Diagnosis Of Lchad/Tfp Deficiency In An At Risk Newborn Using Umbilical Cord Blood Acylcarnitine Analysis, 2017 George Washington University
Diagnosis Of Lchad/Tfp Deficiency In An At Risk Newborn Using Umbilical Cord Blood Acylcarnitine Analysis, Donna Raval, Kristina Cusmano-Ozog, Omar Ayyub, Callie Jenevein, Laura Kofman, Brendan Lanpher, Natalie Hauser, Debra Regier
Pathology Faculty Publications
Trifunctional protein deficiency/Long-chain hydroxyacyl-CoA dehydrogenase deficiency (LCHAD/TFP) deficiency is a disorder of fatty acid oxidation and ketogenesis. Severe neonatal lactic acidosis, cardiomyopathy, and hepatic dysfunction are caused by the accumulation of toxic long-chain acylcarnitines. The feasibility of umbilical cord blood use in screening for acylcarnitine analysis and free carnitine has been hypothesized but not reported in LCHAD/TFP neonates.
We present a 4 week old female who was at risk of inheriting LCHAD/TFP deficiency and was diagnosed at the time of delivery using umbilical cord blood. Umbilical cord blood was collected at delivery and sent for acylcarnitine ...
Homppi: A Class Of Sequence Homology Based Protein-Protein Interface Prediction Methods, 2017 Iowa State University
Homppi: A Class Of Sequence Homology Based Protein-Protein Interface Prediction Methods, Li C. Xue, Drena Dobbs, Vasant Honavar
Results We studied more than 300,000 pair-wise alignments of protein sequences from structurally characterized protein complexes, including both obligate and transient complexes. We identified sequence similarity criteria required for accurate homology-based inference of interface residues in a query protein sequence. Based on these analyses, we developed HomPPI, a class of sequence homology-based methods for predicting protein-protein interface residues. We present two variants of HomPPI: (i) NPS-HomPPI (Non partner-specific HomPPI), which can be used to predict interface residues of a query protein in the absence of knowledge of the interaction partner; and (ii) PS-HomPPI (Partner-specific HomPPI), which can be used ...
G-Quadruplex (G4) Motifs In The Maize (Zea Mays L.) Genome Are Enriched At Specific Locations In Thousands Of Genes Coupled To Energy Status, Hypoxia, Low Sugar, And Nutrient Deprivation, 2017 United States Department of Agriculture
G-Quadruplex (G4) Motifs In The Maize (Zea Mays L.) Genome Are Enriched At Specific Locations In Thousands Of Genes Coupled To Energy Status, Hypoxia, Low Sugar, And Nutrient Deprivation, Carson M. Andorf, Mykhailo Kopylov, Drena Dobbs, Karen E. Koch, M. Elizabeth Stroupe, Carolyn J. Lawrence, Hank W. Bass
The G-quadruplex (G4) elements comprise a class of nucleic acid structures formed by stacking of guanine base quartets in a quadruple helix. This G4 DNA can form within or across single-stranded DNA molecules and is mutually exclusive with duplex B-form DNA. The reversibility and structural diversity of G4s make them highly versatile genetic structures, as demonstrated by their roles in various functions including telomere metabolism, genome maintenance, immunoglobulin gene diversification, transcription, and translation. Sequence motifs capable of forming G4 DNA are typically located in telomere repeat DNA and other non-telomeric genomic loci. To investigate their potential roles in a large-genome ...
Pridb: A Protein–Rna Interface Database, 2017 Iowa State University
Pridb: A Protein–Rna Interface Database, Benjamin A. Lewis, Rasna R. Walia, Michael Terribilini, Jeff Ferguson, Charles Zheng, Vasant Honavar, Drena Dobbs
The Protein–RNA Interface Database (PRIDB) is a comprehensive database of protein–RNA interfaces extracted from complexes in the Protein Data Bank (PDB). It is designed to facilitate detailed analyses of individual protein–RNA complexes and their interfaces, in addition to automated generation of user-defined data sets of protein–RNA interfaces for statistical analyses and machine learning applications. For any chosen PDB complex or list of complexes, PRIDB rapidly displays interfacial amino acids and ribonucleotides within the primary sequences of the interacting protein and RNA chains. PRIDB also identifies ProSite motifs in protein chains and FR3D motifs in RNA chains ...
