Environmental DNA-based biodiversity profiling along the Houdong River in north-eastern Taiwan.

Background: This paper describes two datasets: species occurrences, which were determined by environmental DNA (eDNA) metabarcoding and their associated DNA sequences, originating from a research project which was carried out along the Houdong River (), Jiaoxi Township, Yilan, Taiwan. The Houdong River begins at an elevation of 860 m and flows for approximately 9 km before it empties into the Pacific Ocean. Meandering through mountains, hills, plains and alluvial valleys, this short river system is representative of the fluvial systems in Taiwan. The primary objective of this study was to determine eukaryotic species occurrences in the riverine ecosystem through the use of the eDNA analysis. The second goal was, based on the current dataset, to establish a metabarcoding eDNA data template that will be useful and replicable for all users, particularly the Taiwan community. The species occurrence data are accessible at the Global Biodiversity Information Facility (GBIF) portal and its associated DNA sequences have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI, respectively. A total of 12 water samples from the study yielded an average of 1.5 million reads. The subsequent species identification from the collected samples resulted in the classification of 432 Operational Taxonomic Units (OTUs) out of a total of 2,734. Furthermore, a total of 1,356 occurrences with taxon matches in GBIF were documented (excluding 4,941 incertae sedis, accessed 05-12-2023). These data will be of substantial importance for future species and habitat monitoring within the short river, such as assessment of biodiversity patterns across different elevations, zonations and time periods and its correlation to water quality, land uses and anthropogenic activities. Further, these datasets will be of importance for regional ecological studies, in particular the freshwater ecosystem and its status in the current global change scenarios. New information: The datasets are the first species diversity description of the Houdong River system using either eDNA or traditional monitoring processes.

Gluconeogenesis in the extraembryonic yolk syncytial layer of the zebrafish embryo.

Yolk-consuming (lecithotrophic) embryos of oviparous animals, such as those of fish, need to make do with the maternally derived yolk. However, in many cases, yolk possesses little carbohydrates and sugars, including glucose, the essential monosaccharide. Interestingly, increases in the glucose content were found in embryos of some teleost fishes; however, the origin of this glucose has been unknown. Unveiling new metabolic strategies in fish embryos has a potential for better aquaculture technologies. In the present study, using zebrafish, we assessed how these embryos obtain the glucose. We employed stable isotope (13C)-labeled substrates and injected them to the zebrafish embryos. Our liquid chromatography-mass spectrometry-based isotope tracking revealed that among all tested substrate, glutamate was most actively metabolized to produce glucose in the zebrafish embryos. Expression analysis for gluconeogenic genes found that many of these were expressed in the yolk syncytial layer (YSL), an extraembryonic tissue found in teleost fishes. Generation 0 (G0) knockout of pck2, a gene encoding the key enzyme for gluconeogenesis from Krebs cycle intermediates, reduced gluconeogenesis from glutamate, suggesting that this gene is responsible for gluconeogenesis from glutamate in the zebrafish embryos. These results showed that teleost YSL undergoes gluconeogenesis, likely contributing to the glucose supplementation to the embryos with limited glucose source. Since many other animal lineages lack YSL, further comparative analysis will be interesting.

Anthropogenic nitrogen pollution inferred by stable isotope records of crustose coralline algae.

Since reef ecosystems can offer intricate habitats for various marine organisms, calcified reefs may contain valuable long-term environmental data. This study investigated stable isotopic composition of marine organisms from the Taoyuan and Linshanbi crustose coralline algae (CCA) reef ecosystems to understand sewage pollution. CCA samples from Taoyuan (Palaeo Xin A: ∼1000 years old and Palaeo G: ∼7000 years old) and Linshanbi (Palaeo L: ∼7000 years old and modern CCA) had significantly lower δ15N values (2.5-5.6 ‰) compared to modern CCA from Taoyuan (10.2 ± 1.2 ‰). Intertidal organisms from the Taoyuan CCA reef also showed higher δ15N values than those from Linshanbi CCA reef, indicating anthropogenic stress in both ecosystems. Long-term pollution monitoring and effective strategies to mitigate sewage pollution are recommended for these CCA reef ecosystems.

