Biotechnology Commons^™

Empirical Analysis Of The Str Profiles Resulting From Conceptual Mixtures, David R. Paoletti, Travis E. Doom, Carissa M. Krane, Michael L. Raymer, Dan E. Krane

Biology Faculty Publications

Samples containing DNA from two or more individuals can be difficult to interpret. Even ascertaining the number of contributors can be challenging and associated uncertainties can have dramatic effects on the interpretation of testing results. Using an FBI genotypes dataset, containing complete genotype information from the 13 Combined DNA Index System (CODIS) loci for 959 individuals, all possible mixtures of three individuals were exhaustively and empirically computed. Allele sharing between pairs of individuals in the original dataset, a randomized dataset and datasets of generated cousins and siblings was evaluated as were the number of loci that were necessary to reliably …

When The Public Does Not Have A Right To Know: How The California Public Records Act Is Deterring Bioscience Research And Development, Nader Mousavi, Matthew J. Kleiman

Duke Law & Technology Review

Many bioscience firms collaborate with public research universities to conduct innovative research through sponsored research agreements. Companies sponsoring this research usually require strict confidentiality from their academic partners in order to protect sensitive information that, if revealed, could put them at a competitive disadvantage and threaten their ability to obtain future patents. Yet, ambiguous disclosure requirements in the California Public Records Act preclude California's public research universities from guaranteeing that proprietary information provided in connection with sponsored research agreements will remain confidential. Entering into such agreements with public universities in California is therefore a risky proposition for the sponsors. This …

Atypical Pkciota Contributes To Poor Prognosis Through Loss Of Apical-Basal Polarity And Cyclin E Overexpression In Ovarian Cancer, Astrid M. Eder, Xiaomei Sui, Daniel G. Rosen, Laura K. Nolden, Kwai Wa Cheng, John P. Lahad, Madhuri Kango-Singh, Karen H. Lu, Carla L. Warneke, Edward N. Atkinson, Isabelle Bedrosian, Khandan Keyomarsi, Wen-Lin Kuo, Joe W. Gray, Jerry C. P. Yin, Jinsong Liu, Georg Halder, Gordon B. Mills

Biology Faculty Publications

We show that atypical PKCι, which plays a critical role in the establishment and maintenance of epithelial cell polarity, is genomically amplified and overexpressed in serous epithelial ovarian cancers. Furthermore, PKCι protein is markedly increased or mislocalized in all serous ovarian cancers. An increased PKCι DNA copy number is associated with decreased progression-free survival in serous epithelial ovarian cancers. In a Drosophila in vivo epithelial tissue model, overexpression of persistently active atypical PKC results in defects in apical-basal polarity, increased Cyclin E protein expression, and increased proliferation. Similar to the Drosophila model, increased PKCι proteins levels are associated with …

Metaheuristic Applications And Their Solutions Quality, Dr. Zahid Hussain

International Conference on Information and Communication Technologies

Over the past few decades, a wide variety of classes of combinatorial problems (e.g. the assignment problem, the knapsack problem, the vehicle routing problem, etc.) have emerged - from such areas as management science, telecommunication, AI, VLSI design and many others. Many large combinatorial problems are NP-hard problems because of the combinatorial growth of their solution search space with the problem size. Such problems are commonly solved by some version of a prominent metaheuristic (e.g. Genetic Algorithms, Tabu Search, Simulated Annealing and etc.). These heuristics seek good but approximate solutions at a reasonable computational cost. These heuristics are of stochastic …

Group 13 Hox Proteins Interact With The Mh2 Domain Of R-Smads And Modulate Smad Transcriptional Activation Functions Independent Of Hox Dna Binding Capability, Thomas M. Williams, Melissa E. Williams, Joanne H. Heaton, Thomas D. Gelehrter, Jeffrey W. Innis

Biology Faculty Publications

Interactions with co-factors provide a means by which HOX proteins exert specificity. To identify candidate protein interactors of HOXA13, we created and screened an E11.5–E12.5, distal limb bud yeast two-hybrid prey library. Among the interactors, we isolated the BMP-signaling effector Smad5, which interacted with the paralogous HOXD13 but not with HOXA11 or HOXA9, revealing unique interaction capabilities of the AbdB-like HOX proteins. Using deletion mutants, we determined that the MH2 domain of Smad5 is necessary for HOXA13 interaction.

This is the first report demonstrating an interaction between HOX proteins and the MH2 domain of Smad proteins. HOXA13 and HOXD13 …

Ua3/9/5 Sygen Announcement, Wku President's Office

WKU Administration Documents

Program and talking points used by WKU president Gary Ransdell when announcing $2.5 million gift from Sygen and the creation of the Sygen Chair in Biotechnology.

