@article{giacomini_adler_reading_irwin_2023, title={Differential bumble bee gene expression associated with pathogen infection and pollen diet}, volume={24}, ISSN={1471-2164}, url={http://dx.doi.org/10.1186/s12864-023-09143-5}, DOI={10.1186/s12864-023-09143-5}, abstractNote={Diet and parasitism can have powerful effects on host gene expression. However, how specific dietary components affect host gene expression that could feed back to affect parasitism is relatively unexplored in many wild species. Recently, it was discovered that consumption of sunflower (Helianthus annuus) pollen reduced severity of gut protozoan pathogen Crithidia bombi infection in Bombus impatiens bumble bees. Despite the dramatic and consistent medicinal effect of sunflower pollen, very little is known about the mechanism(s) underlying this effect. However, sunflower pollen extract increases rather than suppresses C. bombi growth in vitro, suggesting that sunflower pollen reduces C. bombi infection indirectly via changes in the host. Here, we analyzed whole transcriptomes of B. impatiens workers to characterize the physiological response to sunflower pollen consumption and C. bombi infection to isolate the mechanisms underlying the medicinal effect. B. impatiens workers were inoculated with either C. bombi cells (infected) or a sham control (un-infected) and fed either sunflower or wildflower pollen ad libitum. Whole abdominal gene expression profiles were then sequenced with Illumina NextSeq 500 technology.Among infected bees, sunflower pollen upregulated immune transcripts, including the anti-microbial peptide hymenoptaecin, Toll receptors and serine proteases. In both infected and un-infected bees, sunflower pollen upregulated putative detoxification transcripts and transcripts associated with the repair and maintenance of gut epithelial cells. Among wildflower-fed bees, infected bees downregulated immune transcripts associated with phagocytosis and the phenoloxidase cascade.Taken together, these results indicate dissimilar immune responses between sunflower- and wildflower-fed bumble bees infected with C. bombi, a response to physical damage to gut epithelial cells caused by sunflower pollen, and a strong detoxification response to sunflower pollen consumption. Identifying host responses that drive the medicinal effect of sunflower pollen in infected bumble bees may broaden our understanding of plant-pollinator interactions and provide opportunities for effective management of bee pathogens.}, number={1}, journal={BMC Genomics}, publisher={Springer Science and Business Media LLC}, author={Giacomini, Jonathan J. and Adler, Lynn S. and Reading, Benjamin J. and Irwin, Rebecca E.}, year={2023}, month={Mar} }
 @article{williams_kowalchyk_collins_reading_2023, title={Discovery Proteomics and Absolute Protein Quantification Can Be Performed Simultaneously on an Orbitrap-Based Mass Spectrometer}, volume={3}, ISSN={["2470-1343"]}, url={https://doi.org/10.1021/acsomega.2c07614}, DOI={10.1021/acsomega.2c07614}, abstractNote={Mass spectrometry (MS) has steadily moved into the forefront of quantification-centered protein research. Protein cleavage isotope dilution MS is a proven way for quantifying proteins by using an isotope-labeled analogue of a peptide fragment of the parent protein as an internal standard. Parallel reaction monitoring (PRM) has become the go-to approach for such quantification on an Orbitrap-based instrument as it is assumed that the instrument sensitivity is enhanced. We performed a comparative study on data-dependent acquisition (DDA) and PRM-based workflows to quantify egg yolk protein precursors or vitellogenins (VTGs) Aa, Ab, and C in striped bass (Morone saxatilis). VTG proportions serve as a developmental measure of egg quality, possibly changing with the environment, and have been studied as an indicator of the health of North Carolina stocks. Based on single-factor analysis of variance comparisons of mean VTG amounts across fish from the same sample groupings, our results indicate that there is no statistical difference between MS1-based and MS2-based VTG quantification. We further conclude that DDA is able to deliver both discovery data and absolute quantification data in the same experiment.}, number={13}, journal={ACS OMEGA}, author={Williams, Taufika Islam and Kowalchyk, Cara and Collins, Leonard B. and Reading, Benjamin J.}, year={2023}, month={Mar} }
 @article{flores_carvalho_reading_fahrenholz_ferket_grimes_2023, title={Machine learning and data mining methodology to predict nominal and numeric performance body weight values using Large White male turkey datasets}, volume={32}, ISSN={["1537-0437"]}, DOI={10.1016/j.japr.2023.100366}, abstractNote={Large biological data sets with many variables and a small number of biological replicates ("omics" sciences and industry data) are challenging to analyze with traditional inferential statistics. Statistical models can be applied to data containing more observations than variables, and they are strongly suited for this purpose. However, the power to detect actual differences is reduced when the number of comparisons exceeds the number of experimental replicates or observations. Machine learning (ML) allows researchers to evaluate treatments groups or multiple categories of variables with fewer observations. Thus, it has become a tool used to predict phenomena and evaluate relationships within datasets that are less suited for traditional statistics. Data mining (DM) helps researchers to identify the most critical variables in an ML predictive model and can be used akin to "statistical significance" for interpretation. This current effort aimed to develop ML and DM methodologies while applying them to predict Large White male turkey body weight (BW). Data from a previously reported study were used. Bird BW, weekly BW gain (BWG), feed intake (FI), feed conversion ratio (FCR), small intestine pH, cloacal temperature, density, microbiome taxa, litter content of Mn and Zn, were used as variables for the ML analysis. A total of 253 variables were used in ML and DM analysis. BW and FI at 18 wk were classified as low, objective, and high based on a 5% for BW and 3% for FI margin of the Aviagen male turkey objectives for ML analysis. The WEKA 3.8.5 Experimenter tool used various classification and regression algorithms with a 10-fold cross-validation system to predict 18 wk BW based on input data. A single algorithm made the most practical model, from 3 models constructed, with a correlation of 0.73 and a root square error of 0.26 based only on turkey 14 wk BW. In conclusion, these ML and DM tools could be applied to turkey research and production systems by analyzing large data sets to predict growth performance.}, number={4}, journal={JOURNAL OF APPLIED POULTRY RESEARCH}, author={Flores, K. R. and Carvalho, L. V. F. M. and Reading, B. J. and Fahrenholz, A. and Ferket, P. R. and Grimes, J. L.}, year={2023}, month={Dec} }
 @article{newell_jima_reading_patisaul_2023, title={Machine learning reveals common transcriptomic signatures across rat brain and placenta following developmental organophosphate ester exposure}, volume={7}, ISSN={["1096-0929"]}, DOI={10.1093/toxsci/kfad062}, abstractNote={Toxicogenomics is a critical area of inquiry for hazard identification and to identify both mechanisms of action and potential markers of exposure to toxic compounds. However, data generated by these experiments are highly dimensional and present challenges to standard statistical approaches, requiring strict correction for multiple comparisons. This stringency often fails to detect meaningful changes to low expression genes and/or eliminate genes with small but consistent changes particularly in tissues where slight changes in expression can have important functional differences, such as brain. Machine learning offers an alternative analytical approach for 'omics data that effectively sidesteps the challenges of analyzing highly dimensional data. Using three rat RNA transcriptome sets, we utilized an ensemble machine learning approach to predict developmental exposure to a mixture of organophosphate esters (OPEs) in brain (newborn cortex and day ten hippocampus) and late gestation placenta of male and female rats, and identified genes that informed predictor performance. OPE exposure had sex specific effects on hippocampal transcriptome, and significantly impacted genes associated with mitochondrial transcriptional regulation and cation transport in females, including voltage-gated potassium and calcium channels and subunits. To establish if this holds for other tissues, RNAseq data from cortex and placenta, both previously published and analyzed via a more traditional pipeline, were reanalyzed with the ensemble machine learning methodology. Significant enrichment for pathways of oxidative phosphorylation and electron transport chain was found, suggesting a transcriptomic signature of OPE exposure impacting mitochondrial metabolism across tissue types and developmental epoch. Here we show how machine learning can complement more traditional analytical approaches to identify vulnerable "signature" pathways disrupted by chemical exposures and biomarkers of exposure.}, journal={TOXICOLOGICAL SCIENCES}, author={Newell, Andrew J. and Jima, Dereje and Reading, Benjamin and Patisaul, Heather B.}, year={2023}, month={Jul} }
 @article{prior_lange_salger_reading_peatman_beck_2022, title={The effect of piscidin antimicrobial peptides on the formation of Gram-negative bacterial biofilms}, volume={45}, DOI={10.1111/jfd.13540}, abstractNote={Fish-derived antimicrobial peptides are an important part of the innate immune system due to their potent antimicrobial properties. Piscidins are a class of antimicrobial peptides first described in hybrid striped bass (Morone chrysops x Morone saxatilis) but have also been identified in many other fish species. Previous work demonstrated the broad antimicrobial activity of piscidins against Gram-negative and Gram-positive bacterial species. This study sought to determine the extent to which class I (striped bass piscidin 1, white bass piscidin 1 and striped bass/white bass piscidin 3) and class II (striped bass piscidin 4 and white bass piscidin 5) piscidins inhibit biofilm formation of different Gram-negative bacteria. In general, the class I and II piscidins demonstrate potent activity against Escherichia coli and Flavobacterium columnare biofilms. The class II piscidins showed more activity against E. coli and F. columnare isolates than did the class I piscidins. The piscidins in general were much less effective against inhibiting Aeromonas hydrophila and A. veronii biofilm growth. Only the class I piscidins showed significant growth inhibition among the Aeromonas spp. examined.}, journal={JOURNAL OF FISH DISEASES}, author={Prior, Benjamin S. and Lange, Miles D. and Salger, Scott A. and Reading, Benjamin J. and Peatman, Eric and Beck, Benjamin H.}, year={2022}, month={Sep}, pages={99–105} }
 @article{reading_andersen_2022, title={Where Does Our Seafood Come From?}, url={https://doi.org/10.52750/273688}, DOI={10.52750/273688}, abstractNote={Aquaculture is the farming of aquatic organisms and it is the major source of seafood produced globally.The majority of seafood products consumed in the United States, however, are imported from foreign countries.}, author={Reading, Benjamin and Andersen, Linnea}, year={2022}, month={Aug} }
 @article{giacomini_adler_reading_irwin_2021, title={Differential Bumble Bee Gene Expression Associated With Pathogen Infection And Pollen Diet}, url={https://doi.org/10.21203/rs.3.rs-912647/v1}, DOI={10.21203/rs.3.rs-912647/v1}, abstractNote={Abstract Background: Diet and parasitism can have powerful effects on host gene expression. However, how specific dietary components affect host gene expression that could feed back to affect parasitism is relatively unexplored in many wild species. Recently, it was discovered that consumption of sunflower ( Helianthus annuus ) pollen reduced severity of gut protozoan pathogen Crithidia bombi infection in Bombus impatiens bumble bees. Despite the dramatic and consistent medicinal effect of sunflower pollen, very little is known about the mechanism(s) underlying this effect. However, sunflower pollen extract increases rather than suppresses C. bombi growth in vitro , suggesting that sunflower pollen reduces C. bombi infection indirectly via changes in the host. Here, we analyzed whole transcriptomes of B. impatiens workers to characterize the physiological response to sunflower pollen consumption and C. bombi infection to isolate the mechanisms underlying the medicinal effect. B. impatiens workers were inoculated with either C. bombi cells (infected) or a sham control (un-infected) and fed either sunflower or wildflower pollen ad libitum . Whole abdominal gene expression profiles were then sequenced with Illumina NextSeq 500 technology. Results: Among infected bees, sunflower pollen upregulated immune transcripts, including the anti-microbial peptide hymenoptaecin, Toll receptors and serine proteases. In both infected and un-infected bees, sunflower pollen upregulated putative detoxification transcripts and transcripts associated with the repair and maintenance of gut epithelial cells. Among wildflower-fed bees, infected bees downregulated immune transcripts associated with phagocytosis and the phenoloxidase cascade. Conclusions: Taken together, these results indicate dissimilar immune responses between sunflower- and wildflower-fed bumble bees infected with C. bombi , a response to physical damage to gut epithelial cells caused by sunflower pollen, and a strong detoxification response to sunflower pollen consumption. Identifying host responses that drive the medicinal effect of sunflower pollen in infected bumble bees may broaden our understanding of plant-pollinator interactions and provide opportunities for effective management of bee pathogens.}, author={Giacomini, Jonathan J. and Adler, Lynn S. and Reading, Benjamin J. and Irwin, Rebecca E.}, year={2021}, month={Nov} }
