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A Single Mechanism Of Biogenesis, Initiated And Directed By Piwi Proteins, Explains Pirna Production In Most Animals, Phillip D. Zamore, Ildar Gainetdinov, Cansu Colpan, Katharine Cecchini 2018 University of Massachusetts Medical School

A Single Mechanism Of Biogenesis, Initiated And Directed By Piwi Proteins, Explains Pirna Production In Most Animals, Phillip D. Zamore, Ildar Gainetdinov, Cansu Colpan, Katharine Cecchini

University of Massachusetts Medical School Faculty Publications

In animals, piRNAs guide PIWI-proteins to silence transposons and regulate gene expression. The mechanisms for making piRNAs have been proposed to differ among cell types, tissues, and animals. Our data instead suggest a single model that explains piRNA production in most animals. piRNAs initiate piRNA production by guiding PIWI proteins to slice precursor transcripts. Next, PIWI proteins direct the stepwise fragmentation of the sliced precursor transcripts, yielding tail-to-head strings of phased pre-piRNAs. Our analyses detect evidence for this piRNA biogenesis strategy across an evolutionarily broad range of animals including humans. Thus, PIWI proteins initiate and sustain piRNA biogenesis by the ...


Effect Of Potassium Bromate On Oxr1 Gene Expression And Cell Growth In Tetrahymena Thermophila, Brendan McMahon, Scott Kahle 2018 Carroll College

Effect Of Potassium Bromate On Oxr1 Gene Expression And Cell Growth In Tetrahymena Thermophila, Brendan Mcmahon, Scott Kahle

Carroll College Student Undergraduate Research Festival

Investigation of Tetrahymena Thermophila’s Response to Oxidative Damage

The purpose of our experiment was to answer the question: Does oxidative damage, induced by potassium bromate (KBrO3), affect the growth rate and the expression of the OXR1 gene in Tetrahymena Thermophila? It was hypothesized that the expression of OXR1 would increase in Tetrahymena that were exposed to potassium bromate and that their growth rate would decrease. The exact mechanism and function of the OXR1 gene is still unknown, however, the literature suggests that it is required for oxidative damage resistance. To test the hypothesis Tetrahymena were randomly assigned to either ...


Exploiting Glycan Topography For Computational Design Of Env Glycoprotein Antigenicity, Wen-Han Yu, Peng Zhao, Monia Draghi, Claudia Arevalo, Christina B. Karsten, Todd J. Suscovich, Bronwyn Gunn, Hendrik Streeck, Abraham L. Brass, Michael Tiemeyer, Michael Seaman, John R. Mascola, Lance Wells, Douglas A. Lauffenburger, Galit Alter 2018 Massachusetts Institute of Technology

Exploiting Glycan Topography For Computational Design Of Env Glycoprotein Antigenicity, Wen-Han Yu, Peng Zhao, Monia Draghi, Claudia Arevalo, Christina B. Karsten, Todd J. Suscovich, Bronwyn Gunn, Hendrik Streeck, Abraham L. Brass, Michael Tiemeyer, Michael Seaman, John R. Mascola, Lance Wells, Douglas A. Lauffenburger, Galit Alter

Open Access Articles

Mounting evidence suggests that glycans, rather than merely serving as a "shield", contribute critically to antigenicity of the HIV envelope (Env) glycoprotein, representing critical antigenic determinants for many broadly neutralizing antibodies (bNAbs). While many studies have focused on defining the role of individual glycans or groups of proximal glycans in bNAb binding, little is known about the effects of changes in the overall glycan landscape in modulating antibody access and Env antigenicity. Here we developed a systems glycobiology approach to reverse engineer the complexity of HIV glycan heterogeneity to guide antigenicity-based de novo glycoprotein design. bNAb binding was assessed against ...


