularly PS and PC extracted from grain sorghum and its DDGS using reflux and Soxtec methods. Corn and …

Thermal Degradation Kinetics Of Distillers Grains And Solubles In Nitrogen And Air, Lijun Wang, Ajay Kumar, Milford Hanna, Curtis L. Weller, D. D. Jones

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The pyrolysis and oxidation kinetics of distillers grains and solubles were determined using thermogravimetric analysis. The starting temperature of pyrolysis and oxidation of distillers grains and solubles increased with the increase of heating rate and initial moisture content. The pyrolysis and oxidation of distillers grains and solubles were completed at 650°C and 850°C, respectively, which were independent of the heating rate and the initial moisture content. The residual weights of distillers grains and solubles after pyrolysis and oxidation were 27.15% and 5.49% of the original dry mass of distillers grains and solubles. Thermogravimetrical analysis data was used to determine kinetic …

Indirect Land Use Emissions In The Life Cycle Of Biofuels: Regulations Vs. Science, Adam J. Liska, Richard K. Perrin

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Recent legislative mandates have been enacted at state and federal levels with the purpose of reducing life cycle greenhouse gas (GHG) emissions from transportation fuels. This legislation encourages the substitution of fossil fuels with “low-carbon” fuels. The burden is put on regulatory agencies to determine the GHG-intensity of various fuels, and those agencies naturally look to science for guidance. Even though much progress has been made in determining the direct life cycle emissions from the production of biofuels, the science underpinning the estimation of potentially significant emissions from indirect land use change (ILUC) is in its infancy. As legislation requires …

Sorghum Distillers Dried Grain Lipid Extract Increases Cholesterol Excretion And Decreases Plasma And Liver Cholesterol Concentration In Hamsters, Jia Tse Hoi, Curtis L. Weller, Vicki Schlegel, Susan L. Cuppett, Ji-Young Lee, Timothy P. Carr

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Grain sorghum is a rich source of phytochemicals. In this study, male hamsters were fed AIN-93M diets supplemented with a hexane-extractable lipid fraction from sorghum distillers dried grains with solubles (DDGS). Diets contained 0.0%, 0.5%, 1.0%, and 5.0% (w/w) DDGS lipid extract. After 4 wk, the 5.0% DDGS lipids group had significantly lower plasma non-HDL cholesterol and liver esterified cholesterol concentration. Fecal neutral sterol (i.e., cholesterol) excretion was significantly higher in the 5.0% DDGS lipids group compared to the other treatments (66% higher compared to controls). Bile acid excretion was not affected by DDGS lipid intake. Fecal cholesterol excretion was …

Antiproliferation Properties Of Grain Sorghum Dry Distiller’S Grain Lipids In Caco-2 Cells, Richard Zbasnik, Timothy P. Carr, Curtis L. Weller, Keum Taek Hwang, Lijun Wang, Susan L. Cuppett, Vicki Schlegel

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Antiproliferative properties of lipids extracted from grain sorghum (GS) dry distiller’s grain (DDG) were analyzed to determine the feasibility of developing GS coproducts as a source for human health dietary ingredients. The lipid extract of GSDDG was delivered to human colon carcinoma (Caco-2) cells by solubilizing 0−1000 μg/mL of GS-DDG lipids in 100 μg/mL increments with micelles. A significant reduction in cell viability (25−50%) resulted at treatment levels of 400−1000 μg/mL GS-DDG lipids (p < 0.05). Alternatively, total protein levels of cells treated with 400, 500, and 600 μg/mL of GS-DDG lipid were not significantly different from the control, indicating cell growth during the treatment period. Total cell counts for the control were not significantly different from the GS-DDG lipid treated cells, but dead cell counts increased by 10% for the latter sample with a concomitant increase of the intercellular protein lactate dehydrogenase leakage (30−40%) in the medium. Preliminary analysis by the fluorescence-activated cell method (FACs) demonstrated that nonviable cells were in either the early apoptotic, late apoptotic, or necrotic stage post-treatment with 400, 500, and 600 μg/mL GS-DDG lipids. Physiochemical characterization of the GS-DDG lipids used for the antiproliferation study showed the presence of vitamin E (predominantly γ-tocopherol), triacylglycerides (predominantly linoleic acid), policosanols, aldehydes, and sterols (predominantly campesterol and stigmasterol), each of which or as synergistic/additive group of constituents may be responsible for the antiproliferative effect.

