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Foreword: Immunogenetics special issue 2017

Ronald E. Bontrop
2017 Immunogenetics  
The Ministry of Environment (ME) has been producing and providing various environmental spatial information including land-cover maps in order to effectively cope with environmental issues. With the advent of the 4th industrial revolution era and the frequent occurrence of environmental disasters, the necessity of combining the environmental spatial information with the newest technology is increasing. By considering the increased necessity, the ME and the Korean Society of Remote Sensing held
more » ... he 2017 Environmental Spatial Information Research Paper Competition with the aim of both discovering new application fields of environmental spatial information and supporting outstanding researchers. The outstanding 9 papers were finally selected after reviewing 51 papers submitted for the competition. This special issue includes the 9 papers that address advanced methodologies and application results based on environmental spatial information, as well as recent environmental issues. We expect the methodologies and applications presented in this special issue would be a reference anthology for users of environmental spatial information.
doi:10.1007/s00251-017-1012-8 pmid:28695281 fatcat:l67yg4hdpfbuzksvmwsuritdwq

Diversity of microRNAs in human and chimpanzee brain

Eugene Berezikov, Fritz Thuemmler, Linda W van Laake, Ivanela Kondova, Ronald Bontrop, Edwin Cuppen, Ronald H A Plasterk
2006 Nature Genetics  
We used massively parallel sequencing to compare the microRNA (miRNA) content of human and chimpanzee brains, and we identified 447 new miRNA genes. Many of the new miRNAs are not conserved beyond primates, indicating their recent origin, and some miRNAs seem species specific, whereas others are expanded in one species through duplication events. These data suggest that evolution of miRNAs is an ongoing process and that along with ancient, highly conserved miRNAs, there are a number of emerging
more » ... miRNAs. miRNAs are B22-nt RNA molecules that are processed from larger hairpin precursors and can regulate gene expression 1 . The role of miRNAs in diverse developmental processes and disease is increasingly recognized 2 . Several hundred miRNA genes have been identified by sequencing of size-fractionated small RNA libraries in human and other vertebrates 3 , and computational analyses have indicated that there could be substantially more miRNAs in the human genome 4,5 . To discover miRNAs that have escaped cloning in previous studies, we applied massively parallel sequencing technology 6 to obtain a total of B400,000 reads from small RNA libraries prepared from human fetal brain and different regions of adult chimpanzee brain. (All experiments were approved by the ethics committee of University Medical Center Utrecht, and written permission was obtained for the use of human fetal tissue.) We developed a computational pipeline to process the sequencing data and to distinguish miRNA candidates from other types of small RNAs (Supplementary Methods online). We mapped more than 87,000 human reads and 140,000 chimpanzee reads to the respective genome sequences and retrieved annotations for the mapped loci from the Ensembl database. Known miRNAs represented 80% and 60% of the reads in the human and chimpanzee library, respectively (Fig. 1) . The fraction of reads derived from repeat elements, rRNAs, tRNAs, other noncoding RNA and repeat-related regions was three times higher in the chimpanzee library (31% versus 11%). This category includes repeat-associated small interfering RNAs (rasiRNAs) that, in Drosophila melanogaster, originate predominantly from the antisense strand of repeats 7 . In our data set, different repeat types showed different strand biases: L2 and CR1 long interspersed nuclear elements (LINEs) had more antisense small RNAs, whereas L1
doi:10.1038/ng1914 pmid:17072315 fatcat:kbbbypf6fzegtlhsbk6ryh4gey

Immunogenetics special issue 2020: nomenclature, databases, and bioinformatics in immunogenetics

Can Kesmir, Ronald Bontrop
2019 Immunogenetics  
This article is part of the Topical Collection on "Nomenclature, databases and bioinformatics in Immunogenetics" * Can Kesmir c.kesmir@uu.nl * Ronald Bontrop bontrop@bprc.nl 1 Theoretical Biology  ...  This time the focus was on MHC/KIR in health and disease (Bontrop 2017) . Again, the various contributions provided a state-of-the-art overview of the most recent advances in the field.  ... 
doi:10.1007/s00251-019-01150-9 pmid:31848642 fatcat:6fukuy2srjalbjb4ihgcv6tvsu

