Digital Commons Network^™

Epsvr And Epmeta: Prediction Of Antigenic Epitopes Using Support Vector Regression And Multiple Server Results, Shide Liang, Dandan Zheng, Daron M. Standley, Bo Yao, Martin Zacharias, Chi Zhang

School of Biological Sciences: Faculty Publications

Background: Accurate prediction of antigenic epitopes is important for immunologic research and medical applications, but it is still an open problem in bioinformatics. The case for discontinuous epitopes is even worse - currently there are only a few discontinuous epitope prediction servers available, though discontinuous peptides constitute the majority of all B-cell antigenic epitopes. The small number of structures for antigen-antibody complexes limits the development of reliable discontinuous epitope prediction methods and an unbiased benchmark to evaluate developed methods.

Results: In this work, we present two novel server applications for discontinuous epitope prediction: EPSVR and EPMeta, where EPMeta …

Stream Invertebrate Responses To A Catastrophic Decline In Consumer Diversity, Jose Checo Colón-Gaud, Matt R. Whiles, Karen R. Lips, Catherine M. Pringle, Susan Kilham, Roberto Brenes, Scot D. Peterson

Biology: Faculty Publications

Tadpoles are often abundant and diverse consumers in headwater streams in the Neotropics. However, their populations are declining catastrophically in many regions, in part because of a chytrid fungal pathogen. These declines are occurring along a moving disease front in Central America and offer the rare opportunity to quantify the consequences of a sudden, dramatic decline in consumer diversity in a natural system. As part of the Tropical Amphibian Declines in Streams (TADS) project, we examined stream macroinvertebrate assemblage structure and production for 2 y in 4 stream reaches at 2 sites in Panama. One site initially had healthy amphibians …

Plasticity Of Acquired Secondary Metabolites In Clathria Prolifera (Demospongia: Poecilosclerida): Putative Photoprotective Role Of Carotenoids In A Temperate Intertidal Sponge, Jonathan D. Dattelbaum, Drew Sieg, Malcolm Hill, Chris M. Manieri, Giles Thomson

Chemistry Faculty Publications

Several marine sponges sequester high concentrations of carotenoids in their tissues. The diversity of carotenoid compounds has been described in detail for a handful of species, but to date, little attention has been paid to natural variability in the concentration and constituency of carotenoid pools. Also lacking are experimental tests of some of the proposed adaptive benefits of carotenoids to the sponge. To address some of these deficits in our understanding of sponge ecology, we used a combination of analytic chemistry, field surveys, and manipulative experiments to determine what function these compounds might play. Attention was focused on the common, …

Low Cost Production Of Proinsulin In Tobacco And Lettuce Chloroplasts For Injectable Or Oral Delivery Of Functional Insulin And, Diane Burberry

Electronic Theses and Dissertations

Current treatment for type I diabetes includes delivery of insulin via injection or pump, which is highly invasive and expensive. The production of chloroplast-derived proinsulin should reduce cost and facilitate oral delivery. Therefore, tobacco and lettuce chloroplasts were transformed with the cholera toxin B subunit fused with human proinsulin (A, B, and C peptides) containing three furin cleavage sites (CTB-PFx3). Transplastomic lines were confirmed for site-specific integration of transgene and homoplasmy. Old tobacco leaves accumulated proinsulin up to 47% of total leaf protein (TLP). Old lettuce leaves accumulated proinsulin up to 53% TLP. Accumulation was so stable that up to …

Acetazolamide-Induced Decrease Of Apical Fluid Flow In Choroid Plexus Is Independent Of The Concomitant Changes In Aquaporin-1 Expression, Pouya Alexander Ameli

Electronic Theses and Dissertations

Acetazolamide (AZA), the only drug approved for treatment of hydrocephalus, is effective in only 25-30% of patients while its effect on fluid flow in the choroid plexus (CP) is unknown. The drug reversibly inhibits Aquaporin 4 (AQP4), the most highly expressed „water pore‟ in the brain, and it is postulated that it reduces cerebrospinal fluid (CSF) production by modulating AQP1 (mostly found in the apical membrane of the CP). In this study, we sought to elucidate the effect of AZA on AQP1 and fluid flow in CP. Primary CP culture from p10 Sprague-Dawley rats and TRCSF-B cell line were grown …

Purification And Properties Of Amycolatopsis Mediterranei Dsm 43304 Lipase And Its Potential In Flavour Ester Synthesis, Dharmendra Dheeman, Gary Henehan, Jesus Maria Frias

