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Mapping Molecular Datasets Back To The Brain Regions They Are Extracted From: Remembering The Native Countries Of Hypothalamic Expatriates And Refugees, Arshad M. Khan, Alice H. Grant, Anais Martinez, Gully APC Burns, Brendan S. Thatcher, Vishwanath T. Anekonda, Benjamin W. Thompson, Zachary S. Roberts, Daniel H. Moralejo, James E. Blevins 2018 University of Texas at El Paso

Mapping Molecular Datasets Back To The Brain Regions They Are Extracted From: Remembering The Native Countries Of Hypothalamic Expatriates And Refugees, Arshad M. Khan, Alice H. Grant, Anais Martinez, Gully Apc Burns, Brendan S. Thatcher, Vishwanath T. Anekonda, Benjamin W. Thompson, Zachary S. Roberts, Daniel H. Moralejo, James E. Blevins

Arshad M. Khan, Ph.D.

This article, which includes novel unpublished data along with commentary and analysis,
focuses on approaches to link transcriptomic, proteomic, and peptidomic datasets mined from
brain tissue to the original locations within the brain that they are derived from using digital atlas
mapping techniques. We use, as an example, the transcriptomic, proteomic and peptidomic
analyses conducted in the mammalian hypothalamus. Following a brief historical overview, we
highlight studies that have mined biochemical and molecular information from the hypothalamus
and then lay out a strategy for how these data can be linked spatially to the mapped locations in a
canonical brain atlas ...


Exploiting Click-Chemistry And Microfluidics To Map The Neuronal Itinerary Of App Processing And Amyloid-Beta Generation, Namratha Srinivas 2018 Washington University in St. Louis

Exploiting Click-Chemistry And Microfluidics To Map The Neuronal Itinerary Of App Processing And Amyloid-Beta Generation, Namratha Srinivas

Engineering and Applied Science Theses & Dissertations

Alzheimer’s disease (AD) is a chronic neurodegenerative disease and is the sixth leading cause of death in the United States with approximately 5.5 million Americans diagnosed with it. The neuropathological hallmark includes extracellular senile plaques and intraneuronal neurofibrillary tangles. Recent GWAS studies have identified genes associated with AD, and have revealed several classes of genes implicated in disease pathogenesis. In particular, three general pathways associated with an increased risk of AD included: 1) cholesterol metabolism, innate immune system, and the membrane trafficking. Our lab has focused on intracellular trafficking as it relates to the processing of amyloid precursor ...


Development Of Lc-Ms For The Identification And Characterization Of Non-Adjacent Dna Photoproduct Formation In G-Quadruplex Forming Sequences, Claudia Posadas 2018 Washington University in St. Louis

Development Of Lc-Ms For The Identification And Characterization Of Non-Adjacent Dna Photoproduct Formation In G-Quadruplex Forming Sequences, Claudia Posadas

Arts & Sciences Electronic Theses and Dissertations

Ultraviolet light is well known to induce cyclobutane pyrimidine dimers (CPD) and pyrimidine (6–4) pyrimidone photoproducts in duplex DNA, which interfere with DNA replication and transcription. Recently, a new class of DNA photoproducts known as anti cyclobutanepyrimidine dimers have been discovered, which form in G-quadruplex forming sequences in solution. G-quadruplex structures have been proposed to form in human DNA telomeres and certain promoters in vivo but evidence for their existence has been lacking. Since anti-cyclobutante pyrimidine dimers have been shown to form in G-quadruplex forming sequences, their formation in irradiated human cells could be used to confirm the ...


