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A Rationally Engineered Capsid Variant Of Aav9 For Systemic Cns-Directed And Peripheral Tissue-Detargeted Gene Delivery In Neonates, Dan Wang, Shaoyong Li, Dominic J. Gessler, Jun Xie, Li Zhong, Jia Li, Karen Tran, Kim Van Vliet, Lingzhi Ren, Qin Su, Ran He, Jason E. Goetzmann, Terence R. Flotte, Mavis Agbandje-McKenna, Guangping Gao 2018 University of Massachusetts Medical School

A Rationally Engineered Capsid Variant Of Aav9 For Systemic Cns-Directed And Peripheral Tissue-Detargeted Gene Delivery In Neonates, Dan Wang, Shaoyong Li, Dominic J. Gessler, Jun Xie, Li Zhong, Jia Li, Karen Tran, Kim Van Vliet, Lingzhi Ren, Qin Su, Ran He, Jason E. Goetzmann, Terence R. Flotte, Mavis Agbandje-Mckenna, Guangping Gao

Open Access Articles

Adeno-associated virus (AAV) has provided the gene therapy field with the most powerful in vivo gene delivery vector to realize safe, efficacious, and sustainable therapeutic gene expression. Because many clinically relevant properties of AAV-based vectors are governed by the capsid, much research effort has been devoted to the development of AAV capsids for desired features. Here, we combine AAV capsid discovery from nature and rational engineering to report an AAV9 capsid variant, designated as AAV9.HR, which retains AAV9's capability to traverse the blood-brain barrier and transduce neurons. This variant shows reduced transduction in peripheral tissues when delivered through ...


Polygenic Scores For Metabolic Traits And Related Drug Prescriptions In The Michigan Genomics Initiative, Samuel K. Handelman, Xiaomeng Du, Yanhua H. Chen, Elizabeth K. Speliotes 2018 University of Michigan-Ann Arbor

Polygenic Scores For Metabolic Traits And Related Drug Prescriptions In The Michigan Genomics Initiative, Samuel K. Handelman, Xiaomeng Du, Yanhua H. Chen, Elizabeth K. Speliotes

Biology and Medicine Through Mathematics Conference

No abstract provided.


Modeling Stochastic Viral Evolution: A Multiscale Wright Fisher Model, Marco Hamins-Puertolas 2018 North Carolina State University at Raleigh

Modeling Stochastic Viral Evolution: A Multiscale Wright Fisher Model, Marco Hamins-Puertolas

Biology and Medicine Through Mathematics Conference

No abstract provided.


Population Genetics And Bumble Bee Conservation: Saving Species By Thinking Small, Cady Greenslit 2018 Lawrence University

Population Genetics And Bumble Bee Conservation: Saving Species By Thinking Small, Cady Greenslit

Lawrence University Honors Projects

Pollinators have experienced a severe decline over the last few decades, and this includes bumble bee populations (g. Bombus). Bumble bees are important native pollinators, and here I investigate the health of local populations with molecular tools. The field of conservation genetics has created useful methodology for investigating the health and informing management strategies of threatened populations. This work investigates and describes the applications of population genetics, which uses span across the board. These applications are then brought back into the context of bumble bee conservation, and how they fit into the experimental plan I originally designed. I designed an ...


Characterizing Virus-Induced Gene Silencing At The Cellular Level With In Situ Multimodal Imaging, Sadie J. Burkhow, Nicole M. Stephens, Yu Mei, Maria Emilia Duenas, Daniel J. Freppon, Geng Ding, Shea C. Smith, Young-Jin Lee, Basil J. Nikolau, Steven A. Whitham, Emily A. Smith 2018 Iowa State University and Ames Laboratory

Characterizing Virus-Induced Gene Silencing At The Cellular Level With In Situ Multimodal Imaging, Sadie J. Burkhow, Nicole M. Stephens, Yu Mei, Maria Emilia Duenas, Daniel J. Freppon, Geng Ding, Shea C. Smith, Young-Jin Lee, Basil J. Nikolau, Steven A. Whitham, Emily A. Smith

Chemistry Publications

Background: Reverse genetic strategies, such as virus-induced gene silencing, are powerful techniques to study gene function. Currently, there are few tools to study the spatial dependence of the consequences of gene silencing at the cellular level.