Articles

An extracellular thermostable lipase from Amycolatopsis mediterranei DSM 43304 has been purified to homogeneity using ammonium sulphate precipitation followed by anion exchange chromatography and hydrophobic interaction chromatography. This protocol resulted in 398 fold purification with 36% final recovery. The purified A. mediterranei DSM 43304 lipase (AML) has an apparent molecular mass of 33 kDa. The N-terminal sequence, AANPYERGPDPTTASIEATR, showed highest similarity to a lipase from Streptomyces exfoliatus. The values of and for p-nitrophenyl palmitate (p-NPP) under optimal temperature (60°C) and pH (8.0) conditions were 0.10 ± 0.01 mM and 2.53 ± 0.06 mmol/minmg, respectively. The purified …

The 3rd Computational Structural Bioinformatics Workshop, Jing He, Di Wu

Computer Science Faculty Publications

As many other domains in biology, molecular structures have proposed challenging but interesting computational problems. The unique challenge of the 3-dimensional molecular structures comes from the combination of the fundamental concepts of physics, chemistry, biology and geometry, and it is often computationally intensive to search for the correct structure. The Computational Structural Bioinformatics Workshop (CSBW) is a workshop that focuses on the fundamental computational work that is related to 3-dimensional molecular structures. This workshop aims to bring together researchers with expertise in bioinformatics, computational biology, structural biology, data mining, optimization and high performance computing to discuss recent results, new techniques, …

Genetic Connections Between Neurological Disorders And Cholesterol Metabolism, Ingemar Bjorkhem, Valerio Leoni, Steve Meaney

Articles

Cholesterol is an essential component of both the peripheral and central nervous systems of mammals. Over the last decade, evidence has accumulated that disturbances in cholesterol metabolism are associated with the development of various neurological conditions. In addition to genetically defined defects in cholesterol synthesis, which will be covered in another review in this Thematic Series, defects in cholesterol metabolism (cerebrotendinous xanthomatosis) and intracellular transport (Niemann Pick Syndrome) lead to neurological disease. A subform of hereditary spastic paresis (type SPG5) and Huntington's disease are neurological diseases with mutations in genes that are of importance for cholesterol metabolism. Neurodegeneration is generally …

The Distribution Of Gnrh And Erbeta In Pre- And Post-Pubertal Male Rats, Maysaa Nageeb

Master's Theses

The hypothalamic-pituitary- gonadal axis is intrinsic in regulating reproductive function. Each part orchestrates the synthesis and release of a key hormone. At the level of the hypothalamus, Gonadotropin- releasing hormone (GnRH) is released and it is the

most upstream regulator of sexual maturation. GnRH neurons express a type of estrogen receptor, ERbeta, which suggests that estradiol (E2) plays a direct role in modulating GnRH function (Herbison and Pape 2001). The objective of this study was to determine if gonadal steroid hormones regulate the expression of ERbeta and GnRH mRNA in the male brain during pubertal development. In-situ hybridization was used …

Developmental Characterization Of Cara Mitad: A Drosophila Nuclear Receptor Co-Regulator, Chhavi Chauhan

Dissertations

In insects and vertebrates, hormone titers drive cellular proliferation and differentiation events that guide proper development. Nuclear receptors (NR) respond to these hormone signals by activating cascades of gene expression, along with coregulator protein complexes. In Drosophila melanogaster, fluctuating titers of the steroid hormone ecdysone are responsible for coordinating the timing of organismal development. Despite major advances in our understanding of Drosophila NR activities, we lack essential knowledge of the coregulators that are required for their proper function.

We have recently identified the Drosophila cara mitad (cmi) (`dear half') gene. The deduced CMI protein is closely related to the N-terminal …

Lysine Specific Demethylase-1 And The Brahma Chromatin Remodeling Complex Regulate Conserved Signaling Pathways During Drosophila Wing Development, Brenda Jean Curtis

Dissertations

The conserved SWI/SNF chromatin remodeling complex uses the energy from ATP hydrolysis to alter local chromatin environments by disrupting DNA-histone contacts. The Drosophila SWI/SNF counterpart, the Brahma complex, has been shown to have an essential role in regulating the proper expression of many developmentally important genes, including those required for eye and wing tissue morphogenesis. A temperature sensitive mutation in one of the core subunits, SNR1 (SNF5/Ini1/SMARC B1), results in reproducible wing patterning phenotypes that can be enhanced and suppressed by extragenic mutations. SNR1 functions as a regulatory subunit to modulate chromatin remodeling activities of the Brahma complex on target …

Localization And Functional Analysis Of Plasmodium Falciparum Genes Pfl2550w And Pff0750w, Carolyn Jane Strobel

