Digital Commons Network^™

Economic Comparison Of The Relative Costs And Efficiency Of Using Thermo Fisher Scientific Rapidhit™ Id System Versus Traditional Dna Laboratory Analysis, Paul J. Speaker

Faculty & Staff Scholarship

With the emergence of any new technology, economic questions arise regarding the efficacy of the new technology in comparison to existing analytical techniques. While the question of ultimate interest concerns the return on investment (ROI) of the new technology, that ROI requires both an evaluation of the net benefits of the technology and an examination of the costs to implement the technology. In this report, we examine the full-loaded cost structure of traditional DNA analysis using fiscal year 2021 data from Project FORESIGHT and compare the cost per sample with the price structure of the Thermo Fischer Scientific RapidHit technology. …

Using Multiple Taxa And Wetland Classification Schemes For Enhanced Detection Of Biological Response Signatures To Human Impairment, Walter Veselka Iv, Walter S. Kordek, James T. Anderson

Faculty & Staff Scholarship

Wetland indices of biological integrity (IBIs) are a common component in monitoring the wetland water resources as required by the United States’ Clean Water Act (CWA). The effectiveness of an IBI to monitor disturbance is dependent on the metrics being consistently responsive to measures of human disturbance within a described classification category. We present IBIs designed for two types of commonly used wetland classification systems – the hydrogeomorphic (HGM) and the National Wetlands Inventory (NWI). The metrics making up the IBIs were derived from anuran, avian, macroinvertebrate, and vegetation communities; each representing increasing levels of resources associated with gathering the …

The Rise To Dominance Of Genetic Model Organisms And The Decline Of Curiosity-Driven Organismal Research, Sarah M. Farris

Faculty & Staff Scholarship

Curiosity-driven, basic biological research “…performed without thought of practical ends…” establishes fundamental conceptual frameworks for future technological and medical breakthroughs. Traditionally, curiosity-driven research in biological sciences has utilized experimental organisms chosen for their tractability and suitability for studying the question of interest. This approach leverages the diversity of life to uncover working solutions (adaptations) to problems encountered by living things, and evolutionary context as to the extent to which these solutions may be generalized to other species. Despite the well-documented success of this approach, funding portfolios of United States granting agencies are increasingly filled with studies on a few species …

Saccharomyces Arboricola And Its Hybrids’ Propensity For Sake Production: Interspecific Hybrids Reveal Increased Fermentation Abilities And A Mosaic Metabolic Profile, Matthew J. Winans, Yuki Yamamoto, Yuki Fujimaru, Yuki Kusaba, Jennifer E G Gallagher, Hiroshi Kitagaki

Faculty & Staff Scholarship

The use of interspecific hybrids during the industrial fermentation process has been well established, positioning the frontier of advancement in brewing to capitalize on the potential of Saccharomyces hybridization. Interspecific yeast hybrids used in modern monoculture inoculations benefit from a wide range of volatile metabolites that broaden the organoleptic complexity. This is the first report of sake brewing by Saccharomyces arboricola and its hybrids. S. arboricola x S. cerevisiae direct-mating generated cryotolerant interspecific hybrids which increased yields of ethanol and ethyl hexanoate compared to parental strains, important flavor attributes of fine Japanese ginjo sake rice wine. Hierarchical clustering heatmapping with …

Oxidative Stress Responses And Nutrient Starvation In Mchm Treated Saccharomyces Cerevisiae, Michael C. Ayers, Zachary N. Sherman, Jennifer E. G. Gallagher

Faculty & Staff Scholarship

In 2014, the coal cleaning chemical 4-methylcyclohexane methanol (MCHM) spilled into the water supply for 300,000 West Virginians. Initial toxicology tests showed relatively mild results, but the underlying effects on cellular biology were underexplored. Treated wildtype yeast cells grew poorly, but there was only a small decrease in cell viability. Cell cycle analysis revealed an absence of cells in S phase within thirty minutes of treatment. Cells accumulated in G1 over a six-hour time course, indicating arrest instead of death. A genetic screen of the haploid knockout collection revealed 329 high confidence genes required for optimal growth in MCHM. These …

