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Genome Wide Co-Expression Among The Starch Debranching Enzyme Genes Atisa1, Atisa2, And Atisa3 In Arabidopsis Thaliana, Ling Li, Hilal Ilarslan, Martha G. James, Alan M. Myers, Eve Syrkin Wurtele 2017 Iowa State University

Genome Wide Co-Expression Among The Starch Debranching Enzyme Genes Atisa1, Atisa2, And Atisa3 In Arabidopsis Thaliana, Ling Li, Hilal Ilarslan, Martha G. James, Alan M. Myers, Eve Syrkin Wurtele

Eve Wurtele

Each of four starch debranching enzymes (DBE) is distinct and highly conserved across the plant kingdom; however, the specific functions of these proteins in carbohydrate metabolism are not well understood. DBEs function in both biosynthesis and degradation of starch, and two have been shown to function as multimers in various quarternary structures that can contain one or more DBE proteins, i.e. ISA1 homomultimers and ISA1/ISA2 heteromultimers. This study characterizes potential functional relationships between the three isoamylase-type DBE proteins (ISA) of Arabidopsis using a comprehensive bioinformatics analysis and promoter fusion approach to determine tissue-, subcellular-, and temporal specificity of ...


Jennifer Maurer Phd Thesis.Pdf, Jennifer Maurer 2017 University of Massachusetts Medical School

Jennifer Maurer Phd Thesis.Pdf, Jennifer Maurer

Jennifer Maurer


Signaling cascades, such as the extracellular signal-regulated kinase (ERK) pathway, play vital roles in early vertebrate development. Signals through these pathways are initiated by a growth factor or hormone, are transduced through a kinase cascade, and result in the expression of specific downstream genes that promote cellular proliferation, growth, or differentiation.Tight regulation of these signals is provided by positive or negative modulators at varying levels in the pathway, and is required for proper development and function. Two members of the dual-specificity phosphatase (Dusp) family, dusp6 and dusp2, are believed to be negative regulators of the ERK pathway and are ...


Characterization Of Acaricide Resistance, Plant-Mediated Rnai Against Two-Spotted Spider Mites (Tetranychus Urticae Koch), And Assessing Off- And Non-Target Effects, Hooman Hosseinzadeh Namin 2017 The University of Western Ontario

Characterization Of Acaricide Resistance, Plant-Mediated Rnai Against Two-Spotted Spider Mites (Tetranychus Urticae Koch), And Assessing Off- And Non-Target Effects, Hooman Hosseinzadeh Namin

Electronic Thesis and Dissertation Repository

The two-spotted spider mite (TSSM), Tetranychus urticae (Koch), is one of the most damaging agricultural pests in the world. It feeds on over 150 crops, causing considerable yield losses in greenhouses and agricultural fields. Currently, using synthetic acaricides is the main method to control TSSM. However, it can develop resistance to acaricides with repeated exposure, and typically resistance can occur within two to four years. To understand the underlying mechanisms of spider mite adaptation to acaricides is an essential part of resistance management strategy. The resistance ratio of the pyridaben-selected strain compared with the pre-selection strain was estimated at greater ...


Characterization Of A Novel Mitochondrial Plasmid In Brassica, Mackenzie Strehle 2017 University of Nebraska - Lincoln

Characterization Of A Novel Mitochondrial Plasmid In Brassica, Mackenzie Strehle

UCARE Research Products

Possessing some of the largest and most complex genomes of any eukaryotic organelles, plant mitochondria are notorious for their rapidly rearranging genetic framework. In addition to containing a large and complex mitochondrial genome, the mitochondria of several plants in the genus Brassica have also been shown to contain an independent, self-replicating linear plasmid. Interestingly, the plasmid appears to be able to move independently between the cytoplasm and the mitochondria, and it can be paternally inherited, unlike the rest of the mitochondrial genome. The plasmid also has features similar to those of adenoviruses, including terminal inverted repeats and covalently bound proteins ...


