Life Sciences Commons^™

Recurring Patterns Among Scrambled Genes In The Encrypted Genome Of The Ciliate Oxytricha Trifallax, Jonathan Burns, Denys Kukushkin, Xiao Chen, Laura F Landweber, Masahico Saito, Nataša Jonoska

Mathematics and Statistics Faculty Publications

Some genera of ciliates, such as Oxytricha and Stylonychia, undergo massive genome reorganization during development and provide model organisms to study DNA rearrangement. A common feature of these ciliates is the presence of two types of nuclei: a germline micronucleus and a transcriptionally-active somatic macronucleus containing over 16,000 gene sized "nano-chromosomes". During conjugation the old parental macronucleus disintegrates and a new macronucleus forms from a copy of the zygotic micronucleus. During this process, macronuclear chromosomes assemble through DNA processing events that delete 90-98% of the DNA content of the micronucleus. This includes the deletion of noncoding DNA segments that interrupt …

Pharmacogenetic Discovery In Calgb (Alliance) 90401 And Mechanistic Validation Of A Vac14 Polymorphism That Increases Risk Of Docetaxel-Induced Neuropathy, Heather E. Wheeler

Bioinformatics Faculty Publications

Purpose: Discovery of SNPs that predict a patient's risk of docetaxel-induced neuropathy would enable treatment individualization to maximize efficacy and avoid unnecessary toxicity. The objectives of this analysis were to discover SNPs associated with docetaxel-induced neuropathy and mechanistically validate these associations in preclinical models of drug-induced neuropathy.

Experimental Design: A genome-wide association study was conducted in metastatic castrate-resistant prostate cancer patients treated with docetaxel, prednisone and randomized to bevacizumab or placebo on CALGB 90401. SNPs were genotyped on the Illumina HumanHap610-Quad platform followed by rigorous quality control. The inference was conducted on the cumulative dose at occurrence of grade 3+ …

Positive Selection Linked With Generation Of Novel Mammalian Dentition Patterns, Joao P. Machado, Siby Philip, Emanuel Maldonado, Stephen J. O'Brien, Warren E. Johnson

Biology Faculty Articles

A diverse group of genes are involved in the tooth development of mammals. Several studies, focused mainly on mice and rats, have provided a detailed depiction of the processes coordinating tooth formation and shape. Here we surveyed 236 tooth-associated genes in 39 mammalian genomes and tested for signatures of selection to assess patterns of molecular adaptation in genes regulating mammalian dentition. Of the 236 genes, 31 (∼13.1%) showed strong signatures of positive selection that may be responsible for the phenotypic diversity observed in mammalian dentition. Mammalian-specific tooth-associated genes had accelerated mutation rates compared with older genes found across all vertebrates. …

Perseverance: Psychospiritual And Genetic Perspectives, Tony N. Jelsma, Arielle Johnston, Bruce Vermeer

Faculty Work Comprehensive List

Perseverance constitutes a quality that motivates humankind to press onward usually in the face of significant adversity and resistance. Perseverance is also important in the Christian life. The apostle Paul, using athletic training metaphors, frequently urges his readers to persevere in the faith, even describing his own life as a fight and a race (2 Tim.4:7). Yet, certain groups of people seem to possess a greater measure of perseverance than others have. We are therefore led to ask, “Can our ability to persevere be, in God’s providence, at least partly genetically influenced?”

Alcohol Discrimination And Preferences In Two Species Of Nectar-Feeding Primate, Samuel R. Gochman, Michael B. Brown, Nathaniel J. Dominy

Dartmouth Scholarship

Recent reports suggest that dietary ethanol, or alcohol, is a supplemental source of calories for some primates. For example, slow lorises (Nycticebus coucang) consume fermented nectars with a mean alcohol concentration of 0.6% (range: 0.0–3.8%). A similar behaviour is hypothesized for aye-ayes (Daubentonia madagascariensis) based on a single point mutation (A294V) in the gene that encodes alcohol dehydrogenase class IV (ADH4), the first enzyme to catabolize alcohol during digestion. The mutation increases catalytic efficiency 40-fold and may confer a selective advantage to aye-ayes that consume the nectar of Ravenala madagascariensis. It is uncertain, however, whether alcohol exists in this nectar …

Examining The Relative Contributions Of Genes, Diet, And The Gut Microbiome To The Development Of Obesity And Diabetes, Laura C. Bridgewater

Journal of Undergraduate Research

This project began as a collaboration with Dr. Julianne Grose in MMBIO to study the effect of PAS kinase on diabetes and obesity in a mouse model system. Due to our initial findings, the study has grown to include Dr. Ben Bickman in PDBIO (an expert in metabolism) and Dr. Scott Weber in MMBIO (an immunologist). We have found that PAS kinase knockout mice have an increased metabolic rate—not only in their overall system but also specifically in skeletal muscle. Metabolic rate can have a profound influence on the immune system, so we began working with Dr. Weber to measure …

The Transcription Factors Adr1 Or Cat8 Are Required For Rtg Pathway Activation And Evasion From Yeast Acetic Acid-Induced Programmed Cell Death In Raffinose, Zhengchang Liu, Luna Laera, Nicoletta Guaragnella, Maša Ždralević, Domenico Marzulli, Sergio Giannattasio

