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A Novel In Vivo Protein Refolding Technique, Yuefei Huang

Wayne State University Dissertations

Proteins perform their functions in their native folded states and misfolding of proteins may cause severe diseases, including Alzheimer's disease, Parkinson's disease, prion disease and diabetes. Understanding protein folding is important for us to engineer proteins to treat these diseases. For protein therapeutics, large quantities of properly folded and functional proteins are required. The current technology produces recombinant proteins using either eukaryotic or prokaryotic expression system, both of them have major problems that prevent production of large quantities of properly folded and functional human proteins for protein therapeutics.

Although the eukaryotic cells have comprehensive folding machinery that contains chaperones and …

The Selaginella Genome Identifies Changes In Gene Content Associated With The Evolution Of Vascular Plants, J. A. Banks, T. Nishiyama, M. Hasebe, J. L. Bowman, M. Gribskov, C. Depamphilis, Paul G. Wolf

Biology Faculty Publications

Vascular plants appeared ~410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in …

The Role Of Co-Infection In The Spread Of Hiv In Sub-Saharan Africa, Diego Fernando Cuadros

Theses and Dissertations--Biology

The cause of the high HIV prevalence in sub-Saharan Africa is incompletely understood, with heterosexual penile-vaginal transmission proposed as the main mechanism. Heterosexual HIV transmission has a very low probability; further, a single estimation of heterosexual probability of HIV transmission fails to reproduce the variation associated with important biological cofactors. In particular, studies of HIV incidence suggest that co-infection with other infectious diseases influence the HIV transmission, and therefore might substantially vary the pattern of the spread of the infection. To assess the effect of co-infection on the spread of HIV, I developed and analyzed several mathematical and statistical models …

Paleoepidemiology Of Intestinal Parasites And Lice In Pre-Columbian South America, Adauto Araujo, Karl Reinhard, Daniela Leles, Luciana Sianto, Alena M. Iñiguez, Martin Fugassa, Bernardo Arriaza, Nancy Orellana, Luis Fernando Ferreira

Karl Reinhard Publications

Some human parasites originated in prehominid ancestors in Africa. Nematode species, such as Enterobius vermicularis (pinworm), hookworms and Trichuris trichiura are shared by humans and other close phylogenetic primates (Pan and Gorilla), showing that they infected a common ancestor to this group. When humans migrated from Africa to other continents they carried these parasites wherever climate conditions allowed parasite transmission from host to host. Other parasites, however, were acquired throughout human biological and social evolutive history when new territories were occupied. Paleoparasitology data is a valuable source to recover emergence and disappearance of parasite infections through analysis of …

A Survey On Tersilochinae (Hymenoptera: Ichneumonidae) Species Of Turkey, With A Key To European Genera, Andrey Ivanovich Khalaim, Murat Yurtcan

Turkish Journal of Zoology

Thirty-five species from 7 genera of Tersilochinae (Hymenoptera: Ichneumonidae) occur in Turkey. Of these, 20 species are new records for Turkish fauna. The general distribution and data on the biology of Turkish species are provided. Keys to all European genera and subgenera are given, with a short annotation on the taxonomy, distribution and biology of each genus.

Synthesis, Self-Assembly And Biological Properties Of Self-Folding Cu(Ii) Coordination Polymers, Alejandro Arzola-Rubio

Open Access Theses & Dissertations

The synthesis of materials via molecular self-assembly is a powerful bottom-up approach for fabricating matter in the nano- and micro-meter scales. This methodology involves the spontaneous and reversible organization of small molecules that interact with one another to create larger structures driven by non-covalent interactions such as hydrogen bonding, hydrophobic forces and metal-ligand coordination interactions. In this thesis, the design, synthesis and characterization of a new set of molecules that spontaneously self-organize in water to form three-dimensional nanoscale toroidal structures was investigated. These supramolecular structures were designed with an intrinsic affinity to bind and condense DNA strands with the intent …

Using Archaeological Fish Remains To Determine The Native Status Of Anadromous Salmonids In The Upper Klamath Basin (Oregon, Usa) Through Mtdna And Geochemical Analysis, Alexander E. Stevenson