 @article{andersen_clark_hopper_hodson_schilling_daniels_woods_kovach_berlinsky_kenter_et al._2021, title={Methods of domestic striped bass (Morone saxatilis) spawning that do not require the use of any hormone induction}, volume={533}, ISSN={["1873-5622"]}, DOI={10.1016/j.aquaculture.2020.736025}, abstractNote={Nineteen batch spawning trials were conducted using 5th and 6th generation domestic striped bass (Morone saxatilis) to demonstrate the ability of these fish to volitionally spawn in large tanks to produce larvae using only photothermal and salinity conditioning. The findings described are the first report of multiple striped bass successfully batch spawning in captivity without exogenous hormone administration. The results of these trials indicate that an approximately 1:1 ratio of female to male striped bass in a single batch spawning unit is more favorable for production, that a minimum of at least 10 fish of each sex is required to elicit this particular spawning behavior, and that using 25 fish of each sex will yield commercially scalable larval production. This batch spawning method has been employed to effectively and consistently spawn over half of the female striped bass in the National Program for Genetic Improvement and Selective Breeding for the Hybrid Striped Bass Industry (N = 202 of 334 female fish over five years) to produce 44,608,181 swim-up larvae (26.6% hatching rate). Microsatellite genotyping and parentage assignment demonstrates that females will reproduce with between 2 and 18 males and that males will reproduce with between 1 and 6 females. Moreover, the effective broodstock size (Nb) of these batch spawning units is 33 and when accounting for multiple partners and unequal family sizes (Nbv) is 28. Lastly, the reported results include the successful spawning of female striped bass staged at and beyond 15 Bayless hours, or those that would have previously been considered ineligible for spawning even with the use of exogenous hormone treatment.}, journal={AQUACULTURE}, author={Andersen, L. K. and Clark, R. W. and Hopper, M. S. and Hodson, R. G. and Schilling, J. and Daniels, H. V. and Woods, L. C., III and Kovach, A. I. and Berlinsky, D. L. and Kenter, L. W. and et al.}, year={2021}, month={Feb} }
 @article{andersen_abernathy_berlinsky_bolton_booker_borski_brown_cerino_ciaramella_clark_et al._2021, title={The status of striped bass, <scp><i>Morone saxatilis</i>,</scp> as a commercially ready species for U.S. marine aquaculture}, volume={52}, ISSN={0893-8849 1749-7345}, url={http://dx.doi.org/10.1111/jwas.12812}, DOI={10.1111/jwas.12812}, abstractNote={Striped bass, Morone saxatilis , is an anadromous fish native to the North American Atlantic Coast and is well recognized as one of the most important and highly regarded recreational fisheries in the United States. Decades of research have been conducted on striped bass and its hybrid (striped bass (cid:1) white bass Morone chrysops ) and culture methods have been established, particularly for the hybrid striped bass, the fourth largest finfish aquaculture industry in the United States (US $50 million). Domesticated striped bass have been developed since the 1990s and broodstock are available from the government for commercial fry production using novel hormone-free methods along with traditional hormone-induced tank and strip spawning. No commercial-scale intensive larval rearing technologies have been developed at present and current fingerling production is conducted in fertilized freshwater ponds. Larval valued at about US $8.45 to US $9.25 per kg whole; the farm gate value for cultured striped bass may be as much as US $10.00 or more per kg depending on demand and market. The ideal market size is between 1.36 and 2.72 kg/fish, which is considerably larger than the traditional 0.68 to 0.90 kg/fish for the hybrid striped bass market. 0.57 0.91 US or US for 2.5 lb or fish). Recent for striped bass in in ranged from US $26.45 to US $41.89 per kg (US $12.00 – US $19.00 per lb) for boneless, skin-on fillets of wild caught striped bass. Market surveys conducted with Locals Seafood in North Carolina found that marketing value-added, boneless, skin-on fillets of aquacultured striped bass in the mid-Atlantic region is feasible even with a final product price of US $39.68 per kg (US $18.00 per lb). Based on these survey data, we estimate the U.S. farm gate value for striped bass can be as low as US $10.14 per kg (US $4.60 per lb) and as high as US $13.23 per kg (US $6.00 per lb) based on a 50.0% to 70.0% mark-up margin. Furthermore, assessments have shown consumer willingness to pay premium prices for striped bass (Quagrainie, 2019). These data show a clear economic and market potential for aquaculture production of striped bass, which already has a wide consumer acceptance and appeal.}, number={3}, journal={Journal of the World Aquaculture Society}, publisher={Wiley}, author={Andersen, Linnea K. and Abernathy, Jason and Berlinsky, David L. and Bolton, Greg and Booker, Matthew M. and Borski, Russell J. and Brown, Travis and Cerino, David and Ciaramella, Michael and Clark, Robert W. and et al.}, year={2021}, month={May}, pages={710–730} }
 @book{bashura_burke_lapitan_mikulec_owens_reading_richt_spencer_valdivia-granda_weekes_et al._2021, place={Washington, D.C.}, title={Threats to Food and Agricultural Resources}, url={https://www.dhs.gov/sites/default/files/publications/threats_to_food_and_agriculture_resources.pdf}, institution={United States Department of Homeland Security, Office of Intelligence and Analysis}, author={Bashura, J. and Burke, M. and Lapitan, R. and Mikulec, J., Jr. and Owens, T. and Reading, B.J. and Richt, J.A. and Spencer, D. and Valdivia-Granda, W. and Weekes, J. and et al.}, year={2021} }
 @article{demi_taylor_reading_tordoff_dunn_2021, title={Understanding the evolution of nutritive taste in animals: Insights from biological stoichiometry and nutritional geometry}, volume={6}, ISSN={["2045-7758"]}, DOI={10.1002/ece3.7745}, abstractNote={A major conceptual gap in taste biology is the lack of a general framework for understanding the evolution of different taste modalities among animal species. We turn to two complementary nutritional frameworks, biological stoichiometry theory and nutritional geometry, to develop hypotheses for the evolution of different taste modalities in animals. We describe how the attractive tastes of Na, Ca, P, N and C containing compounds are consistent with principles of both frameworks based on their shared focus on nutritional imbalances and consumer homeostasis. Specifically, we suggest that the evolution of multiple nutritive taste modalities can be predicted by identifying individual elements that are typically more concentrated in the tissues of animals than plants. Additionally, we discuss how consumer homeostasis can inform our understanding of why some taste compounds (i.e., Na, Ca and P salts) can be either attractive or aversive depending on concentration. We also discuss how these complementary frameworks can help to explain the phylogenetic distribution of different taste modalities and improve our understanding of the mechanisms that lead to loss of taste capabilities in some animal lineages. The ideas presented here will stimulate research that bridges the fields of evolutionary biology, sensory biology and ecology.}, journal={ECOLOGY AND EVOLUTION}, author={Demi, Lee M. and Taylor, Brad W. and Reading, Benjamin J. and Tordoff, Michael G. and Dunn, Robert R.}, year={2021}, month={Jun} }
 @article{andersen_clark_mcginty_hopper_kenter_salger_schilling_hodson_kovach_berlinsky_et al._2021, title={Volitional tank spawning of domestic striped bass (Morone saxatilis) using human chorionic gonadotropin (hCG) and gonadotropin releasing hormone analogue (GnRHa)- induced 'pace-setting' females}, volume={532}, ISSN={["1873-5622"]}, DOI={10.1016/j.aquaculture.2020.735967}, abstractNote={Seventy-one tank spawning trials were conducted to evaluate the efficacy of exogenous hormone compounds and a novel “pace-set” strategy for inducing volitional tank spawning behavior in 5th generation domestic striped bass. Female fish (4.74 ± 0.73 kg; mean ± standard deviation) were treated with human chorionic gonadotropin (hCG; 29 trials), gonadotropin releasing hormone analog (GnRHa; 39 trials) or received no hormone treatment (control; 3 trials). Spawning trials were conducted using single females placed in spawning tanks with two (12 trials) or three (38 trials) males or with paired females placed in spawning tanks with three (4 trials) males. Significant differences in egg production, fry production, hatching rate, and fry/kg female body weight were generally not observed between exogenous hormone treatment groups (alpha = 0.05), with the exception of egg production differing between paired females spawning with three males (Student's t-test, p = 0.0255). However, a trend suggesting that increasing the number of males or females within the tanks improves yield of larvae (fry/kg female body weight) was observed. The untreated control females failed to spawn within 7 days. The pace-set spawning was conducted whereby one female treated with either hCG (7 trials) or GnRHa (7 trials) was placed in a spawning tank with one untreated female and multiple males. The results of these trials show for the first time that a hormone-induced female striped bass can be used to stimulate successful volitional spawning of an untreated female in the same tank with fry/kg female body weight production similar to that of hormone-treated fish. Microsatellite-based parentage of select tank spawns and four additional trials conducted with an increased number of males (19 trials total) showed that female striped bass typically spawn with at least two males; a single pair mating was only observed for one spawning trial. These data allowed for the determination of effective broodstock size (Nb) of each tank spawning trial at between 2.00 and 5.60 when considering all male contributions. The Nb generally increased as the number of males and female fish in the tank increased (from 2.53 for one female and two males to 5.52 for two females and six males). These results indicate that domestic striped bass are promiscuous and will generally reproduce in captivity using tank spawning procedures that allow for a high level of genetic diversity to be retained among the offspring. The pace-set method reduces hormone use and may be applied to commercial striped bass production as well as captive spawning of other fish species.}, journal={AQUACULTURE}, author={Andersen, L. K. and Clark, R. W. and McGinty, A. S. and Hopper, M. S. and Kenter, L. W. and Salger, S. A. and Schilling, J. and Hodson, R. G. and Kovach, A. I. and Berlinsky, D. L. and et al.}, year={2021}, month={Feb} }
 @article{guillette_mccord_guillette_polera_rachels_morgeson_kotlarz_knappe_reading_strynar_et al._2020, title={Elevated levels of per- and polyfluoroalkyl substances in Cape Fear River Striped Bass (Morone saxatilis) are associated with biomarkers of altered immune and liver function}, volume={136}, ISSN={["1873-6750"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85079172705&partnerID=MN8TOARS}, DOI={10.1016/j.envint.2019.105358}, abstractNote={Per- and polyfluoroalkyl substances (PFAS) are anthropogenic chemicals of concern that persist in the environment. Environmental monitoring revealed high concentrations of hexafluoropropylene oxide dimer acid (HFPO-DA) and other novel PFAS in the lower Cape Fear River; however, there is limited information on PFAS exposures and effects of this contamination on aquatic biota. Serum concentrations of 23 PFAS in Striped Bass (Morone saxatilis) from the Cape Fear River (n = 58) and a reference population from an aquaculture laboratory on the Pamlico/Tar watershed (n = 29) were quantified using liquid chromatography and high-resolution mass spectrometry, and correlations between PFAS concentrations and health-related serum biomarkers were evaluated. Perfluorooctane sulfonate, the predominant PFAS in Cape Fear River Striped Bass serum, was detectable in every sample with serum concentrations reaching 977 ng/mL. Perfluorononanoic and perfluorodecanoic acid were also detected in all samples, with perfluorohexanesulfonic acid present in >98% of the samples. HFPO-DA (range <0.24-5.85 ng/mL) and Nafion byproduct 2 (range <0.2-1.03 ng/mL) were detected in 48% and 78% of samples, respectively. The mean total PFAS concentration found in domestic Striped Bass raised in well-water under controlled aquaculture conditions was 40 times lower, with HPFO-DA detected in 10% of the samples, and Nafion byproduct 2 was not detected. The elevated PFAS concentrations found in the Cape Fear River Striped Bass were associated with biomarkers of alterations in the liver and immune system.}, journal={ENVIRONMENT INTERNATIONAL}, author={Guillette, T. C. and McCord, James and Guillette, Matthew and Polera, M. E. and Rachels, Kyle T. and Morgeson, Clint and Kotlarz, Nadine and Knappe, Detlef R. U. and Reading, Benjamin J. and Strynar, Mark and et al.}, year={2020}, month={Mar} }