The Use Of Potato (Solanum Tuberosum) Suspension Cells For Rapid Screening Of Chloroplast Transformation Vectors, Lindsey Shover 2018 University of Tennessee, Knoxville

The Use Of Potato (Solanum Tuberosum) Suspension Cells For Rapid Screening Of Chloroplast Transformation Vectors, Lindsey Shover

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Chloroplast genetic engineering is unique in that it allows for high levels of gene expression while providing a means of natural bio-confinement. Although the chloroplast genome sequence of over 800 plant species is known, the elements that naturally regulate chloroplast gene expression are poorly understood. Recently, our lab has developed a 264 part modular cloning kit that contains known chloroplast regulatory elements. This kit can be used for the construction of novel chloroplast transformation cassettes; however, functional testing of these cassettes is currently hindered by standard chloroplast transformation technologies. Therefore, the aim of this experiment was to develop a rapid ...


Same-Sex Marriage And The Baby Carriage: A Post-Obergefell Analysis Of Art Funding For Same-Sex Couples In The United States, Charmaine Mech 2018 University of Georgia School of Law

Same-Sex Marriage And The Baby Carriage: A Post-Obergefell Analysis Of Art Funding For Same-Sex Couples In The United States, Charmaine Mech

Georgia Journal of International & Comparative Law

No abstract provided.


Optimizing Genetic Manipulation Of Methanogens Through Faster Cloning Techniques, Merrisa Jennings 2018 University of Arkansas, Fayetteville

Optimizing Genetic Manipulation Of Methanogens Through Faster Cloning Techniques, Merrisa Jennings

Biological and Agricultural Engineering Undergraduate Honors Theses

Methanogenesis is the biological production of methane. Only anaerobic archaea known as methanogens are capable of such a metabolic feat. They have strict living conditions and substrate sources which determine their rate of metabolism. This is of particular importance from a greenhouse gas reduction perspective or biogas capturing perspective. One of the best ways to optimize methanogen methane production is via genetic manipulation. The current procedures are timely though, therefore a faster cloning processes should be developed. The objective of this study was to optimize a premade genetic transformation kit known as the Gibson Kit. The Gibson Kit was supposed ...


Ketone Bodies And Signaling In Pancreatic Cancer Cell Lines, Kyla B. Buettner, Pankaj K. Singh, Surendra K. Shukla 2018 University of Nebraska at Omaha

Ketone Bodies And Signaling In Pancreatic Cancer Cell Lines, Kyla B. Buettner, Pankaj K. Singh, Surendra K. Shukla

Theses/Capstones/Creative Projects

Pancreatic cancer is the fourth leading cause of cancer-related deaths in the United States, and 95% of these cases are caused by PDAC (pancreatic ductal adenocarcinoma). Ketone bodies have previously been shown to decrease cell proliferation and cancer-induced cachexia. The molecular mechanism of ketone body-mediated growth inhibition of pancreatic cancer cells is not well understood. Research conducted thus far has not explored which molecular pathways are affected by ketone body treatment in pancreatic cancer cells. In the current study, the effect of the ketone body sodium hydroxybutyrate on the JAK-STAT and mTOR pathways and cell migration was explored. A decrease ...


Restoration Of Phage Growth On A Non-Permissive Host By Bypassing Transcription Termination Signals, Millicent Ronkainen 2018 Western Kentucky University

Restoration Of Phage Growth On A Non-Permissive Host By Bypassing Transcription Termination Signals, Millicent Ronkainen

Honors College Capstone Experience/Thesis Projects

RNA polymerase is the central enzyme in all gene expression. The rpoCY75N mutation in the zinc-binding domain of the β’ subunit of E. coli RNA polymerase blocks a unique RNA-based mechanism of transcription antitermination utilized by bacteriophage HK022 and its relatives. Here, we describe the characterization of mutant phage, orc0368, which overcomes the rpoCY75N mutation. The orc0368 genome varies from the wild type phage genome by 4 single base pair mutations. Three of these mutations were not characterized because they occur in intergenic regions but the fourth was chosen for study because of its location between a series ...


