Other Cell and Developmental Biology Commons^™

The Significance Of Crispr/Cas9-Directed Cul3 Knockout On Human Colorectal Cancer Cells, Zoe A. Lautz

Departmental Honors Projects

Cancer, the second leading cause of death in the US, is caused by mutations in select genes that alter cellular function leading to uncontrolled proliferation. Understanding the specific genes that drive cancer can lead to the generation of novel cancer therapies. To identify novel genes that drive cancer in the colon (CRC), lungs, and ovaries in mice, Starr et al. employed a transposon-based insertional mutagenesis system. One of the genes identified, APC, is mutated in 70-80% of human CRCs. CUL3, suspected to be a general driver gene, was discovered in the lung cancer screen. CUL3 was analyzed for its role …

Expression And Characterization Of Ecm14, A Metallocarboxypeptidase From Saccharomyces Cerevisiae, Matthew James Schott

Master's Theses

Metallocarboxypeptidases are found in most organisms and function in the digestion and maturation of proteins. Ecm14 is a putative metallocarboxypeptidase found in the yeast Saccharomyces cerevisiae vacuole. The function of Ecm14 as an enzyme has been unclear due to the presence of active site amino acids not typically found in metallocarboxypeptidases, suggesting either no enzymatic activity or a unique mechanism. In order to investigate the enzymatic mechanism of Ecm14, expression of histidine-tagged Ecm14 protein was attempted in human HEK293T cell culture, S. cerevisiae, and baculovirus expression systems. No expression was detected in HEK293T cells in preliminary experiments. Expression in the …

Clique Topology Reveals Intrinsic Geometric Structure In Neural Correlations, Chad Giusti, Eva Pastalkova, Carina Curto, Vladimir Itskov

Department of Mathematics: Faculty Publications

Detecting meaningful structure in neural activity and connectivity data is challenging in the presence of hidden nonlinearities, where traditional eigenvalue-based methods may be misleading. We introduce a novel approach to matrix analysis, called clique topology, that extracts features of the data invariant under nonlinear monotone transformations. These features can be used to detect both random and geometric structure, and depend only on the relative ordering of matrix entries. We then analyzed the activity of pyramidal neurons in rat hippocampus, recorded while the animal was exploring a 2D environment, and confirmed that our method is able to detect geometric organization using …

Abcb5 Identifies Immunoregulatory Dermal Cells, Tobias Schatton, Jun Yang, Sonja Kleffel, Mayuko Uehara, Steven R. Barthel, Christoph Schlapbach, Qian Zhan, Stephen Dudeney, Hansgeorg Mueller, Nayoung Lee, Juliane C. De Vries, Barbara Meier, Seppe Vander Beken, Mark M. Kluth, Christoph Ganss, Arlene H. Sharpe, Ana Maria Waaga-Gasser, Mohamed H. Sayegh, Reza Abdi, Karin Scharffetter-Kochanek, George F. Murphy, Thomas S. Kupper, Natasha Y. Frank, Markus H. Frank

Research outputs 2014 to 2021

Cell-based strategies represent a new frontier in the treatment of immune-mediated disorders. However, the paucity of markers for isolation of molecularly defined immunomodulatory cell populations poses a barrier to this field. Here, we show that ATP-binding cassette member B5 (ABCB5) identifies dermal immunoregulatory cells (DIRCs) capable of exerting therapeutic immunoregulatory functions through engagement of programmed cell death 1 (PD-1). Purified Abcb5+ DIRCs suppressed T cell proliferation, evaded immune rejection, homed to recipient immune tissues, and induced Tregs in vivo. In fully major-histocompatibility-complex-mismatched cardiac allotransplantation models, allogeneic DIRCs significantly prolonged allograft survival. Blockade of DIRC-expressed PD-1 reversed the inhibitory effects of …

Detection And Tracking Of T Cells In Time-Lapse Imaging, Cody Arbuckle, Milton L. Greenberg, Erik J. Linstead

Mathematics, Physics, and Computer Science Faculty Articles and Research

The effective classification and tracking of cells obtained from modern staining techniques has significant limitations due to the necessity of having to train and utilize a human expert in the field who must manually identify each cell in each slide. Often times these slides are filled with noise cells that are not of particular interest to the researcher. The use of computational methods has the ability to effectively and efficiently enhance image quality, as well as identify and track target cell types over large data sets. Here we present a computational approach to the in vitro tracking of T cells …

An Activity Aimed At Improving Student Explanations Of Biological Mechanisms, Caleb M. Trujillo, Trevor R. Anderson, Nancy J. Pelaez

PIBERG Instructional Innovation Materials

This document is intended for use by instructors and their students. The activity contains steps to introduce students to the MACH model involving analyzing and discussing explanations about biological mechanisms. Initially, students read modified articles about biological mechanisms during class, although instructors may prefer to assign readings outside of class before the activity. During the activity, students are required to analyze the readings for evidence of research methods, analogies, context, and mechanisms. In so doing, students learn how to integrate the information pertaining to each of the MACH model components into a coherent explanation about their biological mechanism. After performing …

