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1. Types Of Alignment: Presentations & Demos Assignment, Sarah O'Leary-Driscoll 2016 Illinois Mathematics and Science Academy

1. Types Of Alignment: Presentations & Demos Assignment, Sarah O'Leary-Driscoll

Sequence Alignments

Pairwise Alignment: DNA

Pairwise Alignment: Protein

Multiple Sequence Alignment: DNA

Multiple Sequence Alignment: Protein


Bringing Toxicology Into The 21st Century: A Global Call To Action, Troy Seidle, Martin Stephens 2016 Humane Society International

Bringing Toxicology Into The 21st Century: A Global Call To Action, Troy Seidle, Martin Stephens

Martin Stephens, Ph.D.

Conventional toxicological testing methods are often decades old, costly and low-throughput, with questionable relevance to the human condition. Several of these factors have contributed to a backlog of chemicals that have been inadequately assessed for toxicity. Some authorities have responded to this challenge by implementing large-scale testing programmes. Others have concluded that a paradigm shift in toxicology is warranted. One such call came in 2007 from the United States National Research Council (NRC), which articulated a vision of ‘‘21st century toxicology” based predominantly on non-animal techniques. Potential advantages of such an approach include the capacity to examine a far greater ...


A Mechanical Study Of Cancer Drug-Receptor Interactions, Specifically In G-Quadruplex Dna And Topoisomerase I Enzymes, Kelly Ann Mulholland 2016 Rowan University

A Mechanical Study Of Cancer Drug-Receptor Interactions, Specifically In G-Quadruplex Dna And Topoisomerase I Enzymes, Kelly Ann Mulholland

Theses and Dissertations

Computational methods are becoming essential in drug discovery as they provide information that traditional drug development methods lack. Using these methods to understand drug-receptor interactions in detail, researchers are able to efficiently design promising drug candidates. In this study, extra precision Glide docking, molecular dynamics simulations and MMGBSA binding energy calculations provided information about the binding behavior of small molecules to two specific targets for current cancer therapeutics: G-quadruplex DNA and Topoisomerase I enzyme. The first study focuses on the compound Telomestatin, which induces apoptosis of various cancer cells with a relatively low effect on somatic cells due to its ...


Metabolomics As A Hypothesis-Generating Functional Genomics Tool For The Annotation Of Arabidopsis Thaliana Genes Of “Unknown Function”, Stephanie M. Quanbeck, Libuse Brachova, Alexis A. Campbell, Xin Guan, Ann Perera, Kun He, Seung Y. Rhee, Preeti Bais, Julie A. Dickerson, Philip M. Dixon, Gert Wohlgemuth, Oliver Fiehn, Lenore Barkan, Iris Lange, B. Markus Lange, Insuk Lee, Diego Cortes, Carolina Salazar, Joel Shuman, Vladimir Shulaev, David V. Huhman, Lloyd W. Sumner, Mary R. Roth, Ruth Welti, Hilal Ilarslan, Eve S. Wurtele, Basil J. Nikolau 2016 Iowa State University

Metabolomics As A Hypothesis-Generating Functional Genomics Tool For The Annotation Of Arabidopsis Thaliana Genes Of “Unknown Function”, Stephanie M. Quanbeck, Libuse Brachova, Alexis A. Campbell, Xin Guan, Ann Perera, Kun He, Seung Y. Rhee, Preeti Bais, Julie A. Dickerson, Philip M. Dixon, Gert Wohlgemuth, Oliver Fiehn, Lenore Barkan, Iris Lange, B. Markus Lange, Insuk Lee, Diego Cortes, Carolina Salazar, Joel Shuman, Vladimir Shulaev, David V. Huhman, Lloyd W. Sumner, Mary R. Roth, Ruth Welti, Hilal Ilarslan, Eve S. Wurtele, Basil J. Nikolau

Basil Nikolau

Metabolomics is the methodology that identifies and measures global pools of small molecules (of less than about 1,000 Da) of a biological sample, which are collectively called the metabolome. Metabolomics can therefore reveal the metabolic outcome of a genetic or environmental perturbation of a metabolic regulatory network, and thus provide insights into the structure and regulation of that network. Because of the chemical complexity of the metabolome and limitations associated with individual analytical platforms for determining the metabolome, it is currently difficult to capture the complete metabolome of an organism or tissue, which is in contrast to genomics and ...


