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Introduction To Gene Enrichment Analysis Tools, Rolando Garcia-Milian 2015 Yale University

Introduction To Gene Enrichment Analysis Tools, Rolando Garcia-Milian

Rolando Garcia-Milian

Bioinformatics enrichment tools play an important role in identifying, annotating, and functionally analyzing large list of genes generated by high-throughput technologies (e.g. microarrary, RNA-seq, ChIP-chip). This workshop will provide an overview of the principle, type of enrichments, and the infrastructure of enrichment tools. By using concrete examples, it will also introduce some of the most popular tools for gene enrichment analysis such as DAVID, GSEA, and WebGestalt.


Cell Viability Assessment Using The Alamar Blue Assay: A Comparison Of 2d And 3d Cell Culture Models, Franck Bonnier, Mark Keating, Tomasz P. Wrobel, Katarsyna Majzner, Malgorzata Baranska, Amaya Garcia, Alfonso Blanco, Hugh J. Byrne 2015 Dublin Institute of Technology

Cell Viability Assessment Using The Alamar Blue Assay: A Comparison Of 2d And 3d Cell Culture Models, Franck Bonnier, Mark Keating, Tomasz P. Wrobel, Katarsyna Majzner, Malgorzata Baranska, Amaya Garcia, Alfonso Blanco, Hugh J. Byrne

Articles

Comparisons of 2D and 3D cell culture models in literature have indicated differences in cellular morphology and metabolism, commonly attributed the better representation of in vivo conditions of the latter cell culture environment. Thus, interest in the use of 3D collagen gels for in vitro analysis has been growing. Although comparative studies to date have indicated an enhanced resistance of cells on collagen matrices against different toxicants, in the present study it is demonstrated that non-adapted protocols can lead to misinterpretation of results obtained from classical colorometric dye-based cytotoxic assays. Using the well established Alamar Blue assay, the ...


Iron Alters Cell Survival In A Mitochondria-Dependent Pathway In Ovarian Cancer Cells., Edward Haller 2015 University of South Florida

Iron Alters Cell Survival In A Mitochondria-Dependent Pathway In Ovarian Cancer Cells., Edward Haller

Edward Haller

ABSTRACT The role of iron in the development of cancer remains unclear. We previously reported that iron reduces cell survival in a Ras/mitogen-activated protein kinase (MAPK)-dependent manner in ovarian cells; however, the underlying downstream pathway leading to reduced survival was unclear. Although levels of intracellular iron, ferritin/CD71 protein and reactive oxygen species did not correlate with iron-induced cell survival changes, we identified mitochondrial damage (via TEM) and reduced expression of outer mitochondrial membrane proteins (translocase of outer membrane: TOM20 and TOM70) in cell lines sensitive to iron. Interestingly, Ru360 (an inhibitor of the mitochondrial calcium uniporter) reversed ...


"Targeting Cell Cycle Proteins In Breast Cancer Cells With Sirna By Using Lipid-Substituted Polyethylenimines" Data Files, Manoj Parmar, Hamidreza Montazeri Aliabadi, Parvin Mahdipoor, Cezary Kucharski, Robert Maranchuk, Judith C. Hugh, Hasan Uludag 2015 Chapman University

"Targeting Cell Cycle Proteins In Breast Cancer Cells With Sirna By Using Lipid-Substituted Polyethylenimines" Data Files, Manoj Parmar, Hamidreza Montazeri Aliabadi, Parvin Mahdipoor, Cezary Kucharski, Robert Maranchuk, Judith C. Hugh, Hasan Uludag

Pharmacy Faculty Data Sets

The cell cycle proteins are key regulators of cell cycle progression whose de-regulation is one of the causes of breast cancer. RNA interference (RNAi) is an endogenous mechanism to regulate gene expression and it could serve as the basis of regulating aberrant proteins including cell cycle proteins. Since the delivery of small interfering RNA (siRNA) is a main barrier for implementation of RNAi therapy, we explored the potential of a non-viral delivery system, 2.0 kDa polyethylenimines substituted with linoleic acid and caprylic acid, for this purpose. Using a library of siRNAs against cell cycle proteins, we identified cell division ...


