Biotechnology Commons^™

Reporters For The Analysis Of N-Glycosylation In Candida Albicans, Shahida Shahana, Hector M. Mora-Montes, Luis Castillo, Iryna Bohovych, Chirag C. Sheth, Frank C. Odds, Neil A.R. Gow, Alistair J.P. Brown

Department of Biochemistry: Faculty Publications

A large proportion of Candida albicans cell surface proteins are decorated post-translationally by glycosylation. Indeed N-glycosylation is critical for cell wall biogenesis in this major fungal pathogen and for its interactions with host cells. A detailed understanding of N-glycosylation will yield deeper insights into host-pathogen interactions. However, the analysis of N-glycosylation is extremely challenging because of the complexity and heterogeneity of these structures. Therefore, in an attempt to reduce this complexity and facilitate the analysis of N-glycosylation, we have developed new synthetic C. albicans reporters that carry a single N-linked glycosylation site derived from Saccharomyces cerevisiae Suc₂. These …

Probing Arabidopsis Chloroplast Diacylglycerol Pools By Selectively Targeting Bacterial Diacylglycerol Kinase To Suborganellar Membranes, Bagyalakshmi Muthan, Rebecca Roston, John E. Froehlich, Christoph Benning

Department of Biochemistry: Faculty Publications

Diacylglycerol (DAG) is an intermediate in metabolism of both triacylglycerols and membrane lipids. Probing the steady-state pools of DAG and understanding how they contribute to the synthesis of different lipids is important when designing plants with altered lipid metabolism. However, traditional methods of assaying DAG pools are difficult, because its abundance is low and because fractionation of subcellular membranes affects DAG pools. To manipulate and probe DAG pools in an in vivo context, we generated multiple stable transgenic lines of Arabidopsis (Arabidopsis thaliana) that target an Escherichia coli DAGkinase (DAGK) to each leaflet of each chloroplast envelope membrane. …

A Comprehensive, Multi-Scale Dynamical Model Of Erbb Receptor Signal Transduction In Human Mammary Epithelial Cells, Tomáš Helikar, Naomi Kochi, Bryan Kowal, Manjari Dimri, Mayumi Naramura, Srikumar M. Raja, Vimla Band, Hamid Band, Jim A. Rogers

Department of Biochemistry: Faculty Publications

The non-receptor tyrosine kinase Src and receptor tyrosine kinase epidermal growth factor receptor (EGFR/ErbB1) have been established as collaborators in cellular signaling and their combined dysregulation plays key roles in human cancers, including breast cancer. In part due to the complexity of the biochemical network associated with the regulation of these proteins as well as their cellular functions, the role of Src in EGFR regulation remains unclear. Herein we present a new comprehensive, multi-scale dynamical model of ErbB receptor signal transduction in human mammary epithelial cells. This model, constructed manually from published biochemical literature, consists of 245 nodes representing proteins …

Sbml Qualitative Models: A Model Representation Format And Infrastructure To Foster Interactions Between Qualitative Modelling Formalisms And Tools, Claudine Chaouiya, Duncan Bérenguier, Sarah M. Keating, Aurélien Naldi, Martijn P. Van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan Kowal, Benjamin Wicks, Emanuel Gonçalves, Julien Dorier, Michel Page, Pedro T. Monteiro, Axel Von Kamp, Ioannis Xenarios, Hidde De Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomáš Helikar

Department of Biochemistry: Faculty Publications

Background: Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative data, and that they are well-suited for studies of large networks. While numerous groups have developed specific computational tools that provide original methods to analyse qualitative models, a standard format to exchange qualitative models has been missing.

Results: We present the Systems Biology Markup Language (SBML) Qualitative Models Package (“qual”), an extension of the SBML Level 3 standard designed for computer representation of qualitative …

Selenodb 2.0: Annotation Of Selenoprotein Genes In Animals And Their Genetic Diversity In Humans, Frederic Romagne, Didac Santesmasses, Louise White, Gaurab K. Sarangi, Marco Mariotti, Ron Hübler, Antje Weihmann, Genis Parra, Vadim N. Gladyshev, Roderic Guigo, Sergi Castellano

Department of Biochemistry: Faculty Publications

SelenoDB (http://www.selenodb.org) aims to provide high-quality annotations of selenoprotein genes, proteins and SECIS elements. Selenoproteins are proteins that contain the amino acid selenocysteine (Sec) and the first release of the database included annotations for eight species. Since the release of SelenoDB 1.0 many new animal genomes have been sequenced. The annotations of selenoproteins in new genomes usually contain many errors in major databases. For this reason, we have now fully annotated selenoprotein genes in 58 animal genomes. We provide manually curated annotations for human selenoproteins, whereas we use an automatic annotation pipeline to annotate selenoprotein genes in other animal genomes. …