 @article{phillips_reading_livingston_livingston_ashwell_2020, title={Evaluation via Supervised Machine Learning of the Broiler Pectoralis Major and Liver Transcriptome in Association With the Muscle Myopathy Wooden Breast}, volume={11}, ISSN={["1664-042X"]}, DOI={10.3389/fphys.2020.00101}, abstractNote={The muscle myopathy wooden breast (WB) has recently appeared in broiler production and has a negative impact on meat quality. WB is described as hard/firm consistency found within the pectoralis major (PM). In the present study, we use machine learning from our PM and liver transcriptome dataset to capture the complex relationships that are not typically revealed by traditional statistical methods. Gene expression data was evaluated between the PM and liver of birds with WB and those that were normal. Two separate machine learning algorithms were performed to analyze the data set including the sequential minimal optimization (SMO) of support vector machines (SVMs) and Multilayer Perceptron (MLP) Artificial Neural Network (ANN). Machine learning algorithms were compared to identify genes within a gene expression data set of approximately 16,000 genes for both liver and PM, which can be correctly classified from birds with or without WB. The performance of both machine learning algorithms SMO and MLP was determined using percent correct classification during the cross-validations. By evaluating the WB transcriptome datasets by 5× cross-validation using ANNs, the expression of nine genes ranked based on Shannon Entropy (Information Gain) from PM were able to correctly classify if the individual bird was normal or exhibited WB 100% of the time. These top nine genes were all protein coding and potential biomarkers. When PM gene expression data were evaluated between normal birds and those with WB using SVMs they were correctly classified 95% of the time using 450 of the top genes sorted ranked based on Shannon Entropy (Information Gain) as a preprocessing step. When evaluating the 450 attributes that were 95% correctly classified using SVMs through Ingenuity Pathway Analysis (IPA) there was an overlap in top genes identified through MLP. This analysis allowed the identification of critical transcriptional responses for the first time in both liver and muscle during the onset of WB. The information provided has revealed many molecules and pathways making up a complex molecular mechanism involved with the progression of wooden breast and suggests that the etiology of the myopathy is not limited to activity in the muscle alone, but is an altered systemic pathology.}, journal={FRONTIERS IN PHYSIOLOGY}, author={Phillips, Chelsea A. and Reading, Benjamin J. and Livingston, Matthew and Livingston, Kimberly and Ashwell, Chris M.}, year={2020}, month={Feb} }
 @article{leblanc_gahagan_andrews_avery_puncher_reading_buhariwalla_curry_whiteley_pavey_2020, title={Genomic population structure of Striped Bass (Morone saxatilis) from the Gulf of St. Lawrence to Cape Fear River}, volume={13}, ISSN={["1752-4571"]}, DOI={10.1111/eva.12990}, abstractNote={Striped Bass, Morone saxatilis (Walbaum, 1792), is an anadromous fish species that supports fisheries throughout North America and is native to the North American Atlantic Coast. Due to long coastal migrations that span multiple jurisdictions, a detailed understanding of population genomics is required to untangle demographic patterns, understand local adaptation, and characterize population movements. This study used 1,256 single nucleotide polymorphism (SNP) loci to investigate genetic structure of 477 Striped Bass sampled from 15 locations spanning the North American Atlantic coast from the Gulf of St. Lawrence, Canada, to the Cape Fear River, United States. We found striking differences in neutral divergence among Canadian sites, which were isolated from each other and US populations, compared with US populations that were much less isolated. Our SNP dataset was able to assign 99% of Striped Bass back to six reporting groups, a 39% improvement over previous genetic markers. Using this method, we found (a) evidence of admixture within Saint John River, indicating that migrants from the United States and from Shubenacadie River occasionally spawn in the Saint John River; (b) Striped Bass collected in the Mira River, Cape Breton, Canada, were found to be of both Miramichi River and US origin; (c) juveniles in the newly restored Kennebec River population had small and nonsignificant differences from the Hudson River; and (d) tributaries within the Chesapeake Bay showed a mixture of homogeny and small differences among each other. This study introduces new hypotheses about the dynamic zoogeography of Striped Bass at its northern range and has important implications for the local and international management of this species.}, number={6}, journal={EVOLUTIONARY APPLICATIONS}, author={LeBlanc, Nathalie M. and Gahagan, Benjamin I. and Andrews, Samuel N. and Avery, Trevor S. and Puncher, Gregory N. and Reading, Benjamin J. and Buhariwalla, Colin F. and Curry, R. Allen and Whiteley, Andrew R. and Pavey, Scott A.}, year={2020}, month={Jul}, pages={1468–1486} }
 @article{kenter_kovach_wojtusik_reading_berlinsky_2020, title={Paternal Strain Effects on Growth and Body Shape in Hybrid Striped Bass (White Bass female x Striped Bass male)}, volume={82}, ISSN={["1548-8454"]}, DOI={10.1002/naaq.10162}, abstractNote={Abstract The farming of hybrid Striped Bass (HSB; White Bass Morone chrysops ♀ × Striped Bass Morone saxatilis ♂ ) has been an established aquaculture industry in the United States for decades, but high production costs associated with performance variability remain a significant problem. To investigate the paternal effects on hybrid performance, Striped Bass males from Virginia, South Carolina, Florida, Texas and a fifth‐generation domestic strain selected for growth were used as sires in a half‐sibling, hybrid growth study. Eggs from individual White Bass ( n = 11) were divided equally and fertilized with the fresh sperm from different Striped Bass sires ( n = 18) to produce 53 hybrid families. Resulting larvae were stocked communally into ponds, seined as fingerlings, and separated into large‐grade, small‐grade, or ungraded groups for grow out. Juvenile HSB representing the three size‐grades were stocked into replicated indoor recirculating systems and grown until they attained market size (680 g [1.5 lb]). An additional group of the large graded fish was grown in outdoor tanks at a separate facility to observe genotype × environment interactions. Fin clips were collected during final measurements for genotyping and parentage assignment. The results indicated that large, small, and ungraded hybrids required 12, 14, and 17 months, respectively, to attain market size indoors. Wild‐strain‐sired HSB displayed a lower range in final weights compared to domestic fish and grew larger in the ungraded treatment only. Florida‐strain‐sired fish were the largest and had the greatest condition factor ( K ), Virginia‐strain‐sired fish generally had the lowest K , and the other strains had intermediate K ‐values. No differences in final weight were found in the small or large graded fish from recirculating systems, but the domestic strain produced the largest HSB grown in outdoor tanks. These results demonstrated that HSB growth is influenced by sire strain, culture environment, and grading strategies.}, number={4}, journal={NORTH AMERICAN JOURNAL OF AQUACULTURE}, author={Kenter, Linas W. and Kovach, Adrienne I and Wojtusik, Kristopher J. and Reading, Benjamin J. and Berlinsky, David L.}, year={2020}, month={Oct}, pages={405–413} }
 @misc{berlinsky_kenter_reading_goetz_2020, title={Regulating reproductive cycles for captive spawning}, ISSN={1546-5098}, url={http://dx.doi.org/10.1016/bs.fp.2020.09.001}, DOI={10.1016/bs.fp.2020.09.001}, abstractNote={The ultimate goal of broodstock management, to provide sufficient high-quality, genetically improved larvae for reliable production on grow-out farms, is currently achievable only for relatively few fish species. This is primarily because (a) broodstock, except in the case of mature industries, are typically acquired from the wild, or a few generations removed from the wild, (b) insufficient information is available about the environmental and social cues regulating spawning, (c) inadvertant hatchery stressors negatively impact gametogenesis and (d) inadequate, species-specific hormone-induction regimes and reliable markers for gamete quality are currently available. The purpose of this chapter is to review the physiological mechanisms that regulate gonadal development and spawning in fishes and how these processes can be manipulated to ensure successful reproduction in captivity, through volitional spawning or the collection of gametes for in vitro fertilization. As excellent, thorough, reviews are available, we will only briefly review the reproductive processes involved in broodstock development and reproduction (sexual differentiation, puberty, gametogenesis and gamete release), and instead identify control points important for broodstock management in the aquaculture industry.}, journal={Fish Physiology}, publisher={Elsevier}, author={Berlinsky, David L. and Kenter, Linas W. and Reading, Benjamin J. and Goetz, Frederick W.}, year={2020}, pages={1–52} }
 @article{aruho_walakira_bugenyi_rutaisire_reading_2019, title={Morphology and functional ontogeny of the digestive tract of Barbus altianalis larvae}, volume={54}, ISSN={1562-7020 2224-073X}, url={http://dx.doi.org/10.1080/15627020.2019.1642140}, DOI={10.1080/15627020.2019.1642140}, abstractNote={The ontogenetic development of digestive structures in Ripon barbel (Barbus altianalis) larvae was investigated using standard histological and histochemical procedures from hatching up to 60 days after hatching (DAH). The study was conducted to determine the best period of exogenous feeding and the stage when the digestive tract is able to digest processed microdiets. Results indicated that at hatching, the digestive tract, mouth and anus were closed. The opening of the mouth and anus were observed 3–4 DAH, whereas complete separation of the entire gut was observed on 5 DAH. Exogenous feeding started 5–6 DAH, but complete yolk exhaustion occurred 7–8 DAH, indicating a period of mixed feeding. Mucosal epithelial folds were first noted 3 DAH in the anterior intestine and became profound with some goblet cells (mucous cells) by 6 DAH. At 7 DAH the mucous cells had started secreting both neutral and acid glycoconjugates. The first intestinal single loop occurred at 28–30 DAH and a double loop at 45–50 DAH. Each coiling was proceeded by larval weight increase. By 7 DAH the buccopharyngeal cavity was lined by a layer of squamous epithelial cells with scattered goblet cells and tastebuds that became numerous by 15 DAH. At hatching, the liver and the pancreas were undifferentiated, but on 3 DAH the hepatocytes and zymogen granules of the pancreas became clear. By 7 DAH both organs enlarged, making extensions into the posterior. Intestines coiling at 28–30 DAH coincided with the beginning of external dressing of the scales, a period when B. altianalis started transforming into a juvenile. By 7–8 DAH the digestive structure showed all the necessary digestive features that could enable the larvae to digest any compound diet suggesting that it may be feasible to substitute or offer a complete microdiet during larvae nursing with reduced larval mortality.}, number={3}, journal={African Zoology}, publisher={Informa UK Limited}, author={Aruho, Cassius and Walakira, John K and Bugenyi, Fred and Rutaisire, Justus and Reading, Benjamin J}, year={2019}, month={Oct}, pages={137–149} }
 @article{woods_li_ding_liu_reading_fuller_song_2018, title={DNA methylation profiles correlated to striped bass sperm fertility}, volume={19}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-018-4548-6}, abstractNote={Striped bass (Morone saxatilis) spermatozoa are used to fertilize in vitro the eggs of white bass (M. chrysops) to produce the preferred hybrid for the striped bass aquaculture industry. Currently, only one source of domestic striped bass juveniles is available to growers that is not obtained from wild-caught parents and is thus devoid of any genetic improvement in phenotypic traits of importance to aquaculture. Sperm epigenetic modification has been predicted to be associated with fertility, which could switch genes on and off without changing the DNA sequence itself. DNA methylation is one of the most common epigenetic modification types and changes in sperm epigenetics can be correlated to sub-fertility or infertility in male striped bass. The objective of this study was to find the differentially methylated regions (DMRs) between high-fertility and sub-fertility male striped bass, which could potentially regulate the fertility performance. In our present study, we performed DNA methylation analysis of high-fertility and sub-fertility striped bass spermatozoa through MBD-Seq methods. A total of 171 DMRs were discovered in striped bass sperm correlated to fertility. Based on the annotation of these DMRs, we conducted a functional classification analysis and two important groups of genes including the WDR3/UTP12 and GPCR families, were discovered to be related to fertility performance of striped bass. Proteins from the WDR3/UTP12 family are involved in forming the sperm flagella apparatus in vertebrates and GPCRs are involved in hormonal signaling and regulation of tissue development, proliferation and differentiation. Our results contribute insights into understanding the mechanism of fertility in striped bass, which will provide powerful tools to maximize reproductive efficiencies and to identify those males with superior gametes for this important aquaculture species.}, journal={BMC GENOMICS}, author={Woods, L. Curry, III and Li, Yaokun and Ding, Yi and Liu, Jianan and Reading, Benjamin J. and Fuller, S. Adam and Song, Jiuzhou}, year={2018}, month={Apr} }
 @inbook{reading_mcginty_clark_hopper_woods iii_baltzegar_2018, place={Beijing}, title={Genomic Enablement of Temperate Bass Aquaculture (Family Moronidae)}, booktitle={Breeding and Culture of Perch and Bass}, publisher={Science China Press (Chinese Academy of Sciences)}, author={Reading, BJ and McGinty, AS and Clark, RW and Hopper, MS and Woods III, LC and Baltzegar, DA}, editor={Wang, H. and Liang, X.Editors}, year={2018}, pages={314–317} }
