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Exploring Molecular Mechanisms Of Paradoxical Activation In The Braf Kinase Dimers: Atomistic Simulations Of Conformational Dynamics And Modeling Of Allosteric Communication Networks And Signaling Pathways, Amanda Tse, Gennady M. Verkhivker 2016 Chapman University

Exploring Molecular Mechanisms Of Paradoxical Activation In The Braf Kinase Dimers: Atomistic Simulations Of Conformational Dynamics And Modeling Of Allosteric Communication Networks And Signaling Pathways, Amanda Tse, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

The recent studies have revealed that most BRAF inhibitors can paradoxically induce kinase activation by promoting dimerization and enzyme transactivation. Despite rapidly growing number of structural and functional studies about the BRAF dimer complexes, the molecular basis of paradoxical activation phenomenon is poorly understood and remains largely hypothetical. In this work, we have explored the relationships between inhibitor binding, protein dynamics and allosteric signaling in the BRAF dimers using a network-centric approach. Using this theoretical framework, we have combined molecular dynamics simulations with coevolutionary analysis and modeling of the residue interaction networks to determine molecular determinants of paradoxical activation. We ...


Technology Transfer: A View From The Trenches, Harvey Drucker 2016 University of New Hampshire

Technology Transfer: A View From The Trenches, Harvey Drucker

RISK: Health, Safety & Environment

Dr. Drucker, who has lab-wide responsibility for technology transfer at Argonne National Laboratory, argues that transferring rights in discoveries made through tax supported research to private entities can contribute to public welfare in many ways.


Overview Of Federal Technology Transfer, Lawrence Rudolph 2016 University of New Hampshire

Overview Of Federal Technology Transfer, Lawrence Rudolph

RISK: Health, Safety & Environment

Mr. Rudolph reviews approximately thirteen years of legal and political developments that have contributed to laws governing the extent to which private firms may secure rights in technology at least partly developed with federal funds.


Book Review, Kristin S. Shrader-Frechette 2016 University of New Hampshire

Book Review, Kristin S. Shrader-Frechette

RISK: Health, Safety & Environment

Review of the following: ELAINE DRAPER, RiskY BUSINESS: GENETIC TESTING AND EXCLUSIONARY PRACTICES IN THE HAZARDOUS WORKPLACE. (Cambridge University Press 1991) [315 pp.] Index of names and subjects, glossary, notes, references. LC 90-28112; ISBN 0-521-37027-2 (cloth $49.50); ISBN 0-42248-5 (paper $15.95). [40 W. 20th St., New York NY 10011.]


Optimization Of A Genomic Editing System Using Crispr/Cas9-Induced Site-Specific Gene Integration, Jillian L. McCool Ms., Nick Hum, Gabriela G. Loots 2016 California State University, Chico

Optimization Of A Genomic Editing System Using Crispr/Cas9-Induced Site-Specific Gene Integration, Jillian L. Mccool Ms., Nick Hum, Gabriela G. Loots

STAR (STEM Teacher and Researcher) Presentations

The CRISPR-Cas system is an adaptive immune system found in bacteria which helps protect against the invasion of other microorganisms. This system induces double stranded breaks at precise genomic loci (1) in which repairs are initiated and insertions of a target are completed in the process. This mechanism can be used in eukaryotic cells in combination with sgRNAs (1) as a tool for genome editing. By using this CRISPR-Cas system, in addition to the “safe harbor locus,” ROSAβ26, the incorporation of a target gene into a site that is not susceptible to gene silencing effects can be achieved through few ...


Comparative Genomics, Transcriptomics, And Physiology Distinguish Symbiotic From Free-Living Chlorella Strains, Cristian F. Quispe, Olivia Sonderman, Maya Khasin, Wayne R. Riekhof, James Van Etten, Kenneth Nickerson 2016 University of Nebraska-Lincoln

Comparative Genomics, Transcriptomics, And Physiology Distinguish Symbiotic From Free-Living Chlorella Strains, Cristian F. Quispe, Olivia Sonderman, Maya Khasin, Wayne R. Riekhof, James Van Etten, Kenneth Nickerson

Kenneth Nickerson Papers

Most animal–microbe symbiotic interactions must be advantageous to the host and provide nutritional benefits to the endosymbiont. When the host provides nutrients, it can gain the capacity to control the interaction, promote self-growth, and increase its fitness. Chlorella-like green algae engage in symbiotic relationships with certain protozoans, a partnership that significantly impacts the physiology of both organisms. Consequently, it is often challenging to grow axenic Chlorella cultures after isolation from the host because they are nutrient fastidious and often susceptible to virus infection. We hypothesize that the establishment of a symbiotic relationship resulted in natural selection for nutritional and ...


