Molecular Biology Commons^™

An Analysis Of Crispr-Cas Gene Editing In Agriculture, Ashley Laliberte

Honors Scholar Theses

The CRISPR-Cas system is a promising form of gene editing, especially for the agriculture industry. The ability to make single-nucleotide edits within a gene of interest, without the need to introduce foreign DNA, is a powerful tool for designing healthier and more efficient crops and food animals. This system provides opportunity for increased nutritional value, decreased food waste, and more economically and environmentally sustainable food production. Though this biotechnology is facing mechanistic limitations due to off-target effects and inefficient homology-directed repair, vast improvements have already been made to improve its efficacy. The CRISPR-Cas system is already the most advanced form …

Effect Of Zinc On Microcystis Aeruginosa And Its Toxin Production, Jose L. Perez

Seton Hall University Dissertations and Theses (ETDs)

Cyanobacteria harmful algal blooms (CHABs) are globally increasing biomasses of detrimental cyanobacteria due to anthropogenic water phosphorous and nitrogen loading and climate change. CHABs often produce secondary metabolites, cyanotoxins, that cause harmful effects to organisms, most water systems, and socioeconomic infrastructures. Additionally, the presence of heavy metal pollutant runoff in CHAB affected environments may result in CHAB population changes – aggravating toxigenicity. Zinc metal resistance and stress response were studied in microcystin (MC) cyanotoxin-producing Microcystis aeruginosa UTEX LB 2385 (M. aeruginosa UTEX LB 2385) and non-MC producing Microcystis aeruginosa UTEX LB 2386 (M. aeruginosa UTEX LB 2386) cyanobacteria. Molecular analysis …

Mutagenesis Of Claudins To Probe In Vivo Interactions And Assemblies, Currey Zalman, Alex J. Vecchio

UCARE: Research Products

Paracellular transport of solutes and the control of the flow of molecules through the intracellular space in vertebrate epithelia is directed by tight junctions (TJs). Claudins form paracellular barriers and pores that determine tight junction permeability. This investigation attempts to explain the molecular bases for destruction and reconstruction of tight junctions within epithelial cells, occurring via both natural and disease-causing mechanisms. This interdisciplinary research is important in the advancement of our understanding of human biology and health, as different disruptions to epithelial tight junctions are hallmarks of many human diseases. The overall objective was to take previously made Claudin containing …

The Role Of Reactive Oxygen Species In The Gut Immune Response Of Cat Fleas (Ctenocephalides Felis), Clark Hall

Honors College Theses

Fleas transmit numerous deadly and debilitating diseases, including the causative agents of murine typhus and plague. Because initial entry of these infectious agents occurs while blood feeding, the immune response in the flea gut is considered to be the first line of defense against invading microbes. However, relatively few studies have identified the flea immune molecules that effectively resist or limit infection in the gut. In other hematophagous insects, an immediate immune response to imbibed pathogens is the generation of reactive oxygen species (ROS). In this study, we utilized cat fleas (Ctenocephalides felis) to investigate whether natural infections …

Methylation Of Salmonella Typhimurium Flagella Promotes Bacterial Adhesion And Host Cell Invasion, Julia A Horstmann, Michele Lunelli, Hélène Cazzola, Johannes Heidemann, Caroline Kühne, Pascal Steffen, Sandra Szefs, Claire Rossi, Ravi K Lokareddy, Chu Wang, Laurine Lemaire, Kelly T Hughes, Charlotte Uetrecht, Hartmut Schlüter, Guntram A Grassl, Theresia E B Stradal, Yannick Rossez, Michael Kolbe, Marc Erhardt

Department of Biochemistry and Molecular Biology Faculty Papers

The long external filament of bacterial flagella is composed of several thousand copies of a single protein, flagellin. Here, we explore the role played by lysine methylation of flagellin in Salmonella, which requires the methylase FliB. We show that both flagellins of Salmonella enterica serovar Typhimurium, FliC and FljB, are methylated at surface-exposed lysine residues by FliB. A Salmonella Typhimurium mutant deficient in flagellin methylation is outcompeted for gut colonization in a gastroenteritis mouse model, and methylation of flagellin promotes bacterial invasion of epithelial cells in vitro. Lysine methylation increases the surface hydrophobicity of flagellin, and enhances flagella-dependent adhesion of …