Master's Theses

Malaria is a parasitic disease that causes over a million deaths worldwide each year. Understanding development through the parasite's life cycle is necessary to stop disease transmission. As the genetic basis for the crucial transition from the erythrocytic asexual cycle to gametocytogenesis is unknown, we hope to better understand this transition by studying sexual stage genes and their roles in gametocytogenesis. PFL2550w and PFF0750w are genes upregulated during gametocytogenesis that were identified by a whole-genome microarray comparing gene expression between gametocyte-producing and gametocyte-deficient strains. In this study, PFL2550w was shown to be a soluble protein that is exported from the …

Structure-Function Relationship Studies Of The Udp-Glucose Pyrophosphorylase From Escherichia Coli, Agnieszka Maria Orlof

Master's Theses

UDP-Glucose Pyrophosphorylase (UDP-Glc PPase) is a key enzyme of the carbohydrate metabolic pathway widely used among prokaryotes and eukaryotes. In plants, UDP-Glc PPase is necessary for sucrose synthesis while mammals utilize this enzyme for the production of glycogen. A bacterium such as Escherichia coli uses UDP-Glc PPase for biosynthesis of the lipopolysscharide core which forms a cell wall.

This study focused on UDP-Glc PPase from Escherichia coli which is encoded by both galU and galF genes. The first part of this project investigated amino acids that could play an important role in the function of UDP Glc PPase (GalU). Based …

The Globin Gene Family Of The Cephalochordate Amphioxus: Implications For Chordate Globin Evolution, Bettina Ebner, Georgia Panopoulou, Serge N. Vinogradov, Laurent Kiger, Michael C. Marden, Thorsten Burmester, Thomas Hankeln

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

The lancelet amphioxus (Cephalochordata) is a close relative of vertebrates and thus may enhance our understanding of vertebrate gene and genome evolution. In this context, the globins are one of the best studied models for gene family evolution. Previous biochemical studies have demonstrated the presence of an intracellular globin in notochord tissue and myotome of amphioxus, but the corresponding gene has not yet been identified. Genomic resources of Branchiostoma floridae now facilitate the identification, experimental confirmation and molecular evolutionary analysis of its globin gene repertoire.

Results

We show that B. floridae harbors at least fifteen paralogous globin genes, …

Ipla2Β, Alternative Splicing And Apoptosis Of Pancreatic Islets, Bhargavi Emani

Theses and Dissertations

Ceramides are bioactive lipids that can promote splicing of apoptosis-related genes, including caspase 9 and BCL-x. A recent study demonstrated that expression of neutral sphingomyelinase (NSMase), an enzyme that hydrolyzes sphingomyelins to generate ceramide, is regulated by Group VIA phospholipase A2 (iPLA2β)-dependent mechanism during β-cell apoptosis. This prompted us to hypothesize that iPLA2 is upstream of ceramide generation in the process regulating splicing of apoptotic genes. To test this, Jurkat T cells were treated with the selective inhibitor of iPLA2β, bromoenol lactone (BEL), RNA was isolated and converted to cDNA, and caspase 9 and BCL-x mRNA viii species were amplified …

Influence Of Retinal States On The Development And Maintenance Of Retinofugal Projections, Duncan Morhardt

Theses and Dissertations

Vision provides a critical interface with the physical world. This work examines visual development and vision loss in mice to glean the influence of the retinal state on visual connections. I first assessed the impact of retinal activity on the eye-specific segregation of retinal afferents in the lateral geniculate nucleus (LGN) of young Gβ5 -/- mice. Gβ5 is the fifth member of the β subfamily of heterotrimeric G proteins. Gβ5 binds and stabilizes the R7 family of regulators of G-protein signaling (RGS), which accelerate Gi/o GTP hydrolysis. Gβ5 -/- mice, which lack R7RGS activity, have malformed synapses in the outer …

Cell-Cell Junction Signaling Regulating Dna Double-Strand Break Repair In Breast Cells, Sinduja Ethiraj

Theses and Dissertations

Genomic instability and acquisition of invasiveness through the basement membrane extracellular matrix (ECM) are two major processes for epithelial cell malignancy in breast cancer. DNA double-strand break repair (DSBR) is one of the processes that get misregulated during breast cancer progression. In addition, radiation induced breaks such as those induced during radiation therapy to treat breast cancer patients are repaired by DSBR, rendering this pathway relevant for therapy as well. DSBR can occur either by homologous recombination (HR) or non-homologous end-joining (NHEJ). HR is accepted as the more error-free pathway. HR is regulated by the cell cycle status such that …