Genetic Analysis Reveals A Hierarchy Of Interactions Between Polycystin-Encoding Genes And Genes Controlling Cilia Function During Left-Right Determination, Daniel T. Grimes, Jennifer L. Keynton, Maria T. Buenavista, Xingjian Jin, Saloni H. Patel, Shinohara Kyosuke, Jennifer Vibert, Debbie J. Williams, Hiroshi Hamada, Rohana Hussain, Surya M. Nauli, Dominic P. Norris 2016 MRC Harwell

Genetic Analysis Reveals A Hierarchy Of Interactions Between Polycystin-Encoding Genes And Genes Controlling Cilia Function During Left-Right Determination, Daniel T. Grimes, Jennifer L. Keynton, Maria T. Buenavista, Xingjian Jin, Saloni H. Patel, Shinohara Kyosuke, Jennifer Vibert, Debbie J. Williams, Hiroshi Hamada, Rohana Hussain, Surya M. Nauli, Dominic P. Norris

Pharmacy Faculty Articles and Research

During mammalian development, left-right (L-R) asymmetry is established by a cilia-driven leftward fluid flow within a midline embryonic cavity called the node. This ‘nodal flow’ is detected by peripherally-located crown cells that each assemble a primary cilium which contain the putative Ca2+ channel PKD2. The interaction of flow and crown cell cilia promotes left side-specific expression of Nodal in the lateral plate mesoderm (LPM). Whilst the PKD2-interacting protein PKD1L1 has also been implicated in L-R patterning, the underlying mechanism by which flow is detected and the genetic relationship between Polycystin function and asymmetric gene expression remains unknown. Here, we ...


Identification Of Qtls For Resistance Against Rhizoctonia Solani And Phoma Glycinicola In Soybeans (Glycine Max L. Merr), Herbert Sserunkuma 2016 University of Nebraska-Lincoln

Identification Of Qtls For Resistance Against Rhizoctonia Solani And Phoma Glycinicola In Soybeans (Glycine Max L. Merr), Herbert Sserunkuma

Theses, Dissertations, and Student Research in Agronomy and Horticulture

A QTL (Quantitative trait locus) is a chromosome location of a gene controlling a specific phenotypic trait. The trait maybe governed by multiple genes. Fungal pathogens are responsible for over 50% of all soybean diseases. Rhizoctonia solani Kühn causes seedling dumping off, root and hypocotyl rots and other disease in soybeans. Phoma glycinicola de Gruyter & Boerema causes Red leaf blotch disease, predominantly in Sub-Saharan Africa. There is no reported complete resistance against these fungal pathogens in soybeans. Reaction to R.solani is reportedly a quantitative trait controlled by major and minor genes. Three QTLs contributing to reaction to R. solani ...


The Effects Of Epigenetics On Stress Response, Kevin Suddarth 2016 San Jose State University

The Effects Of Epigenetics On Stress Response, Kevin Suddarth

Themis: Research Journal of Justice Studies and Forensic Science

Despite the vast amount of resources at the disposal of humanity today, the intricacies of human biology are often a mystery. The chemical and biological products of the human genome have been well studied and documented, but many of the chemical and neurological pathways are missing quite a few details. The human stress response is one of the most primal and valuable functions of this code that developed as a self- preservation mechanism (Hans, 1975) to naturally increase the odds of procreation. However, this function is prone to overload, particularly in individuals with certain epigenetic traits instilled by early life ...


Beyond Dna: Epigenetics And Proteomics In Forensic Science, Diane F. Eilerts 2016 San Jose State University

Beyond Dna: Epigenetics And Proteomics In Forensic Science, Diane F. Eilerts

Themis: Research Journal of Justice Studies and Forensic Science

The use of genetic evidence in criminal cases is well established and has improved the public opinion and credibility of forensic science. However, several shortcomings associated with current genetic profiling techniques exist. Scientific research aimed at increasing the overall knowledge and understanding of biological factors will lead to the development of methods capable of improving the discriminating power of DNA evidence, overcoming limitations associated with DNA evidence, or complementing current methods of DNA profiling. Increased research in the fields of epigenetics and proteomics are particularly promising and relevant to forensic science. Research suggests that epigenetic biomarkers can be used to ...