Effect Of Vitrification On Epigenetic Modifications And The Meiotic Spindle Of Bovine Oocytes, Emilio Jose Gutierrez-Castillo 2018 Louisiana State University

Effect Of Vitrification On Epigenetic Modifications And The Meiotic Spindle Of Bovine Oocytes, Emilio Jose Gutierrez-Castillo

LSU Master's Theses

While oocyte vitrification has become a common practice, it still faces some challenges such as the low survival rates after warming, probably related to cryoinjuries and cryoprotectant (CPA) toxicity. Evidence suggests that vitrification might have an effect on the patterns of some epigenetic marks including DNA methylation and histone acetylation. During fertilization and embryogenesis, key events for healthy and adequate embryo development take place, not only governed by the information contained within the DNA sequence, but also by epigenetic mechanisms.

This study was aimed at determining the effect of vitrification and CPA exposure, using a combination of ethylene glycol (EG ...


Intellectual Property, Surrogate Licensing, And Precision Medicine, Jacob S. Sherkow, Jorge L. Contreras 2018 New York Law School

Intellectual Property, Surrogate Licensing, And Precision Medicine, Jacob S. Sherkow, Jorge L. Contreras

IP Theory

The fruits of the biotechnology revolution are beginning to be harvested. Recent regulatory approvals of a variety of advanced therapies—Keytruda (pembrolizumab), Kymriah (tisagenlecleucel), and patisiran—have ushered in an age of “precision medicine” treatments that target patients’ specific genetic, physiological, and environmental profiles rather than generalized diagnoses of disease. Therapies like these may soon be supplemented by gene editing technologies such as CRISPR, which could enable the targeted eradication of deleterious genetic variants to improve human health. But the intellectual property (IP) surrounding precision therapies and their foundational technology remain controversial. Precision therapies ultimately rely—and are roughly congruent ...


Intraperitoneal Nanotherapy For Metastatic Ovarian Cancer Based On Sirna-Mediated Suppression Of Dj-1 Protein Combined With A Low Dose Of Cisplatin, Canan Schumann, Stephanie Chan, Jess A. Miller, Yuliya Bortnyak, Katherine Carey, Alex Fedchyk, Leon Wong, Tetiana Korzun, Abraham S. Moses, Anna Lorenz, Delany Shea, Olena Taratula, Oleh Khalimonchuk, Oleh Taratula 2018 Oregon State University

Intraperitoneal Nanotherapy For Metastatic Ovarian Cancer Based On Sirna-Mediated Suppression Of Dj-1 Protein Combined With A Low Dose Of Cisplatin, Canan Schumann, Stephanie Chan, Jess A. Miller, Yuliya Bortnyak, Katherine Carey, Alex Fedchyk, Leon Wong, Tetiana Korzun, Abraham S. Moses, Anna Lorenz, Delany Shea, Olena Taratula, Oleh Khalimonchuk, Oleh Taratula

Biochemistry -- Faculty Publications

Herein, we report an efficient combinatorial therapy for metastatic ovarian cancer based on siRNA-mediated suppression of DJ-1 protein combined with a low dose of cisplatin. DJ-1 protein modulates, either directly or indirectly, different oncogenic pathways that support and promote survival, growth, and invasion of ovarian cancer cells. To evaluate the potential of this novel therapy, we have engineered a cancer-targeted nanoplatform and validated that DJ-1 siRNA delivered by this nanoplatform after intraperitoneal injection efficiently downregulates the DJ-1 protein in metastatic ovarian cancer tumors and ascites. In vivo experiments revealed that DJ-1 siRNA monotherapy outperformed cisplatin alone by inhibiting tumor growth ...


Media Portrayal Of Gm Science And Citrus Greening In State And National Newspapers, Jeremy D'Angelo, Jason D. Ellis Ph.D., Katherine Burke Ph.D., Taylor Ruth 2018 Kansas State University

Media Portrayal Of Gm Science And Citrus Greening In State And National Newspapers, Jeremy D'Angelo, Jason D. Ellis Ph.D., Katherine Burke Ph.D., Taylor Ruth

Journal of Applied Communications

Huanglongbing (HLB), commonly known as citrus greening, is a bacterial disease severely affecting the profitability and continuation of the citrus industry in Florida and is threatening the citrus industry in other states as well. Currently, the disease only can be managed, not cured. Gene-based therapies, such as GM science, have been identified as a viable long-term solution. However, consumer acceptance of genetically modified food is low and their understanding and acceptance of new technologies is largely dependent on what they receive through mass media. Therefore, the purpose of this research is to understand news coverage of both citrus greening and ...


