Life Sciences Commons^™

Pathogenicity Of Acinetobacter Calcoaceticus, Kaitlan A. Sullivan

MUSC Theses and Dissertations

Acinetobacter is a genus of gram-negative bacteria that have been appearing frequently in hospitals contributing to infections in the blood, lungs, urinary tract, and other parts of the body. It infects patients with weakened immune systems that are placed on ventilators, after the use of catheters, or have any other open wounds produced by prolonged hospital stays. This genus of bacteria is problematic due to its high probability of becoming resistant to multiple classes of antibiotics. Thus, we are determining the pathogenicity of clinical isolates of Acinetobacter calcoaceticus using the organism Caenorhabditis elegans as a model.

We are testing …

Cry1 Expression During Postnatal Development Is Critical For The Establishment Of Normal Circadian Period, Aaron Schirmer, Vivek Kumar, Andrew Schook, Eun Joo Song, Michael S. Marshall, Joseph S. Takahashi

Biology Faculty Publications

The mammalian circadian system generates an approximate 24-h rhythm through a complex autoregulatory feedback loop. Four genes, Period1 (Per1), Period2 (Per2), Cryptochrome1 (Cry1), and Cryptochrome2 (Cry2), regulate the negative feedback within this loop. Although these proteins have distinct roles within the core circadian mechanism, their individual functions are poorly understood. Here, we used a tetracycline trans-activator system (tTA) to examine the role of transcriptional oscillations in Cry1 and Cry2 in the persistence of circadian activity rhythms. We demonstrate that rhythmic Cry1 expression is an important regulator of circadian period. We then define a critical period from birth to postnatal day …

Progress Towards Peptide And Protein Synthesis Involving Thiol Moieties, Ryan Lo Chen

Biological Sciences

Polypeptides and proteins play crucial roles in biological systems, including enzymatic activity regulation, molecule transport, and cell and tissue structural support. Amino acids are the building blocks of peptides and proteins, and peptides can act as hormones, neurotransmitters, and enzymes. Proteins are made up of one or more polypeptide chains and have diverse functions such as catalyzing chemical reactions, transporting molecules, and providing structural support. Protein preparation can be done biologically by expression systems or isolation and purification from natural sources. While these methods have their advantages, they also have their shortcomings. Chemical synthesis is an alternative method that allows …

Characterizing The Functional Role Of Transcription Factor E In Archaeal Transcription, Madolyn Hofstetter, Michael Bartlett

Student Research Symposium

Archaea and eukaryotes share many homologous proteins and essential mechanisms for survival and DNA replication. It is proposed that Archaea are the ancestors of eukaryotes, suggesting that eukaryotic transcription evolved from the basic archaeal mechanisms. By studying the fundamentals of archaeal transcription, we are in turn understanding more about how eukaryotic transcription functions. Many human diseases are linked to mishaps and mutations in the process of transcribing DNA to mRNA, so it is essential to explore structures and how mutations in these structures affect the essential function of transcription, and if these mutations also play a role in human disease.

Mutant Viruses From Hell: Comparing The Capsid Structure Of Vp1 Mutants To The Wild-Type, Jenni Tran, Thejanee Liyanaarachchi, Ignacio De La Higuera, Jono Abshier, Ken Stedman

Student Research Symposium

Viruses can be defined as genetic material tightly packed in a protein coat called the capsid. The spindle-shaped fuselloviruses are found worldwide in hot springs at over 80°C and below pH 4. Sulfolobus spindle-shaped virus 1 (SSV1) is a fusellovirus known to infect the archaea, Saccharolobus solfataricus. This research will provide further insights into the survival of macromolecules, particularly proteins, that are present in extreme environments. To study the interaction of proteins within these extreme environments, we are studying the capsid structure of SSV1. The capsid of SSV1 is composed of two main proteins, VP1 (major) and VP3 (minor). There …

Biol 352 Cell Biology: Journey From The Center Of The Cell, Meredith A. Rowe Ph.D.

Open Educational Resources

This project is intended to be a long-term, scaffolded project across an entire semester course. Due dates are spread throughout the semester, and points are distributed as the professor deems appropriate across the sections of the project.