 @article{pigg_reading_2018, title={Knowing Bass: Accounting for Information Environments in Designing Online Public Outreach}, volume={4}, ISSN={["2056-6700"]}, DOI={10.16995/olh.377}, abstractNote={Social media and online news sites have become common outlets through which publics encounter information that shape their knowledge, values, and opinions about food. This article extends scholarship at the intersections of user experience design and online public outreach by focusing on the role of social media and online news sites in information environments that impact public site users’ knowledge about and practices of seafood production and consumption. First, we introduce an ongoing design project about North Carolina seafood production and consumption to provide an example of how and why site designers should account for how online information affects public understanding. Next, we contextualize the challenges of this project by introducing a conceptual framework that helps to explain why the values and practices of understanding seafood production are so complex. Finally, through this case and framework, we argue that designers of online public outreach projects should become more aware of designing in contexts shaped by social media. The potential for public learning is affected by how people search for, encounter, and discuss information about the issues that matter to their lives. We offer a classroom heuristic for identifying and addressing the role of information environments in rhetoric and/or technical communication courses.}, number={2}, journal={OPEN LIBRARY OF HUMANITIES}, author={Pigg, Stacey and Reading, Benjamin J.}, year={2018} }
 @article{douros_baltzegar_reading_seale_lerner_grau_borski_2018, title={Leptin Stimulates Cellular Glycolysis Through a STAT3 Dependent Mechanism in Tilapia}, volume={9}, ISSN={["1664-2392"]}, DOI={10.3389/fendo.2018.00465}, abstractNote={We assessed if leptin, a cytokine hormone known to enhance energy expenditure by promoting lipid and carbohydrate catabolism in response to physiologic stress, might directly regulate cellular glycolysis. A transcriptomic analysis of prolactin cells in the tilapia (Oreochromis mossambicus) pituitary rostral pars distalis (RPD) revealed that recombinant leptin (rtLep) differentially regulates 1,995 genes, in vitro. Machine learning algorithms and clustering analyses show leptin influences numerous cellular gene networks including metabolism; protein processing, transport, and metabolism; cell cycle and the hypoxia response. Leptin stimulates transcript abundance of the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (gapdh) in a covariate manner to the hypoxic stress gene network. Orthogonal tests confirm that rtLepA dose-dependently increases gapdh gene expression in the RPD along with transcript abundance of 6-phosphofructo-1-kinase (pfk1), the rate limiting glycolytic enzyme. Functional testing demonstrated that leptin stimulates PFK activity and glycolytic output, while Stattic (a STAT3 blocker) was sufficient to suppress these responses, indicating leptin stimulates glycolysis through a STAT3-dependent mechanism. Leptin also stimulated pfk1 gene expression and lactate production in primary hepatocyte incubations in a similar manner to those shown for the pituitary RPD. This work characterizes a critical metabolic action of leptin to directly stimulate glycolysis across tissue types in a teleost model system, and suggest that leptin may promote energy expenditure, in part, by stimulating glycolysis. These data in a teleost fish, suggest that one of leptin's ancient, highly-conserved functions among vertebrates may be stimulation of glycolysis to facilitate the energetic needs associated with various stressors.}, journal={FRONTIERS IN ENDOCRINOLOGY}, author={Douros, Jonathan D. and Baltzegar, David A. and Reading, Benjamin J. and Seale, Andre P. and Lerner, Darren T. and Grau, E. Gordon and Borski, Russell J.}, year={2018}, month={Aug} }
 @article{mushirobira_nishimiya_nagata_todo_hara_reading_hiramatsu_2018, title={Molecular cloning of vitellogenin gene promoters and in vitro and in vivo transcription profiles following estradiol-17 beta administration in the cutthroat trout}, volume={267}, ISSN={["1095-6840"]}, DOI={10.1016/j.ygcen.2018.06.017}, abstractNote={Transcription of vitellogenin (vtg) genes are initiated when estradiol-17β (E2)-estrogen receptor (ER) complexes bind estrogen response elements (ERE) located in the gene promoter region. Transcriptional regulation of dual vtg subtypes (major salmonid A-type vtg: vtgAs; minor C-type vtg: vtgC) by E2 was investigated under co-expression of a potential major transcriptional factor, erα1, in cutthroat trout. Two forms of trout vtgAs promoters (1 and 2) and one vtgC promoter were sequenced. These promoters structurally differ based on the number of EREs present. The vtgAs promoter 1 exhibited the highest maximal transcriptional activity by in vitro gene reporter assays. The concentration of E2 that induces 50% of gene reporter activity (half-maximal effective concentrations, EC50) was similar among all vtg promoters and also to the EC50 of E2 administered to induce vtg transcription in vivo. This study revealed a difference in transcriptional properties of multiple vtg promoters for the first time in a salmonid species, providing the basis to understand mechanisms underlying regulation of vitellogenesis via dual vtg gene expression.}, journal={GENERAL AND COMPARATIVE ENDOCRINOLOGY}, author={Mushirobira, Yuji and Nishimiya, Osamu and Nagata, Jun and Todo, Takashi and Hara, Akihiko and Reading, Benjamin J. and Hiramatsu, Naoshi}, year={2018}, month={Oct}, pages={157–166} }
 @article{reading_andersen_ryu_mushirobira_todo_hiramatsu_2018, title={Oogenesis and Egg Quality in Finfish: Yolk Formation and Other Factors Influencing Female Fertility}, volume={3}, ISSN={2410-3888}, url={http://dx.doi.org/10.3390/fishes3040045}, DOI={10.3390/fishes3040045}, abstractNote={Egg quality in fishes has been a topic of research in aquaculture and fisheries for decades as it represents an important life history trait and is critical for captive propagation and successful recruitment. A major factor influencing egg quality is proper yolk formation, as most fishes are oviparous and the developing offspring are entirely dependent on stored egg yolk for nutritional sustenance. These maternally derived nutrients consist of proteins, carbohydrates, lipids, vitamins, minerals, and ions that are transported from the liver to the ovary by lipoprotein particles including vitellogenins. The yolk composition may be influenced by broodstock diet, husbandry, and other intrinsic and extrinsic conditions. In addition, a number of other maternal factors that may influence egg quality also are stored in eggs, such as gene transcripts, that direct early embryonic development. Dysfunctional regulation of gene or protein expression may lead to poor quality eggs and failure to thrive within hours of fertilization. These gene transcripts may provide important markers as their expression levels may be used to screen broodstock for potential spawning success. In addition to such intrinsic factors, stress may lead to ovarian atresia or reproductive failure and can impact fish behavior, fecundity, and ovulation rate. Finally, postovulatory aging may occur when eggs become overripe and the fish fails to spawn in a timely fashion, leading to low fertility, often encountered during manual strip spawning of fish.}, number={4}, journal={Fishes}, publisher={MDPI AG}, author={Reading, Benjamin and Andersen, Linnea and Ryu, Yong-Woon and Mushirobira, Yuji and Todo, Takashi and Hiramatsu, Naoshi}, year={2018}, month={Nov}, pages={45} }
 @article{kenter_kovach_woods_reading_berlinsky_2018, title={Strain evaluation of striped bass (Morone saxatilis) cultured at different salinities}, volume={492}, ISSN={["1873-5622"]}, DOI={10.1016/j.aquaculture.2018.04.017}, abstractNote={Striped bass (Morone saxatilis) and their hybrids have been well studied and are widely cultured in freshwater ponds as food and gamefish. Recent industry expansion has generated an interest in strain-specific broodstock development for marine netpen and pond culture. In this effort, Atlantic and Gulf coast striped bass strains were cultured in recirculating aquaculture systems (RAS) at different salinities for up to two years and production and morphometric parameters (specific growth, feed conversion, fillet yield, condition factor and stripe patterns) were compared. Striped bass juveniles produced from wild-caught broodstock from rivers in Nova Scotia, Delaware, Virginia, North and South Carolina, Florida, Texas and a selected, domesticated strain were reared in triplicate fresh (0 ppt), brackish (5 ppt) and saltwater recirculating (30 ppt) systems. After one year of age, a subset of fish were implanted with passive integrated transponder (PIT) tags, combined into a larger, “common-garden”, saltwater, recirculating system and monitored over an additional year. Parental broodstock and cultured offspring were fin-clipped and genotyped to identify juvenile family origin. Final weights of fish after one and two years averaged approximately 0.5 and 2.5 kg, respectively and did not differ by water salinity. Growth rates and condition factors differed by strain, but condition factor was not correlated with fillet yield. Consistent with other studies, juvenile fish from South Carolina and Nova Scotia were found to be slow growing compared to migratory Atlantic and Gulf strains. Mixed model analyses showed that family, and family by strain interactions were significant, but accounted for less growth variance than strain alone. These results indicate that family-based selection by strain may be useful in striped bass broodstock development programs.}, journal={AQUACULTURE}, author={Kenter, Linas W. and Kovach, Adrienne I and Woods, L. Curry, III and Reading, Benjamin J. and Berlinsky, David L.}, year={2018}, month={Jul}, pages={215–225} }
 @article{ryan_adamson_aktipis_andersen_austin_barnes_beasley_bedell_briggs_chapman_et al._2018, title={The role of citizen science in addressing grand challenges in food and agriculture research}, volume={285}, ISSN={0962-8452 1471-2954}, url={http://dx.doi.org/10.1098/rspb.2018.1977}, DOI={10.1098/rspb.2018.1977}, abstractNote={The power of citizen science to contribute to both science and society is gaining increased recognition, particularly in physics and biology. Although there is a long history of public engagement in agriculture and food science, the term ‘citizen science’ has rarely been applied to these efforts. Similarly, in the emerging field of citizen science, most new citizen science projects do not focus on food or agriculture. Here, we convened thought leaders from a broad range of fields related to citizen science, agriculture, and food science to highlight key opportunities for bridging these overlapping yet disconnected communities/fields and identify ways to leverage their respective strengths. Specifically, we show that (i) citizen science projects are addressing many grand challenges facing our food systems, as outlined by the United States National Institute of Food and Agriculture, as well as broader Sustainable Development Goals set by the United Nations Development Programme, (ii) there exist emerging opportunities and unique challenges for citizen science in agriculture/food research, and (iii) the greatest opportunities for the development of citizen science projects in agriculture and food science will be gained by using the existing infrastructure and tools of Extension programmes and through the engagement of urban communities. Further, we argue there is no better time to foster greater collaboration between these fields given the trend of shrinking Extension programmes, the increasing need to apply innovative solutions to address rising demands on agricultural systems, and the exponential growth of the field of citizen science.}, number={1891}, journal={Proceedings of the Royal Society B: Biological Sciences}, publisher={The Royal Society}, author={Ryan, S. F. and Adamson, N. L. and Aktipis, A. and Andersen, L. K. and Austin, R. and Barnes, L. and Beasley, M. R. and Bedell, K. D. and Briggs, S. and Chapman, B. and et al.}, year={2018}, month={Nov}, pages={20181977} }
 @article{abdelrahman_elhady_alcivar-warren_allen_al-tobasei_bao_beck_blackburn_bosworth_buchanan_et al._2017, title={Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research}, volume={18}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-017-3557-1}, abstractNote={Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships. In addition, it is also important to understand the mechanisms of regulation and evolutionary conservation at the levels of genome, transcriptome, proteome, epigenome, and systems biology. With genomic information and information between the genomes and phenomes, technologies for marker/causal mutation-assisted selection, genome selection, and genome editing can be developed for applications in aquaculture. A set of genomic tools and resources must be made available including reference genome sequences and their annotations (including coding and non-coding regulatory elements), genome-wide polymorphic markers, efficient genotyping platforms, high-density and high-resolution linkage maps, and transcriptome resources including non-coding transcripts. Genomic and genetic control of important performance and production traits, such as disease resistance, feed conversion efficiency, growth rate, processing yield, behaviour, reproductive characteristics, and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salinity, must be understood. QTL need to be identified, validated across strains, lines and populations, and their mechanisms of control understood. Causal gene(s) need to be identified. Genetic and epigenetic regulation of important aquaculture traits need to be determined, and technologies for marker-assisted selection, causal gene/mutation-assisted selection, genome selection, and genome editing using CRISPR and other technologies must be developed, demonstrated with applicability, and application to aquaculture industries.Major progress has been made in aquaculture genomics for dozens of fish and shellfish species including the development of genetic linkage maps, physical maps, microarrays, single nucleotide polymorphism (SNP) arrays, transcriptome databases and various stages of genome reference sequences. This paper provides a general review of the current status, challenges and future research needs of aquaculture genomics, genetics, and breeding, with a focus on major aquaculture species in the United States: catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters, and shrimp. While the overall research priorities and the practical goals are similar across various aquaculture species, the current status in each species should dictate the next priority areas within the species. This paper is an output of the USDA Workshop for Aquaculture Genomics, Genetics, and Breeding held in late March 2016 in Auburn, Alabama, with participants from all parts of the United States.}, journal={BMC GENOMICS}, author={Abdelrahman, Hisham and ElHady, Mohamed and Alcivar-Warren, Acacia and Allen, Standish and Al-Tobasei, Rafet and Bao, Lisui and Beck, Ben and Blackburn, Harvey and Bosworth, Brian and Buchanan, John and et al.}, year={2017}, month={Feb} }