Results: We report the use of multimodal Raman and mass spectrometry imaging to study the cellular-level biochemical changes that occur from silencing the phytoene desaturase (pds) gene using a Foxtail mosaic virus (FoMV) vector in maize leaves. The multimodal imaging method allows the localized carotenoid distribution to be measured and reveals differences lost in the spatial average when analyzing a carotenoid extraction of the ...


Population Structure, Demographic History, And Environmental Niche Of The Sand Fly Disease Vector Lutzomyia Shannoni (Dyar) (Diptera: Psychodidae) In The U.S., Mexico, And Colombia, Matthew E. Wolkoff 2018 University of Texas at Tyler

Population Structure, Demographic History, And Environmental Niche Of The Sand Fly Disease Vector Lutzomyia Shannoni (Dyar) (Diptera: Psychodidae) In The U.S., Mexico, And Colombia, Matthew E. Wolkoff

Biology Theses

Lutzomyia shannoni (Dyar, 1929) (Diptera: Psychodidae) is the only known sand fly vector of vesicular stomatitis virus, a putative leishmaniasis vector, and also boasts the widest distribution of any sand fly in the New World. Research on Lu. shannoni in Central and South America has revealed genetically divergent subpopulations; however, tentative analysis of Lu. shannoni in the U.S. has failed to detect any significant population structure, even between specimens collected from highly disparate localities.

The present study used four molecular markers to more closely investigate the population structure of Lu. shannoni in the U.S., and assess the species ...


Integration Of Local And Regional Regulatory Information In The Human Genome, Hemangi Govind Chaudhari 2018 Washington University in St. Louis

Integration Of Local And Regional Regulatory Information In The Human Genome, Hemangi Govind Chaudhari

Arts & Sciences Electronic Theses and Dissertations

Gene regulation involves the integration of different sources of information at multiple levels. The action of transcription factors is integrated at cis-regulatory sequences (CRSs). Information from many CRSs is combined to drive spatiotemporally regulated gene expression. Prediction of CRS activity from DNA sequence is challenging because most occurrences of transcription factor binding sites (TFBS) are not functional. I assayed the activity of thousands of genomic sequences with Activator Protein 1 (AP-1) binding sites in K562 cells to identify features in flanking sequences that distinguish functional from non-functional TFBS. I find that sequence features directly adjacent to the AP-1 core motif ...


Discovering Rare Hematopoietic Clones Harboring Leukemia-Associated Mutations Using Error-Corrected Sequencing, Andrew Lee Young 2018 Washington University in St. Louis

Discovering Rare Hematopoietic Clones Harboring Leukemia-Associated Mutations Using Error-Corrected Sequencing, Andrew Lee Young

Arts & Sciences Electronic Theses and Dissertations

Cancer is a heterogeneous group of diseases that currently takes over half a million lives per year in the United States alone. Our understanding of cancer has improved dramatically over the last forty years, beginning with the discovery that cancer is a disease of the genome. Currently, the set of somatic mutations found in malignancy are largely known. The specific somatic mutations driving an individual’s disease can be readily assessed at clinical presentation. Additionally, the functional consequences for many of these mutations are known as well as their role in tumorigenesis. Despite this understanding, a cure for cancer remains ...


