Search Results (40)

The yellowtail kingfish (Seriola aureovittata), a commercially important marine species, encounters significant survival challenges under low-temperature conditions during winter aquaculture. To elucidate its molecular adaptation mechanisms, this study employed RNA-Seq to analyze transcriptional responses in juvenile muscle tissues under acute cold stress (10 °C) at 0, 6, 12, and 24 h. Differential gene expression analysis revealed time-dependent patterns, with 269, 863, and 984 differentially expressed genes (DEGs) identified at 6, 12, and 24 h, respectively. Key pathways were identified, including lipid metabolism, carbohydrate metabolism, and stress response. Sestrin3 upregulation implicated AMPK-mediated energy homeostasis in cold adaptation. These findings provide novel insights into the molecular strategies underlying cold adaptation in yellowtail kingfish, offering potential targets for breeding cold-resistant strains and improving aquaculture resilience. Full article

Wastewater-based epidemiology (WBE) has historically proven to be a powerful surveillance tool, particularly during the SARS-CoV-2 pandemic. Effective WBE depends on the sensitive detection of pathogens in wastewater. However, determining the process limit of detection (PLOD) of WBE through a comprehensive evaluation that accounts for pathogen concentration, nucleic acid extraction, and molecular analysis has rarely been documented. We prepared dilution series with known concentrations of S. Typhi, V. cholerae, rotavirus, and SARS-CoV-2 in surface water and wastewater. Pathogen concentration was performed using Nanotrap particles with the KingFisher™ Apex robotic platform, followed by nucleic acid extraction. Quantitative real-time PCR (qPCR) and digital PCR (dPCR) were used to detect the extracted nucleic acids of the pathogens. The PLODs and recovery efficiencies for each of the four pathogens in surface water and wastewater were determined. Overall, the observed PLODs for S. Typhi, V. cholerae, and rotavirus in surface water and wastewater were approximately 3 log₁₀ loads (2.1–2.8 × 10³/10 mL) using either qPCR or dPCR as the detection method. For SARS-CoV-2, the PLOD in surface water was 2.9 × 10⁴/10 mL with both RT-qPCR and dPCR, one log₁₀ higher than the PLODs of the other three pathogens. In wastewater, the PLOD for SARS-CoV-2 was 2.9 × 10⁴/10 mL using RT-qPCR and 2.9 × 10³/10 mL using dPCR. The mean recovery rates of S. Typhi, V. cholerae, rotavirus, and SARS-CoV-2 for dPCR in both surface water and wastewater were below 10.4%, except for S. Typhi and V. cholerae in wastewater, which showed significantly higher recoveries, from 26.5% at 4.6 × 10⁵/10 mL for S. Typhi to 58.8% at 4.8 × 10⁵/10 mL for V. cholerae. Our study demonstrated that combining qPCR or dPCR analysis with automated Nanotrap particle concentration and nucleic acid extraction using the KingFisher™ platform enables the sensitive detection of S. Typhi, V. cholerae, rotavirus, and SARS-CoV-2 in surface water and wastewater. Full article

We have used a rapid, portable assay (Bacterisk) to determine the bacterial water quality along several inland waters in SW England. Water samples were compared by a conventional membrane filter and culture methods for faecal indicator bacteria (FIB; E. coli and enterococci) and endotoxin measurement by Bacterisk. The Bacterisk data, measured in near-real-time, correlate well with both E. coli and enterococci, but also allow the presence of potential pathogens of a non-faecal origin to be detected. The sensitivity was calculated to be 92.96% with a specificity of 46.3% for E. coli with an expanded uncertainty of 22.07% and an Endotoxin Risk detection limit of 25 units. The presence of Bacterisk detectable non-faecal pathogenic bacteria in the water samples was successfully confirmed by Illumina MiSeq sequencing followed by target species-specific qPCR. Sequencing showed the presence of pathogens including Pseudomonas aeruginosa, Salmonella typhi, Acinetobacter baumannii, Shigella spp., and Legionella spp. as well as antimicrobial resistance genes. Furthermore, the portable Bacterisk assay was able to acquire data on the water quality from different locations and at different time points, providing a comprehensive surveillance tool that challenges the time to results by conventional methods (minutes instead of days), yielding compatible results. Full article

