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Stochastic Modeling Of Neuronal Transport In Various Cellular Geometries, Abhishek Choudhary Mr., Peter Kramer 2019 Rensselaer Polytechnic Institute

Stochastic Modeling Of Neuronal Transport In Various Cellular Geometries, Abhishek Choudhary Mr., Peter Kramer

Biology and Medicine Through Mathematics Conference

No abstract provided.


Modeling Mechanisms Behind Force Generation By Actin Polymerization, Seyed Fowad Motahari 2019 Washington University in St. Louis

Modeling Mechanisms Behind Force Generation By Actin Polymerization, Seyed Fowad Motahari

Arts & Sciences Electronic Theses and Dissertations

Actin polymerization is the primary mechanism for overcoming the large turgor pressure that opposes endocytosis in yeast. While generation of pushing forces by actin polymerization is fairly well understood, it is not clear how actin polymerization produces pulling forces. In order to understand this process, it is necessary to simulate polymerization of filaments having various types of interactions with the membrane. Since existing methodologies in the literature do not treat such problems correctly, we develop a thermodynamically consistent methodology for treating polymerization of filaments having arbitrary interaction potentials with the membrane. Then I perform stochastic simulations for a system of ...


Bridging From Intramuscular To Limb Perfusion Delivery Of Raav: Optimization In A Non-Human Primate Study, Alisha Gruntman, Gwladys Gernoux, Qiushi Tang, Guo-Jie Ye, Dave R. Knop, Gensheng Wang, Janet Benson, Kristen E. Coleman, Allison M. Keeler, Christian Mueller, Louis G. Chicoine, Jeffrey D. Chulay, Terence R. Flotte 2019 University of Massachusetts Medical School

Bridging From Intramuscular To Limb Perfusion Delivery Of Raav: Optimization In A Non-Human Primate Study, Alisha Gruntman, Gwladys Gernoux, Qiushi Tang, Guo-Jie Ye, Dave R. Knop, Gensheng Wang, Janet Benson, Kristen E. Coleman, Allison M. Keeler, Christian Mueller, Louis G. Chicoine, Jeffrey D. Chulay, Terence R. Flotte

Christian Mueller

Phase 1 and phase 2 gene therapy trials using intramuscular (IM) administration of a recombinant adeno-associated virus serotype 1 (rAAV1) for replacement of serum alpha-1 antitrypsin (AAT) deficiency have shown long-term (5-year) stable transgene expression at approximately 2% to 3% of therapeutic levels, arguing for the long-term viability of this approach to gene replacement of secreted serum protein deficiencies. However, achieving these levels required 100 IM injections to deliver 135 mL of vector, and further dose escalation is limited by the scalability of direct IM injection. To further advance the dose escalation, we sought to bridge the rAAV-AAT clinical development ...


Subcellular-Level Resolution Maldi-Ms Imaging Of Maize Leaf Metabolites By Maldi-Linear Ion Trap-Orbitrap Mass Spectrometer, Andrew R. Korte, Marna D. Yandeau-Nelson, Basil J. Nikolau, Young-Jin Lee 2019 Iowa State University

Subcellular-Level Resolution Maldi-Ms Imaging Of Maize Leaf Metabolites By Maldi-Linear Ion Trap-Orbitrap Mass Spectrometer, Andrew R. Korte, Marna D. Yandeau-Nelson, Basil J. Nikolau, Young-Jin Lee

Marna Yandeau-Nelson

A significant limiting factor in achieving high spatial resolution for matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS) imaging is the size of the laser spot at the sample surface. Here, we present modifications to the beam-delivery optics of a commercial MALDI-linear ion trap-Orbitrap instrument, incorporating an external Nd:YAG laser, beam-shaping optics, and an aspheric focusing lens, to reduce the minimum laser spot size from ~50 μm for the commercial configuration down to ~9 μm for the modified configuration. This improved system was applied for MALDI-MS imaging of cross sections of juvenile maize leaves at 5-μm spatial resolution using an oversampling ...


