Biotechnology Commons^™

Morphological Characteristics And Species Separation Of Hawaiian Postlarval Amphidromous Fishes, M. Eric Benbow, Albert J. Burky, Carl M. Way

Biology Faculty Publications

There are five Hawaiian amphidromous fishes (Gobiidae: Lentipes concolor, Awaous guamensis, Sicyopterus stimpsoni, Stenogobius hawaiiensis; Eleotridae: Eleotris sandwicensis). Amphidromous adults deposit eggs on the stream bottom. After hatching, larvae drift to the ocean for growth followed by postlarval migration back into the streams. Postlarvae were collected to construct a dichotomous identification key based on 12 morphological measures and ray counts from four fins. Overall, the presense of fused pelvic fins, standard length (SL), and fin ray numbers were the most useful in species separation. Gobies were separated from the eleotrid by the former having fused …

Computational Protein Biomarker Prediction: A Case Study For Prostate Cancer, Michael Wagner, Dayanand N. Naik, Alex Pothen, Srinivas Kasukurti, Raghu Ram Devineni, Bao-Ling Adam, O. John Semmes, George L. Wright Jr.

Mathematics & Statistics Faculty Publications

Background: Recent technological advances in mass spectrometry pose challenges in computational mathematics and statistics to process the mass spectral data into predictive models with clinical and biological significance. We discuss several classification-based approaches to finding protein biomarker candidates using protein profiles obtained via mass spectrometry, and we assess their statistical significance. Our overall goal is to implicate peaks that have a high likelihood of being biologically linked to a given disease state, and thus to narrow the search for biomarker candidates.

Results: Thorough cross-validation studies and randomization tests are performed on a prostate cancer dataset with over 300 patients, obtained …

5-Hydroxydecanoate Is Metabolised In Mitochondria And Creates A Rate-Limiting Bottleneck For Β-Oxidation Of Fatty Acids, Peter J. Hanley, Stefan Dröse, Ulrich Brandt, Rachel A. Lareau, Abir L. Banerjee, D. K. Srivastava, Leonard J. Banaszak, Joseph J. Barycki, Paul P. Van Veldhoven, Jürgen Daut

Department of Biochemistry: Faculty Publications

5-Hydroxydecanoate (5-HD) blocks pharmacological and ischaemic preconditioning, and

has been postulated to be a specific inhibitor of mitochondrial ATP-sensitive K+ (KATP)

channels. However, recent work has shown that 5-HD is activated to 5-hydroxydecanoyl-CoA

(5-HD-CoA), which is a substrate for the first step of β-oxidation. We have now

analysed the complete β-oxidation of 5-HD-CoA using specially synthesised (and purified)

substrates and enzymes, as well as isolated rat liver and heart mitochondria, and compared

it with the metabolism of the physiological substrate decanoyl-CoA. At the second step of

β-oxidation, catalysed by enoyl-CoA hydratase, enzyme kinetics were …

Mobilization Of Intracellular Copper Stores By The Ctr2 Vacuolar Copper Transporter, Erin M. Rees, Jaekwon Lee, Dennis J. Thiele

Department of Biochemistry: Faculty Publications

Copper plays an essential role in processes including signaling to the transcription and protein trafficking machinery, oxidative phosphorylation, iron mobilization, neuropeptide maturation, and normal development. Whereas much is known about intracellular mobilization of ions such as calcium, little information is available on how eukaryotic cells mobilize intracellular copper stores. We describe a mechanism by which the Saccharomyces cerevisiae Ctr2 protein provides bioavailable copper via mobilization of intracellular copper stores. Whereas Ctr2 exhibits structural similarity to the Ctr1 plasma membrane copper importer, microscopic and biochemical fractionation studies localize Ctr2 to the vacuole membrane. We demonstrate that Ctr2 mobilizes vacuolar copper stores …

Interactions Between Small Heat Shock Protein Subunits And Substrate In Small Heat Shock Protein-Substrate Complexes, Kenneth L. Friedrich,, Kim C. Giese, Nicole R. Buan, 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 temperature …

Initial State Of The Drosophila Eye Before Dorsoventral Specification Is Equivalent To Ventral, Amit Singh, Kwang-Wook Choi