Neural Processing Of Communication Signals: The Extent Of Sender–Receiver Matching Varies Across Species Of Apteronotus, Kathryne M. Allen, Gary Marsat

Faculty & Staff Scholarship

As communication signal properties change, through genetic drift or selective pressure, the sensory systems that receive these signals must also adapt to maintain sensitivity and adaptability in an array of contexts. Shedding light on this process helps us to understand how sensory codes are tailored to specific tasks. In a species of weakly electric fish, Apteronotus albifrons, we examined the unique neurophysiological properties that support the encoding of electrosensory communication signals that the animal encounters in social exchanges. We compare our findings to the known coding properties of the closely related species Apteronotus leptorhynchus to establish how these animals …

Fourteen Polymorphic Microsatellite Markers For The Widespread Labrador Tea (Rhododendron Groenlandicum), Mathew L. Sheik, Kitty L. Labounty, Erika Mitchell, Emily L. Gillespie

Faculty & Staff Scholarship

PREMISE: Microsatellite markers were developed for Labrador tea (Rhododendron groenlandicum, Ericaceae) to facilitate downstream genetic investigation of this species and the extremely closely related, circumboreal Rhododendron subsect. Ledum. METHODS AND RESULTS: Forty-eight primer pairs were designed using Illumina data and screened for excellent amplification. Sixteen successful pairs were developed as microsatellite markers using fluorescently labeled amplification to generate chromatogram data. These data were evaluated for intrapopulation and interpopulation variability in three populations from Alaska and Maine, USA, and the Northwest Territories, Canada. Fourteen polymorphic markers genotyped reliably, each with one to eight alleles. Cluster analysis indicates that across the range, …

Increased Dementia Mortality In West Virginia Counties With Mountaintop Removal Mining?, A. K. Salm, Michael J. Benson

Faculty & Staff Scholarship

(MTM), a practice that has been ongoing in some counties of West Virginia (WV) USA since the 1970s. PM inhalation has been linked to central nervous system pathophysiology, including cognitive decline and dementia. Here we compared county dementia mortality statistics in MTM vs. non-MTM WV counties over a period spanning 2001–2015. We found significantly elevated age-adjusted vascular or unspecified dementia mortality/100,000 population in WV MTM counties where, after adjusting for socioeconomic variables, dementia mortality was 15.60 (±3.14 Standard Error of the Mean (S.E.M.)) times higher than that of non-MTM counties. Further analyses with satellite imaging data revealed a highly significant …

Finding New Cell Wall Regulatory Genes In Populus Trichocarpa Using Multiple Lines Of Evidence, Anna Furches, David Kainer, Deborah Weighill, Annabel Large, Piet Jones, Angelica M. Walker, Jonathon Romero, Joao Gabriel Felipe Machado Gazolla, Wayne Joubert, Manesh Shah, Jared Streich, Priya Ranjan, Jeremy Schmutz, Avinash Sreedasayam, David Macaya-Sanz, Nan Zhao, Madhavi Z. Martin, Xiaolan Rao, Richard A. Dixon, Stephen Difazio, Timothy J. Tschaplinski, Jin-Giu Chen, Gerald A. Tuskan, Daniel Jacobson

Faculty & Staff Scholarship

Understanding the regulatory network controlling cell wall biosynthesis is of great interest in Populus trichocarpa, both because of its status as a model woody perennial and its importance for lignocellulosic products. We searched for genes with putatively unknown roles in regulating cell wall biosynthesis using an extended network-based Lines of Evidence (LOE) pipeline to combine multiple omics data sets in P. trichocarpa, including gene coexpression, gene comethylation, population level pairwise SNP correlations, and two distinct SNP-metabolite Genome Wide Association Study (GWAS) layers. By incorporating validation, ranking, and filtering approaches we produced a list of nine high priority gene candidates for …

Prepontine Non-Giant Neurons Drive Flexible Escape Behavior In Zebrafish, Gregory D. Marquart, Kathryn M. Tabor, Sadie A. Bergeron, Kevin L. Briggman, Harold A. Burgess