Dynamic Matrix Composition In Engineered Cartilage With Stochastic Supplementation Of Growth Factors, Asit K. Saha, J. (Jagannath) Mazumdar, Sean S. Kohles

Mechanical and Materials Engineering Faculty Publications and Presentations

Dynamic extracellular matrix (ECM) synthesis is explored in a hypothesized engineered cartilage construct. Growth (α) and decay (β) rate parameters are developed from a previous engineered cartilage model. The presented mathematical model was constructed from the parameterized experimental data using a deterministic and stochastic examination of ECM synthesis based on a negative feedback control mechanism. A growth factor supplementation is incorporated in a probabilistic mathematical approach. The growth factor component modified an initial deterministic model through a Gaussian white noise fluctuation. As the primary constituents of ECM, the mathematical tool is intended to characterize the probable steady state distribution of …

A New Interpretation Of The Drug Levodopa In The Treatment Of Parkinson's Disease, Joanne T. Vannah

Graduate Masters Theses

An argument for levodopa induced dyskinesias (LID) as an expression of long term potentiation (LTP) in the striatum is presented. Normally, with an intact nigrostriatal dopamine (DA) input, long term depression (LTD) is expressed in the striatum, however, striatal LTD is lost following DA denervation and chronic levodopa treatment. It is possible that these changes in synaptic efficacy are due to two other chemical modulators, achetylcholine (ACh) and glutamate, which in turn leads to the induction of striatal LTP. ACh and glutamate may produce these changes in motor behavior by affecting the striosomal pathway in addition to their effect on …

Taking Biologics For Granted? Takings, Trade Secrets, And Off-Patent Biological Products, Andrew Wasson

Duke Law & Technology Review

Biologics are complex medicines which are often genetically engineered, and which are sure to play an important role in curing some of humankind's worst diseases. Not surprisingly, generic companies want a part of the biologic market. The FDA believes that it has the authority to approve off-patent versions of biologics that were originally regulated under the Food, Drug & Cosmetic Act, but in order to effectively do so the FDA would have to rely on findings based on data produced by the brand name companies. This iBrief examines whether the FDA's reliance on previous findings would give rise to a …

Effect Of Heat Schock On Browning-Related Enzymes In Minimally Processed Iceberg Lettuce And Crude Extracts, Ana Belen Martin-Diana, Daniel Rico, Catherine Barry-Ryan, Jemina Mulcahy, Jesus Maria Frias, Gary Henehan

Articles

The effects of heat shock on PPO and POD activity in minimally processed Iceberg lettuce was examined during storage (10 days). The results were compared with the effect of temperature on crude extracts of these enzymes (in vitro analysis). Fresh-cut lettuce washed at 50 °C showed significantly lower PPO and POD activity throughout storage than lettuce washed at 4 °C and 25 °C. These results were consistent with a sensory analysis in which the panellists found the lowest browning scores in those samples treated at 50 °C. When PPO and POD were analysed in vitro, the samples treated …

Disclosure Of Clinical Trial Data: Why Exemption 4 Of The Freedom Of Information Act Should Be Restored, Janene Boyce

Duke Law & Technology Review

Clinical trial data generated during the FDA drug approval process can be very valuable. While patients and doctors desperately need this information to make informed choices about medical treatment, drug sponsors strive to keep this resource secret to ensure their ability to profit from their own research. In the wake of the controversy over antidepressant use in children, both the public and Congress have called for the disclosure of all clinical trial data. However, rather than taking an all-or-nothing approach that could harm the development of new drugs, this iBrief argues that Congress should address the issue of trial data …

Regulating Innovative Medicine: Fitting Square Pegs In Round Holes, Mark Lavender

Duke Law & Technology Review

Increasingly, innovative medical products are creating a quandary for the Food and Drug Administration ("FDA") because they often transcend the FDA's traditional categorical approach to regulating medical products. In a recent attempt to simplify this process, the FDA has proposed a new rule for regulating "combination products." This iBrief discusses the FDA's current approach and analyzes the possible affects of the proposed regulation. Because of the many shortcomings of both systems, this iBrief concludes that the FDA should instead stop assigning center jurisdiction based on a product's "primary mode of action," and give the Office of Combination Products internal agency …

Nanosecond Pulsed Electric Fields: A New Stimulus To Activate Intracellular Signaling, Stephen J. Beebe, Karl H. Schoenbach