Transferable Multiresistance Plasmids Carrying Cfr In Enterococcus Spp. From Swine And Farm Environment, Yang Liu, Yang Wang, Stefan Schwarz, Yun Li, Zhangqi Shen, Qijing Zhang, Congming Wu, Jianzhong Shen 2017 China Agricultural University

Transferable Multiresistance Plasmids Carrying Cfr In Enterococcus Spp. From Swine And Farm Environment, Yang Liu, Yang Wang, Stefan Schwarz, Yun Li, Zhangqi Shen, Qijing Zhang, Congming Wu, Jianzhong Shen

Qijing Zhang

Seventy-seven porcine Enterococcus isolates with florfenicol MICs of ≥16 μg of were/ml screened for the presence of the multiresistance gene cfr, its location on plasmids, and its genetic environment. Three isolates—Enterococcus thailandicus 3-38 (from a porcine rectal swab collected at a pig farm), Enterococcus thailandicus W3, and Enterococcus faecalis W9-2 (the latter two from sewage at a different farm), carried the cfr gene. The SmaI pulsed-field gel electrophoresis patterns of the three isolates differed distinctly. In addition, E. faecalis W9-2 was assigned to a new multilocus sequence type ST469. Mating experiments and Southern blot analysis indicated that cfr ...


Synergistic Effects Of Anti-Cmea And Anti-Cmeb Peptide Nucleic Acids On Sensitizing Campylobacter Jejuni To Antibiotics, Yang Mu, Zhangqi Shen, Byeonghwa Jeon, Lei Dai, Qijing Zhang 2017 Iowa State University

Synergistic Effects Of Anti-Cmea And Anti-Cmeb Peptide Nucleic Acids On Sensitizing Campylobacter Jejuni To Antibiotics, Yang Mu, Zhangqi Shen, Byeonghwa Jeon, Lei Dai, Qijing Zhang

Qijing Zhang

The CmeABC efflux pump in Campylobacter jejuni confers resistance to structurally divergent antimicrobials, and inhibition of CmeABC represents a promising strategy to control antibiotic-resistant Campylobacter. Antisense peptide nucleic acids (PNAs) targeting the three components of CmeABC were evaluated for inhibition of CmeABC expression. The result revealed a synergistic effect of the PNAs targeting CmeA and CmeB on sensitizing C. jejuni to antibiotics. This finding further demonstrates the feasibility of using PNAs to potentiate antibiotics against antibiotic-resistant Campylobacter.


Mutational And Transcriptomic Changes Involved In The Development Of Macrolide Resistance In Campylobacter Jejuni, Haihong Hao, Zonghui Yuan, Zhangqi Shen, Jing Han, Orhan Sahin, Peng Liu, Qijing Zhang 2017 Iowa State University

Mutational And Transcriptomic Changes Involved In The Development Of Macrolide Resistance In Campylobacter Jejuni, Haihong Hao, Zonghui Yuan, Zhangqi Shen, Jing Han, Orhan Sahin, Peng Liu, Qijing Zhang

Qijing Zhang

Macrolide antibiotics are important for clinical treatment of infections caused by Campylobacter jejuni. Development of resistance to this class of antibiotics in Campylobacter is a complex process, and the dynamic molecular changes involved in this process remain poorly defined. Multiple lineages of macrolide-resistant mutants were selected by stepwise exposure of C. jejuni to escalating doses of erythromycin or tylosin. Mutations in target genes were determined by DNA sequencing, and the dynamic changes in the expression of antibiotic efflux transporters and the transcriptome of C. jejuni were examined by real-time reverse transcription-PCR, immunoblotting, and DNA microarray analysis. Multiple types of mutations ...


High Incidence And Endemic Spread Of Ndm-1-Positive Enterobacteriaceae In Henan Province, China, Shangshang Qin, Ying Fu, Qijing Zhang, Hui Qi, Jian Guo Wen, Hui Xu, Lijuan Xu, Li Zeng, Hao Tian, Lijuan Rong, Yonghong Li, Lihong Shan, Hongde Xu, Yunsong Yu, Xianju Feng, Hong-Min Liu 2017 Zhengzhou University

High Incidence And Endemic Spread Of Ndm-1-Positive Enterobacteriaceae In Henan Province, China, Shangshang Qin, Ying Fu, Qijing Zhang, Hui Qi, Jian Guo Wen, Hui Xu, Lijuan Xu, Li Zeng, Hao Tian, Lijuan Rong, Yonghong Li, Lihong Shan, Hongde Xu, Yunsong Yu, Xianju Feng, Hong-Min Liu

Qijing Zhang

The emergence and spread of New Delhi metallo-β-lactamase 1 (NDM-1)-producing carbapenem-resistant Enterobacteriaceae (CRE) present an urgent threat to human health. In China, the blaNDM-1 gene has been reported mostly in Acinetobacter spp. but is rarely found in Enterobacteriaceae. Here, we report a high incidence and endemic spread of NDM-1-producing CRE in Henan Province in China. Sixteen (33.3%) of the 48 CRE isolates obtained from patients during June 2011 to July 2012 were positive for blaNDM-1, and the gene was found to be carried on plasmids of various sizes (∼55 to ∼360 kb). These plasmids were readily transferrable to ...