Faculty & Staff Scholarship

Many species execute ballistic escape reactions to avoid imminent danger. Despite fast reaction times, responses are often highly regulated, reflecting a trade-off between costly motor actions and perceived threat level. However, how sensory cues are integrated within premotor escape circuits remains poorly understood. Here, we show that in zebrafish, less precipitous threats elicit a delayed escape, characterized by flexible trajectories, which are driven by a cluster of 38 prepontine neurons that are completely separate from the fast escape pathway. Whereas neurons that initiate rapid escapes receive direct auditory input and drive motor neurons, input and output pathways for delayed escapes …

Wavelet-Based Genomic Signal Processing For Centromere Identification And Hypothesis Generation, Deborah Weighill, David Macaua-Sanz, Stephen Paul Difiazio, Wayne Joubert, Manesh Shah, Jeremy Schmutz, Avinash Sreedasyam, Gerald Tuska, Daniel Jacobson

Faculty & Staff Scholarship

Various ‘omics data types have been generated for Populus trichocarpa, each providing a layer of information which can be represented as a density signal across a chromosome. We make use of genome sequence data, variants data across a population as well as methylation data across 10 different tissues, combined with wavelet-based signal processing to perform a comprehensive analysis of the signature of the centromere in these different data signals, and successfully identify putative centromeric regions in P. trichocarpa from these signals. Furthermore, using SNP (single nucleotide polymorphism) correlations across a natural population of P. trichocarpa, we find evidence for the …

Ancient Polyploidy And Genome Evolution In Palms, Craig F. Barrett, Michael R. Mckain, Brandon T. Sinn, Xue Jun Ge, Yuqu Zhang, Alexandre Antonelli, Christine D. Bacon

Faculty & Staff Scholarship

Mechanisms of genome evolution are fundamental to our understanding of adaptation and the generation and maintenance of biodiversity, yet genome dynamics are still poorly characterized in many clades. Strong correlations between variation in genomic attributes and species diversity across the plant tree of life suggest that polyploidy or other mechanisms of genome size change confer selective advantages due to the introduction of genomic novelty. Palms (order Arecales, family Arecaceae) are diverse, widespread, and dominant in tropical ecosystems, yet little is known about genome evolution in this ecologically and economically important clade. Here, we take a phylogenetic comparative approach to investigate …

Mutualist-Provisioned Resources Impact Vector Competency, Rita V. M. Rio, Anna K. S. Jozwick, Amy F. Savage, Afsoon Sabet, Aurelien Vigneron, Yineng Wu, Serap Aksoy, Brian L. Weiss

Faculty & Staff Scholarship

ABSTRACT Many symbionts supplement their host’s diet with essential nutrients. However, whether these nutrients also enhance parasitism is unknown. In this study, we investigated whether folate (vitamin B9) production by the tsetse fly (Glossina spp.) essential mutualist, Wigglesworthia, aids auxotrophic African trypanosomes in completing their life cycle within this obligate vector. We show that the expression of Wigglesworthia folate biosynthesis genes changes with the progression of trypanosome infection within tsetse. The disruption of Wigglesworthia folate production caused a reduction in the percentage of flies that housed midgut (MG) trypanosome infections. However, decreased folate did not prevent MG trypanosomes from migrating …

Comparative Genomic Analysis Of Six Glossina Genomes, Vectors Of African Trypanosomes, Geoffrey M. Attardo, Adly M. M. Abd-Alla, Alvaro Acosta-Serrano, James E. Allen, Rosemary Bateta, Joshua B. Benoit, Kostas Bourtzis, Jelle Caers, Guy Caljon, Mikkel B. Christensen, David W. Farrow, Markus Friedrich, Aurélie Hua-Van, Emily C. Jennings, Denis M. Larkin, Daniel Lawson, Michael J. Lehane, Vasileios P. Lenis, Ernesto Lowy-Gallego, Rosaline W. Macharia, Anna R. Malacrida, Heather G. Marco, Daniel Masiga, Gareth L. Maslen, Irina Matetovic, Richard P. Meisel, Irene Meki, Veronika Michalkova, Wolfgang J. Miller, Patrick Minx, Paul O. Mireji, Lino Ometto, Andrew G. Parker, Rita Rio, Clair Rose, Andrew J. Rosendale, Omar Rota-Stabelli, Grazia Savini, Liliane Schoofs, Francesca Scolari, Martin T. Swain, Peter Takáč, Chad Tomlinson, George Tsiamis, Jan Van Abbeele, Aurelien Vigneron, Jingwen Wang, Wesley C. Warren, Robert M. Waterhouse, Mathew T. Weirauch, Brian L. Weiss, Richard K. Wilson, Xin Zhao, Serap Aksoy