Analysis Of The Immunological Biomarker Profile During Acute Zika Virus Infection Reveals The Overexpression Of Cxcl10, A Chemokine Linked To Neuronal Damage., Felipe Gomes Naveca, Gemilson Soares Pontes, Aileen Yu-Hen Chang, George Allan Villarouco da Silva, Valdinete Alves do Nascimento, Dana Cristina da Silva Monteiro, +several additional authors 2018 George Washington University

Analysis Of The Immunological Biomarker Profile During Acute Zika Virus Infection Reveals The Overexpression Of Cxcl10, A Chemokine Linked To Neuronal Damage., Felipe Gomes Naveca, Gemilson Soares Pontes, Aileen Yu-Hen Chang, George Allan Villarouco Da Silva, Valdinete Alves Do Nascimento, Dana Cristina Da Silva Monteiro, +Several Additional Authors

Medicine Faculty Publications

BACKGROUND: Infection with Zika virus (ZIKV) manifests in a broad spectrum of disease ranging from mild illness to severe neurological complications and little is known about Zika immunopathogenesis.

OBJECTIVES: To define the immunologic biomarkers that correlate with acute ZIKV infection.

METHODS: We characterized the levels of circulating cytokines, chemokines, and growth factors in 54 infected patients of both genders at five different time points after symptom onset using microbeads multiplex immunoassay; comparison to 100 age-matched controls was performed for statistical analysis and data mining.

FINDINGS: ZIKV-infected patients present a striking systemic inflammatory response with high levels of pro-inflammatory mediators. Despite ...


Are We Genetically Adapted To The Neolithic Diet?, Nicola E. Hale 2018 None

Are We Genetically Adapted To The Neolithic Diet?, Nicola E. Hale

Journal of Evolution and Health

No abstract provided.


The Receptor Protein Tyrosine Phosphatase Clr-1 Is Required For Synaptic Partner Recognition, Aruna Varshney, Kelli Benedetti, Katherine Watters, Raakhee Shankar, David Tatarakis, Doris Coto Villa, Khristina Magallanes, Venia Agenor, William Wung, Fatima Farah, Nebat Ali, Nghi Le, Jacqueline Pyle, Amber Farooqi, Zanett Kieu, Martina Bremer, Miri VanHoven 2018 San Jose State University

The Receptor Protein Tyrosine Phosphatase Clr-1 Is Required For Synaptic Partner Recognition, Aruna Varshney, Kelli Benedetti, Katherine Watters, Raakhee Shankar, David Tatarakis, Doris Coto Villa, Khristina Magallanes, Venia Agenor, William Wung, Fatima Farah, Nebat Ali, Nghi Le, Jacqueline Pyle, Amber Farooqi, Zanett Kieu, Martina Bremer, Miri Vanhoven

Faculty Publications

During neural circuit formation, most axons are guided to complex environments, coming into contact with multiple potential synaptic partners. However, it is critical that they recognize specific neurons with which to form synapses. Here, we utilize the split GFP-based marker Neuroligin-1 GFP Reconstitution Across Synaptic Partners (NLG-1 GRASP) to visualize specific synapses in live animals, and a circuit-specific behavioral assay to probe circuit function. We demonstrate that the receptor protein tyrosine phosphatase (RPTP) clr-1 is necessary for synaptic partner recognition (SPR) between the PHB sensory neurons and the AVA interneurons in C. elegans. Mutations in clr-1/RPTP result in reduced ...


The Receptor Protein Tyrosine Phosphatase Clr-1 Is Required For Synaptic Partner Recognition, Aruna Varshney, Kelli Benedetti, Katherine Watters, Raakhee Shankar, David Tatarakis, Doris Coto Villa, Khristina Magallanes, Venia Agenor, William Wung, Fatima Farah, Nebat Ali, Nghi Le, Jacqueline Pyle, Amber Farooqi, Zanett Kieu, Martina Bremer, Miri VanHoven 2018 San Jose State University

The Receptor Protein Tyrosine Phosphatase Clr-1 Is Required For Synaptic Partner Recognition, Aruna Varshney, Kelli Benedetti, Katherine Watters, Raakhee Shankar, David Tatarakis, Doris Coto Villa, Khristina Magallanes, Venia Agenor, William Wung, Fatima Farah, Nebat Ali, Nghi Le, Jacqueline Pyle, Amber Farooqi, Zanett Kieu, Martina Bremer, Miri Vanhoven