Evolution of HLA-DRB Genes

Gaby G.M. Doxiadis, Ilka Hoof, Nanine de Groot, Ronald E. Bontrop
2012 Molecular biology and evolution  
2004) and class II DRB genes (Andersson et al. 1987; Mayer et al. 1993; Mnukova-Fajdelova et al. 1994; Klein and O'HUigin 1995; Satta et al. 1996; Andersson et al. 1998; Fernandez-Soria et al. 1998; Bontrop  ...  highlighted. analyzed in various introns gives a more complete picture than the analysis of parts of the intron sequences alone (Satta et al. 1996; Bergstrom et al. 1998) or of only certain TE sequences (Bontrop  ... 
doi:10.1093/molbev/mss186 pmid:22826457 pmcid:PMC3494273 fatcat:5hxv3npe7rfbznolnvpawlzksu

The mosaic of KIR haplotypes in rhesus macaques

Jeroen H. Blokhuis, Marit K. van der Wiel, Gaby G. M. Doxiadis, Ronald E. Bontrop
2010 Immunogenetics  
All animals had been haplotyped by different methods for their Mamu-A, -B and -DR allelic repertoire (Bontrop et al. 1995; Otting et al. 2005; Doxiadis et al. 2006) .  ...  macaques (Macaca mulatta) are often used as animal models for human disease or biology: for instance, with regard to infectious diseases, autoimmunity and transplantation (Knechtle and Burlingham 2004; Bontrop  ... 
doi:10.1007/s00251-010-0434-3 pmid:20204612 pmcid:PMC2858804 fatcat:3zprkgwz5nczddqsujq73qi7xa

Rapid characterization of complex genomic regions using Cas9 enrichment and Nanopore sequencing [article]

Jesse Bruijnesteijn, Marit van der Wiel, Natasja G de Groot, Ronald E Bontrop
2021 bioRxiv   pre-print
Long-read sequencing approaches have considerably improved the quality and contiguity of genome assemblies. Such platforms bear the potential to resolve even extremely complex regions, such as multigenic families and repetitive stretches of DNA. Deep sequencing coverage, however, is required to overcome low nucleotide accuracy, especially in regions with high homopolymer density, copy number variation, and sequence similarity, such as the MHC and KIR gene clusters of the immune system.
more » ... , we have adapted a targeted enrichment protocol in combination with long-read sequencing to efficiently annotate complex genomic regions. Using Cas9 endonuclease activity, segments of the complex KIR gene cluster were enriched and sequenced on an Oxford Nanopore Technologies platform. This provided sufficient coverage to accurately resolve and phase highly complex KIR haplotypes. Our strategy facilitates rapid characterization of large and complex multigenic regions, including its epigenetic footprint, in multiple species, even in the absence of a reference genome.
doi:10.1101/2021.03.11.434935 fatcat:yvbvaycafndyvoinx6tksjshcu

Modeling human arthritic diseases in nonhuman primates

Michel P M Vierboom, Margreet Jonker, Ronald E Bontrop, Bert 't Hart
2005 Arthritis Research & Therapy  
Furthermore, the Mamu-A26-associated CIA resistance was mainly observed in rhesus monkeys of Indian origin (B 't Hart, RE Bontrop, personal observation).  ... 
doi:10.1186/ar1773 pmid:15987497 pmcid:PMC1175046 fatcat:x2opfytdcjaqzmd4eajhipgau4

The HIV-1 pandemic: does the selective sweep in chimpanzees mirror humankind's future?

Natasja G de Groot, Ronald E Bontrop
2013 Retrovirology  
An HIV-1 infection progresses in most human individuals sooner or later into AIDS, a devastating disease that kills more than a million people worldwide on an annual basis. Nonetheless, certain HIV-1-infected persons appear to act as long-term non-progressors, and elite control is associated with the presence of particular MHC class
doi:10.1186/1742-4690-10-53 pmid:23705941 pmcid:PMC3667106 fatcat:4322ps6ar5cwbjj64hspxtg6wq

