Interactions and functionalities of the gut revealed by computational approaches
Benis, Nirupama - \ 2017
Wageningen University. Promotor(en): M.A. Smits; V.A.P. Martins dos Santos, co-promotor(en): D. Schokker; M. Suarez-Diez. - Wageningen : Wageningen University - ISBN 9789463434546 - 247
pigs - mice - digestive tract - digestive system - intestinal microorganisms - intestinal mucosa - computational science - immune system - feeds - animal nutrition - nutrition physiology - animal health - varkens - muizen - spijsverteringskanaal - spijsverteringsstelsel - darmmicro-organismen - darmslijmvlies - computational science - immuunsysteem - voer - diervoeding - voedingsfysiologie - diergezondheid
The gastrointestinal tract is subject of much research for its role in an organism’s health owing to its role as gatekeeper. The tissue acts as a barrier to keep out harmful substances like pathogens and toxins while absorbing nutrients that arise from the digestion of dietary components in in the lumen. There is a large population of microbiota that plays an important role in the functioning of the gut. All these sub-systems of the gastrointestinal tract contribute to the normal functioning of the gut. Due to its various functionalities, the gut is able to respond to different types of stimuli and bring the system back to homeostasis after perturbations.
The work done in this thesis uses several bioinformatic tools to improve our understanding of the functioning of the gut. This was achieved with data from model animals, mice and pigs which were subjected to changing environments before their gastrointestinal response was measured. Different types of stimuli were studied (eg, antibiotic exposure, changing diets and infection with pathogens) in order to understand the response of the gut to varying environments. This data was analysed using different data integration techniques that provide a holistic view of the gut response.
Vertical data integration techniques look for associations between different types of ~omics data to highlight possible interactions between the measured variables. Lateral integration techniques allow the study of one type of ~omics data over several time points or several experimental conditions. Using these techniques, we show proof of interactions between different sub-systems of the gut and the functional plasticity of the gut. Of the several hypotheses generated in this thesis we have validated several using existing literature and one using an in-vitro system. Further validation of these hypotheses will increase understanding of the responses of the gut and the interactions involved.
Ecophysiology of novel intestinal butyrate-producing bacteria
Bui, Thi Phuong Nam - \ 2016
Wageningen University. Promotor(en): Willem de Vos, co-promotor(en): Caroline Plugge. - Wageningen : Wageningen University - ISBN 9789462577015 - 202
butyrates - butyric acid bacteria - intestines - microbial interactions - faecal examination - mice - man - infants - genomics - intestinal physiology - microbial physiology - biochemical pathways - lysine - sugar - butyraten - boterzuurbacteriën - darmen - microbiële interacties - fecesonderzoek - muizen - mens - zuigelingen - genomica - darmfysiologie - microbiële fysiologie - biochemische omzettingen - lysine - suiker
The human intestinal tract harbours a trillion on microbial cells, predominantly anaerobes. The activity and physiology of these anaerobes is strongly associated with health and disease. This association has been investigated for a long time.However, this has not been fully understood. One of the reasons is the limited availability of cultured representatives. It is estimated that there may be more than 3000 species colonised in the gut of healthy individuals, however, only a bit over 1000 species have been isolated and characterised. Among the intestinal microbes, butyrate-producing bacteria are of special interest as the butyrate produced, is crucial to maintain a healthy gut. In addition, butyrate-producing bacteria have shown a reverse correlation with several intestinal diseases. In Chapter 2 we described a novel species Anaerostipes rhamnosivorans 1y2T isolated from an infant stool. This strain belonged to genus Anaerostipes within Clostridium cluster XIVa. A. rhamnosivorans had a capability of converting rhamnose into butyrate that is unique within intestinal butyrate-producing bacteria. The genomic analysis also revealed the entire rhamnose fermentation pathway as well as the acetyl-CoA pathway for butyrate production. This bacterium is able to produce butyrate from a wide range of sugars as well as lactate plus acetate. In Chapter 3, we described the microbial interactions between A. rhamnosivorans and Bacteriodes thetaiotaomicron in dietary pectins; Blautia hydrogenotrophica in lactate and small amount of acetate; Methanobrevibacter smithii in glucose. We observed that A. rhamnosivorans was able to benefit from its partners in all cocultures for butyrate production. This is likely due to its high metabolic flexibility. While the interaction between A. rhamnosivorans and B. thetaiotaomicron appeared as syntrophy, the interaction between A. rhamnosivorans and hydrogenotrohic microbes were cross-feeding type where hydrogen was transferred between two species. The latter resulted in an increase in butyrate level. In Chapter 4 we described a novel species Intestinimonas butyriciproducens SRB521T representing a novel genus Intestinimonas from a mouse caecum within Clostridium cluster IV. This bacterium produced butyrate and acetate as end products from Wilkins-Chalgren-Anaerobe broth.