Bioelectrics Publications

When new technologies are introduced into the scientific community, controversy is expected and both excitement and disappointment enrich the lives of those who initiate the new ideas. It becomes the mission of the “inventors” to embrace the burden of proof to establish their ideas and convince the skeptics and disbelievers who will undoubtedly temper their enthusiasm and test their patience. While open mindedness is generally a scientific motto, those who review patents, manuscripts, and grants do not always readily practice it, even when the evidence is convincingly presented; old ideas and concepts often die hard. So it has been and …

Selective Field Effects On Intracellular Vacuoles And Vesicle Membranes With Nanosecond Electric Pulses, Ephrem Tekle, Hammou Oubrahim, Sergey M. Dzekunov, Juergen F. Kolb, Karl H. Schoenbach

Bioelectrics Publications

Electric pulses across intact vesicles and cells can lead to transient increase in permeability of their membranes. We studied the integrity of these membranes in response to external electric pulses of high amplitude and submicrosecond duration with a primary aim of achieving selective permeabilization. These effects were examined in two separate model systems comprising of 1), a mixed population of 1,2-di-oleoyl-sn-glycero-3-phosphocholine phospholipid vesicles and in 2), single COS-7 cells, in which large endosomal membrane vacuoles were induced by stimulated endocytosis. It has been shown that large and rapidly varying external electric fields, with pulses shorter than the charging time of …

Computer-Assisted Docking Of Flavodoxin With The Atp:Co(I)Rrinoid Adenosyltransferase (Coba) Enzyme Reveals Residues Critical For Protein-Protein Interactions But Not For Catalysis, Nicole R. Baun, Jorge C. Escalante-Semerena

Department of Biochemistry: Faculty Publications

The activity of the housekeeping ATP:co(I)rrinoid adenosyltransferase

(CobA) enzyme of Salmonella enterica sv. Typhimurium

is required to adenosylate de novo biosynthetic intermediates

of adenosylcobalamin and to salvage incomplete and complete

corrinoids from the environment of this bacterium. In vitro,

reduced flavodoxin (FldA) provides an electron to generate the

co(I)rrinoid substrate in the CobA active site. To understand how

CobAand FldA interact, a computer model of aCobA-FldA complex

was generated. This model was used to guide the introduction of

mutations into CobA using site-directed mutagenesis and the synthesis

of a peptide mimic of FldA. Residues Arg-9 and Arg-165 of

CobA …

High-Temperature Fluorescent In Situ Hybridization For Detecting Escherichia Coli In Seawater Samples, Using Rrna-Targeted Oligonucleotide Probes And Flow Cytometry, Ying Zhong Tang, Karina Yew Hoong Gin, Tok Hoon Lim

OES Faculty Publications

Fluorescence in situ hybridization (FISH) is a widely used method to detect environmental microorganisms. The standard protocol is typically conducted at a temperature of 46°C and a hybridization time of 2 or 3 h, using the fluorescence signal intensity as the sole parameter to evaluate the performance of FISH. This paper reports our results for optimizing the conditions of FISH using rRNA-targeted oligonucleotide probes and flow cytometry and the application of these protocols to the detection of Escherichia coli in seawater spiked with E. coli culture. We obtained two types of optimized protocols for FISH, which showed rapid results with …

The Effect Of Antioxidant Supplementation On Human Sperm Cryopreservation, Katrina E. Taylor

Theses : Honours

Semen cryopreservation has an important role in assisted reproductive technology however, the cooling, freezing and thawing processes often result in a significant loss of sperm motility, viability and nuclear integrity. The destructive effects of cryopreservation are significantly exacerbated in samples exhibiting low sperm number and poor morphological characteristics. Recent research into infertility has focused on the correlation between excessive oxidation and subfertility, in particular radical induced lipid peroxidation within the phospholipid bilayer of the spermatozoon plasma membrane and the promotion of cellular damage as a result of antioxidant insufficiency. The aim of this study was to evaluate the effect of …

Effect Of Humic Substance Photodegradation On Bacterial Growth And Respiration In Lake Water, Alexandre M. Anesio, William Granéli, George R. Aiken, David J. Kieber, Kenneth Mopper

Chemistry & Biochemistry Faculty Publications

This study addresses how humic substance (HS) chemical composition and photoreactivity affect bacterial growth, respiration, and growth efficiency (BGE) in lake water. Aqueous solutions of HSs from diverse aquatic environments representing different dissolved organic matter sources (autochthonous and allochthonous) were exposed to artificial solar UV radiation. These solutions were added to lake water passed through a 0.7-μm pore-size filter (containing grazer-free lake bacteria) followed by dark incubation for 5, 43, and 65 h. For the 5-h incubation, several irradiated HSs inhibited bacterial carbon production (BCP) and this inhibition was highly correlated with H₂O₂ photoproduction. The H_{2 …}