 @article{mizuta_mushirobira_nagata_todo_hara_reading_sullivan_hiramatsu_2017, title={Ovarian expression and localization of clathrin (Cltc) components in cutthroat trout, Oncorhynchus clarki: Evidence for Cltc involvement in endocytosis of vitellogenin during oocyte growth}, volume={212}, ISSN={["1531-4332"]}, DOI={10.1016/j.cbpa.2017.06.021}, abstractNote={To evaluate potential involvement of clathrin in endocytosis of vitellogenin (Vtg) by teleost oocytes, cDNAs encoding clathrin heavy chain (cltc) were cloned from ovaries of cutthroat trout. Quantitative PCR revealed three types of cltc (cltc-a1, cltc-a2, cltc-b) to be expressed in 10 different tissues including the ovary. The cltc-a1 alone exhibited a significant decrease in ovarian expression during vitellogenesis; this was correlated with a corresponding decrease in transcripts encoding the major Vtg receptor (Vtgr). No development-related changes in ovarian cltc-a2 or cltc-b transcript levels were observed. In situ hybridization revealed a strong ctlc signal in pre-vitellogenic oocytes, but not in vitellogenic oocytes. Western blotting using a rabbit antiserum (a-Cltc) raised against a recombinant Cltc preparation detected a polypeptide band with an apparent mass of ~170kDa in vitellogenic ovary extracts. Immunohistochemistry using a-Cltc revealed Cltc to be uniformly distributed throughout the ooplasm of perinucleolus stage oocytes, translocated to the periphery of lipid droplet stage oocytes, and localized to the oolemma during vitellogenesis. These patterns of cltc/Cltc distribution and abundance during oogenesis, which are identical to those previously reported for vtgr/Vtgr in this species, constitute the first empirical evidence that cltc-a1/Cltc-a1 is involved in Vtg endocytosis via the Vtgr in teleost fish.}, journal={COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY}, author={Mizuta, Hiroko and Mushirobira, Yuji and Nagata, Jun and Todo, Takashi and Hara, Akihiko and Reading, Benjamin J. and Sullivan, Craig V. and Hiramatsu, Naoshi}, year={2017}, month={Oct}, pages={24–34} }
 @article{salger_reading_noga_2017, title={Tissue localization of piscidin host-defense peptides during striped bass (Morone saxatilis) development}, volume={61}, ISSN={["1095-9947"]}, DOI={10.1016/j.fsi.2016.12.034}, abstractNote={Infectious diseases are a major cause of larval mortality in finfish aquaculture. Understanding ontogeny of the fish immune system and thus developmental timing of protective immune tissues and cells, may help to decrease serious losses of larval fishes when they are particularly vulnerable to infection. One component of the innate immune system of fishes is the host-defense peptides, which include the piscidins. Piscidins are small, amphipathic, α-helical peptides with a broad-spectrum of action against viral, bacterial, fungal, and protozoan pathogens. We describe for the first time the cellular and tissue localization of three different piscidins (1, 3, and 4) during striped bass (Morone saxatilis) larval ontogeny using immunofluorescent histochemistry. From 16 days post hatch to 12 months of age, piscidin staining was observed in cells of the epithelial tissues of gill, digestive tract, and skin, mainly in mast cells. Staining was also seen in presumptive hematopoietic cells in the head kidney. The three piscidins showed variable cellular and tissue staining patterns, possibly relating to differences in tissue susceptibility or pathogen specificity. This furthers our observation that the piscidins are not a monolithic family of antimicrobials, but that different AMPs have different (more specialized) functions. Furthermore, no immunofluorescent staining of piscidins was observed in post-vitellogenic oocytes, embryos, or larvae from hatch to 14 days post hatch, indicating that this critical component of the innate immune system is inactive in pre-hatch and young larval striped bass.}, journal={FISH & SHELLFISH IMMUNOLOGY}, author={Salger, Scott A. and Reading, Benjamin J. and Noga, Edward J.}, year={2017}, month={Feb}, pages={173–180} }
 @inbook{reading_sullivan_schilling_2017, place={Maryland Heights, Missouri}, edition={2nd edition}, title={Vitellogenesis in Fishes}, booktitle={Encyclopedia of Fish Physiology: From Genome to Environment. Reference Module in Life Sciences}, publisher={Elsevier}, author={Reading, B.J. and Sullivan, C.V. and Schilling, J.}, year={2017} }
 @article{salger_cassady_reading_noga_2016, title={A Diverse Family of Host-Defense Peptides (Piscidins) Exhibit Specialized Anti-Bacterial and Anti-Protozoal Activities in Fishes}, volume={11}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0159423}, abstractNote={Conventional antibiotics and other chemical-based drugs are currently one of the most common methods used to control disease-related mortality in animal agriculture. Use of the innate immune system to decrease disease related mortalities is a novel alternative to conventional drugs. One component of the innate immune system is the host-defense peptides, also known as antimicrobial peptides. Host-defense peptides are typically small, amphipathic, α-helical peptides with a broad-spectrum of action against viral, bacterial, fungal, and/or protozoal pathogens. Piscidins are host-defense peptides first discovered in the hybrid striped bass (white bass, Morone chrysops, x striped bass, M. saxatilis). In this paper we identify four new piscidin isoforms in the hybrid striped bass and describe their tissue distributions. We also determine the progenitor species of origin of each piscidin (orthology) and propose a revised nomenclature for this newly described piscidin family based on a three class system. The Class I piscidins (22 amino acids in length; striped bass and white bass piscidin 1 and piscidin 3) show broad-spectrum activity against bacteria and ciliated protozoans, while the Class III piscidins (55 amino acids in length; striped bass and white bass piscidin 6 and striped bass piscidin 7) primarily show anti-protozoal activity. The Class II piscidins (44–46 amino acids in length; striped bass and white bass piscidin 4 and white bass piscidin 5) have a level of activity against bacteria and protozoans intermediate to Classes I and III. Knowledge of piscidin function and activity may help in the future development of disease-resistant lines of striped bass and white bass that could be used to produce superior hybrids for aquaculture.}, number={8}, journal={PLOS ONE}, author={Salger, Scott A. and Cassady, Katherine R. and Reading, Benjamin J. and Noga, Edward J.}, year={2016}, month={Aug} }
 @article{reading_wills_heidinger_heist_2016, title={Genetic variability in meiotic gynogenetic muskellunge, Esox masquinongy (Mitchell), estimated from segregation of microsatellite alleles}, volume={47}, ISSN={["1365-2109"]}, DOI={10.1111/are.12718}, abstractNote={Muskellunge, Esox masquinongy, is an important recreational freshwater fish native to North America. Since muskellunge populations are often maintained through stocking efforts, advances in muskellunge reproductive technologies are of direct relevance to fishery enhancement. We evaluated the efficiency of inbreeding through induced meiotic diploid gynogenesis. Eggs from six female muskellunge were manually stripped and activated using ultra violet-irradiated yellow perch, Perca flavescens, sperm. Hydrostatic pressure shocking regimes (48 263 kPa) were then applied to the eggs to prevent second polar body expulsion producing unambiguous meiotic gynogens. Six female dams and samples of 12–20 of their gynogenetic progeny were genotyped at seven polymorphic microsatellite loci. Chromosomal recombination frequencies of microsatellite loci based on retention of heterozygosity among gynogens ranged from 0.043 to 0.839 (0.576 � 0.237). There were no statistical differences in recombination frequency among females at any of the loci. The average inbreeding coefficient (F-value) ranged from 0.581 to 0.979, equivalent to three to fourteen generations of full-sibling crosses respectively. The average F-value overall was 0.712, equivalent to between five and six generations of full-sibling crosses. Centromere map distances of the seven microsatellite loci ranged from 2.15 to 41.95 cM and meiotic gynogenesis was useful in eliminating heterozygosity at loci proximal to the centromere, but not distal. Since the age at maturity of female muskellunge is approximately 5 years, gynogenesis may pose an expeditious alternative to traditional breeding strategies for creation of homozygous pedigrees for some loci that may be outcrossed to introduce positive heterozygosity effects in the offspring.}, number={9}, journal={AQUACULTURE RESEARCH}, author={Reading, Benjamin J. and Wills, Paul S. and Heidinger, Roy C. and Heist, Edward J.}, year={2016}, month={Sep}, pages={2705–2715} }
 @article{schilling_nepomuceno_planchart_yoder_kelly_muddiman_daniels_hiramatsu_reading_2015, title={Machine learning reveals sex-specific 17β-estradiol-responsive expression patterns in white perch (Morone americana) plasma proteins}, volume={15}, ISSN={1615-9853}, url={http://dx.doi.org/10.1002/pmic.201400606}, DOI={10.1002/pmic.201400606}, abstractNote={With growing abundance and awareness of endocrine disrupting compounds (EDCs) in the environment, there is a need for accurate and reliable detection of EDC exposure. Our objective in the present study was to observe differences within and between the global plasma proteomes of sexually mature male and female white perch (Morone americana) before (Initial Control, IC) and after 17β‐estradiol (E2) induction. Semiquantitative nanoLC‐MS/MS data were analyzed by machine learning support vector machines (SVMs) and by two‐way ANOVA. By ANOVA, the expression levels of 44, 77, and 57 proteins varied significantly by gender, treatment, and the interaction of gender and treatment, respectively. SVMs perfectly classified male and female perch IC and E2‐induced plasma samples using the protein expression data. E2‐induced male and female perch plasma proteomes contained significantly higher levels of the yolk precursors vitellogenin Aa and Ab (VtgAa, VtgAb), as well as latrophilin and seven transmembrane domain‐containing protein 1 (Eltd1) and kininogen 1 (Kng1). This is the first report that Eltd1 and Kng1 may be E2‐responsive proteins in fishes and therefore may be useful indicators of estrogen induction.}, number={15}, journal={PROTEOMICS}, publisher={Wiley}, author={Schilling, Justin and Nepomuceno, Angelito I. and Planchart, Antonio and Yoder, Jeffrey A. and Kelly, Robert M. and Muddiman, David C. and Daniels, Harry V. and Hiramatsu, Naoshi and Reading, Benjamin J.}, year={2015}, month={Jun}, pages={2678–2690} }
 @article{schilling_loziuk_muddiman_daniels_reading_2015, title={Mechanisms of Egg Yolk Formation and Implications on Early Life History of White Perch (Morone americana)}, volume={10}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0143225}, abstractNote={The three white perch (Morone americana) vitellogenins (VtgAa, VtgAb, VtgC) were quantified accurately and precisely in the liver, plasma, and ovary during pre-, early-, mid-, and post-vitellogenic oocyte growth using protein cleavage-isotope dilution mass spectrometry (PC-IDMS). Western blotting generally mirrored the PC-IDMS results. By PC-IDMS, VtgC was quantifiable in pre-vitellogenic ovary tissues and VtgAb was quantifiable in pre-vitellogenic liver tissues however, neither protein was detected by western blotting in these respective tissues at this time point. Immunohistochemistry indicated that VtgC was present within pre-vitellogenic oocytes and localized to lipid droplets within vitellogenic oocytes. Affinity purification coupled to tandem mass spectrometry using highly purified VtgC as a bait protein revealed a single specific interacting protein (Y-box binding protein 2a-like [Ybx2a-like]) that eluted with suramin buffer and confirmed that VtgC does not bind the ovary vitellogenin receptors (LR8 and Lrp13). Western blotting for LR8 and Lrp13 showed that both receptors were expressed during vitellogenesis with LR8 and Lrp13 expression highest in early- and mid-vitellogenesis, respectively. The VtgAa within the ovary peaked during post-vitellogenesis, while VtgAb peaked during early-vitellogenesis in both white perch and the closely related striped bass (M. saxatilis). The VtgC was steadily accumulated by oocytes beginning during pre-vitellogenesis and continued until post-vitellogenesis and its composition varies widely between striped bass and white perch. In striped bass, the VtgC accounted for 26% of the vitellogenin-derived egg yolk, however in the white perch it comprised only 4%. Striped bass larvae have an extended developmental window and these larvae have yolk stores that may enable them to survive in the absence of food for twice as long as white perch after hatch. Thus, the VtgC may play an integral role in providing nutrients to late stage fish larvae prior to the onset of exogenous feeding and its composition in the egg yolk may relate to different early life histories among this diverse group of animals.}, number={11}, journal={PLOS ONE}, author={Schilling, Justin and Loziuk, Philip L. and Muddiman, David C. and Daniels, Harry V. and Reading, Benjamin J.}, year={2015}, month={Nov} }
