Biotechnology Commons^™

Quantitative Reagent-Free Detection Of Fibrinogen Levels In Human Blood Plasma Using Raman Spectroscopy, Kelvin Poon, Fiona Lyng, Peter Knief, Orla L. Howe, Aidan Meade, James Curtin, Hugh Byrne, Joseph Vaughan

Articles

Fibrinogen assays are commonly used as part of clinical screening tests to investigate haemorrhagic states, for detection of disseminated intravascular coagulation and as a predictor of a variety of cardiovascular events. The Clauss assay, which measures thrombin clotting time, is the most commonly used method for measuring fibrinogen levels. Nevertheless, inconsistencies are present in inter-manufacturer reagent sources, calibration standards and methodologies. Automated coagulation analysers, which measure changes in optical density during the prothrombin time (PT-Fg), have found use in many hospitals. However, the PT-Fg method is found to give falsely elevated values due to varying choices of calibrants, reagents and …

A Thousand Tiny Pieces: The Federal Circuit’S Fractured Myriad Ruling, Lessons To Be Learned, And The Way Forward, Jonathan R. K. Stroud

IP Theory

No abstract provided.

Amelioration Of Amyloid Burden In Advanced Human And Mouse Alzheimer's Disease Brains By Oral Delivery Of Myelin Basic Protein Bioencapsulated In Plant Cells, Neha Kohli

Electronic Theses and Dissertations

One of the pathological hallmarks of Alzheimer's disease (AD) is the amyloid plaque deposition in aging brains by aggregation of amyloid-β (Aβ) peptides. In this study, the effect of chloroplast derived myelin basic protein (MBP) fused with cholera toxin subunit B (CTB) was investigated in advanced diseased stage of human and mouse AD brains. The CTB-fusion protein in chloroplasts facilitates transmucosal delivery in the gut by the natural binding ability of CTB pentameric form with GM1 receptors on the intestinal epithelium. Further, bioencapsulation of the MBP within plant cells confers protection from enzymes and acids in the digestive system. Here, …

Identification Of Novel Antimalarial Scaffolds From Marine Natural Products, Bracken Roberts

Electronic Theses and Dissertations

Malaria, the disease caused by Plasmodium sp., claims the lives of over 1 million people every year, with Plasmodium falciparum causing the highest morbidity. Rapidly acquiring drug resistance is threatening to exhaust our antimalarial drug arsenal and already requires the utilization of combination drug therapy in most cases. The global need for novel antimalarial chemical scaffolds has never been greater. Screening of natural product libraries is known to have higher hit rates than synthetic chemical libraries. This elevated hit rate is somewhat attributed to the greater biodiversity available in natural products. Marine life is the most biodiverse system on the …

Light-Activated Binary Nucleotide Reagent For Inactivation Of Dna Polymerase, Evan M. Cornett

Electronic Theses and Dissertations

This work explores a binary reagent approach to increase the specificity of covalent inhibitors. In this approach, two ligand analogs equipped with inert pre-reactive groups specifically bind a target biopolymer. The binding event brings the pre-reactive groups in proximity with each other. The two groups react, generating active chemical intermediates that covalently modify and inactivate the target. In the present study we compare the new approach with the traditional single-component reagent strategy using DNA polymerase from bacteriophage T4 as a model target biopolymer. We report the design and synthesis of two analogs of deoxythymidine triphosphate, a natural DNA polymerase substrate. …

Usc Image Center, Allison Marsh

Section 1: Introduction

No abstract provided.

Powers Of Ten, Allison Marsh

Section 1: Introduction

No abstract provided.

Imaging In 3-D, Allison Marsh

Section 1: Introduction

No abstract provided.

Questioning Images, Allison Marsh

Section 1: Introduction

No abstract provided.

How Small Is Small?, Allison Marsh

Section 1: Introduction

No abstract provided.

Why Do We Collect?, Allison Marsh

Section 2: Imaging the Microscopic

No abstract provided.

Spotlight On Usc: A.C. Moore Herbarium, Allison Marsh

Section 2: Imaging the Microscopic

No abstract provided.

Imaging And Aesthetics, Allison Marsh

Section 2: Imaging the Microscopic

No abstract provided.

Observing The Minuscule, Allison Marsh

Section 2: Imaging the Microscopic

No abstract provided.

Spotlight On Usc: South Carolina Institute For Anthropology And Archaeology, Allison Marsh

Section 4: Imaging the Concealed

No abstract provided.

Mapping The Ocean Frontier, Allison Marsh

Section 4: Imaging the Concealed

No abstract provided.

Seeing With Sound, Allison Marsh

Section 4: Imaging the Concealed

No abstract provided.

World Ocean Floor, Courtesy Of The Library Of Congress, Allison Marsh

Section 4: Imaging the Concealed

No abstract provided.

Marie Tharp At Her Drafting Table, Courtesy Of The Lamont-Doherty Earth Observatory, Earth Institute, Columbia University, Allison Marsh

Section 4: Imaging the Concealed

No abstract provided.