Single-worm long-read sequencing reveals genome diversity in free-living nematodes.

Obtaining sufficient genetic material from a limited biological source is currently the primary operational bottleneck in studies investigating biodiversity and genome evolution. In this study, we employed multiple displacement amplification (MDA) and Smartseq2 to amplify nanograms of genomic DNA and mRNA, respectively, from individual Caenorhabditis elegans. Although reduced genome coverage was observed in repetitive regions, we produced assemblies covering 98% of the reference genome using long-read sequences generated with Oxford Nanopore Technologies (ONT). Annotation with the sequenced transcriptome coupled with the available assembly revealed that gene predictions were more accurate, complete and contained far fewer false positives than de novo transcriptome assembly approaches. We sampled and sequenced the genomes and transcriptomes of 13 nematodes from early-branching species in Chromadoria, Dorylaimia and Enoplia. The basal Chromadoria and Enoplia species had larger genome sizes, ranging from 136.6 to 738.8 Mb, compared with those in the other clades. Nine mitogenomes were fully assembled, and displayed a complete lack of synteny to other species. Phylogenomic analyses based on the new annotations revealed strong support for Enoplia as sister to the rest of Nematoda. Our result demonstrates the robustness of MDA in combination with ONT, paving the way for the study of genome diversity in the phylum Nematoda and beyond.

Duplicated paralog of sulfide: quinone oxidoreductase contributes to the adaptation to hydrogen sulfide-rich environment in the hydrothermal vent crab, Xenograpsus testudinatus.

The hydrothermal crab, Xenograpsus testudinatus (xtcrab) inhabits shallow-water, hydrogen sulfide (H2S)-rich hydrothermal vent regions. Until now, the adaptative strategy of xtcrab to this toxic environment was unknown. Herein, we investigated the sulfide tolerance and detoxification mechanisms of xtcrabs collected in their high-sulfide hydrothermal vent habitat. Experimental immersion of xtcrab in various sulfide concentrations in the field or in aquaria assessed its high sulfide tolerance. HPLC measurement of hemolymph sulfur compounds highlighted xtcrab detoxification capacity via catabolism of sulfide into much less toxic thiosulfate. We focused on a key enzyme for H2S detoxification, sulfide: quinone oxidoreductase (SQR). Cloning and phylogenetic analysis revealed two SQR paralogs in xtcrab, that we named xtSQR1 and xtSQR2. As shown by qPCR, xtSQR2 and xtSQR1 were expressed in the digestive gland, suggesting the involvement of both paralogs in the detoxification of food-related H2S. In contrast, xtSQR1 transcript was highly expressed in the gill, while xtSQR2 was not detectable, suggesting a specific role of SQR1 in gill detoxification of H2S of environmental origin. Comparison between xtcrabs in their hydrogen sulfide-rich hydrothermal habitat, and xtcrabs maintained for one month in sulfide-free seawater aquarium, showed higher transcript levels of gill xtSQR1 in sulfide-rich habitat, further supporting the specific role of xtSQR1 paralog in environmental H2S detoxification in the gill. Gill SQR protein level as measured by Western blot, and gill SQR enzyme activity were also higher in sulfide-rich habitat. Immunohistochemical staining further showed that SQR expression was co-localized with Na+/K+-ATPase-positive epithelial and pillar cells of the gill filament. This is the first evidence of duplicate SQR genes in crustaceans. Overall, our study suggests that the subfunctionalization of duplicate xtSQR genes may play an important role in sulfide detoxification to maintain the sulfide homeostasis in X. testudinatus, providing an ecophysiological basis for its adaptation to the high-sulfide hydrothermal vent environment.

Cellular mechanisms underlying extraordinary sulfide tolerance in a crustacean holobiont from hydrothermal vents.

