Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Profile hidden Markov models trained on aligned KEGG Orthology sequences for enzyme annotation
Rodenburg, Y.A. ; Ridder, D. de; Govers, F. ; Seidl, M.F. - \ 2019
Wageningen University & Research
annotation - bioinformatics - enzymes - hidden Markov models - HMM - homology - KEGG - Kyoto Encyclopedia of Genes and Genomes - proteins
Profile hidden Markov models trained on aligned KEGG Orthology sequences for enzyme annotation. These HMMs were used to reconstruct metabolic networks for the manuscript: The genome of Peronospora belbahrii reveals high heterozygosity, a low number of canonical effectors and CT-rich promoters
Aspergillus niger citrate exporter revealed by comparison of two alternative citrate producing conditions
Odoni, Dorett I. ; Vazquez-Vilar, Marta ; Gaal, Merlijn P. van; Schonewille, Tom ; Martins Dos Santos, Vitor A.P. ; Tamayo-Ramos, Juan Antonio ; Suarez-Diez, Maria ; Schaap, Peter J. - \ 2019
FEMS Microbiology Letters 366 (2019)7. - ISSN 0378-1097
Aspergillus niger - citrate - homology - MDR - transcriptomics - transport

Currently, there is no consensus regarding the mechanism underlying Aspergillus niger citrate biosynthesis and secretion. We hypothesise that depending on the experimental setup, extracellular citrate accumulation can have fundamentally different underlying transcriptomic landscapes. We show that varying the amount and type of supplement of an arginine auxotrophic A. niger strain results in transcriptional down-regulation of citrate metabolising enzymes in the condition in which more citrate is accumulated extracellularly. This contrasts with the transcriptional adaptations when increased citrate production is triggered by iron limitation. By combining gene expression data obtained from these two very distinct experimental setups with hidden Markov models and transporter homology approaches, we were able to compile a shortlist of the most likely citrate transporter candidates. Two candidates (An17g01710 and An09g06720m.01) were heterologously expressed in the yeast Saccharomyces cerevisiae, and one of the resultant mutants showed the ability to secrete citrate. Our findings provide steps in untangling the complex interplay of different mechanisms underlying A. niger citrate accumulation, and we demonstrate how a comparative transcriptomics approach complemented with further bioinformatics analyses can be used to pinpoint a fungal citrate exporter.

Review and simulation of homoplasy and collision in AFLP
Gort, G. ; Eeuwijk, F.A. van - \ 2012
Euphytica 183 (2012)3. - ISSN 0014-2336 - p. 389 - 400.
fragment length distributions - in-silico - markers - bands - probabilities - homology - size
In this paper we give a short review of the problems of homoplasy and collision in AFLP, and describe a software tool that we developed to illustrate these problems. AFLP is a DNA fingerprinting technique, producing profiles of bands, the result of the separation of DNA fragments by length on a gel or microcapillary system. The profiles are usually interpreted as binary band absence/presence patterns. We focus on two major problems: (1) Within a profile two or more fragments of the same length but of different genomic origin may have been selected, colliding into a single band. This collision problem, akin to the birthday problem, may be surprisingly large. (2) In a pair of profiles two equally long fragments of different genomic origin may have been selected, appearing as identical bands in the two profiles. This is called homoplasy. Both problems are quantified by modeling AFLP as a random sampling technique of fragment lengths. AFLP may be used in phylogenetic studies to estimate the pairwise genetic similarity of individuals. Similarity coefficients like Dice and Jaccard coefficients overestimate the true genetic similarity because of homoplasy, with increasing bias for higher numbers of bands per profile. Corrected estimators are described, which do not suffer from bias. The ideas are illustrated using a new software tool. Data from studies on Arabidopsis and tomato serve as examples. Finally, we make some recommendations with respect to the use of AFLP.