Two Distinct Domains Contribute To The Substrate Acyl Chain Length Selectivity Of Plant Acyl-Acp Thioesterase, Fuyuan Jing, Le Zhao, Marna D. Yandeau-Nelson, Basil J. Nikolau 2018 Iowa State University

Two Distinct Domains Contribute To The Substrate Acyl Chain Length Selectivity Of Plant Acyl-Acp Thioesterase, Fuyuan Jing, Le Zhao, Marna D. Yandeau-Nelson, Basil J. Nikolau

Genetics, Development and Cell Biology Publications

The substrate specificity of acyl-ACP thioesterase (TE) plays an essential role in controlling the fatty acid profile produced by type II fatty acid synthases. Here we identify two groups of residues that synergistically determine different substrate specificities of two acyl-ACP TEs from Cuphea viscosissima (CvFatB1 and CvFatB2). One group (V194, V217, N223, R226, R227, and I268 in CvFatB2) is critical in determining the structure and depth of a hydrophobic cavity in the N-terminal hotdog domain that binds the substrate’s acyl moiety. The other group (255-RKLSKI-260 and 285-RKLPKL-289 in CvFatB2) defines positively charged surface patches that may facilitate binding of ...


Evidence For A Unique Dna-Dependent Rna Polymerase In Cereal Crops, Joshua T. Trujillo, Arun S. Seetharam, Matthew B. Hufford, Mark A. Beilstein, Rebecca A. Mosher 2018 University of Arizona

Evidence For A Unique Dna-Dependent Rna Polymerase In Cereal Crops, Joshua T. Trujillo, Arun S. Seetharam, Matthew B. Hufford, Mark A. Beilstein, Rebecca A. Mosher

Genome Informatics Facility Publications

Gene duplication is an important driver for the evolution of new genes and protein functions. Duplication of DNA-dependent RNA polymerase (Pol) II subunits within plants led to the emergence of RNA Pol IV and V complexes, each of which possess unique functions necessary for RNA-directed DNA Methylation. Comprehensive identification of Pol V subunit orthologs across the monocot radiation revealed a duplication of the largest two subunits within the grasses (Poaceae), including critical cereal crops. These paralogous Pol subunits display sequence conservation within catalytic domains, but their carboxy terminal domains differ in length and character of the Ago-binding platform, suggesting unique ...


Functionalizing Titanium Implants With Bioactive Peptides To Increase Osseointegration, Neil Bernard 2018 The University of Akron

Functionalizing Titanium Implants With Bioactive Peptides To Increase Osseointegration, Neil Bernard

Honors Research Projects

Orthopedic surgeries have continued to increase, but the material of choice remains constant: titanium. Titanium has become the benchmark implant material due to its durability and non-immunogenic properties. However, while high rates of success are correlated with joint replacement surgery, certain patients with predisposed diseases such as diabetes or arthritis may have increased complications.1 This can be due to lack of osseointegration due to decreased bone formation and mineralization,2 which will lead to increased rates of infection or aseptic loosening of the implant from the bone. 3 Current methods to alleviate these complications include invasive revisional surgeries, which ...


Characterization Of Tetraethyl Orthosilicate-Based Dynamic Hydrogels For Use As Reversible 3-D Cell Culture Matrices, Krisitan Stipe 2018 University of Montana, Missoula

Characterization Of Tetraethyl Orthosilicate-Based Dynamic Hydrogels For Use As Reversible 3-D Cell Culture Matrices, Krisitan Stipe

Graduate Student Theses, Dissertations, & Professional Papers

No abstract provided.