Plantmetabolomics.Org: Mass Spectrometry-Based Arabidopsis Metabolomics—Database And Tools Update, Preeti Bais, Stephanie M. Moon-Quanbeck, Basil J. Nikolau, Julie A. Dickerson 2016 Iowa State University

Plantmetabolomics.Org: Mass Spectrometry-Based Arabidopsis Metabolomics—Database And Tools Update, Preeti Bais, Stephanie M. Moon-Quanbeck, Basil J. Nikolau, Julie A. Dickerson

Basil Nikolau

The PlantMetabolomics (PM) database (http://www.plantmetabolomics.org) contains comprehensive targeted and untargeted mass spectrum metabolomics data for Arabidopsis mutants across a variety of metabolomics platforms. The database allows users to generate hypotheses about the changes in metabolism for mutants with genes of unknown function. Version 2.0 of PlantMetabolomics.org currently contains data for 140 mutant lines along with the morphological data. A web-based data analysis wizard allows researchers to select preprocessing and data-mining procedures to discover differences between mutants. This community resource enables researchers to formulate models of the metabolic network of Arabidopsis and enhances the research community ...


Channa Striatus Tnfr-1: Molecular Cloning, Characterization And Gene Expression, Rajesh Palanisamy 2016 SRM Institute of Science and Technology

Channa Striatus Tnfr-1: Molecular Cloning, Characterization And Gene Expression, Rajesh Palanisamy

2nd International Conference of Fish & Shellfish Immunology

No abstract provided.


A Comparative Statement On Molecular Approach Of Large Hsps From Macrobrachium Rosenbergii, Mukesh Kumar Chaurasia 2016 SRM UNIVERSITY

A Comparative Statement On Molecular Approach Of Large Hsps From Macrobrachium Rosenbergii, Mukesh Kumar Chaurasia

2nd International Conference of Fish & Shellfish Immunology

No abstract provided.


Rasp-Qs: Efficient And Confidential Query Services In The Cloud, Zohreh S. Alavi, Lu Zhou, James L. Powers, Keke Chen 2016 Wright State University - Main Campus

Rasp-Qs: Efficient And Confidential Query Services In The Cloud, Zohreh S. Alavi, Lu Zhou, James L. Powers, Keke Chen

Keke Chen

Hosting data query services in public clouds is an attractive solution for its great scalability and significant cost savings. However, data owners also have concerns on data privacy due to the lost control of the infrastructure. This demonstration shows a prototype for efficient and confidential range/kNN query services built on top of the random space perturbation (RASP) method. The RASP approach provides a privacy guarantee practical to the setting of cloudbased computing, while enabling much faster query processing compared to the encryption-based approach. This demonstration will allow users to more intuitively understand the technical merits of the RASP approach ...


Exploration Of Chemical And Biological Management Strategies For Diaphorina Citri The Primary Vector Of Candidatus Liberibacter Asiaticus, Gretta Marie Sharp 2016 University of Texas at Tyler

Exploration Of Chemical And Biological Management Strategies For Diaphorina Citri The Primary Vector Of Candidatus Liberibacter Asiaticus, Gretta Marie Sharp

Biology Theses

Diaphorina citri (Hemipteran: Psyllidae), the Asian citrus psyllid, is a phloem-feeding, invasive species endemic to southern Asia that was first identified in the United States in Florida in 1998. Since introduction, D. citri has spread across the major citrus growing regions of the United States. This is of great concern to the citrus industry because D. citri is the primary vector of Candidatus Liberibacter asiaticus the causal agent of Haunglongbing (HLB). Haunglongbing is the most economically devastating disease of citrus causing an estimated 8.92 billion dollars lost in revenue and 4.62 billion dollars lost in gross domestic product ...


Measuring The Human Gut Microbiome: New Tools And Non Alcoholic Fatty Liver Disease, Ruth G. Wong 2016 The University of Western Ontario

Measuring The Human Gut Microbiome: New Tools And Non Alcoholic Fatty Liver Disease, Ruth G. Wong

Electronic Thesis and Dissertation Repository

With the advent of next generation DNA and RNA sequencing, scientists can obtain a more comprehensive snapshot of the bacterial communities on the human body (known as the `human microbiome'), leading to information about the bacterial composition, what genes are present, and what proteins are produced. The scientific community is in a phase of developing the experiments and accompanying statistical techniques to investigate the mechanisms by which the human microbiome affects health and disease. In this thesis, I explore alternatives to the standard weighted and unweighted UniFrac distance metric that measure the difference between microbiome samples. These alternative weightings allow ...