Constitutive Expression Of Thioglucoside Glucohydrolase 1 (Tgg1) Decreases Intercellular Trafficking In Arabidopsis Thaliana, Alessandro Francesco Sarno 2018 University of Tennessee, Knoxville

Constitutive Expression Of Thioglucoside Glucohydrolase 1 (Tgg1) Decreases Intercellular Trafficking In Arabidopsis Thaliana, Alessandro Francesco Sarno

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Plasmodesmata (PD) are pores that traverse plant cell walls, providing a route for intercellular trafficking of essential metabolites, nutrients, and signaling molecules between adjacent plant cells, thereby aiding communication. The increased size exclusion limit 2 (ise2) mutant of Arabidopsis thaliana has an increased abundance of branched PD, as well as a greater flux of intercellular trafficking. A search for proteins that interact with ISE2 identified THIOGLUCOSIDE GLUCOHYDROLASE 2 (a myrosinase). A. thaliana also encodes a second, closely-related myrosinase, TGG1. Myrosinases are enzymes that catalyze the hydrolysis of glucosinolates, a type of secondary metabolite that are amino acid derivatives. The breakdown ...


A Multisession, Undergraduate Molecular Biology Lab Experiment Using Green Fluorescent Protein Including Subcloning And Color Changing Mutagenesis, Nathan S. Winter 2018 St. Cloud State University

A Multisession, Undergraduate Molecular Biology Lab Experiment Using Green Fluorescent Protein Including Subcloning And Color Changing Mutagenesis, Nathan S. Winter

Chemistry Faculty Publications

This paper describes a series of experiments involving handling and manipulating the DNA coding for Green Fluorescent Protein (GFP) including the subcloning of this gene, and mutating the DNA so that Cyan Fluorescent Protein (CFP) or Blue Fluorescent protein (BFP) are expressed. The primers needed for the PCR based subcloning of GFP are presented, as are those needed to mutate the GFP to either CFP or BFP.


The Effects Of Inulin And Galactooligosaccharides On The Production Of Reuterin By Lactobacillus Reuteri, Micah Forshee 2018 Olivet Nazarene University

The Effects Of Inulin And Galactooligosaccharides On The Production Of Reuterin By Lactobacillus Reuteri, Micah Forshee

Scholar Week 2016 - present

The microbiome is a dynamic community that can positively and negatively influence host health. Lactobacillus reuteri is a probiotic that has received much attention for its ability to inhibit pathogens such as Salmonella Typhimurium, Escherichia coli, and Clostridium difficile. It does so by its unique ability to metabolize glycerol into the antimicrobial compound 3-HPA, which is commonly referred to as reuterin. The ability to secrete reuterin is dependent not only on glycerol availability but also the concentration of glucose. In fact, there appears to be a “goldilocks” ratio between glucose and glycerol as either too much or too little glucose ...


An Automated Bayesian Pipeline For Rapid Analysis Of Single-Molecule Binding Data, Carlas Smith, Karina Jouravleva, Maximiliaan Huisman, Samson M. Jolly, Phillip D. Zamore, David Grünwald 2018 University of Massachusetts Medical School

An Automated Bayesian Pipeline For Rapid Analysis Of Single-Molecule Binding Data, Carlas Smith, Karina Jouravleva, Maximiliaan Huisman, Samson M. Jolly, Phillip D. Zamore, David Grünwald

University of Massachusetts Medical School Faculty Publications

Single-molecule binding assays enable the study of how molecular machines assemble and function. Current algorithms can identify and locate individual molecules, but require tedious manual validation of each spot. Moreover, no solution for high-throughput analysis of single-molecule binding data exists. Here, we describe an automated pipeline to analyze single-molecule data over a wide range of experimental conditions. We benchmarked the pipeline by measuring the binding properties of the well-studied, DNA-guided DNA endonuclease, TtAgo, an Argonaute protein from the Eubacterium Thermus thermophilus. We also used the pipeline to extend our understanding of TtAgo by measuring the protein's binding kinetics at ...


The Role Of Phosphohistidine Phosphatase 1 In Ethanol-Induced Liver Injury, Daniel Richard Martin 2018 University of South Florida

The Role Of Phosphohistidine Phosphatase 1 In Ethanol-Induced Liver Injury, Daniel Richard Martin

Graduate Theses and Dissertations

Chronic liver diseases, which includes alcoholic liver disease (ALD), are consistently among the top 15 leading causes of death in the United States. ALD is characterized by progression from a normal liver to fatty liver disease (hepatic steatosis), which can lead to cirrhosis, alcoholic hepatitis, and liver failure. We have identified a novel role of phosphohistidine signaling, mediated through phosphohistidine phosphatase 1 (PHPT1), in the onset of hepatic steatosis. We have identified PHPT1 as a target of selective oxidation following acute ethanol exposure as well as being downregulated following chronic ethanol exposure. We mapped the oxidative modification site and developed ...