Butyrate production is assumed to derive from carbohydrate employing acetyl-CoA pathway. No gut bacterium is known to convert proteins or amino acids to butyrate although butyrogenic pathways from amino acid degradation have been detected in the human gut using metagenomic approach. In Chapter 5 we discovered a novel butyrate synthesis pathway from the amino acid lysine and the Amadori product fructoselysine in Intestinimonas butyriciproducens AF211 that was isolated from human stool. This strain appeared to grow much better in lysine as compared to sugars although lysine and acetyl-CoA pathways were both detected in its complete genome. Moreover, the strain AF211 was able to metabolise efficiently fructoselysine into butyrate, and acetate was found to affect the fructoselysine fermentation, representing the impact of the environmental conditions where acetate is abundant in the gut. While the lysine pathway was found in the gut of many individuals, the fructoselysine pathway was present in only half of those samples. The finding that strain I. butyriciproducens AF211 is capable of the butyrogenic conversion of amino acid lysine and fructoselysine, an Amadori product formed in heated foods via the Maillard reaction, indicated a missing link that coupling protein metabolism and butyrate formation. As this Amadori product has been implicated to play a role in aging process, the use of strain AF211 as fructoselysine clearance in the gut needs further investigation. In Chapter 6 we performed genomic and physiological comparison between the I. butyriciproducens strain AF211 (human isolate) and SRB521T (mouse isolate). I. butyriciproducens was the most abundant species within the Intestinimonas genus and highly prevalent in humans based on metadata analysis on 16S amplicons. We confirmed that the butyrogenesis from lysine was a shared characteristic between the two I. butyriciproducens strains. We also observed the host specific features including tolerance to bile, cellular fatty acid composition, more efficient capability of converting sugars into butyrate, especially galactose and arabinose, in the human strain AF211. In addition, genomic rearrangements as well as variations in bacteriophages differed among strains.
Terugkerende muizenplagen in Nederland : inventarisatie, sturende factoren en beheersing
Wymenga, E. ; Latour, J. ; Beemster, N. ; Bos, D. ; Bosma, N. ; Haverkamp, J. ; Hendriks, R.F.A. ; Roerink, G.J. ; Kasper, G.J. ; Roelsma, J. ; Scholten, S. ; Wiersma, P. ; Zee, E. van der - \ 2016
Altenburg & Wymenga (A&W-rapport 2123) - 137
muizen - woelmuizen - plagen - schadelijke dieren - schade - graslanden - knaagdierenbestrijding - dijken - waterschappen - mice - voles - pests - noxious animals - damage - grasslands - rodent control - dykes - polder boards
2014 en 2015 zullen de geschiedenis in gaan als jaren met een uitzonderlijk grote veldmuizenplaag in Fryslân en op beperkte schaal elders in Nederland. In de loop van de zomer van 2014 meldden agrariërs schade aan graslanden. De werkelijke omvang bleek pas in het najaar en de winter van 2014-2015 en was zonder precedent. Ook uit andere provincies kwamen dergelijke meldingen. De economische schade werd door LTO Noord berekend op 73 miljoen euro (de Boer 2015). Uit een schouw van Wetterskip Fryslân bleek dat ook veel waterkeringen te maken hadden met muizenschade. Daarnaast was het waterschap beducht op een mogelijk verhoogde uitspoeling van meststoffen vanuit polders naar het oppervlaktewater. Bovengenoemde zaken waren aanleiding voor verschillende organisaties om in samenwerking met LTO Noord en het Actiecomité een onderzoek te starten naar de achtergronden van de terugkerende muizenplagen en de mogelijke maatregelen om die te beheersen. Ook de STOWA - Stichting Toegepast Onderzoek Waterbeheer – richtte haar vizier op de muizenplaag, om uit te zoeken in hoeverre de recente muizenplaag voor waterschappen relevant was. De overkoepelende doelstelling van beide onderzoeken was om kennis en bouwstenen te leveren voor een strategie om in de toekomst muizenplagen vroegtijdig te signaleren en de schade te beheersen.
