Abstracts 2019 Focus Sessions
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In Vitro Testicular Toxicity Models : Opportunities for Advancement Via Biomedical Engineering Techniques
Erschienen in: Alternatives to Animal Experimentation : ALTEX ; 30 (2013), 3. - S. 353-377 http://dx.doi.org/10.14573/altex.2013.3.353 t4 Report* In Vitro Testicular Toxicity Models: Opportunities for Advancement via Biomedical Engineering Techniques Louise Parks Saldutti 1, Bruce K. Beyer 2, William Breslin 3, Terry R. Brown 4, Robert E. Chapin 5, Sarah Campion 5, Brian Enright 6, Elaine Faustman 7, Paul M. D. Foster 8, Thomas Hartung 9, William Kelce 10, James H. Kim 11, Elizabeth G. Loboa 12, Aldert H. Piersma 13, David Seyler 14, Katie J. Turner 15, Hanry Yu 16, Xiaozhong Yu 17, and Jennifer C. Sasaki 18 1 2 Department of Development & Reproduction, Merck & Co., West Point, PA, USA; Department of Disposition, Safety 3 and Animal Research – Preclinical Safety, Sanofi U.S. Inc., Bridgewater, NJ, USA; Eli Lilly and Company, Lilly Research 4 Laboratories, Indianapolis, IN, USA; Department of Biochemistry & Molecular Biology, Johns Hopkins Bloomberg School of 5 Public Health, Baltimore, MD, USA; Pfizer Inc., Global R&D, Developmental and Reproductive Toxicology Group, Groton, 7 CT, USA; 6AbbVie Inc., North Chicago, IL, USA; University of Washington, Department of Environmental and Occupational 8 Health Sciences, Institute for Risk Analysis and Risk Communication, Seattle, WA, USA; National Toxicology Program, National Institutes of Environmental Health Sciences, National Institute of Health, Department of Health and Human Services, 9 Research Triangle Park, NC, USA; Johns Hopkins University, Bloomberg School of Public Health, Center for -
DISSERTATION PROTEOMIC PROFILING of the RAT RENAL PROXIMAL CONVOLUTED TUBULE in RESPONSE to CHRONIC METABOLIC ACIDOSIS Submitted
DISSERTATION PROTEOMIC PROFILING OF THE RAT RENAL PROXIMAL CONVOLUTED TUBULE IN RESPONSE TO CHRONIC METABOLIC ACIDOSIS Submitted by Dana Marie Freund Department of Biochemistry and Molecular Biology In partial fulfillment of the requirements For the Degree of Doctor of Philosophy Colorado State University Fort Collins, Colorado Spring 2013 Doctoral Committee: Advisor: Norman Curthoys Co-Advisor: Jessica Prenni Jennifer Nyborg Olve Peersen Karen Dobos ABSTRACT PROTEOMIC PROFILING OF THE RAT RENAL PROXIMAL CONVOLUTED TUBULE IN RESPONSE TO CHRONIC METABOLIC ACIDOSIS The human kidneys contain more than one million glomeruli which filter nearly 200 liters of plasma per day. The proximal tubule is the segment of the nephron that immediately follows the glomeruli. This portion of the nephron contributes to fluid, electrolyte and nutrient homeostasis by reabsorbing 60-70% of the filtered water and NaCl and an even greater proportion of NaHCO3. The initial or convoluted portion of the proximal tubule reabsorbs nearly all of the nutrients in the glomerular filtrate and is the site of active secretion and many of the metabolic functions of the kidney. For example, the proximal convoluted tubule is the primary site of renal ammoniagenesis and gluconeogenesis, processes that are significantly activated during metabolic acidosis. Metabolic acidosis is a common clinical condition that is characterized by a decrease in blood pH and bicarbonate concentration. Metabolic acidosis also occurs frequently as a secondary complication, which adversely affects the outcome of patients with various life- threatening conditions. This type of acidosis can occur acutely, lasting for a few hours to a day, or as a chronic condition where acid-base balance is not fully restored. -