Papillomaviruses are small, circular DNA viruses that infect epithelial and mucosal cells, which have co-evolved with their hosts over time. While certain mammalian papillomaviruses—especially those linked to disease—are well studied, there is limited knowledge about papillomaviruses associated with avian species. In this study, we identified two avian papillomaviruses from eye/choana swabs of the sacred kingfisher (Todiramphus sanctus) and the little corella (Cacatua sanguinea), collected in Queensland, Australia. The genomes of these viruses, designated as todiramphus sanctus papillomavirus 1 (TsPV1) and cacatua sanguinea papillomavirus 1 (CsPV1), were found to be 7883 and 7825 base pairs in length, respectively. The TsPV1 and CsPV1 genomes exhibited the highest nucleotide sequence identity (>56%) with papillomavirus genomes previously sequenced from mallards or wild ducks in the United States, followed by those from black-legged kittiwakes and Atlantic puffins (>54%) in Newfoundland, Canada. Both TsPV1 and CsPV1 share approximately a 65% nucleotide sequence identity in the L1 gene with anas platyrhynchos papillomavirus 3 (AplaPV3), indicating that they represent novel avian papillomaviruses. Notably, the two genomes in this study were nearly identical (99.69%), and their L1 proteins shared 100% sequence identity. Phylogenetic analysis positioned TsPV1 and CsPV1 within a clade of avian papillomaviruses associated with closely related avian hosts, including the mallard, African grey parrot, common chaffinch, and Atlantic canary. These findings underscore the importance of further research on studying additional Australian bird species longitudinally, which will help to establish potential disease associations and ecological impacts of previously unrecognised and novel papillomaviruses in Australian wild birds. Full article

The United States is facing outbreaks of highly pathogenic avian influenza H5N1 in birds and dairy cattle, along with threats of African swine fever, classical swine fever, and foot-and-mouth disease. While the National Animal Health Laboratory Network (NAHLN) depends on high-throughput testing, the KingFisher Duo Prime, IndiMag 48s, and IndiMag 2 are viable alternatives to aid in outbreak assessments. This study evaluates extraction platforms and the IndiMag Pathogen Kit for detecting the previous listed pathogens. Samples and reference materials were extracted using the MagMAX Viral RNA Isolation Kit, MagMAX CORE Nucleic Acid Purification Kit, and IndiMag Pathogen Kit. Real-time RT-PCR was performed following NAHLN protocols to assess analytical and diagnostic performance. Comparable limits of detection across extraction chemistries, instrumentation, and pathogens were demonstrated, with PCR efficiency ranging between 82.5% and 107.6%. The precision variability was low, with the coefficient of variation ranging from 0.16% to 1.76%. Diagnostic sensitivity and specificity were 100%, with a kappa coefficient of 1.0, indicating strong agreement between methods. These findings support the KingFisher Duo Prime, IndiMag 48s, IndiMag 2, and IndiMag Pathogen Kits as reliable options for NAHLN-approved testing, increasing equipment and reagent alternatives to enhance diagnostic resilience and improve response capabilities to emerging animal health threats. Full article

Until recently, the sihek (Guam kingfisher, Todiramphus cinnamominus) has persisted entirely in managed care since a breeding program was established in the 1980s. Understanding the growth and developmental milestones of the sihek from hatch to fledging is critical to enhancing conservation efforts and improving management practices that promote positive welfare. In this study, we summarized data collected on the growth patterns, developmental milestones, and rearing differences in sihek chicks raised at Brookfield Zoo Chicago from 1989 to 2023. We found that hand-reared chicks reached the fledging stage significantly earlier than parent-reared chicks that received supplemental feeding from staff. Additionally, we found that hatch weight was a significant predictor of survival to fledging, highlighting the importance of collecting weight data at all stages of life. These insights into sihek development in managed care provide important data for the development of welfare-focused management practices that improve the success of conservation efforts while also prioritizing the wellbeing of each individual chick. Full article