Bosmuizen verlicht [door studenten / promovendi]
Sindram, Janneke - \ 2015
De Levende Natuur 116 (2015)2. - ISSN 0024-1520 - p. 71 - 72.
forest ecology - artificial light - fauna - mice - adverse effects - bosecologie - kunstlicht - fauna - muizen - nadelige gevolgen
Kunstlicht heeft op allerlei dieren invloed. Daar zijn veel voorbeelden van te verzinnen. Gecombineerd met het feit dat het in Europa 's nachts steeds lichter is geworden, mag de conclusie getrokken worden dat de natuur hier veel gevolgen van ondervindt. Nader onderzoek wordt verricht door Janneke Sandram, begeleid vanuit Wageningen Universiteit en NIOO.
Hypothalamic regulation of food intake during cancer
Dwarkasing, J.T. - \ 2015
Wageningen University. Promotor(en): Renger Witkamp, co-promotor(en): Klaske van Norren; Mark Boekschoten. - Wageningen : Wageningen University - ISBN 9789462575486 - 147
hypothalamische regulatie - anorexia - eetlustcontrole - voedselopname - cancer - chronische ziekten - diermodellen - muizen - serotonine - hypothalamic regulation - anorexia - appetite control - food intake - cancer - chronic diseases - animal models - mice - serotonin
Appetite is often reduced in patients with chronic illness, including cancer.
Cancer anorexia, loss of appetite, frequently co-exists with cachexia, and the combined clinical picture is known as anorexia-cachexia syndrome. In patients suffering from this syndrome, anorexia considerably contributes to the progression of cachexia, and strongly impinges on quality of life. Inflammatory processes in the hypothalamus are considered to play a crucial role in the development of disease-related anorexia.
The main aim of this thesis was to further elucidate crucial processes involved in the pathogenesis of anorexia in cancer. To investigate mechanisms specifically involved in cancer anorexia, we used two tumour mouse models with opposing food intake behaviours: a C26-colon adenocarcinoma model with increased food intake and a Lewis lung carcinoma model with decreased food intake. In both models, tumour-induced cachexia (body wasting) was strongly present. The contrast in food intake behaviour between tumour-bearing (TB) mice in response to growth of the two different tumours was used to distinguish processes involved in cachexia from those specifically involved in anorexia.
The hypothalamus was used for transcriptomic analysis (Affymetrix chips). We found expression of genes involved in serotonin signalling in the hypothalamus to be differentially regulated between the two tumour models. Furthermore, transcriptional activity of genes involved in serotonin signalling were inversely associated with food intake behaviour. Surprisingly, we also found a strong increase in gene expression of NPY and AgRP, potent orexigenic neuropeptides, in both models, meaning that their expression did not reflect food intake behaviour. However, NPY has also been described to regulate energy storage. Therefore, we hypothesized that this upregulation of NPY/AgRP corresponded to weight loss, which was severe in both tumour models.
