RNAseq analysis of fast skeletal muscle in restriction-fed transgenic coho salmon (Oncorhynchus kisutch) : an experimental model uncoupling the growth hormone and nutritional signals regulating growth

Background Coho salmon (Oncorhynchus kisutch) transgenic for growth hormone (Gh) express Gh in multiple tissues which results in increased appetite and continuous high growth with satiation feeding. Restricting Gh-transgenics to the same lower ration (TR) as wild-type fish (WT) results in similar growth, but with the recruitment of fewer, larger diameter, muscle skeletal fibres to reach a given body size. In order to better understand the genetic mechanisms behind these different patterns of muscle growth and to investigate how the decoupling of Gh and nutritional signals affects gene regulation we used RNA-seq to compare the fast skeletal muscle transcriptome in TR and WT coho salmon. Results Illumina sequencing of individually barcoded libraries from 6 WT and 6 TR coho salmon yielded 704,550,985 paired end reads which were used to construct 323,115 contigs containing 19,093 unique genes of which >10,000 contained >90 % of the coding sequence. Transcripts coding for 31 genes required for myoblast fusion were identified with 22 significantly downregulated in TR relative to WT fish, including 10 (vaspa, cdh15, graf1, crk, crkl, dock1, trio, plekho1a, cdc42a and dock5) associated with signaling through the cell surface protein cadherin. Nineteen out of 44 (43 %) translation initiation factors and 14 of 47 (30 %) protein chaperones were upregulated in TR relative to WT fish. Conclusions TR coho salmon showed increased growth hormone transcripts and gene expression associated with protein synthesis and folding than WT fish even though net rates of protein accretion were similar. The uncoupling of Gh and amino acid signals likely results in additional costs of transcription associated with protein turnover in TR fish. The predicted reduction in the ionic costs of homeostasis in TR fish associated with increased fibre size were shown to involve multiple pathways regulating myotube fusion, particularly cadherin signaling.Publisher PDFPeer reviewe

Cardiac myoglobin deficit has evolved repeatedly in teleost fishes

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Stallion sperm quality after combined ejaculate fractionation and colloidal centrifugation

This study investigated the possible additive benefit of ejaculate fractionation and colloidal centrifugation on stallion sperm quality. Using an open-end artificial vagina, the sperm-rich fraction (FRAC-1) was separated from the rest of the ejaculate (FRAC-2) and a third sperm sample representing the combined ejaculate was reconstituted post-ejaculation (RAW). Each semen sample was processed for colloidal centrifugation. The percentage of abnormal spermatozoa was 17.8 ± 7.0% in RAW and 14.6 ± 9.5% in FRAC-1 but decreased to 11.4 ± 4.7% and 9.6 ± 6.9% respectively, after colloidal centrifugation. A sperm DNA fragmentation index of 10.9 ± 5.1% was observed in RAW and 7.5 ± 2.4% in FRAC-1 semen collected with the AV but this decreased to 7.8 ± 2.8% and 5.2 ± 2.3% after colloidal centrifugation. The rate of increase in sperm DNA fragmentation during the first 6 h of incubation at 37 ºC was 1.8 ± 0.9% per hour in RAW semen and 2.0 ± 2.0% per hour in FRAC-1 but this significantly decreased to 1.3 ± 1.4% and 0.9 ± 0.8% respectively after colloidal centrifugation. While stallion seminal characteristics can be improved using colloidal centrifugation, further enhancement is possible if the ejaculate is initially fractionatedThis research was supported by the Spanish Ministry of Economy and Competitiveness, MINECO (BFU-2013-44290-R

Muscle fibre size optimisation provides flexibility for energy budgeting in calorie-restricted coho salmon transgenic for growth hormone

The study was supported by the Marine Alliance for Science and Technology for Scotland (Scottish Funding Council grant HR09011) and by the Canadian Biotechnology Strategy (to R.H.D.). Deposited in PMC for immediate releaseCoho salmon (Oncorhynchus kisutch) transgenic for growth hormone (GH) show substantially faster growth than wild-type (WT) fish. We fed GH-transgenic salmon either to satiation (1 year; TF) or the same smaller ration of wild-type fish (2 years; TR), resulting in groups matched for body size to WT salmon. The myotomes of TF and WT fish had the same number and size distribution of muscle fibres, indicating a twofold higher rate of fibre recruitment in the GH transgenics. Unexpectedly, calorie restriction was found to decrease the rate of fibre production in transgenics, resulting in a 20% increase in average fibre size and reduced costs of ionic homeostasis. Genes for myotube formation were downregulated in TR relative to TF and WT fish. We suggest that muscle fibre size optimisation allows the reallocation of energy from maintenance to locomotion, explaining the observation that calorie-restricted transgenics grow at the same rate as WT fish whilst exhibiting markedly higher foraging activity.Publisher PDFPeer reviewe

