Christiaan Henkel

Christiaan Henkel
Norwegian University of Life Sciences

About

120
Publications
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Introduction
I am a genome biologist at the Norwegian University of Life Sciences (NMBU).

Publications

Publications (120)
Article
Full-text available
De novo assembly tools play a main role in reconstructing genomes from next-generation sequencing (NGS) data and usually yield a number of contigs. Using paired-read sequencing data it is possible to assess the order, distance and orientation of contigs and combine them into so-called scaffolds. Although the latter process is a crucial step in fini...
Article
Full-text available
The enigmatic life cycle and elongated body of the European eel (Anguilla anguilla L., 1758) have long motivated scientific enquiry. Recently, eel research has gained in urgency, as the population has dwindled to the point of critical endangerment. We have assembled a draft genome in order to facilitate advances in all provinces of eel biology. Her...
Article
Full-text available
Significance Snake venoms are toxic protein cocktails used for prey capture. To investigate the evolution of these complex biological weapon systems, we sequenced the genome of a venomous snake, the king cobra, and assessed the composition of venom gland expressed genes, small RNAs, and secreted venom proteins. We show that regulatory components of...
Article
Full-text available
We have sequenced the genome of the endangered European eel using the MinION by Oxford Nanopore, and assembled these data using a novel algorithm specifically designed for large eukaryotic genomes. For this 860 Mbp genome, the entire computational process takes two days on a single CPU. The resulting genome assembly significantly improves on a prev...
Article
Full-text available
The pituitary is the vertebrate endocrine gland responsible for the production and secretion of several essential peptide hormones. These, in turn, control many aspects of an animal’s physiology and development, including growth, reproduction, homeostasis, metabolism, and stress responses. In teleost fish, each hormone is presumably produced by a s...
Article
Full-text available
Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum is evolutionarily one of the closest non-tuberculous species related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen, we have previ...
Preprint
Full-text available
Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum is evolutionarily one of the closest non-tuberculous species related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen, we have previ...
Article
Full-text available
In seasonally breeding mammals and birds, the production of the hormones that regulate reproduction (gonadotropins) is controlled by a complex pituitary-brain-pituitary pathway. Indeed, the pituitary thyroid-stimulating hormone (TSH) regulates gonadotropin expression in pituitary gonadotropes, via dio2-expressing tanycytes, hypothalamic Kisspeptin,...
Preprint
Full-text available
In vertebrates, pituitary gonadotropins (follicle-stimulating and luteinizing hormones: FSH and LH) regulate gonadal development and maturation, therefore playing an essential role in reproduction. The seasonal regulation of gonadotropins has been widely studied in mammals and birds, and in these taxa thyroid-stimulating hormone (TSH) was found to...
Article
Accurate species phylogenies are a prerequisite for all evolutionary research. Teleosts are the largest and most diversified group of extant vertebrates, but relationships among their three oldest extant lineages remain unresolved. On the basis of seven high-quality new genome assemblies in Elopomorpha (tarpons, eels), we revisited the topology of...
Article
Full-text available
Directing both organismal homeostasis and physiological adaptation, the pituitary is a key endocrine gland in all vertebrates. One of its major tasks is to coordinate sexual maturation through the production and release of hormones stimulating gonad development. In order to study its developmental dynamics in the model fish medaka (Oryzias latipes)...
Article
Full-text available
In fish, prolactin-producing cells (lactotropes) are located in the anterior part of the pituitary and play an essential role in osmoregulation. However, small satellite lactotrope clusters have been described in other parts of the pituitary in several species. The functional and developmental backgrounds of these satellite clusters are not known....
Preprint
Full-text available
We have previously documented that overexpression of the Arabidopsis nuclear protein AHL15 leads to reprogramming of somatic cells to embryonic cells (Karami et al., 2021) and to suppression of plant ageing (Karami et al., 2020). Here we show that transient (4 hours) activation of overexpressed AHL15-GR in Arabidopsis seedlings has long-term effect...
Article
Full-text available
The vertebrate pituitary is a dynamic organ, capable of adapting its hormone secretion to different physiological demands. In this context, endocrinologists have debated for the past 40 years if endocrine cells are mono or multi-hormonal. Since its establishment, the dominant “one cell, one hormone” model has been continuously challenged. In mammal...
Preprint
Full-text available
In fish, prolactin-producing cells (lactotropes) are located in the anterior part of the pituitary and play an essential role in osmoregulation. However, small satellite lactotrope populations have been described in other parts of the pituitary in several species. The functional and developmental backgrounds of these extra populations are not known...
