Fish and invertebrates
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA833406 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:As described in our paper "Aspm knockout ferret reveals an evolutionary mechanism governing cerebral cortical size" (Johnson et al., Nature 2018), we used the standard Drop-seq method and analysis of Macosko et al. (2015) to capture, sequence, and analyze mRNA from single cells from Aspm wild-type, heterozygous, and knock-out littermate ferrets at embryonic day 35. Bulk reference samples were processed using standard Illumina mRNA-seq library prep and sequencing protocols, and the samples were described previously (Johnson, Wang et al., Nature Neurosci 2015)
2018-04-18 | GSE110010 | GEO
Project description:Currently as of 29/05/2019:
https://www.cancerresearchuk.org/about-cancer/find-a-clinical-trial/a-trial-looking-aspirin-and-fish-oil-possible-way-preventing-small-growths-forming-bowel-seafood
Previously:
http://cancerhelp.cancerresearchuk.org/trials/a-trial-looking-aspirin-and-fish-oil-possible-way-preventing-small-growths-forming-bowel-seafood
| 2407543 | ecrin-mdr-crc
Project description:Ricin, a protein found in castor seeds, is a lethal toxin that is designated as a category 2 select agent. Because castor seeds are easy to obtain and the toxin can be easily extracted, cases of attempted ricin poisoning are relatively common. A shotgun proteomics method for ricin identification has recently been developed (manuscript in preparation), in which ricin peptides are identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS) followed by proteomics database search, and peptide-spectrum matches are verified and compared to standard spectra by a human expert. To make this process more reproducible, objective, and high-throughput, we have created a ricin spectral library for peptide identification to supplement the human review step. To construct these spectral libraries, two pure ricin samples (from a proposed standard reference material) and crude castor seed extracts were digested with trypsin and analyzed using a standard shotgun LC-MS/MS protocol. Spectral libraries were created from the filtered search results from four database search tools. The library was then used in a search using SpectraST on samples from castor seeds. Analysis showed that the spectral library search resulted in more peptides identified from crude castor seed samples compared to MS-GF+ and Sequest plus Percolator. These results suggest that computational comparison of putative ricin peptide spectra to library spectra can be an effective method of confirming the presence of ricin, and that spectral library search may be suitable to augment the more manual and subjective aspects of the currently recommended human expert review.
2019-10-02 | PXD013711 | Pride
Project description:N-3 long chain polyunsaturated fatty acids (n-3LC-PUFA) are essential components of vertebrate membrane lipids and are now at critically low levels in modern Western diets. The main human dietary source for n-3LC-PUFA is fish and seafood, and over 50% of global fish production is currently supplied by aquaculture. However, increasing pressure to include vegetable oils, which are devoid of n-3LC-PUFA, in aquaculture feeds reduces their content in farmed fish flesh. The aim of this investigation was to infer mechanisms determining flesh n-3LC-PUFA content in Atlantic salmon. The TRAITS / SGP Atlantic salmon 17k feature cDNA microarray (ArrayExpress accession: A-MEXP-1790) was used to compare hepatic mRNA expression in 8 families, reared under common conditions, which exhibited contrasting high and low flesh n-3LC-PUFA levels at harvest. The microarray interrogations incorporated a common pooled reference design, comprising a total of 16 hybridisations (8 families x 2 - dye swap). Each family sample comprised RNA pooled from six sibs.
2010-05-01 | E-TABM-955 | biostudies-arrayexpress
Project description:We performed a parallel analysis of commonly used pre- and post-bisulfite WGBS library preparation protocols for their performance and quality of sequencing outputs. Our results show that bisulfite conversion per se generates pronounced sequencing biases, and subsequent fragmentation and amplification steps lead to several-fold overrepresentation of these artefacts. Standard pre-bisulfite library preparation methods lead to a significantly biased genomic sequence representation and a marked overestimation of methylation levels. We have integrated a bias diagnostic tool in the Bismark package and propose that amplification-free and post-bisulfite procedures should become the gold standard for WGBS library preparation.
