TY - JOUR TI - Enhanced biodiversity of gut flora and feed efficiency in pond cultured tilapia under reduced frequency feeding strategies AU - Salger, Scott A. AU - Reza, Jimi AU - Deck, Courtney A. AU - Wahab, Md Abdul AU - Baltzegar, David A. AU - Murr, Alexander T. AU - Borski, Russell J. T2 - PLOS ONE AB - Feed constitutes 50-70% of total production costs of tilapia, one of the most widely cultured finfishes in the world. We evaluated reduced-feeding strategies for improving production efficiency of Nile tilapia (Oreochromis niloticus). In a 12-week pond trial, fish were fed daily, every other day, every third day, or not at all. Ponds were fertilized to enhance natural foods. In a fifth group fish were fed daily without pond fertilization. Fish fed daily with or without pond fertilization and fish fed every other day had higher specific growth rates, survivability, and net production than the other two treatments. Fish feed efficiency and benefit to cost ratio was highest for treatments fed in a pulsatile manner (i.e. fed every other day or every third day) with fish fed on alternate days providing the best net return among all groups. Fish fed on alternate days had more moderate gene expression levels of intestinal nutrient transporters which may allow for a more balanced and efficient nutrient uptake. Fecal microbe analyses identified 145 families of prokaryotic and 132 genera of eukaryotic organisms in tilapia. The highest diversity of prokaryotes was found in fish fed either every other day or daily in fertilized ponds and the highest diversity of eukaryotes was found in fish fed every other day. These studies indicate feeding Nile tilapia on alternate days along with weekly pond fertilization has no deleterious effects on growth, survivability, or production versus daily feeding regimes, but enhances feed efficiency by 76% and provides the greatest net return on investments. Our studies also suggest for the first time that combining alternate-day feeding with pond fertilization produces the greatest microbial biodiversity in the intestine that could contribute to enhanced feed efficiency and overall health of tilapia. DA - 2020/7/23/ PY - 2020/7/23/ DO - 10.1371/journal.pone.0236100 VL - 15 IS - 7 SP - SN - 1932-6203 ER - TY - JOUR TI - Transcriptional regulation ofprolactinin a euryhaline teleost: Characterisation of gene promoters through in silico and transcriptome analyses AU - Seale, Andre P. AU - Malintha, Gardi Hewage Tharindu AU - Celino-Brady, Fritzie T. AU - Head, Tony AU - Belcaid, Mahdi AU - Yamaguchi, Yoko AU - Lerner, Darren T. AU - Baltzegar, David A. AU - Borski, Russell J. AU - Stoytcheva, Zoia R. AU - Breves, Jason P. T2 - JOURNAL OF NEUROENDOCRINOLOGY AB - The sensitivity of prolactin (Prl) cells of the Mozambique tilapia (Oreochromis mossambicus) pituitary to variations in extracellular osmolality enables investigations into how osmoreception underlies patterns of hormone secretion. Through the actions of their main secretory products, Prl cells play a key role in supporting hydromineral balance of fishes by controlling the major osmoregulatory organs (ie, gill, intestine and kidney). The release of Prl from isolated cells of the rostral pars distalis (RPD) occurs in direct response to physiologically relevant reductions in extracellular osmolality. Although the particular signal transduction pathways that link osmotic conditions to Prl secretion have been identified, the processes that underlie hyposmotic induction of prl gene expression remain unknown. In this short review, we describe two distinct tilapia gene loci that encode Prl177 and Prl188 . From our in silico analyses of prl177 and prl188 promoter regions (approximately 1000 bp) and a transcriptome analysis of RPDs from fresh water (FW)- and seawater (SW)-acclimated tilapia, we propose a working model for how multiple transcription factors link osmoreceptive processes with adaptive patterns of prl177 and prl188 gene expression. We confirmed via RNA-sequencing and a quantitative polymerase chain reaction that multiple transcription factors emerging as predicted regulators of prl gene expression are expressed in the RPD of tilapia. In particular, gene transcripts encoding pou1f1, stat3, creb3l1, pbxip1a and stat1a were highly expressed; creb3l1, pbxip1a and stat1a were elevated in fish acclimated to SW vs FW. Combined, our in silico and transcriptome analyses set a path for resolving how adaptive patterns of Prl secretion are achieved via the integration of osmoreceptive processes with the control of prl gene transcription. DA - 2020/11// PY - 2020/11// DO - 10.1111/jne.12905 VL - 32 IS - 11 SP - SN - 1365-2826 KW - in silico KW - osmoreception KW - prolactin KW - promoter KW - salinity KW - tilapia KW - transcription factor KW - transcriptome ER - TY - JOUR TI - Differential chromatin accessibility landscape reveals structural and functional features of the allopolyploid wheat chromosomes AU - Jordan, Katherine W. AU - He, Fei AU - Soto, Monica Fernandez AU - Akhunova, Alina AU - Akhunov, Eduard T2 - GENOME BIOLOGY AB - Abstract Background Our understanding of how the complexity of the wheat genome influences the distribution of chromatin states along the homoeologous chromosomes is limited. Using a differential nuclease sensitivity assay, we investigate the chromatin states of the coding and repetitive regions of the allopolyploid wheat genome. Results Although open chromatin is found to be significantly enriched around genes, the majority of MNase-sensitive regions are located within transposable elements (TEs). Chromatin of the smaller D genome is more accessible than that of the larger A and B genomes. Chromatin states of different TEs vary among families and are influenced by the TEs’ chromosomal position and proximity to genes. While the chromatin accessibility of genes is influenced by proximity to TEs, and not by their position on the chromosomes, we observe a negative chromatin accessibility gradient along the telomere-centromere axis in the intergenic regions, positively correlated with the distance between genes. Both gene expression levels and homoeologous gene expression bias are correlated with chromatin accessibility in promoter regions. The differential nuclease sensitivity assay accurately predicts previously detected centromere locations. SNPs located within more accessible chromatin explain a higher proportion of genetic variance for a number of agronomic traits than SNPs located within more closed chromatin. Conclusions Chromatin states in the wheat genome are shaped by the interplay of repetitive and gene-encoding regions that are predictive of the functional and structural organization of chromosomes, providing a powerful framework for detecting genomic features involved in gene regulation and prioritizing genomic variation to explain phenotypes. DA - 2020/7/19/ PY - 2020/7/19/ DO - 10.1186/s13059-020-02093-1 VL - 21 IS - 1 SP - SN - 1474-760X KW - Chromatin accessibility KW - Transposable elements KW - Polyploid wheat KW - MNase KW - DNS-seq KW - Centromere KW - Genome-to-phenome ER -