Dissertations and Theses

Within the Upper Klamath Basin, Oregon, the native status of anadromous salmonids (Oncorhynchus spp.) has been a long standing question. Ongoing efforts to establish if these fish were native to the region prior to the construction of the Copco I Dam on the Klamath River (c.1917) have relied on sparse, contradictory and sometimes unreliable historic documentation and informant testimony. Current restoration projects with very high financial and social costs necessitate accurate and reliable data on salmonid species which once called the region home. Often, archaeolofaunal remains present a novel way to determine species present in an area prior to …

The Energy Landscape Analysis Of Cancer Mutations In Protein Kinases, Anshuman Dixit, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

The growing interest in quantifying the molecular basis of protein kinase activation and allosteric regulation by cancer mutations has fueled computational studies of allosteric signaling in protein kinases. In the present study, we combined computer simulations and the energy landscape analysis of protein kinases to characterize the interplay between oncogenic mutations and locally frustrated sites as important catalysts of allostetric kinase activation. While structurally rigid kinase core constitutes a minimally frustrated hub of the catalytic domain, locally frustrated residue clusters, whose interaction networks are not energetically optimized, are prone to dynamic modulation and could enable allosteric conformational transitions. The results …

A New Approach To Construct Pathway Connected Networks And Its Application In Dose Responsive Gene Expression Profiles Of Rat Liver Regulated By 2,4dnt, Sudhir Chowbina, Youping Deng, Junmei Ai, Xiaogang Wu, Xin Guan, Mitchell S. Wilbanks, Barbara Lynn Escalon, Edward J. Perkins, Jake Y. Chen

Faculty Publications

Background: Military and industrial activities have lead to reported release of 2,4-dinitrotoluene (2,4DNT) into soil, groundwater or surface water. It has been reported that 2,4DNT can induce toxic effects on humans and other organisms. However the mechanism of 2,4DNT induced toxicity is still unclear. Although a series of methods for gene network construction have been developed, few instances of applying such technology to generate pathway connected networks have been reported.

Results: Microarray analyses were conducted using liver tissue of rats collected 24h after exposure to a single oral gavage with one of five concentrations of 2,4DNT. We observed …

The In Situ Function Of A Microbial Community Profiled By Ft-Ir: A Snapshot In Time, Ryan Roberts

Department of Biochemistry: Dissertations, Theses, and Student Research

Photographs of an ecosystem are an important tool in macro-community ecology. The photograph is a permanent record of species phenotype. In microbiology, biochemical activity provides the most descriptive information of an organism’s phenotype. A method for fingerprinting all biochemical activities occurring within a microbial community is analogous to a photograph. Infrared spectroscopy in the region between wavelengths 2500 to 20,000 nm (mid-IR) is a well established instrumental method for fingerprinting the total biochemical profile of axenic cultures. Spectra are complex and sensitive as demonstrated by the ability to discriminate between strains of bacteria, fungi, and algae. This thesis develops the …

Network To Pology In Human Protein Interaction Data Predicts Functional Association, Hua Li

Dissertations and Theses (Open Access)

High-throughput assays, such as yeast two-hybrid system, have generated a huge amount of protein-protein interaction (PPI) data in the past decade. This tremendously increases the need for developing reliable methods to systematically and automatically suggest protein functions and relationships between them. With the available PPI data, it is now possible to study the functions and relationships in the context of a large-scale network. To data, several network-based schemes have been provided to effectively annotate protein functions on a large scale. However, due to those inherent noises in high-throughput data generation, new methods and algorithms should be developed to increase the …

Network Analysis And Comparative Phylogenomics Of Micrornas And Their Respective Messenger Rna Targets Using Twelve Drosophila Species, M Ryan Woodcock

Theses and Dissertations

MicroRNAs represent a special class of small (~21–25 nucleotides) non-coding RNA molecules which exert powerful post-transcriptional control over gene expression in eukaryotes. Indeed microRNAs likely represent the most abundant class of regulators in animal gene regulatory networks. This study describes the recovery and network analyses of a suite of homologous microRNA targets recovered through two different prediction methods for whole gene regions across twelve Drosophila species. Phylogenetic criteria under an accepted tree topology were used as a reference frame to 1) make inference into microRNA-target predictions, 2) study mathematical properties of microRNA-gene regulatory networks, 3) and conduct novel phylogenetic analyses …