Exploring the fate of cattle herds with inconclusive reactors to the tuberculin skin test

Bovine tuberculosis (TB) is an important animal health issue in many parts of the world. In England and Wales, the primary test to detect infected animals is the single intradermal comparative cervical tuberculin test, which compares immunological responses to bovine and avian tuberculins. Inconclusive test reactors (IRs) are animals that demonstrate a positive reaction to the bovine tuberculin only marginally greater than the avian reaction, so are not classified as reactors and immediately removed. In the absence of reactors in the herd, IRs are isolated, placed under movement restrictions and re-tested after 60 days. Other animals in these herds at the time of the IR result are not usually subject to movement restrictions. This could affect efforts to control TB if undetected infected cattle move out of those herds before the next TB test. To improve our understanding of the importance of IRs, this study aimed to assess whether median survival time and the hazard of a subsequent TB incident differs in herds with only IRs detected compared with negative-testing herds. Survival analysis and extended Cox regression were used, with herds entering the study on the date of the first whole herd test in 2012. An additional analysis was performed using an alternative entry date to try to remove the impact of IR retesting and is presented in the Supplementary Material. Survival analysis showed that the median survival time among IR only herds was half that observed for clear herds (2.1 years and 4.2 years respectively; p < 0.001). Extended Cox regression analysis showed that IR-only herds had 2.7 times the hazard of a subsequent incident compared with negative-testing herds in year one (hazard ratio: 2.69; 95% CI: 2.54, 2.84; p < 0.001), and that this difference in the hazard reduced by 63% per year. After 2.7 years the difference had disappeared. The supplementary analysis supported these findings showing that IR only herds still had a greater hazard of a subsequent incident after the IR re-test, but that the effect was reduced. This emphasizes the importance of careful decision making around the management of IR animals and indicates that re-testing alone may not be sufficient to reduce the risk posed by IR only herds in England and Wales

Seasonal associations with light pollution trends for nocturnally migrating bird populations

This project was supported by The Leon Levy Foundation, The Wolf Creek Charitable Foundation, Lyda Hill Philanthropies, Amon G. Carter Foundation, National Aeronautics and Space Administration (80NSSC21K1143), and National Science Foundation (ABI sustaining DBI-1939187, GCR-2123405). Computing support was provided by the National Science Foundation (CNS-1059284 and CCF-1522054), and the Extreme Science and Engineering Discovery Environment (XSEDE; National Science Foundation, ACI-1548562) through allocation TG-DEB200010 run on Bridges at the Pittsburgh Supercomputing Center.Artificial light at night (ALAN) is adversely affecting natural systems worldwide, including the disorienting influence of ALAN on nocturnally migrating birds. Understanding how ALAN trends are developing across species' seasonal distributions will inform mitigation efforts, such as Lights Out programs. Here, we intersect ALAN annual trend estimates (1992-2013) with weekly estimates of relative abundance for 42 nocturnally migrating passerine bird species that breed in North America using observations from the eBird community science database for the combined period 2005-2020. We use a cluster analysis to identify species with similar weekly associations with ALAN trends. Our results identified three prominent clusters. Two contained species that occurred in northeastern and western North America during the breeding season. These species were associated with moderate ALAN levels and weak negative ALAN trends during the breeding season, and low ALAN levels and strong positive ALAN trends during the nonbreeding season. The difference between the breeding and nonbreeding seasons was lower for species that occurred in northern South America and greater for species that occurred in Central America during the nonbreeding season. For species that occurred in South America during the nonbreeding season, positive ALAN trends increased in strength as species migrated through Central America, especially in the spring. The third cluster contained species whose associations with positive ALAN trends remained high across the annual cycle, peaking during migration, especially in the spring. These species occurred in southeastern North America during the breeding season where they were associated with high ALAN levels, and in northern South America during the nonbreeding season where they were associated with low ALAN levels. Our findings suggest reversing ALAN trends in Central America during migration, especially in the spring, would benefit the most individuals of the greatest number of species. Reversing ALAN trends in southeastern North America during the breeding season and Central America during the nonbreeding season would generate the greatest benefits outside of migration.Publisher PDFPeer reviewe