Biological Sciences Faculty Publications

Yeast Saccharomyces cerevisiae grown on glucose undergoes programmed cell death (PCD) induced by acetic acid (AA-PCD), but evades PCD when grown in raffinose. This is due to concomitant relief of carbon catabolite repression (CCR) and activation of mitochondrial retrograde signaling, a mitochondria-to-nucleus communication pathway causing up-regulation of various nuclear target genes, such as CIT2, encoding peroxisomal citrate synthase, dependent on the positive regulator RTG2 in response to mitochondrial dysfunction. CCR down-regulates genes mainly involved in mitochondrial respiratory metabolism. In this work, we investigated the relationships between the RTG and CCR pathways in the modulation of AA-PCD sensitivity under glucose repression …

Herpes Simplex Virus And Interferon Signaling Induce Novel Autophagic Clusters In Sensory Neurons, Sarah Katzenell, David A. Leib

Dartmouth Scholarship

Herpes simplex virus 1 (HSV-1) establishes lifelong infection in the neurons of trigeminal ganglia (TG), cycling between productive infection and latency. Neuronal antiviral responses are driven by type I interferon (IFN) and are crucial to controlling HSV-1 virulence. Autophagy also plays a role in this neuronal antiviral response, but the mechanism remains obscure. In this study, HSV-1 infection of murine TG neurons triggered unusual clusters of autophagosomes, predominantly in neurons lacking detectable HSV-1 antigen. Treatment of neurons with IFN-β induced a similar response, and cluster formation by infection or IFN treatment was dependent upon an intact IFN-signaling pathway. The autophagic …

Pharmacogenetic Allele Nomenclature: International Workgroup Recommendations For Test Result Reporting., L V. Kalman, Jag Agúndez, M Lindqvist Appell, J L. Black, G C. Bell, S Boukouvala, C Bruckner, E Bruford, K Caudle, S A. Coulthard, A K. Daly, Al Del Tredici, J T. Den Dunnen, K Drozda, R E. Everts, D Flockhart, R R. Freimuth, Andrea Gaedigk, H Hachad, T Hartshorne, M Ingelman-Sundberg, T E. Klein, V M. Lauschke, D R. Maglott, H L. Mcleod, G A. Mcmillin, U A. Meyer, D J. Müller, D A. Nickerson, W S. Oetting, M Pacanowski, V M. Pratt, M V. Relling, A Roberts, W S. Rubinstein, K Sangkuhl, M Schwab, S A. Scott, S C. Sim, R K. Thirumaran, L H. Toji, R F. Tyndale, Rhn Van Schaik, M Whirl-Carrillo, Ktj Yeo, U M. Zanger

Manuscripts, Articles, Book Chapters and Other Papers

This article provides nomenclature recommendations developed by an international workgroup to increase transparency and standardization of pharmacogenetic (PGx) result reporting. Presently, sequence variants identified by PGx tests are described using different nomenclature systems. In addition, PGx analysis may detect different sets of variants for each gene, which can affect interpretation of results. This practice has caused confusion and may thereby impede the adoption of clinical PGx testing. Standardization is critical to move PGx forward.

Mouse Osns Express 10,000 Genes, Timothy S. Mcclintock

Physiology Research Data

This Excel file (both full and compressed versions are available) contains processed GeneChip microarray data that allows predictions of whether a gene is expressed in mature olfactory sensory neurons of mice.

Pepper (Capsicum Annuum L.) Anther Culture: Fundamentalresearch And Practical Applications, Teodora Popova Irikova, Spyridon Kintzios, Stanislava Grozeva, Velichka Rodeva

Turkish Journal of Biology

To create new varieties resistant to biotic and abiotic stress factors that possess high productivity and improved fruit quality, breeders require modern breeding methods and techniques. Double haploid (DH) lines are an invaluable breeding element due to their guaranteed, completely homozygous nature. One of the fastest methods for obtaining DH lines is anther culture. Microspore embryogenesis provides considerable opportunities in the areas of breeding and biotechnology and represents a model system for fundamental biological research. The effectiveness of pepper anther culture is still low, which affects the application of DH lines in breeding programs. A detailed study of the anther …

Identification Of A Novel Gene On 10q22.1 Causing Autosomal Dominant Retinitis Pigmentosa (Adrp)., Stephen P Daiger, Lori S Sullivan, Sara J Bowne, Daniel C Koboldt, Susan H Blanton, Dianna K Wheaton, Cheryl E Avery, Elizabeth D Cadena, Robert K Koenekoop, Robert S Fulton, Richard K Wilson, George M Weinstock, Richard A Lewis, David G Birch

Faculty Publications

Whole-genome linkage mapping identified a region on chromosome 10q21.3-q22.1 with a maximum LOD score of 3.0 at 0 % recombination in a six-generation family with autosomal dominant retinitis pigmentosa (adRP). All known adRP genes and X-linked RP genes were excluded in the family by a combination of methods. Whole-exome next-generation sequencing revealed a missense mutation in hexokinase 1, HK1 c.2539G > A, p.Glu847Lys, tracking with disease in all affected family members. One severely-affected male is homozygous for this region by linkage analysis and has two copies of the mutation. No other potential mutations were detected in the linkage region nor were …

The Confluence Of Philosophy And Biology: An Excavation Of Philosophical Issues In Molecular And Developmental Biology, Patrick Johnson Mendie, Emmanuel Bassey Eyo (Ph.D)

Journal of Health Ethics

Philosophical evaluations have played an influential role in the growth and development of molecular and developmental biology to ensure that every individual is born healthy, born wanted and has the privilege to fulfil his or her potentials for a life free from disease and disability. This is why it becomes necessary for biologists to carefully understand human genes, evolution, cells and general human anatomy to fulfil this project. During this process, they are faced with challenges where they also lack the foundation on how to solve them. This challenge gave birth to a philosophical excavation of molecular and developmental biology. …