Methylation Of Salmonella Typhimurium Flagella Promotes Bacterial Adhesion And Host Cell Invasion., Julia A Horstmann, Michele Lunelli, Hélène Cazzola, Johannes Heidemann, Caroline Kühne, Pascal Steffen, Sandra Szefs, Claire Rossi, Ravi K Lokareddy, Chu Wang, Laurine Lemaire, Kelly T Hughes, Charlotte Uetrecht, Hartmut Schlüter, Guntram A Grassl, Theresia E B Stradal, Yannick Rossez, Michael Kolbe, Marc Erhardt

Department of Biochemistry and Molecular Biology Faculty Papers

The long external filament of bacterial flagella is composed of several thousand copies of a single protein, flagellin. Here, we explore the role played by lysine methylation of flagellin in Salmonella, which requires the methylase FliB. We show that both flagellins of Salmonella enterica serovar Typhimurium, FliC and FljB, are methylated at surface-exposed lysine residues by FliB. A Salmonella Typhimurium mutant deficient in flagellin methylation is outcompeted for gut colonization in a gastroenteritis mouse model, and methylation of flagellin promotes bacterial invasion of epithelial cells in vitro. Lysine methylation increases the surface hydrophobicity of flagellin, and enhances flagella-dependent adhesion of …

Possible Roles For Essential Oils In Chemoprevention And Suppression Of Cancer, Chad Kirk Lillestolen

Senior Honors Theses

Cancer represents one of the costliest and most prevalent diseases to afflict the modern world, even though treatments have evolved steadily over the years and produce an increasingly positive outlook with each development and innovation. Essential oils have been used medicinally- among other purposes- for thousands of years and have begun to attract attention for possible applications to the field of oncology. Numerous investigations and publications have shed light on the possible chemopreventative (antioxidant and antimetastatic) uses of these oils, alongside cancer suppressive (apoptosis-inducing and cytotoxic) abilities that they may possess. With the high annual incidence of cancer and the …

Progress Presentation On The Proposed Function Of Protein 4diu Through Bioinformatics Analyses, Melissa Hoff

Biochemistry and Molecular Biology Presentations

The BASIL project is a scientific inquiry project that aims to determine the function of a protein from its structure. Biochemistry students completed wet lab work, while structural biology students worked in silico. The purpose of this study was to determine the function of the protein with PDB ID: 4DIU. Bioinformatics analyses were completed using several databases: BLAST, Dali, Pfam, and Moltimate, and imaging of the protein was completed using PyMOL software. The BLAST database aligned the primary sequence with known protein sequences. The Dali database compared protein structure with known structures through global alignment. The Pfam database matched our …

The Role Of Diet In The Onset Of Depression: A Biochemical Connection Between Nutrition And Mental Health, Katlin Wildeman

Senior Honors Theses

Depression is a major clinical concern, having a complex onset and the presence of multiple, often unidentifiable causes. Depression affects millions of individuals worldwide, with a high prevalence in regions of the world with a Western-style diet as compared to regions with a Mediterranean diet. A Western-style diet consists of foods high in sugar, fat, and processed meats and grains, whereas the Mediterranean diet contains significantly more vegetables, fruits, lean meats, and whole grains. The link between diet and mental health disorders has implications for individuals of all ages who are hesitant to turn to medication. In addition to presenting …