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UNDERSTANDING THE GENETICS UNDERLYING MASTITIS USING A MULTI-PRONGED APPROACH A Dissertation Presented to the Faculty of the Graduate School of Cornell University In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Asha Marie Miles December 2019 © 2019 Asha Marie Miles UNDERSTANDING THE GENETICS UNDERLYING MASTITIS USING A MULTI-PRONGED APPROACH Asha Marie Miles, Ph. D. Cornell University 2019 This dissertation addresses deficiencies in the existing genetic characterization of mastitis due to granddaughter study designs and selection strategies based primarily on lactation average somatic cell score (SCS). Composite milk samples were collected across 6 sampling periods representing key lactation stages: 0-1 day in milk (DIM), 3- 5 DIM, 10-14 DIM, 50-60 DIM, 90-110 DIM, and 210-230 DIM. Cows were scored for front and rear teat length, width, end shape, and placement, fore udder attachment, udder cleft, udder depth, rear udder height, and rear udder width. Independent multivariable logistic regression models were used to generate odds ratios for elevated SCC (≥ 200,000 cells/ml) and farm-diagnosed clinical mastitis. Within our study cohort, loose fore udder attachment, flat teat ends, low rear udder height, and wide rear teats were associated with increased odds of mastitis. Principal component analysis was performed on these traits to create a single new phenotype describing mastitis susceptibility based on these high-risk phenotypes. Cows (N = 471) were genotyped on the Illumina BovineHD 777K SNP chip and considering all 14 traits of interest, a total of 56 genome-wide associations (GWA) were performed and 28 significantly associated quantitative trait loci (QTL) were identified. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
A Gene Expression Resource Generated by Genome-Wide Lacz
© 2015. Published by The Company of Biologists Ltd | Disease Models & Mechanisms (2015) 8, 1467-1478 doi:10.1242/dmm.021238 RESOURCE ARTICLE A gene expression resource generated by genome-wide lacZ profiling in the mouse Elizabeth Tuck1,**, Jeanne Estabel1,*,**, Anika Oellrich1, Anna Karin Maguire1, Hibret A. Adissu2, Luke Souter1, Emma Siragher1, Charlotte Lillistone1, Angela L. Green1, Hannah Wardle-Jones1, Damian M. Carragher1,‡, Natasha A. Karp1, Damian Smedley1, Niels C. Adams1,§, Sanger Institute Mouse Genetics Project1,‡‡, James N. Bussell1, David J. Adams1, Ramiro Ramırez-Soliś 1, Karen P. Steel1,¶, Antonella Galli1 and Jacqueline K. White1,§§ ABSTRACT composite of RNA-based expression data sets. Strong agreement was observed, indicating a high degree of specificity in our data. Knowledge of the expression profile of a gene is a critical piece of Furthermore, there were 1207 observations of expression of a information required to build an understanding of the normal and particular gene in an anatomical structure where Bgee had no essential functions of that gene and any role it may play in the data, indicating a large amount of novelty in our data set. development or progression of disease. High-throughput, large- Examples of expression data corroborating and extending scale efforts are on-going internationally to characterise reporter- genotype-phenotype associations and supporting disease gene tagged knockout mouse lines. As part of that effort, we report an candidacy are presented to demonstrate the potential of this open access adult mouse expression resource, in which the powerful resource. expression profile of 424 genes has been assessed in up to 47 different organs, tissues and sub-structures using a lacZ reporter KEY WORDS: Gene expression, lacZ reporter, Mouse, Resource gene. -
Grhpr Gene, Full Gene Analysis
