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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A Lowly Digestible-Starch Diet after Weaning Enhances Exogenous Glucose Oxidation Rate in Female, but Not in Male, Mice
Fernández-Calleja, José M.S. ; Bouwman, Lianne M.S. ; Swarts, Hans J.M. ; Billecke, Nils ; Oosting, Annemarie ; Keijer, Jaap ; Schothorst, Evert M. van - \ 2019
Nutrients 11 (2019)9. - ISSN 2072-6643
13C-starch - amylase - amylopectin - amylose - C57BL mice - glucose oxidation - glycaemic index - indirect calorimetry

Starches of low digestibility are associated with improved glucose metabolism. We hypothesise that a lowly digestible-starch diet (LDD) versus a highly digestible-starch diet (HDD) improves the capacity to oxidise starch, and that this is sex-dependent. Mice were fed a LDD or a HDD for 3 weeks directly after weaning. Body weight (BW), body composition (BC), and digestible energy intake (dEI) were determined weekly. At the end of the intervention period, whole-body energy expenditure (EE), respiratory exchange ratio (RER), hydrogen production, and the oxidation of an oral 13C-labelled starch bolus were measured by extended indirect calorimetry. Pancreatic amylase activity and total 13C hepatic enrichment were determined in females immediately before and 4 h after administration of the starch bolus. For both sexes, BW, BC, and basal EE and RER were not affected by the type of starch, but dEI and hydrogen production were increased by the LDD. Only in females, total carbohydrate oxidation and starch-derived glucose oxidation in response to the starch bolus were higher in LDD versus HDD mice; this was not accompanied by differences in amylase activity or hepatic partitioning of the 13C label. These results show that starch digestibility impacts glucose metabolism differently in females versus males.

Introducing gene deletions by mouse zygote electroporation of Cas12a/Cpf1
Dumeau, Charles Etienne ; Monfort, Asun ; Kissling, Lucas ; Swarts, Daan C. ; Jinek, Martin ; Wutz, Anton - \ 2019
Transgenic Research (2019). - ISSN 0962-8819
Cas12a - Cpf1 - CRISPR-Cas - Electroporation - Gene deletion - Mouse embryo - Mutation

CRISPR-associated (Cas) nucleases are established tools for engineering of animal genomes. These programmable RNA-guided nucleases have been introduced into zygotes using expression vectors, mRNA, or directly as ribonucleoprotein (RNP) complexes by different delivery methods. Whereas microinjection techniques are well established, more recently developed electroporation methods simplify RNP delivery but can provide less consistent efficiency. Previously, we have designed Cas12a-crRNA pairs to introduce large genomic deletions in the Ubn1, Ubn2, and Rbm12 genes in mouse embryonic stem cells (ESC). Here, we have optimized the conditions for electroporation of the same Cas12a RNP pairs into mouse zygotes. Using our protocol, large genomic deletions can be generated efficiently by electroporation of zygotes with or without an intact zona pellucida. Electroporation of as few as ten zygotes is sufficient to obtain a gene deletion in mice suggesting potential applicability of this method for species with limited availability of zygotes.

Extended indirect calorimetry with isotopic CO2 sensors for prolonged and continuous quantification of exogenous vs. total substrate oxidation in mice
Fernández-Calleja, José M.S. ; Bouwman, Lianne M.S. ; Swarts, Hans J.M. ; Oosting, Annemarie ; Keijer, Jaap ; Schothorst, Evert M. van - \ 2019
Scientific Reports 9 (2019). - ISSN 2045-2322

Indirect calorimetry (InCa) estimates whole-body energy expenditure and total substrate oxidation based on O2 consumption and CO2 production, but does not allow for the quantification of oxidation of exogenous substrates with time. To achieve this, we incorporated 13CO2 and 12CO2 gas sensors into a commercial InCa system and aimed to demonstrate their performance and added value. As a performance indicator, we showed the discriminative oscillations in 13CO2 enrichment associated with food intake in mice fed diets containing naturally low (wheat) vs high (maize) 13C enrichment. To demonstrate the physiological value, we quantified exogenous vs total carbohydrate and fat oxidation continuously, in real time in mice varying in fat mass. Diet-induced obese mice were fed a single liquid mixed meal containing 13C-isotopic tracers of glucose or palmitate. Over 13 h, ~70% glucose and ~48% palmitate ingested were oxidised. Exogenous palmitate oxidation depended on body fat mass, which was not the case for exogenous glucose oxidation. We conclude that extending an InCa system with 13CO2 and 12CO2 sensors provides an accessible and powerful technique for real-time continuous quantification of exogenous and whole-body substrate oxidation in mouse models of human metabolic physiology.