The shallow-water hydrothermal vent system of Kueishan Island has been described as one of the world's most acidic and sulfide-rich marine habitats. The only recorded metazoan species living in the direct vicinity of the vents is Xenograpsus testudinatus, a brachyuran crab endemic to marine sulfide-rich vent systems. Despite the toxicity of hydrogen sulfide, X. testudinatus occupies an ecological niche in a sulfide-rich habitat, with the underlying detoxification mechanism remaining unknown. Using laboratory and field-based experiments, we characterized the gills of X. testudinatus that are the major site of sulfide detoxification. Here sulfide is oxidized to thiosulfate or bound to hypotaurine to generate the less toxic thiotaurine. Biochemical and molecular analyses demonstrated that the accumulation of thiosulfate and hypotaurine is mediated by the sodium-independent sulfate anion transporter (SLC26A11) and taurine transporter (Taut), which are expressed in gill epithelia. Histological and metagenomic analyses of gill tissues demonstrated a distinct bacterial signature dominated by Epsilonproteobacteria. Our results suggest that thiotaurine synthesized in gills is used by sulfide-oxidizing endo-symbiotic bacteria, creating an effective sulfide-buffering system. This work identified physiological mechanisms involving host-microbe interactions that support life of a metazoan in one of the most extreme environments on our planet.

Teleostean fishes may have developed an efficient Na+ uptake for adaptation to the freshwater system.

Understanding Na+ uptake mechanisms in vertebrates has been a research priority since vertebrate ancestors were thought to originate from hyperosmotic marine habitats to the hypoosmotic freshwater system. Given the evolutionary success of osmoregulator teleosts, these freshwater conquerors from the marine habitats are reasonably considered to develop the traits of absorbing Na+ from the Na+-poor circumstances for ionic homeostasis. However, in teleosts, the loss of epithelial Na+ channel (ENaC) has long been a mystery and an issue under debate in the evolution of vertebrates. In this study, we evaluate the idea that energetic efficiency in teleosts may have been improved by selection for ENaC loss and an evolved energy-saving alternative, the Na+/H+ exchangers (NHE3)-mediated Na+ uptake/NH4 + excretion machinery. The present study approaches this question from the lamprey, a pioneer invader of freshwater habitats, initially developed ENaC-mediated Na+ uptake driven by energy-consuming apical H+-ATPase (VHA) in the gills, similar to amphibian skin and external gills. Later, teleosts may have intensified ammonotelism to generate larger NH4 + outward gradients that facilitate NHE3-mediated Na+ uptake against an unfavorable Na+ gradient in freshwater without consuming additional ATP. Therefore, this study provides a fresh starting point for expanding our understanding of vertebrate ion regulation and environmental adaptation within the framework of the energy constraint concept.

Temperature increases induce metabolic adjustments in the early developmental stages of bigfin reef squid (Sepioteuthis lessoniana).

Climate changes, such as extreme temperature shifts, can have a direct and significant impact on animals living in the ocean system. Ectothermic animals may undergo concerted metabolic shifts in response to ambient temperature changes. The physiological and molecular adaptations in cephalopods during their early life stages are largely unknown due to the challenge of rearing them outside of a natural marine environment. To overcome this obstacle, we established a pelagic bigfin reef squid (Sepioteuthis lessoniana) culture facility, which allowed us to monitor the effects of ambient thermal elevation and fluctuation on cephalopod embryos/larvae. By carefully observing embryonic development in the breeding facility, we defined 23 stages of bigfin reef squid embryonic development, beginning at stage 12 (blastocyst; 72 h post-egg laying) and continuing through hatching (~1 month post-egg laying). Since temperature recordings from the bigfin reef squid natural habitats have shown a steady rise over the past decade, we examined energy substrate utilization and cellular/metabolic responses in developing animals under different temperature conditions. As the ambient temperature increased by 7 °C, hatching larvae favored aerobic metabolism by about 2.3-fold. Short-term environmental warming stress inhibited oxygen consumption but did not affect ammonium excretion in stage (St.) 25 larvae. Meanwhile, an aerobic metabolism-related marker (CoxI) and a cellular stress-responsive marker (HSP70) were rapidly up-regulated upon acute warming treatments. In addition, our simulations of temperature oscillations mimicking natural daily rhythms did not result in significant changes in metabolic processes in St. 25 animals. As the ambient temperature increased by 7 °C, referred to as heatwave conditions, CoxI, HSP70, and antioxidant molecule (SOD) were stimulated, indicating the importance of cellular and metabolic adjustments. As with other aquatic species with high metabolic rates, squid larvae in the tropical/sub-tropical climate zone undergo adaptive metabolic shifts to maintain physiological functions and prevent excessive oxidative stress under environmental warming.