Characterization Of Phenotypic Traits Related To Loss-Of-Function And Ectopic Expression Of Bhlh093 And Bhlh061 In Arabidopsis Thaliana, Leila Belhadjali

WWU Graduate School Collection

bHLH093 and bHLH061 are members of sub-group IIIb of basic helix-loop-helix (bHLH) Arabidopsis thaliana transcription factors. Although bHLH proteins are the second largest transcription factor family in Arabidopsis, only a small proportion of them have been functionally characterized. Here, we investigated the phenotypic impact of bHLH061 and bHLH093 ectopic overexpression and loss-of-function to confirm previously published results and provide new insight into their role in development. bHLH093 and bHLH061 are homologs of two stomatal development genes, SCREAM1/ICE1 and SCREAM2 and have been shown to dimerize with two master regulators of stomata development, FAMA and MUTE. While no evidence was found …

Investigation Into The Akirin Subcellular Localization And Developmental Interactions, Riley Wildeman

Master of Science in Integrative Biology Theses

Akirin is a highly conserved nuclear protein ubiquitously expressed in nonfungal eukaryotic species and is known to be involved in many biological processes such as embryonic muscle patterning and innate immune function. Akirin functionality is essential for the prevention of disease and developmental defects. This investigation focused on both the subcellular localization of Akirin based on a putative nuclear localization signal and the genetic interaction between Akirin and the Nucleosome Remodeling Deacetylase (NuRD) complex. Through transfection of Drosophila S2 cells with Akirin mutant constructs we were able to visualize the localization patterns of Akirin and how the patterns relate to …

Characterization Of Yellow Family Proteins In Gryllus Bimaculatus, Alexandra W. Rubenstein

Honors Projects

Neuronal plasticity occurs in developing nervous systems, with adult organisms rarely able to recover from neurological damage. The cricket, Gryllus bimaculatus, is useful to study neuronal plasticity due to its reorganization of the auditory system in response to injury beyond development. When a cricket ear is removed and auditory afferents severed, a rare phenomenon occurs: the dendrites of interneurons on the deafferented side cross the typically-respected midline of the prothoracic ganglion to form functional synapses with auditory afferents from the opposite side. To find proteins involved in this phenomenon, the Horch Lab assembled a de novo transcriptome from neurons in …

Cloning And Expression Of Hydra Innexin 2, A Gap Junction Protein Required For Coordinated Contraction Of The Body Column, Ashley O'Brien

Biology Theses

In invertebrates gap junctions are formed by the innexin family of proteins. Remarkably, the genome of Hydra magnipapillata contains 17 innexin genes. This study focused on Hydra innexin-2 (h-Inx2) which is expressed in nerve cells and plays a role in contraction of the body column. The gene sequence of H-Inx2 was obtained from the National Center for Biotechnology Information (NCBI), the gene was synthesized externally and transferred to a vector suitable for expression in Xenopus oocytes (pcDNA3.1 CT-GFP TOPO). The TOPO CT-GFP vector includes a priming site for RNA polymerase which allows in vitro preparation of RNA. Another advantage is …

The Binding Site Between The Adenoviral Protein E4 11k And The Cellular Protein Ddx6, O'Nekia Samuel

Georgia College Student Research Events

Adenovirus is a nonenveloped virus that consists of an icosahedral capsid that contains double-stranded DNA. Viruses of this type can cause the common cold, conjunctivitis, and diarrhea. An important gene of adenoviruses is an early viral gene called E4 ORF3, which encodes the protein, E4 11k. This gene is responsible for changing the cellular environment, which aids in viral replication and prevents the host cell’s synthesis of proteins. E4 11k binds to Ddx6, a cellular protein located in P-bodies, and disrupts its localization. P-bodies are granules in the cytoplasm that contain mRNAs that have been repressed and proteins that are …

Development Of A Prolyl Endopeptidase Expression System In Lactobacillus Reuteri To Reduce The Clinical Manifestation Of Celiac Disease, Kara Lynn Jew

Master's Theses

Celiac Disease (CD) is an autoimmune disorder that emerges due to the ingestion of gluten, a protein found in a variety of common grains such as wheat, rye, and barley. Approximately 1 in 100 individuals in the US suffer from CD, making it the most commonly diagnosed gastrointestinal disorder (Ciclitira et. al., 2005). These proline-rich gluten peptides are resistant to proteolysis and accumulate in the duodenum of the small intestine. Once in the duodenum, these peptides illicit an autoimmune response resulting in villous atrophy. Current treatment for CD requires a rigorous adherence to a gluten-free diet. Nevertheless, gluten-containing grains are …

Targeting The Pin Domain Of Type Ii Toxins Is A Novel Approach To Treat Infections Caused By Nontypeable Haemophilus Influenzae, Ashley Lynne Molinaro