Targeting Cell Cycle Proteins In Breast Cancer Cells With Sirna By Using Lipid-Substituted Polyethylenimines, Manoj Parmar, Hamidreza Montazeri Aliabadi, Parvin Mahdipoor, Cezary Kucharski, Robert Maranchuk, Judith C. Hugh, Hasan Uludag 2015 Chapman University

Targeting Cell Cycle Proteins In Breast Cancer Cells With Sirna By Using Lipid-Substituted Polyethylenimines, Manoj Parmar, Hamidreza Montazeri Aliabadi, Parvin Mahdipoor, Cezary Kucharski, Robert Maranchuk, Judith C. Hugh, Hasan Uludag

Pharmacy Faculty Articles and Research

The cell cycle proteins are key regulators of cell cycle progression whose de-regulation is one of the causes of breast cancer. RNA interference (RNAi) is an endogenous mechanism to regulate gene expression and it could serve as the basis of regulating aberrant proteins including cell cycle proteins. Since the delivery of small interfering RNA (siRNA) is a main barrier for implementation of RNAi therapy, we explored the potential of a non-viral delivery system, 2.0 kDa polyethylenimines substituted with linoleic acid and caprylic acid, for this purpose. Using a library of siRNAs against cell cycle proteins, we identified cell division ...


The Leishmania Years At Unl (Or, My Life As A Cell Biologist, 1966-1981), John J. Janovy Jr. 2015 University of Nebraska-Lincoln

The Leishmania Years At Unl (Or, My Life As A Cell Biologist, 1966-1981), John J. Janovy Jr.

Faculty Publications from the Harold W. Manter Laboratory of Parasitology

Slides for a talk during which Professor Janovy discussed the methods he used in researching Leishmania during the years 1966-1981. Includes lists of references.


Evaluation Of The Developmental Toxicity Of Lead In The Danio Rerio Body, Nicole M. Roy, Sarah DeWolf, Bruno Carneiro 2015 Sacred Heart University

Evaluation Of The Developmental Toxicity Of Lead In The Danio Rerio Body, Nicole M. Roy, Sarah Dewolf, Bruno Carneiro

Biology Faculty Publications

Lead has been utilized throughout history and is widely distributed and mobilized globally. Although lead in the environment has been somewhat mitigated, the nature of lead and its extensive uses in the past prohibit it from being completely absent from our environment and exposure to lead is still a public health concern. Most studies regarding lead toxicity have focused on the brain. However, little is found in the literature on the effects of lead in other tissues. Here, we utilize the zebrafish model system to investigate effects of lead exposure during early developmental time windows at 24, 48 and 72 ...


Arsenic Targets Neural Plate Border Specifier Cells In P19 Cells, Christopher McCoy 2015 Clemson University

Arsenic Targets Neural Plate Border Specifier Cells In P19 Cells, Christopher Mccoy

All Theses

Epidemiological studies have shown that arsenic exposure during early embryogenesis can cause reduced weight gain and neurological deficits later on in life. In addition, in vitro and in vivo studies have indicated that arsenic suppresses neurogenesis and myogenesis. The exact mechanism of how arsenic causes these undesired developmental outcomes is poorly understood, however both skeletal muscle and sensory neuron development require the Wnt/β-catenin signaling pathway to initiate the specific differentiation of precursor cells. We were interested in determining the target cell population of arsenic and its metabolites. Arsenic's metabolites were of interest because they have been shown to ...


Effects Of Cannabidiol On Contractions And Calcium Signaling In Rat Ventricular Myocytes, Ramez M. Ali, Lina T. Al Kury, Keun-Hang Susan Yang, Anwar Qureshi, Mohanraj Rajesh, Sehamuddin Galadari, Yaroslav M. Shuba, Frank Christopher Howarth, Murat Oz 2015 UAE University, Al Ain, Abu Dhabi, UAE

Effects Of Cannabidiol On Contractions And Calcium Signaling In Rat Ventricular Myocytes, Ramez M. Ali, Lina T. Al Kury, Keun-Hang Susan Yang, Anwar Qureshi, Mohanraj Rajesh, Sehamuddin Galadari, Yaroslav M. Shuba, Frank Christopher Howarth, Murat Oz

Mathematics, Physics, and Computer Science Faculty Articles and Research

Cannabidiol (CBD), a major nonpsychotropic cannabinoid found in Cannabis plant, has been shown to influence cardiovascular functions under various physiological and pathological conditions. In the present study, the effects of CBD on contractility and electrophysiological properties of rat ventricular myocytes were investigated. Video edge detection was used to measure myocyte shortening. Intracellular Ca2+ was measured in cells loaded with the Ca2+ sensitive fluorescent indicator fura-2 AM. Whole-cell patch clamp was used to measure action potential and Ca2+ currents. Radioligand binding was employed to study pharmacological characteristics of CBD binding. CBD (1 μM) caused a significant decrease in the amplitudes of ...