Conclusion Panel, Allison Marsh

Section 6: Conclusion

No abstract provided.

Complete Genome Sequence Of Clostridium Clariflavum Dsm 19732, Javier A. Izquierdo, Lynne Goodwin, Karen W. Davenport, Hazuki Teshima

Dartmouth Scholarship

Clostridium clariflavum is a Cluster III Clostridium within the family Clostridiaceae isolated from thermophilic anaerobic sludge (Shiratori et al, 2009). This species is of interest because of its similarity to the model cellulolytic organism Clostridium thermocellum and for the ability of environmental isolates to break down cellulose and hemicellulose. Here we describe features of the 4,897,678 bp long genome and its annotation, consisting of 4,131 protein-coding and 98 RNA genes, for the type strain DSM 19732.

Microfluidic Impedance Spectroscopy As A Tool For Quantitative Biology And Biotechnology, Ahmet C. Sabuncu, Jie Zhuang, Juergen F. Kolb, Ali Beskok

Mechanical & Aerospace Engineering Faculty Publications

A microfluidic device that is able to perform dielectric spectroscopy is developed. The device consists of a measurement chamber that is 250 μm thick and 750 μm radius. Around 1000 cells fit inside the chamber assuming average quantities for cell radius and volume fraction. This number is about 1000 folds lower than the capacity of conventional fixtures. A T-cell leukemia cell line Jurkat is tested using the microfluidic device. Measurements of deionized water and salt solutions are utilized to determine parasitic effects and geometric capacitance of the device. Physical models, including Maxwell-Wagner mixture and double shell models, are used to …

Udp-Glucose Dehydrogenase Polymorphisms From Patients With Congenital Heart Valve Defects Disrupt Enzyme Stability And Quaternary Assembly, Annastasia S. Hyde, Erin L. Farmer, Katherine E. Easley, Kristy Van Lammeren, Vincent M. Christoffels, Joseph J. Barycki, Jeroen Bakkers, Melanie A. Simpson

Department of Biochemistry: Faculty Publications

Background: UDP-glucose dehydrogenase (UGDH) polymorphisms were identified in a screen of candidate genes for heart valve defects.

Results: Two individual mutants fail to rescue cardiac valve defects in UGDH-deleted zebrafish and have reduced stability in vitro.

Conclusion: UGDH loss of function mutations result in a subset of human congenital cardiac valve defects caused by reduced enzyme activity during morphogenesis.

Significance: Screening these alleles could predict valve defects.

Genome, Functional Gene Annotation, And Nuclear Transformation Of The Heterokont Oleaginous Alga Nannochloropsis Oceanica Ccmp1779, Astrid Vieler, Guangxi Wu, Chia-Hong Tsai, Blair Bullard, Adam J. Cornish, Christopher Harvey, Ida-Barbara Reca, Chelsea Thornburg, Rujira Achawanantakun, Christopher J. Buehl, Michael S. Campbell, David Cavalier, Kevin L. Childs, Teresa J. Clark, Rahul Deshpande, Erika Erickson, Ann Armenia Ferguson, Witawas Handee, Que Kong, Xiaobo Li, Bensheng Liu, Steven Lundback, Cheng Peng, Rebecca Roston, Michigan State University, Jeffrey P. Simpson, Allan Terbush, Jaruswan Warakanont, Simone Zäuner, Eva M. Farre, Eric L. Hegg, Ning Jiang, Min-Hao Kuo, Yan Lu, Krishna K. Niyogi, John Ohlrogge, Katherine W. Osteryoung, Yair Shachar-Hill, Barbara B. Sears, Yanni Sun, Hideki Takahashi, Mark Yandell, Shin-Han Shiu, Christoph Benning

Department of Biochemistry: Faculty Publications

Unicellular marine algae have promise for providing sustainable and scalable biofuel feedstocks, although no single species has emerged as a preferred organism. Moreover, adequate molecular and genetic resources prerequisite for the rational engineering of marine algal feedstocks are lacking for most candidate species. Heterokonts of the genus Nannochloropsis naturally have high cellular oil content and are already in use for industrial production of high-value lipid products. First success in applying reverse genetics by targeted gene replacement makes Nannochloropsis oceanica an attractive model to investigate the cell and molecular biology and biochemistry of this fascinating organism group. Here we present the …

Cellular Responses Of Candida Albicans To Phagocytosis And The Extracellular Activities Of Neutrophils Are Critical To Counteract Carbohydrate Starvation, Oxidative And Nitrosative Stress, Pedro Miramón, Christine Dunker, Hanna Windecker, Iryna Bohovych, Alistair J.P. Brown, Oliver Kurzai, Bernhard Hube

Department of Biochemistry: Faculty Publications

Neutrophils are key players during Candida albicans infection. However, the relative contributions of neutrophil activities to fungal clearance and the relative importance of the fungal responses that counteract these activities remain unclear. We studied the contributions of the intra- and extracellular antifungal activities of human neutrophils using diagnostic Green Fluorescent Protein (GFP)-marked C. albicans strains. We found that a carbohydrate starvation response, as indicated by upregulation of glyoxylate cycle genes, was only induced upon phagocytosis of the fungus. Similarly, the nitrosative stress response was only observed in internalised fungal cells. In contrast, the response to oxidative stress was observed in …