Investigation Of Alcohol-Induced Changes In Hepatic Histone Modifications Using Mass Spectrometry Based Proteomics, Crystina Leah Kriss 2018 University of South Florida

Investigation Of Alcohol-Induced Changes In Hepatic Histone Modifications Using Mass Spectrometry Based Proteomics, Crystina Leah Kriss

Graduate Theses and Dissertations

Alcohol liver disease (ALD) is a major health concern throughout the world. Currently, in the United States, 17 million people suffer from alcoholism, of which 1.4 million people are receiving treatment [1, 2]. The link between ethanol metabolism, reactive oxygen species (ROS) and liver injury in ALD has been well characterized over the last couple decades [3-10]. Ethanol metabolism relies on the availability of the cofactor NAD+ for the oxidation of ethanol into acetate, consequently causing alterations in redox potential. Redox dysfunction within the mitochondria can affect multiple pathways important in maintaining cellular homeostasis. Chapter 1 provides an introduction ...


Intron-Containing Rna From The Hiv-1 Provirus Activates Type I Interferon And Inflammatory Cytokines, Sean M. McCauley, Kyusik Kim, Anetta Nowosielska, Ann Dauphin, Leonid Yurkovetskiy, William E. Diehl, Jeremy Luban 2018 University of Massachusetts Medical School

Intron-Containing Rna From The Hiv-1 Provirus Activates Type I Interferon And Inflammatory Cytokines, Sean M. Mccauley, Kyusik Kim, Anetta Nowosielska, Ann Dauphin, Leonid Yurkovetskiy, William E. Diehl, Jeremy Luban

Program in Molecular Medicine Publications and Presentations

HIV-1-infected people who take drugs that suppress viremia to undetectable levels are protected from developing AIDS. Nonetheless, these individuals have chronic inflammation associated with heightened risk of cardiovascular pathology. HIV-1 establishes proviruses in long-lived CD4+ memory T cells, and perhaps other cell types, that preclude elimination of the virus even after years of continuous antiviral therapy. Though the majority of proviruses that persist during antiviral therapy are defective for production of infectious virions, many are expressed, raising the possibility that the HIV-1 provirus or its transcripts contribute to ongoing inflammation. Here we found that the HIV-1 provirus activated innate immune ...


Mutagenic Potential Of Phthalates In Mammalian Cells, Chanelle Hunter, Virginia Lane, Adrian Torres, Shahd Mohamed, Alicia Hawthorne, Emily Bradshaw 2018 University of Central Florida

Mutagenic Potential Of Phthalates In Mammalian Cells, Chanelle Hunter, Virginia Lane, Adrian Torres, Shahd Mohamed, Alicia Hawthorne, Emily Bradshaw

Chanelle Hunter

Several popular industrial chemicals, such as Phthalates and Bisphenol A (BPA), are commonly found in many of the personal products used in daily life. This includes plastics present in water bottles, medical equipment such as IV fluid transporters, storage containers of food, PVC piping, children’s toys, cooking utensils, printing inks, and even baby pacifiers. Although plastic enhances the quality of life, phthalates and BPA have both been linked to genetic mutations. BPA can cause increased chromosomal mutations, and phthalates can cause germline mutations in sperm. These genetic changes can result in adverse effects on human health in areas including ...


Cloning, Purification, And Preliminary Dna-Binding And Unfolding Results For The Dna Polymerase I From The Psychrophile Psychromonas Ingrahamii, John Tod Baker 2018 Louisiana State University and Agricultural and Mechanical College

Cloning, Purification, And Preliminary Dna-Binding And Unfolding Results For The Dna Polymerase I From The Psychrophile Psychromonas Ingrahamii, John Tod Baker

LSU Master's Theses

Psychromonas ingrahamii is a psychrophilic bacterium that lives in Arctic polar sea ice and grows at a temperature range of -12 to 10º C. This bacterium resides within veins inside the ice where the salinity is high, resulting in a freezing point depression and liquid water. The large fragment of DNA polymerase I from Psychromonas ingrahamii, called Klenpin, has been cloned, expressed, and purified in our laboratory. Although enzyme kinetic studies have been performed on a few psychrophilic enzymes, the thermodynamics of ligand binding and of protein stability have not been well studied for this class of extremophilic proteins. Here ...