Comparative Metabolic Profiling Of Haberlea Rhodopensis, Thellungiella Halophyla, And Arabidopsis Thaliana Exposed To Low Temperature, Maria Benina, Toshihiro Obata, Nikolay Mehterov, Ivan Ivanov, Veselin Petrov, Valentina Toneva, Alisdair R. Fernie, Tsanko S. Gechev

Department of Biochemistry: Faculty Publications

Haberlea rhodopensis is a resurrection species with extreme resistance to drought stress and desiccation but also with ability to withstand low temperatures and freezing stress. In order to identify biochemical strategies which contribute to Haberlea's remarkable stress tolerance, the metabolic reconfiguration of H. rhodopensis during low temperature (4^◦C) and subsequent return to optimal temperatures (21^◦C) was investigated and compared with that of the stress tolerant Thellungiella halophyla and the stress sensitive Arabidopsis thaliana. Metabolic analysis by GC-MS revealed intrinsic differences in the metabolite levels of the three species even at 21^◦C. H. rhodopensis …

Elucidating Causes Of Diporeia Decline In The Great Lakes Via Metabolomics: Physiological Responses After Exposure To Different Stressors, Suman Maity, Amber Jannasch, Jiri Adamec, James M. Watkins, Thomas Nalepa, Tomas O. Höök, Maria S. Sepúlveda

Department of Biochemistry: Faculty Publications

The benthic macroinvertebrate Diporeia spp. have been extirpated from many areas of the Laurentian Great Lakes, but the mechanisms underlying such declines are not fully understood. Diporeia declines coinciding with the invasion of exotic dreissenid mussels (zebra and quagga) have led to the hypothesis that Diporeia declines are a result of decreased food availability from increasing competition with dreissenids for diatoms. There is additional evidence that Diporeia are negatively affected when in close proximity to dreissenids, probably because of exposure to toxins present in the mussels’ pseudofeces. Diporeia are also known to be sensitive to anthropogenic contaminants (such as polychlorinated …

Microrna Function In Human Diseases, Sathish Kumar Natarajan, Mary Anne Smith, Cody J. Wehrkamp, Ashley M. Mohr, Justin L. Mott

Department of Biochemistry: Faculty Publications

MicroRNAs are emerging as a hot topic in research, and rightfully so. They show great promise as targets of treatment and as markers for common human diseases, such as cancer and metabolic diseases. In this review, we address some of the basic questions regarding micro- RNA function in human disease and the clinical significance of microRNAs. Specifically, micro- RNAs in epigenetics, cancer, and metabolic diseases are discussed, with examples taken from cholangiocarcinoma and nonalcoholic fatty liver disease.

Is Breakdown Of Fatty Acid Peroxides Involved In The Induction Of Apolipoprotein A1?, Rajat Gupta

Electronic Theses and Dissertations

Over the past few years the number of deaths caused due to cardiovascular diseases has been increasing and is of major concern. In the United States, 75% of cardiovascular-related deaths have been attributed to atherosclerosis. Western diets containing large quantities of peroxidized lipids are considered atherogenic. Heated oil in the form of fried food brings high levels of peroxidized fat and its decomposition products in the diet. Peroxidized lipids are known to increase the susceptibility of serum lipoproteins to undergo oxidation, thereby contributing to the progression of atherosclerosis. The intestinal cells are responsible for the absorption of dietary fatty acid …

Next-Peak: A Normal-Exponential Two-Peak Model For Peak-Calling In Chip-Seq Data, Nak-Kyeong Kim, Rasika V. Jayatillake, John L. Spouge

Mathematics & Statistics Faculty Publications

Background: Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) can locate transcription factor binding sites on genomic scale. Although many models and programs are available to call peaks, none has dominated its competition in comparison studies.

Results: We propose a rigorous statistical model, the normal-exponential two-peak (NEXT-peak) model, which parallels the physical processes generating the empirical data, and which can naturally incorporate mappability information. The model therefore estimates total strength of binding (even if some binding locations do not map uniquely into a reference genome, effectively censoring them); it also assigns an error to an estimated binding location. The comparison study …

The Contested Vision For Agriculture's Future: Sustainable Intensive Agriculture And Agroecology, Drew L. Kershen

Faculty Articles

No abstract provided.

Response To "Sodium Current Inhibition By Nanosecond Pulsed Electric Field (Nspef) - Fact Or Artifact?" By Verkerk Et Al, Andrei G. Pakhomov

Bioelectrics Publications

It was nice to learn that our studies of nanosecond pulsed electric field (nsPEF) effects on membrane currents [Nesin et al., 2012; Nesin and Pakhomov, 2012] gained the attention of scientists outside the immediate field of bioelectromagnetics.

The Hyaluronan Receptor For Endocytosis (Hare) Activates Nf-Κb-Mediated Gene Expression In Response To 40–400-Kda, But Not Smaller Or Larger, Hyaluronans, Madhu S. Pandey, Bruce A. Baggenstoss, Jennifer Washburn, Edward N. Harris, Paul H. Weigel

Department of Biochemistry: Faculty Publications

Background: HARE mediates systemic clearance of hyaluronan (HA), which turns over continuously in tissues.