A Tetrahedral Version Of The Mach Model For Explaining Biological Mechanisms, Caleb M. Trujillo, Trevor R. Anderson, Nancy J. Pelaez

PIBERG Instructional Innovation Materials

This document is intended for both instructors and students. Modified from the original MACH model this version, once cut and folded, creates a tetrahedral model that can conveniently be used as a teaching and learning tool to inform and guide students on how to write expert quality explanations of biological mechanisms. Each vertex of the tetrahedron represents a component of the model namely, Methods, Analogy, Context, and How. For a coherent and complete explanation about molecular mechanisms, it is important to integrate information pertaining to all four components of the model. The tetrahedral MACH model has been tested in both …

Peptide Arrays For Detecting Naphthenic Acids In Oil Sands Process Affected Water, Kamaljit Kaur, Subir Bhattacharjee, Rajesh G. Pillai, Sahar Ahmed, Sarfuddin Azmi

Pharmacy Faculty Articles and Research

Naphthenic acids (NAs) are water-soluble components of petroleum. The characterization and quantification of NAs by analytical methods have proved quite challenging, whilst the toxic effects of these water-soluble compounds on a variety of organisms adversely affecting reproduction and steroid production is becoming apparent. In this study, we report a fluorescence-based competitive binding method for rapid sensing of the presence of NAs using cellulosic peptide array strips as sensors. The peptide array was designed from sequences derived from the estrogen receptor (ER). Several of these peptides were able to detect the presence of NAs at low micromolar (∼5 mg L^{−1 …}

Neural Stem Cells As A Model To Study Huntington’S Disease, Rawan Bakhsh

Dissertations, Masters Theses, Capstones, and Culminating Projects

Huntington’s disease (HD) is a heritable neurodegenerative disorder that affects muscle coordination and diminishes cognitive abilities, by affecting the medium spiny neurons in the brain. In HD patients, neurons are damaged and destroyed because of the toxicity of the mutant Huntington protein (mHtt). The mechanism of how mHtt protein affects the neurons is unknown. In this study we explored the effects of mHtt expression by looking at changes in huntingtin localization, changes in the expression and co-localization of related proteins and differences in cell morphology. We examine how this expression affects the cytoskeletal structures using neural stem cells Q7 (wild …

Phthalates And Phthalate Alternatives: Effects On Proliferative And Estrogenic Target Genes In Ishikawa Cells, Ranjani Sundar '15, Ping Yin, Serdar E. Bulun

Student Publications & Research

Phthalates are used as plasticizers in many of the products found in medical, household, and industrial applications. Much research has not been completed on the effects of these phthalates as potential endocrine disrupting chemicals (EDCs). As these chemicals are ingested, the mechanism by which they affect the reproductive system is largely unknown. The purpose of this study was to observe how 2 phthalates, Di-n-butyl phthalate (DBP) and Diisononyl phthalate (DINP), and 2 phthalate alternatives, Dioctyl terephthalate (DOTP) and BHT (butylated hydroxytoluene)affect uterine cells in comparison to a vehicle treatment and 17β-Estradiol treatment. Changes in expression of mRNA were observed using …

Analysis Of The Chondroitinase Operon Of Flavobacterium Columnare, Erin L. Sorlien

Senior Honors Projects

Analysis of the chondroitinase operon of Flavobacterium columnare

Erin Sorlien

Major

Cell and Molecular Biology, Chemistry

Advisor

Dr. David R. Nelson

Date

May 2, 2013

Keywords

Flavobacterium columnare, columnaris disease, chondroitin AC lyase, complementation, csl operon

Abstract
Flavobacterium columnare, an opportunistic bacterial pathogen of fish, is the causative agent of columnaris disease (CD). The bacterium is a Gram-negative rod that exhibits gliding motility and avidly forms biofilms. CD affects both wild and cultured freshwater fish, and continues to cause large economic losses to the fish farming industry. According to an investigation conducted by the National Animal Health Monitoring System, CD …

Investigating The Roles Of The P63 Isoforms In The Microrna Biogenesis Pathway, Deepavali Chakravarti

Dissertations and Theses (Open Access)

MicroRNAs play roles in various biological processes like development, tumorigenesis, metastasis and pluripotency. My thesis work has demonstrated roles for p63, a p53 family member, in the upstream regulation of microRNA biogenesis. The p63 gene has a complex gene structure and has multiple isoforms. The TAp63 isoforms contain an acidic transcription activation domain. The ΔNp63 isoforms, lack the TA domain, but have a proline rich region critical for gene transactivation. To understand the functions of these isoforms, the Flores lab generated TAp63 and ΔNp63 conditional knock out mice. Using these mice and tissues and cells from these mice we have …

Aqueous Extract Of Nigella Sativa Seeds Suppresses Testicular Steroidogenesis In Mice Leydig Cells In Vitro., 5sheikh A. Saeed, Naheed Anwar, Qaiser Jabeen, Anwar Hassan Gilani