Biomedical Sciences Theses & Dissertations

Toxin-antitoxin (TA) gene pairs have been identified in nearly all bacterial genomes sequenced to date and are thought to facilitate persistence and antibiotic tolerance. TA loci are classified into various types based upon the characteristics of their antitoxins, with those in type II expressing proteic antitoxins. Many toxins from type II modules are ribonucleases that maintain a PilT N-terminus (PIN) domain containing conserved amino acids considered essential for activity. The vapBC (virulence associated protein) TA system is the largest subfamily in this class and has been linked to pathogenesis of nontypeable Haemophilus influenzae (NTHi). This dissertation presents three studies investigating …

Interfacial Stress In The Development Of Biologics: Fundamental Understanding, Current Practice, And Future Perspective, Jinjiang Li, Mary E. Krause, Xiaodong Cheng, Yuan Cheng, Weiguo Dai, John J. Hill, Min Huang, Susan Jordan, Daniel Lacasse, Linda Narhi, Evgenyi Shalaev, Ian C. Shieh, Justin C. Thomas, Raymond Tu, Songyan Zheng, Lily Zhu

Publications and Research

Biologic products encounter various types of interfacial stress during development, manufacturing, and clinical administration. When proteins come in contact with vapor–liquid, solid–liquid, and liquid–liquid surfaces, these interfaces can significantly impact the protein drug product quality attributes, including formation of visible particles, subvisible particles, or soluble aggregates, or changes in target protein concentration due to adsorption of the molecule to various interfaces. Protein aggregation at interfaces is often accompanied by changes in conformation, as proteins modify their higher order structure in response to interfacial stresses such as hydrophobicity, charge, and mechanical stress. Formation of aggregates may elicit immunogenicity concerns; therefore, it …

Structural Characterization Of Black Widow Spider Dragline Silk Proteins Crp1 And Crp4, Mikayla Shanafelt

University of the Pacific Theses and Dissertations

Spider dragline silk is a biomaterial with outstanding material properties, possessing high-tensile strength and toughness. In nature, dragline silk serves a central role during spider locomotion and web construction. Today, scientists are racing to elucidate the molecular machinery governing silk extrusion, attempting to translate this knowledge into a mimicry process in the laboratory to create synthetic fibers for a wide range of different applications. During extrusion, it has been established that biochemical and mechanical forces govern spidroin folding, aggregation, and assembly. In black widow spiders, at least 7 different proteins have been identified as constituents of dragline silk fibers. These …

The Evolution Of Molecular Compatibility Between Bacteriophage Φx174 And Its Host, Alexander Kula, Joseph Saelens, Jennifer Cox, Alyxandria M. Schubert, Michael Travisano, Catherine Putonti

Biology: Faculty Publications and Other Works

Viruses rely upon their hosts for biosynthesis of viral RNA, DNA and protein. This dependency frequently engenders strong selection for virus genome compatibility with potential hosts, appropriate gene regulation and expression necessary for a successful infection. While bioinformatic studies have shown strong correlations between codon usage in viral and host genomes, the selective factors by which this compatibility evolves remain a matter of conjecture. Engineered to include codons with a lesser usage and/or tRNA abundance within the host, three different attenuated strains of the bacterial virus ФX174 were created and propagated via serial transfers. Molecular sequence data indicate that biosynthetic …

Animal Agriculture And American Health: The Search For Sustainable Protein, Britta Brinkmann

Biology: Student Scholarship & Creative Works

This study examines the impact large-scale animal agriculture has on the environment. It links the environment and health. The goal is to find protein sources that are sustainable and nutritious in order to replace typical meat and dairy products. A study is proposed to measure the impact of the typical American diet, a vegan diet, an insect-supplemented diet and a diet heavy in seafood.

Detrital Protein Contributes To Oyster Nutrition And Growth In The Damariscotta Estuary, Maine, Usa, Cheyenne M. Adams

Electronic Theses and Dissertations

Oyster aquaculture is an expanding industry that relies on identifying and utilizing natural estuarine conditions for the economically viable production of a filter-feeding crop. The eastern oyster, Crassostrea virginica, is the principal species currently cultured in Maine. In addition to preferentially consumed phytoplankton, various detrital complexes (non-algal and/or non-living organic matter) may provide some nutrition to C. virginica between times of phytoplankton abundance. Here I investigated the importance of detrital proteins in supporting the growth of oysters cultured in the upper Damariscotta Estuary. Oyster aquaculture in this area is highly successful and previous reports indicate that labile detrital protein …

Constrained Sequence Alignment, Kyle Daling

WWU Honors College Senior Projects

Constrained Sequence Alignment: A new algorithm designed to help biologists produce better alignment for protein sequences.