Agri 115: Biotechnology – Food, Health And Environment, A Peer Review Of Teaching Project Benchmark Portfolio, Leah Sandall 2018 University of Nebraska-Lincoln

Agri 115: Biotechnology – Food, Health And Environment, A Peer Review Of Teaching Project Benchmark Portfolio, Leah Sandall

UNL Faculty Course Portfolios

No abstract provided.


Total Mercury Determination In Muscle And Liver Tissue Samples From Brazilian Amazon Fish Using Slurry Sampling, João Vitor de Queiroz, José Cavalcante Souza Vieira, Izabela da Cunha Bataglioli, Alis Correia Bittarello, Camila Pereira Braga, Grasieli de Oliveira, Cilene do Carmo Federici Padilha, Pedro de Magalhães Padilha 2018 São Paulo State University

Total Mercury Determination In Muscle And Liver Tissue Samples From Brazilian Amazon Fish Using Slurry Sampling, João Vitor De Queiroz, José Cavalcante Souza Vieira, Izabela Da Cunha Bataglioli, Alis Correia Bittarello, Camila Pereira Braga, Grasieli De Oliveira, Cilene Do Carmo Federici Padilha, Pedro De Magalhães Padilha

Biochemistry -- Faculty Publications

This paper presents a slurry sampling method for total mercury determination by graphite furnace atomic absorption spectrometry (GFAAS) in tissue of fish from the Amazon. The tissue samples were lyophilized and macerated, and then the slurry samples were prepared by putting 20 mg of tissue, added to a solution containing Triton X-100, Suprapur HNO3, and zirconium nitrate directly in sampling vials of a spectrometer. Mercury standard solutions were prepared under the same conditions as the slurry samples. The slurry samples and the mercury standard solutions were sonicated for 20 s. Twenty microliters of slurry samples were injected into the ...


Cancerdiscover: An Integrative Pipeline For Cancer Biomarker And Cancer Class Prediction From High-Throughput Sequencing Data, Akram Mohammed, Greyson Biegert, Jiri Adamec, Tomáš Helikar 2018 University of Nebraska-Lincoln

Cancerdiscover: An Integrative Pipeline For Cancer Biomarker And Cancer Class Prediction From High-Throughput Sequencing Data, Akram Mohammed, Greyson Biegert, Jiri Adamec, Tomáš Helikar

Biochemistry -- Faculty Publications

Accurate identification of cancer biomarkers and classification of cancer type and subtype from High Throughput Sequencing (HTS) data is a challenging problem because it requires manual processing of raw HTS data from various sequencing platforms, quality control, and normalization, which are both tedious and timeconsuming. Machine learning techniques for cancer class prediction and biomarker discovery can hasten cancer detection and significantly improve prognosis. To date, great research efforts have been taken for cancer biomarker identification and cancer class prediction. However, currently available tools and pipelines lack flexibility in data preprocessing, running multiple feature selection methods and learning algorithms, therefore, developing ...


Assessment Of Resistance To Botrytis Cinerea In Arabidopsis Expressing Grapevine Sts Genes And Analysis Of New Grapevine Vein Clearing Virus Isolates, Li Su 2018 Missouri State University

Assessment Of Resistance To Botrytis Cinerea In Arabidopsis Expressing Grapevine Sts Genes And Analysis Of New Grapevine Vein Clearing Virus Isolates, Li Su

MSU Graduate Theses

Grapevine stilbene synthase gene (STS) family is unusually large with more than 32 members of full-length genes. Resveratrol and piceid are synthesized in VaSTS7-, VvSTS22-, VaSTS22-transgenic Arabidopsis. To study the function of these STS genes in the resistance against Botrytis cinerea in vivo, lesion sizes on these STS transgenic Arabidopsis were compared to that on non-transgenic control Col-0, at 96 hours post inoculation with B. cinerea spores at 0, 200, or 1,000 spores/μl. In each experiment there were three biological replicates. Three lesion sizes from each replicate were averaged. The experiment was repeated three times. The results ...


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