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Human-Nonhuman Chimeras, Ontology, And Dignity: A Constructivist Approach To The Ethics Of Conducting Research On Cross-Species Hybrids, Jonathan M. Vajda 2017 Western Michigan University

Human-Nonhuman Chimeras, Ontology, And Dignity: A Constructivist Approach To The Ethics Of Conducting Research On Cross-Species Hybrids, Jonathan M. Vajda

The Hilltop Review

Developments in biological technology in the last few decades highlight the surprising and ever-expanding practical benefits of stem cells. With this progress, the possibility of combining human and nonhuman organisms is a reality, with ethical boundaries that are not readily obvious. These inter-species hybrids are of a larger class of biological entities called “chimeras.” As the concept of a human-nonhuman creature is conjured in our minds, either incredulous wonder or grotesque horror is likely to follow. This paper seeks to mitigate those worries and demotivate reasonable concerns raised against chimera research, all the while pressing current ethical positions toward their ...


Exploration Of Dna Transfer In The Nyc Subway, Sannia K. Tauqeer 2016 CUNY John Jay College

Exploration Of Dna Transfer In The Nyc Subway, Sannia K. Tauqeer

Student Theses

The ability to detect “touch” DNA has complicated the interpretation of DNA profiles in the field of forensics because it leads to the introduction of the concept of DNA transfer, persistence and background into casework. This project is geared towards understanding DNA transfer in the NYC subways and has relevance in groping and attempted sexual assault cases, where garments are submitted as evidence. The study involved 10 volunteers who were asked to wear a clean jacket during their trips on the subway for one week and the DNA from these jackets was collected, extracted, quantified, amplified and typed. The results ...


American Chestnut Sem Portfolio, Dakota Matthews 2016 SUNY College of Environmental Science and Forestry

American Chestnut Sem Portfolio, Dakota Matthews

N.C. Brown Center for Ultrastructure Studies

Scanning electron microscopy micrographs of transgenic american chestnut pollen and anthers. Chinkapin anthers and pollen imaged also.


Molecular Measurement Of Toxicity In Fish; Case Examples And Policy Implications, Jessica A. Freedman 2016 University of Rhode Island

Molecular Measurement Of Toxicity In Fish; Case Examples And Policy Implications, Jessica A. Freedman

Senior Honors Projects

Stormwater and oil are common urban contaminants that can be harmful to fish species. One way of recognizing exposed and impaired fish is by monitoring gene expression and gene induction. This study focused on the identification and validation of reference genes for measuring contaminant-induced changes in gene expression due to urban influence. In this study, reference genes (which are genes used to normalize data and remain consistent in varying exposures regardless of organism and tissue type) were established. Six genes were identified as reference genes (ef1a, wdtc1, mtm1, spop, rxrba and tuba1) from a longer list of potential reference genes ...


Examination Of The Relevance Of Pi3k And Pten Pathway In Ustilago Maydis., Nathaniel Edward Dalton 2016 University of Louisville

Examination Of The Relevance Of Pi3k And Pten Pathway In Ustilago Maydis., Nathaniel Edward Dalton

Electronic Theses and Dissertations

Ustilago maydis is a fungal pathogen that is an obligate parasite on Zea mays (Corn) in order to undergo and complete its sexual life cycle. The cells grow as a haploid form until they meet a compatible partner and undergo a dimorphic switch from a budding yeast-like cell type to a filamentous dikaryon. Infection of the host plant is characterized by leaf chlorosis, anthocyanin content, and formation of large galls that develop on the stem, leaves, cobs, and flowers. Many signaling cascades such as MAPK and PKA are involved in the regulation of the infection lifecycle. The Phosphatidylinosotiol 3 Kinase ...