Using hypothalamic cell lines we further explored how serotonin might act on food intake regulatory pathways. We showed that serotonin was able to inhibit neuronal NPY secretion, while not affecting gene expression. Inflammatory markers IL-6 and TNFα were also measured in plasma and it was found that C26 TB mice had a lower inflammatory response than LL TB mice. These differences in inflammatory response could be implicated in the differences in feeding behaviour and serotonin signalling between C26 and LL TB mice. We therefore investigated the direct influence of inflammation on hypothalamic serotonin turnover and its contribution to the development of anorexia. To this end, different doses of TNF and IL-6 were administered by injection to healthy mice, inducing an acute inflammatory response. The injected cytokine doses were estimated from their corresponding plasma levels measured in tumour bearing (TB) mice. Also in this cytokine induced-anorexia model, where anorexia was exclusively induced by an inflammatory response, serotonin metabolism in the hypothalamus was affected. Both TNF and IL-6 increased hypothalamic serotonin turnover while also inducing anorectic behaviour. Furthermore, the effect of cytokines on increasing serotonin turnover was supported by in vitro experiments with hypothalamic neuronal cell lines.
In conclusion, we identified hypothalamic serotonin signalling to play a major role in the decrease in food intake during cancer. Serotonin signalling itself is modulated by inflammatory mediators. Therefore, hypothalamic inflammation is an important trigger in the failure of hypothalamic food-intake regulation, probably by affecting serotonergic signalling, which acts as an upstream modulator of various orexigenic and anorexigenic systems.
Mucus and gut barrier in health and disease
Sovran, B. - \ 2015
Wageningen University. Promotor(en): Jerry Wells; P. de Vos, co-promotor(en): J. Dekker. - Wageningen : Wageningen University - ISBN 9789462574892 - 233
slijm - spijsverteringskanaal - darmen - muizen - probiotica - eilandjes van peyer - colitis - transcriptomen - immunohistologie - veroudering - geslacht (sex) - homeostase - gezondheid - ziekten - mucus - digestive tract - intestines - mice - probiotics - peyer patches - colitis - transcriptomes - immunohistology - senescence - sex - homeostasis - health - diseases
This publication describes his work as a PhD student in the Host-Microbe Interactomics Chair group at Wageningen University within the Gastrointestinal Health theme. It has been completed under the supervision of Prof. Dr Jerry M Wells, Dr Jan Dekker and the TIFN project leader, Prof. Dr Paul de Vos.
Mucus serves as a protective layer between the intestinal content and the intestinal wall. It facilitates the passage of the luminal content through the intestine, reducing the risk of mechanical damage to the intestinal epithelium. The overarching goal of this thesis was to investigate the role of mucus in the maintenance of the intestinal immune barrier and the effects of ageing and gender differences on mucus production and the gut barrier.
We found by using a mouse model that decreased mucus production leads to changes in microbiota and mucosal stress responses, without the appearance of pathology, demonstrating the importance of mucus in intestinal homeostasis. The mucus barrier was shown to deteriorate during aging but this could be prevented with specific probiotics. Furthermore gender-specific differences in the effects of ageing on the mucosal barrier were found. Increased knowledge on these mechanisms might contribute significantly to disease prevention and treatment, for instance by optimizing gender-specific dietary and pharmacological requirements.
The study presented in this thesis was performed within the framework of Top Institute Food and Nutrition, within the GH002 project.
Deze zomer veel tekenbeten verwacht
Vliet, A.J.H. van; Wijngaard, K. van den - \ 2015
Nature Today (2015)9 juli.
tekenbeten - ziekten overgebracht door teken - lyme-ziekte - muizen - borrelia burgdorferi - tekenbesmettingen - registratie - tick bites - tickborne diseases - lyme disease - mice - tick infestations - registration
Naar verwachting zullen komende maand een half miljoen mensen door een teek gebeten worden. Afgelopen maand werden aanzienlijk meer tekenbeten gemeld via Tekenradar.nl dan in eerdere jaren. Teken kunnen met een beet de ziekte van Lyme overbrengen. Het is daarom belangrijk dat mensen zich na een bezoek ‘in het groen’ goed controleren op tekenbeten. Mensen die toch de ziekte van Lyme oplopen, kunnen meedoen aan het onderzoek naar langdurige klachten na Lyme. De gezondheid van de deelnemers wordt een jaar lang gevolgd. Dit jaar kunnen nog 500 mensen meedoen aan het onderzoek.