Preprint
Full-text available
Accurate species phylogenies are a prerequisite for evolutionary research. Teleosts are by far the largest and the most diversified group of extant vertebrates, but relationships among the three oldest lineages of extant teleosts remain unresolved. Based on seven high-quality new genome assemblies in Elopomorpha (tarpons, eels), we revisited the to...
Article
Full-text available
Objective Currently the majority of non-culturable microbes in sea water are yet to be discovered, Nanopore offers a solution to overcome the challenging tasks to identify the genomes and complex composition of oceanic microbiomes. In this study we evaluate the utility of Oxford Nanopore Technologies (ONT) sequencing to characterize microbial diver...
Article
Full-text available
Molecular genetic data have recently been incorporated in attempts to reconstruct the ecology of the ancestral snake, though this has been limited by a paucity of data for one of the two main extant snake taxa, the highly fossorial Scolecophidia. Here we present and analyse vision genes from the first eye transcriptomic and genome-wide data for Sco...
Article
Full-text available
In vertebrates, the anterior pituitary plays a crucial role in regulating several essential physiological processes via the secretion of at least seven peptide hormones by different endocrine cell types. Comparative and comprehensive knowledge of the spatial distribution of those endocrine cell types is required to better understand their physiolog...
Preprint
Full-text available
Directing both organismal homeostasis and physiological adaptation, the pituitary is a key endocrine gland in all vertebrates. It communicates the needs of the organism to different organs by secreting hormones into the bloodstream. Here, we have used the model fish medaka to investigate the developmental dynamics in the pituitary using a comprehen...
Preprint
Full-text available
In vertebrates, the anterior pituitary plays a crucial role in regulating several essential physiological processes via the secretion of at least seven peptide hormones by different endocrine cell types. Comparative and comprehensive knowledge of the spatial distribution of those endocrine cell types is required to better understand their role duri...
Preprint
Full-text available
The pituitary is the vertebrate endocrine gland responsible for the production and secretion of several essential peptide hormones. These, in turn, control many aspects of an animal’s physiology and development, including growth, reproduction, homeostasis, metabolism and stress responses. In teleost fish, each hormone is presumably produced by a sp...
Article
Full-text available
The life cycle of European eel (Anguilla anguilla), a catadromous species, is complex and enigmatic. In nature, during the silvering process prior to their long spawning migration, reproductive development is arrested, and they cease feeding. In studies of reproduction using hormonal induction, eels are equivalently not feed. Therefore, in female e...
Preprint
Full-text available
Objective Currently the majority of non-culturable microbes in sea water are yet to be discovered, Nanopore offers a solution to overcome the challenging tasks to identify the genomes and complex composition of oceanic microbiomes. In this study we evaluate the utility of Oxford Nanopore Technologies (ONT) sequencing to characterize microbial diver...
Preprint
Full-text available
Objective: Currently the majority of non-culturable microbes in sea water are yet to be discovered, Nanopore offers a solution to overcome the challenging tasks to identify the genomes and complex composition of oceanic microbiomes. In this study we evaluate the utility of Oxford Nanopore Technologies (ONT) sequencing to characterize microbial dive...
Article
Full-text available
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 in fish. The aim of this study was to determine whether sustained swimming exercise can enhance brain plasticity in juvenile Atlantic salmon. Brain plasticity was assess...
Preprint
Full-text available
Currently the majority of non-culturable microbes in sea water are yet to be discovered, Nanopore offers a solution to overcome the challenging tasks to identify the genomes and complex composition of oceanic microbiomes. In this study we evaluate the utility of Oxford Nanopore Technologies (ONT) sequencing to characterize microbial diversity in se...
Chapter
Bioinformatics applies specialised computer programs to search and process biological data. The fast development of fundamental (bio) medical data and technology facilitates advanced molecular diagnostics. High-throughput diagnostics has become the reality with increasing accuracy. The volume and complexity of data require computer-assisted process...
Chapter
Over the past decades, it has become almost routine to determine the identity and order of nucleotide bases in any piece of nucleic acid. DNA sequencing has evolved from analysing one nucleotide at a time, by using costly and time-consuming assays, to massively parallel ‘next- and third-generation sequencing’ approaches. Over the past 15 years, sub...