Influence Of Cultivation Conditions On The Production Of A Thermostable Extracellular Lipase From Amycolatopsis Mediterranei Dsm 43304, Dharmdendra Dheeman, Jesus Maria Frias, Gary Henehan

Articles

Among several lipase producing actinomycete strains screened, Amycolatopsis mediterranei DSM 43304 was found to produce a thermostable, extracellular lipase. Culture condition and nutrient source modification studies involving carbon sources, nitrogen sources, incubation temperature and medium pH were carried out. Lipase activity of 1.37 ± 0.103 IU/ml of culture medium was obtained in 96 h at 28 °C and pH 7.5 using linseed oil and fructose as carbon sources and a combination of phytone peptone and yeast extract (5:1) as nitrogen sources. In optimal culture conditions the lipase activity was enhanced 12-fold with a 2-fold increase in lipase specific activity. The …

Improving Predicted Protein Loop Structure Ranking Using A Pareto-Optimality Consensus Method, Yaohang Li, Ionel Rata, See-Wing Chiu, Erik Jakobsson

Computer Science Faculty Publications

Background

Accurate protein loop structure models are important to understand functions of many proteins. Identifying the native or near-native models by distinguishing them from the misfolded ones is a critical step in protein loop structure prediction.

Results

We have developed a Pareto Optimal Consensus (POC) method, which is a consensus model ranking approach to integrate multiple knowledge- or physics-based scoring functions. The procedure of identifying the models of best quality in a model set includes: 1) identifying the models at the Pareto optimal front with respect to a set of scoring functions, and 2) ranking them based on the fuzzy …

Protein Folding, Aggregation And Unfolding In Monte Carlo Simulations, Sandipan Mohanty, Anders Irbäck, Simon Mitternacht, Giorgio Favrin, U. H.E. Hansmann

Michigan Tech Publications, Part 1

An implicit water all-atom model is used to study folding, aggregation and mechanical unfolding of small proteins. Physically reasonable results obtained for a variety of applications indicate healthy global properties of the interaction potential.

Uncultivated Environmental Tm7 Model To Study Human Disease-Associated Tm7 Bacteria, David Barton

Master's Theses

The TM7 bacterial phylum has no cultivated species and includes members that span a broad range of environmental and human habitats, some of which are associated with human periodontitis. In this project, activated wastewater TM7 bacteria were analyzed and their relatedness compared to human-associated TM7 bacteria for the long-term goal of using an environmental TM7 to better understand TM7 pathogenesis in humans. DNA was extracted from activated wastewater and PCR amplified using TM7 16S rRNA gene- specific primers. The ~1,170 base pair PCR products were then cloned and sequenced. DNA sequencing and phylogenetic analysis identified environmental TM7 clones with high …

Studies On Inositol Polyphosphates And Their Role In Programmed Cell Death, Rakhee Agarwal

Theses and Dissertations

The agents that induce apoptosis in cancerous cells are considered as potential candidates for cancer therapy. Inositol polyphosphates, the naturally occurring compounds, regulate diverse cellular processes including induction of apoptosis in certain cancerous cells and hence can be considered as potential anticancer agents. The aim of this research dissertation was to establish firmly the role of inositol polyphosphates in induction of apoptosis by examining their mechanism of action. The overall hypothesis was that alterations in intracellular levels of inositol polyphosphates would bring about apoptotic changes. The hypothesis was tested by changing endogenous inositol polyphosphates by way of chemical treatments known …

The Danger Signal Adenosine Induces Persistence Of Chlamydial Infection Through Stimulation Of A2b Receptors, Matthew A. Pettengill, Verissa W. Lam, David M. Ojcius

All Dugoni School of Dentistry Faculty Articles

Infections with intracellular bacteria such as chlamydiae affect the majority of the world population. Infected tissue inflammation and granuloma formation help contain the short-term expansion of the invading pathogen, leading also to local tissue damage and hypoxia. However, the effects of key aspects of damaged inflamed tissues and hypoxia on continued infection with intracellular bacteria remain unknown. We find that development of Chlamydia trachomatis is reversibly retarded by prolonged exposure of infected cells to extracellular adenosine, a hallmark of hypoxia and advanced inflammation. In epithelial cells, this effect was mediated by the A2b adenosine receptor, unique in the adenosine receptor …

Progress Toward The Total Synthesis Of Lyconadin A, Yu Zhang

Theses and Dissertations

Lyconadin A is a pentacyclic Lycopodium alkaloid isolated from the club moss Lycopodium complanatum with antitumor properties. We have developed a novel 7-exo/6-exo acyl radical cascade cyclization as a method of making the bicyclo[5.4.0]undecane ring system of lyconadin A. The model products are trans-fused ring systems, while a cis-fused ring system is needed in lyconadin A. We have discovered a method to convert the trans-fused model cascade cyclization product into the desired cis isomer. Based on Donohoe's pyridone synthesis, we developed a method for the construction of 5-alkyl and 3,5-dialkyl-6-carbomethoxy-2-pyridones, the former of which …

Overexpression And Partial Purification Of Serine Hydroxymethyltransferase, Kimberly Rose Stevens

Chemistry and Biochemistry

No abstract provided.