Department of Biological & Biomedical Sciences

10ABSTRACT 11Nigella sativa (black seed) is an important medicinal herb with folkloric use in wide range of diseases. It is 12well studied for its biological activities. However, there is limited information regarding its effect on the 13male reproductive system. This study describes the effect of the aqueous extract of N. sativa (NSE) on 14 testicular steroidogenesis from mice Leydig cells in vitro. Mice testicular cells were incubated in a media 15 containing either no treatment or NSE or LH alone or combination of LH and NSE. Incubations were 16 carried out for three hours in a shaking water bath at …

Identification Of Ebs1, Lsm6 And Nup159 As Suppressors Of Spt10 Effects At Adh2 In Saccharomyces Cerevisiae Suggests Post-Transcriptional Defects Affect Mrna Synthesis, Bradley Anderson, Carrie Ann May, Clyde L. Denis

New Hampshire Agricultural Experiment Station Publications

Suppression of the effects of an spt10 mutation on ADH2 expression is a phenotype shared by a small number of genes whose protein products are either components of the CCR4-NOT complex required for mRNA deadenylation and degradation (CCR4, CAF1, NOT4) or have been shown to interact with the complex (DBF2, SRB9, SRB10). In this work, we conducted a screen for additional suppressors of spt10 at ADH2 to identify new factors related to CCR4 function. In addition to reisolating ccr4 and caf1 alleles, three previously unidentified suppressors …

Characterization Of The Infectivity Of Non-Replicating Human Immunodeficiency Virus (Hiv)-Derived Viral Vectors., Vanessa E. Rodriguez, Manuel Llano, Luis Valdes

COURI Symposium Abstracts, Summer 2012

The ability of HIV-derived viral vectors to integrate genes of interest into the host genome causing permanent phenotypic modifications makes them excellent tools in gene therapy. However, integration also causes insertional mutagenesis and controlling integration site selection will increase the biosafety of these molecular tools. HIV DNA integration site selection is influenced by LEDGF/p75, a chromatin-bound cellular protein that interacts with the viral enzyme integrase through the integrase binding domain (IBD). Integrase catalyzes viral DNA integration and non-covalently associates with the HIV genome forming the pre-integration complex (PIC). Therefore, interaction of chromatin-bound LEDGF/p75 with the PIC-associated integrase tethers the HIV …

The Effects Of Cytokinin On The Transcriptional Regulation Of Pin Expression In Arabidopsis Thaliana, Elizabeth Burgess

Honors Theses and Capstones

The processes of cell division and differentiation are critical to the development of any multicellular organism. During the formation of plant roots these processes take place at a region of the root tip called the meristem. Cytokinin and auxin are two plant growth hormones that influence this process. Although these two growth hormones are both necessary they also appear in many ways to have an antagonistic relationship. As meristematic root cells undergo differentiation they cease dividing. It has been proposed that the size of the root meristem and thus the overall rate of root growth are determined by the balance …

Endotoxin-Induced Inflammation & Morphine-Induced Conditioned Place Preference In The Hiv-1 Transgenic Rat, Natasha F. Homji-Mishra

Seton Hall University Dissertations and Theses (ETDs)

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Use Of Two-Dimensional Agarose-Gel Analysis To Characterize Processing Of Uv-Irradiated Plasmids And The Composition Of The Replisome Following Uv-Induced Arrest, Harout Arthur Jeiranian

Dissertations and Theses

In this thesis, I address two fundamental questions related to our understanding of how DNA damage is processed and repaired during replication. Using Two-dimensional (2-D) agarose gel analysis, I first examine whether DNA damage on plasmids introduced by transformation is processed in a manner similar to that observed on endogenously replicating plasmids and the chromosome. The original intent for using this approach was to develop a technique that could examine how different DNA adducts would be repaired in various sequence contexts. However, I found that distinct differences exist between the processing of DNA damage on transforming plasmids and the chromosome. …

Gata-Family Transcription Factors In Magnaporthe Oryzae, Cristian F. Quispe

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

The filamentous fungus, Magnaporthe oryzae, responsible for blast rice disease, destroys around 10-30% of the rice crop annually. Infection begins when the specialized infection structure, the appressorium, generates enormous internal turgor pressure through the accumulation of glycerol. This turgor acts on a penetration peg emerging at the base of the cell, causing it to breach the leaf surface allowing its infection.

The enzyme trehalose-6- phosphate synthase (Tps1) is a central regulator of the transition from appressorium development to infectious hyphal growth. In the first chapter we show that initiation of rice blast disease requires a regulatory mechanism involving an …

The Impact Of Tricaine Methanesulfonate, 2-Phenoxyethanol, And Carvone-Methyl Salicylate On The Innate Immune Response Of Zebrafish (Danio Rerio), Charles R. Wulff

Honors Theses

Anesthesia plays a vital role in the maintenance of aquaculture species, where it is used to minimize stress during complex handling tasks such as transport, assessment, and harvesting. However, anesthetics have been shown to suppress the innate immune response, which could impact immunity and increase risk of infection. Tricaine methanesulfonate (MS-222) and 2-Phenoxyethanol (2-PE) represent two of the most commonly used anesthetics in aquaculture, with R-(+)-carvone, in the form of carvone-methyl salicylate (CMS) has recently been proposed as an alternative anesthetic for food fish. These three anesthetics were used to assess the influence of anesthetics on the immune system of …