Biology Faculty Publications

Dorsoventral (DV) patterning is crucial for eye development in invertebrates and higher animals. DV lineage restriction is the primary event in undifferentiated early eye primordia of Drosophila. InDrosophila eye disc, a dorsal-specific GATA family transcription factor pannier (pnr) controls Iroquois-Complex (Iro-C) genes to establish the dorsal eye fate whereas Lobe (L), which is involved in controlling a Notch ligand Serrate (Ser), is specifically required for ventral growth. However, fate of eye disc cells before the onset of dorsal expression of pnr and Iro-C is not known. We show that L/Ser …

Are Biotech Crops And Conventional Crops Like Products? An Analysis Under Gatt, Julian Wong

Duke Law & Technology Review

The transatlantic debate over the use of genetically modified organisms ("GMO"s) as food products, with the US as a proponent on one side, and the European Union ("EU") as an opponent on the other, is set to take center stage. The US has initiated formal legal action under the World Trade Organization Dispute Settlement System, charging that the EU violates several agreements of international trade law, including Article III of GATT, an anti-protectionist measure which forbids a country from favoring its own products over imported "like products." The US claims that GMOs and conventional crops are "like products,, and that …

Hatch–Waxman Reform And Accelerated Market Entry Of Generic Drugs: Is Faster Necessarily Better?, Sarah E. Eurek

Duke Law & Technology Review

Recently there has been a considerable amount of pressure to accelerate consumer access to generic drugs, which are significantly less expensive than their brand-name counterparts. One way to bring generic drugs on to the market sooner is through revision of the existing law relating to pharmaceutical patents. This iBrief describes recent regulatory changes to the Drug Price Competition and Patent Term Restoration Act (the Hatch-Waxman Act), which governs the patenting process for new drug products, as well as current legislative efforts to speed generic access through Hatch-Waxman reform. This iBrief also assesses whether these changes will be beneficial to consumers …

Reviving Informed Consent: Using Risk Perception In Clinical Trials, Dana Ziker

Duke Law & Technology Review

The current doctrine of informed consent falls far short of its potential to serve as a valuable safeguard for human research subjects. Instead of providing a channel of communication between physician and subject, informed consent is a lifeless entity responsible for a large portion of the misunderstanding existing between these parties. Acknowledging risk perception principles may help transform the informed consent process into an effective communication of health risks.

Life Cycle Of A Torrenticolous Hawaiian Chironomid (Telmatogeton Torrenticola): Stream Flow And Microhabitat Effects, M. Eric Benbow, Albert J. Burky, Carl M. Way

Biology Faculty Publications

In this study we documented the instar densities and life cycle of Telmatogeton torrenticola Terry (Chironomidae : Telmatogetoninae) from Kinihapai Stream, Maui, Hawaii. Greatest larval densities of this midge are found on substrates of high velocity, shallow flows of cascades, and splash zones of waterfalls, with lower densities in riffles. In the summer of 1994 we compared the effects of two microhabitats (termed optimal and suboptimal) on inter-instar density and relative abundance. In a second year (1995), we evaluated the effect of long-term reduced stream flow on these variables only in optimal microhabitats. A significant reduction in stream flow from …

The Effects Of Intense Submicrosecond Electrical Pulses On Cells, Jingdong Deng, Karl H. Schoenbach, E. Stephen Buescher, Pamela S. Hair, Paula M. Fox, Stephen J. Beebe

Bioelectrics Publications

A simple electrical model for living cells predicts an increasing probability for electric field interactions with intracellular substructures of both prokaryotic and eukaryotic cells when the electric pulse duration is reduced into the submicrosecond range. The validity of this hypothesis was verified experimentally by applying electrical pulses (durations 100 μs– 60 ns, electric field intensities 3–150 kV/cm) to Jurkat cells suspended in physiologic buffer containing propidium iodide. Effects on Jurkat cells were assessed by means of temporally resolved fluorescence and light microscopy. For the longest applied pulses, immediate uptake of propidium iodide occurred consistent with electroporation as the cause of …

Real-Time Study Of Multidrug Resistance Mechanism In Pseudomonas Aeruginosa Using Nanoparticle Optics And Single Live Cell Imaging, Sophia Vasou Kyriacou

Chemistry & Biochemistry Theses & Dissertations

This thesis centers on the study of the xenobiotic efflux system in Pseudomonas aeruginosa, which is a ubiquitous bacterium. It resists many structurally and functionally diverse substrates due to expression of Mex-extrusion pumps, including MexAB-OprM, MexCD-OprJ, MexEF-OprN and MexXY-OprM systems. Despite extensive research, the structure and mechanism of multidrug resistance is unclear (1-9). For example, (i) how do MexA, MexB and OprM proteins assemble to extrude antibiotics? (ii) What is the antibiotic susceptibility of MexA, MexB, and OprM proteins? (iii) How do substrates cross the outer membrane of P. aeruginosa? (iv) Where are antibiotics accumulated inside the cell? This thesis …