Mcnamara 201412 Nih Scap Innocentive Challenge Solution - T-Bow Rainbow T-Cells And Tumor Cells Spatial Multiplexing Gene Expression Reporter System – Plus Supplement Plus Posters - 20141228s, George McNamara 2014 M.D. Anderson Cancer Center

Mcnamara 201412 Nih Scap Innocentive Challenge Solution - T-Bow Rainbow T-Cells And Tumor Cells Spatial Multiplexing Gene Expression Reporter System – Plus Supplement Plus Posters - 20141228s, George Mcnamara

George McNamara

McNamara 201412 NIH SCAP InnoCentive Challenge Solution - T-Bow Rainbow T-cells and Tumor Cells Spatial Multiplexing Gene Expression Reporter System – plus supplement plus posters - 20141228S

The download is my/Cooper lab solution (submission) to the 2014 NIH Single Cell Analysis Program (SCAP) InnoCentive Challenge, "Follow That Cell". I submitted the Solution on 20141215Mon (with 20 minutes to spare). The Challenge web page is

https://www.innocentive.com/ar/challenge/9933618

Our Solution is to revolutionize live cell transcriptional reporter assays. Specifically, we propose to multiplex five promoter response elements to drive expression of different color fluorescent proteins that would bind to ...


An Activity Aimed At Improving Student Explanations Of Biological Mechanisms, Caleb M. Trujillo, Trevor R. Anderson, Nancy J. Pelaez 2014 Purdue University

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 2014 Purdue University

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 ...


Lkb1 Deficient Non-Small Cell Lung Cancer Cells Are Vulnerable To Energy Stress Induced By Atp Depletion, Chao Yang 2014 UT GSBS

Lkb1 Deficient Non-Small Cell Lung Cancer Cells Are Vulnerable To Energy Stress Induced By Atp Depletion, Chao Yang

UT GSBS Dissertations and Theses (Open Access)

Lung cancer is the second most frequent cancer in United States, which represents about 13.5% of new cancer cases every year. It accounts for about 27.2% of all cancer related deaths, which is more than the sum of deaths caused by prancretic, breast and colorectal. On average, only about 16% of lung cancer patients survive beyond 5 years. LKB1 is the third most mutated gene in lung cancer. It has been shown that LKB1 is mutated in at least 15% to 30% of NSCLC. Tumor with LKB1 mutation is associated with poor differentiation, high metastasis and worse response ...


The Drosophila T-Box Transcription Factor Midline Functions Within The Insulin/Akt And C-Jun-N-Terminal Kinase Signaling Pathways To Regulate Interomatidial Bristle Formation And Cell Survival, Qichuan Chen 2014 University of Southern Mississippi

The Drosophila T-Box Transcription Factor Midline Functions Within The Insulin/Akt And C-Jun-N-Terminal Kinase Signaling Pathways To Regulate Interomatidial Bristle Formation And Cell Survival, Qichuan Chen

Master's Theses

From a genetic and allelic modifier screen, we report that the Drosophila melanogaster T-box transcription factor midline (mid), a homolog to the human TBX20 gene, interacts with dFOXO within the insulin receptor (InR) and the c-Jun-N-terminal kinase (JNK) signaling pathways to regulate interommatidial bristle (IOB) formation. Previous studies have identified mid’s role in cell fate specification of sensory organ precursor cells in conjunction with the Notch-Delta signaling pathway (Das et al., 2013). The Notch, InR, and JNK signaling pathways regulate dFOXO activity under conditions of stress. Thus, we determined the effects of oxidative stress and metabolic stress by exposing ...


Glutaredoxin 2 (Grx2) Gene Deletion Induces Early Onset Of Age-Dependent Cataracts In Mice, Hongli Wu, Yibo Yu, Larry David, Ye-Shih Ho, Marjorie F. Lou 2014 University of North Texas Health Science Center

Glutaredoxin 2 (Grx2) Gene Deletion Induces Early Onset Of Age-Dependent Cataracts In Mice, Hongli Wu, Yibo Yu, Larry David, Ye-Shih Ho, Marjorie F. Lou

Papers in Veterinary and Biomedical Science

Glutaredoxin 2 (Grx2) is an isozyme of glutaredoxin1 (thioltransferase) present in the mitochondria and nucleus with disulfide reductase and peroxidase activities, and it controls thiol/ disulfide balance in cells. In this study, we investigated whether Grx2 gene deletion could induce faster age-related cataract formation and elucidated the biochemical changes effected by Grx2 gene deletion that may contribute to lens opacity. Slit lamp was used to examine the lenses in Grx2 knock-out (KO) mice and age-matched wild-type (WT) mice ages 1 to 16 months. In the Grx2 null mice, the lens nuclear opacity began at 5 months, 3 months sooner than ...