Article
Full-text available
p>This Article contains errors. Since the publication of this Article, the website hosting the assembly data has become inactive. The data has now been re-deposited in the DataverseNO repository. As such, the corrected Data Availability section should be as follows. Data Availability The nanopore sequencing data are available in the European Nucleo...
Article
Full-text available
Background: The introduction of the MinION sequencing device by Oxford Nanopore Technologies may greatly accelerate whole genome sequencing. Nanopore sequence data offers great potential for de novo assembly of complex genomes without using other technologies. Furthermore, Nanopore data combined with other sequencing technologies is highly useful f...
Article
Full-text available
Background: The introduction of the MinION TM sequencing device by Oxford Nanopore Technologies may greatly accelerate whole genome sequencing. It has been shown that the nanopore sequence data, in combination with other sequencing technologies, is highly useful for accurate annotation of all genes in the genome. However, it also offers great poten...
Article
Full-text available
The rapidly growing world population has a greatly increasing demand for plant biomass, thus creating a great interest in the development of methods to enhance the growth and biomass accumulation of crop species. In this study, we used zinc finger artificial transcription factor (ZF-ATF)-mediated genome interrogation to manipulate the growth charac...
Data
A to scale overview of the phenotypes and sizes of wild-type Col-0 plants, VP16-02-003 plants (T3) and plants of retransformant lines reconstituted from VP16-02-003 that have significantly larger RSA than the wild-type Col-0 (T2; segregating). A) Representative individuals of Col-0 (out of 48 plants), VP16-02-003 and retransformant lines harboring...
Data
Quantification of the relative fresh weight (A) and dry weight (B) of wild-type Col-0 plants, VP16-05-014 plants (T3; segregating) and retransformant plants reconstituted from VP16-05-014 (T2; segregating) compared to the wild-type Col-0 (28 dpg). The fresh and dry weights of plants of the indicated genotypes was calculated in terms of percentage o...
Data
Overview of Differentially Expressed Genes (DEGs) compared to the wild-type Col-0 in the RNA sequencing data sets of the indicated 3F-EAR transgenic lines (p < 0.0001). ‘Background’ refers to RNA expression data derived from the pool of lines expressing 3F-EAR fusions similar to the specific 3F-EAR fusion expressed in the selected lines, but withou...
Data
Overview of the 157 Differentially Expressed Genes (DEGs) compared to the wild-type Col-0 that are shared in the RNA sequencing data sets of the 3F-EAR transgenic lines EAR-13-68, EAR-15-025 and EAR-15-053 (p < 0.0001). The 10 DEGs that were not found in the transcriptomes of background pools are shaded in grey. (PDF)
Data
Overview of significantly enriched GO categories (p < 0.05) found for the 104 upregulated (Up) and 53 downregulated (Down) DEGs compared to the wild-type Col-0 that are shared in the RNA sequencing data sets of the three larger 3F-EAR transgenic lines, EAR-13-68, EAR-15-025 and EAR-15-053. (PDF)
Data
Overview of the 116 Differentially Expressed Genes (DEGs) compared to the Col-0 that are shared in all RNA sequencing data sets derived from 3F-EAR transgenic lines and background pools (p < 0.0001). (PDF)
Data
Overview of significantly enriched GO categories (p < 0.05) found for the selection of 10 out of 157 DEGs compared to the Col-0 that are shared in the RNA sequencing data sets of the three larger 3F-EAR transgenic lines, but are not found in the transcriptomes of background pools. (PDF)
Data
Growth curves of the Col-0, VP16-05-014 (T3; segregating) and retransformants reconstituted from VP16-05-014 (T2; segregating) (n = 36 for Col-0, n = 18 for the other genotypes). In this experiment we were not able to reproduce the increase in RSA of VP16-05-014. Significant differences with Col-0 at 28 dpg are indicated by an * (p < 0.05). For eac...
Data
Growth curves of the wild-type Col-0, VP16-02-003 (T3) and retransformants reconstituted from VP16-02-003 in the binary vector construct p35S-VP16-Kana (T2; segregating) (n = 84 for Col-0, n = 11–18 for the transgenic lines). Significant differences with Col-0 at 27 dpg are indicated by an * (p < 0.05). For each genotype the average relative growth...