TEST ID: GRHPZ GRHPR GENE, FULL GENE ANALYSIS CLINICAL INFORMATION MOBILE APPS FROM MAYO MEDICAL LABORATORIES Primary hyperoxaluria type 2 (PH2) is a hereditary disorder of glyoxylate metabolism caused by deficiency of the hepatic enzyme glyoxylate reductase/hydroxypyruvate reductase (GRHPR). Lab Catalog for iPad and Absence of GRHPR activity results in excess oxalate and usually L-glycerate excreted in the Lab Reference for iPhone urine leading to nephrolithiasis (kidney stones) and sometimes renal failure. and iPod Touch Onset of PH2 is typically in childhood or adolescence with symptoms related to kidney stones. In some cases, kidney failure may be the initial presenting feature. Nephrocalcinosis, as seen by renal ultrasound, is observed less frequently in individuals with PH2 than primary Requires iOS 5.1+ hyperoxaluria type 1 (PH1). End-stage renal disease (ESRD) is also less common and of later onset than PH1; however, once ESRD develops, oxalate deposition in other organs such as REFERENCE VALUES bone, retina, and myocardium can occur. An interpretive report will be While the exact prevalence and incidence of PH2 are not known, it is thought that PH2 is less provided. common than PH1, which has an estimated prevalence rate of 1 to 3 per million population and an incidence of 0.1 per million/year. ANALYTIC TIME Biochemical testing is indicated in patients with possible primary hyperoxaluria. Measurement 14 days of urinary oxalate in a timed, 24-hour urine collection is strongly preferred, with correction to adult body surface area in pediatric patients (HYOX / Hyperoxaluria Panel, Urine; OXU / Oxalate, Urine). In very young children (incapable of performing a timed collection), random urine oxalate to creatinine ratios may be used for determination of oxalate excretion. -
Methods in and Applications of the Sequencing of Short Non-Coding Rnas" (2013)
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2013 Methods in and Applications of the Sequencing of Short Non- Coding RNAs Paul Ryvkin University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Bioinformatics Commons, Genetics Commons, and the Molecular Biology Commons Recommended Citation Ryvkin, Paul, "Methods in and Applications of the Sequencing of Short Non-Coding RNAs" (2013). Publicly Accessible Penn Dissertations. 922. https://repository.upenn.edu/edissertations/922 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/922 For more information, please contact [email protected]. Methods in and Applications of the Sequencing of Short Non-Coding RNAs Abstract Short non-coding RNAs are important for all domains of life. With the advent of modern molecular biology their applicability to medicine has become apparent in settings ranging from diagonistic biomarkers to therapeutics and fields angingr from oncology to neurology. In addition, a critical, recent technological development is high-throughput sequencing of nucleic acids. The convergence of modern biotechnology with developments in RNA biology presents opportunities in both basic research and medical settings. Here I present two novel methods for leveraging high-throughput sequencing in the study of short non- coding RNAs, as well as a study in which they are applied to Alzheimer's Disease (AD). The computational methods presented here include High-throughput Annotation of Modified Ribonucleotides (HAMR), which enables researchers to detect post-transcriptional covalent modifications ot RNAs in a high-throughput manner. In addition, I describe Classification of RNAs by Analysis of Length (CoRAL), a computational method that allows researchers to characterize the pathways responsible for short non-coding RNA biogenesis. -