 @article{mushirobira_mizuta_luo_todo_hara_reading_sullivan_hiramatsu_2015, title={Molecular Cloning and Partial Characterization of a Low-Density Lipoprotein Receptor-Related Protein 13 (Lrp13) Involved in Vitellogenin Uptake in the Cutthroat Trout (Oncorhynchus clarki)}, volume={82}, ISSN={["1098-2795"]}, DOI={10.1002/mrd.22579}, abstractNote={Multiple ovarian membrane proteins that bind vitellogenin (Vtg) have been detected in teleosts. One of these Vtg receptors was recently identified as low‐density lipoprotein receptor‐related protein 13 (lrp13/Lrp13) in perciform species, but little is known about this Vtg receptor in salmonid fish. In this study, a cDNA encoding a putative Vtg receptor with 13+1 ligand binding repeats (lr13+1) was cloned from the ovary, and identified as an lrp13 ortholog for cutthroat trout (Oncorhynchus clarki). This lrp13 was predominantly expressed in the pre‐vitellogenic stage ovary, and its expression decreased during vitellogenesis. Ovarian localization of Lrp13 was observed by immunohistochemistry using specific antiserum against recombinant Lrp13. Lrp13 immunoreactivity was observed at the oolemma, throughout the zona radiata, and within the perivitelline space between the zona radiata and granulosa cells in ovarian follicles at both the lipid‐droplet and vitellogenic stages of growth—an expression pattern that mimics that of a lr8/LR8‐type Vtg receptor in this species and of lrp13/Lrp13 in Morone species. Six discrete Vtg‐binding proteins were detected in cutthroat trout ovarian membrane proteins when probing with a digoxygenin‐labeled salmonid A‐type Vtg (VtgAs) followed by chemiluminescent ligand detection. Western blotting using the anti‐Lrp13 serum revealed a broad signal consisting of two proteins with masses ranging from ∼190 to ∼210 kDa, which corresponded with some of the VtgA‐binding proteins. These findings suggest that, in addition to lr8/LR8, lrp13/Lrp13 acts as a VtgA receptor in trout. Mol. Reprod. Dev. 82: 986–1000, 2015. © 2015 Wiley Periodicals, Inc.}, number={12}, journal={MOLECULAR REPRODUCTION AND DEVELOPMENT}, author={Mushirobira, Yuji and Mizuta, Hiroko and Luo, Wenshu and Todo, Takashi and Hara, Akihiko and Reading, Benjamin J. and Sullivan, Craig V. and Hiramatsu, Naoshi}, year={2015}, month={Dec}, pages={986–1000} }
 @article{hiramatsu_todo_sullivan_schilling_reading_matsubara_ryu_mizuta_luo_nishimiya_et al._2015, title={Ovarian yolk formation in fishes: Molecular mechanisms underlying formation of lipid droplets and vitellogenin-derived yolk proteins}, volume={221}, ISSN={["1095-6840"]}, DOI={10.1016/j.ygcen.2015.01.025}, abstractNote={Fish egg yolk is largely derived from vitellogenins, which are synthesized in the liver, taken up from the maternal circulation by growing oocytes via receptor-mediated endocytosis and enzymatically processed into yolk proteins that are stored in the ooplasm. Lipid droplets are another major component of fish egg yolk, and these are mainly composed of neutral lipids that may originate from maternal plasma lipoproteins. This review aims to briefly summarize our current understanding of the molecular mechanisms underlying yolk formation in fishes. A hypothetical model of oocyte growth is proposed based on recent advances in our knowledge of fish yolk formation.}, journal={GENERAL AND COMPARATIVE ENDOCRINOLOGY}, author={Hiramatsu, Naoshi and Todo, Takashi and Sullivan, Craig V. and Schilling, Justin and Reading, Benjamin J. and Matsubara, Takahiro and Ryu, Yong-Woon and Mizuta, Hiroko and Luo, Wenshu and Nishimiya, Osamu and et al.}, year={2015}, month={Sep}, pages={9–15} }
 @article{sullivan_chapman_reading_anderson_2015, title={Transcriptomics of mRNA and egg quality in farmed fish: Some recent developments and future directions}, volume={221}, ISSN={["1095-6840"]}, DOI={10.1016/j.ygcen.2015.02.012}, abstractNote={Maternal mRNA transcripts deposited in growing oocytes regulate early development and are under intensive investigation as determinants of egg quality. The research has evolved from single gene studies to microarray and now RNA-Seq analyses in which mRNA expression by virtually every gene can be assessed and related to gamete quality. Such studies have mainly focused on genes changing two- to several-fold in expression between biological states, and have identified scores of candidate genes and a few gene networks whose functioning is related to successful development. However, ever-increasing yields of information from high throughput methods for detecting transcript abundance have far outpaced progress in methods for analyzing the massive quantities of gene expression data, and especially for meaningful relation of whole transcriptome profiles to gamete quality. We have developed a new approach to this problem employing artificial neural networks and supervised machine learning with other novel bioinformatics procedures to discover a previously unknown level of ovarian transcriptome function at which minute changes in expression of a few hundred genes is highly predictive of egg quality. In this paper, we briefly review the progress in transcriptomics of fish egg quality and discuss some future directions for this field of study.}, journal={GENERAL AND COMPARATIVE ENDOCRINOLOGY}, author={Sullivan, Craig V. and Chapman, Robert W. and Reading, Benjamin J. and Anderson, Paul E.}, year={2015}, month={Sep}, pages={23–30} }
 @article{schilling_nepomuceno_schaff_muddiman_daniels_reading_2014, title={Compartment Proteomics Analysis of White Perch (Morone americana) Ovary Using Support Vector Machines}, volume={13}, ISSN={["1535-3907"]}, DOI={10.1021/pr401067g}, abstractNote={Compartment proteomics enable broad characterization of target tissues. We employed a simple fractionation method and filter-aided sample preparation (FASP) to characterize the cytosolic and membrane fractions of white perch ovary tissues by semiquantitative tandem mass spectrometry using label-free quantitation based on normalized spectral counts. FASP depletes both low-molecular-weight and high-molecular-weight substances that could interfere with protein digestion and subsequent peptide separation and detection. Membrane proteins are notoriously difficult to characterize due to their amphipathic nature and association with lipids. The simple fractionation we employed effectively revealed an abundance of proteins from mitochondria and other membrane-bounded organelles. We further demonstrate that support vector machines (SVMs) offer categorical classification of proteomics data superior to that of parametric statistical methods such as analysis of variance (ANOVA). Specifically, SVMs were able to perfectly (100% correct) classify samples as either membrane or cytosolic fraction during cross-validation based on the expression of 242 proteins with the highest ANOVA p-values (i.e., those that were not significant for enrichment in either fraction). The white perch ovary cytosolic and membrane proteomes and transcriptome presented in this study can support future investigations into oogenesis and early embryogenesis of white perch and other members of the genus Morone.}, number={3}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Schilling, Justin and Nepomuceno, Angelito and Schaff, Jennifer E. and Muddiman, David C. and Daniels, Harry V. and Reading, Benjamin J.}, year={2014}, month={Mar}, pages={1515–1526} }
 @article{reading_hiramatsu_schilling_molloy_glassbrook_mizuta_luo_baltzegar_williams_todo_et al._2014, title={Lrp13 is a novel vertebrate lipoprotein receptor that binds vitellogenins in teleost fishes}, volume={55}, ISSN={["1539-7262"]}, DOI={10.1194/jlr.m050286}, abstractNote={Transcripts encoding a novel member of the lipoprotein receptor superfamily, termed LDL receptor-related protein (Lrp)13, were sequenced from striped bass (Morone saxatilis) and white perch (Morone americana) ovaries. Receptor proteins were purified from perch ovary membranes by protein-affinity chromatography employing an immobilized mixture of vitellogenins Aa and Ab. RT-PCR revealed lrp13 to be predominantly expressed in striped bass ovary, and in situ hybridization detected lrp13 transcripts in the ooplasm of early secondary growth oocytes. Quantitative RT-PCR confirmed peak lrp13 expression in the ovary during early secondary growth. Quantitative mass spectrometry revealed peak Lrp13 protein levels in striped bass ovary during late-vitellogenesis, and immunohistochemistry localized Lrp13 to the oolemma and zona radiata of vitellogenic oocytes. Previously unreported orthologs of lrp13 were identified in genome sequences of fishes, chicken (Gallus gallus), mouse (Mus musculus), and dog (Canis lupus familiaris). Zebrafish (Danio rerio) and Nile tilapia (Oreochromis niloticus) lrp13 loci are discrete and share genomic synteny. The Lrp13 appears to function as a vitellogenin receptor and may be an important mediator of yolk formation in fishes and other oviparous vertebrates. The presence of lrp13 orthologs in mammals suggests that this lipoprotein receptor is widely distributed among vertebrates, where it may generally play a role in lipoprotein metabolism.}, number={11}, journal={JOURNAL OF LIPID RESEARCH}, author={Reading, Benjamin J. and Hiramatsu, Naoshi and Schilling, Justin and Molloy, Katelyn T. and Glassbrook, Norm and Mizuta, Hiroko and Luo, Wenshu and Baltzegar, David A. and Williams, Valerie N. and Todo, Takashi and et al.}, year={2014}, month={Nov}, pages={2287–2295} }
 @article{williams_reading_hiramatsu_amano_glassbrook_hara_sullivan_2014, title={Multiple vitellogenins and product yolk proteins in striped bass, Morone saxatilis: molecular characterization and processing during oocyte growth and maturation}, volume={40}, ISSN={["1573-5168"]}, DOI={10.1007/s10695-013-9852-0}, abstractNote={The multiple vitellogenin (Vtg) system of striped bass, a perciform species spawning nearly neutrally buoyant eggs in freshwater, was investigated. Vitellogenin cDNA cloning, Western blotting of yolk proteins (YPs) using Vtg and YP type-specific antisera, and tandem mass spectrometry (MS/MS) of the YPs revealed the complex mechanisms of yolk formation and maturation in this species. It was discovered that striped bass possesses a tripartite Vtg system (VtgAa, VtgAb, and VtgC) in which all three forms of Vtg make a substantial contribution to the yolk. The production of Vtg-derived YPs is generally similar to that described for other perciforms. However, novel amino-terminal labeling of oocyte YPs prior to MS/MS identified multiple alternative sites for cleavage of these proteins from their parent Vtg, revealing a YP mixture far more complex than reported previously. This approach also revealed that the major YP product of each form of striped bass Vtg, lipovitellin heavy chain (LvH), undergoes limited degradation to smaller polypeptides during oocyte maturation, unlike the case in marine fishes spawning buoyant eggs in which LvHAa undergoes extensive proteolysis to osmotically active free amino acids. These differences likely reflect the lesser need for hydration of pelagic eggs spawned in freshwater. The detailed characterization of Vtgs and their proteolytic fate(s) during oocyte growth and maturation establishes striped bass as a freshwater model for investigating teleost multiple Vtg systems.}, number={2}, journal={FISH PHYSIOLOGY AND BIOCHEMISTRY}, author={Williams, V. N. and Reading, B. J. and Hiramatsu, N. and Amano, H. and Glassbrook, N. and Hara, A. and Sullivan, C. V.}, year={2014}, month={Apr}, pages={395–415} }
 @article{chapman_reading_sullivan_2014, title={Ovary Transcriptome Profiling via Artificial Intelligence Reveals a Transcriptomic Fingerprint Predicting Egg Quality in Striped Bass, Morone saxatilis}, volume={9}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0096818}, abstractNote={Inherited gene transcripts deposited in oocytes direct early embryonic development in all vertebrates, but transcript profiles indicative of embryo developmental competence have not previously been identified. We employed artificial intelligence to model profiles of maternal ovary gene expression and their relationship to egg quality, evaluated as production of viable mid-blastula stage embryos, in the striped bass (Morone saxatilis), a farmed species with serious egg quality problems. In models developed using artificial neural networks (ANNs) and supervised machine learning, collective changes in the expression of a limited suite of genes (233) representing <2% of the queried ovary transcriptome explained >90% of the eventual variance in embryo survival. Egg quality related to minor changes in gene expression (<0.2-fold), with most individual transcripts making a small contribution (<1%) to the overall prediction of egg quality. These findings indicate that the predictive power of the transcriptome as regards egg quality resides not in levels of individual genes, but rather in the collective, coordinated expression of a suite of transcripts constituting a transcriptomic “fingerprint”. Correlation analyses of the corresponding candidate genes indicated that dysfunction of the ubiquitin-26S proteasome, COP9 signalosome, and subsequent control of the cell cycle engenders embryonic developmental incompetence. The affected gene networks are centrally involved in regulation of early development in all vertebrates, including humans. By assessing collective levels of the relevant ovarian transcripts via ANNs we were able, for the first time in any vertebrate, to accurately predict the subsequent embryo developmental potential of eggs from individual females. Our results show that the transcriptomic fingerprint evidencing developmental dysfunction is highly predictive of, and therefore likely to regulate, egg quality, a biologically complex trait crucial to reproductive fitness.}, number={5}, journal={PLOS ONE}, author={Chapman, Robert W. and Reading, Benjamin J. and Sullivan, Craig V.}, year={2014}, month={May} }
