Effects of the photovoltaic fishery culture model on muscle nutritional quality and volatile flavor compounds of .

This study used to compare the muscle nutritional quality and volatile flavor compounds of animals raised in the photovoltaic fishery culture model (PM) and the common pond breeding model (CM). Amino acids, fatty acids, and volatile flavor substances were identified and analyzed using an automatic amino acid analyzer and headspace solid phase microextraction(HS-SPME) combined with GC/MS. There were no significant differences between the two culture models in terms of general nutrients, mineral contents, and amino acid compositions in the muscles of .

Effects of different temperatures on Leiocassis longirostris gill structure and intestinal microbial composition.

Fish are poikilothermic vertebrates and their physiological activities are affected by water temperature. In recent years, extreme weather has occurred frequently, and temperature changes have adversely affected the growth of farmed fish. To explore the changes in gill tissue structure caused by changing the water temperature and the relationship between the intestinal microbiota and the Leiocassis longirostris host adaptation mechanism, gill tissue sections and intestinal microbial 16S rRNA amplicon sequencing were conducted under different temperature stress (low temperature 4 °C, normal temperature 26 °C and high temperature 32 °C).

Single-nuclei RNA-seq reveals skin cell responses to infection in Chinese longsnout catfish .

As the primary natural barrier that protects against adverse environmental conditions, the skin plays a crucial role in the innate immune response of fish, particularly in relation to bacterial infections. However, due to the diverse functionality and intricate anatomical and cellular composition of the skin, deciphering the immune response of the host is a challenging task. In this study, single nuclei RNA-sequencing (snRNA-seq) was performed on skin biopsies obtained from Chinese longsnout catfish (), comparing -infected subjects to healthy control subjects.

Study on the Adaptive Regulation of Light on the Stress Response of Mandarin Fish () with Re-Feeding after Starvation.

Light influences the stress response to environmental stimuli and feeding behaviors of and, thus, is an important regulator of normal growth and development. In this study, we first explored the important role of light on the digestive and stress capacity of by studying the changes in physiological and biochemical indicators of , taking the re-feeding after starvation as the constant environmental stimulus and the light intensity as the adjustable environmental stimulus. The activity of protease and lipase was generally higher in the stomach tissues than in the intestinal tissues, especially lipase, which was higher in stomach tissues under all light conditions, and the protease and lipase activity peaked in the stomach tissues of at a light intensity of 18.

PacBio single-molecule long-read sequencing provides new insights into the complexity of full-length transcripts in oriental river prawn, macrobrachium nipponense.

Background: Oriental river prawn (Macrobrachium nipponense) is one of the most dominant species in shrimp farming in China, which is a rich source of protein and contributes to a significant impact on the quality of human life. Thus, more complete and accurate annotation of gene models are important for the breeding research of oriental river prawn.

Results: A full-length transcriptome of oriental river prawn muscle was obtained using the PacBio Sequel platform.

Integrated analysis of how gender and body weight affect the intestinal microbial diversity of Gymnocypris chilianensis.

Intestinal microorganisms that living in the mucosa and contents of the gastrointestinal tract of animals, have close links with their hosts over a long evolutionary history. The community structure of the fish intestinal microbiota is associated with food, living environment, and the growth stage. To screen for potential probiotics that can be used for regulating breeding behaviors, this study focused on the diversity of fish intestinal microorganisms.

Studies on the molecular level changes and potential resistance mechanism of under temperature stimulation.

In this study, we used transcriptome and proteome technology to analyze molecular level changes in tissues of cultured at high temperature (HT) and low temperature (LT). We also screened for specific anti-stress genes and proteins and evaluated the relationships between them. We identified 201,803 unigenes and 10,623 proteins.

Toxic metals in rice-fish co-culture systems and human health.