DNA-guided DNA cleavage at moderate temperatures by Clostridium butyricum Argonaute
Hegge, Jorrit W. ; Swarts, Daan C. ; Chandradoss, Stanley D. ; Cui, Tao Ju ; Kneppers, Jeroen ; Jinek, Martin ; Joo, Chirlmin ; Oost, John van der - \ 2019
Nucleic acids research 47 (2019)11. - ISSN 0305-1048 - p. 5809 - 5821.

Prokaryotic Argonaute proteins (pAgos) constitute a diverse group of endonucleases of which some mediate host defense by utilizing small interfering DNA guides (siDNA) to cleave complementary invading DNA. This activity can be repurposed for programmable DNA cleavage. However, currently characterized DNA-cleaving pAgos require elevated temperatures (≥65°C) for their activity, making them less suitable for applications that require moderate temperatures, such as genome editing. Here, we report the functional and structural characterization of the siDNA-guided DNA-targeting pAgo from the mesophilic bacterium Clostridium butyricum (CbAgo). CbAgo displays a preference for siDNAs that have a deoxyadenosine at the 5'-end and thymidines at nucleotides 2-4. Furthermore, CbAgo mediates DNA-guided DNA cleavage of AT-rich double stranded DNA at moderate temperatures (37°C). This study demonstrates that certain pAgos are capable of programmable DNA cleavage at moderate temperatures and thereby expands the scope of the potential pAgo-based applications.

Non-invasive continuous real-time in vivo analysis of microbial hydrogen production shows adaptation to fermentable carbohydrates in mice
Fernández Calleja, J.M.S. ; Konstanti, Prokopis ; Swarts, J.J.M. ; Bouwman, L.M.S. ; Garcia-Campayo, Vicenta ; Billecke, Nils ; Oosting, Annemarie ; Smidt, H. ; Keijer, J. ; Schothorst, E.M. van - \ 2018
PRJEB23475 - ERP105229
The gut microbiome interacts continuously with the host and its diet. Studying these interactions and their evolution in vivo as soon as they happen have been impossible. Here we develop a method to study microbiota-host-diet interactions continuously, non-invasively, and in real time, by measuring hydrogen (H2) and methane (CH4) production in mice housed in indirect calorimetry chambers.
Direct and Long-Term Metabolic Consequences of Lowly vs. Highly-Digestible Starch in the Early Post-Weaning Diet of Mice
Fernández-Calleja, José M.S. ; Bouwman, Lianne M.S. ; Swarts, Hans J.M. ; Oosting, Annemarie ; Keijer, Jaap ; Schothorst, Evert M. van - \ 2018
Nutrients 10 (2018)11. - ISSN 2072-6643
adipose tissue - amylopectin - amylose - C57BL mice - carbohydrates - glycemic index - indirect calorimetry - metabolic flexibility - nutrition - sexual dimorphism

Starches of low and high digestibility have different metabolic effects. Here, we examined whether this gives differential metabolic programming when fed in the immediate post-weaning period. Chow-fed mice were time-mated, and their nests were standardized and cross-fostered at postnatal days 1⁻2. After postnatal week (PW) 3, individually housed female and male offspring were switched to a lowly-digestible (LDD) or highly-digestible starch diet (HDD) for three weeks. All of the mice received the same high-fat diet (HFD) for nine weeks thereafter. Energy and substrate metabolism and carbohydrate fermentation were studied at the end of the HDD/LDD and HFD periods by extended indirect calorimetry. Glucose tolerance (PW 11) and metabolic flexibility (PW14) were analyzed. Directly in response to the LDD versus the HDD, females showed smaller adipocytes with less crown-like structures in gonadal white adipose tissue, while males had a lower fat mass and higher whole body fat oxidation levels. Both LDD-fed females and males showed an enlarged intestinal tract. Although most of the phenotypical differences disappeared in adulthood in both sexes, females exposed to LDD versus HDD in the early post-weaning period showed improved metabolic flexibility in adulthood. Cumulatively, these results suggest that the type of starch introduced after weaning could, at least in females, program later-life health.

