☆ 4.6 Article

Prediction of Feed Efficiency and Performance-Based Traits in Fish via Integration of Multiple Omics and Clinical Covariates

BIOLOGY-BASEL (2023)

相关参考文献

注意：仅列出部分参考文献，下载原文获取全部文献信息。

Article Fisheries

Opportunities for improving feed efficiency and spinal health in New Zealand farmed Chinook salmon (Oncorhynchus tshawytscha) using genomic information

Megan Scholtens et al.

Summary: This study aimed to determine the potential for selecting improved feed conversion ratio (FCR) and reduced spinal curvature while also improving growth in Chinook salmon. The results showed that weight and condition factor had high heritabilities, while spinal curvature had a moderate heritability. Growth, feed intake, and FCR traits had low to moderate heritabilities, indicating potential for improvement through selection. Genetic correlations suggested that selection for growth could lead to some progress in improving FCR, but quantifying feed intake would result in larger gains. Additionally, an unfavorable genetic correlation was found between condition factor and spinal curvature, which should be considered in commercial breeding goals.

AQUACULTURE (2023)

添加到收藏夹

Article Fisheries

An integrated proteomics and metabolomics investigation of feed efficiency in seawater reared Chinook salmon (Oncorhynchus tshawytscha) br

Noah Esmaeili et al.

Summary: In this study, a multi-omics approach was used to investigate the molecular basis of feed efficiency (FE) in Chinook salmon. The results showed that protein synthesis was enriched in the liver and white muscle tissues of the efficient group, while pathways associated with protein degradation and glucose metabolism were affected in the inefficient group. Metabolite data revealed enrichment in pyruvate metabolism in the efficient group's liver, and phenylalanine, tyrosine, and tryptophan metabolism in the efficient group's plasma. Glutathione metabolism and valine, leucine, and isoleucine metabolism were the top enriched pathways in the inefficient group's plasma and muscle samples.

AQUACULTURE (2023)

添加到收藏夹

Review Biochemistry & Molecular Biology

Recent advances in data- and knowledge-driven approaches to explore primary microbial metabolism

Bartosz Jan Bartmanski et al.

Summary: With the advancement of metabolomics and sequencing technologies, more data on the metabolome of single microbes and their communities are available, revealing the potential of microorganisms to metabolize various chemical compounds. However, the analysis of microbial metabolomics datasets remains challenging, involving compound identification and annotation, as well as distinguishing metabolite sources in mixed samples. This review discusses recent advances in computational methods for analyzing primary microbial metabolism and the perspective of combining these approaches to further investigate primary metabolism in mixed microbial samples.

CURRENT OPINION IN CHEMICAL BIOLOGY (2023)

添加到收藏夹

Article Biochemistry & Molecular Biology

Effects of fasting and temperature on the biological parameters, proximal composition, and fatty acid profile of Chinook salmon (Oncorhynchus tshawytscha) at different life stages

Bruno C. Araujo et al.

Summary: The study found that fasting did not significantly impact body weight of chinook salmon, but fasting at 17 degrees Celsius negatively affected fillet weight and total fatty acid daily loss. Saturated, monounsaturated, and n-6 series fatty acids were preserved in fish at 17 degrees Celsius, while higher losses of DHA, EPA, and n-3 PUFA were observed in fish at this temperature and in smaller fish at 13 degrees Celsius.

COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY (2022)

添加到收藏夹

Review Fisheries

Aquatic disease in New Zealand: synthesis and future directions

Henry S. Lane et al.

Summary: Dedicated studies on aquatic disease in New Zealand began in 1974, with a focus on aquatic disease ecology and diseases of commercial species. However, aquatic disease in New Zealand has not received much attention and there is a need to address knowledge gaps on future threats such as climate change, invasive species, and pollution. More attention from the wider marine science community is needed.

NEW ZEALAND JOURNAL OF MARINE AND FRESHWATER RESEARCH (2022)

添加到收藏夹

Article Fisheries

The relationship of feed intake, growth, nutrient retention, and oxygen consumption to feed conversion ratio of farmed saltwater Chinook salmon (Oncorhynchus tshawytscha)

Jordan E. Elvy et al.

Summary: The feed conversion ratio (FCR) is important for reducing feed costs and environmental impacts. This study examined the correlation between FCR and physiological traits in farmed saltwater Chinook salmon. The results showed that high DWG and low DFI were strongly correlated with FCR efficiency.

AQUACULTURE (2022)

添加到收藏夹

Article Fisheries

Proteomic investigation of brain, liver and intestine in high feed intake and low feed intake Chinook salmon (Oncorhynchus tshawytscha)

Noah Esmaeili et al.