Effect Of Bm-Hpme® Free Protein On Hbm-Mscs In Benchtop Bioreactor With Microcarriers, Adam Talbot

Biology Posters

Mesenchymal stem cell (MSC)-based therapies have great potential for treating many age-related diseases. When harvested from human bone marrow (hBM), these cells are relatively scarce and thus is is necessary for the cells to be expanded to achieve the necessary numbers needed for any therapeutic application and for many research applications. In order for the potential of MSCs to be unlocked, a strategy must be developed to expand these cells in the most efficient and effective way possible. Here we present a method to expand MSCs in a benchtop bioreactor with microcarriers and quantify the effect of the addition of …

Optimizing A Method For Simultaneous Recovery Of Proteins And Dna From Fingerprints, Steven Kranes

Student Theses

DNA testing on touched objects is a valuable tool in forensic investigations, but DNA is usually present in low amounts, causing poor STR typing results. For touch DNA evidence, there is a clear need for additional individualization, especially for highly probative samples. This could be achieved by testing genetically variable proteins. The goal of this project was to develop a DNA/protein co-extraction method to facilitate DNA and protein testing on the same evidence item. Existing DNA extraction methods were carefully adjusted to allow for downstream mass spectrometry analysis. Initial experiments on saliva and fingerprints placed on glass suggested that trypsin …

Thylakoid Protein Targeting/Insertion By A Signal Recognition Particle In Chloroplasts, Priyanka Sharma

Graduate Theses and Dissertations

Protein targeting is a fundamental cellular process that directs proteins from their site of synthesis to the site where they function. The signal recognition particle (SRP) dependent targeting pathway is conserved in both eukaryotes and prokaryotes where it co-translationally targets polypeptide chains emerging from ribosomes to the endoplasmic reticulum (eukaryotes) or cytoplasmic membrane (prokaryotes). A structurally unique form of SRP is found in chloroplasts where it functions to post-translationally bind and target a subset of integral thylakoid membrane proteins, the light harvesting chlorophyll binding proteins (LHCPs). Mature LHCPs bind chlorophyll a/b and function in photosynthetic light capture. Like many other …

Inquiry Into Perilipin-5a Expression In Triacylglycerol Rich Vs Normal Fed Mouse Tissue, Kobi Agyepong

Undergraduate Honors Thesis Projects

The steep rise in both childhood and adult obesity over the past three decades has moved to the forefront of public consciousness in recent years. This development has generated a marked increase in general health awareness and lifestyle changes for a vast number of individuals, most notably in the form of increased physical activity and diet alterations. The latter point is especially salient in a biochemical context, because of the myriad factors that can result in “fat accumulation”. Chief among these factors is the Perilipin 5A gene, (known as PLIN5A) which encodes the protein Perilipin 5A of the Perilipin family …

Ticks Elicit Variable Fibrinogenolytic Activities Upon Feeding On Hosts With Different Immune Backgrounds, Ashish Vora, Vikas Taank, John F. Anderson, Durland Fish, Daniel E. Sonenshine, John D. Catravas, Hameeda Sultana, Girish Neelakanta

Biological Sciences Faculty Publications

Ticks secrete several anti-hemostatic factors in their saliva to suppress the host innate and acquired immune defenses against infestations. Using Ixodes scapularis ticks and age-matched mice purchased from two independent commercial vendors with two different immune backgrounds as a model, we show that ticks fed on immunodeficient animals demonstrate decreased fibrinogenolytic activity in comparison to ticks fed on immunocompetent animals. Reduced levels of D-dimer (fibrin degradation product) were evident in ticks fed on immunodeficient animals in comparison to ticks fed on immunocompetent animals. Increased engorgement weights were noted for ticks fed on immunodeficient animals in comparison to ticks fed on …