Jazz: A Jam Session

This is the poster for the Jazz Jam Session held on November 17, 2023, in Dr. Jack\u27s Coffee House. The session featured Dr. Austin Motley on trombone, pianist Kristen La Madrid, Dr. Bruce Johnston on bass, and Dr. Ryan Lewis on drums

Characterization of the transcriptome of fast and slow muscle myotomal fibres in the pacu (Piaractus mesopotamicus)

MDPS and EAM were supported by FAPESP, Proc. n° 12/02489-4 and 2011/09346-1. This work also received funding from CAPES, Proc. n° 2524/12. IAJ and DGDLS were supported by the Marine Alliance for Science and Technology for Scotland pooling initiative and Scottish Funding Council grant number HR09011.Background: The Pacu (Piaractus mesopotamicus) is a member of the Characiform family native to the Prata Basin (South America) and a target for the aquaculture industry. A limitation for the development of a selective breeding program for this species is a lack of available genetic information. The primary objectives of the present study were 1) to increase the genetic resources available for the species, 2) to exploit the anatomical separation of myotomal fibres types to compare the transcriptomes of slow and fast muscle phenotypes and 3) to systematically investigate the expression of Ubiquitin Specific Protease (USP) family members in fast and slow muscle in response to fasting and refeeding. Results: We generated 0.6 Tb of pair-end reads from slow and fast skeletal muscle libraries. Over 665 million reads were assembled into 504,065 contigs with an average length of 1,334 bp and N50=2,772 bp. We successfully annotated nearly 47% of the transcriptome and identified around 15,000 unique genes and over 8000 complete coding sequences. 319 KEGG metabolic pathways were also annotated and 380 putative microsatellites were identified. 956 and 604 genes were differentially expressed between slow and fast skeletal muscle, respectively. 442 paralogues pairs arising from the teleost-specific whole genome duplication were identified, with the majority showing different expression patterns between fibres types (301 in slow and 245 in fast skeletal muscle). 45 members of the USP family were identified in the transcriptome. Transcript levels were quantified by qPCR in a separate fasting and refeeding experiment. USP genes in fast muscle showed a similar transient increase in expression with fasting as the better characterized E3 ubiquitin ligases. Conclusion: We have generated a 53-fold coverage transcriptome for fast and slow myotomal muscle in the pacu (Piaractus mesopotamicus) significantly increasing the genetic resources available for this important aquaculture species. We describe significant differences in gene expression between muscle fibre types for fundamental components of general metabolism, the Pi3k/Akt/mTor network and myogenesis, including detailed analysis of paralogue expression. We also provide a comprehensive description of USP family member expression between muscle fibre types and with changing nutritional status.Publisher PDFPeer reviewe

Association of polymorphisms in genes coding for antioxidant enzymes and human male infertility

This is the peer reviewed version of the following article: Annals of Human Genetics 83.1 (2019): 63-72, which has been published in final form at https://doi.org/10.1111/ahg.12286. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived VersionsPurpose: Although oxidative stress is thought to be an important cause of male infertility, primarily due to DNA and cell membrane damage, little is known about the genetic causes underlying suboptimal function of the seminal enzymatic antioxidant system. The aim of this study was to investigate the relationship of four potentially functional polymorphisms associated with oxidative stress pathway genes (superoxide dismutase—SOD2 lle58Thr and SOD2 rs4880, catalase—CAT C-262T, glutathione peroxidase 1—GPX1 Pro200Leu) and two null variants of the glutathione S transferase (GSTT and GSTM) genes and infertility risk. Methods: A case control study was conducted on 313 infertile patients and 80 fertile donors. Each ejaculate was subjected to a seminal analysis that included the classical parameters seminal volume, sperm concentration, sperm motility, and sperm morphology, as well as sperm DNA fragmentation (patients only). Polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) and PCR multiplex methods were carried out for genotyping. Results: Statistically significant differences were found between fertile donors and infertile patients for SNP CAT C-262T; the CC genotype was related with a twofold increased risk of infertility (odds ratio [OR] = 2.262; 95% confidence interval [CI] = 1.369–3.733; P = 0.001), whereas the CT genotype was associated with a protective effect (OR = 0.401; 95% CI = 0.241–0.667; P = 0.001). Surprisingly, the SOD2 Ile58ssThr SNP was not represented in the sample population, so its frequency in the current population frequenting fertility clinics in Madrid may be very low. Conclusions: Our results suggest that the CAT SNP C-262T is potentially associated with an increased risk of male infertilityThe Ministry of Economy, Industry and Competitiveness of Spain supported this stud