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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 …

Demographic Hallmarks Of An Overbrowsed Population State In American Ginseng, James B. Mcgraw, Jennifer L. Chandler

Faculty & Staff Scholarship

Effects of high deer herbivory in North America on populations of favored plant browse species have been well-documented, however since less palatable plants now dominate the understory, we asked whether these species could be vulnerable as well, and if so, what symptoms might signal that this was occurring? Using American ginseng (Panax quinque- foliusL.) as our representative less palatable understory plant, we compared two sub- populations within a single natural population that were differentially exposed to browse; one isolated from deer by growing atop a large, flat-topped boulder, and a browse-exposed subpopulation in the surrounding low-lying area. We tested the …

Pleiotropic And Epistatic Network-Based Discovery: Integrated Networks For Target Gene Discovery, Deborah Weighill, Piet Jones, Manesh Shah, Priya Ranjan, Wellington Muchero, Jeremy Schmutz, Avinash Sreedasyam, David Macaya-Sanz, Robert Sykes, Nan Zhao, Madhavi Z. Martin, Stephen Difazio, Timothy J. Tschaplinski, Gerald Tuskan, Daniel Jacobson

Faculty & Staff Scholarship

Biological organisms are complex systems that are composed of functional networks of interacting molecules and macro-molecules. Complex phenotypes are the result of orchestrated, hierarchical, heterogeneous collections of expressed genomic variants. However, the effects of these variants are the result of historic selective pressure and current environmental and epigenetic signals, and, as such, their co-occurrence can be seen as genome-wide correlations in a number of different manners. Biomass recalcitrance (i.e., the resistance of plants to degradation or deconstruction, which ultimately enables access to a plant’s sugars) is a complex polygenic phenotype of high importance to biofuels initiatives. This study makes use …

Large Effect Quantitative Trait Loci For Salicinoid Phenolic Glycosides In Populus: Implications For Gene Discovery, Scott A. Woolbright, Brian J. Rehill, Richard L. Lindroth, Stephen P. Difazio, Gregory D. Martinsen, Matthew S. Zinkgraf, Gerard J. Allan, Paul Keim, Thomas G. Whitham

Faculty & Staff Scholarship

Genomic studies have been used to identify genes underlying many important plant secondary metabolic pathways. However, genes for salicinoid phenolic glycosides (SPGs)—ecologically important compounds with significant commercial, cultural, and medicinal applications—remain largely undescribed. We used a linkage map derived from a full-sib population of hybrid cottonwoods (Populus spp.) to search for quanti- tative trait loci (QTL) for the SPGs salicortin and HCH-salicortin. SSR markers and primer sequences were used to anchor the map to the V3.0 P. trichocarpa genome. We discovered 21 QTL for the two traits, including a major QTL for HCH-salicortin (R2 = .52) that colocated with a …

Theaflavin-3,3′-Digallate Enhances The Inhibitory Effect Of Cisplatin By Regulating The Copper Transporter 1 And Glutathione In Human Ovarian Cancer Cells, Haibo Pan, Eunhye Kim, Gary O. Rankin, Yon Rojanasakul, Youying Tu, Yi Charlie Chen

Faculty & Staff Scholarship

Ovarian cancer has the highest fatality rate among the gynecologic cancers. The side effects, high relapse rate, and drug resistance lead to low long-term survival rate (less than 40%) of patients with advanced ovarian cancer. Theaflavin-3,3′-digallate (TF3), a black tea polyphenol, showed less cytotoxicity to normal ovarian cells than ovarian cancer cells. We aimed to investigate whether TF3 could potentiate the inhibitory effect of cisplatin against human ovarian cancer cell lines. In the present study, combined treatment with TF3 and cisplatin showed a synergistic cytotoxicity against A2780/CP70 and OVCAR3 cells. Treatment with TF3 could increase the intracellular accumulation of platinum …

A Functional Signature Ontology (Fusion) Screen Detects An Ampk Inhibitor With Selective Toxicity Toward Human Colon Tumor Cells, Binita Das, Beth K. Neilsen, Kurt W. Fisher, Drew Gehring, Youcai Hu, Deanna J. Volle, Hyun Seok Kim, Jamie L. Mccall, David L. Kelly, John B. Macmillian, Michael A. White, Robert E. Lewis

Faculty & Staff Scholarship

AMPK is a serine threonine kinase composed of a heterotrimer of a catalytic, kinase-containing α and regulatory β and γ subunits. Here we show that individual AMPK subunit expression and requirement for survival varies across colon cancer cell lines. While AMPKα1 expression is relatively consistent across colon cancer cell lines, AMPKα1 depletion does not induce cell death. Conversely, AMPKα2 is expressed at variable levels in colon cancer cells. In high expressing SW480 and moderate expressing HCT116 colon cancer cells, siRNA-mediated depletion induces cell death. These data suggest that AMPK kinase inhibition may be a useful component of future therapeutic strategies. …

The Antioxidant Xanthorrhizol Prevents Amyloid-Β-Induced Oxidative Modification And Inactivation Of Neprilysin, Chol Seung Lim, Jung-Soo Han