Role Of The Glycerophosphocholine Acyltransferase, Gpc1, In Phosphatidylcholine (Pc) Biosynthesis And Remodeling In Saccharomyces Cerevisiae, Sanket Anaokar 2019 Duquesne University

Role Of The Glycerophosphocholine Acyltransferase, Gpc1, In Phosphatidylcholine (Pc) Biosynthesis And Remodeling In Saccharomyces Cerevisiae, Sanket Anaokar

Electronic Theses and Dissertations

Biomembranes are permeable barriers that enclose the cell and the intracellular organelles in a cell. The selective nature of these robust barriers acts as the first line of defense towards the harsh factors that can compromise cell survival. Biomembranes primarily consist of membrane lipids that are organized into layers to form a dynamic bilayer structure. The dynamic nature of the membrane requires the synchronized modulation of lipid composition through de novo synthesis, degradation, intracellular movement, and remodeling. Phospholipids are the major membrane lipid class, and phosphatidylcholine (PC) is the most abundant phospholipid in most eukaryotic biomembranes.

PC is primarily produced ...


On The Ability Of Pnicogen Atoms To Engage In Both Σ And Π-Hole Complexes. Heterodimers Of Zf2C6H5 (Z = P, As, Sb, Bi) And Nh3, Wiktor Zierkiewicz, Mariusz Michalczyk, Rafał Wysokiński, Steve Scheiner 2019 Wrocław University of Science and Technology

On The Ability Of Pnicogen Atoms To Engage In Both Σ And Π-Hole Complexes. Heterodimers Of Zf2C6H5 (Z = P, As, Sb, Bi) And Nh3, Wiktor Zierkiewicz, Mariusz Michalczyk, Rafał Wysokiński, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

When bound to a pair of F atoms and a phenyl ring, a pyramidal pnicogen (Z) atom can form a pnicogen bond wherein an NH3 base lies opposite one F atom. In addition to this σ-hole complex, the ZF2C6H5 molecule can distort in such a way that the NH3 approaches on the opposite side to the lone pair on Z, where there is a so-called π-hole. The interaction energies of these π-hole dimers are roughly 30 kcal/mol, much larger than the equivalent quantities for the σ-hole complexes, which are only 4–13 ...


Enhanced Cas12a Editing In Mammalian Cells And Zebrafish, Pengpeng Liu, Kevin Luk, Masahiro Shin, Feston Idrizi, Samantha F. Kwok, Benjamin P. Roscoe, Esther Mintzer, Sneha Suresh, Kyle Morrison, Josias B. Frazao, Mehmet Fatih Bolukbasi, Karthikeyan Ponnienselvan, Jeremy Luban, Lihua Julie Zhu, Nathan D. Lawson, Scot A. Wolfe 2019 University of Massachusetts Medical School

Enhanced Cas12a Editing In Mammalian Cells And Zebrafish, Pengpeng Liu, Kevin Luk, Masahiro Shin, Feston Idrizi, Samantha F. Kwok, Benjamin P. Roscoe, Esther Mintzer, Sneha Suresh, Kyle Morrison, Josias B. Frazao, Mehmet Fatih Bolukbasi, Karthikeyan Ponnienselvan, Jeremy Luban, Lihua Julie Zhu, Nathan D. Lawson, Scot A. Wolfe

Open Access Articles

Type V CRISPR-Cas12a systems provide an alternate nuclease platform to Cas9, with potential advantages for specific genome editing applications. Here we describe improvements to the Cas12a system that facilitate efficient targeted mutagenesis in mammalian cells and zebrafish embryos. We show that engineered variants of Cas12a with two different nuclear localization sequences (NLS) on the C terminus provide increased editing efficiency in mammalian cells. Additionally, we find that pre-crRNAs comprising a full-length direct repeat (full-DR-crRNA) sequence with specific stem-loop G-C base substitutions exhibit increased editing efficiencies compared with the standard mature crRNA framework. Finally, we demonstrate in zebrafish embryos that the ...