Supplemental Information
Supplemental information Dissection of the genomic structure of the miR-183/96/182 gene. Previously, we showed that the miR-183/96/182 cluster is an intergenic miRNA cluster, located in a ~60-kb interval between the genes encoding nuclear respiratory factor-1 (Nrf1) and ubiquitin-conjugating enzyme E2H (Ube2h) on mouse chr6qA3.3 (1). To start to uncover the genomic structure of the miR- 183/96/182 gene, we first studied genomic features around miR-183/96/182 in the UCSC genome browser (http://genome.UCSC.edu/), and identified two CpG islands 3.4-6.5 kb 5’ of pre-miR-183, the most 5’ miRNA of the cluster (Fig. 1A; Fig. S1 and Seq. S1). A cDNA clone, AK044220, located at 3.2-4.6 kb 5’ to pre-miR-183, encompasses the second CpG island (Fig. 1A; Fig. S1). We hypothesized that this cDNA clone was derived from 5’ exon(s) of the primary transcript of the miR-183/96/182 gene, as CpG islands are often associated with promoters (2). Supporting this hypothesis, multiple expressed sequences detected by gene-trap clones, including clone D016D06 (3, 4), were co-localized with the cDNA clone AK044220 (Fig. 1A; Fig. S1). Clone D016D06, deposited by the German GeneTrap Consortium (GGTC) (http://tikus.gsf.de) (3, 4), was derived from insertion of a retroviral construct, rFlpROSAβgeo in 129S2 ES cells (Fig. 1A and C). The rFlpROSAβgeo construct carries a promoterless reporter gene, the β−geo cassette - an in-frame fusion of the β-galactosidase and neomycin resistance (Neor) gene (5), with a splicing acceptor (SA) immediately upstream, and a polyA signal downstream of the β−geo cassette (Fig. -
The Centriole Protein CEP76 Negatively Regulates PLK1 Activity in the Cytoplasm for Proper Mitotic Progression
© 2020. Published by The Company of Biologists Ltd | Journal of Cell Science (2020) 133, jcs241281. doi:10.1242/jcs.241281 RESEARCH ARTICLE The centriole protein CEP76 negatively regulates PLK1 activity in the cytoplasm for proper mitotic progression Yutaka Takeda, Kaho Yamazaki, Kaho Hashimoto, Koki Watanabe, Takumi Chinen*,‡ and Daiju Kitagawa*,‡ ABSTRACT are important for accurate mitotic progression (Golsteyn, 1995; Polo-like kinase 1 (PLK1) dynamically changes its localization and Schmucker and Sumara, 2014). Several factors regulate PLK1 plays important roles in proper mitotic progression. In particular, strict localization during mitosis. PLK1 is recruited to centrosomes in a control of cytoplasmic PLK1 is needed to prevent mitotic defects. CDK1-dependent manner (Lee et al., 2014). The initial recruitment However, the regulation of cytoplasmic PLK1 is not fully understood. In of PLK1 to kinetochores is mediated by its interaction with PBIP1 this study, we show that CEP76, a centriolar protein, physically (also known as CENPU; Kang et al., 2006). During anaphase, PLK1 interacts with PLK1 and tightly controls the activation of cytoplasmic binds to PRC1 and changes its localization to the midbody (Hu et al., PLK1 during mitosis in human cells. We found that removal of 2012). In addition, strict control of PLK1 in the cytoplasm is needed centrosomes induced ectopic aggregation of PLK1, which is highly to prevent its aggregation and mitotic defects (Mukhopadhyay and phosphorylated, in the cytoplasm during mitosis. Importantly, a Dasso, 2010; Schmit et al., 2012; Zhao et al., 2016). However, the targeted RNAi screen revealed that depletion of CEP76 resulted in a detailed mechanisms through which the localization, expression and similar phenotype. -
Is Cep70, a Centrosomal Protein with New Roles in Breast Cancer Dissemination and Metastasis, a Facilitator of Epithelial-Mesenchymal Transition?