High-quality RNA is crucial in clinical diagnostics and precision medicine. Formalin-fixed and paraffin-embedded (FFPE) tissues pose a challenge due to nucleic acid fragmentation and crosslinking. In this pilot study, various commercially available techniques for extracting RNA from small FFPE samples were compared. We evaluated the KingFisher Duo automated system or the manual MagMAX FFPE DNA/RNA Ultra Kit as an RNA extraction method combined with either a xylene, d-limonene, or AutoLys M tubes deparaffinization method. Additionally, the automated Maxwell RSC RNA FFPE kit and the High Pure FFPET RNA Isolation Kit were examined using FFPE samples from inflammatory bowel disease (IBD) patients, as well as samples from ovarian, kidney, and breast cancer and the skin. The KingFisher Duo system gave a higher yield and more consistent RNA quantities, especially from small volumes of IBD samples, compared to manual extraction. The deparaffinization method also impacted results, with AutoLys M tubes proving effective in combination with the KingFisher Duo system. Conversely, the High Pure kit exhibited higher yields for larger FFPE samples. While RNA integrity is a critical factor, particularly for messenger RNA (mRNA) expression studies, its role is less prominent in microRNA (miRNA) analyses. Recognizing this, our study focused on RNA yield and purity (A260/A230) to evaluate RNA extraction methods for various sample types. These findings emphasize the importance of selecting appropriate RNA extraction methods based on sample characteristics and research goals, highlighting the performance of automated methods and the impact of deparaffinization choices. The findings contribute to refining RNA extraction for molecular biology analyses, suggesting avenues for further exploration, including cost-effectiveness under specific experimental conditions. Full article

Maritime activities have become increasingly frequent with the deepening of economic globalization, highlighting the burgeoning significance of maritime rescue. However, in practical applications, UAVs for maritime rescue face numerous challenges, such as limited endurance and inadequate autonomous planning capabilities. To optimize flight routes and circumvent adverse sea conditions, an improved Pied Kingfisher Optimizer (IPKO) that incorporates refraction reverse learning, variable spiral search, and Cauchy mutation strategies was proposed. Comparative experiments conducted on CEC2005 and CEC2022 datasets with seven traditional algorithms demonstrate that the proposed algorithm exhibits superior precision and convergence speed. Subsequently, a path planning objective function was constructed based on trajectory cost and threat cost to simulate a 3D space for UAV maritime rescue missions, and the IPKO algorithm was applied to address the UAV path planning problem. The results showed that the total cost incurred by the IPKO algorithm decreased by 5.77% compared to the PKO algorithm and by 51.19% compared to the SCA algorithm. Finally, through UAV flight tests validating its practical applicability, it is ascertained that IPKO can enhance rescue efficiency in complex maritime rescue environments. Full article

Automated nucleic acid extractors are useful instruments for the high-throughput processing of bio-samples and are expected to improve research throughput in addition to decreased inter-sample variability inherent to manual processing. We evaluated three commercial nucleic acid extractors Bioer GenePure Pro (Bioer Technology, Hangzhou, China), Maxwell RSC 16 (Promega Corporation, Madison, WI, USA), and KingFisher Apex (ThermoFisher Scientific, Waltham, MA, USA) based on their DNA yield, DNA purity, and 16S rRNA gene amplicon results using both human fecal samples and a mock community (ZymoBIOMICS Microbial Community Standard (Zymo Research Corp., Irvine, CA, USA)). Bead-beating provided incremental yield to effectively lyse and extract DNA from stool samples compared to lysis buffer alone. Differential abundance analysis and comparison of prevalent bacterial species revealed a greater representation of Gram-positive bacteria in samples subjected to mechanical lysis, regardless of sample type. All three commercial extractors had differences in terms of yield, inter-sample variability, and subsequent sequencing readouts, which we subsequently share in the paper and believe are significant considerations for all researchers undertaking human fecal microbiota research. Full article

Tea polyphenols (TPs) are a critical indicator for evaluating the quality of tea leaves and are esteemed for their beneficial effects. The non-destructive detection of this component is essential for enhancing precise control in tea production and improving product quality. This study developed an enhanced PKO-SVR (support vector regression based on the Pied Kingfisher Optimization Algorithm) model for rapidly and accurately detecting tea polyphenol content in Fu brick tea using hyperspectral reflectance data. During this experiment, chemical analysis determined the tea polyphenol content, while hyperspectral imaging captured the spectral data. Data preprocessing techniques were applied to reduce noise interference and improve the prediction model. Additionally, several other models, including K-nearest neighbor (KNN) regression, neural network regression (BP), support vector regression based on the sparrow algorithm (SSA-SVR), and support vector regression based on particle swarm optimization (PSO-SVR), were established for comparison. The experiment results demonstrated that the improved PKO-SVR model excelled in predicting the polyphenol content of Fu brick tea (R² = 0.9152, RMSE = 0.5876, RPD = 3.4345 for the test set) and also exhibited a faster convergence rate. Therefore, the hyperspectral data combined with the PKO-SVR algorithm presented in this study proved effective for evaluating Fu brick tea’s polyphenol content. Full article