Grand Challenges For Biological Engineering, Jeong-Yeol Yoon, Mark R. Riley

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Biological engineering will play a significant role in solving many of the world's problems in medicine, agriculture, and the environment. Recently the U.S. National Academy of Engineering (NAE) released a document "Grand Challenges in Engineering," covering broad realms of human concern from sustainability, health, vulnerability and the joy of living. Biological engineers, having tools and techniques at the interface between living and non-living entities, will play a prominent role in forging a better future. The 2010 Institute of Biological Engineering (IBE) conference in Cambridge, MA, USA will address, in part, the roles of biological engineering in solving the challenges presented …

Impact Of Microclimatic Data Measured Above Maize And Grass Canopies On Penman‐Monteith Reference Evapotranspiration Calculations, Suat Irmak, Lameck O. Odhiambo

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Estimation of reference evapotranspiration (ET_ref) using measured microclimatic data and the Penman‐Monteith (PM) method provides a powerful means of quantifying actual plant evapotranspiration (ET_a) needed for use in various disciplines. When applying the PM method to estimate ET_ref, it is desirable to measure the required microclimatic data over a reference grass or alfalfa surface rather than above non‐reference surfaces. However, in reality, establishing and maintaining a reference surface for long periods of time is a difficult task. Other surface energy balance systems, such as the Bowen ratio energy balance system (BREBS), eddy covariance system, …

Special Issue On Evapotranspiration Measurement And Modeling, Samuel Ortega-Farias, Suat Irmak, R. H. Cuenca

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Water availability for irrigation throughout the world has been reduced in recent years due to a combination of frequent droughts and competition for water resources among agricultural, industrial, and urban users. In addition, some major agricultural areas face moderate to significant reductions of rainfall, or changes in timing of stream flow due to changes in timing of snowmelt, as a result of global climate change. Under such conditions, sophisticated irrigation water management will be required to optimize water use efficiency and maintain sufficient levels of crop productivity and quality. A key factor to achieve these targets is the estimation of …

Integration Of An Extended Octagonal Ring Transducer And Soil Coulterometer For Identifying Soil Compaction, Santosh Pitla, L. G. Wells, S. A. Shearer

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The soil coulterometer is an “on‐the‐go” electro‐mechanical system which collects impedance force data at multiple depths using an oscillating coulter. During the initial testing (summer 2006), only vertical soil impedance force data was collected using a pressure sensor. To improve the performance of the coulterometer, an extended octagonal ring transducer was integrated into the system to collect both the horizontal and vertical impedance forces given by the soil. In the summer of 2007, data was collected using the revised sensor from a typical central Kentucky field setting in a 0.8‐ha (2‐acre) plot. Four passes were made with the coulterometer. Seventy …

N-Glycosylation Microheterogeneity And Site Occupancy Of An Asn-X-Cys Sequon In Plasma-Derived And Recombinant Protein C, Geun-Cheol Gil, William H. Velander, Kevin E. Van Cott

Kevin Van Cott Publications

Human protein C (hPC) is glycosylated at three Asn-X-Ser/Thr and one atypical Asn-X-Cys sequons. We have characterized the micro- and macro-heterogeneity of plasma-derived hPC and compared the glycosylation features with recombinant protein C (tg-PC) produced in a transgenic pig bioreactor from two animals having approximately tenfold different expression levels. The N-glycans of hPC are complex di- and tri-sialylated structures, and we measured 78% site occupancy at Asn-329 (the Asn-X-Cys sequon). The N-glycans of tg-PC are complex sialylated structures, but less branched and partially sialylated. The porcine mammary epithelial cells glycosylate the Asn-X-Cys sequon with a similar efficiency as human hepatocytes …

The Selenoproteome Of Clostridium Sp. Ohilas: Characterization Of Anaerobic Bacterial Selenoprotein Methionine Sulfoxide Reductase A, Hwa Young, Yan Zhang, Byung Cheon Lee, Jae-Ryong Kim, Vadim N. Gladyshev