Comparison Of Methods For Dna Isolation From Food Samples For Detection Of Shiga Toxin-Producing Escherichia Coli By Real-Time Pcr, Loree C. Heller, Carisa R. Davis, K. Kealy Peak, David Wingfield, Andrew C. Cannons, Philip T. Amuso, Jacqueline Cattani

Bioelectrics Publications

In this study, food samples were intentionally contaminated with Escherichia coli O157:H7, and then DNA was isolated by using four commercial kits. The isolated DNA samples were compared by using real-time PCR detection of the Shiga toxin genes. The four kits tested worked similarly.

The Case For National Dna Identification Cards, Ben Quarmby

Duke Law & Technology Review

Foes of the United States have demonstrated their ability to strike at the heart of this country. Fear of renewed attacks and a desire for greater national security have now prompted many to call for improvements in the national personal identification system. In particular, the possibility of a national identification card containing the carrier's DNA information is being seriously considered. However, this raises difficult questions. Would such a card system, and the extraction of individuals' DNA it entails, violate the 4th Amendment of the Constitution? This article will show that such a card system could in fact be found to …

Trends. Security, Stigma, And Biological Weapons, Ibpp Editor

International Bulletin of Political Psychology

This Trends article discusses the political psychology of security concerns pertaining to unclassified information relating to biological weapons and/or biosecurity and how it might be used to harm US security.

Patenting Genome Research Tools And The Law., Rebecca S. Eisenberg

Articles

Patenting genes encoding therapeutic proteins was relatively uncontroversial in the early days of biotechnology. Controversy arose in the era of high-throughput DNA sequencing, when gene patents started to look less like patents on drugs and more like patents on scientific information. Evolving scientific and business strategies for exploiting genomic information raised concerns that patents might slow subsequent research. The trend towards stricter enforcement of the utility and disclosure requirements by the patent offices should help clarify the current confusion.

Power, Privilege, And Special Interests: Rent Seeking And Subsidies In Agriculture, Matt Bogard

Agriculture Department Seminar Series

This presentation covers what Public Choice economists refer to as ‘rent seeking,’ generally seeking favor or special privilege from government through subsidies or regulatory advantages. Particularly, the biotech industry is the area of focus for this presentation. Problems with rent seeking in the biotech industry involve less innovation and industry consolidation. Policies related to biotech regulation, school lunch programs, the Clean Air Act, and ethanol subsidies are discussed. A game theoretic approach is used and it is concluded that issues related to rent seeking and special interests are not adequately addressed by recent campaign finance reform efforts. Alternatives such as …

Site‐Selective In Vivo Targeting Of Cytosine‐5 Dna Methylation By Zinc‐Finger Proteins, Christopher D. Carvin, Rebecca D. Parr, Michael P. Kladde

Faculty Publications

Cytosine‐5 DNA methylation is a critical signal defining heritable epigenetic states of transcription. As aberrant methylation patterns often accompany disease states, the ability to target cytosine methylation to preselected regions could prove valuable in re‐establishing proper gene regulation. We employ the strategy of targeted gene methylation in yeast, which has a naturally unmethylated genome, selectively directing de novo DNA methylation via the fusion of C5 DNA methyltransferases to heterologous DNA‐binding proteins. The zinc‐finger proteins Zif268 and Zip53 can target DNA methylation by M.CviPI or M.SssI 5–52 nt from single zinc‐factor binding sites. Modification at specific GC (M.CviPI) or CG (M.SssI) …

Transmembrane Movement Of Exogenous Long-Chain Fatty Acids: Proteins, Enzymes, And Vectorial Esterification, Paul N. Black, Concetta C. Dirusso

Department of Biochemistry: Faculty Publications

INTRODUCTION......................................................................................................................................................454

FATTY ACIDS AND BIOLOGICAL MEMBRANES.............................................................................................455

Fatty Acid Transport Defined ...............................................................................................................................456

MODEL SYSTEMS TO INVESTIGATE FATTY ACID TRANSPORT ..............................................................456

Genetic Foundations of Fatty Acid Transport....................................................................................................456

PROTEINS IMPLICATED IN FATTY ACID TRANSPORT ...............................................................................456