Miri VanHoven

During neural circuit formation, most axons are guided to complex environments, coming into contact with multiple potential synaptic partners. However, it is critical that they recognize specific neurons with which to form synapses. Here, we utilize the split GFP-based marker Neuroligin-1 GFP Reconstitution Across Synaptic Partners (NLG-1 GRASP) to visualize specific synapses in live animals, and a circuit-specific behavioral assay to probe circuit function. We demonstrate that the receptor protein tyrosine phosphatase (RPTP) clr-1 is necessary for synaptic partner recognition (SPR) between the PHB sensory neurons and the AVA interneurons in Celegans. Mutations in clr-1/RPTP result in reduced ...


Fine Grained Compositional Analysis Of Port Everglades Inlet Microbiome Using High Throughput Dna Sequencing, Lauren M. O'Connell, Song Gao, Donald S. McCorquodale Jr., Jay M. Fleisher, Jose Lopez 2018 Nova Southeastern University

Fine Grained Compositional Analysis Of Port Everglades Inlet Microbiome Using High Throughput Dna Sequencing, Lauren M. O'Connell, Song Gao, Donald S. Mccorquodale Jr., Jay M. Fleisher, Jose Lopez

Oceanography Faculty Articles

Background

Similar to natural rivers, manmade inlets connect inland runoff to the ocean. Port Everglades Inlet (PEI) is a busy cargo and cruise ship port in South Florida, which can act as a source of pollution to surrounding beaches and offshore coral reefs. Understanding the composition and fluctuations of bacterioplankton communities (“microbiomes”) in major port inlets is important due to potential impacts on surrounding environments. We hypothesize seasonal microbial fluctuations, which were profiled by high throughput 16S rRNA amplicon sequencing and analysis.

Methods & Results

Surface water samples were collected every week for one year. A total of four samples per ...


Characterization Of An N-Terminal Non-Core Domain Of Rag1 Gene Disrupted Syrian Hamster Model Generated By Crispr Cas9, Jinxin Miao, Baoling Ying, Rong Li, Ann E. Tollefson, Jacqueline F. Spencer, William S.M. Wold, Seok-Hwan Song, Il-Keun Kong, Karoly Toth, Yaohe Wang, Zhongde Wang 2018 Zhengzhou University

Characterization Of An N-Terminal Non-Core Domain Of Rag1 Gene Disrupted Syrian Hamster Model Generated By Crispr Cas9, Jinxin Miao, Baoling Ying, Rong Li, Ann E. Tollefson, Jacqueline F. Spencer, William S.M. Wold, Seok-Hwan Song, Il-Keun Kong, Karoly Toth, Yaohe Wang, Zhongde Wang

Animal, Dairy, and Veterinary Science Faculty Publications

The accumulating evidence demonstrates that Syrian hamsters have advantages as models for various diseases. To develop a Syrian hamster (Mesocricetus auratus) model of human immunodeficiency caused by RAG1 gene mutations, we employed the CRISPR/Cas9 system and introduced an 86-nucleotide frameshift deletion in the hamster RAG1 gene encoding part of the N-terminal non-core domain of RAG1. Histological and immunohistochemical analyses demonstrated that these hamsters (referred herein as RAG1-86nt hamsters) had atrophic spleen and thymus, and developed significantly less white pulp and were almost completely devoid of splenic lymphoid follicles. The RAG1-nt86 hamsters had barely detectable CD3+ and CD4+ T cells ...


