Plantmetabolomics.org: mass spectrometry-based Arabidopsis metabolomics—database and tools update

The PlantMetabolomics (PM) database (http://www.plantmetabolomics.org) contains comprehensive targeted and untargeted mass spectrum metabolomics data for Arabidopsis mutants across a variety of metabolomics platforms. The database allows users to generate hypotheses about the changes in metabolism for mutants with genes of unknown function. Version 2.0 of PlantMetabolomics.org currently contains data for 140 mutant lines along with the morphological data. A web-based data analysis wizard allows researchers to select preprocessing and data-mining procedures to discover differences between mutants. This community resource enables researchers to formulate models of the metabolic network of Arabidopsis and enhances the research community's ability to formulate testable hypotheses concerning gene functions. PM features new web-based tools for data-mining analysis, visualization tools and enhanced cross links to other databases. The database is publicly available. PM aims to provide a hypothesis building platform for the researchers interested in any of the mutant lines or metabolites

Policiklički aromatski ugljikovodici u zraku okolice plinskog polja Molve

Small-volume air samples (~7 m3 per 24 h) of airborne PM10 particle fraction were collected on quartz fibre filters at two measuring sites in the vicinity of the gas field Molve in April and July 2006. It took five to seven days for each sample to collect and one month to collect five to seven samples. Mass concentrations of PM10 fractions were determined by gravimetry while PAHs were analysed using a HPLC with a fluorescent detector. The analysis included fluoranthene (Flu), pyrene (Pyr), benzo(a)anthracene (BaA), chrysene (Cry), benzo(b)fluoranthene (BbF), benzo(k)fluoranthene (BkF), benzo(a)pyrene (BaP), benzo(ghi)perylene (BghiP) and indene(1,2,3-cd)pyrene (Ind). Average concentrations of all PAHs in April at site A were slightly higher than at site B while in July they were lower and similar on both sites. Average BaP concentration measured at site A in April was 0.156 ng m-3 and at site B 0.129 ng m-3, while July BaP averages were 0.022 ng m-3 at both sites. In both months, the mass concentration of BaP was lower than the limit value (1 ng m-3) and well below the tolerant value (2 ng m-3) set by a Croatian regulation of 2005. This suggests that the air near gas field Molve was of acceptable quality in respect to BaP at the time of the measurement.Uzorci PM10 frakcije lebdećih čestica skupljani su prosisavanjem malog volumena zraka (~7 m3 za 24 h) kroz filtre od kvarcnih vlakana. Svaki je uzorak skupljan tijekom pet do sedam dana na dva mjerna mjesta u okolici plinskog polja Molve. Uzorkovanje je provedeno tijekom travnja i srpnja 2006. godine. Masene koncentracije PM10 frakcije određene su gravimetrijski, dok je analiza policikličkih aromatskih ugljikovodika (PAU) rađena tekućinskom kromatografijom visoke djelotvornosti (HPLC) s fluorescentnim detektorom. Mjereni su sljedeći PAU: fluoranten, piren, benzo(a)antracen, krizen, benzo(b)fluoranten, benzo(k)fluoranten, benzo(a)piren, benzo(ghi)perilen i indeno(1,2,3-cd)piren. Srednje vrijednosti masenih koncentracija svih PAU u travnju na mjernome mjestu A bile su neznatno više od onih na mjernome mjestu B, dok su u srpnju na oba mjerna mjesta bile vrlo slične. Srednja vrijednost koncentracije BaP izmjerenog u travnju na mjernome mjestu A bila je viša od vrijednosti izmjerene na mjernome mjestu B. U srpnju su srednje vrijednosti bile znatno niže i na oba mjerna mjesta iznosile su 0.022 ng m-3. Iz rezultata dobivenih mjerenjem vidljivo je da je koncentracija benzo(a)pirena bila znatno niža od granične vrijednosti (1 ng m-3) i tolerantne vrijednosti (1 ng m-3, Uredba iz 2005.), pa možemo zaključiti da je zrak u okolici plinskog polja Molve tijekom istraživanog razdoblja bio prve kategorije kakvoće

Metabolomics as a Hypothesis-Generating Functional Genomics Tool for the Annotation of Arabidopsis thaliana Genes of “Unknown Function”

Metabolomics is the methodology that identifies and measures global pools of small molecules (of less than about 1,000 Da) of a biological sample, which are collectively called the metabolome. Metabolomics can therefore reveal the metabolic outcome of a genetic or environmental perturbation of a metabolic regulatory network, and thus provide insights into the structure and regulation of that network. Because of the chemical complexity of the metabolome and limitations associated with individual analytical platforms for determining the metabolome, it is currently difficult to capture the complete metabolome of an organism or tissue, which is in contrast to genomics and transcriptomics. This paper describes the analysis of Arabidopsis metabolomics data sets acquired by a consortium that includes five analytical laboratories, bioinformaticists, and biostatisticians, which aims to develop and validate metabolomics as a hypothesis-generating functional genomics tool. The consortium is determining the metabolomes of Arabidopsis T-DNA mutant stocks, grown in standardized controlled environment optimized to minimize environmental impacts on the metabolomes. Metabolomics data were generated with seven analytical platforms, and the combined data is being provided to the research community to formulate initial hypotheses about genes of unknown function (GUFs). A public database (www.PlantMetabolomics.org) has been developed to provide the scientific community with access to the data along with tools to allow for its interactive analysis. Exemplary datasets are discussed to validate the approach, which illustrate how initial hypotheses can be generated from the consortium-produced metabolomics data, integrated with prior knowledge to provide a testable hypothesis concerning the functionality of GUFs

SARS-CoV-2 Orphan Gene ORF10 Contributes to More Severe COVID-19 Disease

The orphan gene of SARS-CoV-2, ORF10, is the least studied gene in the virus responsible for the COVID-19 pandemic. Recent experimentation indicated ORF10 expression moderates innate immunity in vitro. However, whether ORF10 affects COVID-19 in humans remained unknown. We determine that the ORF10 sequence is identical to the Wuhan-Hu-1 ancestral haplotype in 95% of genomes across five variants of concern (VOC). Four ORF10 variants are associated with less virulent clinical outcomes in the human host: three of these affect ORF10 protein structure, one affects ORF10 RNA structural dynamics. RNA-Seq data from 2070 samples from diverse human cells and tissues reveals ORF10 accumulation is conditionally discordant from that of other SARS-CoV-2 transcripts. Expression of ORF10 in A549 and HEK293 cells perturbs immune-related gene expression networks, alters expression of the majority of mitochondrially-encoded genes of oxidative respiration, and leads to large shifts in levels of 14 newly-identified transcripts. We conclude ORF10 contributes to more severe COVID-19 clinical outcomes in the human host.This preprint is made available through medRxiv at doi:https://doi.org/10.1101/2023.11.27.23298847. It is made available under a CC-BY 4.0 International license