Evolution In Light Of Mitonuclear Landscapes An Examination Of Mitochondrial Replacement In Killifish (Fundulus Spp.), Stephen D. Flanagan 2016 University of Southern Mississippi

Evolution In Light Of Mitonuclear Landscapes An Examination Of Mitochondrial Replacement In Killifish (Fundulus Spp.), Stephen D. Flanagan

Dissertations

The mitochondria are responsible for the bulk of energy production in eukaryotes. They possess their own genome that works in conjunction with the nuclear genome to accomplish the extraordinarily important task of energy conversion. When species hybridize there will be a mismatch in evolutionary histories between these two genomes. The deleterious interactions of these genomes have been studied in great detail (i.e. hybrid breakdown). However, little work has been conducted to understand the population genetic, and morphological consequences of wide-ranging replacement. The Fundulus notatus complex is comprised of 3 species: F. notatus, F. olivaceus, and F. euryzonus. Within the ...


Chip-Seq And Rna-Seq Reveal An Amrz-Mediated Mechanism For Cyclic Di-Gmp Synthesis And Biofilm Development By Pseudomonas Aeruginosa, Christopher J. Jones, David Newsom, Benjamin Kelly, Yasuhiko Irie, Laura K. Jennings, Binjie Xu, Dominique H. Limoli, Joe J. Harrison, Matthew R. Parsek, Peter White, Daniel J. Wozniak 2016 The Ohio State University

Chip-Seq And Rna-Seq Reveal An Amrz-Mediated Mechanism For Cyclic Di-Gmp Synthesis And Biofilm Development By Pseudomonas Aeruginosa, Christopher J. Jones, David Newsom, Benjamin Kelly, Yasuhiko Irie, Laura K. Jennings, Binjie Xu, Dominique H. Limoli, Joe J. Harrison, Matthew R. Parsek, Peter White, Daniel J. Wozniak

Yasuhiko Irie

The transcription factor AmrZ regulates genes important for P. aeruginosa virulence, including type IV pili, extracellular polysaccharides, and the flagellum; however, the global effect of AmrZ on gene expression remains unknown, and therefore, AmrZ may directly regulate many additional genes that are crucial for infection. Compared to the wild type strain, a ΔamrZ mutant exhibits a rugose colony phenotype, which is commonly observed in variants that accumulate the intracellular second messenger cyclic diguanylate (c-di-GMP). Cyclic di-GMP is produced by diguanylate cyclases (DGC) and degraded by phosphodiesterases (PDE). We hypothesized that AmrZ limits the intracellular accumulation of c-di-GMP through transcriptional repression ...


The Cababc Operon Essential For Biofilm And Rugose Colony Development In Vibrio Vulnificus, Jin Hwan Park, Youmi Jo, Song Yee Jang, Haenaem Kwon, Yasuhiko Irie, Matthew R. Parsek, Myung Hee Kim, Sang Ho Choi 2016 Seoul National University

The Cababc Operon Essential For Biofilm And Rugose Colony Development In Vibrio Vulnificus, Jin Hwan Park, Youmi Jo, Song Yee Jang, Haenaem Kwon, Yasuhiko Irie, Matthew R. Parsek, Myung Hee Kim, Sang Ho Choi

Yasuhiko Irie

A transcriptome analysis identified Vibrio vulnificus cabABC genes which were preferentially expressed in biofilms. The cabABC genes were transcribed as a single operon. The cabA gene was induced by elevated 3′,5′-cyclic diguanylic acid (c-di-GMP) and encoded a calcium-binding protein CabA. Comparison of the biofilms produced by the cabA mutant and its parent strain JN111 in microtiter plates using crystal-violet staining demonstrated that CabA contributed to biofilm formation in a calcium-dependent manner under elevated c-di-GMP conditions. Genetic and biochemical analyses revealed that CabA was secreted to the cell exterior through functional CabB and CabC, distributed throughout the biofilm matrix ...