Results: HARE uptake of 40–400-kDa, but not larger or smaller, HA stimulated NF-κB activation.

Conclusion: HA-HARE signal complexes activate NF-κB and gene transcription only with optimally sized HA.

Significance: HARE responsiveness to a narrow size range ofHAdegradation products may be a sensing system to detect tissue ECM stress.

Optimizing Electrode Design For Microbial Fuel Cells Used For Wastewater Treatment, Lindsay Nichols, John A. Hogan

STAR Program Research Presentations

Microbial fuel cells (MFC) utilize bacteria to generate an electrical current that can be used in the decomposition of sludge and human urine. In a MFC there is an anode (for oxidation of organic compounds), cathode (reduction of oxygen or carbon dioxide), and a proton exchange membrane (PEM, allows protons to migrate); reduction-oxidation reactions between the anode and cathode produce a measurable current. Bacteria that are found in sludge can be used to produce electrons in a voltaic cell, but optimizing conditions for harnessing the energy is crucial to making a MFC efficient. Research has shown that the ratios of …

Using Printed Anhydrous Carbohydrate Glass To Create Water Soluble Scaffolding For Use In Tissue Engineering, Tanner Carden, Devon Bane, Courtney Bane, Gavon Carden

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

The Effects Of Hydrostatic Pressure On Early Endothelial Tubulogenic Processes, Ryan M. Underwood

Theses and Dissertations--Biomedical Engineering

The effects of mechanical forces on endothelial cell function and behavior are well documented, but have not been fully characterized. Specifically, fluid pressure has been shown to elicit physical and chemical responses known to be involved in the initiation and progression of endothelial cell-mediated vascularization. Central to the process of vascularization is the formation of tube-like structures. This process—tubulogenesis—is essential to both the physiological and pathological growth of tissues. Given the known effects of pressure on endothelial cells and its ubiquitous presence in the vasculature, we investigated pressure as a magnitude-dependent parameter for the regulation of endothelial tubulogenic activity. To …

Biomedical Patents At The Supreme Court: A Path Forward, Arti K. Rai

Faculty Scholarship

Although most would argue that software patents pose a bigger challenge, the U.S. Supreme Court has recently focused on biomedical patents. Two of the Court's recent decisions scaling back such patents, Mayo v. Prometheus and AMP v. Myriad, have provoked justifiable anxiety for those concerned about biomedical innovation, particularly in the area of personalized medicine. While acknowledging significant limitations in the Court's reasoning in both cases, this Essay sketches a reading that is consistent with the results and innovation-friendly.

Real-Time In Vivo Imaging Of Size-Dependent Transport And Toxicity Of Gold Nanoparticles In Zebrafish Embryos Using Single Nanoparticle Plasmonic Spectroscopy, Lauren M. Browning, Tao Huang, Xiao-Hong Nancy Xu

Chemistry & Biochemistry Faculty Publications

Noble metal nanoparticles (NPs) show distinctive plasmonic optical properties and superior photostability, enabling them to serve as photostable multicoloured optical molecular probes and sensors for real-time in vivo imaging. To effectively study biological functions in vivo, it is essential that the NP probes are biocompatible and can be delivered into living organisms non-invasively. In this study, we have synthesized, purified and characterized stable (non-aggregated) gold (Au) NPs (86.2 +/- 10.8 nm). We have developed dark-field single NP plasmonic microscopy and spectroscopy to study their transport into early developing zebrafish embryos (cleavage stage) and their effects on embryonic development …

Role Of Host Immune Response And Bacterial Autolysin Atl In Human Nasal Colonization By Staphylococcus Aureus, Vanathy Paramanandam

Electronic Theses and Dissertations

Staphylococcus aureus (SA) is a major human pathogen that colonizes the anterior nares in 30% of the human population. Though nasal carriage of SA is a known risk factor for the subsequent spread of SA infections, the dynamics of SA nasal colonization is poorly understood. Our research focuses on understanding the host and bacterial factors that might contribute to the human nasal colonization by SA. In an attempt to elucidate the host response to SA, we performed an autologous human in vivo nasal colonization study, which showed decreased survival rates of SA in hosts who elicited a robust immune response. …

Towards Elucidation Of A Viral Dna Packaging Motor, Chad T. Schwartz

Theses and Dissertations--Pharmacy

Previously, gp16, the ATPase protein of phi29 DNA packaging motor, was an enigma due to its tendency to form multiple oligomeric states. Recently we employed new methodologies to decipher both its stoichiometry and also the mechanism in which the protein functions to hydrolyze ATP and provide the driving force for DNA packaging. The oligomeric states were determined by biochemical and biophysical approaches. Contrary to many reported intriguing models of viral DNA packaging, it was found that phi29 DNA packaging motor permits the translocation of DNA unidirectionally and driven cooperatively by three rings of defined shape. The mechanism for the generation …