Extent Of Cysteine Modification Of Snap-25 In Vitro, Alex McGregor DaBell 2014 Brigham Young University - Provo

Extent Of Cysteine Modification Of Snap-25 In Vitro, Alex Mcgregor Dabell

All Theses and Dissertations

Exocytosis, the fusion of a vesicle to a cellular membrane, involves a protein named SNAP-25. This protein, containing two alpha helices connected with a linker region, is localized to the cell membrane via palmitic acids attached to the cysteine residues of its linker region in a process called palmitoylation. Are cysteine residues of the SNAP-25 linker region palmitoylated in an ordered manner and to a particular extent? The answer to this question may give insight into the regulated nature of exocytosis. While it is generally accepted that SNAP-25 must be palmitoylated in order to perform its exocytotic functions, the details ...


Structure-Based Network Analysis Of Activation Mechanisms In The Erbb Family Of Receptor Tyrosine Kinases: The Regulatory Spine Residues Are Global Mediators Of Structural Stability And Allosteric Interactions, Kevin A. James, Gennady M. Verkhivker 2014 Chapman University

Structure-Based Network Analysis Of Activation Mechanisms In The Erbb Family Of Receptor Tyrosine Kinases: The Regulatory Spine Residues Are Global Mediators Of Structural Stability And Allosteric Interactions, Kevin A. James, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

The ErbB protein tyrosine kinases are among the most important cell signaling families and mutation-induced modulation of their activity is associated with diverse functions in biological networks and human disease. We have combined molecular dynamics simulations of the ErbB kinases with the protein structure network modeling to characterize the reorganization of the residue interaction networks during conformational equilibrium changes in the normal and oncogenic forms. Structural stability and network analyses have identified local communities integrated around high centrality sites that correspond to the regulatory spine residues. This analysis has provided a quantitative insight to the mechanism of mutation-induced ‘‘superacceptor’’ activity ...


Gadph Single Molecule Mrna Fish 20141104tue, George McNamara 2014 M.D. Anderson Cancer Center

Gadph Single Molecule Mrna Fish 20141104tue, George Mcnamara

George McNamara

GADPH single molecule mRNA FISH 20141104Tue

Raw data on NVidia TITAN GPU card deconvolution using original Bruce and Butte 2013 Optics Express software running inside Fiji ImageJ.

B&B GPU Deconvolution Reference:

http://www.opticsinfobase.org/oe/fulltext.cfm?uri=oe-21-4-4766&id=249375

Acquired at 63x1x using leica plan apo 1.4 NA objective lens on Cooper lab Leica DMI6000 microscope, SOLA (initial release) LED lamp using only "green" LED, 554x Semrock exciter filter (in ASI ex wheel), Leica N3 (Cy3) filter cube, center 600 nm emission wavelength.

Hamamatsu FLASH4.0 sCMOS, 100 ms exposure time so 6.4 seconds ...


Majority Of Cells Lining The Walls Of The 3rd Ventricle In The Adult Rat Brain Are Not Neural Progenitor Cells, C. Hasken, S. Vermilyea, M. Hendrickson, R. Kalil 2014 DePauw University

Majority Of Cells Lining The Walls Of The 3rd Ventricle In The Adult Rat Brain Are Not Neural Progenitor Cells, C. Hasken, S. Vermilyea, M. Hendrickson, R. Kalil

Science Research Fellows Posters

No abstract provided.


Identifying Diagnostic Dna Methylation Profiles For Facioscapulohumeral Muscular Dystrophy In Blood And Saliva Using Bisulfite Sequencing, Takako I. Jones, Chi Yan, Peter Sapp, Diane McKenna-Yasek, Peter B. Kang, Colin Quinn, Johnny S. Salameh, Oliver D. King, Peter L. Jones 2014 University of Massachusetts Medical School

Identifying Diagnostic Dna Methylation Profiles For Facioscapulohumeral Muscular Dystrophy In Blood And Saliva Using Bisulfite Sequencing, Takako I. Jones, Chi Yan, Peter Sapp, Diane Mckenna-Yasek, Peter B. Kang, Colin Quinn, Johnny S. Salameh, Oliver D. King, Peter L. Jones

Peter Jones Lab

BACKGROUND: Facioscapulohumeral muscular dystrophy (FSHD) is linked to chromatin relaxation due to epigenetic changes at the 4q35 D4Z4 macrosatellite array. Molecular diagnostic criteria for FSHD are complex and involve analysis of high molecular weight (HMW) genomic DNA isolated from lymphocytes, followed by multiple restriction digestions, pulse-field gel electrophoresis (PFGE), and Southern blotting. A subject is genetically diagnosed as FSHD1 if one of the 4q alleles shows a contraction in the D4Z4 array to below 11 repeats, while maintaining at least 1 repeat, and the contraction is in cis with a disease-permissive A-type subtelomere. FSHD2 is contraction-independent and cannot be diagnosed ...


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