Primate Immunodeficiency Virus Vpx And Vpr Counteract Transcriptional Repression Of Proviruses By The Hush Complex, Leonid Yurkovetskiy, Mehmet Hakan Guney, Kyusik Kim, Shih Lin Goh, Sean M. McCauley, Ann Dauphin, William E. Diehl, Jeremy Luban 2018 University of Massachusetts Medical School

Primate Immunodeficiency Virus Vpx And Vpr Counteract Transcriptional Repression Of Proviruses By The Hush Complex, Leonid Yurkovetskiy, Mehmet Hakan Guney, Kyusik Kim, Shih Lin Goh, Sean M. Mccauley, Ann Dauphin, William E. Diehl, Jeremy Luban

University of Massachusetts Medical School Faculty Publications

Drugs that inhibit HIV-1 replication and prevent progression to AIDS do not eliminate HIV-1 proviruses from the chromosomes of long-lived CD4+ memory T cells. To escape eradication by these antiviral drugs, or by the host immune system, HIV-1 exploits poorly defined host factors that silence provirus transcription. These same factors, though, must be overcome by all retroviruses, including HIV-1 and other primate immunodeficiency viruses, in order to activate provirus transcription and produce new virus. Here we show that Vpx and Vpr, proteins from a wide range of primate immunodeficiency viruses, activate provirus transcription in human CD4+ T cells. Provirus activation ...


The Characterization Of The Transcription Factor Msab And Its Role In Staphylococcal Virulence, Justin Batte 2018 The University of Southern Mississippi

The Characterization Of The Transcription Factor Msab And Its Role In Staphylococcal Virulence, Justin Batte

Dissertations

Staphylococcus aureus is a common human pathogen that is responsible for a wide range of infections, ranging from relative minor skin infections to life-threatening disease such as bacteremia, septicemia, and endocarditis. S. aureus possesses many different virulent factors that aid in its ability to cause this wide array of infections. One major virulence factor includes the production of capsular polysaccharide (CP). The production of CP plays a major role in the virulence response during infection specifically by providing S. aureus an antiphagocytic mechanism that allows the pathogen to evade phagocytosis during an infection. S. aureus has developed complex genetic regulatory ...


Tracing Actin Filament Bundles In Three-Dimensional Electron Tomography Density Maps Of Hair Cell Stereocilia, Salim Sazzed, Junha Song, Julio Kovacs, Willi Wriggers, Manfred Auer, Jing He 2018 Old Dominion University

Tracing Actin Filament Bundles In Three-Dimensional Electron Tomography Density Maps Of Hair Cell Stereocilia, Salim Sazzed, Junha Song, Julio Kovacs, Willi Wriggers, Manfred Auer, Jing He

Computer Science Faculty Publications

Cryo-electron tomography (cryo-ET) is a powerful method of visualizing the three-dimensional organization of supramolecular complexes, such as the cytoskeleton, in their native cell and tissue contexts. Due to its minimal electron dose and reconstruction artifacts arising from the missing wedge during data collection, cryo-ET typically results in noisy density maps that display anisotropic XY versus Z resolution. Molecular crowding further exacerbates the challenge of automatically detecting supramolecular complexes, such as the actin bundle in hair cell stereocilia. Stereocilia are pivotal to the mechanoelectrical transduction process in inner ear sensory epithelial hair cells. Given the complexity and dense arrangement of actin ...


The Synthesis And Function Of The Peritrophic Matrix In Drosophila Melanogaster, Sean Conway 2018 Marquette University

The Synthesis And Function Of The Peritrophic Matrix In Drosophila Melanogaster, Sean Conway

Dissertations (2009 -)

Maintenance of functional barrier structures separating an organism from and regulating its interaction with the environment is critical for many aspects of fitness. Arguably, the most dynamic interface between an animal and its environment is the gut, as the organism must balance the primary functions, digestion and nutrient acquisition, with several homeostatic and defensive systems including pathogen defense, microbiome maintenance and stem cell renewal. Many animals secrete extracellular barrier structures along their guts to organize and modulate these interactions, including intestinal mucosal secretions in humans and a semi-permeable structure in insects called the peritrophic matrix (PM). In Drosophila, the PM ...