Microwave-assisted mechanical rock breaking represents an innovative technology in the realm of mining excavation. The intricate and variable characteristics of geological formations necessitate a comprehensive understanding of the interplay between microwave-induced rock damage and the subsequent deterioration in rock strength. This study conducted microwave irradiation damage assessments on 78 distinct rock samples, encompassing granite, sandstone, and marble. A total of ten critical parameters were identified: Microwave Irradiation Time (MIT), Microwave Irradiation Power (MIP), Longitudinal Wave Velocity prior to Microwave Treatment (LWVB), Longitudinal Wave Velocity post-Microwave Treatment (LWVA), Percentage Decrease in Longitudinal Wave Velocity (LWVP), Porosity before Microwave Treatment (PB), Porosity after Microwave Treatment (PA), Percentage Increase in Porosity (PP), and Uniaxial Compressive Strength following Microwave Treatment (UCSA). Utilizing the Pied Kingfisher Optimizer (PKO) alongside Extreme Gradient Boosting (XGBoost), we developed a PKO-XGBoost machine learning model to elucidate the relationship between UCSA and the nine additional parameters. This model was benchmarked against other prevalent machine learning frameworks, with Shapley additive explanatory methods employed to assess each parameter’s influence on UCSA. The findings reveal that the PKO-XGBoost model provides superior accuracy in delineating relationships among rock physical properties, microwave irradiation variables, microscopic attributes of rocks, and UCSA. Notably, PA emerged as having the most significant effect on UCSA, indicating that microwave-induced microscopic damage is a primary contributor to reductions in rock strength. Additionally, MR exhibited substantial influence; under identical microwave irradiation conditions, rocks with lower density demonstrated greater susceptibility to strength degradation. Furthermore, during microwave-assisted rock breaking operations, it is imperative to establish optimal MIT and MIP values to effectively diminish UCSA while facilitating mechanical cutting processes. The insights derived from this research offer a more rapid, cost-efficient approach for accurately assessing correlations between microwave irradiation parameters and resultant rock damage—providing essential data support for enhancing mechanical rock-breaking efficiency. Full article

The farming mode of yellowtail kingfish (Seriola aureovittata) in China tends to be mature. However, there are some problems with environmental impact and economic benefits that cannot be ignored in the sustainable farming process. This study focused on a yellowtail kingfish aquaculture company in Dalian, China, and carried out a life cycle environmental and cost assessment (LCA and LCC) study to evaluate the environmental impact and economic benefits of the yellowtail kingfish farming process. According to the LCA and LCC results, the environmental impact is significantly influenced by fossil energy consumption and feed production. Moreover, five improvement scenarios were proposed and discussed, and the results show that replacing coal and thermal power generation with wind power generation will comprehensively (scenario 5) reduce environmental impact by 82.14% and decrease costs by 24.25%. The results of this study can provide effective improvement scenarios for yellowtail kingfish aquaculture enterprises and enrich the international aquaculture LCA basic database with data support. Full article

The yellowtail kingfish is a highly active and fast-growing marine fish with promising potential for aquaculture. In this study, essential insights were gained into the energy economy of this species by heart rate and acceleration logging during a swim-fitness test and a subsequent stress challenge test. Oxygen consumption values of the 600–800 g fish, when swimming in the range of 0.2 up to 1 m·s⁻¹, were high—between 550 and 800 mg·kg⁻¹·h⁻¹—and the heart rate values—up to 228 bpm—were even among the highest ever measured for fishes. When swimming at these increasing speeds, their heart rate increased from 126 up to 162 bpm, and acceleration increased from 11 up to 26 milli-g. When exposed to four sequential steps of increasing stress load, the decreasing peaks of acceleration (baseline values of 12 to peaks of 26, 19 and 15 milli-g) indicated anticipatory behavior, but the heart rate increases (110 up to 138–144 bpm) remained similar. During the fourth step, when fish were also chased, peaking values of 186 bpm and 44 milli-g were measured. Oxygen consumption and heart rate increased with swimming speed and was well reflected by increases in tail beat and head width frequencies. Only when swimming steadily near the optimal swimming speed were these parameters strongly correlated. Full article