Summary: This study investigated the proteomic profiles of the brain, liver, and intestine in high feed intake (HFI) and low feed intake (LFI) Chinook salmon to understand the mechanisms underlying feed intake. The results showed that protein synthesis was enriched in the intestine and liver of HFI fish, while lipid metabolism was the most enriched pathway in the brain. The share of the meal was significantly higher in the HFI group, suggesting dominance among individuals. The LFI group showed signs of proteolysis and stress response, possibly due to internal or external stressors.

AQUACULTURE (2022)

添加到收藏夹

Review Biochemistry & Molecular Biology

Computational approaches for network-based integrative multi-omics analysis

Francis E. Agamah et al.

Summary: Advances in omics technologies have enabled the holistic study of biological systems. Network-based integrative approaches have revolutionized multi-omics analysis by capturing interactions between different layers of omics data. These approaches can identify biomarkers, disease subtypes, crosstalk, causality, and molecular drivers, providing insights into the understanding and treatment of diseases like COVID-19. However, challenges remain in terms of reproducibility, heterogeneity, and interpretability of results in multi-omics network-based analysis.

FRONTIERS IN MOLECULAR BIOSCIENCES (2022)

添加到收藏夹

Review Biochemical Research Methods

A comprehensive survey of the approaches for pathway analysis using multi-omics data integration

Zeynab Maghsoudi et al.

Summary: The use of pathway analysis in multi-omics setups has provided new insights into disease phenotype associations and the discovery of novel pathways. Different methods and integration strategies have been developed to aggregate multiple views and formulate new hypotheses in disease ideation and treatment targets. The review aims to assist users in selecting suitable tools for analysis purposes and highlights the challenges that need to be addressed for future development in the field.

BRIEFINGS IN BIOINFORMATICS (2022)

添加到收藏夹

Review Biochemical Research Methods

Large-scale benchmark study of survival prediction methods using multi-omics data

Moritz Herrmann et al.

Summary: This study investigates the prediction of disease outcomes using multi-omics data from TCGA. Methods that consider the multi-omics structure show slightly better prediction performance. The utility of multi-omics data for prediction purposes in the TCGA studies was found to be limited.

BRIEFINGS IN BIOINFORMATICS (2021)

添加到收藏夹

Review Fisheries

Use of glycerol in fish nutrition: a review

Marlise Teresinha Mauerwerk et al.

Summary: Crude glycerol and its purified forms can be utilized as substitutes for fish feed, showing great potential and versatility. However, factors such as digestibility and inclusion levels need to be carefully evaluated for successful implementation.

REVIEWS IN AQUACULTURE (2021)

添加到收藏夹

Article Fisheries

Effects of feed ration and temperature on Chinook salmon (Oncorhynchus tshawytscha) microbiota in freshwater recirculating aquaculture systems

Ruixiang Zhao et al.

Summary: The feed ration is crucial for fish growth performance and gut health, while temperature significantly affects water microbiota. The faecal microbiota is stable, distinct from water or feed microbiota, and dominated by Photobacterium piscicola in samples with higher water content.

AQUACULTURE (2021)

添加到收藏夹

Article Physiology

An in vitro study of urea and ammonia production and transport by the intestinal tract of fed and fasted rainbow trout: responses to luminal glutamine and ammonia loading

Ellen H. Jung et al.

Summary: Digestion of dietary protein in teleosts results in high levels of ammonia within the intestine, which can be detoxified via arginolysis. The study shows that rainbow trout intestinal tissues have the ability to produce urea and detoxify ammonia, likely through direct arginolysis.

JOURNAL OF COMPARATIVE PHYSIOLOGY B-BIOCHEMICAL SYSTEMS AND ENVIRONMENTAL PHYSIOLOGY (2021)

添加到收藏夹

Article Agricultural Engineering

Production of market-size European strain Atlantic salmon (Salmo salar) in land-based freshwater closed containment aquaculture systems

Curtis Crouse et al.

Summary: Interest in land-based farms using recirculating aquaculture systems for market-size Atlantic salmon continues to grow. This research on European-sourced Atlantic salmon reared in land-based aquaculture systems confirmed the feasibility of growing Atlantic salmon to market-size, but controlling early maturation of diploid salmon remains a challenge. All-female groups generally grew faster than mixed-sex groups, with early maturation rates varying among different groups.

AQUACULTURAL ENGINEERING (2021)

添加到收藏夹

Review Immunology

Development of Fish Parasite Vaccines in the OMICs Era: Progress and Opportunities

Saloni Shivam et al.

