Search Results (11)

Background: Hypoxia triggers stress, leading to significant alterations in gene expression patterns, which in turn affect fish’s growth and development. Real-time quantitative PCR (RT-qPCR) is a pivotal technique for assessing changes in gene expression. However, its accuracy is highly contingent upon the stable expression of reference genes. Ribosomal RNA (18s), β-actin (actb), elongation factor 1-α (ef1a), α tubulin (tuba), and ribosomal protein L17 (rpl17) are the widely used reference genes, but their expression stability in the tissues of black rockfish under hypoxic conditions remains unclear. Methods: The expression of genes was detected by RT-qPCR and the stability was assessed by Delta Ct, geNorm, NormFinder, and BestKeeper algorithms. Results: Results showed that tuba exhibited stable expression in liver, heart, gill tissues under normoxic conditions, and in the liver and head kidney under hypoxic conditions. Ef1a was identified as the most stably expressed gene in gill tissue under hypoxia. For hypoxic heart studies, rpl17 and tuba were recommended as reference genes. 18s showed high stability in spleen tissue under hypoxic conditions. Actb was the most stably expressed gene in spleen and head kidney tissues under normoxic conditions. Conclusions: The identified reference genes exhibited tissue-specific stability, and it was necessary to select appropriate reference genes based on the specific tissue type for gene expression studies under hypoxic conditions. These findings help in enhancing the accuracy of gene expression analysis in the mechanism of hypoxia for black rockfish. Full article

Humpback grouper (Cromileptes altivelis) is an economically important fish, but the increasing density of its farming has led to more severe disease outbreaks. To address this challenge, we established brain (CAB) and kidney (CAK) cell lines in our laboratory previously, providing a valuable tool for in vitro studies on immune responses. In this study, we used quantitative real-time polymerase chain reaction (qRT-PCR) to identify the optimal reference gene from six reference genes for CAB and CAK cells, under both normal conditions and after stimulation with LPS or Poly I: C. The qRT-PCR data were analyzed using geNorm, NormFinder, and BestKeeper software (Version 3.5) to ensure comprehensve evaluation. The results showed that RPL13 was the most stable reference gene for both CAB and CAK cells under normal conditions. Following LPS stimulation, TTLL1 was the best reference gene for CAB cells, while RPL13 remained the most suitable for CAK cells. For Poly I: C stimulation, EF1A and Actin were identified as the most stable reference genes for CAB and CAK cells, respectively. To confirm the reliability of the selected reference genes, we analyzed the expression of the cytokine genes IL-6 and IFN-h, demonstrating the dependability of these reference genes. This study lays a solid foundation for exploring gene expression patterns in humpback grouper cell lines under various experimental conditions, providing essential insights for future research into immune processes and disease control strategies in aquaculture. Full article

The spotted scat (Scatophagus argus) is the most widely commercially cultured fish in eastern and southern Asia that possess potential economic value. However, up to date, there are no studies reported on the selection of suitable reference genes in this fish, which is crucial for guaranteeing accurate and reliable results in RT-qPCR analyses. This study aimed at screening the most stable reference genes in the ovary and pituitary at different ovarian stages, which is of great significance for further research on the reproductive regulation mechanism of female S. argus. In this study, we selected twenty-one genes as the candidate reference genes, including four genes in the ovary (EEF1A, ACTB, B2M, and HPRT1), and seventeen genes in the pituitary (B2M, APOA1, CGBA, RPLP0, GNRHR, GUSB, TBP, SLC25A5, RPL4, PLA1A, GAPDH, GNB2L1, CTFS, HPRT1, RPS2, TFRC, and TUBB4B). To analyze the stability of the potential reference genes, we first used four commonly used software, BestKeeper, GeNorm, NormFinder, and ΔCt, and then we established comprehensive rankings with ReFinder. The results indicate that RPL4 and GNB2L1, and EEF1A and HPRT1 were the most appropriate reference genes for the pituitary and ovary of S. argus, respectively, in the three developmental stages of the ovary. Additionally, GeNorm analysis suggested that for the accurate normalization of gene expression, two reference genes were reliable in the ovary and pituitary of S. argus. To the best of our knowledge and understanding, this is the first study to identify appropriate reference genes for analyzing gene expression in S. argus. Consequently, this study can be used as a foundation for future research on the reproduction of S. argus. Full article

The spatial extent of a dual-frequency echosounder and its potential impact on cetacean species were examined. Sound emissions of output frequencies of 83 kHz and 200 kHz were tested at a maximum distance of 400 m. This is the minimum vessel approach distance for killer whales (Orcinus orca) in southern British Columbia, which was introduced as a measure for limiting disturbance of southern resident killer whales (SRKWs). The experiment was conducted in shallow (34 m) and deep (220–235 m) water. Recordings were made at depths of 5 and 30 m for both locations, as well as at 100 and 200 m in the deeper water to examine the effect of the echosounder through the water column and at SRKW diving depths. The recordings showed that 200 kHz echosounder emissions were contained within a 250 m radius of the source, with most of the acoustic energy focused within 100 m in shallow waters. For the 83 kHz signal and for deeper water testing of the 200 kHz signal, the echosounder transmissions exceeded the 400 m threshold, intimating that whales could experience noise additions of 30 dB or more above the ambient level at the minimum vessel approach distance. Evaluating the noise additions to the ambient level from the echosounder in frequencies used by SRKWs for echolocation (15–100 kHz) further showed the potential impact on whales in close proximity to vessels (≤400 m) when using echosounders or fish-finders. Full article