Vadim Gladyshev Publications

Selenocysteine (Sec) is incorporated into proteins in response to UGA codons. This residue is frequently found at the catalytic sites of oxidoreductases. In this study, we characterized the selenoproteome of an anaerobic bacterium, Clostridium sp. (also known as Alkaliphilus oremlandii) OhILA, and identified 13 selenoprotein genes, five of which have not been previously described. One of the detected selenoproteins was methionine sulfoxide reductase A (MsrA), an antioxidant enzyme that repairs oxidatively damaged methionines in a stereospecific manner. To date, little is known about MsrA from anaerobes. We characterized this selenoprotein MsrA which had a single Sec residue at the catalytic …

X-Ray Fluorescence Microscopy Reveals The Role Of Selenium In Spermatogenesis, Sebastian Kehr, Mikalai I. Malinouski, Lydia Finney, Stefan Vogt, Vyacheslav M. Labunskyy, Marina V. Kasaikina, Bradley A. Carlson, You Zhou, Dolph L. Hatfield, Vadim N. Gladyshev

Vadim Gladyshev Publications

Selenium (Se) is a trace element with important roles in human health. Several selenoproteins have essential functions in development. However, the cellular and tissue distribution of Se remains largely unknown because of the lack of analytical techniques that image this element with sufficient sensitivity and resolution. Herein, we report that X-ray fluorescence microscopy (XFM) can be used to visualize and quantify the tissue, cellular and subcellular topography of Se. We applied this technique to characterize the role of Se in spermatogenesis and identified a dramatic Se enrichment specifically in late spermatids, a pattern that was not seen in any other …

Comparative Genomic Analyses Of Nickel, Cobalt And Vitamin B12 Utilization, Yan Zhang, Dmitry Rodionov, Mikhail Gelfand, Vadim N. Gladyshev

Vadim Gladyshev Publications

Background: Nickel (Ni) and cobalt (Co) are trace elements required for a variety of biological processes. Ni is directly coordinated by proteins, whereas Co is mainly used as a component of vitamin B₁₂. Although a number of Ni and Co-dependent enzymes have been characterized, systematic evolutionary analyses of utilization of these metals are limited. Results: We carried out comparative genomic analyses to examine occurrence and evolutionary dynamics of the use of Ni and Co at the level of (i) transport systems, and (ii) metalloproteomes. Our data show that both metals are widely used in bacteria and archaea. Cbi/NikMNQO …

Eukaryotic Selenoproteins And Selenoproteomes, Alexey V. Lobanov, Dolph L. Hatfield, Vadim N. Gladyshev

Vadim Gladyshev Publications

Selenium is an essential trace element for which both beneficial and toxic effects in human health have been described. It is now clear that the importance of having adequate amounts of this micronutrient in the diet is primarily due to the fact that selenium is required for biosynthesis of selenocysteine, the twenty first naturally occurring amino acid in protein. In this review, we provide an overview of eukaryotic selenoproteins and selenoproteomes, which are sets of selenoproteins in these organisms. In eukaryotes, selenoproteins show a mosaic occurrence, with some organisms, such as vertebrates and algae, having dozens of these proteins, while …

Overexpression Of Methionine-R-Sulfoxide Reductases Has No Influence On Fruit Fly Aging, Valentina A. Shchedrina, Gerd Vorbrüggen, Byung Cheon Lee, Hwa-Young Kim, Hadise Kabil, Lawrence G. Harshman, Vadim N. Gladyshev

Vadim Gladyshev Publications

Methionine sulfoxide reductases (Msrs) are enzymes that repair oxidized methionine residues in proteins. This function implicated Msrs in antiox¬idant defense and the regulation of aging. There are two known Msr types in animals: MsrA specific for the reduction of methionine-S-sulfoxide, and MsrB that catalyzes the reduction of methionine-R-sulfoxide. In a previous study, overexpression of MsrA in the nervous system of Drosophila was found to extend lifespan by 70%. Overexpression of MsrA in yeast also extended lifespan, whereas MsrB overexpression did so only under cal¬orie restriction conditions. The effect of MsrB overexpression on lifespan has not yet been characterized in animal …

Characterization And Performance Of A Near-Infrared 2-Deoxyglucose Optical Imaging Agent For Mouse Cancer Models, Joy L. Kovar, William Volcheck, Eva Sevick-Muraca, Melanie A. Simpson, D. Michael Olive