Data
Overview of significantly enriched GO categories (p < 0.05) found for the 24 upregulated (Up) and 92 downregulated (Down) DEGs compared to the Col-0 that are shared in the RNA sequencing data sets derived from 3F-EAR transgenic lines and background pools. (PDF)
Data
DEGs shared by the original EAR and VP16 lines. (XLSX)
Data
ZF motif search of DEGs shared by VP16-02-003 and VP16-05-014 allowing for one or two mismatches at the 2th and 3th nucleotide of each GNN-triplet. (XLSX)
Data
Growth curves of the wild-type Col-0, VP16-05-014 (T3) and retransformants reconstituted from VP16-05-014 in the binary vector construct p35S-VP16-Kana (T2; segregating) (n = 84 for Col-0, n = 11–18 for the transgenic lines). Significant differences with Col-0 at 27 dpg are indicated by an * (p < 0.05). For each genotype the average relative growth...
Data
Overview of Differentially Expressed Genes (DEGs) compared to the Col-0 in the RNA sequencing data sets of the indicated 3F-VP16 transgenic lines (p < 0.0001). ‘Background’ refers to RNA expression data derived from the pool of lines expressing 3F-VP16 fusions similar to the specific 3F-VP16 fusion expressed in the selected lines, but without a not...
Data
Overview of the 239 Differentially Expressed Genes (DEGs) compared to the Col-0 that are shared in the RNA sequencing data sets of the two larger 3F-VP16 transgenic lines, VP16-02-003 and VP16-005-014 (p < 0.0001). The 2 DEGs that were also found in the transcriptomes of background pools are shaded. (PDF)
Data
Overview of significantly enriched GO categories (p < 0.05) found for the 146 upregulated (Up) and 93 downregulated (Down) DEGs compared to the wild-type Col-0 that are shared in the RNA sequencing data sets of the two larger 3F-VP16 transgenic lines, VP16-02-003 and VP16-005-014. (PDF)
Data
Cq values of QPCR on Col-0, VP16-02-003 and the retransformant lines harboring 3F-VP16 constructs reconstituted from VP16-02-003 under control of either the RPS5a promoter or the CaMV 35S promoter. (XLSX)
Preprint
Full-text available
We have sequenced the genome of the endangered European eel using the MinION by Oxford Nanopore, and assembled these data using a novel algorithm specifically designed for large eukaryotic genomes. For this 860 Mbp genome, the entire computational process takes two days on a single CPU. The resulting genome assembly significantly improves on a prev...
Article
Full-text available
Snake genome sequencing is in its infancy—very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinol...
Article
Full-text available
Background: The common carp (Cyprinus carpio) is the oldest, most domesticated and one of the most cultured fish species for food consumption. Besides its economic importance, the common carp is also highly suitable for comparative physiological and disease studies in combination with the animal model zebrafish (Danio rerio). They are genetically...
Article
During Agrobacterium-mediated transformation of plant cells a part of the tumour inducing plasmid, T-DNA, is integrated into the host genome. In addition, a number of virulence proteins are translocated into the host cell. The virulence protein VirE3 binds to the Arabidopsis thaliana pBrp protein, a plant-specific general transcription factor of th...
Article
Complete sexual maturation of European eels (Anguilla anguilla) in captivity can only be achieved via injections with gonadotropins. For female eels this procedure takes 4-6months and the response ranges from "unresponsive" to final maturation and ovulation. Reproductive success could be significantly increased via early selection of responders bas...
Article
Full-text available
RNA-seq has become a widely used method to study transcriptomes, and it is now possible to perform RNA-seq on almost any sample. Nevertheless, samples obtained from small cell populations are particularly challenging, as biases associated with low amounts of input RNA can have strong and detrimental effects on downstream analyses. Here we compare d...
Article
Full-text available
We have sequenced the complete genome of the plant pathogen Agrobacterium tumefaciens strain LBA4213, a derivative of the wild-type strain A. tumefaciens Ach5 and the ancestor of A. tumefaciens strain LBA4404 used in genetic engineering. The genome consists of a circular chromosome and a linear chromosome, as well as a megaplasmid and a tumor-induc...
Article
Full-text available
Significance The molecular basis of morphological and physiological adaptations in snakes is largely unknown. Here, we study these phenotypes using the genome of the Burmese python ( Python molurus bivittatus ), a model for extreme phenotypic plasticity and metabolic adaptation. We discovered massive rapid changes in gene expression that coordinate...
Article
Full-text available
Sensitivity and throughput of transcriptomic and proteomic technologies have advanced tremendously in recent years. With the use of deep sequencing of RNA samples (RNA-seq) and mass spectrometry technology for protein identification and quantitation, it is now feasible to compare gene and protein expression on a massive scale and for any organism f...