Molecular and physiological assessment of metabolic health : adipose tissue, transcriptome analysis and challenge tests
Duivenvoorde, L.P.M. - \ 2015
Wageningen University. Promotor(en): Jaap Keijer, co-promotor(en): Evert van Schothorst. - Wageningen : Wageningen University - ISBN 9789462573017 - 186
muizen - metabolisme - gezondheid - vetweefsel - transcriptomen - stofwisselingsstoornissen - fysiologie - laboratoriumdieren - mice - metabolism - health - adipose tissue - transcriptomes - metabolic disorders - physiology - laboratory animals
Summary of main findings
Maintenance of metabolic health not only ensures that energy is made available in times of need and stored in times of excess, but also prevents resistance to nutritional cues, ectopic lipid accumulation and dysfunction of metabolic organs. The proportion of humans that is at risk for reduced metabolic health increases worldwide due to the current epidemic of obesity and the increase in both mean and maximum life span. Better understanding of the various factors that influence metabolic health may offer opportunities to fight this threat to human health. This thesis aims to assess metabolic health using transcriptome analysis and non-invasive challenge tests. Special focus is on the development and validation of InCa-based non-invasive challenge tests. In most chapters of this thesis white adipose tissue (WAT) formed the major organ of interest because of its key role in whole-body energy homeostasis. WAT function was, among others, studied with whole-genome gene expression analysis, which, compared to single parameter analysis, extends the scale and depth of understanding biological processes.
Metabolic health was also quantified as metabolic flexibility, with the use of non-invasive, indirect calorimetry (InCa) based challenge tests. One of the InCa based challenge tests described in this thesis, the oxygen restriction (OxR) challenge, is a novel approach to investigate metabolic flexibility in mice. In each study, OxR was applied acute ([O2] reduction within 30 minutes) and for a short period of 6 hours in fasted mice. The other two InCa-based challenge tests: fasting and re-feeding and fasting and glucose consumption are nutrient-based and were described previously, although in different formats and settings.
In chapter 2 we demonstrate that dietary restriction on a high-fat diet (HF-DR) improves metabolic health of mice compared with mice receiving the same diet on an ad libitum basis (HF-AL). Already after five weeks of restriction, the serum levels of cholesterol and leptin were significantly decreased in HF-DR mice, whereas their glucose tolerance and serum adiponectin levels were increased. The body weight and measured serum parameters remained stable in the following 7 weeks of restriction, implying metabolic adaptation. To understand the molecular events associated with this adaptation, we analysed gene expression in WAT with whole genome microarrays. HF-DR strongly influenced gene expression in WAT; in total, 8643 genes were differentially expressed between both groups of mice, with a major role for genes involved in lipid metabolism and mitochondrial functioning. DR also increases mitochondrial density in WAT. These results show that WAT, indeed, has an important role in the improvement of metabolic health of dietary restricted mice and suggest that the development of substrate efficiency plays an important role in the observed changes in health status. Finally, mitochondrial density might be used as a marker for WAT health status.
Chapter 3 shows how indirect calorimetry can be used to noninvasively assess metabolic and age-related flexibility in mice. In this study, we tested the sensitivity and response stability over time of three InCa-based treatments in old versus adult mice. For the first treatment, diurnal patterns of respiratory exchange ratio were followed for 24 hours under standard conditions. For the second and third treatment, which were both based on a challenge approach, mice were fasted and either received a glucose bolus to test switch-effectiveness from fat to glucose oxidation (Treatment 2), or were exposed to oxygen restriction (OxR, Treatment 3) in the InCa system, which was introduced as a novel approach to asses metabolic flexibility. Opposite to the mice that were dietary restricted (chapter 2), aging appeared to increase adiposity and decrease WAT mitochondrial density, which further suggests that WAT mitochondrial density might be used as a marker for WAT health. We observed that the test results of the first treatment were not stable between test periods, possibly because of behavioural differences within the group of old mice between both measurements. For the second treatment, no differences between groups were observed. With Treatment 3, however, stable significant differences could be detected: old mice did not maintain reduced oxygen consumption under OxR during both measurements, whereas adult mice did. Further biochemical and gene expression analyses showed that OxR affected glucose and lactate homeostasis in liver and WAT of adult mice, supporting the observed differences in oxygen consumption. This was the first study to show that InCa analysis of the response to OxR is a sensitive and reproducible treatment to noninvasively measure age-impaired metabolic health in mice. Evaluation of metabolic health under non-challenged conditions may be confounded by behavioural-induced variation between animals