Faculty & Staff Scholarship

Background: Tsetse flies (Glossina sp.) are the vectors of human and animal trypanosomiasis throughout subSaharan Africa. Tsetse flies are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood-specific diet by both sexes, and obligate bacterial symbiosis. This work describes the comparative analysis of six Glossina genomes representing three sub-genera: Morsitans (G. morsitans morsitans, G. pallidipes, G. austeni), Palpalis (G. palpalis, G. fuscipes), and Fusca (G. brevipalpis) which represent different habitats, host preferences, and vectorial capacity. Results: Genomic analyses validate established evolutionary relationships and sub-genera. Syntenic analysis of Glossina relative …

The Regulatory Landscape Of A Core Maize Domestication Module Controlling Bud Dormancy And Growth Repression, Zhaobin Dong, Yuguo Xiao, Rajanikanth Govindarajulu, Regina Feil, Muriel L. Siddoway, Torrey Nielsen, John E. Lunn, Jennifer Hawkins, Clinton Whipple, George Chuck

Faculty & Staff Scholarship

Many domesticated crop plants have been bred for increased apical dominance, displaying greatly reduced axillary branching compared to their wild ancestors. In maize, this was achieved through selection for a gain-of-function allele of the TCP transcription factor teosinte branched1 (tb1). The mechanism for how a dominant Tb1 allele increased apical dominance, is unknown. Through ChIP seq, RNA seq, hormone and sugar measurements on 1 mm axillary bud tissue, we identify the genetic pathways putatively regulated by TB1. These include pathways regulating phytohormones such as gibberellins, abscisic acid and jasmonic acid, but surprisingly, not auxin. In addition, metabolites involved in sugar …

A New Transgenic Reporter Line Reveals Wnt-Dependent Snai2 Re-Expression And Cranial Neural Crest Differentiation In Xenopus, Jiejing Li, Mark Perfetto, Christopher Materna, Rebecca Li, Hong Thi Tran, Kris Vleminckx, Melinda K. Duncan, Shuo Wei

Faculty & Staff Scholarship

During vertebrate embryogenesis, the cranial neural crest (CNC) forms at the neural plate border and subsequently migrates and diferentiates into many types of cells. The transcription factor Snai2, which is induced by canonical Wnt signaling to be expressed in the early CNC, is pivotal for CNC induction and migration in Xenopus. However, snai2 expression is silenced during CNC migration, and its roles at later developmental stages remain unclear. We generated a transgenic X. tropicalis line that expresses enhanced green fuorescent protein (eGFP) driven by the snai2 promoter/enhancer, and observed eGFP expression not only in the pre-migratory and migrating CNC, but …

Soil And Tree Nutrient Status Of High Elevation Mixed Red Spruce (Picea Rubens Sarg.) And Broadleaf Deciduous Forests, Phillip M. Crim, Louis M. Mcdonald, Jonathan R. Cumming

Faculty & Staff Scholarship

Abstract: Anthropogenic and industrial emissions have resulted in historically high levels of acidic deposition into central Appalachian forests. Despite the reduction in acidic inputs due to legislation curbing industrial emissions in the United States, continued N deposition may impact forest ecosystems. Soil and foliar samples were collected from four high elevation red spruce sites along a modeled gradient of historic N deposition. The three most abundant tree species at all sites, Acer rubrum L., Betula alleghaniensis Britt., and Picea rubens Sarg., were sampled. Bulk soil beneath the canopies of individual trees were collected from the top 15-cm and separated into …