Small But Crucial: The Novel Small Heat Shock Protein Hsp21 Mediates Stress Adaptation And Virulence In Candida Albicans, Francois L. Mayer, Duncan Wilson, Ilse D. Jacobsen, Pedro Miramón, Silvia Slesiona, Iryna Bohovych, Alistair J.P. Brown, Bernhard Hube

Department of Biochemistry: Faculty Publications

Small heat shock proteins (sHsps) have multiple cellular functions. However, the biological function of sHsps in pathogenic microorganisms is largely unknown. In the present study we identified and characterized the novel sHsp Hsp21 of the human fungal pathogen Candida albicans. Using a reverse genetics approach we demonstrate the importance of Hsp21 for resistance of C. albicans to specific stresses, including thermal and oxidative stress. Furthermore, a hsp21∆/∆ mutant was defective in invasive growth and formed significantly shorter filaments compared to the wild type under various filamentinducing conditions. Although adhesion to and invasion into human-derived endothelial and oral epithelial cells …

Oligomerization Of Heme O Synthase In Cytochrome Oxidase Biogenesis Is Mediated By Cytochrome Oxidase Assembly Factor Coa2, Oleh Khalimonchuk, Hyung Kim, Talina Watts, Xochitl Perez-Martinez, Dennis R. Winge

Department of Biochemistry: Faculty Publications

The synthesis of the heme a cofactor used in cytochrome c

oxidase (CcO) is dependent on the sequential action of heme o

synthase (Cox10) and heme a synthase (Cox15). The active state of

Cox10 appears to be a homo-oligomeric complex,andformation of

this complex is dependent on the newly synthesized CcO subunit

Cox1 and the presence of an early Cox1 assembly intermediate.

Cox10 multimerization is triggered by progression of Cox1 from

the early assembly intermediate todownstreamintermediates.The

CcOassembly factor Coa2 appears important in coupling the presence

of newly synthesized Cox1 to Cox10 oligomerization. Cells

lacking Coa2 are impaired in Cox10 complex formation …

Selective Oma1 Protease-Mediated Proteolysis Of Cox1 Subunit Of Cytochrome Oxidase In Assembly Mutants, Oleh Khalimonchuk, Mi-Young Jeong, Talina Watts, Elliott Ferris, Dennis R. Winge

Department of Biochemistry: Faculty Publications

Background: Yeast lacking Coa2 are deficient in cytochrome c oxidase due to Cox1 degradation.

Results: Oma1 mediates Cox1 degradation in coa2∆ cells but not other mutants stalled in oxidase biogenesis.

Conclusion: Impaired hemylation of Cox1 in coa2∆ cells leads to misfolding and facile degradation by Oma1.

Significance: Oma1 functions in quality control of cytochrome oxidase assembly.

The Evolutionary Rewiring Of Ubiquitination Targets Has Reprogrammed The Regulation Of Carbon Assimilation In The Pathogenic Yeast Candida Albicans, Doblin Sandai, Zhikang Yin, Laura Selway, David Stead, Janet Walker, Michelle D. Leach, Iryna Bohovych, Iuliana V. Ene, Stavroula Kastora, Susan Budge, Carol A. Munro, Frank C. Odds, Neil A.R. Gow, Alistair J.P. Brown

Department of Biochemistry: Faculty Publications

Microbes must assimilate carbon to grow and colonize their niches. Transcript profiling has suggested that Candida albicans, a major pathogen of humans, regulates its carbon assimilation in an analogous fashion to the model yeast Saccharomyces cerevisiae, repressing metabolic pathways required for the use of alterative nonpreferred carbon sources when sugars are available. However, we show that there is significant dislocation between the proteome and transcriptome in C. albicans. Glucose triggers the degradation of the ICL1 and PCK1 transcripts in C. albicans, yet isocitrate lyase (Icl1) and phosphoenolpyruvate carboxykinase (Pck1) are stable and are retained. Indeed, numerous …

Role Of Apoptosis-Inducing Factor, Proline Dehydrogenase, And Nadph Oxidase In Apoptosis And Oxidative Stress, Sathish Kumar Natarajan, Donald F. Becker

Department of Biochemistry: Faculty Publications

Flavoproteins catalyze a variety of reactions utilizing flavin mononucleotide or flavin adenine dinucleotide as cofactors. The oxidoreductase properties of flavoenzymes implicate them in redox homeostasis, oxidative stress, and various cellular processes, including programmed cell death. Here we explore three critical flavoproteins involved in apoptosis and redox signaling, ie, apoptosis-inducing factor (AIF), proline dehydrogenase, and NADPH oxidase. These proteins have diverse biochemical functions and influence apoptotic signaling by unique mechanisms. The role of AIF in apoptotic signaling is two-fold, with AIF changing intracellular location from the inner mitochondrial membrane space to the nucleus upon exposure of cells to apoptotic stimuli. In …