Protein-Rna Interface Residue Prediction Using Machine Learning: An Assessment Of The State Of The Art, 2017 Iowa State University
Protein-Rna Interface Residue Prediction Using Machine Learning: An Assessment Of The State Of The Art, Rasna R. Walia, Cornelia Caragea, Benjamin A. Lewis, Fadi Towfic, Michael Terribilini, Yasser El-Manzalawy, Drena Dobbs, Vasant Honavar
Background: RNA molecules play diverse functional and structural roles in cells. They function as messengers for transferring genetic information from DNA to proteins, as the primary genetic material in many viruses, as catalysts (ribozymes) important for protein synthesis and RNA processing, and as essential and ubiquitous regulators of gene expression in living organisms. Many of these functions depend on precisely orchestrated interactions between RNA molecules and specific proteins in cells. Understanding the molecular mechanisms by which proteins recognize and bind RNA is essential for comprehending the functional implications of these interactions, but the recognition ‘code’ that mediates interactions between proteins ...
Zfngenome: A Comprehensive Resource For Locating Zinc Finger Nuclease Target Sites In Model Organisms, 2017 Iowa State University
Zfngenome: A Comprehensive Resource For Locating Zinc Finger Nuclease Target Sites In Model Organisms, Deepak Reyon, Jessica R. Kirkpatrick, Jeffry D. Sander, Feng Zhang, Daniel F. Voytas, J Keith Joung, Drena Dobbs, Clark R. Coffman
Background: Zinc Finger Nucleases (ZFNs) have tremendous potential as tools to facilitate genomic modifications, such as precise gene knockouts or gene replacements by homologous recombination. ZFNs can be used to advance both basic research and clinical applications, including gene therapy. Recently, the ability to engineer ZFNs that target any desired genomic DNA sequence with high fidelity has improved significantly with the introduction of rapid, robust, and publicly available techniques for ZFN design such as the Oligomerized Pool ENgineering (OPEN) method. The motivation for this study is to make resources for genome modifications using OPEN-generated ZFNs more accessible to researchers by ...
Computational Modeling Suggests Dimerization Of Equine Infectious Anemia Virus Rev Is Required For Rna Binding, 2017 Iowa State University
Computational Modeling Suggests Dimerization Of Equine Infectious Anemia Virus Rev Is Required For Rna Binding, Chijioke N. Umunnakwe, Hyelee Loyd, Kinsey Cornick, Jerald R. Chavez, Drena Dobbs, Susan Carpenter
Background The lentiviral Rev protein mediates nuclear export of intron-containing viral RNAs that encode structural proteins or serve as the viral genome. Following translation, HIV-1 Rev localizes to the nucleus and binds its cognate sequence, termed the Rev-responsive element (RRE), in incompletely spliced viral RNA. Rev subsequently multimerizes along the viral RNA and associates with the cellular Crm1 export machinery to translocate the RNA-protein complex to the cytoplasm. Equine infectious anemia virus (EIAV) Rev is functionally homologous to HIV-1 Rev, but shares very little sequence similarity and differs in domain organization. EIAV Rev also contains a bipartite RNA binding domain ...
Predicting Protein-Protein Interface Residues Using Local Surface Structural Similarity, 2017 Iowa State University
Predicting Protein-Protein Interface Residues Using Local Surface Structural Similarity, Rafael R. Jordan, Yasser El-Manzalawy, Drena Dobbs, Vasant Honavar
Identification of the residues in protein-protein interaction sites has a significant impact in problems such as drug discovery. Motivated by the observation that the set of interface residues of a protein tend to be conserved even among remote structural homologs, we introduce PrISE, a family of local structural similarity-based computational methods for predicting protein-protein interface residues.
We present a novel representation of the surface residues of a protein in the form of structural elements. Each structural element consists of a central residue and its surface neighbors. The PrISE family of interface prediction methods uses a representation of structural ...
Zifit (Zinc Finger Targeter): An Updated Zinc Finger Engineering Tool, 2017 Massachusetts General Hospital
Zifit (Zinc Finger Targeter): An Updated Zinc Finger Engineering Tool, Jeffry D. Sander, Morgan L. Maeder, Deepak Reyon, Daniel F. Voytas, J. Keith Joung, Drena Dobbs
ZiFiT (Zinc Finger Targeter) is a simple and intuitive web-based tool that provides an interface to identify potential binding sites for engineered zinc finger proteins (ZFPs) in user-supplied DNA sequences. In this updated version, ZiFiT identifies potential sites for ZFPs made by both the modular assembly and OPEN engineering methods. In addition, ZiFiT now integrates additional tools and resources including scoring schemes for modular assembly, an interface with the Zinc Finger Database (ZiFDB) of engineered ZFPs, and direct querying of NCBI BLAST servers for identifying potential off-target sites within a host genome. Taken together, these features facilitate design of ZFPs ...