Diseases pose a significant and pressing concern for the sustainable development of the aquaculture sector, particularly as their impact continues to grow due to climatic shifts such as rising water temperatures. While various approaches, ranging from biosecurity measures to vaccines, have been devised to combat infectious diseases, their efficacy is disease and species specific and contingent upon a multitude of factors. The fields of genetics and genomics offer effective tools to control and prevent disease outbreaks in aquatic animal species. In this study, we present the key findings from our recent research, focusing on the genetic resistance to three specific diseases: White Spot Syndrome Virus (WSSV) in white shrimp, Bacterial Necrotic Pancreatitis (BNP) in striped catfish, and skin fluke (a parasitic ailment) in yellowtail kingfish. Our investigations reveal that all three species possess substantial heritable genetic components for disease-resistant traits, indicating their potential responsiveness to artificial selection in genetic improvement programs tailored to combat these diseases. Also, we observed a high genetic association between disease traits and survival rates. Through selective breeding aimed at enhancing resistance to these pathogens, we achieved substantial genetic gains, averaging 10% per generation. These selection programs also contributed positively to the overall production performance and productivity of these species. Although the effects of selection on immunological traits or immune responses were not significant in white shrimp, they yielded favorable results in striped catfish. Furthermore, our genomic analyses, including shallow genome sequencing of pedigreed populations, enriched our understanding of the genomic architecture underlying disease resistance traits. These traits are primarily governed by a polygenic nature, with numerous genes or genetic variants, each with small effects. Leveraging a range of advanced statistical methods, from mixed models to machine and deep learning, we developed prediction models that demonstrated moderate-to-high levels of accuracy in forecasting these disease-related traits. In addition to genomics, our RNA-seq experiments identified several genes that undergo upregulation in response to infection or viral loads within the populations. Preliminary microbiome data, while offering limited predictive accuracy for disease traits in one of our studied species, underscore the potential for combining such data with genome sequence information to enhance predictive power for disease traits in our populations. Lastly, this paper briefly discusses the roles of precision agriculture systems and AI algorithms and outlines the path for future research to expedite the development of disease-resistant genetic lines tailored to our target species. In conclusion, our study underscores the critical role of genetics and genomics in fortifying the aquaculture sector against the threats posed by diseases, paving the way for more sustainable and resilient aquaculture development. Full article

Urine provides a diverse source of information related to a patient’s health status and is ideal for clinical proteomics due to its ease of collection. To date, most methods for the preparation of urine samples lack the throughput required to analyze large clinical cohorts. To this end, we developed a novel workflow, urine-HILIC (uHLC), based on an on-bead protein capture, clean-up, and digestion without the need for bottleneck processing steps such as protein precipitation or centrifugation. The workflow was applied to an acute kidney injury (AKI) pilot study. Urine from clinical samples and a pooled sample was subjected to automated sample preparation in a KingFisher™ Flex magnetic handling station using the novel approach based on MagReSyn^® HILIC microspheres. For benchmarking, the pooled sample was also prepared using a published protocol based on an on-membrane (OM) protein capture and digestion workflow. Peptides were analyzed by LCMS in data-independent acquisition (DIA) mode using a Dionex Ultimate 3000 UPLC coupled to a Sciex 5600 mass spectrometer. The data were searched in Spectronaut™ 17. Both workflows showed similar peptide and protein identifications in the pooled sample. The uHLC workflow was easier to set up and complete, having less hands-on time than the OM method, with fewer manual processing steps. Lower peptide and protein coefficient of variation was observed in the uHLC technical replicates. Following statistical analysis, candidate protein markers were filtered, at ≥8.35-fold change in abundance, ≥2 unique peptides and ≤1% false discovery rate, and revealed 121 significant, differentially abundant proteins, some of which have known associations with kidney injury. The pilot data derived using this novel workflow provide information on the urinary proteome of patients with AKI. Further exploration in a larger cohort using this novel high-throughput method is warranted. Full article