2017-02-16 | GSE77961 | GEO
Project description:Vibrio harveyi, which belongs to family Vibrionaceae of class Gammaproteobacteria, includes the species V. carchariae and V. trachuri as its junior synonyms. The organism is a well-recognized and serious bacterial pathogen of marine fish and invertebrates, including penaeid shrimp, in aquaculture. Diseased fish may exhibit a range of lesions, including eye lesions/blindness, gastro-enteritis, muscle necrosis, skin ulcers, and tail rot disease. In shrimp, V. harveyi is regarded as the etiological agent of luminous vibriosis in which affected animals glow in the dark. There is a second condition of shrimp known as Bolitas negricans where the digestive tract is filled with spheres of sloughed-off tissue. It is recognized that the pathogenicity mechanisms of V. harveyi may be different in fish and penaeid shrimp. In shrimp, the pathogenicity mechanisms involved the endotoxin lipopolysaccharide, and extracellular proteases, and interaction with bacteriophages. In fish, the pathogenicity mechanisms involved extracellular hemolysin (encoded by duplicate hemolysin genes), which was identified as a phospholipase B and could inactivate fish cells by apoptosis, via the caspase activation pathway. V. harveyi may enter the so-called viable but nonculturable (VBNC) state, and resuscitation of the VBNC cells may be an important reason for vibriosis outbreaks in aquaculture. Disease control measures center on dietary supplements (including probiotics), nonspecific immunostimulants, and vaccines and to a lesser extent antibiotics and other antimicrobial compounds.
| S-EPMC7223180 | biostudies-literature
Project description:The application of machine learning has recently gained interest from ecotoxicological fields for its ability to model and predict chemical and/or biological processes, such as the prediction of bioconcentration. However, comparison of different models and the prediction of bioconcentration in invertebrates has not been previously evaluated. A comparison of 24 linear and machine learning models is presented herein for the prediction of bioconcentration in fish and important factors that influenced accumulation identified. R2 and root mean square error (RMSE) for the test data (n?=?110 cases) ranged from 0.23-0.73 and 0.34-1.20, respectively. Model performance was critically assessed with neural networks and tree-based learners showing the best performance. An optimised 4-layer multi-layer perceptron (14 descriptors) was selected for further testing. The model was applied for cross-species prediction of bioconcentration in a freshwater invertebrate, Gammarus pulex. The model for G. pulex showed good performance with R2 of 0.99 and 0.93 for the verification and test data, respectively. Important molecular descriptors determined to influence bioconcentration were molecular mass (MW), octanol-water distribution coefficient (logD), topological polar surface area (TPSA) and number of nitrogen atoms (nN) among others. Modelling of hazard criteria such as PBT, showed potential to replace the need for animal testing. However, the use of machine learning models in the regulatory context has been minimal to date and is critically discussed herein. The movement away from experimental estimations of accumulation to in silico modelling would enable rapid prioritisation of contaminants that may pose a risk to environmental health and the food chain.
| S-EPMC6234108 | biostudies-literature
Project description:Industrial-scale harvest of species at risk of extinction is controversial and usually highly regulated on land and for charismatic marine animals (e.g. whales). In contrast, threatened marine fish species can be legally caught in industrial fisheries. To determine the magnitude and extent of this problem, we analyze global fisheries catch and import data and find reported catch records of 91 globally threatened species. Thirteen of the species are traded internationally and predominantly consumed in European nations. Targeted industrial fishing for 73 of the threatened species accounts for nearly all (99%) of the threatened species catch volume and value. Our results are a conservative estimate of threatened species catch and trade because we only consider species-level data, excluding group records such as 'sharks and rays.' Given the development of new fisheries monitoring technologies and the current push for stronger international mechanisms for biodiversity management, industrial fishing of threatened fish and invertebrates should no longer be neglected in conservation and sustainability commitments.
| S-EPMC7506527 | biostudies-literature
Project description:Proteomic analysis of serum antibodies is challenging due to the non-germline origin of immunoglobulin (Ig) sequences and the complexity of Ig primary structure, with regions of hypervariable sequence interspersed within highly conserved framework sections resulting in an unusually high frequency of peptide-spectrum mis-identification using standard reference database search methods. Using a strategy of differential cysteine labeling with two alkylating reagents, we examined peptide-spectrum matches and decoy-based error modeling for the interpretation of antibody-derived mass spectral data.
2014-04-24 | PXD000916 | Pride
Project description:For data-independent acquisition by means of sequential window acquisition of all theoretical fragment ion spectra (SWATH), a reference library of data-dependent acquisition (DDA) runs is typically used to correlate the quantitative data from the fragment ion spectra with peptide identifications. The quality and coverage of such a reference library is therefore essential when processing SWATH data. In general, library sizes can be increased by reducing the impact of DDA precursor selection with replicate runs or fractionation. However, these strategies can affect the match between the library and SWATH measurement, and thus larger library sizes do not necessarily correspond to improved SWATH quantification. Here, three fractionation strategies to increase local library size were compared to standard library building using replicate DDA injection: protein SDS-PAGE fractionation, peptide high-pH RP-HPLC fractionation and MS-acquisition gas phase fractionation. The impact of these libraries on SWATH performance was evaluated in terms of the number of extracted peptides and proteins, the match quality of the peptides and the extraction reproducibility of the transitions. These analyses were conducted using the hydrophilic proteome of differentiating human embryonic stem cells.
2017-07-04 | PXD006190 | Pride