The threat of contamination with toxic metals (TMs) to food security and human health has become a high priority in recent decades. Hence, countless studies have investigated the safe cultivation of rice and fish, respectively, as the main food crop and protein source worldwide. For the present study, a literature search of the PubMed, Web of Science, ScienceDirect, and China National Knowledge Infrastructure databases identified 11 studies that met the inclusion criteria and provided sufficient data to assess the relationship between TM contamination of rice, fish, and shrimp products from rice-fish co-culture systems and carcinogenic risk (CR) and non-carcinogenic risk (non-CR) to humans.

Toxic Metals in a Paddy Field System: A Review.

The threat of toxic metals to food security and human health has become a high-priority issue in recent decades. As the world's main food crop source, the safe cultivation of rice has been the focus of much research, particularly the restoration of toxic metals in paddy fields. Therefore, in this paper, we focus on the effects of toxic metals on rice, as well as the removal or repair methods of toxic metals in paddy fields.

Integrated analysis of the miRNA and mRNA expression profiles in Leiocassis longirostris at gonadal maturation.

Leiocassis longirostris is a commercially important fish species that shows a sexually dimorphic growth pattern. A lack of molecular data from the gonads of this species has hindered research and selective breeding efforts. In this study, we conducted a comprehensive analysis of the expression profile of miRNA and mRNA to explore their regulatory roles in the gonadal maturation stage of L.

Integrated analysis about the effects of heat stress on physiological responses and energy metabolism in Gymnocypris chilianensis.

The temperature of the rivers in the Qilian Mountains, China varies widely from day to night, and Gymnocypris chilianensis living in these rivers may experience a change of 10 °C to 20 °C within a day. To explore the mechanisms underlying G. chilianensis responses to heat stress, we conducted an acute temperature stress experiment.

Integrative analysis identifies the quality advantage and corresponding regulatory mechanism of paddy field-cultured crayfish (Procambarus clarkii).

Procambarus clarkii is the dominant economic variety of crayfish in China, and paddy field shrimp cultivation is an organic mode of traditional rice-fish cultivation, with paddy field shrimp being the country's prevailing aquatic product. However, little has been reported on the differences in meat quality and digestive ability between paddy field and pond fish. In this study, the muscle composition and digestive function regulation of P.

MiRNA-seq analysis of spleen and head kidney tissue from aquacultured largemouth bass (Micropterus salmoides) in response to Aeromonas hydrophila infection.

Recently, the same fish diseases, which have been found in pond farming, have been found in the newly tested largemouth bass (Micropterus salmoides) system. Bacterial septicemia caused by Aeromonas hydrophila occurs frequently in largemouth bass culture leading to significant economic losses. To investigate the role miRNA in the largemouth bass disease resistance, twelve (2 tissues (spleen and head kidney) × 2 experimental groups (infected and control) × three biological replicates) small RNA libraries were constructed and sequenced with miRNA-seq.

A hybrid correcting method considering heterozygous variations by a comprehensive probabilistic model.

Background: The emergence of the third generation sequencing technology, featuring longer read lengths, has demonstrated great advancement compared to the next generation sequencing technology and greatly promoted the biological research. However, the third generation sequencing data has a high level of the sequencing error rates, which inevitably affects the downstream analysis. Although the issue of sequencing error has been improving these years, large amounts of data were produced at high sequencing errors, and huge waste will be caused if they are discarded.

Differential transcriptomic analysis of crayfish (Procambarus clarkii) from a rice coculture system challenged by Vibrio parahaemolyticus.

Rice-crayfish (Procambarus clarkii) coculture is an effective farming mode and has been promoted in various regions of China. However, infection in crayfish can be a significant economic drain. We found crayfish infected with Vibrio parahemolyticus (VP), and to understand the molecular mechanisms of the immune responses of crayfish to VP infection, Illumina sequencing was employed to identify changes in the mRNA of hepatopancreatic tissue.

A machine learning framework for genotyping the structural variations with copy number variant.

Background: Genotyping of structural variation is an important computational problem in next generation sequence data analysis. However, in cancer genomes, the copy number variant(CNV) often coexists with other types of structural variations which significantly reduces the accuracy of the existing genotype methods. The bias on sequencing coverage and variant allelic frequency can be observed on a CNV region, which leads to the genotyping approaches that misinterpret the heterozygote as a homozygote.