Non-invasive continuous real-time in vivo analysis of microbial hydrogen production shows adaptation to fermentable carbohydrates in mice
Fernández-Calleja, José M.S. ; Konstanti, Prokopis ; Swarts, Hans J.M. ; Bouwman, Lianne M.S. ; Garcia-Campayo, Vicenta ; Billecke, Nils ; Oosting, Annemarie ; Smidt, Hauke ; Keijer, Jaap ; Schothorst, Evert M. van - \ 2018
Scientific Reports 8 (2018)1. - ISSN 2045-2322 - 16 p.

Real time in vivo methods are needed to better understand the interplay between diet and the gastrointestinal microbiota. Therefore, a rodent indirect calorimetry system was equipped with hydrogen (H2) and methane (CH4) sensors. H2 production was readily detected in C57BL/6J mice and followed a circadian rhythm. H2 production was increased within 12 hours after first exposure to a lowly-digestible starch diet (LDD) compared to a highly-digestible starch diet (HDD). Marked differences were observed in the faecal microbiota of animals fed the LDD and HDD diets. H2 was identified as a key variable explaining the variation in microbial communities, with specific taxa (including Bacteroides and Parasutterella) correlating with H2 production upon LDD-feeding. CH4 production was undetectable which was in line with absence of CH4 producers in the gut. We conclude that real-time in vivo monitoring of gases provides a non-invasive time-resolved system to explore the interplay between nutrition and gut microbes in a mouse model, and demonstrates potential for translation to other animal models and human studies.

Bacteriophage DNA glucosylation impairs target DNA binding by type I and II but not by type V CRISPR–Cas effector complexes
Vlot, Marnix ; Houkes, Joep ; Lochs, Silke J.A. ; Swarts, Daan C. ; Zheng, Peiyuan ; Kunne, Tim ; Mohanraju, Prarthana ; Anders, Carolin ; Jinek, Martin ; Oost, John Van Der; Dickman, Mark J. ; Brouns, Stan J.J. - \ 2018
Nucleic acids research 46 (2018)2. - ISSN 0305-1048 - p. 873 - 885.
Prokaryotes encode various host defense systems that provide protection against mobile genetic elements. Restriction–modification (R–M) and CRISPR–Cas systems mediate host defense by sequence specific targeting of invasive DNA. T-even bacteriophages employ covalent modifications of nucleobases to avoid binding and therefore cleavage of their DNA by restriction endonucleases. Here, we describe that DNA glucosylation of bacteriophage genomes affects interference of some but not all CRISPR–Cas systems. We show that glucosyl modification of 5-hydroxymethylated cytosines in the DNA of bacteriophage T4 interferes with type I-E and type II-A CRISPR–Cas systems by lowering the affinity of the Cascade and Cas9–crRNA complexes for their target DNA. On the contrary, the type V-A nuclease Cas12a (also known as Cpf1) is not impaired in binding and cleavage of glucosylated target DNA, likely due to a more open structural architecture of the protein. Our results suggest that CRISPR–Cas systems have contributed to the selective pressure on phages to develop more generic solutions to escape sequence specific host defense systems.
No Adverse Programming by Post-Weaning Dietary Fructose of Body Weight, Adiposity, Glucose Tolerance, or Metabolic Flexibility
Bouwman, Lianne M.S. ; Fernández-Calleja, José M.S. ; Swarts, Hans J.M. ; Stelt, Inge van der; Oosting, Annemarie ; Keijer, Jaap ; Schothorst, Evert M. van - \ 2018
Molecular Nutrition & Food Research 62 (2018)2. - ISSN 1613-4125
carbohydrates - indirect calorimetry - metabolic programming - metabolism - monosaccharides
Scope: Metabolic programming can occur not only in the perinatal period, but also post-weaning. This study aims to assess whether fructose, in comparison to glucose, in the post-weaning diet programs body weight, adiposity, glucose tolerance, metabolic flexibility, and health at adult age. Methods and results: Three-week-old male and female C57BL6/JRccHsd mice are given an intervention diet with 32 energy percent (en%) glucose or fructose for only 3 weeks. Next, all animals are switched to the same 40 en% high fat diet for 9 weeks. Neither body weight nor adiposity differs significantly between the animals fed with glucose or fructose diets at any point during the study in both sexes. Glucose tolerance in adulthood is not affected by the post-weaning diet, nor are activity, energy expenditure, and metabolic flexibility, as measured by indirect calorimetry. At the end of the study, only in females fasting serum insulin levels and HOMA-IR index are lower in post-weaning fructose versus glucose diet (p = 0.02), without differences in pancreatic β-cell mass. Conclusions: Our present findings indicate no adverse programming of body weight, adiposity, glucose tolerance, and metabolic flexibility by dietary (solid) fructose in comparison to glucose in the post-weaning diet in mice.
Prokaryotic Argonaute proteins : novel genome-editing tools?
Hegge, Jorrit W. ; Swarts, Daan C. ; Oost, John van der - \ 2018
Nature Reviews Microbiology 16 (2018)1. - ISSN 1740-1526 - p. 5 - 11.