The study described in chapter 4 followed up on the promising results that were obtained with the OxR challenge in chapter 3. In this study we tested whether OxR can also be used to reveal diet-induced health effects in an early stage. Early detection of diet-induced health effects might shorten animal experiments and reduce costs and age-related variation. Timely identification may increase options for reversal. Mice were exposed to a low-fat (LF) or high-fat (HF) diet for only 5 days, after which they were exposed to OxR or remained under normoxic conditions. The response to OxR was assessed by calorimetric measurements, followed by analysis of gene expression in liver and WAT. A novelty described in this chapter was the analysis of serum markers for protein glycation and oxidation, to detect differences in the response to OxR between LF and HF mice. Although HF feeding increased body weight, HF and LF mice did not differ in indirect calorimetric values under normoxic conditions and in a fasting state. Exposure to OxR however, increased oxygen consumption and lipid oxidation in HF mice versus LF mice. Furthermore, OxR induced gluconeogenesis and an antioxidant response in the liver of HF mice, whereas it induced de novo lipogenesis and an antioxidant response in eWAT of LF mice, indicating that HF and LF mice differed in their adaptation to OxR. OxR also increased serum markers of protein glycation and oxidation in HF mice, whereas these changes were absent in LF mice. From this study we concluded that OxR is a promising new method to test food products on potential beneficial effects for metabolic health.
The study described in chapter 5 aimed to assess differences in metabolic health of mice on iso-caloric diets differing in fatty acid composition using the OxR challenge. We also implemented a fasting and re-feeding challenge. One diet, the HFpu diet, predominantly contained poly-unsaturated fatty acids (PUFAs), which are considered to be healthier than saturated fatty acids (SFAs) that mainly made up the fat component of the second diet, the HFs diet. Since health effects of fatty acids also depend on the ratio of dietary omega-6 to omega-3 PUFAs (n6/n3 ratio), this ratio was kept similar between both diets. Mice received the isocaloric high-fat diets for six months, during and after which several biomarkers for health were measured. We found that HFpu and HFs diets only induce minor differences in static health markers: HFpu and HFs mice did not differ in body weight, total adiposity, adipose tissue health, serum adipokines, whole body energy balance, or circadian rhythm. HFpu and HFs mice also had a similar glucose tolerance, even though HFs mice had more triglycerides in liver and skeletal muscle and larger adipocytes in the eWAT depot. Interestingly, HFs mice were less flexible in their response to both fasting and re-feeding and OxR, which shows the relevance and sensitivity of InCa-based challenge tests. We concluded that InCa-based challenge tests are a valuable contribution to the analysis of metabolic health in mice. Challenge tests in the InCa system may, furthermore, reveal relevant consequences of small changes in metabolic health status, such as adipocyte hypertrophy or ectopic lipid storage.
Chapter 6 describes an in-depth study to the response to OxR both at whole body level using InCa and serum metabolomics (amino acids and (acyl)carnitines) and at WAT level using transcriptomics and the analysis of amino acid and (acyl)carnitine levels. Serum and tissue amino acids levels indicate the level of protein catabolism and certain amino acids are, typically, increased in obese individuals. Serum and tissue (acyl)carnitine levels indicate the rate and completeness of mitochondrial fatty acid oxidation; serum acylcarnitine levels are significantly increased in individuals that suffer from ambient oxygen restriction. The metabolic adaptation to OxR was studied in diet-induced moderately obese mice that received a high-fat diet (HFpu diet, as in chapter 5) for 6 weeks, which is expected to lead to WAT expansion and possibly to reduce oxygen availability in WAT. We found that OxR reduced mitochondrial oxidation at whole-body level, as shown by a reduction in whole-body oxygen consumption and an increase in serum long-chain acylcarnitine levels. WAT did not seem to contribute to this serum profile, since only short-chain acylcarnitines were increased in WAT and gene expression analysis indicated an increase in mitochondrial oxidation, based on coordinate down-regulation of Sirt4, Gpam and Chchd3/Minos3. In addition, OxR did not induce oxidative stress in WAT, but increased molecular pathways involved in cell growth and proliferation. OxR increased levels of tyrosine, lysine and ornithine in serum and of leucine/isoleucine in WAT. This study shows that OxR limits oxidative phosphorylation at whole-body level, but in WAT compensatory mechanisms seem to operate. The down-regulation of the mitochondria-related genes Sirt4, Gpam, and Chchd3 may be considered as a biomarker profile for WAT mitochondrial reprogramming in response to acute exposure to limited oxygen availability.