Exploring Molecular Mechanisms Of Paradoxical Activation In The Braf Kinase Dimers: Atomistic Simulations Of Conformational Dynamics And Modeling Of Allosteric Communication Networks And Signaling Pathways, Amanda Tse, Gennady M. Verkhivker 2016 Chapman University

Exploring Molecular Mechanisms Of Paradoxical Activation In The Braf Kinase Dimers: Atomistic Simulations Of Conformational Dynamics And Modeling Of Allosteric Communication Networks And Signaling Pathways, Amanda Tse, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

The recent studies have revealed that most BRAF inhibitors can paradoxically induce kinase activation by promoting dimerization and enzyme transactivation. Despite rapidly growing number of structural and functional studies about the BRAF dimer complexes, the molecular basis of paradoxical activation phenomenon is poorly understood and remains largely hypothetical. In this work, we have explored the relationships between inhibitor binding, protein dynamics and allosteric signaling in the BRAF dimers using a network-centric approach. Using this theoretical framework, we have combined molecular dynamics simulations with coevolutionary analysis and modeling of the residue interaction networks to determine molecular determinants of paradoxical activation. We ...


Expression Of The Primary Carbohydrate Component Of The Bordetella Bronchiseptica Biofilm Matrix Is Dependent On Growth Phase But Independent Of Bvg Regulation, Yasuhiko Irie, Andrew Preston, Ming H. Yuk 2016 University of Dayton

Expression Of The Primary Carbohydrate Component Of The Bordetella Bronchiseptica Biofilm Matrix Is Dependent On Growth Phase But Independent Of Bvg Regulation, Yasuhiko Irie, Andrew Preston, Ming H. Yuk

Yasuhiko Irie

We previously showed that the Bvg virulence control system regulates biofilm formation in Bordetella bronchiseptica (Y. Irie, S. Mattoo, and M. H. Yuk, J. Bacteriol. 186:5692-5698, 2004). Analyses of the extracellular components of B. bronchiseptica biofilm matrix revealed that the major sugar component in the matrix was xylose, and linkage analysis indicated a majority of it to be in a 4-linked polymeric form. The production of xylose was independent of Bvg regulation but instead was dependent on bacterial growth phase. In addition, N-acetyl-glucosamine in the matrix was found to be important for the initial development of the biofilm ...


Fluorescence-Based Reporter For Gauging Cyclic Di-Gmp Levels In Pseudomonas Aeruginosa, Morten T. Rybtke, Bradley R. Borlee, Keiji Murakami, Yasuhiko Irie, Morten Hentzer, Thomas E. Nielsen, Michael Givskov, Matthew R. Parsek, Tim Tolker-Nielsen 2016 University of Copenhagen

Fluorescence-Based Reporter For Gauging Cyclic Di-Gmp Levels In Pseudomonas Aeruginosa, Morten T. Rybtke, Bradley R. Borlee, Keiji Murakami, Yasuhiko Irie, Morten Hentzer, Thomas E. Nielsen, Michael Givskov, Matthew R. Parsek, Tim Tolker-Nielsen

Yasuhiko Irie

The increased tolerance toward the host immune system and antibiotics displayed by biofilm-forming Pseudomonas aeruginosa and other bacteria in chronic infections such as cystic fibrosis bronchopneumonia is of major concern. Targeting of biofilm formation is believed to be a key aspect in the development of novel antipathogenic drugs that can augment the effect of classic antibiotics by decreasing antimicrobial tolerance. The second messenger cyclic di-GMP is a positive regulator of biofilm formation, and cyclic di-GMP signaling is now regarded as a potential target for the development of antipathogenic compounds. Here we describe the development of fluorescent monitors that can gauge ...


Sequence Annotation & Designing Gene-Specific Qpcr Primers (Computational), Raymond A. Enke 2016 enkera@jmu.edu

Sequence Annotation & Designing Gene-Specific Qpcr Primers (Computational), Raymond A. Enke

Ray Enke Ph.D.