Homoplasy corrected estimation of genetic similarity from AFLP bands, and the effect of the number of bands on the precision of estimation
Gort, G. ; Hintum, T.J.L. van; Eeuwijk, F.A. van - \ 2009
Theoretical and Applied Genetics 119 (2009)3. - ISSN 0040-5752 - p. 397 - 416.
fragment length distributions - collision probabilities - species relationships - size homoplasy - diversity - markers - homology - lettuce - genome - barley
AFLP is a DNA fingerprinting technique, resulting in binary band presence–absence patterns, called profiles, with known or unknown band positions. We model AFLP as a sampling procedure of fragments, with lengths sampled from a distribution. Bands represent fragments of specific lengths. We focus on estimation of pairwise genetic similarity, defined as average fraction of common fragments, by AFLP. Usual estimators are Dice (D) or Jaccard coefficients. D overestimates genetic similarity, since identical bands in profile pairs may correspond to different fragments (homoplasy). Another complicating factor is the occurrence of different fragments of equal length within a profile, appearing as a single band, which we call collision. The bias of D increases with larger numbers of bands, and lower genetic similarity. We propose two homoplasy- and collision-corrected estimators of genetic similarity. The first is a modification of D, replacing band counts by estimated fragment counts. The second is a maximum likelihood estimator, only applicable if band positions are available. Properties of the estimators are studied by simulation. Standard errors and confidence intervals for the first are obtained by bootstrapping, and for the second by likelihood theory. The estimators are nearly unbiased, and have for most practical cases smaller standard error than D. The likelihood-based estimator generally gives the highest precision. The relationship between fragment counts and precision is studied using simulation. The usual range of band counts (50–100) appears nearly optimal. The methodology is illustrated using data from a phylogenetic study on lettuce
AFLP markers support separation of Solanum nodiflorum from Solanum americanum sensu strictio (Solanaceae)
Manoko, M.L.K. ; Berg, R.G. van den; Feron, R.M.C. ; Weerden, G.M. van der; Mariani, C. - \ 2007
Plant Systematics and Evolution 267 (2007)1-4. - ISSN 0378-2697 - p. 1 - 11.
genetic-relationships - l. - biosystematics - relatives - homology - barley - wild
This study was aimed at examining the relationships between the African material of Solanum americanum (also designated as S. nodiflorum), accessions of this taxon from other geographical areas, and American S. americanum using AFLP markers. 96 individuals representing 39 accessions of S. americanum sensu lato and related diploid species from the widest possible geographical range, and one accession of S. dulcamara (as outgroup) were used. The AFLP results suggested that American S. americanum differs from S. nodiflorum and that the material investigated in this study can be assigned to three different species: S. americanum sensu stricto, S. nodiflorum and a Solanum species from Brazil. These species can be differentiated based on a combination of floral and fruit characteristics.
Fish on avian lampbrush chromosomes produces higher resolution gene mapping
Galkina, S.A. ; Deryusheva, S. ; Fillon, V. ; Vignal, A. ; Crooijmans, R.P.M.A. ; Groenen, M.A.M. ; Rodionov, A.V. ; Gaginskaya, E. - \ 2006
Genetica 128 (2006)1-3. - ISSN 0016-6707 - p. 241 - 251.
coturnix-coturnix-japonica - japanese-quail - dna-sequence - chicken chromosomes - gallus-domesticus - cytological map - crossing-over - w-chromosome - evolution - homology
Giant lampbrush chromosomes, which are characteristic of the diplotene stage of prophase I during avian oogenesis, represent a very promising system for precise physical gene mapping. We applied 35 chicken BAC and 4 PAC clones to both mitotic metaphase chromosomes and meiotic lampbrush chromosomes of chicken (Gallus gallus domesticus) and Japanese quail (Coturnix coturnix japonica). Fluorescence in situ hybridization (FISH) mapping on lampbrush chromosomes allowed us to distinguish closely located probes and revealed gene order more precisely. Our data extended the data earlier obtained using FISH to chicken and quail metaphase chromosomes 1¿6 and Z. Extremely low levels of inter- and intra-chromosomal rearrangements in the chicken and Japanese quail were demonstrated again. Moreover, we did not confirm the presence of a pericentric inversion in Japanese quail chromosome 4 as compared to chicken chromosome 4. Twelve BAC clones specific for chicken chromosome 4p and 4q showed the same order in quail as in chicken when FISH was performed on lampbrush chromosomes. The centromeres of chicken and quail chromosomes 4 seem to have formed independently after centric fusion of ancestral chromosome 4 and a microchromosome
Pharmacology of stomoxytachykinin receptor depends on second messenger system
Poels, J. ; Nachman, R.J. ; Akerman, K.E. ; Oonk, H.B. ; Guerrero, F. ; Loof, A. de; Janecka, A.E. ; Torfs, H. ; Vanden Broeck, J. - \ 2005
Peptides 26 (2005)1. - ISSN 0196-9781 - p. 109 - 114.