Is Cep70, a centrosomal protein with new roles in breast cancer dissemination and metastasis, a facilitator of epithelial-mesenchymal transition? Pedro A. Lazo 1,2 1 Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, Salamanca, Spain 2 Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Salamanca, Spain Running title: Cep70 and EMT Disclosures: None declared. Contact address: [email protected] 1 Introduction Microtubules are driving mechanisms of chromosomes, intracellular organelle movement, and cell shape and motility. Microtubules are organized on centrosomes, which are assembled in microtubule-organizing centers (MTOC). In mitosis there is no nuclear envelope and centromeres associated to microtubules are mainly involved in chromosome redistribution into daughter cells. In differentiated cells the microtubule- organizing centers are dispersed in the cytoplasm (non centrosomal (ncMTOC)) and interact with the minus end of microtubules through γ-tubulin. 1 However, it is not known if the microtubule contribution to tumor biology is only by facilitating tumor aneuploidy. During tumor dissemination, a process not linked to cell division, important changes take place in cell shape and motility. Microtubules are very dynamic because of their inherent structural instability, and this plasticity facilitates their reorganization during the epithelial-mesenchymal -
Elucidating Biological Roles of Novel Murine Genes in Hearing Impairment in Africa
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 19 September 2019 doi:10.20944/preprints201909.0222.v1 Review Elucidating Biological Roles of Novel Murine Genes in Hearing Impairment in Africa Oluwafemi Gabriel Oluwole,1* Abdoulaye Yal 1,2, Edmond Wonkam1, Noluthando Manyisa1, Jack Morrice1, Gaston K. Mazanda1 and Ambroise Wonkam1* 1Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa. 2Department of Neurology, Point G Teaching Hospital, University of Sciences, Techniques and Technology, Bamako, Mali. *Correspondence to: [email protected]; [email protected] Abstract: The prevalence of congenital hearing impairment (HI) is highest in Africa. Estimates evaluated genetic causes to account for 31% of HI cases in Africa, but the identification of associated causative genes mutations have been challenging. In this study, we reviewed the potential roles, in humans, of 38 novel genes identified in a murine study. We gathered information from various genomic annotation databases and performed functional enrichment analysis using online resources i.e. genemania and g.proflier. Results revealed that 27/38 genes are express mostly in the brain, suggesting additional cognitive roles. Indeed, HERC1- R3250X had been associated with intellectual disability in a Moroccan family. A homozygous 216-bp deletion in KLC2 was found in two siblings of Egyptian descent with spastic paraplegia. Up to 27/38 murine genes have link to at least a disease, and the commonest mode of inheritance is autosomal recessive (n=8). Network analysis indicates that 20 other genes have intermediate and biological links to the novel genes, suggesting their possible roles in HI. -
Mutations Suggests Both Loss-Of-Function and Gain-Of-Function Effects Morag A
© 2021. Published by The Company of Biologists Ltd | Disease Models & Mechanisms (2021) 14, dmm047225. doi:10.1242/dmm.047225 RESEARCH ARTICLE Hearing impairment due to Mir183/96/182 mutations suggests both loss-of-function and gain-of-function effects Morag A. Lewis1,2,*, Francesca Di Domenico1, Neil J. Ingham1,2, Haydn M. Prosser2 and Karen P. Steel1,2 ABSTRACT birth. However, this is not the cause of the hearing loss; even before The microRNA miR-96 is important for hearing, as point mutations in the onset of normal hearing, homozygote hair cells fail to mature humans and mice result in dominant progressive hearing loss. Mir96 both morphologically and physiologically, remaining in their is expressed in sensory cells along with Mir182 and Mir183, but the immature state, and heterozygote hair cells show a developmental roles of these closely-linked microRNAs are as yet unknown. Here, delay. miR-96 is thus thought to be responsible for coordinating we analyse mice carrying null alleles of Mir182, and of Mir183 and hair cell maturation (Chen et al., 2014; Kuhn et al., 2011). Mir96 together to investigate their roles in hearing. We found that Overexpression of the three miRNAs also results in cochlear defects Mir183/96 heterozygous mice had normal hearing and homozygotes and hearing loss (Weston et al., 2018). The complete loss of all were completely deaf with abnormal hair cell stereocilia bundles and mature miRNAs from the inner ear results in early developmental reduced numbers of inner hair cell synapses at 4 weeks of age. defects including a severely truncated cochlear duct (Friedman Mir182 knockout mice developed normal hearing then exhibited et al., 2009; Soukup et al., 2009).