This class tested protocol will guide students through the steps for the following activities:
  • Obtaining and annotating genomic DNA and mRNA sequence information
  • Designing primers for quantitative PCR (qPCR) analysis of a cDNA library


Qpcr Primer Standard Curve Assay (Wet Lab) + Kegg Pathway Analysis (Computational), Raymond A. Enke 2016 enkera@jmu.edu

Qpcr Primer Standard Curve Assay (Wet Lab) + Kegg Pathway Analysis (Computational), Raymond A. Enke

Ray Enke Ph.D.

This class tested protocol will guide students through the steps for the following activities:
  • analyzing qPCR standard curve data to determine primer efficiency
  • analyzing differential gene expression experimental qPCR data
  • applying KEGG pathway analysis of selected candidates genes


An Analysis Of Gene-Enzyme Variability In Natural Populations Of Drosophila Melanogaster And D. Simulans, Stephen J. O'Brien, Ross J. MacIntyre 2016 Cornell University

An Analysis Of Gene-Enzyme Variability In Natural Populations Of Drosophila Melanogaster And D. Simulans, Stephen J. O'Brien, Ross J. Macintyre

Stephen O'Brien

No abstract provided.


Heterologous Expression Of A Rice Mir395 Gene In Nicotiana Tabacum Impairs Sulfate Homeostasis, Ning Yuan, Shuangrong Yuan, Zhigang Li, Dayong Li, Qian Hu, Hong Luo 2016 Clemson University

Heterologous Expression Of A Rice Mir395 Gene In Nicotiana Tabacum Impairs Sulfate Homeostasis, Ning Yuan, Shuangrong Yuan, Zhigang Li, Dayong Li, Qian Hu, Hong Luo

Hong Luo

Sulfur participates in many important mechanisms and pathways of plant development. The most common source of sulfur in soil –SO42−– is absorbed into root tissue and distributed into aerial part through vasculature system, where it is reduced into sulfite and finally sulfide within the subcellular organs such as chloroplasts and mitochondria and used for cysteine and methionine biosynthesis. MicroRNAs are involved in many regulation pathways by repressing the expression of their target genes. MiR395 family in Arabidopsis thaliana has been reported to be an important regulator involved in sulfate transport and assimilation, and a high-affinity sulphate transporter and three ATP ...


Ataluren Stimulates Ribosomal Selection Of Near-Cognate Trnas To Promote Nonsense Suppression, Bijoyita Roy, Westley J. Friesen, Yuki Tomizawa, John D. Leszyk, Jin Zhuo, Briana Johnson, Jumana Dakka, Christopher R. Trotta, Xiaojiao Xue, Venkateshwar Mutyam, Kim M. Keeling, James A. Mobley, Steven M. Rowe, David M. Bedwell, Ellen M. Welch, Allan Jacobson 2016 University of Massachusetts Medical School

Ataluren Stimulates Ribosomal Selection Of Near-Cognate Trnas To Promote Nonsense Suppression, Bijoyita Roy, Westley J. Friesen, Yuki Tomizawa, John D. Leszyk, Jin Zhuo, Briana Johnson, Jumana Dakka, Christopher R. Trotta, Xiaojiao Xue, Venkateshwar Mutyam, Kim M. Keeling, James A. Mobley, Steven M. Rowe, David M. Bedwell, Ellen M. Welch, Allan Jacobson

Microbiology and Physiological Systems Publications and Presentations

A premature termination codon (PTC) in the ORF of an mRNA generally leads to production of a truncated polypeptide, accelerated degradation of the mRNA, and depression of overall mRNA expression. Accordingly, nonsense mutations cause some of the most severe forms of inherited disorders. The small-molecule drug ataluren promotes therapeutic nonsense suppression and has been thought to mediate the insertion of near-cognate tRNAs at PTCs. However, direct evidence for this activity has been lacking. Here, we expressed multiple nonsense mutation reporters in human cells and yeast and identified the amino acids inserted when a PTC occupies the ribosomal A site in ...