Multigenerational inspections of environmental thermal perturbations promote metabolic trade-offs in developmental stages of tropical fish.

Global warming both reduces global temperature variance and increases the frequency of extreme weather events. In response to these ambient perturbations, animals may be subject to trans- or intra-generational phenotype modifications that help to maintain homeostasis and fitness. Here, we show how temperature-associated transgenerational plasticity in tilapia affects metabolic trade-offs during developmental stages under a global warming scenario. Tropical tilapia reared at a stable temperature of 27 °C for a decade were divided into two temperature-experience groups for four generations of breeding. Each generation of one group was exposed to a single 15 °C cold-shock experience during its lifetime (cold-experienced CE group), and the other group was kept stably at 27 °C throughout their lifetimes (cold-naïve CN group). The offspring at early life stages from the CE and CN tilapia were then assessed by metabolomics-based profiling, and the results implied that parental cold-experience might affect energy provision during reproduction. Furthermore, at early life stages, progeny may be endowed with metabolic traits that help the animals cope with ambient temperature perturbations. This study also applied the feature rescaling and Uniform Manifold Approximation and Projection (UMAP) to visualize metabolic dynamics, and the result could effectively decompose the complex omic-based datasets to represent the energy trade-off variability. For example, the carbohydrate to free amino acid conversion and enhanced compensatory features appeared to be hypothermic-responsive traits. These multigenerational metabolic effects suggest that the tropical ectothermic tilapia may exhibit transgenerational phenotype plasticity, which could optimize energy allocation under ambient temperature challenges. Knowledge about such metabolism-related transgenerational plasticity effects in ectothermic aquatic species may allow us to better predict how adaptive mechanisms will affect fish populations in a climate with narrow temperature variation and frequent extreme weather events.

The Ovarian Transcriptome at the Early Stage of Testis Removal-Induced Male-To-Female Sex Change in the Protandrous Black Porgy Acanthopagrus schlegelii.

Unlike gonochoristic fishes, sex is fixed after gonadal differentiation (primary sex determination), and sex can be altered in adults (secondary sex determination) of hermaphroditic fish species. The secondary sex determination of hermaphroditic fish has focused on the differences between testicular tissue and ovarian tissue during the sex change process. However, comprehensive studies analyzing ovarian tissue or testicular tissue independently have not been performed. Hermaphroditic black porgy shows a digonic gonad (ovarian tissue with testicular tissue separated by connective tissue). Protandrous black porgy has stable maleness during the first two reproductive cycles (<2 years old), and approximately 50% enter femaleness (natural sex change) during the third reproductive cycle. Precocious femaleness is rarely observed in the estradiol-17ß (E2)-induced female phase (oocytes maintained at the primary oocyte stage), and a reversible female-to-male sex change is found after E2 is withdrawn in <2-year-old fish. However, precocious femaleness (oocytes entering the vitellogenic oocyte stage) is observed in testis-removed fish in <2-year-old fish. We used this characteristic to study secondary sex determination (femaleness) in ovarian tissue via transcriptomic analysis. Cell proliferation analysis showed that BrdU (5-bromo-2'-deoxyuridine)-incorporated germline cells were significantly increased in the testis-removed fish (female) compared to the control (sham) fish (male) during the nonspawning season (2 months after surgery). qPCR analysis showed that there were no differences in pituitary-releasing hormones (lhb and gtha) in pituitary and ovarian steroidogenesis-related factors (star, cyp11a1, hsd3b1, and cyp19a1a) or female-related genes (wnt4a, bmp15, gdf9, figla, and foxl2) in ovarian tissues between intact and testis-removed fish (2 months after surgery). Low expression of pituitary fshb and ovarian cyp17a1 was found after 2 months of surgery. However, we did find small numbers of genes (289 genes) showing sexual fate dimorphic expression in both groups by transcriptomic analysis (1 month after surgery). The expression profiles of these differentially expressed genes were further examined by qPCR. Our present work identified several candidate genes in ovarian tissue that may be involved in the early period of secondary sex determination (femaleness) in black porgy. The data confirmed our previous suggestion that testicular tissue plays an important role in secondary sex determination in protandrous black porgy.