Crosstalk Among Lncrnas, Micrornas And Mrnas In The Muscle ‘Degradome’ Of Rainbow Trout, Bam Paneru, Ali Ali, Rafet Al-Tobasei, Brett Kenney, Mohamed Salem

Faculty & Staff Scholarship

In fish, protein-coding and noncoding genes involved in muscle atrophy are not fully characterized. In this study, we characterized coding and noncoding genes involved in gonadogenesis-associated muscle atrophy, and investigated the potential functional interplay between these genes. Using RNA- Seq, we compared expression pattern of mRNAs, long noncoding RNAs (lncRNAs) and microRNAs of atrophying skeletal muscle from gravid females and control skeletal muscle from age-matched sterile individuals. A total of 852 mRNAs, 1,160 lncRNAs and 28 microRNAs were differentially expressed (DE) between the two groups. Muscle atrophy appears to be mediated by many genes encoding ubiquitin- proteasome system, autophagy related …

Conjugative Transposons And Their Cargo Genes Vary Across Natural Populations Of Rickettsia Buchneri Infecting The Tick Ixodes Scapularis, Rachael Hagen, Victoria I. Verhoeve, Joseph J. Gillespie, Timothy P. Driscoll

Faculty & Staff Scholarship

Rickettsia buchneri (formerly Rickettsia endosymbiont of Ixodes scapularis, or REIS) is an obligate intracellular endoparasite of the black-legged tick, the primary vector of Lyme disease in North America. It is noteworthy among the rickettsiae for its relatively large genome (1.8 Mb) and extraordinary proliferation of mobile genetic elements (MGEs), which comprise nearly 35% of its genome. Previous analysis of the R. buchneri genome identified several integrative conjugative elements named Rickettsiales amplified genomic elements (RAGEs); the composition of these RAGEs suggests that continued genomic invasions by MGEs facilitated the proliferation of rickettsial genes related to an intracellular lifestyle. In this study, …

Approaches To Denoise The Diffuse Optical Signals For Tissue Blood Flow Measurement, Peng Zhang, Zhiguo Gui, Yu Shang

Faculty & Staff Scholarship

Various diseases are relevant to the abnormal blood flow in tissue. Diffuse correlation spectroscopy (DCS) is an emerging technology to extract the blood flow index (BFI) from light electric field temporal autocorrelation data. To account for tissue heterogeneity and irregular geometry, we developed an innovative DCS algorithm (i.e., the Nth order linear algorithm, or simply the NL algorithm) previously, in which the DCS signals are fully utilized through iterative linear regressions. Under the framework of NL algorithm, the BFI to be extracted is significantly influenced by the linear regression approach adopted. In this study, three approaches were proposed and evaluated …

Bulked-Segregant Analysis Coupled To Whole Genome Sequencing (Bsa-Seq) For Rapid Gene Cloning In Maize, Harry Klein, Yuguo Xiao, Phillip A. Conklin, Rajanikanth Govindarajulu, Jacob A. Kelly, Michael J. Scanlon, Clinton J. Whipple, Madelaine Bartlett

Faculty & Staff Scholarship

Forward genetics remains a powerful method for revealing the genes underpinning organismal form and function, and for revealing how these genes are tied together in gene networks. In maize, forward genetics has been tremendously successful, but the size and complexity of the maize genome made identifying mutant genes an often arduous process with traditional methods. The next generation sequencing revolution has allowed for the gene cloning process to be significantly accelerated in many organisms, even when genomes are large and complex. Here, we describe a bulked-segregant analysis sequencing (BSA-Seq) protocol for cloning mutant genes in maize. Our simple strategy can …

Genetic Assessment Of Inbred Chicken Lines Indicates Genomic Signatures Of Resistance To Marek's Disease, Lingyang Xu, Yanghua He, George E. Liu, Huanmin Zhang, Hans H. Cheng, Robert L. Taylor Jr, Jiuzhou Song

Faculty & Staff Scholarship

Background: Marek’s disease (MD) is a highly contagious pathogenic and oncogenic disease primarily affecting chickens. However, the mechanisms of genetic resistance for MD are complex and not fully understood. MD-resistant line 63 and MD-susceptible line 72 are two highly inbred progenitor lines of White Leghorn. Recombinant Congenic Strains (RCS) were developed from these two lines, which show varied susceptibility to MD.