Fatty Acid Translocase..........................................................................................................................................457

Fatty Acid Binding Protein—Membrane Bound ................................................................................................457

Fatty Acid Transport Protein...............................................................................................................................458

The Long-Chain Fatty Acid Transport Protein FadL .......................................................................................458

Fatty Acyl-CoA Synthetase ...................................................................................................................................459

VECTORIAL ACYLATION: ONE MECHANISM OPERATIONAL IN FATTY ACID TRANSPORT...........460

THE BACTERIAL PARADIGM ...............................................................................................................................460

Energetics of Fatty Acid Transport in Gram-Negative Bacteria......................................................................460

The Fatty Acid Transporter FadL........................................................................................................................461

The Fatty Acyl-CoA Synthetase FadD..................................................................................................................461

Structural Considerations of FACS .....................................................................................................................462

FATTY ACID TRANSPORT AND ACTIVATION IN YEAST: …

The Many Faces Of Vitamin B12: Catalysis By Cobalamin-Dependent Enzymes, Ruma Banerjee, Stephen W. Ragsdale

Department of Biochemistry: Faculty Publications

Vitamin B₁₂ is a complex organometallic cofactor associated with three subfamilies of enzymes: the adenosylcobalamin-dependent isomerases, the methylcobalamin-dependent methyltransferases, and the dehalogenases. Different chemical aspects of the cofactor are exploited during catalysis by the isomerases and the methyltransferases. Thus, the cobalt-carbon bond ruptures homolytically in the isomerases, whereas it is cleaved heterolytically in the methyltransferases. The reaction mechanism of the dehalogenases, the most recently discovered class of B₁₂ enzymes, is poorly understood. Over the past decade our understanding of the reaction mechanisms of B₁₂ enzymes has been greatly enhanced by the availability of large amounts of enzyme …

Defining A New Ethical Standard For Human In Vitro Embryos In The Context Of Stem Cell Research, Sina A. Muscati

Duke Law & Technology Review

This iBrief discusses some of the social, ethical and legal considerations surrounding the use of unimplanted, in vitro embryos in stem cell research. It proposes that a new ethical standard be elucidated for these embryos. The iBrief gives an overview of two proposals for such a standard at opposite ends of the spectrum: treating the in vitro embryo as a legal person versus treating it as mere property. It argues against both approaches. The former can have undesirable social implications including undue interference with female reproductive autonomy, while the latter would objectify potential human life and reproductive potential. The iBrief …

Review Of "The Human Embryonic Stem Cell Debate: Science, Ethics, And Public Policy (Basic Bioethics)," Edited By Suzanne Holland, Karen Lebacqz, And Laurie Zoloth, James Steele

The University of New Hampshire Law Review

[Excerpt] "Perhaps like others, I started "The Human Embryonic Stem Cell Debate" not knowing many of the finer points of embryonic stem cell research, but I certainly had an opinion. This issue is far more complex than I had initially imagined. The editors do a commendable effort of compiling a sample of the innumerable arguments surrounding the debate."

Shar-Pei Mediates Cell Proliferation Arrest During Imaginal Disc Growth In Drosophila, Madhuri Kango-Singh, Riitta Nolo, Chunyao Tao, Patrik Verstreken, P. Robin Hiesinger, Hugo J. Bellen, Georg Halder

Biology Faculty Publications

During animal development, organ size is determined primarily by the amount of cell proliferation, which must be tightly regulated to ensure the generation of properly proportioned organs. However, little is known about the molecular pathways that direct cells to stop proliferating when an organ has attained its proper size. We have identified mutations in a novel gene, shar-pei, that is required for proper termination of cell proliferation during Drosophila imaginal disc development. Clones of shar-pei mutant cells in imaginal discs produce enlarged tissues containing more cells of normal size. We show that this phenotype is the result of both …

Regulating Functional Foods: Pre- And Post-Market Strategy, Dana Ziker

Duke Law & Technology Review

As best we understand the government, its first argument runs along the following lines: that health claims lacking "significant scientific agreement" are inherently misleading because they have such an awesome impact on consumers as to make it virtually impossible for them to exercise any judgment at the point of sale. It would be as if the consumers were asked to buy something while hypnotized, and therefore they are bound to be misled. We think this contention is almost frivolous.