Population Dynamics And Genetic Differentiation Of The Threatened Freshwater Mussel Species Fusconaia Askewi, Fusconaia Lananensis, And Pleurobema Riddellii, Edith D. Plants-Paris 2016 University of Texas at Tyler

Population Dynamics And Genetic Differentiation Of The Threatened Freshwater Mussel Species Fusconaia Askewi, Fusconaia Lananensis, And Pleurobema Riddellii, Edith D. Plants-Paris

Biology Theses

North America has the most diverse freshwater mussel fauna in the world with approximately 300 species; unfortunately, extinction rates for freshwater mussels rivals the rates of many other groups of organisms. Population-level natural life history data is essential in the management of species of conservation concern, yet basic information about freshwater mussel life-history and demographic traits are unknown for many species. To further complicate matters, taxonomic uncertainty exists among some members of the group. The work detailed herein had two goals: to gain further understanding of the taxonomic relationship between Fusconaia lananensis and F. askewi by sequencing genes that had ...


Ethnic Disparity In 21-Hydroxylase Gene Mutations Identified In Pakistani Congenital Adrenal Hyperplasia Patient, Aysha Habib Khan, Muniba Aban, Jamal Raza, Naeem ul Haq, Abdul Jabbar, Tariq Moatter 2016 Aga Khan University

Ethnic Disparity In 21-Hydroxylase Gene Mutations Identified In Pakistani Congenital Adrenal Hyperplasia Patient, Aysha Habib Khan, Muniba Aban, Jamal Raza, Naeem Ul Haq, Abdul Jabbar, Tariq Moatter

Aysha Habib

Background: Congenital adrenal hyperplasia (CAH) is a group of autosomal recessive disorders caused by defects in the steroid 21 hydroxylase gene (CYP21A2). We studied the spectrum of mutations in CYP21A2 gene in a multi-ethnic population in Pakistan to explore the genetics of CAH. Methods: A cross sectional study was conducted for the identification of mutations CYP21A2 and their phenotypic associations in CAH using ARMS-PCR assay. Results: Overall, 29 patients were analyzed for nine different mutations. The group consisted of two major forms of CAH including 17 salt wasters and 12 simple virilizers. There were 14 phenotypic males and 15 females ...


Optimization Of A Genomic Editing System Using Crispr/Cas9-Induced Site-Specific Gene Integration, Jillian L. McCool Ms., Nick Hum, Gabriela G. Loots 2016 California State University, Chico

Optimization Of A Genomic Editing System Using Crispr/Cas9-Induced Site-Specific Gene Integration, Jillian L. Mccool Ms., Nick Hum, Gabriela G. Loots

STAR (STEM Teacher and Researcher) Presentations

The CRISPR-Cas system is an adaptive immune system found in bacteria which helps protect against the invasion of other microorganisms. This system induces double stranded breaks at precise genomic loci (1) in which repairs are initiated and insertions of a target are completed in the process. This mechanism can be used in eukaryotic cells in combination with sgRNAs (1) as a tool for genome editing. By using this CRISPR-Cas system, in addition to the “safe harbor locus,” ROSAβ26, the incorporation of a target gene into a site that is not susceptible to gene silencing effects can be achieved through few ...


Relationship Between Morphogenesis And Secretion In The Filamentous Fungus Aspergillus Nidulans, Lakshmi Preethi Yerra 2016 University of Nebraska-Lincoln

Relationship Between Morphogenesis And Secretion In The Filamentous Fungus Aspergillus Nidulans, Lakshmi Preethi Yerra

Dissertations and Theses in Biological Sciences

Filamentous fungi have a long history in biotechnology for the production of food ingredients, pharmaceuticals and enzymes. The advancements made in recent years have earned filamentous fungi such as Aspergillus species a dominant place among microbial cell factories. Although the model fungus A. nidulans has been extensively studied, the genetic and regulatory networks that underlie morphogenesis and development have yet to be fully characterized. The Rho GTPases (Cdc42 and RacA) are one of the most important regulators of the morphogenetic processes among diverse eukaryotic organisms. Although the functions of these GTPases are relatively well-characterized, little is known about their downstream ...


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