Anticancer And Antifungal Activity Of Copper(Ii) Complexes Of Quinolin-2(1h)-One-Derived Schiff Bases, Bernadette S. Creaven, Brian Duff, Denise A. Egan, Kevin Kavanagh, Georgina Rosair, Venkat Reddy Thangella, Maureen Walsh

Articles

The condensation of substituted aromatic aldehydes with 7-amino-4-methyl-quinolin-2(1H)-one (1) has lead to the isolation of quinolin-2(1H)-one derived Schiff bases (2–14). The copper(II) complexes (2a–14a) of the ligands were also prepared, and together with their corresponding free ligands were fully characterised by elemental analyses, spectral methods (IR, ¹H and ¹³C NMR, AAS, UV–Vis), magnetic and conductance measurements. The bidentate ligands coordinated to the copper(II) ion through the deprotonated phenolic oxygen and the azomethine nitrogen of the ligands in almost all cases. X-ray crystal structures of two of the complexes, 5a and 8a, confirmed the bidentate …

A State Record For The Oconee Scorpionfly, Panorpa Oconee Byers (Mecoptera: Panorpidae), In Florida, Louis A. Somma

Insecta Mundi

I provide the first state record for the Oconee scorpionfly, Panorpa oconee Byers, from Putnam County, Florida. This is the southernmost record for P. oconee, extends its range 321 km south of its known distribution and, if valid, adds a seventh described species of panorpid, and twelfth mecopteran, indigenous to Florida.

Drug Off-Target Effects Predicted Using Structural Analysis In The Context Of A Metabolic Network Model, Roger L. Chang, Lei Xie, Philip E. Bourne, Bernhard O. Palsson

Publications and Research

Recent advances in structural bioinformatics have enabled the prediction of protein-drug off-targets based on their ligand binding sites. Concurrent developments in systems biology allow for prediction of the functional effects of system perturbations using large-scale network models. Integration of these two capabilities provides a framework for evaluating metabolic drug response phenotypes in silico. This combined approach was applied to investigate the hypertensive side effect of the cholesteryl ester transfer protein inhibitor torcetrapib in the context of human renal function. A metabolic kidney model was generated in which to simulate drug treatment. Causal drug off-targets were predicted that have previously been …

The Marine Sponge Metabolite Mycothiazole: A Novel Prototype Mitochondrial Complex I Inhibitor., J Brian Morgan, Fakhri Mahdi, Yang Liu, Veena Coothankandaswamy, Mika B. Jekabsons, Tyler A. Johnson, Koneni V. Sashidhara, Phillip Crews, Dale G. Nagle, Yu-Dong Zhou

Natural Sciences and Mathematics | Faculty Scholarship

A natural product chemistry-based approach was applied to discover small-molecule inhibitors of hypoxia-inducible factor-1 (HIF-1). A Petrosaspongia mycofijiensis marine sponge extract yielded mycothiazole (1), a solid tumor selective compound with no known mechanism for its cell line-dependent cytotoxic activity. Compound 1 inhibited hypoxic HIF-1 signaling in tumor cells (IC(50) 1nM) that correlated with the suppression of hypoxia-stimulated tumor angiogenesis in vitro. However, 1 exhibited pronounced neurotoxicity in vitro. Mechanistic studies revealed that 1 selectively suppresses mitochondrial respiration at complex I (NADH-ubiquinone oxidoreductase). Unlike rotenone, MPP(+), annonaceous acetogenins, piericidin A, and other complex I inhibitors, mycothiazole is a mixed polyketide/peptide-derived compound …

Review Of The Exploitation Of Marine Resources Of The Australian Indian Ocean Territories: The Implications Of Biogeographic Isolation For Tropical Island Fisheries, Matthew Hourston

Fisheries Research Reports

The small islands of the Indian Ocean Territories are isolated reefs in an expanse of open ocean of abyssal depth. The majority of marine species that live on their reefs and lagoons have settled there from remote locations. Colonising individuals are presumed to have come to the island as the result of unusual weather and current conditions and form populations that are, necessarily, largely self-sustaining. The isolated populations that make up many of the fish and invertebrate stocks at the Cocos (Keeling) and Christmas Islands rely almost exclusively on larvae returning to their home reef to settle, grow and ultimately …

Morphological Characterization And Molecular Mediated Genetic Variation Of Thief Ant (Solenopsis Molesta Say, Hymenoptera: Formicidae), Ralph B. Narain