Results: We investigated genetic structure and genomic signatures across the genome, including the line 63 and line 72, six RCSs, and two reciprocally crossed flocks between the lines 63 and 72 (F1 63 × 72 and F1 72 × …

Systematic Analysis Of Transmitter Coexpression Reveals Organizing Principles Of Local Interneuron Heterogeneity, Kristyn M. Lizbinski, Gary Marsat, Andrew M. Dacks

Faculty & Staff Scholarship

Broad neuronal classes are surprisingly heterogeneous across many parameters, and subclasses often exhibit partially overlapping traits including transmitter coexpression. However, the extent to which transmitter coex- pression occurs in predictable, consistent patterns is unknown. Here, we demonstrate that pairwise coexpression of GABA and multiple neuropeptide families by olfactory local interneurons (LNs) of the moth Manduca sexta is highly heterogeneous, with a single LN capable of expressing neuropeptides from at least four peptide families and few instances in which neuropeptides are consistently coexpressed. Using computational modeling, we demonstrate that observed coexpression patterns cannot be explained by independent probabilities of expres- sion …

Genome-Wide Association Analysis With A 50k Transcribed Gene Snp-Chip Identifies Qtl Affecting Muscle Yield In Rainbow Trout, Mohamed Salem, Rafet Al-Tobasei, Ali Ali, Daniela Lourenco, Guangtu Gao, Yniv Palti, Brett Kenney, Timothy D. Leeds

Faculty & Staff Scholarship

Detection of coding/functional SNPs that change the biological function of a gene may lead to identification of putative causative alleles within QTL regions and discovery of genetic markers with large effects on phenotypes. This study has two-fold objectives, first to develop, and validate a 50K transcribed gene SNP-chip using RNA-Seq data. To achieve this objective, two bioinformatics pipelines, GATK and SAMtools, were used to identify ∼21K transcribed SNPs with allelic imbalances associated with important aquaculture production traits including body weight, muscle yield, muscle fat content, shear force, and whiteness in addition to resistance/susceptibility to bacterial cold-water disease (BCWD). SNPs ere …

A Tangled Web: Origins Of Reproductive Parasitism, Joseph J. Gillespie, Timothy P. Driscoll, Victoria I. Verhoeve, Mohammed Sayeedur Rahman, Kevin R. Macaluso

Faculty & Staff Scholarship

While typically a flea parasite and opportunistic human pathogen, the presence of Rickettsia felis (strain LSU-Lb) in the non-blood- feeding, parthenogenetically reproducing booklouse, Liposcelis bostrychophila, provides a system to ascertain factors governing not only host transitions but also obligate reproductive parasitism (RP). Analysis of plasmid pLbAR, unique to R. felis str. LSU-Lb, revealed a toxin–antitoxin module with similar features to prophage-encoded toxin–antitoxin modules utilized by parasitic Wolbachia strains to induce another form of RP, cytoplasmic incompatibility, in their arthropod hosts. Curiously, multiple deubiquitinase and nuclease domains of the large (3,841 aa) pLbAR toxin, as well the entire antitoxin, facilitated the …

Responses Of Early-Successional Songbirds To A Two-Stage Shelterwood Harvest For Oak Forest Regeneration, Eric L. Margenau, Yong Wang, Callie J. Schweitzer

Faculty & Staff Scholarship

Background: The early stage of forest succession following disturbance is characterized by a shift in songbird com- position as well as increased avian richness due to increased herbaceous growth in the forest understory. However, regeneration of woody species eventually outcompetes the herbaceous understory, subsequently shifting vegetation communities and decreasing availability of vital foraging and nesting cover for disturbance-dependent birds, ulti- mately resulting in their displacement. These early stages following forest disturbance, which are declining through- out the eastern United States, are ephemeral in nature and birds depend on such disturbances for nesting and other purposes throughout their lives.