Effects Of Mutating The Mrub_1345 Gene Found In Meiothermus Ruber, Brandon M. Wills, Lori R. Scott 2016 Augustana College, Rock Island Illinois

Effects Of Mutating The Mrub_1345 Gene Found In Meiothermus Ruber, Brandon M. Wills, Lori R. Scott

Celebration of Learning

Meiothermus ruber is a unique, red-pigmented, thermophilic bacterium that preferentially grows in high-temperature environments ranging from 35-70°C. Due to the lack of studies performed on this organism, there is quite a bit of information missing in regard to the genes found within this organism’s genome and their function. This study focuses in on the Mrub_1345 gene in M. ruber, which has been suggested to be orthologous to the proC gene found of E. coli proline biosynthesis pathway. To test if these genes are orthologs, we performed the complementation assay on wild-type proC. Next, we performed site-directed mutagenesis on ...


Using Hadoop To Identify False Positives In Bacterial Strain Typing From Dna Fingerprints, Colin C. Adams 2016 California Polytechnic State University, San Luis Obispo

Using Hadoop To Identify False Positives In Bacterial Strain Typing From Dna Fingerprints, Colin C. Adams

Computer Science

Pyroprinting is a novel technique used by the Department of Biological Sciences to obtain “fingerprints” from the DNA of E. coli isolates in order to categorize them into strains. To determine the number of false positives that occur in the pyroprinting process, isolates with the same pyroprints needed to be sequenced to see if their underlying alleles match. If they do match, this shows they are indeed the same strain and are a true positive. If the alleles don’t match, they are different strains and are a false positive. To do this 100 isolates with nucleotide identifiers were sequenced ...


Homeolog Specific Expression Bias, Ronald D. Smith 2016 College of William and Mary

Homeolog Specific Expression Bias, Ronald D. Smith

Biology and Medicine Through Mathematics Conference

No abstract provided.


Phylogenetic Analysis Of Human Cytomegalovirus Pus27 And Pus28: Ascertaining An Independent Or Linked Evolutionary History, Jessica A. Scarborough 2016 University of San Francisco

Phylogenetic Analysis Of Human Cytomegalovirus Pus27 And Pus28: Ascertaining An Independent Or Linked Evolutionary History, Jessica A. Scarborough

Undergraduate Honors Theses

Human cytomegalovirus (HCMV) is a widespread pathogen that is particularly skilled at evading immune detection and defense mechanisms, largely due to extensive co-evolution with its host’s immune system. One aspect of this co-evolution involves the acquisition of four virally encoded GPCR chemokine receptor homologs, products of the US27, US28, UL33 and UL78 genes. G protein-coupled receptors (GPCR) are the largest family of cell surface proteins, found in organisms from yeast to humans. In this research, phylogenetic analysis was used to investigate the origins of the US27 and US28 genes, which are adjacent in the viral genome. The results indicate ...


Dawn Or Doom: The Risks And Rewards Of Emerging Technologies, Diana Hancock, Steve Tally, Gerry McCartney, Michele Arthur 2016 Purdue University

Dawn Or Doom: The Risks And Rewards Of Emerging Technologies, Diana Hancock, Steve Tally, Gerry Mccartney, Michele Arthur

Purdue P-12 Networking Summit & Poster Session

Dawn or Doom is a free and open to the public conference at Purdue where we focus on benefits and risks surrounding some of the technologies that are both the most disruptive to current practices and being adopted the fastest. A collection of Purdue faculty experts and some outside speakers showcase their many perspectives related to this technology explosion, explore conditions that will foster innovation and investment into the next generation, and address the big-picture issues where both optimism and pessimism are warranted.


Genome-Wide Compensatory Changes Accompany Drug-Selected Mutations In The Plasmodium Falciparum Crt Gene, Hongying Jiang, Jigar J. Patel, Ming Yi, Jianbing Mu, Jinhui Ding, Robert Stephens, Roland A. Cooper, Michael T. Ferdig, Xin-zhuan Su 2016 Old Dominion University

Genome-Wide Compensatory Changes Accompany Drug-Selected Mutations In The Plasmodium Falciparum Crt Gene, Hongying Jiang, Jigar J. Patel, Ming Yi, Jianbing Mu, Jinhui Ding, Robert Stephens, Roland A. Cooper, Michael T. Ferdig, Xin-Zhuan Su

Roland A. Cooper

Mutations in PfCRT (Plasmodium falciparum chloroquine-resistant transporter), particularly the substitution at amino acid position 76, confer chloroquine (CQ) resistance in P. falciparum. Point mutations in the homolog of the mammalian multidrug resistance gene (pfmdr1) can also modulate the levels of CQ response. Moreover, parasites with the same pfcrt and pfmdr1 alleles exhibit a wide range of drug sensitivity, suggesting that additional genes contribute to levels of CQ resistance (CQR). Reemergence of CQ sensitive parasites after cessation of CQ use indicates that changes in PfCRT are deleterious to the parasite. Some CQR parasites, however, persist in the field and grow well ...