protein-coupled receptors - tachykinin-like peptides - drosophila-melanogaster - thyrotropin receptor - insect neuropeptides - nk1 receptor - agonist - expression - homology - family
STKR is a neurokinin receptor derived from the stable fly, Stomoxys calcitrans. Insect tachykinin-related peptides, also referred to as ¿insectatachykinins¿, produce dose-dependent calcium and cyclic AMP responses in cultured Drosophila melanogaster Schneider 2 (S2) cells that were stably transfected with the cloned STKR cDNA. Pronounced differences in pharmacology were observed between agonist-induced calcium and cyclic AMP responses. The results indicate that the pharmacological properties of STKR depend on its coupling to a unique second messenger system. Therefore, a model postulating the existence of multiple active receptor conformations is proposed. This article presents the first evidence that an insect peptide receptor with dual coupling properties to second messenger systems can display agonist-dependent functional differences.
Expression of a cucumber class III chitinase and Nicotiana plumbaginifolia class I glucanase genes in transgenic potato plants
Moravcikova, J. ; Matusikova, I. ; Libantova, J. ; Bauer, M. ; Mlynarova, L. - \ 2004
Plant Cell, Tissue and Organ Culture: an international journal on in vitro culture of higher plants 79 (2004)2. - ISSN 0167-6857 - p. 161 - 168.
tobacco plants - agrobacterium-tumefaciens - antifungal activity - acidic chitinase - tomato plants - beta-1,3-glucanase - dna - resistance - induction - homology
The genes encoding for a cucumber class III chitinase and Nicotiana plumbaginifolia class I glucanase were co-introduced into Slovak potato (Solanum tuberosum L.) breeding line 116/86 using Agrobacterium tumefaciens. For both transgenes the number of integrated copies and level of RNA expression were determined. These analyses demonstrated low variation and significant correlation in expression of the introduced transgenes. The effect of transgene expression on fungal susceptibility of transformants was evaluated in vitro. Hyphal extension assays revealed no obvious differences in the ability of extracts from transformants to inhibit growth of Rhizoctonia solani comparing to non-transformed potato.
Functional analysis of synthetic insectatachykinin analogs on recombinant neurokinin receptor expressing cell lines
Torfs, H. ; Akerman, K.E. ; Nachman, R.J. ; Oonk, H.B. ; Detheux, M. ; Poels, J. ; Loy, T. van; Loof, A. ; Meloen, R.H. ; Vassart, G. ; Parmentier, M. ; Broeck, J. van den - \ 2002
Peptides 23 (2002)11. - ISSN 0196-9781 - p. 1999 - 2005.
tachykinin-related peptides - insect neuropeptides - urechis-unicinctus - myotropic peptides - echiuroid worm - identification - vertebrate - homology - family - cockroach
The activity of a series of synthetic tachykinin-like peptide analogs was studied by means of microscopic calcium imaging on recombinant neurokinin receptor expressing cell lines. A C-terminal pentapeptide (FTGMRa) is sufficient for activation of the stomoxytachykinin receptor (STKR) expressed in Schneider 2 cells. Replacement of amino acid residues at the position of the conserved phenylalanine (F) or arginine (R) residues by alanine (A) results in inactive peptides (when tested at 1 ¿M), whereas A-replacements at other positions do not abolish the biological activity of the resulting insectatachykinin-like analogs. Calcium imaging was also employed to compare the activity of C-terminally substituted tachykinin analogs on three different neurokinin receptors. The results indicate that the major pharmacological and evolutionary difference between tachykinin-related agonists for insect (STKR) and human (NK1 and NK2) receptors resides in the C-terminal amino acid residues (R versus M). A single C-terminal amino acid change can turn an STKR-agonist into an NK-agonist and vice versa
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