Argonaute proteins constitute a highly diverse family of nucleic acid-guided proteins. They were first discovered in eukaryotes as key proteins in RNA interference systems, but homologous prokaryotic Argonaute proteins (pAgos) have also been found in archaea and bacteria. In this Progress article, we focus on long pAgo variants, a class of pAgos that are involved in nucleic acid-guided host defence against invading nucleic acids, and discuss the potential of pAgos in genome editing.

Structural basis for guide RNA processing and seed-dependent DNA targeting and cleavage by CRISPR-Cas12a
Swarts, Daan C. ; Oost, J. van der; Jinek, Martin - \ 2017
DNA - nuclease - RNA - ribonucleases - gel
Raw imaging data belonging to the manuscript 'Structural basis for guide RNA processing and seed-dependent DNA targeting and cleavage by CRISPR-Cas12a', by Swarts et al.
MOLECULAR-CELL-D-16-01367 Swarts et al
Swarts, D.C. - \ 2017
DNA sequencing - data analysis - gel
This data contains the raw imaging data and sequencing data of the manuscript "Autonomous generation and loading of DNA guides by bacterial Argonaute" written by Swarts, Szczepaniak, Sheng et al.
Monosaccharides in post-weaning diet of young mice program body composition and feeding behaviour in adulthood
Fernández Calleja, J.M.S. ; Bouwman, L.M.S. ; Swarts, J.J.M. ; Oosting, Annemarie ; Keijer, J. ; Schothorst, E.M. van - \ 2017
Journal of Developmental Origins of Health and Disease 8 (2017)Supplement 1. - ISSN 2040-1744 - p. S369 - S369.
Monosaccharides in post-weaning diet of young mice program body composition and feeding behaviour in adulthood
Fernández Calleja, J.M.S. ; Bouwman, L.M.S. ; Swarts, J.J.M. ; Oosting, A. ; Keijer, J. ; Schothorst, E.M. van - \ 2017
- 2 p.
No adverse metabolic programming of dietary fructose versus glucose post-weaning by extensive basal and challenged phenotyping in mice
Schothorst, E.M. van; Bouwman, L.M.S. ; Fernández Calleja, J.M.S. ; Swarts, J.J.M. ; Oosting, A. ; Keijer, J. - \ 2017
Body weight cycling with identical diet composition does not affect energy balance and has no adverse affect on metabolic health parameters
Palm, I.F. ; Schram, Rianne ; Swarts, J.J.M. ; Schothorst, E.M. van; Keijer, J. - \ 2017
Nutrients 9 (2017)10. - ISSN 2072-6643 - 13 p.
Background: Body weight (BW) cycling, the yo-yo effect, is generally thought to have adverse effects on human metabolic health. However, human and animal experiments are limited in number and do not provide clear answers, partly due to large variations in experimental design, parameters measured, and definitions of BW cycling. Here, we examined the effect of repetitive BW cycling versus single- and non-cycling control groups, without alterations in diet composition, on steady state BW and metabolic parameters. Methods: We induced well-defined BW cycles on a semi-purified high fat diet in C57BL/6J mice, a well-described animal model for diet-induced obesity, and measured energy expenditure and relevant metabolic parameters. Results: Our setup indeed resulted in the intended BW changes and always reached a stage of energy balance. A history of weight cycling did not result in increased BW or fat mass compared with the control group, nor in deteriorated serum concentrations of glucose, adipokines and serum triglyceride and free fatty acid (FFA) concentrations. If anything, BW tended to be reduced, presumably because of a reduced overall energy intake in BW cycling animals. Conclusion: Repeated cycling in BW without changes in diet composition does not lead to impaired metabolic health nor increased BW (gain).
Transient hypothyroidism: Dual effect on adult-type leydig cell and sertoli cell development
Rijntjes, Eddy ; Lucca Moreira Gomes, Marcos de; Zupanic, Nina ; Swarts, Hans J.M. ; Keijer, Jaap ; Teerds, Katja J. - \ 2017
Frontiers in Physiology 8 (2017). - ISSN 1664-042X - 12 p.
Leydig cell - Macroorchidism - Proliferation - Sertoli cell - Testis - Testosterone - Thyroid hormone