The Impact of MicroRNAs on Brain Aging and Neurodegeneration

Stephan P. Persengiev, Ivanela I. Kondova, Ronald E. Bontrop
2012 Current Gerontology and Geriatrics Research  
The molecular instructions that govern gene expression regulation are encoded in the genome and ultimately determine the morphology and functional specifications of the human brain. As a consequence, changes in gene expression levels might be directly related to the functional decline associated with brain aging. Small noncoding RNAs, including miRNAs, comprise a group of regulatory molecules that modulate the expression of hundred of genes which play important roles in brain metabolism. Recent
more » ... comparative studies in humans and nonhuman primates revealed that miRNAs regulate multiple pathways and interconnected signaling cascades that are the basis for the cognitive decline and neurodegenerative disorders during aging. Identifying the roles of miRNAs and their target genes in model organisms combined with system-level studies of the brain would provide more comprehensive understanding of the molecular basis of brain deterioration during the aging process.
doi:10.1155/2012/359369 pmid:22312330 pmcid:PMC3270527 fatcat:tmfo5nhgrrb5hmrexz7gwhgw54

The Genetic Mechanisms Driving Diversification of the KIR Gene Cluster in Primates

Jesse Bruijnesteijn, Natasja G. de Groot, Ronald E. Bontrop
2020 Frontiers in Immunology  
The activity and function of natural killer (NK) cells are modulated through the interactions of multiple receptor families, of which some recognize MHC class I molecules. The high level of MHC class I polymorphism requires their ligands either to interact with conserved epitopes, as is utilized by the NKG2A receptor family, or to co-evolve with the MHC class I allelic variation, which task is taken up by the killer cell immunoglobulin-like receptor (KIR) family. Multiple molecular mechanisms
more » ... e responsible for the diversification of the KIR gene system, and include abundant chromosomal recombination, high mutation rates, alternative splicing, and variegated expression. The combination of these genetic mechanisms generates a compound array of diversity as is reflected by the contraction and expansion of KIR haplotypes, frequent birth of fusion genes, allelic polymorphism, structurally distinct isoforms, and variegated expression, which is in contrast to the mainly allelic nature of MHC class I polymorphism in humans. A comparison of the thoroughly studied human and macaque KIR gene repertoires demonstrates a similar evolutionarily conserved toolbox, through which selective forces drove and maintained the diversified nature of the KIR gene cluster. This hypothesis is further supported by the comparative genetics of KIR haplotypes and genes in other primate species. The complex nature of the KIR gene system has an impact upon the education, activity, and function of NK cells in coherence with an individual's MHC class I repertoire and pathogenic encounters. Although selection operates on an individual, the continuous diversification of the KIR gene system in primates might protect populations against evolving pathogens.
doi:10.3389/fimmu.2020.582804 pmid:33013938 pmcid:PMC7516082 fatcat:5i6syfndjjbehnekfh6exyjmb4

Definition of Mafa-A and -B haplotypes in pedigreed cynomolgus macaques (Macaca fascicularis)

Nel Otting, Gaby G. M. Doxiadis, Ronald E. Bontrop
2009 Immunogenetics  
The MHC systems in humans (HLA) and in other primate species have been studied extensively (Bontrop 2006) .  ... 
doi:10.1007/s00251-009-0412-9 pmid:19937015 pmcid:PMC2802488 fatcat:mpfqyhkrjndlroz2za6bxokena

5′ Regulatory nucleotide sequence of an HLA-A * 0101null allele

N. M. Lardy, N. Otting, Ann R. van der Horst, Ronald E. Bontrop, Leo P. de Waal
1997 Immunogenetics  
doi:10.1007/s002510050254 pmid:9162102 fatcat:pgdghmo3dbhulggelvvn3asdsq

Differential recombination dynamics within the MHC of macaque species

Nanine de Groot, Gaby G. M. Doxiadis, Nel Otting, Annemiek J. M. de Vos-Rouweler, Ronald E. Bontrop
2014 Immunogenetics  
to study human biology and disease-namely, the rhesus (Macaca mulatta) and the Indonesian/Indochinese cynomolgus macaque (Macaca fascicularis)-has been thoroughly investigated (Blancher et al. 2012b; Bontrop  ... 
doi:10.1007/s00251-014-0783-4 pmid:24934118 pmcid:PMC4156779 fatcat:ifqoj7x645bjfmizpse5lg7p7m

The common marmoset: A new world primate species with limited Mhc class II variability