Faculty & Staff Scholarship

Activity of neprilysin (NEP), the major protease which cleaves amyloid-β peptide (Aβ), is reportedly reduced in the brains of patients with Alzheimer’s disease (AD). Accumulation of Aβ generates reactive oxygen species (ROS) such as 4-hydroxynonenal (HNE), and then reduces activities of Aβ-degrading enzymes including NEP. Xanthorrhizol (Xan), a natural sesquiterpenoid, has been reported to possess antioxidant and anti-inflammatory proper- ties. The present study examined the effects of Xan on HNE- or oligomeric Aβ42-induced ox- idative modification of NEP protein. Xan was added to the HNE- or oligomeric Aβ42-treated SK-N-SH human neuroblastoma cells and then levels, oxidative modification and enzymatic activities …

Transcriptional Profiling Of Saccharomyces Cerevisiae Reveals The Impact Of Variation Of A Single Transcription Factor On Differential Gene Expression In 4nqo, Fermentable, And Nonfermentable Carbon Sources, Xiaoqing Rong-Mullins, Michael C. Ayers, Mahmoud Summers, Jennifer E.G. Gallagher

Faculty & Staff Scholarship

Cellular metabolism can change the potency of a chemical’s tumorigenicity. 4-nitroquinoline-1-oxide (4NQO) is a tumorigenic drug widely used on animal models for cancer research. Polymorphisms of the transcription factor Yrr1 confer different levels of resistance to 4NQO in Saccharomyces cerevisiae. To study how different Yrr1 alleles regulate gene expression leading to resistance, transcriptomes of three isogenic S. cerevisiae strains carrying different Yrr1 alleles were profiled via RNA sequencing (RNA-Seq) and chromatin immunoprecipitation coupled with sequencing (ChIP-Seq) in the presence and absence of 4NQO. In response to 4NQO, all alleles of Yrr1 drove the expression of SNQ2 (a multidrug transporter), which …

Altered Spring Phenology Of North American Freshwater Turtles And The Importance Of Representative Populations, Fredric J. Janzen, Luke A. Hoekstra, Ronald J. Brooks, David M. Carroll, J Whitfield Gibbons, Judith L. Greene, John B. Iverson, Jacqueline D. Litzgus, Edwin D. Michael, Steven G. Parren, Willem M. Roosenburg, Gabriel F. Strain, John K. Tucker, Gordon R. Ultsch

Faculty & Staff Scholarship

Globally, populations of diverse taxa have altered phenology in response to climate change. However, most research has focused on a single population of a given taxon, which may be unrepresentative for comparative analyses, and few long-term studies of phenology in ectothermic amniotes have been published. We test for climate- altered phenology using long-term studies (10–36 years) of nesting behavior in 14 populations representing six genera of freshwater turtles (Chelydra, Chrysemys, Kinosternon, Malaclemys, Sternotherus, and Trachemys). Nesting season initiation oc- curs earlier in more recent years, with 11 of the populations advancing phenology. The onset of nesting for nearly all populations …

Parasitaemia Data And Molecular Characterization Of Haemoproteus Catharti From New World Vultures (Cathartidae) Reveals A Novel Clade Of Haemosporida, Michael J. Yabsley, Ralph E.T. Vanstreels, Ellen S. Martinsen, Alexandra G. Wickson, Amanda E. Holland, Sonia M. Hernandez, Alec T. Thompson, Susan L. Perkins, Christopher A. Lawrence Bryan, Christopher A. Cleveland, Emily Jolly, Justin D. Brown, Dave Mcruer, Shannon Behmke, James C. Beasley

Faculty & Staff Scholarship

Background: New World vultures (Cathartiformes: Cathartidae) are obligate scavengers comprised of seven species in five genera throughout the Americas. Of these, turkey vultures (Cathartes aura) and black vultures (Coragyps atratus) are the most widespread and, although ecologically similar, have evolved differences in morphology, physiology, and behaviour. Three species of haemosporidians have been reported in New World vultures to date: Haemoproteus catharti, Leucocytozoon toddi and Plasmodium elongatum, although few studies have investigated haemosporidian parasites in this important group of species. In this study, morphological and molecular methods were used to investi- gate the epidemiology and molecular biology of haemosporidian parasites of …

Quantitative Acoustic Differentiation Of Cryptic Species Illustrated With King And Clapper Rails, Lydia L. Stiffler, Katie M. Schroeder, James T. Anderson, Susan B. Mcrae, Todd E. Katzner

Faculty & Staff Scholarship

Reliable species identification is vital for survey and monitoring programs. Recently, the development of digital technology for recording and analyzing vocalizations has assisted in acoustic surveying for cryptic, rare, or elusive species. However, the quan- titative tools that exist for species differentiation are still being refined. Using vocali- zations recorded in the course of ecological studies of a King Rail (Rallus elegans) and a Clapper Rail (Rallus crepitans) population, we assessed the accuracy and effective- ness of three parametric (logistic regression, discriminant function analysis, quadratic discriminant function analysis) and six nonparametric (support vector machine, CART, Random Forest, k-nearest neighbor, weighted …