The Evidence For A Nascent Biotechnology Cluster In Cork, John W. Hobbs

Theses

Over the past 30 years, encouraged by Ireland’s low rate of corporation tax (currently 12.5 %), and active promotion of FDI by the IDA, foreign owned pharmaceutical plants have set up and multiplied in the Cork area. To Ireland’s advantages of a low tax rate, an English speaking population, a pro-business environment and membership of EU, Cork offered the added attractions of a deepwater port and large natural harbour, good freight connections, an international airport, an educated workforce and excellent sporting and leisure facilities for sailing, golf, etc. (Pfizer, Eli Lilly, Novartis, GlaxoSmithKline, Johnson & Johnson and Schering Plough have …

On Thacker's Biomedia (2004), Nicholas Ruiz Iii

Reconstruction: Studies in Contemporary Culture

[First paragraph]

Only we could have done it. The Code (DNA and its analogs, etc.) that we perhaps only narrate, never forgetting all of the fictions that narration portends, today consciously edits the text that evolution has edited unconsciously for eons. Thacker considers how humans -- perhaps little more than interactive Code, manipulate the Code -- with the technology of the Code. No other faction of Code has yet to make such heady ‘gains.’ Where posthumanity was always a literary endeavor, a literary bypass, out of instrumental science and into fictive states, it now is a technical endeavor, encompassing a …

The Medicare Prescription Drug, Improvement, & Modernization Act Of 2003: Are We Playing The Lottery With Healthcare Reform?, Melissa Ganz

Duke Law & Technology Review

With millions of Americans unable to cope with the rising costs of prescription drugs, and many even forced to go without health insurance, the mounting pressure on Congress to enact major healthcare reform culminated in the Medicare Prescription Drug, Improvement, & Modernization Act of 2003. This iBrief examines this legislation, and concludes that it provides elusive benefits for seniors and merely creates a windfall for the pharmaceutical and insurance industries.

The Bvg Virulence Control System Regulates Biofilm Formation In Bordetella Bronchiseptica, Yasuhiko Irie, Seema Mattoo, Ming H. Yuk

Biology Faculty Publications

Bordetella species utilize the BvgAS (Bordetella virulence gene) two-component signal transduction system to sense the environment and regulate gene expression among at least three phases: a virulent Bvg⁺ phase, a nonvirulent Bvg⁻ phase, and an intermediate Bvgⁱ phase. Genes expressed in the Bvg⁺ phase encode known virulence factors, including adhesins such as filamentous hemagglutinin (FHA) and fimbriae, as well as toxins such as the bifunctional adenylate cyclase/hemolysin (ACY). Previous studies showed that in the Bvgⁱ phase, FHA and fimbriae continue to be expressed, but ACY expression is significantly downregulated. In this report, we determine …

Synthesis, Characterisation And Biological Activity Of Transition Metal Complexes Of Thiabendazole, Rachel Kelly

Masters

A series of transition metal complexes of 2-(4’-thiazolyl)benzimidazole{thiabendazole}(TBZH) have been prepared and their ability to prevent the growth of the fungal pathogen Candida albicans has been assessed. The compounds were synthesised using the Chloride, Nitrate, Sulfate and Acetate salts of MN(II), Fe(II), Fe(III), Co(II), Ni(II), Zn(II) and Ag(1) resulting in the formation of 29 metal complexes. The complexes were formulated on the basis of their physico-chemical data. Reaction of Fe(NO3)3.9H2) with TBZH yielded the unusual nitrate salt [TBZH2NO3], a compound which could not be generated using simple acid –base chemistry. The X-ray crystal structure of [TBZH2NO3] was determined. TBZH, [TBZH2NO3], …

Drosophila As An Emerging Model To Study Metastasis, Madhuri Kango-Singh, Georg Halder

Biology Faculty Publications

Metastasis is the primary cause of human cancer-related deaths. Two recent studies describe a system for testing how multiple genetic events synergize to promote neoplastic growth and metastasis in Drosophila, paving the way for systematic approaches to understanding metastasis using the powerful tools of Drosophila genetics.