Involvement of IGF-1R-PI3K-AKT-mTOR pathway in increased number of GnRH3 neurons during androgen-induced sex reversal of the brain in female tilapia.

The neuroplastic mechanism of sex reversal in the fish brain remains unclear due to the difficulty in identifying the key neurons involved. Mozambique tilapia show different reproductive behaviours between sexes; males build circular breeding nests while females hold and brood fertilized eggs in their mouth. In tilapia, gonadotropin-releasing hormone 3 (GnRH3) neurons, located in the terminal nerve, regulate male reproductive behaviour. Mature males have more GnRH3 neurons than mature females, and these neurons have been indicated to play a key role in the androgen-induced female-to-male sex reversal of the brain. We aimed to elucidate the signalling pathway involved in the androgen-induced increase in GnRH3 neurons in mature female tilapia. Applying inhibitors to organotypic cultures of brain slices, we showed that the insulin-like growth factor (IGF)-1 receptor (IGF-1R)/PI3K/AKT/mTOR pathway contributed to the androgen-induced increase in GnRH3 neurons. The involvement of IGF-1 and IGF-1R in 11-ketotestosterone (11-KT)-induced development of GnRH3 neurons was supported by an increase in Igf-1 mRNA shortly after 11-KT treatment, the increase of GnRH3 neurons after IGF-1 treatment and the expression of IGF-1R in GnRH3 neurons. Our findings highlight the involvement of IGF-1 and its downstream signalling pathway in the sex reversal of the tilapia brain.

Adaptive metabolic responses in a thermostabilized environment: Transgenerational trade-off implications from tropical tilapia.

Relatively warm environments caused by global warming enhance the productivity of aquaculture activities in tropical/subtropical regions; however, the intermittent cold stress (ICS) caused by negative Arctic Oscillation can still result in major economic losses. In contrast to endotherms, ectothermic fishes experience ambient temperature as an abiotic factor that is central to performance and survival. Therefore, the occurrence of extreme temperatures caused by climate change has ignited a surge of scientific interest from ecologists, economists and physiologists. In this study, we test the transgenerational effects of rearing cold-experienced (CE) and cold-naïve (CN) strains of tropical tilapia. Our results show that compared to CN tilapia, the CE strain preferentially converts carbohydrates into lipids in liver at a regular temperature of 27 °C. Besides, at a low temperature of 22 °C, the CE strain exhibits a broader aerobic scope than CN fish, and their metabolite profile suggests a metabolic shift towards the utilization of glutamate derivatives. Therefore, in response to thermal perturbations, this transgenerational metabolic adjustment provides evidence into the adaptive trade-off mechanisms in tropical fish. Nevertheless, global warming may result in less thermal variation each year, and the stabilized ambient temperature may cause tropical tilapia to gradually exhibit lower energy deposits in liver. In addition to those habitants in cold and temperate regions, a lack of cold exposure to multiple generations of fish may decrease the native cold-tolerance traits of subtropical/tropical organisms; this notion has not been previously explored in terms of the biological effects under anthropogenic climate change.

Estrogen-related receptor γ2 controls NaCl uptake to maintain ionic homeostasis.