Department of Entomology: Dissertations, Theses, and Student Research

The thief ant, Solenopsis molesta (Say), a common nuisance ant species found throughout the United States is genetically related to other stinging ants. This research was undertaken to estimate genetic variation utilizing mitochondrial DNA sequences of cytochrome oxidase I in thief ant populations from various geographic locations. Thief ants were collected from nine states, identified to species using morphologic characteristics from available keys. DNA extractions were completed with Qiagen’s Gentra PUREGENE® DNA Isolation Kit using their solid tissue protocol. PCR reactions were run on the extracted DNA using primers Lep-F1 (forward) and Lep-R1 (reverse). The resulting DNA products were concentrated …

In Vitro Enabling Technologies For Use In The Aquatic Environment, Colm J. O'Dowd

Doctoral

O’Dowd, C., Mothersill, C.E., Cairns, M.T., Austin, B., Lyng, F.M., McClean, B. and Murphy, J.E.J. Assessing the mitochondrion as a biomarker of fish tissue damage using g radiation as a stress model in vitro.

There is an ever-increasing need for biomarkers to identify toxic stress in the aquatic environment. Such techniques need to be accurate, expeditious, ethical and economical. Typically, in vitro based platforms fit these criteria however many of these systems often undergo ‘assay drift’ and consequently do not fully represent the real-life situation.

In recent years, there has been growing interest in the mitochondrion and its (dys)function …

Integrated Fisheries Management Report. West Coast Demersal Scalefish Resource., Department Of Fisheries Western Australia.

Fisheries Management Papers

This report on the West Coast Demersal Scalefish fishery is the third in a series of Integrated Fisheries Management (IFM) resource reports required under the Government policy on IFM. Under this policy, the Chief Executive Officer of the Department of Fisheries is required to approve a sustainability report for each fishery, which includes a clear statement on the recommended harvest level.

Botanical Report Of Tierra Redonda Mountain Blm Area Of Critical Environmental Concern, San Luis Obispo County, California (W120˚59’41”; N35˚45’59”)., Anthony Baniaga, Andrew Theo Fitanides

Biological Sciences

The purpose of this document is to report the results of a botanical survey of a portion of the Tierra Redonda Mountain Area of Critical Environmental Concern. The survey was conducted for the Bureau of Land Management, and executed between October 2009 and June 2010. Tierra Redonda Mountain is the type locality for the Tierra Redonda formation, and has weathered to form steep slopes of exposed chaparral and protected woodlands. Four general community types were found; foothill woodland, chaparral, southern coastal scrub and dune scrub. Alliances determined by The Manual of California Vegetation (2nd ed.) were: Quercus douglasii Woodland, Quercus …

Error Correcting Codes And The Human Genome., Suzanne Mclean Lyle

Electronic Theses and Dissertations

In this work, we study error correcting codes and generalize the concepts with a view toward a novel application in the study of DNA sequences. The author investigates the possibility that an error correcting linear code could be included in the human genome through application and research. The author finds that while it is an accepted hypothesis that it is reasonable that some kind of error correcting code is used in DNA, no one has actually been able to identify one. The author uses the application to illustrate how the subject of coding theory can provide a teaching enrichment activity …

Ampa Receptor Allosterism: Measurement Of The Conformational Changes In The Ligand Binding Domain Of A Functional Receptor, Jennifer Gonzalez-Mcgehee

Dissertations and Theses (Open Access)

Ionotropic glutamate receptors are important excitatory neurotransmitter receptors in the mammalian central nervous system that have been implicated in a number of neuropathologies such as epilepsy, ischemia, and amyotrophic lateral sclerosis. Glutamate binding to an extracellular ligand binding domain initiates a series of structural changes that leads to the formation of a cation selective transmembrane channel, which consequently closes due to desensitization of the receptor. The crystal structures of the AMPA subtype of the glutamate receptor have been particularly useful in providing initial insight into the conformational changes in the ligand binding domain; however, these structures are limited by crystallographic …

Countermeasure Policy On The Samho Brother Benzene Ship Accident, Chin-Long Lin, Jian-Hwa Hu