Metablast! Virtual Cell: A Pedagogical Convergence Between Game Design And Science Education, 2017 Iowa State University
Metablast! Virtual Cell: A Pedagogical Convergence Between Game Design And Science Education, Anson B. Call, Steven Herrnstadt, Eve S. Wurtele, Julie Dickerson, Diane Bassham
MetaBlast! Virtual Cell (from now on referred to as VC) is a game design solution to a specific scientific and educational problem; expressly, how to make advanced, university level plant biology instruction on molecular and anatomical levels an exciting, efficient learning experience. The advanced technologies of 3D modeling and animation, computer programming and game design are united and tempered with strong, scientific guidance for accuracy and art direction for a powerful visual and audio simulation. The additional strength of intense gaming as a powerful tool aiding memory, logic and problem solving has recently become well recognized. Virtual Cell will provide ...
Blood Mercury Levels Of Zebra Finches Are Heritable: Implications For The Evolution Of Mercury Resistance, 2017 College of William and Mary
Blood Mercury Levels Of Zebra Finches Are Heritable: Implications For The Evolution Of Mercury Resistance, Kenton A. Buck, Claire W. Varian-Ramos, Daniel A. Cristol, John P. Swaddle
Mercury is a ubiquitous metal contaminant that negatively impacts reproduction of wildlife and has many other sub-lethal effects. Songbirds are sensitive bioindicators of mercury toxicity and may suffer population declines as a result of mercury pollution. Current predictions of mercury accumulation and biomagnification often overlook possible genetic variation in mercury uptake and elimination within species and the potential for evolution in affected populations. We conducted a study of dietary mercury exposure in a model songbird species, maintaining a breeding population of zebra finches (Taeniopygia guttata) on standardized diets ranging from 0.0–2.4 μg/g methylmercury. We applied a ...
Genetic Architecture And Predictability Of Seedling Root Traits In Maize (Zea Mays L.), 2017 Iowa State University
Genetic Architecture And Predictability Of Seedling Root Traits In Maize (Zea Mays L.), Jordon Michael Pace
The maize (Zea mays L.) root system is important for proper growth and productivity of the plant. There is substantial genetic and phenotypic variation for root architecture, which gives opportunity for selection. Root traits, however, have not been used as selection criterion mainly due to the difficulty in measuring, as well as their quantitative mode of inheritance. Studying seedling roots offer an opportunity to study multiple individuals and to enable repeated measurements per year as compared to adult root phenotyping. Here we have evaluated phenotypic and genotypic variation within seedling root traits for two panels of inbred lines. Constructed maize ...
Review Of: The Human Genome Project And Minority Communities - Ethical, Social, And Political Dilemmas (Raymond A. Zilinskas & Peter J. Balint Eds.), Craig Steven Jepson
RISK: Health, Safety & Environment
Review of the book: The Human Genome Project and Minority Communities -Ethical, Social, and Political Dilemmas (Raymond A. Zilinskas & Peter J.Balint eds., Praeger Publishers 2001). Preface, index, about the contributors. LC 00-032390; ISBN 0-275-96961-4 [160 pp. $54.50.Cloth, 88 Post Road West, Westport, CT 06881].
Review Of: Alan Mchughen, Pandora's Picnic Basket: The Potential And Hazards Of Genetically Modified Foods, 2017 University of New Hampshire
Review Of: Alan Mchughen, Pandora's Picnic Basket: The Potential And Hazards Of Genetically Modified Foods, Shimona Pratap Singh
RISK: Health, Safety & Environment
Review of the book: Alan McHughen, Pandora's Picnic Basket: The Potential and Hazards of Genetically Modified Foods (Oxford University Press 2000).Acknowledgements, introduction, glossary and abbreviations, resources, index. ISBN 0-19-850674-0 [277 pp. $25.00 Cloth, 198 Madison Avenue, New York, NY 10016-4314].
Poorer European Countries Are Less Concerned About Biotechnology Than Richer Countries, 2017 University of New Hampshire
Poorer European Countries Are Less Concerned About Biotechnology Than Richer Countries, Michael Siegrist
RISK: Health, Safety & Environment
The author examines the relationship between GNP, media coverage, and public perceptions of the utility, risk, and acceptability of medical and food-related applications of biotechnology.
