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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Evolutionary regression and species-specific codon usage of TLR15
Voogdt, Carlos G.P. ; Merchant, Mark E. ; Wagenaar, Jaap A. ; Putten, Jos P.M. van - \ 2018
Frontiers in Immunology 9 (2018)NOV. - ISSN 1664-3224
Codon-bias - Protease activated receptor - Reptile - TLR15 - Toll-like receptor

Toll-like receptors (TLRs) form an ancient family of innate immune receptors that detect microbial structures and activate the host immune response. Most subfamilies of TLRs (including TLR3, TLR5, and TLR7) are highly conserved among vertebrate species. In contrast, TLR15, a member of the TLR1 subfamily, appears to be unique to birds and reptiles. We investigated the functional evolution of TLR15. Phylogenetic and synteny analyses revealed putative TLR15 orthologs in bird species, several reptilian species and also in a shark species, pointing to an unprecedented date of origin of TLR15 as well as large scale reciprocal loss of this TLR in most other vertebrates. Cloning and functional analysis of TLR15 of the green anole lizard (Anolis carolinensis), salt water crocodile (Crocodylus porosus), American alligator (Alligator mississippiensis), and chicken (Gallus gallus) showed for all species TLR15 specific protease-induced activation of NF-?B, despite highly variable TLR15 protein expression levels. The variable TLR15 expression was consistent in both human and reptilian cells and could be attributed to species-specific differences in TLR15 codon usage. The species-specific codon bias was not or barely noted for more evolutionarily conserved TLRs (e.g., TLR3). Overall, our results indicate that TLR15 originates before the divergence of chondrichthyes fish and tetrapods and that TLR15 of both avian and reptilian species has a conserved function as protease activated receptor. The species-specific codon usage and large scale loss of TLR15 in most vertebrates suggest evolutionary regression of this ancient TLR.

Homologous recombination between genetically divergent campylobacter fetus lineages supports host-associated speciation
Gilbert, Maarten J. ; Duim, Birgitta ; Graaf-van Bloois, Linda van der; Wagenaar, Jaap A. ; Zomer, Aldert L. - \ 2018
Genome Biology and Evolution 10 (2018)3. - ISSN 1759-6653 - p. 716 - 722.
Campylobacter fetus - Homologous recombination - Host association - Reptile - Speciation - Whole genome sequencing

Homologous recombination is a major driver of bacterial speciation. Genetic divergence and host association are important factors influencing homologous recombination. Here, we study these factors for Campylobacter fetus, which shows a distinct intraspecific host dichotomy. Campylobacter fetus subspecies fetus (Cff) and venerealis are associated with mammals, whereas C. fetus subsp. testudinum (Cft) is associated with reptiles. Recombination between these genetically divergent C. fetus lineages is extremely rare. Previously it was impossible to show whether this barrier to recombination was determined by the differential host preferences, by the genetic divergence between both lineages or by other factors influencing recombination, such as restriction-modification, CRISPR/Cas, and transformation systems. Fortuitously, a distinct C. fetus lineage (ST69) was found, which was highly related to mammal-associated C. fetus, yet isolated from a chelonian. The whole genome sequences of two C. fetus ST69 isolates were compared with those of mammal- and reptile-associated C. fetus strains for phylogenetic and recombination analysis. In total, 5.1-5.5% of the core genome of both ST69 isolates showed signs of recombination. Of the predicted recombination regions, 80.4% were most closely related to Cft, 14.3% to Cff, and 5.6% to C. iguaniorum. Recombination from C. fetus ST69 to Cft was also detected, but to a lesser extent and only in chelonian-associated Cft strains. This study shows that despite substantial genetic divergence no absolute barrier to homologous recombination exists between two distinct C. fetus lineages when occurring in the same host type, which provides valuable insights in bacterial speciation and evolution.

A comparison of UVb compact lamps in enabling cutaneous vitamin D synthesis in growing bearded dragons
Diehl, J.J.E. ; Baines, F.M. ; Heijboer, A.C. ; Leeuwen, J.P. van; Kik, M. ; Hendriks, W.H. ; Oonincx, D.G.A.B. - \ 2018
Journal of Animal Physiology and Animal Nutrition 102 (2018)1. - ISSN 0931-2439 - p. 308 - 316.
25(OH)D - Lizard - Pogona vitticeps - Reptile - Ultraviolet light - Vitamin D - Vitamin D metabolites

The effect of exposure to different UVb compact lamps on the vitamin D status of growing bearded dragons (Pogona vitticeps) was studied. Forty-two newly hatched bearded dragons (<24 h old) were allocated to six treatment groups (n = 7 per group). Five groups were exposed to different UVb compact lamps for two hours per day, with a control group not exposed to UVb radiation. At 120 days of age, blood samples were obtained and concentrations of 25(OH)D3, Ca, P and uric acid were determined. In addition, plasma 25(OH)D3 concentration was determined in free-living adult bearded dragons to provide a reference level. Only one treatment resulted in elevated levels of 25(OH)D3 compared to the control group (41.0 ± 12.85 vs. 2.0 ± 0.0 nmol/L). All UVb-exposed groups had low 25(OH)D3 plasma levels compared to earlier studies on captive bearded dragons as well as in comparison with the free-living adult bearded dragons (409 ± 56 nmol/L). Spectral analysis indicated that all treatment lamps emitted UVb wavelengths effective for some cutaneous vitamin D synthesis. None of these lamps, under this regime, appeared to have provided a sufficient UVb dose to enable synthesis of plasma 25(OH)D3 levels similar to those of free-living bearded dragons in their native habitat.

Comparative genomics of campylobacter iguaniorum to unravel genetic regions associated with reptilian hosts
Gilbert, Maarten J. ; Miller, William G. ; Yee, Emma ; Kik, Marja ; Zomer, Aldert L. ; Wagenaar, Jaap A. ; Duim, Birgitta - \ 2016
Genome Biology and Evolution 8 (2016)9. - ISSN 1759-6653 - p. 3022 - 3029.
Campylobacter Iguaniorum - Comparative Genomics - Evolution - Phylogeny - Recombination - Reptile

Campylobacter iguaniorum is most closely related to the species C. fetus, C. hyointestinalis, andC. lanienae. Reptiles, chelonians and lizards in particular, appear to be a primary reservoir of this Campylobacter species. Here we report the genome comparison of C. iguaniorumstrain 1485E, isolated from a bearded dragon (Pogona vitticeps), and strain 2463D, isolated froma green iguana (Iguana iguana), with the genomes of closely related taxa, in particular with reptile-Associated C. fetus subsp.Testudinum. In contrast to C. fetus, C. iguaniorum is lacking an S-layer encoding region. Furthermore, a defined lipooligosaccharide biosynthesis locus, encoding multiple glycosyltransferases and bounded by waa genes, is absent from C. iguaniorum. Instead, multiple predicted glycosylation regionswere identified inC. iguaniorum.One of these regions is>50 kb withdeviantG+Ccontent, suggesting acquisition via lateral transfer. These similar, but non-homologous glycosylation regions were located at the same position on the genome in both strains. Multiple genes encoding respiratory enzymes not identified to date within the C. fetus clade were present. C. iguaniorum shared highest homology with C. hyointestinalis and C. fetus. As in reptile-Associated C. fetus subsp.Testudinum, a putative tricarballylate catabolism locus was identified. However, despite colonizing a shared host, no recent recombination between both taxa was detected. This genomic study provides a better understanding of host adaptation, virulence, phylogeny, and evolution of C. iguaniorum and related Campylobacter taxa.

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