A5047504832- Aquaculture disease management and microbiota
- Reproductive biology and impacts on aquatic species
- Genomics and Phylogenetic Studies
- Molecular Biology Techniques and Applications
- Identification and Quantification in Food
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Aquaculture Nutrition and Growth
- DNA and Biological Computing
- Advanced biosensing and bioanalysis techniques
- Physiological and biochemical adaptations
- Fish Ecology and Management Studies
- Amphibian and Reptile Biology
- Zebrafish Biomedical Research Applications
- Single-cell and spatial transcriptomics
- Plant Molecular Biology Research
- Adipose Tissue and Metabolism
- interferon and immune responses
- Genetic diversity and population structure
- Cancer-related molecular mechanisms research
- Microbial Community Ecology and Physiology
- Modular Robots and Swarm Intelligence
- RNA and protein synthesis mechanisms
- Neurogenesis and neuroplasticity mechanisms
- Plant tissue culture and regeneration
- Growth Hormone and Insulin-like Growth Factors
Norwegian University of Life Sciences
2013-2025
ZF Screens (Netherlands)
2010-2024
Leiden University
2013-2023
Genomics (United Kingdom)
2020
University of Applied Sciences Leiden
2017-2019
Arab Foundations Forum
2005
Utrecht University
2002
De novo assembly tools play a main role in reconstructing genomes from next-generation sequencing (NGS) data and usually yield number of contigs. Using paired-read it is possible to assess the order, distance orientation contigs combine them into so-called scaffolds. Although latter process crucial step finishing genomes, scaffolding algorithms are often built-in functions de cannot be independently controlled. We here present new tool, called SSPACE, which stand-alone scaffolder...
Significance Snake venoms are toxic protein cocktails used for prey capture. To investigate the evolution of these complex biological weapon systems, we sequenced genome a venomous snake, king cobra, and assessed composition venom gland expressed genes, small RNAs, secreted proteins. We show that regulatory components secretory system may have evolved from pancreatic origin toxin genes were co-opted by distinct genomic mechanisms. After co-option, important capture massively expanded gene...
Snakes possess many extreme morphological and physiological adaptations. Identification of the molecular basis these traits can provide novel understanding for vertebrate biology medicine. Here, we study snake using genome sequence Burmese python (Python molurus bivittatus), a model metabolic adaptation. We compare king cobra genomes along with genomic samples from other snakes perform transcriptome analysis to gain insights into phenotypes python. discovered rapid massive transcriptional...
Accurate species phylogenies are a prerequisite for all evolutionary research. Teleosts the largest and most diversified group of extant vertebrates, but relationships among their three oldest lineages remain unresolved. On basis seven high-quality new genome assemblies in Elopomorpha (tarpons, eels), we revisited topology deepest branches teleost phylogeny using independent gene sequence chromosomal rearrangement phylogenomic approaches. These analyses converged to single scenario that...
The enigmatic life cycle and elongated body of the European eel (Anguilla anguilla L., 1758) have long motivated scientific enquiry. Recently, research has gained in urgency, as population dwindled to point critical endangerment. We assembled a draft genome order facilitate advances all provinces biology. Here, we use investigate eel's complement Hox developmental transcription factors. show that unlike any other teleost fish, retains fully populated, duplicate clusters, which originated at...
We have sequenced the genome of endangered European eel using MinION by Oxford Nanopore, and assembled these data a novel algorithm specifically designed for large eukaryotic genomes. For this 860 Mbp genome, entire computational process takes two days on single CPU. The resulting assembly significantly improves previous draft based short reads only, both in terms contiguity (N50 1.2 Mbp) structural quality. This combination affordable nanopore sequencing light weight promises to make...
The Japanese eel is a much appreciated research object and very important for Asian aquaculture; however, its genomic resources are still limited. We have used streamlined bioinformatics pipeline the de novo assembly of genome sequence from raw Illumina reads. total assembled has size 1.15 Gbp, which divided over 323,776 scaffolds with an N50 52,849 bp, minimum scaffold 200 bp maximum 1.14 Mbp. Direct comparison representative set revealed that all Hox genes their intergenic distances almost...
Research on common carp, Cyprinus carpio, is beneficial for zebrafish research because of resources available owing to its large body size, such as the availability sufficient organ material transcriptomics, proteomics, and metabolomics. Here we describe shot gun sequencing a clonal double-haploid carp line. The assembly consists 511891 scaffolds with an N50 17 kb, predicting total genome size 1.4–1.5 Gb. A detailed analysis ten largest indicates that has considerably lower repeat coverage...