Estrogen-related receptors (ERRs) are known to function in mammalian kidney as key regulators of ion transport-related genes; however, a comprehensive understanding of the physiological functions of ERRs in vertebrate body fluid ionic homeostasis is still elusive. Here, we used medaka (Oryzias melastigma), a euryhaline teleost, to investigate how ERRs are involved in ion regulation. After transferring medaka from hypertonic seawater to hypotonic freshwater (FW), the mRNA expression levels of errγ2 were highly upregulated, suggesting that Errγ2 may play a crucial role in ion uptake. In situ hybridization showed that errγ2 was specifically expressed in ionocytes, the cells responsible for Na+/Cl- transport. In normal FW, ERRγ2 morpholino knockdown caused reductions in the mRNA expression of Na+/Cl- cotransporter (Ncc), the number of Ncc ionocytes, Na+/Cl- influxes of ionocytes, and whole-body Na+/Cl- contents. In FW with low Na+ and low Cl-, the expression levels of mRNA for Na+/H+ exchanger 3 (Nhe3) and Ncc were both decreased in Errγ2 morphants. Treating embryos with DY131, an agonist of Errγ, increased the whole-body Na+/Cl- contents and ncc mRNA expression in Errγ2 morphants. As such, medaka Errγ2 may control Na+/Cl- uptake by regulating ncc and/or nhe3 mRNA expression and ionocyte number, and these regulatory actions may be subtly adjusted depending on internal and external ion concentrations. These findings not only provide new insights into the underpinning mechanism of actions of ERRs, but also enhance our understanding of their roles in body fluid ionic homeostasis for adaptation to changing environments during vertebrate evolution.

To cope with a changing aquatic soundscape: Neuroendocrine and antioxidant responses to chronic noise stress in fish.

Anthropogenic underwater noises that change aquatic soundscapes represent an important issue in marine conservation. While it is evident that strong underwater acoustic pollutants may cause significant damage to fish at short ranges, the physiological effects of long-term exposure to relatively quiet but continuous noise are less well understood. Here, we present a summary of the known impacts of long-term underwater noise on hypothalamic-pituitary-interrenal (HPI) axis-mediated physiological responses, oxidant/antioxidant balance, and neurotransmitter regulation in fish. Cortisol is known to play a central role in physiological stress response, most often as a mediator of acute response. However, recent research indicates that noise exposure may also induce chronic corticosteroid responses, which involve increased rates of cortisol turnover. Moreover, continuous noise affects oxidative stress and antioxidant systems in vertebrates and fish, suggesting that oxidative species may mediate some noise-induced physiological responses and make these systems valuable noise stress markers. Lastly, noise stress is also known to affect neurotransmitters in the brain that may cause neurophysiological and behavioral changes. The neurochemical mechanisms underlying observed behavioral disorders in fish after exposure to changing acoustic environments are a topic of active research. Overall, a growing body of evidence suggests that chronic noise pollution could be a threat to fish populations. In future work, systematic and comparative investigations into long-term and transgenerational adaptive neuronal and metabolic responses to noise will be important to understand the physiological patterns and dynamics of noise response relevant to fish conservation.

Effects of emersion on acid-base regulation, osmoregulation, and nitrogen physiology in the semi-terrestrial mangrove crab, Helice formosensis.

Emersion limits water availability and impairs the gill function of water-breathing animals resulting in a reduced capacity to regulate respiratory gas exchange, acid-base balance, and nitrogenous waste excretion. Semi-terrestrial crustaceans such as Helice formosensis mitigate these physiological consequences by modifying and recycling urine and branchial water shifting some branchial workload to the antennal glands. To investigate how this process occurs, Helice formosensis were emersed for up to 160 h and their hemolymph and urinary acid-base, nitrogenous waste, free amino acids, and osmoregulatory parameters were investigated. Upon emersion, crabs experienced a respiratory acidosis that is restored by bicarbonate accumulation and ammonia reduction within the hemolymph and urine after 24 h. Prolonged emersion caused an overcompensatory metabolic alkalosis potentially limiting the crab's ability to remain emersed. During the alkalosis, hemolymph ammonia was maintained at control levels while urinary ammonia remained reduced by 60% of control values. During emersion, ammonia may be temporarily converted to alanine as part of the Cahill cycle until re-immersion where crabs can revert alanine to ammonia for excretion coinciding with the crabs' observed delayed ammonia excretion response. The presence of high hemolymph alanine concentrations even when immersed may indicate this cycle's use outside of emersion or in preparation for emersion. Furthermore, H. formosensis appears to be uniquely capable of actively suppressing its rate of desiccation in absence of behavioral changes, in part by creating hyperosmotic urine that mitigates evaporative water loss.