Journal of Marine Science and Technology–Taiwan

On October 10th, 2005, the chemical ship SAMHO BROTHER mishap occurred in the Taiwan Strait while transporting a cargo of benzene. Explosive approach was applied but failed, causing the ship wreck sank to a depth of 70 m. Oil spill was recovered in a small amount, leaving about 50 tons of the fuel remained. On the other hand, environmental monitoring at the site of the accident revealed that almost all of the great amount of 3140 m3 benzene remains stored in the nine tanks on the ship and further actions upon such a unique event in the history are urgent. …

Shark Bay Prawn And Scallop Fisheries. Final Review Report, Department Of Fisheries Western Australia

Fisheries Management Papers

In recent times, the Department of Fisheries has received representations from both sectors about the ongoing interaction of the fisheries and their respective management settings. As a result, a decision was made to comprehensively review the fisheries, taking into account matters of fishery sustainability and gear interactions, together with industry economics and market considerations.

The review has also addressed research requirements to ensure an appropriate scientific basis for decision-making into the future.

Shark Bay Prawn And Scallop Fisheries: Final Review Report, Western Australia. Department Of Fisheries

Fisheries Management Papers

The Shark Bay Prawn Fishery and Shark Bay Scallop Fishery operate in the same general areas of Shark Bay (although there are some differences in their areas of operation). The interrelationship between trawling activities for the two target species (prawns and scallops) has raised both management challenges and industry conflicts over time. Harvest level settings for each fishery (in the form of effort levels and the timing and/or location of fishing) are independently set, on the basis of recruitment and abundance surveys of each target species. However, each industry sector strongly believes that the interactions between the fisheries arise because …

A Test Of The Area Of Refuge Hypothesis In Indo-Pacific Marine Biogeography, Jonnell C. Sanciangco

Biological Sciences Theses & Dissertations

Many hypotheses have been proposed to explain the marine biogeographic patterns of species richness of the Indo-Pacific. One of these hypotheses suggests that available habitat area is the main predictor of species richness. This is the basis for the area of refuge hypothesis that attempts to explain the global maxima of species richness found in the Coral Triangle, the area encompassing mostly the Philippines, Indonesia, and Malaysia. This species-area effect also has habitat heterogeneity as a potential component. The purpose of this study is to test the effects of habitat availability predictors, such as shallow water area and coastline length …

Age, Growth And Maturation Of Swordtip Squid (Photololigo Edulis) In The Southern East China Sea, Kae-Yih Wang, Kuo-Tien Lee, Cheng-Hsin Liao

Journal of Marine Science and Technology–Taiwan

The reproductive biology, and age and growth of the swordtip squid (Photololigo edulis) in the East China Sea were examined based on the growth ring of statoliths from 1797 specimens during the period of November 2002 to November 2004. The maximum age observed was 261 days in female and 253 days in male, an evidence showing that swordtip squid has a longevity of about 9 months in both sexes. Growth in mantle length (ML) and body weight (BW) in both sexes was best described by the exponential model. There was significantly difference in somatic or statolith growth between the sexes. …

Perspectives Of Underwater Optics In Biological Oceanography And Plankton Ecology Studies, Hans-Uwe Dahms, Jiang-Shiou Hwang

Journal of Marine Science and Technology–Taiwan

The ever expanding fields of UW (underwater) optics cover principal measurements of the optical properties of the sea, development of new methods of monitoring optical properties, techniques for measurements of organisms or structures in the sea and the development and application of optical instrumentation. In this respect, ocean optics is a multidisciplinary (and multinational) endeavour of science and engineering. Ocean optics has applications in the study of upwelling irradiance and chlorophyll concentrations in the ocean, in the penetration of solar radiation in shallow shelf seas and how this influences temperature profiles and ultimately its effect on sound propagation. Recent development …

Fisheries Occasional Paper No. 77 - Economic Analysis: Fishing Industry Impact Study - Kimberley Lng Project, Econsearch Pty Ltd, Department Of Fisheries Western Australia

Fisheries Occasional Publications

This study, prepared as a part of a broader study for WA fisheries, is concerned with the regional economy of the West Kimberley region and involves an assessment of the impact on the region of a range of fishing industry scenarios associated with development of an LNG processing facility. Specific tasks involved in the study were to prepare the following:

• a standard input-output model for the West Kimberley regional economy for 2007/08 and extend it as a DECON model; and

• estimates of the regional economic and population impact for a range of fishing industry scenarios arising from the …