Development Of Steady-State And Dynamic Flux Models For Broad-Scope Microbial Metabolism Analysis, Lian He 2016 Washington University in St. Louis

Development Of Steady-State And Dynamic Flux Models For Broad-Scope Microbial Metabolism Analysis, Lian He

Engineering and Applied Science Theses & Dissertations

Flux analysis techniques, including flux balance analysis (FBA) and 13C-metabolic flux analysis (MFA), can characterize carbon and energy flows through a cells metabolic network. By employing both 13C-labeling experiments and nonlinear programming, 13C-MFA provides a rigorous way of examining cell flux distributions in the central metabolism. FBA, on the other hand, gives a holistic review of optimal fluxomes on the genome scale. In this dissertation, flux analysis techniques were constructed to investigate the microbial metabolisms.

First, an open-source and programming-free platform of 13C-MFA (WUFlux) with a user-friendly interface in MATLAB was developed, which allowed both mass isotopomer distribution (MID) analysis ...


Design, Implementation And Evaluation Of A Medical Library Program To Support Biomedical Research In The Omics Era, Rolando Garcia-Milian, John Gallagher, Janis Glover 2016 Yale University

Design, Implementation And Evaluation Of A Medical Library Program To Support Biomedical Research In The Omics Era, Rolando Garcia-Milian, John Gallagher, Janis Glover

Rolando Garcia-Milian


Objectives
Design and implement a sustainable program that supports biomedical research at Yale University. Our program responds to the challenges posed by omics (e.g. genomics, transcriptomics, proteomics, etc.) technologies, identifies the role and place of the Yale Cushing/Whitney Medical Library in the high-throughput omics research cycle, and is based on the organizational culture of the institution.

Methods
Key challenges posed by omics technologies on preclinical and clinical research are: rapidly generating high amount of diverse omics data; integrating these diverse data; exponential increase in the biomedical literature and databases; use of pathway and network-based methods to analyze and ...


Design, Implementation And Evaluation Of A Medical Library Program To Support Biomedical Research In The Omics Era, Rolando Garcia-Milian 2016 Yale University

Design, Implementation And Evaluation Of A Medical Library Program To Support Biomedical Research In The Omics Era, Rolando Garcia-Milian

Rolando Garcia-Milian


Objectives
Design and implement a sustainable program that supports biomedical research at Yale University. Our program responds to the challenges posed by omics (e.g. genomics, transcriptomics, proteomics, etc.) technologies, identifies the role and place of the Yale Cushing/Whitney Medical Library in the high-throughput omics research cycle, and is based on the organizational culture of the institution.

Methods
Key challenges posed by omics technologies on preclinical and clinical research are: rapidly generating high amount of diverse omics data; integrating these diverse data; exponential increase in the biomedical literature and databases; use of pathway and network-based methods to analyze and ...


Identification Of Candidate Genes Underlying An Iron Efficiency Quantitative Trait Locus In Soybean, Gregory A. Peiffer, Keith E. King, Andrew J. Severin, Gregory D. May, Silvia R. Cianzio, Shun Fu Lin, Nicholas C. Lauter, Randy C. Shoemaker 2016 Iowa State University

Identification Of Candidate Genes Underlying An Iron Efficiency Quantitative Trait Locus In Soybean, Gregory A. Peiffer, Keith E. King, Andrew J. Severin, Gregory D. May, Silvia R. Cianzio, Shun Fu Lin, Nicholas C. Lauter, Randy C. Shoemaker

Andrew Severin

Prevalent on calcareous soils in the United States and abroad, iron deficiency is among the most common and severe nutritional stresses in plants. In soybean (Glycine max) commercial plantings, the identification and use of iron-efficient genotypes has proven to be the best form of managing this soil-related plant stress. Previous studies conducted in soybean identified a significant iron efficiency quantitative trait locus (QTL) explaining more than 70% of the phenotypic variation for the trait. In this research, we identified candidate genes underlying this QTL through molecular breeding, mapping, and transcriptome sequencing. Introgression mapping was performed using two related near-isogenic lines ...


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