Summary: Parasites are increasingly recognized as catastrophic agents in aquaculture and wild aquatic habitats, leading to significant economic losses. Vaccines are recommended as the most effective solution, but there are limited commercial parasite vaccines available, highlighting the need for more research in vaccine development based on omics technologies.

VACCINES (2021)

添加到收藏夹

Article Fisheries

Comparative assessment of blood biochemistry and haematology normal ranges between Chinook salmon (Oncorhynchus tshawytscha) from seawater and freshwater farms

Paula Casanovas et al.

Summary: Blood biochemistry and haematological parameters in fish are affected by environmental changes, stress, and health status. The study provides baseline data and reference ranges for 34 indicators in Chinook salmon, showing significant differences in some parameters between freshwater and seawater environments. Some parameters were also found to be correlated with fish size.

AQUACULTURE (2021)

添加到收藏夹

Article Genetics & Heredity

A High-Density Genetic Linkage Map and Fine Mapping of QTL For Feed Conversion Efficiency in Common Carp (Cyprinus carpio)

Xiaofeng Zhang et al.

Summary: The study utilized a high-density genetic linkage map to reveal 17 QTL for feed conversion efficiency (FCE) trait in common carp, with one major cluster located on LG28. Additionally, two more QTL clusters were detected on LG32 and LG20, with a total of nine candidate genes identified for the FCE trait.

FRONTIERS IN GENETICS (2021)

添加到收藏夹

Review Biology

Omics Strategies in Current Advancements of Infectious Fish Disease Management

Maya Erna Natnan et al.

Summary: The increasing demand for fish products in aquaculture has led to disease-related issues, and the utilization of multi-omics platforms can offer better strategies for prevention and treatment, as well as the discovery of potential biomarkers.

BIOLOGY-BASEL (2021)

添加到收藏夹

Review Multidisciplinary Sciences

A 20-year retrospective review of global aquaculture

Rosamond L. Naylor et al.

Summary: The sustainability of aquaculture has been intensely debated since 2000, with major contributions coming from inland aquaculture in Asia. There have been significant advances in feed efficiency and fish nutrition, but reliance on marine ingredients remains a challenge. Molluscs and seaweed have potential for ecosystem services and global nutritional security, but their quantification, valuation, and market development are still underexploited.

NATURE (2021)

添加到收藏夹

Article Fisheries

Proteomic investigation of liver and white muscle in efficient and inefficient Chinook salmon (Oncorhynchus tshawytscha): Fatty acid metabolism and protein turnover drive feed efficiency

Noah Esmaeili et al.

Summary: Proteomics was used to compare the protein profiles of efficient and inefficient Chinook salmon, revealing enrichment of lipid metabolism-related gene ontology terms in the liver of efficient fish and protein metabolism pathways in the white muscle. Inefficient fish showed enrichment of protein processing and proteolysis terms in the liver. This study provides a preliminary understanding of the molecular landscape of feed efficiency in Chinook salmon.

AQUACULTURE (2021)

添加到收藏夹

Article Biochemistry & Molecular Biology

MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights

Zhiqiang Pang et al.

Summary: MetaboAnalyst version 5.0 has been introduced to facilitate comprehensive metabolomics data analysis and interpretation, with the aim of narrowing the gap from raw data to functional insights. Three new modules have been developed to assist in this goal, along with various other new functions and improvements in interface, graphics, and codebase. Users can now easily switch between compatible modules for a streamlined data analysis experience.

NUCLEIC ACIDS RESEARCH (2021)

添加到收藏夹

Article Environmental Sciences

Integration of Omics Tools for Understanding the Fish Immune Response Due to Microbial Challenge

Maya E. Natnan et al.

Summary: The increasing demand for fish protein has led to a rise in fish production through aquaculture and wild capture. Pathogen infections in hatcheries and grow-out ponds have resulted in reduced productivity and economic losses for farmers. Utilizing omics datasets and systems biology approaches can help scientists understand complex host-pathogen interactions and identify new targets for combating diseases in aquaculture. Various omics approaches such as genomics, transcriptomics, proteomics, and metabolomics are valuable tools in developing treatment and prevention strategies to address aquaculture diseases caused by microbial infections.

FRONTIERS IN MARINE SCIENCE (2021)

添加到收藏夹

Article Fisheries

Dietary supplementation of N-carbamylglutamate promotes growth performance by modulating the homeostasis of gut microbiota in tilapia (Oreochromis niloticus)

Wei Li et al.

