Automated assembly of species metabolomes through data submission into a public repository
Salek, Reza ; Conesa, Pablo ; Cochrane, Keeva ; Haug, Kenneth ; Williams, M. ; Kale, Namrata ; Moreno, P. ; Jayaseelan, Kalai Vanii ; Macias, Jose Ramon ; Nainala, Venkata Chandrasekhar ; Hall, R.D. ; Reed, Laura ; Viant, Mark ; Donovan, C. ; Steinbeck, Christoph - \ 2017
GigaScience 6 (2017)8. - ISSN 2047-217X - 4 p.
Following similar global efforts to exchange genomic and other biomedical data, global databases in metabolomics have now been established. MetaboLights, the first general purpose, publically available, cross-species, cross-application database in metabolomics, has become the fastest growing data repository at the European Bioinformatics Institute in terms of data volume. Here we present the automated assembly of species metabolomes in MetaboLights, a crucial reference for chemical biology, which is growing through user submissions.
Antimony retention and release from drained and waterlogged shooting range soil under field conditions
Hockmann, K. ; Tandy, S. ; Lenz, M. ; Reiser, R. ; Conesa, H. ; Keller, M. ; Studer, B. ; Schulin, R. - \ 2015
Chemosphere 134 (2015). - ISSN 0045-6535 - p. 536 - 543.
Many soils polluted by antimony (Sb) are subject to fluctuating waterlogging conditions; yet, little is known about how these affect the mobility of this toxic element under field conditions. Here, we compared Sb leaching from a calcareous shooting range soil under drained and waterlogged conditions using four large outdoor lysimeters. After monitoring the leachate samples taken at bi-weekly intervals for >1.5 years under drained conditions, two of the lysimeters were subjected to waterlogging with a water table fluctuating according to natural rainfall water infiltration. Antimony leachate concentrations under drained conditions showed a strong seasonal fluctuation between 110 µg L-1 in summer and
Optimal time scaling for plant growth analysis
Schnabel, S.K. ; Eilers, P.H.C. ; Eeuwijk, F.A. van - \ 2011
In: Proceedings of the 26th International Workshop on Statistical Modelling. - - p. 544 - 547.
In field trials the development of plants is regularly scored on a visual scale. Plots of the data show strongly curved relationships with time. We investigate optimal scaling of the time axis in order to get linear curves and apply it to decay data of potato plants.
Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology
Botton, A. ; Galla, G. ; Conesa, A. ; Bachem, C.W.B. ; Ramina, A. ; Barcaccia, G. - \ 2008
BMC Genomics 9 (2008). - ISSN 1471-2164 - 19 p.
genome-wide expression - pseudo-testcross strategy - poa-pratensis l - cdna-aflp - candidate genes - seed-germination - cell-division - linkage map - identification - markers
Background: After 10-year-use of AFLP (Amplified Fragment Length Polymorphism) technology for DNA fingerprinting and mRNA profiling, large repertories of genome- and transcriptome-derived sequences are available in public databases for model, crop and tree species. AFLP marker systems have been and are being extensively exploited for genome scanning and gene mapping, as well as cDNA-AFLP for transcriptome profiling and differentially expressed gene cloning. The evaluation, annotation and classification of genomic markers and expressed transcripts would be of great utility for both functional genomics and systems biology research in plants. This may be achieved by means of the Gene Ontology (GO), consisting in three structured vocabularies (i.e. ontologies) describing genes, transcripts and proteins of any organism in terms of their associated cellular component, biological process and molecular function in a species-independent manner. In this paper, the functional annotation of about 8,000 AFLP-derived ESTs retrieved in the NCBI databases was carried out by using GO terminology. Results: Descriptive statistics on the type, size and nature of gene sequences obtained by means of AFLP technology were calculated. The gene products associated with mRNA transcripts were then classified according to the three main GO vocabularies. A comparison of the functional content of cDNA-AFLP records was also performed by splitting the sequence dataset into monocots and dicots and by comparing them to all annotated ESTs of Arabidopsis and rice, respectively. On the whole, the statistical parameters adopted for the in silico AFLP-derived transcriptome-anchored sequence analysis proved to be critical for obtaining reliable GO results. Such an exhaustive annotation may offer a suitable platform for functional genomics, particularly useful in non-model species. Conclusion: Reliable GO annotations of AFLP-derived sequences can be gathered through the optimization of the experimental steps and the statistical parameters adopted. The Blast2GO software was shown to represent a comprehensive bioinformatics solution for an annotation-based functional analysis. According to the whole set of GO annotations, the AFLP technology generates thorough information for angiosperm gene products and shares common features across angiosperm species and families. The utility of this technology for structural and functional genomics in plants can be implemented by serial annotation analyses of genome- anchored fragments and organ/tissue-specific repertories of transcriptome-derived fragments.
|Microarray technology in agricultural research
Conesa, A. ; Forment, J. ; Gadea, J. ; Dijk, J.P. van - \ 2007
In: Microarray Technology Through Applications / Falciani, F., Abingdon : Taylor & Francis - ISBN 9780415378536 - p. 173 - 209.
Fecal microbiota changes with the consumption of follow-up formulas containing Bifidobacterium spp. and/or galactooligosaccharides by rats and a follow-up infant formula containing Bifidobacterium spp. by human infants
Perez-Conesa, D. ; Lopez, G. ; Ros, G.H. ; Abellan, P. ; Hartemink, R. - \ 2006
Journal of Food Science 71 (2006)1. - ISSN 0022-1147 - p. M7 - M13.
bottle-fed infants - intestinal microflora - selective medium - human-milk - flora - probiotics - prebiotics - newborn - agar
Seven groups of rats were fed during 1 mo using 1 infant formula containing Bifidobacterium bifidum and Bifidobacterium longum, 3 infant formulas containing 4-galactosyllactose at 1.2%, 5.0%, and 10.0%, and 3 infant formulas containing both ingredients. During 3 periods, corresponding to day 8 to 10, 18 to 20, and 28 to 30, fecal samples were collected for total aerobes, total anaerobes, and bifidobacteria counts. Results showed that bifidobacteria represented an important proportion out of the anaerobe group in the 1st period. However, in the 2nd period bifidobacteria decreased significantly, and in the 3rd period bifidobacteria counts increased, especially in the group fed diet containing galactooligosaccharides 1.2%. In a 2nd study, 12 human infants were fed with the infant formula containing B. bifidum and B. longum, whereas the other 12 were fed using a control infant formula. Fecal samples were collected at the age of 1, 3, 5, 7, 9, and 12 mo for total anaerobes, bacteroides, bifidobacteria, clostridia counts, as well as for fecal pH determination. Infants fed infant formula containing bifidobacteria in samples corresponding to 7th and 9th mo of age had significantly (P<0.05) higher bifidobacteria counts and a lower fecal pH than those fed control infant formula
|Involvement of subventral gland proteins (SVPs) from the potato cyst nematode Globodera rostochiensis in feeding site induction.
Stokkermans, J.P.W.G. ; Goverse, A. ; Smant, G. ; Conesa-Cegarra, A.V. ; Zilverentant, J.F. ; Pomp, R. ; Helder, J. ; Bakker, J. ; Schots, A. - \ 1996
In: Proc. Keystone Symp. on Molecular Helminthology: an integrated approach, Santa Fe, NM (1996)