The Alteration of Intestinal Microbiota Profile and Immune Response in Epinephelus coioides during Pathogen Infection.

Epinephelus coioides, or grouper, is a high economic value fish species that plays an important role in the aquaculture industry in Asia. However, both viral and bacterial diseases have threatened grouper for many years, especially nervous necrosis virus, grouper iridovirus and Vibrio harveyi, which have caused a bottleneck in the grouper industry. Currently, intestinal microbiota can provide novel insights into the pathogenesis-related factors involved in pathogen infection. Hence, we investigated the comparison of intestinal microbiota communities in control group and pathogen-infected grouper through high-throughput sequencing of the 16S rRNA gene. Our results showed that microbial diversity was decreased, whereas microbial richness was increased during pathogen infection. The individuals in each group were distributed distinctly on the PLSDA diagram, especially the GIV group. Proteobacteria and Firmicutes were the most abundant bacterial phyla in all groups. Interestingly, beneficial genera, Faecalibacterium and Bifidobacterium, predominated in the intestines of the control group. In contrast, the intestines of pathogen-infected grouper had higher levels of harmful genera such as Sphingomonas, Atopostipes, Staphylococcus and Acinetobacter. Additionally, we investigated the expression levels of innate and adaptive immune-related genes after viral and bacterial infection. The results revealed that immunoglobulin T and proinflammatory cytokine levels in the intestine increased after pathogen infection. Through these unique bacterial compositions in diseased and uninfected fish, we could establish a novel therapeutic approach and bacterial marker for preventing and controlling these diseases.

L-Carnitine ameliorates congenital myopathy in a tropomyosin 3 de novo mutation transgenic zebrafish.

BACKGROUND: Congenital myopathy (CM) is a group of clinically and genetically heterogeneous muscle disorders, characterized by muscle weakness and hypotonia from birth. Currently, no definite treatment exists for CM. A de novo mutation in Tropomyosin 3-TPM3(E151G) was identified from a boy diagnosed with CM, previously TPM3(E151A) was reported to cause CM. However, the role of TPM3(E151G) in CM is unknown. METHODS: Histopathological, swimming behavior, and muscle endurance were monitored in TPM3 wild-type and mutant transgenic fish, modelling CM. Gene expression profiling of muscle of the transgenic fish were studied through RNAseq, and mitochondria respiration was investigated. RESULTS: While TPM3(WT) and TPM3(E151A) fish show normal appearance, amazingly a few TPM3(E151G) fish display either no tail, a crooked body in both F0 and F1 adults. Using histochemical staining for the muscle biopsy, we found TPM3(E151G) displays congenital fiber type disproportion and TPM3(E151A) resembles nemaline myopathy. TPM3(E151G) transgenic fish dramatically swimming slower than those in TPM3(WT) and TPM3(E151A) fish measured by DanioVision and T-maze, and exhibit weaker muscle endurance by swimming tunnel instrument. Interestingly, L-carnitine treatment on TPM3(E151G) transgenic larvae significantly improves the muscle endurance by restoring the basal respiration and ATP levels in mitochondria. With RNAseq transcriptomic analysis of the expression profiling from the muscle specimens, it surprisingly discloses large downregulation of genes involved in pathways of sodium, potassium, and calcium channels, which can be rescued by L-carnitine treatment, fatty acid metabolism was differentially dysregulated in TPM3(E151G) fish and rescued by L-carnitine treatment. CONCLUSIONS: These results demonstrate that TPM3(E151G) and TPM3(E151A) exhibit different pathogenicity, also have distinct gene regulatory profiles but the ion channels were downregulated in both mutants, and provides a potential mechanism of action of TPM3 pathophysiology. Our results shed a new light in the future development of potential treatment for TPM3-related CM.