The Identity Of Proteins Associated With A Small Heat Shock Protein During Heat Stress In Vivo Indicates That These Chaperones Protect A Wide Range Of Cellular Functions, Eman Basha, Garrett J. Lee, Linda A. Breci, Andrew C. Hausrath, Nicole R. Buan, Kim C. Giese, Elizabeth Vierling

Department of Biochemistry: Faculty Publications

The small heat shock proteins (sHSPs) are a ubiquitous class of ATP-independent chaperones believed to prevent irreversible protein aggregation and to facilitate subsequent protein renaturation in cooperation with ATP-dependent chaperones. Although sHSP chaperone activity has been studied extensively in vitro, understanding the mechanism of sHSP function requires identification of proteins that are sHSP substrates in vivo. We have used both immunoprecipitation and affinity chromatography to recover 42 proteins that specifically interact with Synechocystis Hsp16.6 in vivo during heat treatment. These proteins can all be released from Hsp16.6 by the ATP-dependent activity of DnaK and cochaperones and are heat-labile. Thirteen …

Rosenzweig's Messianic Aesthetics, Jules Simon

Selected Works Temporary Series

No abstract provided.

Sterol Carrier Protein-2 Directly Interacts With Caveolin-1 In Vitro And In Vivo, Minglong Zhou, Rebecca D. Parr, Anca D. Petrescu, H. Ross Payne, Barbara P. Atshaves, Ann B. Kier, Judith M. Ball, Friedhelm Schroeder

Faculty Publications

HDL-mediated reverse-cholesterol transport as well as phosphoinositide signaling are mediated through plasma membrane microdomains termed caveolae/lipid rafts. However, relatively little is known regarding mechanism(s) whereby these lipids traffic to or are targeted to caveolae/lipid rafts. Since sterol carrier protein-2 (SCP-2) binds both cholesterol and phosphatidylinositol, the possibility that SCP-2 might interact with caveolin-1 and caveolae was examined. Double immunolabeling and laser scanning fluorescence microscopy showed that a small but significant portion of SCP-2 colocalized with caveolin-1 primarily at the plasma membrane of L-cells and more so within intracellular punctuate structures in hepatoma cells. In SCP-2 overexpressing L-cells, SCP-2 was detected …

A Method Based On Conserved Multiple Amino Acid Properties To Predict Amino Acid Substitutions Which Maintain The Protein Structure, Avinash M. Baktula

Masters Theses & Specialist Projects

A METHOD BASED ON CONSERVED MULTIPLE AMINO ACID PROPERTIES TO PREDICT AMINO ACID SUBSTITUTIONS WHICH MAINTAIN THE PROTEIN STRUCTURE Avinash M. Baktula September 16, 2004 1-117 Directed by: Claire A. Rinehart, Doug McElroy and Sigrid Jacobshagen Department of Biology Western Kentucky University Proteins often contain several domains, each with a distinct structure. Such domains have evolved as units that, when combined in various arrangements, produce proteins of unique structure. This study was conducted to identify amino acid substitutions that don’t change structure. Amino acid properties which were conserved in proteins with identical structures were used to predict a set of …

Interactions Between Small Heat Shock Protein Subunits And Substrate In Small Heat Shock Protein-Substrate Complexes, Kenneth L. Friedrich, Kim C. Giese, Nicole R. Baun, Elizabeth Vierling

Department of Biochemistry: Faculty Publications

Small heat shock proteins (sHSPs) are dynamic oligomeric

proteins that bind unfolding proteins and protect

them from irreversible aggregation. This binding results

in the formation of sHSP-substrate complexes from

which substrate can later be refolded. Interactions between

sHSP and substrate in sHSP-substrate complexes

and the mechanism by which substrate is transferred to

ATP-dependent chaperones for refolding are poorly defined.

We have established C-terminal affinity-tagged

sHSPs from a eukaryote (pea HSP18.1) and a prokaryote

(Synechocystis HSP16.6) as tools to investigate these issues.

We demonstrate that sHSP subunit exchange for

HSP18.1 and HSP16.6 is temperature-dependent and

rapid at the optimal growth …

The Identity Of Proteins Associated With A Small Heat Shock Protein During Heat Stress In Vivo Indicates That These Chaperones Protect A Wide Range Of Cellular Functions, Eman Basha, Garrett J. Lee, Linda A. Breci, Andrew C. Hausrath, Nicole R. Baun, Kim C. Giese, Elizabeth Vierling

Department of Biochemistry: Faculty Publications

The small heat shock proteins (sHSPs) are a ubiquitous

class of ATP-independent chaperones believed to

prevent irreversible protein aggregation and to facilitate

subsequent protein renaturation in cooperation

with ATP-dependent chaperones. Although sHSP chaperone

activity has been studied extensively in vitro, understanding

the mechanism of sHSP function requires

identification of proteins that are sHSP substrates in

vivo. We have used both immunoprecipitation and affinity

chromatography to recover 42 proteins that specifically

interact with Synechocystis Hsp16.6 in vivo during

heat treatment. These proteins can all be released from

Hsp16.6 by the ATP-dependent activity of DnaK and cochaperones

and are heat-labile. …