Characterization Of Induced Rnai Silencing Of Vaccinia Virus Essential Genes, Kewa Jiang 2016 University of Connecticut

Characterization Of Induced Rnai Silencing Of Vaccinia Virus Essential Genes, Kewa Jiang

University Scholar Projects

Vaccinia virus (VACV) is a large double-stranded DNA virus and the prototypical member of the family Poxviridae and is most notable for its use as the vaccine that eradicated smallpox (variola virus). More recently, VACV has been used to develop recombinant vaccines and immunotherapies. However, many of these processes require VACV replication to be tightly controlled. RNA interference (RNAi) is a powerful tool for in vitro silencing of mRNAs that are complimentary to 19-21 base pairs (bp) of double-stranded RNA (dsRNA). This project outlines the design and preliminary analysis of two inducible RNAi silencing constructs targeting multiple VACV essential genes ...


The Utility Of Genomic Variant Databases In Genetic Counseling, Colleen Ahern, Elly Brokamp 2016 Sarah Lawrence College

The Utility Of Genomic Variant Databases In Genetic Counseling, Colleen Ahern, Elly Brokamp

Human Genetics Theses and Capstones

Organizations such as the American College of Medical Genetics (ACMG) and the National Society of Genetic Counselors (NSGC) are in agreement that public genomic data sharing will benefit patient care. Despite these recommendations, not all clinical laboratories share their variant data onto public databases. As the amount of genetic material being analyzed for patient care continues to increase, more variants of unknown significance (VUS) are reported as well. Genetic counselors need to properly interpret VUS results in order to aid patients in making educated health decisions. For this paper, genetic counselors were asked about genomic data sharing and how they ...


Examining Psychological Outcomes Associated With Genetic Testing For Primary Arrhythmic Disorders In Adult Patients, Samantha Colaiacovo, Erin Kelter 2016 Sarah Lawrence College

Examining Psychological Outcomes Associated With Genetic Testing For Primary Arrhythmic Disorders In Adult Patients, Samantha Colaiacovo, Erin Kelter

Human Genetics Theses and Capstones

The psychological impact of genetic testing for an inherited arrhythmia and its influence on future well-being is highly variable and has not been well studied. Thirty-seven participants completed a survey which included questions from the Multidimensional Impact of Cancer Risk Assessment (MICRA) questionnaire, Impact of Events Scale (IES) and Satisfaction with Decision Scale (SWDS) to provide more information on their genetic testing experience and to allow the authors to search for trends that may improve the genetic counseling experience moving forward. Trends were seen upon the comparison of those who had positive versus negative genetic testing results. Those with positive ...


Studying The Needles In The Haystack: A Qualitative Study Of African-American And Latino Genetic Counselors, Amanda Kass, Larissa Veres 2016 Sarah Lawrence College

Studying The Needles In The Haystack: A Qualitative Study Of African-American And Latino Genetic Counselors, Amanda Kass, Larissa Veres

Human Genetics Theses and Capstones

The field of genetic counseling as a whole significantly lacks ethnic diversity within the ranks of their prospective students and trained professionals. This article describes the importance of understanding underrepresented minorities’ (URM’s) experiences and how their stories can be used to better implement recruitment techniques. In this qualitative study, five practicing genetic counselors and three genetic counseling students who identified as African-American and/or Latino participated in a structured phone interview. These interviews were aimed at better understanding their introduction into the field, their experiences in their training program, and their experiences in the profession. Themes that were explored ...


Assessing Tumor Genomic Profiling Reports For Genetic Counseling Referral Indications, Margaret McDuffee, Michelle Ning 2016 Sarah Lawrence College

Assessing Tumor Genomic Profiling Reports For Genetic Counseling Referral Indications, Margaret Mcduffee, Michelle Ning

Human Genetics Theses and Capstones

Our purpose is two-fold: (1) to identify patients who may benefit from referrals to cancer genetic counseling by characterizing the alterations reported in tumor profiling reports without matched germline control, and (2) to assess the utility of public database ClinVar in providing further information on these alterations. We assessed 160 reports across 66 tumor types. 127 (79%) reports had a mutation in 1 of 86 selected cancer predisposition genes. Of these, 29 (23%) did not meet ACMG/NSGC criteria for referral based on tumor type alone. 19% of mutations in selected genes were found in ClinVar, with 15% reported as ...