Aminoacyl-Trna Synthetases, Miguel Angel Rubio Gomez, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The aminoacyl-tRNA synthetases are an essential and universally distributed family of enzymes that plays a critical role in protein synthesis, pairing tRNAs with their cognate amino acids for decoding mRNAs according to the genetic code. Synthetases help to ensure accurate translation of the genetic code by using both highly accurate cognate substrate recognition and stringent proofreading of noncognate products. While alterations in the quality control mechanisms of synthetases are generally detrimental to cellular viability, recent studies suggest that in some instances such changes facilitate adaption to stress conditions. Beyond their central role in translation, synthetases are also emerging as key …

The Classification Of An Unknown Protein 3h04, Britney Dyszel

Biochemistry and Molecular Biology Presentations

An unclassified protein in the Protein Data Bank, 3H04, was selected as a protein of interest. Research was performed in silico to gain key information on the structure, sequence, and homology of protein 3H04. This research was guided using the BASIL Project’s protocols on in silico research. Several databases were utilized to study protein 3H04. Based on the data gathered, unclassified protein 3H04 is an aminopeptidase that cleaves prolyl-dipeptidyl peptide bonds through alpha beta hydrolase function.

Probing The Function Of Perilipin 5b, Rebekah Dalton

Undergraduate Honors Thesis Projects

Many modern health issues arise from aberrant lipid metabolism, among these are type II diabetes and non-alcoholic fatty liver disease. One commonality these diseases share is neutral lipid metabolism and storage. Regulation of neutral lipid metabolism is of vital importance in the body, and among the proteins responsible for such regulation are the perilipins. Perilipins are a family of five conserved proteins that are found on the surface of lipid storage droplets and play a central role in the regulation of cellular neutral lipid metabolism. Perilipin 5 specifically, is expressed in tissues with a high capacity for fatty acid oxidation …

Methylxanthines Inhibit Primary Amine Oxidase And Monoamine Oxidase Activities Of Human Adipose Tissue, Wiem Haj Ahmed, CéCile Peiro, Jessica Fontaine, Barry J. Ryan, Gemma K. Kinsella, Jeff O’Sullivan, Jean-Louis Grolleau, Gary T.M. Henehan, Christian CarpéNé

Articles

Abstract: Background: Methylxanthines including caffeine and theobromine are widely consumed compounds and were recently shown to interact with bovine copper-containing amine oxidase. To the best of our knowledge, no direct demonstration of any interplay between these phytochemicals and human primary amine oxidase (PrAO) has been reported to date. We took advantage of the coexistence of PrAO and monoamine oxidase (MAO) activities in human subcutaneous adipose tissue (hScAT) to test the interaction between several methylxanthines and these enzymes, which are involved in many key pathophysiological processes. Methods: Benzylamine, methylamine, and tyramine were used as substrates for PrAO and MAO in homogenates …

Genome Sequencing Analysis Of Laboratory Isolate Of Francisella Noatunensis Subs. Orientalis, Joseph Paquette

Senior Honors Projects

Francisella noatunensis subs. orientalis is a known fish pathogen that has been most notably isolated from tilapia (Oreochromis niloticus) in Costa Rica. The genome of this Francisella species pathogen has been sequenced using Next-Generation Sequencing and been made available for the scientific community. Dr. Kathryn Ramsey’s research laboratory in the Department of Cell and Molecular Biology at the University of Rhode Island works with several Francisella species pathogens and is interested in identifying the differences, if any, between the known genome sequence of Francisella noatunensis and that of a laboratory isolate of the same species. With the use …

Npgreat: Hybrid Assembly Of Human Subtelomeres With The Use Of Nanopore And Linked-Read Datasets, Eleni Adam, Desh Ranjan, Harold Riethman

College of Sciences Posters

The telomeres are vitally important regions that are located at the tips of the chromosomes. Their dysfunction, caused by length shortening can lead to senescent cells, which in turn cause age-related diseases, including cancer. The subtelomeres, located next to the telomeres, possess the critical role of regulating the adjacent telomere lengths. Even after many years of research, human subtelomeres have proven to be very hard to assemble due to their morphology. In order to overcome these problems, the hybrid assembly method we develop utilizes two of the latest available types of data, which complement each other: Linked-Reads and ultralong Nanopore …