Assessing The Potential Impact Of Nanotechnology On The Purification Of Water, Noor Khan 2019 Collin College

Assessing The Potential Impact Of Nanotechnology On The Purification Of Water, Noor Khan

Quest

Independent Research Paper

Research in progress for PHYS 2426: University Physics II

Faculty Mentor: Raji Kannampuzha, Ph.D.

The following paper represents research work done by students in a University Physics 2426 class, the second half of a two-semester introductory course in physics. It is a calculus-based physics course, intended primarily for physics, chemistry, math, and engineering majors. Students are introduced to the concept of academic research by learning to ask research-focused questions and then use the library resources to pursue outside research to find answers. For this assignment, students are asked to investigate a physical science, biological science, or ...


Circular Dichroism And Molecular Modeling Yield A Structure For The Complex Of Human Immunodeficiency Virus Type 1 Trans-Activation Response Rna And The Binding Region Of Tat, The Trans-Acting Transcriptional Activator, Erwann P. Loret, Philippe T. Georgel, W. Curtis Johnson Jr., Pui Shing Ho 2019 Marshall University

Circular Dichroism And Molecular Modeling Yield A Structure For The Complex Of Human Immunodeficiency Virus Type 1 Trans-Activation Response Rna And The Binding Region Of Tat, The Trans-Acting Transcriptional Activator, Erwann P. Loret, Philippe T. Georgel, W. Curtis Johnson Jr., Pui Shing Ho

Philippe T. Georgel

Transcription in the human immunodeficiency virus type 1 (HIV-1) retrovirus is regulated by binding the viral Tat protein (trans-acting transcriptional activator) to the trans-activation response (TAR) RNA sequence. Here, vacuum UV circular dichroism (VUV-CD) is used to study the structure of TAR and its complex with two peptide fragments that are important for Tat binding to TAR. The VUV-CD spectrum of TAR is typical of A-form RNA and is minimally perturbed when bound to either the short or the long Tat peptide. The CD spectra ofthe complexes indicate an extended structure in the argnine-rich region of Tat from amino acid ...


Biotransformation Of Praziquantel By Cunninghamella Elegans, Umbelopsis Ramanniana, And Yarrowia Lipolytica Metabolism, Samuel Chivers 2019 University of the Incarnate Word

Biotransformation Of Praziquantel By Cunninghamella Elegans, Umbelopsis Ramanniana, And Yarrowia Lipolytica Metabolism, Samuel Chivers

Samuel Chivers

No abstract provided.


Patterns Of Metabolite Changes Identified From Large-Scale Gene Perturbations In Arabidopsis Using A Genome-Scale Metabolic Network, Taehyong Kim, Kate Dreher, Ricardo Nilo-Poyanco, Insuk Lee, Oliver Fiehn, Bernd Markus Lange, Basil J. Nikolau, Lloyd Sumner, Ruth Welti, Eve S. Wurtele, Seung Y. Rhee 2019 Carnegie Institution for Science

Patterns Of Metabolite Changes Identified From Large-Scale Gene Perturbations In Arabidopsis Using A Genome-Scale Metabolic Network, Taehyong Kim, Kate Dreher, Ricardo Nilo-Poyanco, Insuk Lee, Oliver Fiehn, Bernd Markus Lange, Basil J. Nikolau, Lloyd Sumner, Ruth Welti, Eve S. Wurtele, Seung Y. Rhee

Eve Wurtele

Metabolomics enables quantitative evaluation of metabolic changes caused by genetic or environmental perturbations. However, little is known about how perturbing a single gene changes the metabolic system as a whole and which network and functional properties are involved in this response. To answer this question, we investigated the metabolite profiles from 136 mutants with single gene perturbations of functionally diverse Arabidopsis (Arabidopsis thaliana) genes. Fewer than 10 metabolites were changed significantly relative to the wild type in most of the mutants, indicating that the metabolic network was robust to perturbations of single metabolic genes. These changed metabolites were closer to ...