Deep RNA sequencing (RNA-seq) was performed to provide an in-depth view of the transcriptome red and white skeletal muscle exercised non-exercised rainbow trout (Oncorhynchus mykiss) with specific objective identify expressed genes quantify transcriptomic effects swimming-induced exercise. Pubertal autumn-spawning seawater-raised female were rested (n = 10) or swum for 1176 km at 0.75 body-lengths per second in a 6,000-L swim-flume under reproductive conditions 40 days. Red fish (4 lanes)...
The common carp (Cyprinus carpio) is the oldest, most domesticated and one of cultured fish species for food consumption. Besides its economic importance, also highly suitable comparative physiological disease studies in combination with animal model zebrafish (Danio rerio). They are genetically closely related but offer complementary benefits fundamental research, large body mass presenting possibilities obtaining sufficient cell material advanced transcriptome proteome studies.Here we have...
Seasonal changes in metabolism are crucial for animals to adapt annual environmental fluctuations. However, the molecular mechanisms underlying these adaptations remain poorly understood. Here, we identified a novel gene, photoperiod decoder 1 ( phod1 ), which exhibits unique bimodal expression pattern under long-day conditions Japanese medaka fish Oryzias latipes ). While is conserved across many vertebrates, except eutherians, its function remained unknown. Single-cell RNA sequencing...
In vertebrates, the anterior pituitary plays a crucial role in regulating several essential physiological processes
It is well-established that sustained exercise training can enhance brain plasticity and boost cognitive performance in mammals, but this phenomenon has not received much attention fish. The aim of study was to determine whether swimming juvenile Atlantic salmon. Brain assessed by both mapping the whole telencephalon transcriptome conducting telencephalic region-specific microdissections on target genes. We found 1772 transcripts were differentially expressed between control groups. Gene...
Abstract The pituitary is the vertebrate endocrine gland responsible for production and secretion of several essential peptide hormones. These, in turn, control many aspects an animal’s physiology development, including growth, reproduction, homeostasis, metabolism, stress responses. In teleost fish, each hormone presumably produced by a specific cell type. However, key details on regulation of, communication between these types remain to be resolved. We have therefore used single-cell...
Zebrafish is a natural host of various
Aberrations in gene expression are a hallmark of cancer cells. Differential tumor-specific transcript levels single genes or whole sets may be critical for the neoplastic phenotype and important therapeutic considerations useful as biomarkers. As an approach to filter out such relevant differences from plethora changes noted global profiling studies, we searched that conserved. Transcriptomes massive parallel sequencing different types melanoma medaka were generated compared microarray...
Abstract In seasonally breeding mammals and birds, the production of hormones that regulate reproduction (gonadotropins) is controlled by a complex pituitary-brain-pituitary pathway. Indeed, pituitary thyroid-stimulating hormone (TSH) regulates gonadotropin expression in gonadotropes, via dio2 -expressing tanycytes, hypothalamic Kisspeptin, RFamide-related peptide, gonadotropin-releasing neurons. However, fish, how seasonal environmental signals influence gonadotropins remains unclear....
The common carp is a candidate model system for immunology research.Using nextgeneration sequencing technology, we have generated huge amount of sequence reads from the genome and transcriptome.Currently, our aim to identify genes involved in development innate immune response, particularly TIR domaincontaining genes, preliminary assembly.To achieve this, developed comprehensive gene identification pipeline.This analysis allowed us estimate that has 39 domain-containing transcript isoforms genes.
The common carp is a candidate model system for immunology research. Using next-generation sequencing technology, we have generated huge amount of sequence reads from the genome and transcriptome. Currently, our aim to identify genes involved in development innate immune response, particularly TIR domain-containing genes, preliminary assembly. To achieve this, developed comprehensive gene identification pipeline. This analysis allowed us estimate that has 39 transcript isoforms genes.
We have sequenced the complete genome of plant pathogen Agrobacterium tumefaciens strain LBA4213, a derivative wild-type A. Ach5 and ancestor LBA4404 used in genetic engineering. The consists circular chromosome linear chromosome, as well megaplasmid tumor-inducing plasmid.
Summary During Agrobacterium tumefaciens ‐mediated transformation of plant cells a part the tumour‐inducing plasmid, T‐ DNA , is integrated into host genome. In addition, number virulence proteins are translocated cell. The protein VirE3 binds to Arabidopsis thaliana pB rp protein, plant‐specific general transcription factor TFIIB family. To study possible role for in transcriptional regulation, we stably expressed virE3 A. under control tamoxifen‐inducible promoter. By RNA sequencing showed...