Department of Biochemistry: Faculty Publications

Malignant neoplasms exhibit an elevated rate of glycolysis over normal cells. This characteristic can be exploited for optical imaging of tumors in mice. A near-infrared fluorophore, IRDye 800CW, emission maximum 794 nm, was conjugated to 2-deoxyglucose (2-DG). An immunofluorescent cell-based assay was used to evaluate specificity and sensitivity of the conjugate in cultured cell monolayers. Dose-dependent uptake was established with increasing concentrations of IRDye 800CW 2-DG for epithelial and prostate carcinomas. IRDye 800CW 2-DG was specifically blocked by an antibody against GLUT1 glucose transporter, and by excess unlabeled 2-DG or d-glucose. Signal was increased by a phorbol ester activator of …

Hyaluronan-Binding Proteoglycans, Ed Harris, Paul H. Weigel

Department of Biochemistry: Faculty Publications

Molecular components of the extracellular matrix (ECM) are critical for matrix stabilization, cellular differentiation, and tissue morphogenesis. Once thought to function only as the extracellular glue that primarily binds cells together, proteoglycans in the ECM carry out a diverse array of activities and can be grouped into five functionally based families: (i) hyalectins (lecticans), which contain lectin-like carbohydrate-recognition domains (CRDs) and bind hyaluronan (HA); (ii) heparan sulfate (HS) proteoglycans that sequester growth factors via their HS chains; (iii) small leucine-rich proteoglycans (SLRPs) containing leucine-rich domains that interact with collagens and other ECM proteins; (iv) phosphacans that function primarily as receptor-like …

Functional Aspects Of The Hyaluronan And Chondroitin Sulfate Receptors, Ed Harris, Paul H. Weigel

Department of Biochemistry: Faculty Publications

Glycosaminoglycans (GAGs) are distinct from other sugars/oligosaccharides in that they are polymers of disaccharide units composed of an amino sugar, N-acetylglucosamine (GlcNAc), or N-acetylgalactosamine (GalNAc), and uronic acid, glucuronic acid (GlcUA), or iduronic acid (IdUA). The exception is keratan sulfate (KS) in which the uronic acid is replaced by the neutral sugar galactose. Initially, GAGs were thought to be just part of an extracellular glue or ground substance that held tissues together and provided a liquid-like space between cells for the transport of nutrients. However, research using new technologies and techniques over the last two decades has revealed that the …

Polyploidy Creates Higher Diversity Among Cynodon Accessions As Assessed By Molecular Markers, Osman Gulsen, Songul Sever-Mutlu, Nedim Mutlu, Metin Tuna, Osman Karaguzel, Robert C. Shearman, Terrance P. Riordan, Tiffany M. Heng-Moss

Department of Biochemistry: Faculty Publications

Developing a better understanding of associations among ploidy level, geographic distribution, and genetic diversity of Cynodon accessions could be beneficial to bermudagrass breeding programs, and would enhance our understanding of the evolutionary biology of this warm season grass species. This study was initiated to: (1) determine ploidy analysis of Cynodon accessions collected from Turkey, (2) investigate associations between ploidy level and diversity, (3) determine whether geographic and ploidy distribution are related to nuclear genome variation, and (4) correlate among four nuclear molecular marker systems for Cynodon accessions’ genetic analyses. One hundred and eighty-two Cynodon accessions collected in Turkey from an …

Copper Transport Into The Secretory Pathway Is Regulated By Oxygen In Macrophages, Carine White, Taiho Kambe, Yan G. Fulcher, Sherri W. Sachdev, Ashley I. Bush, Kevin Fritsche, Jaekwon Lee, Thomas P. Quinn, Michael J. Petris

Department of Biochemistry: Faculty Publications

Copper is an essential nutrient for a variety of biochemical processes; however, the redox properties of copper also make it potentially toxic in the free form. Consequently, the uptake and intracellular distribution of this metal is strictly regulated. This raises the issue of whether specific pathophysiological conditions can promote adaptive changes in intracellular copper distribution. In this study, we demonstrate that oxygen limitation promotes a series of striking alterations in copper homeostasis in RAW264.7 macrophage cells. Hypoxia was found to stimulate copper uptake and to increase the expression of the copper importer, CTR1. This resulted in increased copper delivery to …