Methods: We …

Integrated Analysis Of Lncrna And Mrna Expression In Rainbow Trout Families Showing Variation In Muscle Growth And Fillet Quality Traits, Ali Ali, Rafet Al-Tobasei, Brett Kenney, Timothy D. Leeds, Mohamed Salem

Faculty & Staff Scholarship

Muscle yield and quality traits are important for the aquaculture industry and consumers. Genetic selection for these traits is difficult because they are polygenic and result from multifactorial interactions. To study the genetic architecture of these traits, phenotypic characterization of whole body weight (WBW), muscle yield, fat content, shear force and whiteness were measured in ~500 fish representing 98 families from a growth-selected line. RNA-Seq was used to sequence the muscle transcriptome of different families exhibiting divergent phenotypes for each trait. We have identified 240 and 1,280 differentially expressed (DE) protein-coding genes and long noncoding RNAs (lncRNAs), respectively, in fish …

Repeated Translocation Of A Gene Cassette Drives Sex-Chromosome Turnover In Strawberries, Jacob A. Tennessen, Na Wei, Shannon C.K. Straub, Rajanikanth Govindarajulu, Aaron Liston, Tia-Lynn Ashman

Faculty & Staff Scholarship

Turnovers of sex-determining systems represent important diversifying forces across eukary- otes. Shifts in sex chromosomes—but conservation of the master sex-determining genes— characterize distantly related animal lineages. Yet in plants, in which separate sexes have evolved repeatedly and sex chromosomes are typically homomorphic, we do not know whether such translocations drive sex-chromosome turnovers within closely related taxo- nomic groups. This phenomenon can only be demonstrated by identifying sex-associated nucleotide sequences, still largely unknown in plants. The wild North American octoploid strawberries (Fragaria) exhibit separate sexes (dioecy) with homomorphic, female heteroga- metic (ZW) inheritance, yet sex maps to three different chromosomes in …

Mapping The Yearly Extent Of Surface Coal Mining In Central Appalachia Using Landsat And Google Earth Engine, Andrew A. Pericak, Christian J. Thomas, David A. Kroodsma, Matthew F. Wasson, Matthew R.V. Ross, Nicolas E. Clinton, David J. Campagna, Yolandita Franklin, Emily S. Bernhardt, John F. Amos

Faculty & Staff Scholarship

Surface mining for coal has taken place in the Central Appalachian region of the United States for well over a century, with a notable increase since the 1970s. Researchers have quantified the ecosystem and health impacts stemming from mining, relying in part on a geospatial dataset defining surface mining’s extent at a decadal interval. This dataset, how- ever, does not deliver the temporal resolution necessary to support research that could establish causal links between mining activity and environmental or public health and safety outcomes, nor has it been updated since 2005. Here we use Google Earth Engine and Landsat imagery …

In Utero Gene Expression In The Slc39a8(Neo/Neo) Knockdown Mouse, Jing Chen, Marina Galvez-Peralta, Xiang Zhang, Jingyuan Deng, Zijuan Liu, Daniel W. Nebert

Faculty & Staff Scholarship

Slc39a8 encodes ZIP8, a divalent cation/bicarbonate symporter expressed in pluripotent mouse embryonic stem cells, and therefore ubiquitous in adult tissues; ZIP8 influxes Zn2+, Mn2+ and Fe2+. Slc39a8(neo/neo) knockdown mice exhibit 10–15% of wild-type ZIP8 mRNA and protein levels, and show pleiotropic phenotype of stunted growth, neonatal lethality, multi-organ dysmorphogenesis, and dysregulated hematopoiesis manifested as severe anemia. Herein we performed RNA-seq analysis of gestational day (GD)13.5 yolk sac and placenta, and GD16.5 liver, kidney, lung, heart and cerebellum,comparing Slc39a8(neo/neo) with Slc39a8(+/+) wild-type. Meta-data analysis of differentially- expressed genes revealed 29 unique genes from all tissues — having enriched GO categories associated …