Exploring The Role Of Genetic Counselors In Tumor Genomic Sequencing : A Survey Of Genetic Counselors, Michelle Weinberg 2016 Sarah Lawrence College

Exploring The Role Of Genetic Counselors In Tumor Genomic Sequencing : A Survey Of Genetic Counselors, Michelle Weinberg

Human Genetics Theses and Capstones

In the emerging era of genomics-driven medicine, tumor genomic profiling in particular has begun to revolutionize the field of oncology. As the integration of such technologies evolves and affects the management and treatment of cancer, questions arise with regards to the changing roles of healthcare professionals involved in cancer care. One hundred and twenty-eight members of the National Society of Genetic Counselors (NSGC) responded to a survey to assess the current roles of genetic counselors in oncology and the perceived roles that genetic counselors will have in the clinical use of tumor genomic profiling. With regards to current roles in ...


Characterization Of Induced Rnai Silencing Of Vaccinia Virus Essential Genes, Kewa Jiang 2016 University of Connecticut

Characterization Of Induced Rnai Silencing Of Vaccinia Virus Essential Genes, Kewa Jiang

Honors Scholar Theses

Vaccinia virus (VACV) is a large double-stranded DNA virus and the prototypical member of the family Poxviridae and is most notable for its use as the vaccine that eradicated smallpox (variola virus). More recently, VACV has been used to develop recombinant vaccines and immunotherapies. However, many of these processes require VACV replication to be tightly controlled. RNA interference (RNAi) is a powerful tool for in vitro silencing of mRNAs that are complementary to 19-21 base pairs (bp) of double-stranded RNA (dsRNA). This project outlines the design and preliminary analysis of two inducible RNAi silencing constructs targeting multiple VACV essential genes ...


Social And Scientific Implications Of Genetic Testing In The Digital Age, Yaruska A. Ordinola 2016 University of Rhode Island

Social And Scientific Implications Of Genetic Testing In The Digital Age, Yaruska A. Ordinola

Senior Honors Projects

From Mendel’s law of inheritance in the 19th century through Watson and Crick’s revolutionary observations of the double helix in the 20th century, genetics has been a fascinating and continuing topic of discussion in the field of science (Collins & McKusick, 2001). Major studies like the Human Genome Project (HGP), initiated in 1990 and completed in 2003, provided a starting point from which scientists could more thoroughly investigate the human condition on a genetic level. Arising from this study, personal genomics is considered a blooming field in genetics- in which rapidly developing technological advances are able to provide easier ...


Genetic Factors Affecting Hybrid Male Sterility Leading To Speciation, Patrick Opperman, Colin D. Meiklejohn 2016 University of Nebraska - Lincoln

Genetic Factors Affecting Hybrid Male Sterility Leading To Speciation, Patrick Opperman, Colin D. Meiklejohn

UCARE Research Products

The process whereby speciation occurs can come about through the evolution of barriers to gene flow. One of these barriers to gene flow can be an incompatibility, which leaves hybrids dead or sterile. Two theories underlie the work of this experiment, Haldane’s Rule and the large X effect. Haldane’s Rule is the observation that unisexual inviability or sterility among species’ hybrids is almost always found in the heterogametic sex. The large X effect is the observation that substitution of one species’ X-chromosome for another’s has a disproportionately large effect on hybrid fitness compared to similar substitution of ...


Turn Me On Or Off: A Study On Epigenetics And Merleau-Ponty In Angela Carter’S “The Lady Of The House Of Love”, Solsiree Lynn Skarlinsky 2016 Florida International University

Turn Me On Or Off: A Study On Epigenetics And Merleau-Ponty In Angela Carter’S “The Lady Of The House Of Love”, Solsiree Lynn Skarlinsky

FIU Electronic Theses and Dissertations

This study aims to trace points of intersection between the too often divorced disciplines of literature, continental philosophy, and the hard sciences in Angela Carter’s “The Lady of the House of Love.” In short, this thesis will not only explore how such conversations surface within the short story, but will also serve as an explication of Maurice Merleau-Ponty’s philosophy of body and space, and the theory of epigenetics. Through these explications, the thesis itself will also gear one discipline towards the other as both theories intimately bind the environment with the body, and the body with the environment ...


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