 @article{williams_reading_amano_hiramatsu_schilling_salger_williams_gross_sullivan_2014, title={Proportional Accumulation of Yolk Proteins Derived From Multiple Vitellogenins is Precisely Regulated During Vitellogenesis in Striped Bass (Morone saxatilis)}, volume={321}, ISSN={["2471-5646"]}, url={http://europepmc.org/abstract/med/24648375}, DOI={10.1002/jez.1859}, abstractNote={ABSTRACT}, number={6}, journal={JOURNAL OF EXPERIMENTAL ZOOLOGY PART A-ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY}, author={Williams, Valerie N. and Reading, Benjamin J. and Amano, Haruna and Hiramatsu, Naoshi and Schilling, Justin and Salger, Scott A. and Williams, Taufika Islam and Gross, Kevin and Sullivan, Craig V.}, year={2014}, month={Jul}, pages={301–315} }
 @article{baltzegar_reading_douros_borski_2014, title={Role for leptin in promoting glucose mobilization during acute hyperosmotic stress in teleost fishes}, volume={220}, ISSN={["1479-6805"]}, DOI={10.1530/joe-13-0292}, abstractNote={Osmoregulation is critical for survival in all vertebrates, yet the endocrine regulation of this metabolically expensive process is not fully understood. Specifically, the function of leptin in the regulation of energy expenditure in fishes, and among ectotherms, in general, remains unresolved. In this study, we examined the effects of acute salinity transfer (72 h) and the effects of leptin and cortisol on plasma metabolites and hepatic energy reserves in the euryhaline fish, the tilapia (Oreochromis mossambicus). Transfer to 2/3 seawater (23 ppt) significantly increased plasma glucose, amino acid, and lactate levels relative to those in the control fish. Plasma glucose levels were positively correlated with amino acid levels (R2=0.614), but not with lactate levels. The mRNA expression of liver leptin A (lepa), leptin receptor (lepr), and hormone-sensitive and lipoprotein lipases (hslandlpl) as well as triglyceride content increased during salinity transfer, but plasma free fatty acid and triglyceride levels remained unchanged. Both leptin and cortisol significantly increased plasma glucose levelsin vivo, but only leptin decreased liver glycogen levels. Leptin decreased the expression of liverhslandlplmRNAs, whereas cortisol significantly increased the expression of these lipases. These findings suggest that hepatic glucose mobilization into the blood following an acute salinity challenge involves both glycogenolysis, induced by leptin, and subsequent gluconeogenesis of free amino acids. This is the first study to report that teleost leptin A has actions that are functionally distinct from those described in mammals acting as a potent hyperglycemic factor during osmotic stress, possibly in synergism with cortisol. These results suggest that the function of leptin may have diverged during the evolution of vertebrates, possibly reflecting differences in metabolic regulation between poikilotherms and homeotherms.}, number={1}, journal={JOURNAL OF ENDOCRINOLOGY}, author={Baltzegar, David A. and Reading, Benjamin J. and Douros, Jonathon D. and Borski, Russell J.}, year={2014}, month={Jan}, pages={61–72} }
 @article{reading_williams_chapman_williams_sullivan_2013, title={Dynamics of the Striped Bass (Morone saxatilis) Ovary Proteome Reveal a Complex Network of the Translasome}, volume={12}, ISSN={1535-3893 1535-3907}, url={http://dx.doi.org/10.1021/PR3010293}, DOI={10.1021/pr3010293}, abstractNote={We evaluated changes in the striped bass (Morone saxatilis) ovary proteome during the annual reproductive cycle using label-free quantitative mass spectrometry and a novel machine learning analysis based on K-means clustering and support vector machines. Modulated modularity clustering was used to group co-variable proteins into expression modules and Gene Ontology (GO) biological process and KEGG pathway enrichment analyses were conducted for proteins within those modules. We discovered that components of the ribosome along with translation initiation and elongation factors generally decrease as the annual ovarian cycle progresses toward ovulation, concomitant with a slight increase in components of the 26S-proteasome. Co-variation within more than one expression module of components from these two multi-protein complexes suggests that they are not only co-regulated, but that co-regulation occurs through more than one sub-network. These components also co-vary with subunits of the TCP-1 chaperonin system and enzymes of intermediary metabolic pathways, suggesting that protein folding and cellular bioenergetic state play important roles in protein synthesis and degradation. We provide further evidence to suggest that protein synthesis and degradation are intimately linked, and our results support function of a proteasome-ribosome supercomplex known as the translasome.}, number={4}, journal={Journal of Proteome Research}, publisher={American Chemical Society (ACS)}, author={Reading, Benjamin J. and Williams, Valerie N. and Chapman, Robert W. and Williams, Taufika Islam and Sullivan, Craig V.}, year={2013}, month={Mar}, pages={1691–1699} }
 @article{luo_ito_mizuta_massaki_hiramatsu_todo_reading_sullivan_hara_2013, title={Molecular cloning and partial characterization of an ovarian receptor with seven ligand binding repeats, an orthologue of low-density lipoprotein receptor, in the cutthroat trout (Oncorhynchus clarki)}, volume={166}, DOI={10.1016/j.cbpa.2013.06.026}, abstractNote={Teleost fish eggs contain a substantial yolk mass consisting of lipids and proteins that provides essential nutrients for embryonic and larval development. The polar lipid and protein components of the yolk are delivered to oocytes by circulating vitellogenins, however the source(s) of the neutral lipid remains unknown. We cloned a cDNA encoding an orthologue of low-density-lipoprotein receptor (LDLR) from the ovary of cutthroat trout, Oncorhynchus clarki (ct-Ldlr). Predominant expression of ct-ldlr mRNA was observed in the ovary and moderate expression was detected in intestine, gill and brain. The relative abundance of ct-ldlr transcripts was highest in early pre-vitellogenic ovaries and significantly decreased during vitellogenesis, followed by a slight increase during final maturation and in post-ovulatory follicles. In situ hybridization revealed an intense and evenly distributed localization of ct-ldlr transcripts in the ooplasm of pre-vitellogenic oocytes and these signals disappeared in vitellogenic follicles. Collectively, these results suggest that the Ldlr is involved in deposition of yolk lipids in cutthroat trout oocytes. The ct-ldlr transcripts also were detected in theca and granulosa cells, suggesting that this receptor may be involved in cholesterol uptake for ovarian steroidogenesis. This is the first report on partial characterization of an ldlr orthologue in any fish species.}, number={2}, journal={Comparative Biochemistry and Physiology. A, Molecular & Integrative Physiology}, author={Luo, W. S. and Ito, Y. and Mizuta, H. and Massaki, K. and Hiramatsu, N. and Todo, T. and Reading, Benjamin and Sullivan, C. V. and Hara, A.}, year={2013}, pages={263–271} }
 @article{hiramatsu_luo_reading_sullivan_mizuta_ryu_nishimiya_todo_hara_2013, title={Multiple ovarian lipoprotein receptors in teleosts}, volume={39}, ISSN={["1573-5168"]}, DOI={10.1007/s10695-012-9612-6}, abstractNote={Recent investigations have revealed multiplicity in maternal yolk precursors and their corresponding ovarian lipoprotein receptors (LRs) in diverse oviparous vertebrates, including fishes. This mini-review describes further evidence for the system of fish egg yolk formation mediated by multiple ovarian LRs, which have been obtained by studies utilizing a combination of conventional molecular and biochemical analyses, and modern proteome and transcriptome technologies. A hypothetical "multiple ovarian LR" model is proposed based on our current and previous knowledge of fish yolk formation.}, number={1}, journal={FISH PHYSIOLOGY AND BIOCHEMISTRY}, author={Hiramatsu, N. and Luo, W. and Reading, B. J. and Sullivan, C. V. and Mizuta, H. and Ryu, Y. -W. and Nishimiya, O. and Todo, T. and Hara, A.}, year={2013}, month={Feb}, pages={29–32} }
 @article{mizuta_luo_ito_mushirobira_todo_hara_reading_sullivan_hiramatsu_2013, title={Ovarian expression and localization of a vitellogenin receptor with eight ligand binding repeats in the cutthroat trout (Oncorhynchus clarki)}, volume={166}, ISSN={["1879-1107"]}, DOI={10.1016/j.cbpb.2013.07.005}, abstractNote={A cDNA encoding a vitellogenin receptor with 8 ligand binding repeats (vtgr) was cloned from ovaries of the cutthroat trout, Oncorhynchus clarki. In situ hybridization and quantitative PCR analyses revealed that the main site of vtgr mRNA expression was the oocytes. Expression was strongly detected in perinucleous stage oocytes, gradually decreased as oocytes grew, and became hardly detectable in vitellogenic oocytes. A rabbit antibody (a-Vtgr) was raised against a recombinant Vtgr protein in order to immunologically detect and localize Vtgr within the ovarian follicles. Western blotting using a-Vtgr detected a bold band with an apparent mass of ~95-105kDa in an ovarian preparation that also bound Sakhalin taimen, Hucho perryi, vitellogenin in ligand blots. Immunohistochemistry using a-Vtgr revealed that the Vtgr was uniformly distributed throughout the ooplasm of perinucleolus stage oocytes, subsequently translocated to the periphery of lipid droplet stage oocytes, and became localized to the oolemma during vitellogenesis. We provide the first characterization of Vtgr at both the transcriptional and the translational levels in the cutthroat trout, and our results suggest that this receptor is involved in uptake of Vtg by oocytes of this species.}, number={1}, journal={COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY}, author={Mizuta, Hiroko and Luo, Wenshu and Ito, Yuta and Mushirobira, Yuji and Todo, Takashi and Hara, Akihiko and Reading, Benjamin J. and Sullivan, Craig V. and Hiramatsu, Naoshi}, year={2013}, month={Sep}, pages={81–90} }
 @article{baltzegar_reading_brune_borski_2013, title={Phylogenetic revision of the claudin gene family}, volume={11}, ISSN={["1876-7478"]}, DOI={10.1016/j.margen.2013.05.001}, abstractNote={Claudins are four-transmembrane proteins acting to collectively regulate paracellular movement of water and ions across cellular tight junctions in vertebrate tissues. Despite the prominence of zebrafish (Danio rerio) as a developmental model and the existence of an annotated genome, the diversity and evolutionary history of these claudins, with respect to other vertebrate groups, is poorly described. In this study, we identify 54 zebrafish claudins, including 24 that were previously unreported, and infer homology of the encoded polypeptide sequences with other vertebrate claudin groups using Bayesian phylogenetic analysis. In this analysis, 197 vertebrate claudin and claudin-like proteins were classified into discrete 'superclades' of related proteins. Based on these groupings, an interim reclassification is proposed, which will resolve ambiguity in the present nomenclature of several vertebrate models. Fifty-two of the 54 identified claudins were detected in cDNA preparations from whole, adult zebrafish, and 43 exhibited distinct tissue expression profiles. Despite prolific expansion of the claudin gene family in teleost genomes, these claudins can still be broadly separated into two functional groups: (1) "classic" claudins that characteristically contain an equal number of opposing, charged residues in the first extracellular loop (ECL1) and (2) "non-classic" claudins that typically have an ECL1 containing a variable number of charged residues. Functional analysis of these groups indicates that 'classic' claudins may act to reduce overall paracellular permeability to water and dissolved ions, whereas 'non-classic' claudins may constitute pores that facilitate selective ion permeability.}, journal={MARINE GENOMICS}, author={Baltzegar, David A. and Reading, Benjamin J. and Brune, Emily S. and Borski, Russell J.}, year={2013}, month={Sep}, pages={17–26} }