To conclude, the work presented in this thesis provides more insight in the analysis of metabolic health in mice with the use of transcriptome analysis and InCa-based challenge tests. We show that non-invasive tests using the InCa-system are more likely to reveal differences in metabolic flexibility than invasive challenge tests, such as the oral glucose tolerance test. Furthermore, we show that the challenge approach is more sensitive than analysis of metabolic health under non-challenged (free-feeding) conditions. Transcriptome analysis proved to be very valuable to provide in-depth molecular understanding of the mechanisms underlying reduced or improved metabolic health. Ideally, transciptomic or metabolomic approaches should be integrated with InCa-based challenge tests to further extent physiological understanding of diet-induced health effects.
Vreterij in consumptie-aardappelen : inventarisatie van vreterij op aardappelpercelen en in de bewaring
Rozen, K. van; Huiting, H.F. - \ 2015
Lelystad : Praktijkonderzoek Plant & Omgeving, onderdeel van Wageningen UR, Business Unit PPO-agv - 49
akkerbouw - aardappelen - diagnose - gewasbescherming - plagen - agriotes - athous - melolontha melolontha - phyllopertha horticola - naaktslakken - deroceras reticulatum - arion - agrotis - diplopoda - muizen - arable farming - potatoes - diagnosis - plant protection - pests - slugs - mice
In 2012 en 2013 is onderzoek verricht naar de symptomen en de impact van gaten in knollen. Percelen zijn bezocht om de mate van vraat aan de knollen te beoordelen en de oorzaak vast te stellen. Dit leverde schade op door het hele land. Oost-Nederland is de regio waar het meest onderzoek heeft plaatsgevonden. Daar zijn de meeste percelen bezocht en bemonsterd. De meeste schade werd veroorzaakt door ritnaalden. De symptomen zijn beschreven en afgebeeld. De symptomen zijn vergeleken met drycore, een aantasting wat ook gaatjes tot gevolg heeft. Enkele percelen met engerlingen en slakken zijn aangetroffen. Van enkele andere aantasters zijn de symptomen beschreven.
Unravelling mechanisms of dietary flavonoid-mediated health effects: effects on lipid metabolism and genotoxicity
Hoek-van den Hil, E.F. - \ 2015
Wageningen University. Promotor(en): Ivonne Rietjens; Jaap Keijer, co-promotor(en): Peter Hollman. - Wageningen : Wageningen University - ISBN 9789462573031 - 157
flavanoïden - flavonoïden - vetzuren - quercetine - flavonolen - lichaamsgewicht - lipidenmetabolisme - hart- en vaatziekten - lever - vetweefsel - gezondheid - genotoxiciteit - voeding - muizen - flavanoids - flavonoids - fatty acids - quercetin - flavonols - body weight - lipid metabolism - cardiovascular diseases - liver - adipose tissue - health - genotoxicity - nutrition - mice
Consumption of foods containing flavonoids is associated with a reduced risk of cardiovascular diseases (CVD), possibly by lipid-lowering effects. On the other hand, for one of these flavonoids, quercetin, also genotoxicity was shown especially in in vitro bioassays. Therefore, the first aim of this thesis was to identify mechanisms underlying potential beneficial health effects of flavonoids. The focus was on hepatic lipid metabolism and circulating lipids and a molecular and physiological approach was used. Secondly, we aimed to study the potential in vivo genotoxic effects of quercetin by transcriptome analyses in liver and small intestine, since these represent the tissues of first contact exposed to relatively high levels upon oral intake of flavonoids.