Identification Of A Novel Membrane Transporter Mediating Resistance To Organic Arsenic In Campylobacter Jejuni, Zhangqi Shen, Taradon Luangtongkum, Zhiyi Qiang, Byeonghwa Jeon, Liping Wang, Qijing Zhang 2017 Iowa State University

Identification Of A Novel Membrane Transporter Mediating Resistance To Organic Arsenic In Campylobacter Jejuni, Zhangqi Shen, Taradon Luangtongkum, Zhiyi Qiang, Byeonghwa Jeon, Liping Wang, Qijing Zhang

Qijing Zhang

Although bacterial mechanisms involved in the resistance to inorganic arsenic are well understood, the molecular basis for organic arsenic resistance has not been described. Campylobacter jejuni, a major food-borne pathogen causing gastroenteritis in humans, is highly prevalent in poultry and is reportedly resistant to the arsenic compound roxarsone (4-hydroxy-3-nitrobenzenearsonic acid), which has been used as a feed additive in the poultry industry for growth promotion. In this study, we report the identification of a novel membrane transporter (named ArsP) that contributes to organic arsenic resistance in Campylobacter. ArsP is predicted to be a membrane permease containing eight transmembrane helices, distinct ...


The Role Of T-Box Proteins In Vertebrate Germ Layer Formation And Patterning, Sushma Teegala 2017 The Graduate Center, City University of New York

The Role Of T-Box Proteins In Vertebrate Germ Layer Formation And Patterning, Sushma Teegala

All Graduate Works by Year: Dissertations, Theses, and Capstone Projects

All of the tissues in triploblastic organisms, with the exception of the germ cells, arise from the three germ layers, ectoderm, mesoderm and the endoderm. The identification of the genes that underlie the differentiation of these layers is crucial to our understanding of development. T-box family proteins are DNA-binding transcriptional regulators that play important roles during germ layer formation in the early vertebrate embryo. Well-characterized members of this family, including the transcriptional activators Brachyury and VegT, are essential for the proper formation of mesoderm and endoderm, respectively. To date, T-box proteins have not been shown to play a role in ...


Examination Of Contribution Of Pentose Catabolism To Molecular Hydrogen Formation By Targeted Disruption Of Arabinose Isomerase (Araa) In The Hyperthermophilic Bacterium, Thermotoga Maritima, Derrick White 2017 University of Nebraska - Lincoln

Examination Of Contribution Of Pentose Catabolism To Molecular Hydrogen Formation By Targeted Disruption Of Arabinose Isomerase (Araa) In The Hyperthermophilic Bacterium, Thermotoga Maritima, Derrick White

Dissertations and Theses in Biological Sciences

Thermotoga maritima ferments a broad range of sugars to form acetate, carbon dioxide, traces of lactate and near theoretic yields of molecular hydrogen (H2). In this organism, the catabolism of pentose sugars such as arabinose depends on the interaction between the pentose phosphate, Embden Myerhoff and Entner Doudoroff pathways. While values for H2 yield have been determined using pentose supplemented complex media (CM) and predicted by metabolic pathway reconstruction, quantitative in vivo measurements derived from pathway elimination have not been reported reflecting the lack of a genetic method for the creation of targeted mutations. Here, a spontaneous and ...


Amelioration Of Prenatal Alcohol Effects By Environmental Enrichment In A Mouse Model Of Fasd, Aniruddho Chokroborty-Hoque 2017 The University of Western Ontario

Amelioration Of Prenatal Alcohol Effects By Environmental Enrichment In A Mouse Model Of Fasd, Aniruddho Chokroborty-Hoque

Electronic Thesis and Dissertation Repository

Maternal alcohol consumption during pregnancy results in a spectrum of behavioural and cognitive deficits collectively known as Fetal Alcohol Spectrum Disorders (FASD). Currently, little is know about if and how the external environment may modulate these deficits. I have used C57BL/6 mice to study this interaction between prenatal alcohol exposure and the postnatal environment. Alcohol exposure during synaptogenesis produces high levels of anxiety-like traits and decreased memory performance. Alcohol-exposed mice (and matched unexposed controls) were put in 'environmentally-enriched' conditions of voluntary exercise, physical activities and cognitive stimulation to ascertain the effects of a positive postnatal environment. The results show ...