Pcsk9 Genetic Variants And Risk Of Type 2 Diabetes: A Mendelian Randomisation Study, 2017 George Washington University
Pcsk9 Genetic Variants And Risk Of Type 2 Diabetes: A Mendelian Randomisation Study, A. Schmidt, D. Swerdlow, M. Holmes, R. Patel, Z. Fairhurst-Hunter, Cara L. Carty, +Several Additional Authors
Pediatrics Faculty Publications
Statin treatment and variants in the gene encoding HMG-CoA reductase are associated with reductions in both the concentration of LDL cholesterol and the risk of coronary heart disease, but also with modest hyperglycaemia, increased bodyweight, and modestly increased risk of type 2 diabetes, which in no way offsets their substantial benefits. We sought to investigate the associations of LDL cholesterol-lowering PCSK9 variants with type 2 diabetes and related biomarkers to gauge the likely effects of PCSK9 inhibitors on diabetes risk.
In this mendelian randomisation study, we used data from cohort studies, randomised controlled trials, case control studies, and ...
Estimating The Probability Of Clonal Relatedness Of Pairs Of Tumors In Cancer Patients, 2017 Memorial Sloan-Kettering Cancer Center
Estimating The Probability Of Clonal Relatedness Of Pairs Of Tumors In Cancer Patients, Audrey Mauguen, Venkatraman E. Seshan, Irina Ostrovnaya, Colin B. Begg
Memorial Sloan-Kettering Cancer Center, Dept. of Epidemiology & Biostatistics Working Paper Series
Next generation sequencing panels are being used increasingly in cancer research to study tumor evolution. A specific statistical challenge is to compare the mutational profiles in different tumors from a patient to determine the strength of evidence that the tumors are clonally related, i.e. derived from a single, founder clonal cell. The presence of identical mutations in each tumor provides evidence of clonal relatedness, although the strength of evidence from a match is related to how commonly the mutation is seen in the tumor type under investigation. This evidence must be weighed against the evidence in favor of independent ...
Transcriptional And Post-Transcriptional Regulation Of Histone Variant H2a.Z During Sea Urchin Development, 2017 The Graduate Center, City University of New York
Transcriptional And Post-Transcriptional Regulation Of Histone Variant H2a.Z During Sea Urchin Development, Mihai Hajdu
All Graduate Works by Year: Dissertations, Theses, and Capstone Projects
Histone variant H2A.Z promotes chromatin accessibility at transcriptional regulatory elements and is developmentally regulated in metazoans. We characterize the transcriptional and post-transcriptional regulation of H2A.Z in the purple sea urchin Strongylocentrotus purpuratus. H2A.Z depletion by antisense translation-blocking morpholino oligonucleotides during early development causes developmental collapse, in agreement with its previously demonstrated general role in transcriptional multipotency. During H2A.Z peak expression in 24-h embryos, endogenous H2A.Z 3’ UTR sequences stabilize GFP mRNAs relative to those with SV40 3’ UTR sequences, although the 3’UTR of H2A.Z does not determine the spatial distribution of H2A.Z ...
The Subject Librarian Newsletter, Biology, Spring 2017, 2017 University of California, Irvine School of Law
The Subject Librarian Newsletter, Biology, Spring 2017, Sandy Avila
No abstract provided.
High Throughput In Vivo Functional Validation Of Candidate Congenital Heart Disease Genes In Drosophila., 2017 George Washington University
High Throughput In Vivo Functional Validation Of Candidate Congenital Heart Disease Genes In Drosophila., Jun-Yi Zhu, Yulong Fu, Margaret Nettleton, Adam Richman, Zhe Han
Pediatrics Faculty Publications
Genomic sequencing has implicated large numbers of genes and de novo mutations as potential disease risk factors. A high throughput in vivo model system is needed to validate gene associations with pathology. We developed a Drosophila-based functional system to screen candidate disease genes identified from Congenital Heart Disease (CHD) patients. 134 genes were tested in the Drosophila heart using RNAi-based gene silencing. Quantitative analyses of multiple cardiac phenotypes demonstrated essential structural, functional, and developmental roles for more than 70 genes, including a subgroup encoding histone H3K4 modifying proteins. We also demonstrated the use of Drosophila to evaluate cardiac phenotypes resulting ...