Investigating The Role Of Dnc-2 And Dli-1 On Ampa Receptor Mediated Behaviors In Caenorhabditis Elegans, Natalie Oberding 2018 Carroll College, Helena, MT

Investigating The Role Of Dnc-2 And Dli-1 On Ampa Receptor Mediated Behaviors In Caenorhabditis Elegans, Natalie Oberding

Life and Environmental Sciences Undergraduate Theses

Γ-amino-3-hydroxy-5methylisoxazole-4-proprionic acid (AMPA) receptors (AMPARs) are protein complexes involved in excitatory neurotransmission. AMPARs are tetrameric structures consisting of the pairings of GluA1, GluA2, GluA3, and GluA4 subunits. Dctn2 and Dync1li1 were found to interact with GluA2 in an immunoprecipitation screen that was performed on postnatal day 14 rat brains. DNC-2 and DLI-1 were identified as the C. elegans homologs of Dctn2 and Dync1li1, respectively, and are components of motor proteins that transport cargo throughout the cell. The goal of this project was to determine whether knocking down DNC-2 and DLI-1 by RNAi affects AMPA Receptor-mediated behaviors, including mechanosensation and chemosensation ...


Biochemical Analysis Of Dimethyl Suberimidate-Crosslinked Yeast Nucleosomes, Yuichi Ichikawa, Paul D. Kaufman 2018 University of Massachusetts Medical School

Biochemical Analysis Of Dimethyl Suberimidate-Crosslinked Yeast Nucleosomes, Yuichi Ichikawa, Paul D. Kaufman

Open Access Articles

Nucleosomes are the fundamental unit of eukaryotic chromosome packaging, comprised of 147 bp of DNA wrapped around two molecules of each of the core histone proteins H2A, H2B, H3, and H4. Nucleosomes are symmetrical, with one axis of symmetry centered on the homodimeric interaction between the C-termini of the H3 molecules. To explore the functional consequences of nucleosome symmetry, we designed an obligate pair of H3 heterodimers, termed H3X and H3Y, allowing us to compare cells with single or double H3 alterations. Our biochemical validation of the heterodimeric X-Y interaction included intra-nucleosomal H3 crosslinking using dimethyl suberimidate (DMS). Here, we ...


Multiple Molecular Mechanisms Rescue Mtdna Disease In C. Elegans, Suraiya Haroon, Annie Li, Jaye L. Weinert, Clark Fritsch, Nolan G. Ericson, Jasmine Alexander-Floyd, Bart P. Braeckman, Cole M. Haynes, Jason H. Bielas, Tali Gidalevitz, Marc Vermulst 2018 The Children's Hospital of Philadelphia

Multiple Molecular Mechanisms Rescue Mtdna Disease In C. Elegans, Suraiya Haroon, Annie Li, Jaye L. Weinert, Clark Fritsch, Nolan G. Ericson, Jasmine Alexander-Floyd, Bart P. Braeckman, Cole M. Haynes, Jason H. Bielas, Tali Gidalevitz, Marc Vermulst

University of Massachusetts Medical School Faculty Publications

Genetic instability of the mitochondrial genome (mtDNA) plays an important role in human aging and disease. Thus far, it has proven difficult to develop successful treatment strategies for diseases that are caused by mtDNA instability. To address this issue, we developed a model of mtDNA disease in the nematode C. elegans, an animal model that can rapidly be screened for genes and biological pathways that reduce mitochondrial pathology. These worms recapitulate all the major hallmarks of mtDNA disease in humans, including increased mtDNA instability, loss of respiration, reduced neuromuscular function, and a shortened lifespan. We found that these phenotypes could ...


Killi-Data News (Winter), Tyrone Genade 2018 Northwestern College, Iowa

Killi-Data News (Winter), Tyrone Genade

Killifish Research Review

Valued readers, it is with a heavy heart that I inform you that this is the last issue of Killi-Data News. The good news is that we will be back as Killifish Research Review. The dissolution of Killi-Data International created a prob- lem: how can the newsletter of a defunct organization live on without that organization? But other additional problems were building in the background. The first issue numbered 15 pages. The previous issue was 28 pages. The number of killifish related papers is increasing while time on our end (the editorial team) is running out. It takes a lot ...


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