Threshold and spectral sensitivity of vision in medaka Oryzias latipes determined by a novel template wave matching method.

We propose a new analytical method for determining the response threshold in electroretinogram (ERG) in which the wave shows a biphasic slow dc-potential shift. This method uses the recorded wave to the highest intensity stimuli in each wavelength tested as a template wave f(t), and it was compared with other recorded waves obtained under lower intensities g(t). Our test recordings in medaka Oryzias latipes were analogous between the template and the compared waveforms, although there were differences in amplitude and time lag (τ, peak time difference) which occurred as a result of the difference in stimulus intensity. Cross-correlation analysis was applied. Based on the obtained cross-correlation function Cfg(τ) in each comparison, τ was determined as the time lag at which the cross-correlation coefficient Rfg(τ) showed the maximum value. Determined thresholds that were based on both the experimenter's visual inspection and this new method agreed well when the adoption condition was set to satisfy R(τ) ≥ 0.7 and τ ≤ 150 ms in scotopic or τ ≤ 120 ms in photopic conditions. We concluded that this "template wave matching method" is a quick and reliable objective assessment that can be used to determine the threshold. This study analyzed ERG recordings in response to 6 kinds of wavelength light stimuli (380 nm to 620 nm) at different photon flux densities. We report the threshold levels and relative spectral sensitivities in scotopic and photopic vision of medaka.

Specialized adaptations allow vent-endemic crabs (Xenograpsus testudinatus) to thrive under extreme environmental hypercapnia.

Shallow hydrothermal vent environments are typically very warm and acidic due to the mixing of ambient seawater with volcanic gasses (> 92% CO2) released through the seafloor making them potential 'natural laboratories' to study long-term adaptations to extreme hypercapnic conditions. Xenograpsus testudinatus, the shallow hydrothermal vent crab, is the sole metazoan inhabitant endemic to vents surrounding Kueishantao Island, Taiwan, where it inhabits waters that are generally pH 6.50 with maximum acidities reported as pH 5.50. This study assessed the acid-base regulatory capacity and the compensatory response of X. testudinatus to investigate its remarkable physiological adaptations. Hemolymph parameters (pH, [HCO3-], [Formula: see text], [NH4+], and major ion compositions) and the whole animal's rates of oxygen consumption and ammonia excretion were measured throughout a 14-day acclimation to pH 6.5 and 5.5. Data revealed that vent crabs are exceptionally strong acid-base regulators capable of maintaining homeostatic pH against extreme hypercapnia (pH 5.50, 24.6 kPa [Formula: see text]) via HCO3-/Cl- exchange, retention and utilization of extracellular ammonia. Intact crabs as well as their isolated perfused gills maintained [Formula: see text]tensions below environmental levels suggesting the gills can excrete CO2 against a hemolymph-directed [Formula: see text] gradient. These specialized physiological mechanisms may be amongst the adaptations required by vent-endemic animals surviving in extreme conditions.

Insulin-like growth factor 1 triggers salt secretion machinery in fish under acute salinity stress.

Timely adjustment of osmoregulation upon acute salinity stress is essential for the survival of euryhaline fish. This rapid response is thought to be tightly controlled by hormones; however, there are still questions unanswered. In this work, we tested the hypothesis that the endocrine hormone, insulin-like growth factor 1 (Igf1), a slow-acting hormone, is involved in the activation of salt secretion mechanisms in euryhaline medaka (Oryzias melastigma) during acclimation to acute salinity stress. In response to a 30-ppt seawater (SW) challenge, Na+/Cl- secretion was enhanced within 0.5 h, with concomitant organization of ionocyte multicellular complexes and without changes in expression of major transporters. Igf1 receptor inhibitors significantly impair the Na+/Cl- secretion and ionocyte multicellular complex responses without affecting transporter expression. Thus, Igf1 may activate salt secretion as part of the teleost response to acute salinity stress by exerting effects on transporter function and enhancing the formation of ionocyte multicellular complexes. These findings provide new insights into hormonal control of body fluid ionic/osmotic homeostasis during vertebrate evolution.