Continuous monitoring of antimicrobial resistance in bacteria along the food chain is crucial for the assessment of human health risks. Uncritical use of antibiotics in farming over years can be one of the main reasons for increased antibiotic resistance in bacteria. In this study, we aimed to classify 222 presumptive Pseudomonas isolates originating from a salmon processing environment, and to examine the phenotypic and genotypic antibiotic resistance profiles of these isolates. Of all the analyzed isolates 68% belonged to Pseudomonas, and the most abundant species were Pseudomonas fluorescens, Pseudomonas azotoformans, Pseudomonas gessardii, Pseudomonas libanesis, Pseudomonas lundensis, Pseudomonas cedrina and Pseudomonas extremaustralis based on sequencing of the rpoD gene. As many as 27% of Pseudomonas isolates could not be classified to species level. Phenotypic susceptibility analysis by disc diffusion method revealed a high level of resistance towards the antibiotics ampicillin, amoxicillin, cefotaxime, ceftriaxone, imipenem, and the fish farming relevant antibiotics florfenicol and oxolinic acid among the Pseudomonas isolates. Whole genome sequencing and subsequent analysis of AMR determinants by ResFinder and CARD revealed that no isolates harbored any acquired resistance determinants, but all isolates carried variants of genes known from P. aeruginosa to be involved in multidrug efflux pump systems. Full article

The Spanish Toothcarp (Apricaphanius iberus) is a small fish species endemic to the eastern coast of the Iberian Peninsula. Its area of distribution includes a variety of salt and freshwater habitats that experience large fluctuations in temperature and salinity throughout the year. The Spanish Toothcarp belongs to the Cyprinodontiformes order and to the family Aphaniidae. It is currently considered “Endangered” (category IUCN: EN), i.e., facing a very high risk of extinction in the wild. The genetics of A. iberus are not well known since most studies have only evaluated the genetic structure of the species under a conservation framework in order to identify its potential conservation units. In this study, the whole mitochondrial genome of A. iberus was obtained for the first time in the context of an A. iberus genome reference sequencing. The mitogenome was reconstructed and aligned against 83 other cyprinodontiformes and two outgroup taxa. From this, a phylogenetic reconstruction was created using PartitionFinder to test the best evolutionary model for both the 13 protein coding genes and two non-coding ribosomal genes. Following this, a phylogenetics analysis was conducted using two methods: Maximum-Likelihood approximation (IQTree) including bootstrap branching support and Bayesian inference (MrBayes) applying the partitions models obtained. By doing so, it was possible to find the molecular position of A. iberus within the Cyprinodontiformes order. The results showed A. iberus grouped together with Orestias ascotanensis and both species formed a sister group with North American and Caribbean cyprinodontiformes. These new data will be valuable for a better understanding of the evolution of A. iberus and will be highly useful for future genetic studies. Full article

MicroRNA (miRNA) plays essential roles in post-transcriptional regulation of protein coding genes, and the quantitative real-time polymerase chain reaction (qRT-PCR) is the powerful and broadly employed tool to conduct studies of miRNA expression. Identifying appropriate references to normalize quantitative data is a prerequisite to ensure the qRT-PCR accuracy. Until now, there has been no report about miRNA reference for qRT-PCR in Japanese flounder (Paralichthys olivaceus), one important marine cultured fish along the coast of Northern Asia. In this study, combined with miRNA-Seq analysis and literature search, 10 candidates (miR-34a-5p, miR-205-5p, miR-101a-3p, miR-22-3p, miR-23a-3p, miR-210-5p, miR-30c-5p, U6, 5S rRNA, and 18S rRNA) were chosen as potential references to test their expression stability among P. olivaceus tissues, and in livers of P. olivaceus infected with Edwardsiella tarda at different time points. The expression stability of these candidates was analyzed by qRT-PCR and evaluated with Delta CT, BestKeeper, geNorm, as well as NormFinder methods, and RefFinder was employed to estimate the comprehensive ranking according to the four methods. As the result, miR-22-3p and miR-23a-3p were proved to be the suitable combination as reference miRNAs for both P. olivaceus normal tissues and livers infected with E. tarda, and they were successfully applied to normalize miR-7a and miR-221-5p expression in P. olivaceus livers in response to E. tarda infection. All these results provide valuable information for P. olivaceus miRNA quantitative expression analysis in the future. Full article