Transient neonatal 6-propyl-2-thiouracil (PTU) induced hypothyroidism affects Leydig and Sertoli cell numbers in the developing testis, resulting in increased adult testis size. The hypothyroid condition was thought to be responsible, an assumption questioned by studies showing that uninterrupted fetal/postnatal hypothyroidism did not affect adult testis size. Here, we investigated effects of transient hypothyroidism on Leydig and Sertoli cell development, employing a perinatal iodide-deficient diet in combination with sodium perchlorate. This hypothyroidism inducing diet was continued until days 1, 7, 14, or 28 postpartum (pp) respectively, when the rats were switched to a euthyroid diet and followed up to adulthood. Continuous euthyroid and hypothyroid, and neonatal PTU-treated rats switched to the euthyroid diet at 28 days pp, were included for comparison. No effects on formation of the adult-type Leydig cell population or on Sertoli cell proliferation and differentiation were observed when the diet switched at/or before day 14 pp. However, when the diet was discontinued at day 28 pp, Leydig cell development was delayed similarly to what was observed in chronic hypothyroid rats. Surprisingly, Sertoli cell proliferation was 6- to 8-fold increased 2 days after the diet switch and remained elevated the next days. In adulthood, Sertoli cell number per seminiferous tubule cross-section and consequently testis weight was increased in this group. These observations implicate that increased adult testis size in transiently hypothyroid rats is not caused by the hypothyroid condition per se, but originates from augmented Sertoli cell proliferation as a consequence of rapid normalization of thyroid hormone concentrations.

Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a
Swarts, Daan C. ; Oost, John van der; Jinek, Martin - \ 2017
Molecular Cell 66 (2017)2. - ISSN 1097-2765 - p. 221 - 233.e4.
Cas12a - Cas9 - Cpf1 - CRISPR RNA - CRISPR-Cas - crRNA processing - nuclease - R-loop - seed sequence - target DNA cleavage

The CRISPR-associated protein Cas12a (Cpf1), which has been repurposed for genome editing, possesses two distinct nuclease activities: endoribonuclease activity for processing its own guide RNAs and RNA-guided DNase activity for target DNA cleavage. To elucidate the molecular basis of both activities, we determined crystal structures of Francisella novicida Cas12a bound to guide RNA and in complex with an R-loop formed by a non-cleavable guide RNA precursor and a full-length target DNA. Corroborated by biochemical experiments, these structures reveal the mechanisms of guide RNA processing and pre-ordering of the seed sequence in the guide RNA that primes Cas12a for target DNA binding. Furthermore, the R-loop complex structure reveals the strand displacement mechanism that facilitates guide-target hybridization and suggests a mechanism for double-stranded DNA cleavage involving a single active site. Together, these insights advance our mechanistic understanding of Cas12a enzymes and may contribute to further development of genome editing technologies.