Susana G. Antunes, Natasja G. de Groot, Nel Otting, Ronald E. Bontrop
1997 Immunology Letters  
The common marmoset (Callithrix jacchus) is a New World primate species that is highly susceptible to fatal infections caused by various strains of bacteria. We present here a first step in the molecular characterization of the common marmoset's Mhc class II genes by nucleotide sequence analysis of the polymorphic exon 2 segments. For this study, genetic material was obtained from animals bred in captivity as well as in the wild. The results demonstrate that the common marmoset has, like other
more » ... rimates, apparently functional Mhc-DR and -DQ regions, but the Mhc-DP region has been inactivated. At the -DR and -DQ loci, only a limited number of lineages were detected. On the basis of the number of alleles found, the -DQA and -B loci appear to be oligomorphic, whereas only a moderate degree of polymorphism was observed for two of three Mhc-DRB loci. The contact residues in the peptide-binding site of the Caja-DRB1*03 lineage members are highly conserved, whereas the -DRB*W16 lineage members show more divergence in that respect. The latter locus encodes five oligomorphic lineages whose members are not observed in any other primate species studied, suggesting rapid evolution, as illustrated by frequent exchange of polymorphic motifs. All common marmosets tested were found to share one monomorphic type of Caja-DRB*W12 allele probably encoded by a separate locus. Common marmosets apparently lack haplotype polymorphism because the number of Caja-DRB loci present per haplotype appears to be constant. Despite this, however, an unexpectedly high number of allelic combinations are observed at the haplotypic level, suggesting that Caja-DRB alleles are exchanged frequently between chromosomes by recombination, promoting an optimal distribution of limited Mhc polymorphisms among individuals of a given population. This peculiar genetic make up, in combination with the limited variability of the major histocompatability complex class II repertoire, may contribute to the common marmoset's susceptibility to particular bacterial infections.
doi:10.1016/s0165-2478(97)85020-1 fatcat:kgszuq6zmfchdoaotqbus4ny3a

Origins of De Novo Genes in Human and Chimpanzee

Jorge Ruiz-Orera, Jessica Hernandez-Rodriguez, Cristina Chiva, Eduard Sabidó, Ivanela Kondova, Ronald Bontrop, Tomàs Marqués-Bonet, M.Mar Albà, James Noonan
2015 PLoS Genetics  
The birth of new genes is an important motor of evolutionary innovation. Whereas many new genes arise by gene duplication, others originate at genomic regions that did not contain any genes or gene copies. Some of these newly expressed genes may acquire coding or noncoding functions and be preserved by natural selection. However, it is yet unclear which is the prevalence and underlying mechanisms of de novo gene emergence. In order to obtain a comprehensive view of this process, we have
more » ... d in-depth sequencing of the transcriptomes of four mammalian species-human, chimpanzee, macaque, and mouse-and subsequently compared the assembled transcripts and the corresponding syntenic genomic regions. This has resulted in the identification of over five thousand new multiexonic transcriptional events in human and/or chimpanzee that are not observed in the rest of species. Using comparative genomics, we show that the expression of these transcripts is associated with the gain of regulatory motifs upstream of the transcription start site (TSS) and of U1 snRNP sites downstream of the TSS. In general, these transcripts show little evidence of purifying selection, suggesting that many of them are not functional. However, we find signatures of selection in a subset of de novo genes which have evidence of protein translation. Taken together, the data support a model in which frequently-occurring new transcriptional events in the genome provide the raw material for the evolution of new proteins. process. Here we have examined RNA-Seq data from 8 mammalian species in order to define a set of putative newly-born genes in human and chimpanzee and investigate what drives their expression. This is the largest-scale project to date that tries to address this scientific question. We have found thousands of transcripts that are human and/or chimpanzee-specific and which are likely to have originated de novo from previously nontranscribed regions of the genome. We have observed an enrichment in transcription factor binding sites in the promoter regions of these genes when compared to other species; this is consistent with the idea that the gain of new regulatory motifs results in de novo gene expression. We also show that some of the genes encode new functional proteins expressed in brain or testis, which may have contributed to phenotypic novelties in human evolution.
doi:10.1371/journal.pgen.1005721 pmid:26720152 pmcid:PMC4697840 fatcat:nov4l6mz4fanda5b7khugsqusi
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