Hfq Links Translation Repression To Stress-Induced Mutagenesis In E. Coli, Jiandong Chen, Susan Gottesman 2017 National Cancer Institute

Hfq Links Translation Repression To Stress-Induced Mutagenesis In E. Coli, Jiandong Chen, Susan Gottesman

Jiandong Chen

Mismatch repair (MMR) is a conserved mechanism exploited by cells to correct DNA replication errors both in growing cells and under nongrowing conditions. Hfq (host factor for RNA bacteriophage Qβ replication), a bacterial Lsm family RNA-binding protein, chaperones RNA–RNA interactions between regulatory small RNAs (sRNAs) and target messenger RNAs (mRNAs), leading to alterations of mRNA translation and/or stability. Hfq has been reported to post-transcriptionally repress the DNA MMR gene mutS in stationary phase, possibly limiting MMR to allow increased mutagenesis. Here we report that Hfq deploys dual mechanisms to control mutS expression. First, Hfq binds directly to an ...


Intergenerational Effects Of Nicotine In An Animal Model Of Paternal Nicotine Exposure, Markus Parzival Vallaster 2017 University of Massachusetts Medical School

Intergenerational Effects Of Nicotine In An Animal Model Of Paternal Nicotine Exposure, Markus Parzival Vallaster

GSBS Dissertations and Theses

Environmental conditions imposed onto organisms during certain phases of their life cycles such as embryogenesis or puberty can not only impact the organisms’ own health, but also affect subsequent generations. The underlying mechanisms causing intergenerational phenotypes are not encoded in the genome, but the result of reversible epigenetic modifications. This work investigates in a mouse model the impact of paternal nicotine exposure on the next generation regarding addictive behavior modulation, metabolic changes, and molecular mechanisms. It provides evidence that male offspring from nicotine-exposed fathers (NIC offspring) is more resistant to lethal doses of nicotine. This phenotype is gender-specific and depends ...


Performing A Genetic Screen To Identify Factors That Promote Lncrna-Dependent Gene Repression, Chrishan Fernando, Cecilia Yiu, Sara Cloutier, Siwen Wang, Elizabeth Tran 2017 Purdue University

Performing A Genetic Screen To Identify Factors That Promote Lncrna-Dependent Gene Repression, Chrishan Fernando, Cecilia Yiu, Sara Cloutier, Siwen Wang, Elizabeth Tran

The Summer Undergraduate Research Fellowship (SURF) Symposium

Long non-coding RNAs (lncRNAs) were once thought not to have useful functions in organisms but rather to be products of aberrant transcription. However, roles are being found for lncRNAs in beneficial processes such as controlling gene expression. In some of these cases, lncRNAs form R-loops in vivo. R-loops are nucleic acid structures consisting of hybridized strands of single-stranded DNA (ssDNA) and single-stranded RNA (ssRNA) as well as the displaced strand of ssDNA. Formation of these R-loops is important for gene regulation by the lncRNAs. However, factors that promote formation of lncRNA R-loops are not known. The gene PHO84 is being ...


Tumor Formation In Response To Loss Of Chromatin Remodeler Chd5 In Zebrafish, Taylor R. Sabato, Erin L. Sorlien, Dr. Joseph P. Ogas 2017 Purdue University

Tumor Formation In Response To Loss Of Chromatin Remodeler Chd5 In Zebrafish, Taylor R. Sabato, Erin L. Sorlien, Dr. Joseph P. Ogas

The Summer Undergraduate Research Fellowship (SURF) Symposium

Chromodomain helicase DNA binding protein 5 (CHD5) has been identified as a tumor suppressor in humans. Deletion or mutation of CHD5 has been observed in numerous cancers, including neuroblastoma and melanoma. We hypothesize that chd5 is also a tumor suppressor in zebrafish, a powerful model system to study tumorigenesis. Many genes involved in tumorigenesis are conserved in zebrafish, and they develop fully penetrant tumor phenotypes. We have created chd5 knock-out zebrafish using CRISPR/Cas9 and are monitoring them for tumor development. In addition to the chd5 knock-outs, we are undertaking a double-mutant approach by coupling loss of ...