Distribution And Diversity Of Archaeal And Bacterial Ammonia Oxidizers In Salt Marsh Sediments, Nicole S. Moin, Katelyn A. Nelson, Alexander Bush, Anne E. Bernhard

Biology Faculty Publications

Diversity and abundance of ammonia-oxidizing Betaproteobacteria (β-AOB) and archaea (AOA) were investigated in a New England salt marsh at sites dominated by short or tall Spartina alterniflora (SAS and SAT sites, respectively) or Spartina patens (SP site). AOA amoA gene richness was higher than β-AOB amoA richness at SAT and SP, but AOA and β-AOB richness were similar at SAS. β-AOB amoA clone libraries were composed exclusively of Nitrosospira-like amoA genes. AOA amoA genes at SAT and SP were equally distributed between the water column/sediment and soil/sediment clades, while AOA amoA sequences at SAS were primarily affiliated with the …

Charge Switch Nucleotides, John G. K. Williams, Gregory R. Bashford, Jiyan Chen, Dan Draney, Nara Narayanan, Bambi Reynolds, Pamela Sheaff

Biomedical Imaging and Biosignal Analysis Laboratory

The present invention provides compounds, methods and systems for sequencing nucleic acid using single molecule detection. Using labeled NPs that exhibit charged-switching behavior, single-molecule DNA sequencing in a microchannel sorting system is realized. In operation, sequencing products are detected enabling real-time sequencing as successive detectable moieties flow through a detection channel. By electrically sorting charged molecules, the cleaved product molecules are detected in isolation Without interference from unincorporated NPs and Without illuminating the polymerase-DNA complex.

Cloning Of "Animal Cryptochrome" Cdna From The Model Organism Chlamydomonas Reinhardtii For Functional Analysis Of Its Protein Product, Shobha Lavanya Silparasetty

Masters Theses & Specialist Projects

reinhardtii, a unicellular green alga, is a model organism to study the circadian clock. Cryptochromes are the blue light photoreceptors that entrain the clock in some organisms. The CPH1 protein of C. reinhardtii resembles the cryptochromes of the plant model Arabidopsis, but whether CPH1 entrains the circadian clock in C. reinhardtii is not yet known. Recent reports have suggested the existence of one more cryptochrome in C. reinhardtii, which resembles the cryptochromes of animals. However, the amino acid sequence of this protein shows even higher sequence similarity with the 6-4 DNA photolyase of Arabidopsis. DNA photolyases …

Computational Prediction Of The Agregated Structure Of Denatured Lysozyme, Pongsathorn Chotikasemsri

Masters Theses & Specialist Projects

Mis-folded proteins and their associated aggregates are a contributing factor in some human diseases. In this study we used the protein lysozyme as a model to define aggregation structures under denaturing conditions. Sasahara et al. (2007), Frare et al. (2009, 2006), and Rubin et al. (2008) observed conditions where heat denatured lysozyme formed fibril structures that were observed to be 8-17 nanometers in diameter under the electron microscope. Even though the crystal structure of lysozyme is known, the denatured form of this protein is still unknown. Therefore, we used Rosetta++ protein folding and blind docking software to create in silico …

Low-Dose Of Sodium Arsenite Causes Delayed Differentiation In C2c12 Mouse Myoblast Cells Through The Repression Of The Transcription Factor Myogenin, Amanda Steffens

All Theses

A number of epidemiological studies have correlated arsenic exposurwith cancer, skin diseases, cardiovascular diseases, and adverse developmental outcomes such as stillbirths, spontaneous abortions, neonatal mortality, low birth weight, and delays in the use of musculature. The current study used C2C12 mouse myoblast cells to examine whether low concentrations of arsenic could alter their differentiation into myotubes, which would indicate that arsenic has the ability to act as a developmental toxicant. Myoblast cells were exposed to 20nM sodium arsenite and allowed to differentiate into myotubes and expression of the muscle-specific transcription factor myogenin, along with the expression of myosin light chain …