Electric Field Enhanced Plasmid Delivery To Liver Hepatocellular Carcinomas, Richard Gilbert, Mark J. Jaroszeski, Loree Heller, Richard Heller

Bioelectrics Publications

Electric field enhanced molecular delivery for cancer research and treatment is a new technology that has demonstrated its effectiveness in clinical trials using bleomycin or cisplatin (Heller, R., Gilbert, R., Jaroszeski, M. J. Clinical applications of electrochemotherapy, Advanced Drug Delivery Reviews 35,119-129, 1999), as chemotherapeutic agents. The technology is being investigated in research applications for applicability as a method to enhance gene expression in a target tumor. Success is predicated on an appropriate effective electric field mediated delivery protocol that triggers significant appropriate gene expression duration and levels. An electric field mediated delivery protocol includes a set of conditions …

Electrically Mediated Delivery Of Vector Plasmid Dna Elicits An Antitumor Effect, L. Heller, D. Coppola

Bioelectrics Publications

In vivo electroporation is an efficient means of increasing plasmid DNA delivery to normal tissues, such as skin and muscle, as well as directly to tumors. In the experiments described here, plasmid DNA was delivered by in vivo electroporation to B16 mouse melanomas using two very different pulsing protocols. Reporter expression increased 21- or 42-fold, respectively with electroporation over injection alone. The growth of experimental melanomas with an approximate diameter of 4 mm on the day of treatment was monitored after electroporation delivery of reporter plasmid DNA. Remarkably, short-term complete regressions using one of these pulsing protocols occurred in up …

Genetic Testing In The Workplace: The Employer’S Coin Toss, Samantha French

Duke Law & Technology Review

A toss of the coin by the modern-day employer reveals two options regarding genetic testing in the workplace. The employer may choose to take advantage of increasingly precise, available, and affordable genetic testing in order to ascertain the genetic characteristics - and deficiencies - of its employees. This outcome exposes the employer to a vast array of potential litigation and liability relating to the Americans with Disabilities Act, the Fourth Amendment, Title VII of the Civil Rights Act, and state legislation designed to protect genetic privacy. Alternatively, the employer may neglect to indulge in this trend of genetic testing and …

Eye Suppression, A Novel Function Of Teashirt, Requires Wingless Signaling, Amit Singh, Madhuri Kango-Singh, Y. Henry Sun

Biology Faculty Publications

Teashirt (tsh) encodes a Drosophila zinc-finger protein. Misexpression of tsh has been shown to induce ectopic eye formation in the antenna. We report that tsh can suppress eye development. This novel function of tsh is due to the induction of homothorax (hth), a known repressor of eye development, and requires Wingless (WG) signaling. Interestingly, tsh has different functions in the dorsal and ventral eye, suppressing eye development close to the ventral margin, while promoting eye development near the dorsal margin. It affects both growth of eye disc and retinal cell differentiation.

The Atp:Co(I)Rrinoid Adenosyltransferase (Coba) Enzyme Of Salmonella Enterica Requires The 2'-Oh Group Of Atp For Function And Yields Inorganic Triphosphate As Its Reaction Byproduct, Maris V. Fonseca, Nicole R. Buan, Alexander R. Horswill, Ivan Rayment, Jorge C. Escalante-Semerena

Department of Biochemistry: Faculty Publications

The specificity of the ATP:corrinoid adenosyltransferase (CobA) enzyme of Salmonella enterica serovar Typhimurium LT2 for its nucleotide substrate was tested using ATP analogs and alternative nucleotide donors. The enzyme showed broad specificity for the nucleotide base and required the 2’-OH group of the ribosyl moiety of ATP for activity. ³¹P NMR spectroscopy was used to identify inorganic triphosphate (PPP_i) as the byproduct of the reaction catalyzed by the CobA enzyme. Cleavage of triphosphate into pyrophosphate and orthophosphate did not occur, indicating that triphosphate cleavage was not required for release of the adenosylcorrinoid product. Triphosphate was a strong …

Customizing Conception: A Survey Of Preimplantation Genetic Diagnosis And The Resulting Social, Ethical, And Legal Dilemmas, Jason Christopher Roberts

Duke Law & Technology Review

One in six American couples experience difficulties conceiving a child. With fertility rates at an all time low, the business of treating infertility is booming. However, due to the United States prohibition on government funding for embryonic research, the $4 billion industry of assisted reproductive technologies (ART) has been incompletely monitored and largely removed from oversight. Additionally, due to the fervent abortion debate, in vitro fertilization (IVF) was introduced in the United States without a research phase and procedures have been forced to evolve in the private sector. Thus, the checks and balances on medical innovation that are generally imposed …