Expression Of Fam171b Protein In Mouse Brain Tissue, Quan Tran

All Graduate Theses, Dissertations, and Other Capstone Projects

Polyglutamine (polyQ) diseases are inherited fatal neurodegenerative disorders caused by expansion of trinucleotide cytosine-adenine-guanine (CAG) repeats, encoding abnormally long glutamine tracts in respective disease proteins. Currently, there are nine polyQ diseases- including Huntington’s disease and a number of Spinocerebellar ataxias. Interestingly, expanded polyQ proteins are prone to aggregate, and this aggregation may underlie neurodegeneration. In this study, we investigate the expression and localization of FAM171B (a novel polyQ protein) in the brain. Western blotting reveals that FAM171B protein is indeed expressed in the developing and adult mouse brain. Furthermore, immunohistochemical analyses suggests widespread localization of FAM171B to many brain regions …

The Relationship Between Protein And Phosphorus Digestion And Retention In Growing Pigs And Broiler Chickens, Pengcheng Xue

Open Access Dissertations

Xue, Pengcheng. Ph.D., Purdue University, December 2016. The Relationship between Protein and Phosphorus Digestion and Retention in Growing Pigs and Broiler Chickens. Major Professor: Dr. Layi Adeola. The objective of this study was to investigate the relationship between protein and P digestion and retention in growing pigs and broiler chickens. The methodology of determining the digestibility of AA and P and the effect of dietary N and P on the digestion and retention of these two nutrients were investigated.

An experiment was conducted in growing pigs to investigate the additivity of AID or SID of CP and AA in mixed …

Developmental Functions Of Mir156-Regulated Squamosa Promoter Binding Protein-Like (Spl) Genes In Arabidopsis Thaliana, Mingli Xu, Tieqiang Hu, Jianfei Zhao, Mee-Yeon Park, Keith W. Earley, Gang Wu, Li Yang, R. Scott Poethig

Faculty Publications

Correct developmental timing is essential for plant fitness and reproductive success. Two important transitions in shoot development—the juvenile-to-adult vegetative transition and the vegetative-to-reproductive transition—are mediated by a group of genes targeted by miR156, SQUAMOSA PROMOTER BINDING PROTEIN (SBP) genes. To determine the developmental functions of these genes in Arabidopsis thaliana, we characterized their expression patterns, and their gain-of-function and loss-of-function phenotypes. Our results reveal that SBP-LIKE (SPL) genes in Arabidopsis can be divided into three functionally distinct groups: 1) SPL2, SPL9, SPL10, SPL11, SPL13 and SPL15 contribute to both the juvenile-to-adult vegetative transition …

Regulation Of Ampa-Type Glutamate Receptor Homolog Glr-1 By Erad Ubiquitin Ligases In C. Elegans, Sam Witus

Scholars Week

Endoplasmic reticulum-associated degradation (ERAD) maintains cellular health by removing misfolded proteins from the endoplasmic reticulum (ER). ERAD is ubiquitin-dependent, and ubiquitination of target proteins can be catalyzed by ER-resident E3 ubiquitin ligases. In C. elegans, genes for three putative ERAD E3 ubiquitin ligases have been identified: hrd-1, hrdl-1, and marc-6 (HRD-1, GP78/AMFR, and MARCH-6 in mammalian systems). In C. elegans, these three genes cooperate to maintain the overall health of animals during ER stress. We are testing the roles of hrd-1, hrdl-1, and marc-6 in the neurons of C. elegans. GLR-1 is a glutamate receptor that is expressed in a …

Spider Aggregate Glue Sequence Characterization And Expression, Kyle Berg

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Orb-weaving spiders create a glue which is secreted onto the web to capture and retain insects. This glue is made from aggregate protein. Aggregate glue is sticky when wet and can stretch far when pulled at slow speeds, and pull back with a greater force if pulled at high speeds which helps it achieve its purpose as the adhesive that keeps insects in the web. These features also make it an attractive target for applications such as a surgical glue or underwater adhesive. Unfortunately, very little is known about the aggregate glue gene, and knowledge of the genetic sequence is …

The Effect Of Degrading The Transcription Factor Nf-Kb Subunit Proteins On Nf-Kb' S Oncological Activity, Seongmin Lee

Honors Theses

Nuclear factor-kappa B (NF-κB) is a transcription factor that becomes functional when any two of its five component proteins (p50, p52, p65, c-Rel, and RelB) join together. NF-κB plays an important role in bringing out cell proliferation, or cell growth. When NF-κB malfunctions and becomes hyperactive, excessive NF-κB activity promotes abnormally high cell growth, which is a symptom of cancer. Because of its tie to cancer, NF-κB is commonly subjected to modification to curb cancer growth. In this project, each component protein of NF- κB was degraded via a method called RNAi to see if it would have any negative …