Targeting The Fatty Acid Transport Proteins (Fatp) To Understand The Mechanisms Linking Fatty Acid Transport To Metabolism, Paul N. Black, Angel Sandoval, Elsa Arias-Barrau, Concetta C. Dirusso

Department of Biochemistry: Faculty Publications

One principal process driving fatty acid transport is vectorial acylation, where fatty acids traverse the membrane concomitant with activation to CoA thioesters. Current evidence is consistent with the proposal that specific fatty acid transport (FATP) isoforms alone or in concert with specific long chain acyl CoA synthetase (Acsl) isoforms function to drive this energy-dependent process. Understanding the details of vectorial acylation is of particular importance as disturbances in lipid metabolism many times leads to elevated levels of circulating free fatty acids, which in turn increases fatty acid internalization and ectopic accumulation of triglycerides. This is associated with changes in fatty …

Glucose Promotes Stress Resistance In The Fungal Pathogen Candida Albicans, Alexandra Rodaki, Iryna M. Bohovych, Brice Enjalbert, Tim Young, Frank C. Odds, Neil A.R. Gow, Alistair J.P. Brown

Department of Biochemistry: Faculty Publications

Metabolic adaptation, and in particular the modulation of carbon assimilatory pathways during disease progression, is thought to contribute to the pathogenicity of Candida albicans. Therefore, we have examined the global impact of glucose upon the C. albicans transcriptome, testing the sensitivity of this pathogen to wide-ranging glucose levels (0.01, 0.1, and 1.0%). We show that, like Saccharomyces cerevisiae, C. albicans is exquisitely sensitive to glucose, regulating central metabolic genes even in response to 0.01% glucose. This indicates that glucose concentrations in the bloodstream (approximate range 0.05–0.1%) have a significant impact upon C. albicans gene regulation. However, in contrast …

A Role For The Atp7a Copper-Transporting Atpase In Macrophage Bactericidal Activity, Carine White, Jaekwon Lee, Taiho Kambe, Kevin Fritsche, Michael J. Petris

Department of Biochemistry: Faculty Publications

Copper is an essential micronutrient that is necessary for healthy immune function. This requirement is underscored by an increased susceptibility to bacterial infection in copper-deficient animals; however, a molecular understanding of its importance in immune defense is unknown. In this study, we investigated the effect of proinflammatory agents on copper homeostasis in RAW264.7 macrophages. Interferon-γ was found to increase expression of the high affinity copper importer, CTR1, and stimulate copper uptake. This was accompanied by copper-stimulated trafficking of the ATP7A copper exporter from the Golgi to vesicles that partially overlapped with phagosomal compartments. Silencing of ATP7A expression attenuated bacterial killing, …

Copper Transport Activity Of Yeast Ctr1 Is Down-Regulated Via Its C Terminus In Response To Excess Copper, Xiaobin Wu, Devis Sinani, Heejeong Kim, Jaekwon Lee

Department of Biochemistry: Faculty Publications

Copper is an essential yet toxic trace element. The Ctr1 family of proteins plays a critical role for copper uptake in eukaryotes. However, the mechanisms of action of Ctr1 are largely unknown. Our previous data demonstrated that copper transport induces conformational changes in the cytosolic C terminus of the yeast Saccharomyces cerevisiae Ctr1. To define the physiological significance of this molecular event and gain better insights into the mechanism of Ctr1-mediated copper uptake, we have characterized the functional roles of the Ctr1 C terminus.ACtr1 mutant lacking the entire C-terminal cytosolic tail is functional in high affinity copper uptake; however, yeast …

Contribution Of Impaired Myocardial Insulin Signaling To Mitochondrial Dysfunction And Oxidative Stress In The Heart, Sihem Boudina, Heiko Bugger, Sandra Sena, Brian T. O'Neill, Vlad G. Zaha, Olesya Ilkun, Jordan J. Wright, Pradip K. Mazumber, Eric Palfreyman, Timothy J. Tidwell, Heather Theobald, Oleh Khalimonchuk, Benjamin Wayment, Xiaoming Sheng, Kenneth J. Rodnick, Ryan Centini, Dong Chen, Sheldon E. Litwin, Bart E. Weimer, E. Dale Abel

Department of Biochemistry: Faculty Publications

Background—Diabetes-associated cardiac dysfunction is associated with mitochondrial dysfunction and oxidative stress, which may contribute to LV dysfunction. The contribution of altered myocardial insulin action, independently of associated changes in systemic metabolism is incompletely understood. The present study tested the hypothesis that perinatal loss of insulin signaling in the heart impairs mitochondrial function.