Aeromonas hydrophila are ubiquitous in the environment and are highly distributed in aquatic habitats. They have long been known as fish pathogens but are opportunistic human pathogens. Aeromonas spp. have persisted through food-processing safeguards and have been isolated from fresh grocery vegetables, dairy, beef, pork, poultry products and packaged ready-to-eat meats, thus providing an avenue to foodborne illness. A beta-hemolytic, putative Escherichia coli strain collected from diarrheic neonatal pigs in Oklahoma was subsequently identified as A. hydrophila, and designated CVM861. Here we report the whole-genome sequence of A. hydrophila CVM861, SRA accession number, SRR12574563; BioSample number, SAMN1590692; Genbank accession number SRX9061579. The sequence data for CVM861 revealed four Aeromonas-specific virulence genes: lipase (lip), hemolysin (hlyA), cytonic enterotoxin (ast) and phospholipid-cholesterolacyltransferase (GCAT). There were no alignments to any virulence genes in VirulenceFinder. CVM861 contained an E. coli resistance plasmid identified as IncQ1_1__M28829. There were five aminoglycoside, three beta-lactam, and one each of macrolide, phenicol, sulfonamide, tetracycline and trimethoprim resistance genes, all with over 95% identity to genes in the ResFinder database. Additionally, there were 36 alignments to mobile genetic elements using MobileElementFinder. This shows that an aquatic pathogen, rarely considered in human disease, contributes to the resistome reservoir and may be capable of transferring resistance and virulence genes to other more prevalent foodborne strains such as E. coli or Salmonella in swine or other food production systems. Full article

A novel hydrocyclone including a cylindrical screen embedded in a conventional hydrocyclone (CH), named three products hydrocyclone screen (TPHS), has been successfully designed. In TPHS, the combination of centrifugal classification and screening was employed to separate particles. In this paper, Grey theory, as an effective means to the laws of both complex and uncertainty system’s behavior with small samples, was used to investigate the operational (feed concentration and feed pressure) and structural (aperture size, spigot diameter, and vortex finder diameter) parameters on performance evaluation Hancock classification efficiency (HE), imperfection (I), and cut size (d_50c). The experiments of coal sample (0–1 mm) show that TPHS with coarser particles in underflow exhibited the absent “fish-hook”. The closeness calculated using the Grey System algorithm indicates that the performance of TPHS was closely related to the operation and structure parameters. Further, the order of grey incidence degree between different parameters and HE (or I or d_50c) is the spigot diameter and aperture size with the highest value, the feed pressure and vortex finder diameter with the middle value, and the feed concentration with the lowest value. The prediction using the GM(1, N) algorithm implies that the dynamic prediction model for the performance evaluation can be created depending on the operation, structure and previous performance value. The mean relative errors between the predicted and actual HE, I, and d₅₀ were 2.84%, 5.83%, and 3.57%, respectively, which exhibit the accurate prediction. Full article

Sonar survey of shallow water bodies has challenged scientists for a long time. Although these water courses are small, still they have an increasing ecological, touristic and economical role. As maritime sonars are non-ideal tools for shallow waters, the bathymetric survey of these rivers has been taken with cross-sectional methods. Due to recent developments, interferometric surveying technology have also burst into the market of recreational-grade fish-finders. The objective of the current study was the development of a novel, complex and integrated surveying technique which is affordable, robust and applicable even at low water levels. A recreational-grade sonar system was assembled and mounted on a double-hull vessel and connected with a geodetic Global Navigation Satellite System (GNSS) device. We have developed a novel software which enables the bridging between a closed sonar file format and the commonly used Geographic Information System (GIS) datasets. As a result, the several month-long conventional bathymetric survey of the 146 km-long reach of the Drava River was reduced to 20 days and provided channel bathymetry of many orders of magnitude higher than the classical methods. Additionally, a large number of spatial derivatives were generated which enables the analysis of channel morphology, textural variation of channel sediments and the accurate delineation of navigational routes. Full article

Rhode Island, New Zealand, and southern California recently reported sharp increases in sexually transmitted diseases (STDs). Health department officials stated that these increases appeared to be due to the more widespread use of social media like Tinder, Grindr, and Facebook, which allow users to readily connect with and meet others. The purpose of this study was to see if U.S. states that have more users of social networking sites, dating sites, and dating apps like Match.com, Ashley Madison, Our Time, Down Dating, Bumble, Zoosk, Hinge, Score, At First Sight, Plenty of Fish, Eharmony, Adult Friend Finder, Tinder, Grindr, and Facebook have more cases of STDs after controlling for population, race, age, income, education, and population density. It was found that states with more users of Match.com, OKCupid, and Down Dating had a larger number of cases of STDs, while states with more users of Our Time, Ashley Madison, Facebook, How About We, Hinge, Adult Friend Finder, Grindr, Bumble, Score, Tinder, and At First Sight had fewer cases of STDs. While social networking sites make it easier for individuals to be exposed to an STD since in-network individuals may share an STD, many sites either attract individuals who are not interested in a short-term sexual relationship or who take precautions to avoid contracting an STD. Full article