Accurately estimating the length distributions of genomic micro-satellites by tumor purity deconvolution.

Background: Genomic micro-satellites are the genomic regions that consist of short and repetitive DNA motifs. Estimating the length distribution and state of a micro-satellite region is an important computational step in cancer sequencing data pipelines, which is suggested to facilitate the downstream analysis and clinical decision supporting. Although several state-of-the-art approaches have been proposed to identify micro-satellite instability (MSI) events, they are limited in dealing with regions longer than one read length.

[Reconstruction of tumor clonal haplotypes based on an improved spanning algorithm].

Objective: To reconstruct tumor clonal haplotypes based on the third-generation sequencing data to effectively identify tumor heterogeneity.

Methods: We developed an algorithm for extracting somatic mutational event from the mixed tumor data and determining the connection weight of each somatic cell mutation site through the probability function. A reconstruction algorithm of the haplotype was designed based on the maximum spanning tree, and following the principle of inheritance between tumor clones, the connection pattern was determined at each mutation site in the clonal maximum spanning tree in a stepwise manner.

A graph-based algorithm for estimating clonal haplotypes of tumor sample from sequencing data.

Background: Haplotype phasing is an important step in many bioinformatics workflows. In cancer genomics, it is suggested that reconstructing the clonal haplotypes of a tumor sample could facilitate a comprehensive understanding of its clonal architecture and further provide valuable reference in clinical diagnosis and treatment. However, the sequencing data is an admixture of reads sampled from different clonal haplotypes, which complicates the computational problem by exponentially increasing the solution-space and leads the existing algorithms to an unacceptable time-/space- complexity.

An Efficient Algorithm for Sensitively Detecting Circular RNA from RNA-seq Data.

Circular RNA (circRNA) is an important member of non-coding RNA family. Numerous computational methods for detecting circRNAs from RNA-seq data have been developed in the past few years, but there are dramatic differences among the algorithms regarding the balancing of the sensitivity and precision of the detection and filtering strategies. To further improve the sensitivity, while maintaining an acceptable precision of circRNA detection, a novel and efficient detection algorithm, CIRCPlus, is proposed in this paper.

Synstable Fusion: A Network-Based Algorithm for Estimating Driver Genes in Fusion Structures.

Gene fusion structure is a class of common somatic mutational events in cancer genomes, which are often formed by chromosomal mutations. Identifying the driver gene(s) in a fusion structure is important for many downstream analyses and it contributes to clinical practices. Existing computational approaches have prioritized the importance of oncogenes by incorporating prior knowledge from gene networks.

An improved burden-test pipeline for identifying associations from rare germline and somatic variants.

Background: Identifying rare germline and somatic variants associated with cancer progression is an important research topic in cancer genomics. Although many approaches are proposed for rare variant association study, they are not fit for cancer sequencing data due to multiple issues, such as overly relying on pre-selection, losing sight of interacting hotspots, etc.

Results: In this article, we propose an improved pipeline to identify germline variant and somatic mutation interactions influencing cancer susceptibility from pair-wise cancer sequencing data.

Identifying interacting genetic variations by fish-swarm logic regression.

Understanding associations between genotypes and complex traits is a fundamental problem in human genetics. A major open problem in mapping phenotypes is that of identifying a set of interacting genetic variants, which might contribute to complex traits. Logic regression (LR) is a powerful multivariant association tool.

A probabilistic method for identifying rare variants underlying complex traits.

Background: Identifying the genetic variants that contribute to disease susceptibilities is important both for developing methodologies and for studying complex diseases in molecular biology. It has been demonstrated that the spectrum of minor allelic frequencies (MAFs) of risk genetic variants ranges from common to rare. Although association studies are shifting to incorporate rare variants (RVs) affecting complex traits, existing approaches do not show a high degree of success, and more efforts should be considered.