The Worlds Of Splicing And Chromatin Collide, J. Adam Hall, Philippe T. Georgel 2019 Marshall University

The Worlds Of Splicing And Chromatin Collide, J. Adam Hall, Philippe T. Georgel

Philippe T. Georgel

Both transcription and splicing take place in a nuclear environment which, at face value, may seem refractory to the efficiency afforded by the coupling of both processes. This environment, chromatin, was once viewed as only a passive packaging system for genetic material, with very little contribution to the variety of nuclear activities occurring within and around it. However, overwhelming evidence now points to the chromatin environment as being highly dynamic, and an active player in nuclear activities.


Effect Of Turmeric On The Promoter Activity Of The Cyp6a8 Gene Of Drosophila Melanogaster, Alexa Stroh 2019 University of Tennessee, Knoxville

Effect Of Turmeric On The Promoter Activity Of The Cyp6a8 Gene Of Drosophila Melanogaster, Alexa Stroh

Chancellor’s Honors Program Projects

No abstract provided.


Spatial Reorganization Of Histone-Like Nucleoid Structuring Proteins Caused By Silver Nanoparticles, Meaad Alqahtany 2019 University of Arkansas, Fayetteville

Spatial Reorganization Of Histone-Like Nucleoid Structuring Proteins Caused By Silver Nanoparticles, Meaad Alqahtany

Theses and Dissertations

Silver nanoparticles (AgNPs) and ions (Ag+) can be the new generation of antibiotics due to their antimicrobial effects against bacteria and other microbes. Many studies have shown that AgNPs and suppress the growth of bacteria and damage the cell walls of the microbes; therefore, treating bacterial cells with AgNPs may be a promising method to terminate multi-resistant bacteria. In this work, the effect of AgNPs with two different surface coatings on the spatial reorganization of histone-like nucleoid structuring (H-NS) proteins in Escherichia coli bacteria was investigated using quantitative super-resolution fluorescence microscopy to understand the toxicity and antimicrobial mechanism of AgNPs ...


Brown Fat Organogenesis And Maintenance Requires Akt1 And Akt2, Joan Sanchez-Gurmaches, Camila Martinez Calejman, Su Myung Jung, Huawei Li, David A. Guertin 2019 University of Massachusetts Medical School

Brown Fat Organogenesis And Maintenance Requires Akt1 And Akt2, Joan Sanchez-Gurmaches, Camila Martinez Calejman, Su Myung Jung, Huawei Li, David A. Guertin

Open Access Articles

OBJECTIVE: Understanding the signaling mechanisms that control brown adipose tissue (BAT) development is relevant to understanding energy homeostasis and obesity. The AKT kinases are insulin effectors with critical in vivo functions in adipocytes; however, their role in adipocyte development remains poorly understood. The goal of this study was to investigate AKT function in BAT development.

METHODS: We conditionally deleted Akt1 and Akt2 either individually or together with Myf5-Cre, which targets early mesenchymal precursors that give rise to brown adipocytes. Because Myf5-Cre also targets skeletal muscle and some white adipocyte lineages, comparisons were made between AKT function in BAT versus white ...


Biotransformation Of Natural Antioxidants Osajin And Pomiferin By Cunninghamella Elegans (Atcc® 9245tm), Stephen Luis 2019 University of the Incarnate Word

Biotransformation Of Natural Antioxidants Osajin And Pomiferin By Cunninghamella Elegans (Atcc® 9245tm), Stephen Luis

Theses & Dissertations

Osajin and pomiferin, prenylated isoflavones extracted from the fruit of the osage orange tree (Maclura pomifera) have been reported as antioxidant compounds. The purpose of this study is to analyze the metabolization of osajin and pomiferin by the fungi Cunninghamella elegans (ATCC 9245) and supporting strains Umbelopsis ramanniana and Aspergillus fumigatus fresnius.

HPLC analysis of the extracts showed new, more polar compounds were formed, evidenced by peaks at lower retention times for each strain of fungi. To further investigate the metabolites produced, HPLC-guided chromatographic purification will be performed, and the pure metabolites will be analyzed through nuclear magnetic resonance and ...