A Rapid Colorimetric Peptide Nucleic Acid Loop-Mediated Isothermal Amplification Assay For The Detection Of The Idh1 Mutation In Glioblastoma, Edward J. Raack 2017 eraack

A Rapid Colorimetric Peptide Nucleic Acid Loop-Mediated Isothermal Amplification Assay For The Detection Of The Idh1 Mutation In Glioblastoma, Edward J. Raack

All NMU Master's Theses

The IDH1 mutation is an important diagnostic and prognostic biomarker used to characterize glioblastoma (GBM). Patients harboring the IDH1 mutation have improved overall survival following maximal resection. Knowledge of the IDH1 mutation status allows the surgeon to modify the surgical plan; however, no existing molecular test can provide this information intraoperatively. We designed a novel colorimetric peptide nucleic acid loop-mediated isothermal amplification (PNA-LAMP) method that rapidly detects the IDH1 R132H mutation in GBM. PNA-LAMP amplifies target DNA under isothermal conditions with high specificity and speed. The PNA prevents amplification of wild-type IDH1 DNA, while allowing amplification of the R132H variant ...


Pirna Biogenesis And Transposon Silencing In Drosophila: A Dissertation, Zhao Zhang 2017 University of Massachusetts Medical School

Pirna Biogenesis And Transposon Silencing In Drosophila: A Dissertation, Zhao Zhang

Zhao Zhang

piRNAs guide PIWI proteins to silence transposons in animal germ cells. In Drosophila, the heterochromatic piRNA clusters transcribe piRNA precursors to be transported into nuage, a perinuclear structure for piRNA production and transposon silencing. At nuage, reciprocal cycles of piRNA-directed RNA cleavage—catalyzed by the PIWI proteins Aubergine (Aub) and Argonaute3 (Ago3) in Drosophila—destroy the sense transposon mRNA and expand the population of antisense piRNAs in response to transposon expression, a process called the Ping-Pong cycle. Heterotypic Ping-Pong between Aub and Ago3 ensures that antisense piRNAs predominate. My thesis research mainly focuses on two fundamental questions about the piRNA ...


Engineering And Verifying Requirements For Programmable Self-Assembling Nanomachines, Robyn Lutz, Jack Lutz, James Lathrop, Titus Klinge, Eric Henderson, Davita Mathur, Dalia Abo Sheasha 2017 Iowa State University

Engineering And Verifying Requirements For Programmable Self-Assembling Nanomachines, Robyn Lutz, Jack Lutz, James Lathrop, Titus Klinge, Eric Henderson, Davita Mathur, Dalia Abo Sheasha

Robyn Lutz

We propose an extension of van Lamsweerde's goal-oriented requirements engineering to the domain of programmable DNA nanotechnology. This is a domain in which individual devices (agents) are at most a few dozen nanometers in diameter. These devices are programmed to assemble themselves from molecular components and perform their assigned tasks. The devices carry out their tasks in the probabilistic world of chemical kinetics, so they are individually error-prone. However, the number of devices deployed is roughly on the order of a nanomole (a 6 followed by fourteen 0s), and some goals are achieved when enough of these agents achieve ...


Cellular/Molecular Analysis Of Interspecies Sterile Male Hybrids In Drosophila, Rachelle L. Kanippayoor 2017 The Unviersity of Western Ontario

Cellular/Molecular Analysis Of Interspecies Sterile Male Hybrids In Drosophila, Rachelle L. Kanippayoor

Electronic Thesis and Dissertation Repository

Over time, genetic differences can accumulate between populations that are geographically separated. This genetic divergence can lead to the evolution of reproductive isolating mechanisms that reduce gene flow between the populations and, upon secondary contact, result in distinct species. The process of speciation is, thus, what accounts for the multitude of species that contribute to the rich biodiversity on Earth. Interspecies hybrid sterility is a postzygotic isolating mechanism that affects the development of hybrids, rendering them sterile. A notable trend, known as Haldane's Rule, describes that heterogametic individual (e.g. males in Drosophila) are more susceptible to sterility than ...


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