Effects of a wide range of dietary nicotinamide riboside (NR) concentrations on metabolic flexibility and white adipose tissue (WAT) of mice fed a mildly obesogenic diet
Shi, W. ; Hegeman, M.A. ; Dartel, D.A.M. van; Tang, J. ; Suarez, M. ; Swarts, H. ; Hee, B. van der; Arola, L. ; Keijer, J. - \ 2017
Molecular Nutrition & Food Research 61 (2017)8. - ISSN 1613-4125
Metabolic flexibility - NAD - Niacin - Nicotinamide riboside - Vitamin B3
Scope: Metabolic flexibility is the ability to switch metabolism between carbohydrate oxidation (CHO) and fatty acid oxidation (FAO) and is a biomarker for metabolic health. The effect on metabolic health of nicotinamide riboside (NR) as an exclusive source of vitamin B3 is unknown and is examined here for a wide range of NR. Design and methods: Nine-week-old male C57BL/6JRcc mice received a semi-purified mildly obesogenic (40 en% fat) diet containing 0.14% L-tryptophan and either 5, 15, 30, 180, or 900 mg NR per kg diet for 15 weeks. Body composition and metabolic parameters were analyzed. Metabolic flexibility was measured using indirect calorimetry. Gene expression in epididymal white adipose tissue (eWAT) was measured using qRT-PCR. Results: The maximum delta respiratory exchange ratio when switching from CHO to FAO (maxΔRERCHO1→FAO) and when switching from FAO to CHO (maxΔRERFAO→CHO2) were largest in 30 mg NR per kg diet (30NR). In eWAT, the gene expression of Pparγ, a master regulator of adipogenesis, and of Sod2 and Prdx3, two antioxidant genes, were significantly upregulated in 30NR compared to 5NR. Conclusion: 30NR is most beneficial for metabolic health, in terms of metabolic flexibility and eWAT gene expression, of mice on an obesogenic diet.
Prolonged hypothyroidism severely reduces ovarian follicular reserve in adult rats
Meng, Li ; Rijntjes, Eddy ; Swarts, Hans J.M. ; Keijer, Jaap ; Teerds, Katja J. - \ 2017
Journal of Ovarian Research 10 (2017)1. - ISSN 1757-2215
AMH - Follicular atresia - Growing follicle population - Hypothyroidism - Ovary - Primordial follicle reserve

Background: There is substantial evidence both in humans and in animals that a prolonged reduction in plasma thyroid hormone concentration leads to reproductive problems, including disturbed folliculogenesis, impaired ovulation and fertilization rates, miscarriage and pregnancy complications. The objective of the present study is to examine the consequences of chronic hypothyroidism, induced in adulthood, for the size of the ovarian follicle pool. In order to investigate this, adult female rats were provided either a control or an iodide deficient diet in combination with perchlorate supplementation to inhibit iodide uptake by the thyroid. Sixteen weeks later animals were sacrificed. Blood was collected for hormone analyses and ovaries were evaluated histologically. Results: At the time of sacrifice, plasma thyroid-stimulating hormone concentrations were 20- to 40-fold increased, thyroxine concentrations were negligible while tri-iothyronin concentrations were decreased by 40% in the hypothyroid group, confirming that the animals were hypothyroid. Primordial, primary and preantral follicle numbers were significantly lower in the hypothyroid ovaries compared to the euthyroid controls, while a downward trend in antral follicle and corpora lutea numbers was observed. Surprisingly the percentage of atretic follicles was not significantly different between the two groups, suggesting that the reduced preantral and antral follicle numbers were presumably not the consequence of increased degeneration of these follicle types in the hypothyroid group. Plasma anti-Müllerian hormone (AMH) levels showed a significant correlation with the growing follicle population represented by the total ovarian number of primary, preantral and antral follicles, suggesting that also under hypothyroid conditions AMH can serve as a surrogate marker to assess the growing ovarian follicle population. Conclusions: The induction of a chronic hypothyroid condition in adult female rats negatively affects the ovarian follicular reserve and the size of the growing follicle population, which may impact fertility.

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