Pre-Administration Of Medium Chain Triglycerides In Vivo Can Attenuate Or Block The Effects Of Recurrent Hypoglycemia, Dhanisha Nandigama 2019 University at Albany, State University of New York

Pre-Administration Of Medium Chain Triglycerides In Vivo Can Attenuate Or Block The Effects Of Recurrent Hypoglycemia, Dhanisha Nandigama

Biological Sciences

Hypoglycemia is a state of abnormally low blood glucose. Many patients who use insulin, primarily for the treatment of diabetes, experience multiple bouts of hypoglycemia, termed recurrent hypoglycemia (RH). Because RH impairs cognitive function and ability to appropriately respond to a subsequent episode of hypoglycemia, it is critical to develop treatments. One approach, which we have taken here, is to attempt to preserve neuronal fuel supply during a hypoglycemic episode. Medium-chain triglycerides are medium-chain fatty acid (MCT) esters of glycerol that can provide an alternative fuel source to the brain via ketones; the hippocampus is known to express transporters for ...


The Effect Of Cysteine-Reactive Catechol Antioxidants On Alcohol Dehydrogenase As A Model For Oxidative Stress In Neurodegenerative Disease, Rachel Smith 2019 William & Mary

The Effect Of Cysteine-Reactive Catechol Antioxidants On Alcohol Dehydrogenase As A Model For Oxidative Stress In Neurodegenerative Disease, Rachel Smith

Undergraduate Honors Theses

The cellular mechanisms underlying age-related neurodegeneration, especially in disease states, are poorly understood. Oxidative stress has been heavily implicated as one factor both produced by and contributing to the progression of neurodegenerative diseases such as Alzheimer’s disease. In particular, it can destroy a cell’s ability to produce energy through aerobic and anaerobic respiration, thus leading to the death of individual cells and brain tissues as a whole. This study focuses on the relationship between oxidative stress and energy production in disease states. In particular, we examine the ability of catechol molecules to take on pro-oxidative properties and modify ...


Regulation Of The Drosophila Imd Pathway By Signaling Amyloids, Anni Kleino, Neal S. Silverman 2019 Aarhus University

Regulation Of The Drosophila Imd Pathway By Signaling Amyloids, Anni Kleino, Neal S. Silverman

Open Access Articles

Fruit flies elicit effective defense responses against numerous microbes. The responses against Gram-negative bacteria are mediated by the Imd pathway, an evolutionarily conserved NF-kappaB pathway recognizing meso-diaminopimelic acid (DAP)-type peptidoglycan from bacterial cell walls. Several reviews already provide a detailed view of ligand recognition and signal transduction during Imd signaling, but the formation and regulation of the signaling complex immediately downstream of the peptidoglycan-sensing receptors is still elusive. In this review, we focus on the formation of the Imd amyloidal signaling center and post-translational modifications in the assembly and disassembly of the Imd signaling complex.


The Effects Of Eicosapentaenoic Acid (Epa) And Docosahexaenoic Acid (Dha) On Brown Adipogenesis In Stem Cell Culture, Darynne Dahlem 2019 University of Arkansas, Fayetteville

The Effects Of Eicosapentaenoic Acid (Epa) And Docosahexaenoic Acid (Dha) On Brown Adipogenesis In Stem Cell Culture, Darynne Dahlem

Animal Science Undergraduate Honors Theses

Polyunsaturated fatty acids (PUFAs), especially eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), are major maternal dietary supplements due to their positive benefits on neurological tissue growth during the first 12 weeks of gestation. Previous studies show that EPA and DHA inhibit muscle formation but promote adipogenesis. However, no research has addressed the question whether high intake of EPA and DHA affects brown fat development during gestation. The objective of this study was to measure the effect of EPA and DHA supplement on brown adipogenesis and potential pathways related to mitochondrial biosynthesis using fibroblasts as in vitro model. Using Oil-Red-O staining ...


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