 @article{reading_chapman_schaff_scholl_opperman_sullivan_2012, title={An ovary transcriptome for all maturational stages of the striped bass (Morone saxatilis), a highly advanced perciform fish}, volume={5}, ISSN={1756-0500}, url={http://dx.doi.org/10.1186/1756-0500-5-111}, DOI={10.1186/1756-0500-5-111}, abstractNote={The striped bass and its relatives (genus Morone) are important fisheries and aquaculture species native to estuaries and rivers of the Atlantic coast and Gulf of Mexico in North America. To open avenues of gene expression research on reproduction and breeding of striped bass, we generated a collection of expressed sequence tags (ESTs) from a complementary DNA (cDNA) library representative of their ovarian transcriptome.Sequences of a total of 230,151 ESTs (51,259,448 bp) were acquired by Roche 454 pyrosequencing of cDNA pooled from ovarian tissues obtained at all stages of oocyte growth, at ovulation (eggs), and during preovulatory atresia. Quality filtering of ESTs allowed assembly of 11,208 high-quality contigs ≥ 100 bp, including 2,984 contigs 500 bp or longer (average length 895 bp). Blastx comparisons revealed 5,482 gene orthologues (E-value < 10-3), of which 4,120 (36.7% of total contigs) were annotated with Gene Ontology terms (E-value < 10-6). There were 5,726 remaining unknown unique sequences (51.1% of total contigs). All of the high-quality EST sequences are available in the National Center for Biotechnology Information (NCBI) Short Read Archive (GenBank: SRX007394). Informative contigs were considered to be abundant if they were assembled from groups of ESTs comprising ≥ 0.15% of the total short read sequences (≥ 345 reads/contig). Approximately 52.5% of these abundant contigs were predicted to have predominant ovary expression through digital differential display in silico comparisons to zebrafish (Danio rerio) UniGene orthologues. Over 1,300 Gene Ontology terms from Biological Process classes of Reproduction, Reproductive process, and Developmental process were assigned to this collection of annotated contigs.This first large reference sequence database available for the ecologically and economically important temperate basses (genus Morone) provides a foundation for gene expression studies in these species. The predicted predominance of ovary gene expression and assignment of directly relevant Gene Ontology classes suggests a powerful utility of this dataset for analysis of ovarian gene expression related to fundamental questions of oogenesis. Additionally, a high definition Agilent 60-mer oligo ovary 'UniClone' microarray with 8 × 15,000 probe format has been designed based on this striped bass transcriptome (eArray Group: Striper Group, Design ID: 029004).}, number={1}, journal={BMC Research Notes}, publisher={Springer Science and Business Media LLC}, author={Reading, Benjamin J and Chapman, Robert W and Schaff, Jennifer E and Scholl, Elizabeth H and Opperman, Charles H and Sullivan, Craig V}, year={2012}, pages={111} }
 @article{reading_hiramatsu_sullivan_2011, title={Disparate Binding of Three Types of Vitellogenin to Multiple Forms of Vitellogenin Receptor in White Perch}, volume={84}, ISSN={["1529-7268"]}, DOI={10.1095/biolreprod.110.087981}, abstractNote={Three types of white perch (Morone americana) vitellogenin (VtgAa, VtgAb, and VtgC) were purified, labeled with digoxigenin (DIG), and subjected to Vtg receptor (Vtgr) binding assays in 96-well plates coated with perch ovarian membrane proteins or to ligand blotting procedures. Binding specificity was evaluated by incubating membrane protein preparations with constant amounts of DIG-Vtg tracer (VtgAa, VtgAb, VtgC, or a mixture of VtgAa and VtgAb [VtgAa/b]) alone or in the presence of unlabeled Vtg ligands. At 250-fold excess molar concentration relative to the tracer, VtgAa and VtgAb were each able to displace only approximately 50% of bound DIG-VtgAa/b, but VtgAa/b could fully displace DIG-VtgAa and DIG-VtgAb under the same conditions. Over a broad range of excess molar ratios, unlabeled VtgAa and VtgAb each displaced their respective DIG-Vtg tracer much more effectively than each did the heterologous tracer (DIG-VtgAb and DIG-VtgAa, respectively). Ligand blotting revealed three forms of Vtgr, a large receptor (>212 kDa) that bound only to VtgAa and two smaller receptors (∼116 and ∼110.5 kDa) that bound preferentially to VtgAb. The VtgC did not specifically bind to ovarian membrane proteins in either assay. Collectively, these results indicate the presence of a system of multiple ovarian Vtgrs with disparate binding to the three types of Vtg present in higher-order teleosts (Acanthomorpha). To our knowledge, this is the first report on binding of multiple types of Vtg to multiple forms of Vtgr in any vertebrate.}, number={2}, journal={BIOLOGY OF REPRODUCTION}, author={Reading, Benjamin J. and Hiramatsu, Naoshi and Sullivan, Craig V.}, year={2011}, month={Feb}, pages={392–399} }
 @article{salger_reading_baltzegar_sullivan_noga_2011, title={Molecular characterization of two isoforms of piscidin 4 from the hybrid striped bass (Morone chrysops x Morone saxatilis)}, volume={30}, ISSN={["1095-9947"]}, DOI={10.1016/j.fsi.2010.10.009}, abstractNote={As one of the key components of innate immune system, piscidins are likely to play pivotal role in the first defense line in fish. Piscidins own multiple resistance activity. A novel piscidin 5-like type 4 was excavated from Larimichthys crocea (termed Lc-P5L4) liver transcriptome immuned by Cryptocaryon irritans, and upregulated at 7 days post infection when secondary bacterial infection occurred. In the study, we characterized the antibacterial activity of Lc-P5L4. The liquid growth inhibition assay detected the recombinant Lc-P5L4 (rLc-P5L) had potent antibacterial activity to Photobacterium damselae. Scanning electron microscope (SEM) observed the cell surface of P. damselae collapsed to form pit, and membrane of some bacteria ruptured after co-incubation with rLc-P5L. Further, transmission electron microscope (TEM) was also employed to observe the intracellular microstructural damage, rLc-P5L4 caused cytoplasm contraction, pores formation and contents leakage. After knowing about its antibacterial effects, the preliminary antibacterial mechanism was also explored, western blot analysis showed rLc-P5L4 could bind to P. damselae through targeting to LPS. Agarose gel eletrophoresis analysis further showed rLc-P5L4 could also penetrate into cells and brought about genome DNA degradation. Therefore, rLc-P5L4 was of potential being a candidate to explore new antimicrobial drug or additive agent, especially to P. damselae.}, number={1}, journal={FISH & SHELLFISH IMMUNOLOGY}, author={Salger, Scott A. and Reading, Benjamin J. and Baltzegar, David A. and Sullivan, Craig V. and Noga, Edward J.}, year={2011}, month={Jan}, pages={420–424} }
 @inbook{reading_sullivan_2011, place={London}, title={Vitellogenesis in Fishes}, booktitle={Encyclopedia of Fish Physiology: From Genome to Environment}, publisher={Elsevier}, author={Reading, B.J. and Sullivan, C.V.}, editor={Farrell, A.P.Editor}, year={2011}, pages={635–646} }
 @misc{reading_hiramatsu_sawaguchi_matsubara_hara_lively_sullivan_2009, title={Conserved and Variant Molecular and Functional Features of Multiple Egg Yolk Precursor Proteins (Vitellogenins) in White Perch (Morone americana) and other Teleosts}, volume={11}, ISSN={["1436-2236"]}, DOI={10.1007/s10126-008-9133-6}, abstractNote={Three complete cDNAs encoding different forms of vitellogenin (Vtg) were isolated from a white perch (Morone americana) liver cDNA library and characterized with respect to immunobiochemical and functional features of the three Vtgs and their product yolk proteins (YPs) in this species and in the congeneric striped bass (Morone saxatilis). The two longest cDNAs encoded Vtgs with a complete suite of yolk protein domains that, based on comparisons with vtg sequences from other species, were categorized as VtgAa and VtgAb using the current nomenclature for multiple teleost Vtgs. The shorter cDNA encoded a Vtg that lacked a phosvitin domain, had a shortened C-terminus, and was categorized as VtgC. Mapping of peptide sequences from the purified Vtgs and their derived YPs to Vtg sequences deduced from the cDNAs definitively identified the white perch VtgAa, VtgAb, and VtgC proteins. Detailed comparisons of the primary structures of each Vtg with partial or complete sequences of Morone yolk proteins or of Vtgs from other fishes revealed conserved and variant structural elements of teleost Vtgs with functional significance, including, as examples, signal peptide cleavage sites, dimerization sites, cathepsin D protease recognition sites, and receptor-binding domains. These comparisons also yielded an interim revision of the classification scheme for multiple teleost Vtgs.}, number={2}, journal={MARINE BIOTECHNOLOGY}, author={Reading, Benjamin J. and Hiramatsu, Naoshi and Sawaguchi, Sayumi and Matsubara, Takahiro and Hara, Akihiko and Lively, Mark O. and Sullivan, Craig V.}, year={2009}, month={Apr}, pages={169–187} }
 @inproceedings{reading_hiramatsu_matsubara_hara_sullivan_2008, title={Deduced primary structures of three vitellogenins and specific binding to putative multiple ovarian receptors in white perch (Morone americana)}, volume={32}, number={2}, booktitle={Cybium}, author={Reading, B. J. and Hiramatsu, N. and Matsubara, T. and Hara, A. and Sullivan, C. V.}, year={2008}, pages={159–161} }
 @article{davis_hiramatsu_hiramatsu_reading_matsubara_hara_sullivan_pierce_hirano_grau_2007, title={Induction of three vitellogenins by 17beta-estradiol with concurrent inhibition of the growth hormone-insulin-like growth factor 1 axis in a euryhaline teleost, the tilapia (Oreochromis mossambicus)}, volume={77}, ISSN={["1529-7268"]}, DOI={10.1095/biolreprod.107.060947}, abstractNote={Abstract The objective of the present study was to utilize the male Mozambique tilapia (Oreochromis mossambicus) as a model for examining the molecular mechanisms that mediate the physiological transition between somatic and gonadal growth in female teleost fish, and in vertebrates in general. Partial cDNAs that encode multiple forms of vitellogenin (Vtg), which is the major precursor of yolk proteins, were cloned from estrogen-treated males and utilized to develop real-time quantitative RT-PCR assays, which were supplemented by an assay for Vtg immunoreactivity in the plasma. Alignment analyses of the amino acid sequences deduced from the vtg cDNAs revealed three distinct tilapia Vtgs, which were categorized as Aa-, Ab-, and C-type Vtgs. A single injection of male tilapias with 17beta-estradiol (E2) at 5 μg/g body weight significantly increased the plasma E2 and hepatic levels of all three vtg transcripts within 1 day. Plasma E2 levels declined after 3 days, whereas the plasma Vtg immunoreactivity and hepatic levels of the three vtg transcripts continued to increase. Hepatic expression of the estrogen receptor (esr) 1 gene, but not the esr2 gene, also increased markedly 1 day after E2 injection and remained elevated for 5 days. While plasma growth hormone (Gh) levels were unaffected, hepatic expression of transcripts that encoded the Gh receptor and insulin-like growth factor 1 (Igf1) was suppressed by E2, as were the plasma Igf1 levels. These results clearly suggest a distinct negative interplay between the growth and reproductive axes at the molecular level of key hepatic regulatory pathways involved in the control of energy utilization by gonadal and somatic growth processes.}, number={4}, journal={BIOLOGY OF REPRODUCTION}, author={Davis, Lori K. and Hiramatsu, Naoshi and Hiramatsu, Kaori and Reading, Benjamin J. and Matsubara, Takahiro and Hara, Akihiko and Sullivan, Craig V. and Pierce, Andrew L. and Hirano, Tetsuya and Grau, Gordon}, year={2007}, month={Oct}, pages={614–625} }
 @article{reading_wills_heidinger_heist_2003, title={Development of microsatellite markers for muskellunge (Esox masquinongy) and cross-species amplification in two other esocids}, volume={3}, ISSN={1471-8278 1471-8286}, url={http://dx.doi.org/10.1046/j.1471-8286.2003.00479.x}, DOI={10.1046/j.1471-8286.2003.00479.x}, abstractNote={AbstractWe report the development of seven polymorphic microsatellite loci in muskellunge ( Esoxmasquinongy ) using an unenriched subgenomic library. Polymorphic loci exhibited 2–11alleles with observed heterozygosities ranging from 0.190 to 0.917 ( n = 24). All seven lociamplified by their respective primer pairs resulted in monomorphic products in northernpike ( E. lucius ) whereas three loci amplified monomorphic products in grass pickerel( E. americanus americanus ); these results imply conservation of flanking sequence butloss of polymorphism between these closely related species. Only one of six microsatelliteprimers developed in a previous study in northern pike amplified polymorphic productsin muskellunge. Keywords : Esox , grass pickerel, microsatellite, muskellunge, northern pike Received 17 February 2003; revision received 14 May 2003; accepted 14 May 2003 The muskellunge ( Esox masquinongy ) is a large predatoryfish common to lakes and large rivers in northern USand Canada. Despite the important ecological role that themuskellunge plays as the apex predator in many fresh-water ecosystems and the value of the species to recre-ational fisheries there has been very little investigationof the genetic population structure of this species. In theonly published study of muskellunge genetic variationKoppleman & Philipp (1986) found significant variation atseveral allozyme markers between muskellunge fromwidespread localities within North America. The potentialfor genetic stock structure may be of particular importanceconsidering the widespread stocking of muskellungethroughout North America. Microsatellites have beenisolated for the northern pike (}, number={3}, journal={Molecular Ecology Notes}, publisher={Wiley}, author={Reading, Benjamin J. and Wills, Paul S. and Heidinger, Roy C. and Heist, Edward J.}, year={2003}, month={Sep}, pages={447–449} }
 @article{heist_jenkot_keeney_lane_moyer_reading_smith_2003, title={Isolation and characterization of polymorphic microsatellite loci in nurse shark (Ginglymostoma cirratum)}, volume={3}, ISSN={1471-8278 1471-8286}, url={http://dx.doi.org/10.1046/j.1471-8286.2003.00348.x}, DOI={10.1046/j.1471-8286.2003.00348.x}, abstractNote={We report on the development of nine polymorphic microsatellite loci in nurse shark ( Ginglymostoma cirratum ) using a combination of enriched and unenriched subgenomic libraries. Based on the small percentage of positive clones in the unenriched library (0.4%) it appears that microsatellites are very scarce in nurse shark genomes. Numbers of alleles at polymorphic loci ranged from two to 15; observed heterozygosity ranged from 0.17 to 0.90. We expect these loci to be useful for studies of breeding structure and paternity.}, number={1}, journal={Molecular Ecology Notes}, publisher={Wiley}, author={Heist, Edward J. and Jenkot, Jennifer L. and Keeney, Devon B. and Lane, Ryan L. and Moyer, Gregory R. and Reading, Benjamin J. and Smith, Noelle L.}, year={2003}, month={Jan}, pages={59–61} }