Summary: The supplementation of N-carbamylglutamate (NCG) has been shown to promote the synthesis of arginine, improve physiological parameters, and modulate gut function in fish. This study found that NCG supplementation in tilapia led to higher weight gain and specific growth rates, as well as a reshaping of the gut microbiota community with an enrichment in nutritional metabolism related functions. Furthermore, key bacterial taxa identified in response to NCG supplementation played a fundamental role in nitrogen-fixing, indicating potential benefits in amino acid biosynthesis and growth promotion in tilapia.

AQUACULTURE REPORTS (2021)

添加到收藏夹

Article Agriculture, Dairy & Animal Science

Hematology parameters as potential indicators of feed efficiency in pigs

Amanda K. Lindholm-Perry et al.

Summary: This study aimed to investigate the association between hematology parameters in pigs and feed efficiency metrics. Platelet count, lymphocyte count, neutrophil, RBC counts, hemoglobin, hematocrit, and changes in these parameters were found to be correlated with average daily gain and average daily feed intake. Changes in RBC measurements, particularly hematocrit, were identified as potentially useful measurements to supplement feed efficiency phenotypes in swine.

TRANSLATIONAL ANIMAL SCIENCE (2021)

添加到收藏夹

Article Biotechnology & Applied Microbiology

Synergetic Effects ofLactobacillus plantarumand β-Glucan on Digestive Enzyme Activity, Intestinal Morphology, Growth, Fatty Acid, and Glucose-Related Gene Expression of Genetically Improved Farmed Tilapia

Mahmoud A. O. Dawood et al.

PROBIOTICS AND ANTIMICROBIAL PROTEINS (2020)

添加到收藏夹

Review Fisheries

A Proteomics and other Omics approach in the context of farmed fish welfare and biomarker discovery

Claudia Sofia Ferreira Raposo de Magalhaes et al.

REVIEWS IN AQUACULTURE (2020)

添加到收藏夹

Article Fisheries

Production cost and competitiveness in major salmon farming countries 2003-2018

Audun Iversen et al.

AQUACULTURE (2020)

添加到收藏夹

Article Agriculture, Dairy & Animal Science

Effects of in ovo feeding of N-acetyl-L-glutamate on early intestinal development and growth performance in broiler chickens

Jiguang Wang et al.

POULTRY SCIENCE (2020)

添加到收藏夹

Article Microbiology

Mucosal Microbiota and Metabolome along the Intestinal Tract Reveal a Location-Specific Relationship

Ce Yuan et al.

MSYSTEMS (2020)

添加到收藏夹

Article Fisheries

Improving winter production of Nile tilapia: What can be done?

Renata Oselame Nobrega et al.

AQUACULTURE REPORTS (2020)

添加到收藏夹

Article Agriculture, Dairy & Animal Science

Genomic regions and signaling pathways associated with indicator traits for feed efficiency in juvenile Atlantic salmon (Salmo salar)

Hanne Dvergedal et al.

GENETICS SELECTION EVOLUTION (2020)

添加到收藏夹

Article Biochemical Research Methods

Variable selection and validation in multivariate modelling

Lin Shi et al.

BIOINFORMATICS (2019)

添加到收藏夹

Article Chemistry, Analytical

Systematic Error Removal Using Random Forest for Normalizing Large-Scale Untargeted Lipidomics Data

Sili Fan et al.

ANALYTICAL CHEMISTRY (2019)

添加到收藏夹

Article Fisheries

Agonistic behaviour behaviour and feed efficiency in juvenile Nile tilapia Oreochromis niloticus

Hugues de Verdal et al.

AQUACULTURE (2019)

添加到收藏夹

Article Fisheries

Application of a Fourier transform-near infrared reflectance spectroscopy method for the rapid proximate analysis of the greenshell mussel (Perna canaliculus) and king (Chinook) salmon (Oncorhynchus tshawytscha)

Matthew R. Miller et al.

AQUACULTURE RESEARCH (2019)

添加到收藏夹

Article Biochemical Research Methods

Block Forests: random forests for blocks of clinical and omics covariate data

Roman Hornung et al.

BMC BIOINFORMATICS (2019)

添加到收藏夹

Article Fisheries

Rainbow trout (Oncorhynchus mykiss) urea cycle and polyamine synthesis gene families show dynamic expression responses to inflammation

T. C. Clark et al.

FISH & SHELLFISH IMMUNOLOGY (2019)

添加到收藏夹

Article Biochemistry & Molecular Biology

Metabolic Effects of Dietary Glycerol Supplementation in Muscle and Liver of European Seabass and Rainbow Trout by 1H NMR Metabolomics

Mariana Palma et al.

METABOLITES (2019)

添加到收藏夹

Article Biochemical Research Methods

Evaluation of variable selection methods for random forests and omics data sets

Frauke Degenhardt et al.