Elucidation Of The Mechanisms By Which Anesthetics Induce Blood-Brain Barrier Breakdown And Delirium In The Elderly, George A. Godsey Ii

Graduate School of Biomedical Sciences Theses and Dissertations

Delirium is a highly prevalent neuropsychiatric or neurocognitive disorder that presents a major problem to modern healthcare. Patients suffering from delirium normally have a worse prognosis, prolonged hospital stay, increased hospital cost, long-term cognitive impairment, and higher mortality rates. Many factors can predispose one to develop delirium, which makes treating this disorder a daunting task. Unfortunately, delirium is the most common psychiatric syndrome found in the hospital setting. In fact, a form of delirium known as postoperative delirium (POD) is one of the most common postoperative complications faced by elderly patients undergoing surgery.

POD is a major problem in modern …

Diversity Of The Major Histocompatibility Complex In African Penguins (Spheniscus Demersus) In Situ, Athena Schalk

Undergraduate Honors Thesis Projects

The Major Histocompatibility Complex (MHC) is responsible for the immune response in all jawed vertebrates and protects individuals against a variety of pathogens and diseases. Maintaining genetic diversity within the MHC exons is critical to protecting endangered species. African penguins (Spheniscus demersus) are in danger of losing their MHC diversity in isolated populations due to reductions in population size associated with environmental changes and human activity. This study analyzes the diversity within the exons in the DNA encoding the MHC by amplifying the exons through polymerase chain reaction and identifying alleles through denaturing gradient gel electrophoresis. Wild populations of …

Functional Sites Within The Ihnv Nonvirion Protein That Regulate Host Cellular Responses, Jeff Ringiesn, Bartolomeo Gorgoglione, Douglas W. Leaman

Celebration of Undergraduate & Graduate Research, Scholarship, and Creative Activities Materials

Fish Rhabdoviruses are responsible for causing fatal epizootics within commercial and wild populations of various fish species around the world. Infectious hematopoietic necrosis virus (IHNV), also known as the Salmonid novirhabdovirus, is enzootic along the Pacific Coast of North America and is comprised of five genogroups, each of which is endemic to a specific geographical location. Once the virus enters the host through the fin epithelia, IHNV infection causes infectious hematopoietic necrosis in salmonid species. The disease is highly fatal and presents with signs such as abdominal distension, bulging of the eyes, anemia, and necrosis of vital organs such as …

Tip60 Regulation Of Δnp63Α Is Associated With Cisplatin Resistance, Akshay Hira, Andrew Stacy, Jin Zhang, Michael P. Craig, Madhavi Kadakia

Celebration of Undergraduate & Graduate Research, Scholarship, and Creative Activities Materials

About 5.4 million basal and squamous cell skin cancers are diagnosed every year in the US. ΔNp63a, a member of the p53 transcription factor family, is overexpressed in non-melanoma skin cancer and regulates cell survival, migration and invasion. TIP60 is histone acetyltransferase (HAT) which mediates cellular processes such as transcription and the DNA damage response (DDR). Previous studies in our lab have shown that overexpression of TIP60 induces ΔNp63a protein stabilization in a catalytic-dependent manner. Since ΔNp63a is known to transcriptionally regulate several DDR genes and promote cisplatin resistance, its stabilization by TIP60 may contribute to the failure of platinum-based …

Optimization Of Methods For Cross-Species Infection Of Cell Cultures With Wolbachia, Sarah J. Lane

Honors Thesis

The common intracellular endosymbiont genus of bacteria called Wolbachia is of interest due to the promise it shows for playing a role in disease control. Wolbachia have a number of widely variable effects on its many species of host insects. In combination with these roles, Wolbachia largely affects reproduction and development of its host species. It can lead to feminization and cytoplasmic incompatibility (Werren et al. 2008). Furthermore, this species is vertically transmitted which means that it passes from mother to offspring (Caragata et al., 2016). In combination with its effects on reproduction, which can allow Wolbachia to propagate through …