Effects Of Mitochondrial Nadp+-Dependent Isocitrate Dehydrogenase Deficiency On Fructose-Induced Obesity In Mice, Allison Michelle Montalbano, Kaleigh Elizabeth Beane 2018 University of Arkansas, Fayetteville

Effects Of Mitochondrial Nadp+-Dependent Isocitrate Dehydrogenase Deficiency On Fructose-Induced Obesity In Mice, Allison Michelle Montalbano, Kaleigh Elizabeth Beane

Human Nutrition and Hospitality Innovation Undergraduate Honors Theses

Obesity prevalence in the United States continues to increase and is associated with health consequences such as type 2 diabetes, hypertension, atherosclerosis, and hyperlipidemia. Among many contributing factors to obesity, fructose may be one of the major reasons as it disrupts the antioxidant system thereby resulting in an accumulation of reactive oxidative species and leading to obese conditions. The enzyme, isocitrate dehydrogenase 2 (IDH2), reduces nicotinamide adenine dinucleotide phosphate from the TCA Cycle, hence might be implicated with not only energy metabolism but also cellular redox homeostasis. Therefore, the hypothesis was that IDH2 deficiency in mice would exacerbate hepatic lipid ...


Evolutionary Conservation Of Midline Repulsion By Robo Family Receptors In Flies And Mice, Allison Loy 2018 University of Arkansas, Fayetteville

Evolutionary Conservation Of Midline Repulsion By Robo Family Receptors In Flies And Mice, Allison Loy

Biological Sciences Undergraduate Honors Theses

As the nervous system develops in animal embryos, neuronal axons are guided to their synaptic targets by extra cellular cues that signal through axon guidance receptors expressed on the surface of the axon. In animals with bilateral symmetry, one of the important decisions made by nearly every axon in the embryonic nervous system is whether to stay on its own side of the body, or to cross the midline and connect to cells on the opposite side. The Roundabout (Robo) family is an evolutionarily conserved group of axon guidance receptors that regulate midline crossing in a wide range of animal ...


A Forensic Investigation Into The Possible Origins Of Three Human Skeletons, Jefferson P. Sinnott 2018 State University of New York College at Buffalo - Buffalo State College

A Forensic Investigation Into The Possible Origins Of Three Human Skeletons, Jefferson P. Sinnott

Forensic Science Theses

The Anthropology Department at Buffalo State has three human skeletons that have been part of the department’s collection for several years. The origin of the skeletons is currently unknown. Modern DNA techniques coupled with forensic anthropological techniques may now allow us to determine with some certainty the geographic origin of the skeletons. Ancestry, sex, age, and stature were assessed using current anthropological techniques. Afterwards, one tooth from each of the three skeletons was extracted, pulverized and DNA was isolated. Y-STR fragment size analysis of the DNA samples can provide information about the patrilineage of male individuals. Mitochondrial DNA sequencing ...


Involvement Of The Ino80 Complex In Chromosome Segregation, Jesus Moreno 2018 University of Arkansas, Fayetteville

Involvement Of The Ino80 Complex In Chromosome Segregation, Jesus Moreno

Theses and Dissertations

Chromatin remodeling complexes are multi-protein complexes that regulate the dynamics of the nucleosomes in the genome. The INO80 chromatin remodeling complex participates in varied biological processes such as: transcription, DNA repair, DNA replication and chromosome integrity. It catalyzes the eviction of the H2A.Z variant histone as well as whole nucleosome eviction. This complex is comprised of 15 subunits and the contribution of each to chromosome segregations remains unknown. To evaluate the contribution of each subunit to chromosome segregation, we tested deletion mutants of the non-essential subunits for DNA content and benomyl sensitivity. Also, we assessed members of the SWR1 ...


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 ...


Functional Studies Of The E. Coli Proc And A Putative Ortholog Mrub_1345, Mourin Azar, Dr. Lori Scott 2018 Augustana College, Rock Island Illinois

Functional Studies Of The E. Coli Proc And A Putative Ortholog Mrub_1345, Mourin Azar, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of Escherichia coli and Meiothermus ruber proC genes using the complementation assay. In this research project, mutants of varying severity to the functional state of the protein were developed. The results showed that two or more amino acid deletions reduced or eliminated ProC function. Amino acid substitutions, on the other hand, were not severe enough to impact ProC function. Double and triple mutants ...


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