Methods and Results—In 8-week-old mice with cardiomyocyte deletion of insulin receptors (CIRKO), inotropic reserves were reduced and mitochondria manifested respiratory defects for pyruvate that was associated with proportionate reductions in catalytic subunits of pyruvate dehydrogenase. Progressive age-dependent defects in oxygen consumption and ATP synthesis with the substrates glutamate …

Sdh5, A Gene Required For Flavination Of Succinate Dehydrogenase, Is Mutated In Paraganglioma, Huai-Xiang Hao, Oleh Khalimonchuk, Margit Schraders, Noah Dephoure, Jean-Pierre Bayley, Henricus Kunst, Peter Devilee, Cor W.R.J. Cremers, Joshua D. Schiffman, Brandon G. Bentz, Steven P. Gygi, Dennis R. Winge, Hannie Kremer, Jared Rutter

Department of Biochemistry: Faculty Publications

Mammalian mitochondria contain about 1100 proteins, nearly 300 of which are uncharacterized. Given the well-established role of mitochondrial defects in human disease, functional characterization of these proteins may shed new light on disease mechanisms. Starting with yeast as a model system, we investigated an uncharacterized but highly conserved mitochondrial protein (named here Sdh5). Both yeast and human Sdh5 interact with the catalytic subunit of the succinate dehydrogenase (SDH) complex, a component of both the electron transport chain and the tricarboxylic acid cycle. Sdh5 is required for SDH-dependent respiration and for Sdh1 flavination (incorporation of the flavin adenine dinucleotide cofactor). Germline …

Chemchains: A Platform For Simulation And Analysis Of Biochemical Networks Aimed To Laboratory Scientists, Tomáš Helikar, Jim A. Rogers

Department of Biochemistry: Faculty Publications

Background: New mathematical models of complex biological structures and computer simulation software allow modelers to simulate and analyze biochemical systems in silico and form mathematical predictions. Due to this potential predictive ability, the use of these models and software has the possibility to compliment laboratory investigations and help refine, or even develop, new hypotheses. However, the existing mathematical modeling techniques and simulation tools are often difficult to use by laboratory biologists without training in high-level mathematics, limiting their use to trained modelers.

Results: We have developed a Boolean network-based simulation and analysis software tool, ChemChains, which combines the advantages of …

Ulk-Atg13-Fip200 Complexes Mediate Mtor Signaling To The Autophagy Machinery, Chang Hwa Jung, Chang Bong Jun, Seung-Hyun Ro, Young-Mi Kim, Neil Michael Otto, Jing Cao, Mondira Kundu, Do-Hyung Kim

Department of Biochemistry: Faculty Publications

Autophagy, the starvation-induced degradation of bulky cytosolic components, is up-regulated in mammalian cells when nutrient supplies are limited. Although mammalian target of rapamycin (mTOR) is known as the key regulator of autophagy induction, the mechanism by which mTOR regulates autophagy has remained elusive. Here, we identify that mTOR phosphorylates a mammalian homologue of Atg13 and the mammalian Atg1 homologues ULK1 and ULK2. The mammalian Atg13 binds both ULK1 and ULK2 and mediates the interaction of the ULK proteins with FIP200. The binding of Atg13 stabilizes and activates ULK and facilitates the phosphorylation of FIP200 by ULK, whereas knockdown of Atg13 …

Editorial: Dietary Lipid Absorption, Concetta Dirusso, Paul N. Black

Department of Biochemistry: Faculty Publications

The composition of dietary fat influences tissue fatty acid composition, which in turn impacts cellular function through a number of different processes. This includes changes in signaling, lipid metabolism, and transcriptional activities that normally function to maintain intracellular fatty acid homeostasis. The consumption of high levels of dietary fat in excess of caloric expenditure is linked with obesity and the disruption of normal homeostatic mechanisms governing lipid metabolism. Data from the Centers for Disease Control and Prevention show that obesity (defined as a BMI≥30) represents a considerable health concern in the United States. Of particular note is that for adult …