BRIEFINGS IN BIOINFORMATICS (2019)

添加到收藏夹

Article Agriculture, Dairy & Animal Science

Selection for feed efficiency in Atlantic salmon using individual indicator traits based on stable isotope profiling

Hanne Dvergedal et al.

GENETICS SELECTION EVOLUTION (2019)

添加到收藏夹

Review Fisheries

Improving feed efficiency in fish using selective breeding: a review

Hugues de Verdal et al.

REVIEWS IN AQUACULTURE (2018)

添加到收藏夹

Article Biochemical Research Methods

SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses

Tomas Vetrovsky et al.

BIOINFORMATICS (2018)

添加到收藏夹

Article Cell Biology

Infant and Adult Gut Microbiome and Metabolome in Rural Bassa and Urban Settlers from Nigeria

Funmilola A. Ayeni et al.

CELL REPORTS (2018)

添加到收藏夹

Review Geriatrics & Gerontology

Random Forest Algorithm for the Classification of Neuroimaging Data in Alzheimer's Disease: A Systematic Review

Alessia Sarica et al.

FRONTIERS IN AGING NEUROSCIENCE (2017)

添加到收藏夹

Article Microbiology

Microbiome Datasets Are Compositional: And This Is Not Optional

Gregory B. Gloor et al.

FRONTIERS IN MICROBIOLOGY (2017)

添加到收藏夹

Article Biochemical Research Methods

UpSetR: an R package for the visualization of intersecting sets and their properties

Jake R. Conway et al.

BIOINFORMATICS (2017)

添加到收藏夹

Article Chemistry, Analytical

Coupling Targeted and Untargeted Mass Spectrometry for Metabolome-Microbiome-Wide Association Studies of Human Fecal Samples

Alexey V. Melnik et al.

ANALYTICAL CHEMISTRY (2017)

添加到收藏夹

Article Biochemical Research Methods

Integration of multi-omics data for prediction of phenotypic traits using random forest

Animesh Acharjee et al.

BMC BIOINFORMATICS (2016)

添加到收藏夹

Article Ecology

Atlantic Salmon (Salmo salar L.) Gastrointestinal Microbial Community Dynamics in Relation to Digesta Properties and Diet

Kamarul Zaman Zarkasi et al.

MICROBIAL ECOLOGY (2016)

添加到收藏夹

Article Biochemical Research Methods

Integrative random forest for gene regulatory network inference

Francesca Petralia et al.

BIOINFORMATICS (2015)

添加到收藏夹

Article Endocrinology & Metabolism

Sauvignon blanc metabolomics: grape juice metabolites affecting the development of varietal thiols and other aroma compounds in wines

Farhana R. Pinu et al.

METABOLOMICS (2014)

添加到收藏夹

Article Fisheries

Feeding behavior and stress response explain individual differences in feed efficiency in juveniles of Nile tilapia Oreochromis niloticus

Catarina I. M. Martins et al.

AQUACULTURE (2011)

添加到收藏夹

Article Biochemical Research Methods

Metab: an R package for high-throughput analysis of metabolomics data generated by GC-MS

Raphael Aggio et al.

BIOINFORMATICS (2011)

添加到收藏夹

Article Biochemistry & Molecular Biology

Alkylation or Silylation for Analysis of Amino and Non-Amino Organic Acids by GC-MS?

Silas G. Villas-Boas et al.

METABOLITES (2011)

添加到收藏夹

Article Biochemical Research Methods

Analytical platform for metabolome analysis of microbial cells using methyl chloroformate derivatization followed by gas chromatography-mass spectrometry

Kathleen F. Smart et al.

NATURE PROTOCOLS (2010)

添加到收藏夹

Article Endocrinology & Metabolism

Fat and Fatty Acid Terminology, Methods of Analysis and Fat Digestion and Metabolism: A Background Review Paper

W. M. Nimal Ratnayake et al.

ANNALS OF NUTRITION AND METABOLISM (2009)

添加到收藏夹

Article Multidisciplinary Sciences

Feeding aquaculture in an era of finite resources

Rosamond L. Naylor et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

添加到收藏夹

Article Biochemistry & Molecular Biology

Effects of exercise on nitrogen excretion, carbamoyl phosphate synthetase III activity and related urea cycle enzymes in muscle and liver tissues of juvenile rainbow trout (Oncorhynchus mykiss)

AE Todgham et al.

COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR AND INTEGRATIVE PHYSIOLOGY (2001)

添加到收藏夹

© Peeref 2019-2024. All rights reserved.