Circulating lipids are important CVD-related risk markers, which are in general determined with commercially available enzyme-based assays. However, the usual enzyme in these assays, peroxidase, has previously been reported to be inhibited by flavonoids. Therefore, we have studied in chapter 2 whether these assays can adequately be used in flavonoid research. We observed that various flavonoid aglycones interfere with peroxidase used in triglycerides (TG) and free fatty acids (FFA) enzymatic assays, reporting incorrect lower TG and FFA levels than actually present. Furthermore, addition of metabolites such as isorhamnetin or quercetin-3-O-glucuronide, the major metabolite of quercetin in human and rat plasma, to murine serum also resulted in a significant reduction of the detected TG levels, while a trend was seen towards reduced FFA levels. It can be concluded that when applying these biochemical assays, vigilance is needed and alternative analytical methods assessing FFA or TG levels should preferably be applied for studying the biological effects of flavonoids on TG and FFA levels.
In chapter 3 mechanistic and physiological effects of quercetin on hepatic lipid metabolism were studied. C57BL/6JOlaHsd male adult mice received a mild high-fat (30 en%) diet without or with supplementation of 0.33% (w/w) quercetin for 12 weeks. Gas chromatography and 1H-NMR were used to quantitatively measure serum lipid profiles. Whole genome microarray analysis of liver tissue was used to identify potential mechanisms underlying altered circulating lipid levels by quercetin supplementation. Body weight, energy intake and hepatic lipid accumulation did not differ significantly between the quercetin and the control group. In serum of quercetin-fed mice, TG levels were decreased by 14% (p<0.001) and total poly unsaturated fatty acids (PUFA) levels were increased by 13% (p<0.01). Levels of palmitic acid, oleic acid, and linoleic acid were all decreased by 9-15% (p<0.05) in quercetin-fed mice. Both palmitic acid and oleic acid can be oxidized by omega-oxidation. Gene expression profiling showed indeed that quercetin increased hepatic lipid metabolism, especially omega-oxidation. At the gene level, this was reflected by the up-regulation of cytochrome P450 (Cyp) 4a10, Cyp4a14, Cyp4a31 and Acyl-CoA thioesterase 3 (Acot3). Two relevant regulators, cytochrome P450 oxidoreductase (Por, rate limiting for cytochrome P450 activities) and the transcription factor constitutive androstane receptor (Car; official symbol Nr1i3) were also up- regulated in the quercetin-fed mice. We concluded that quercetin intake increased hepatic lipid omega-oxidation and lowered corresponding circulating lipid levels, which may contribute to potential beneficial effects of quercetin on CVD.
Subsequently, in chapter 4 effects of quercetin supplementation were studied in mice given a high-fat (40 en%) background diet. The set-up of the experiment was the same as in chapter 3, with the exception of the background diet that was used, which was different in fat content and composition. This high-fat diet-induced body weight gain, and serum and hepatic lipid accumulation, which are all known risk factors for CVD. The aim of this study was to investigate the effects and underlying molecular mechanisms of the effects of the flavonoid quercetin on hepatic lipid metabolism in mice given this high-fat diet background. C57BL/6JOlaHsd male adult mice received the high-fat diet without or with supplementation of 0.33% (w/w) quercetin for 12 weeks. Body weight gain was 29% lower in quercetin fed mice versus control mice (p<0.01), while the energy intake was not significantly different. Quercetin supplementation lowered high-fat diet-induced hepatic lipid accumulation to 29% of the amount present in the control mice (p<0.01). 1H-NMR serum lipid profiling revealed that the supplementation also significantly lowered high-fat diet-induced increases in serum lipid levels. Global gene expression profiling of liver showed that cytochrome P450 2b (Cyp2b) genes, key target genes of the transcription factor Car, were down-regulated. However, the induction of omega-oxidation observed by quercetin supplementation to a mild high-fat (30en%) diet (chapter 3), was not observed this time with the high-fat (40en%) diet. Cumulatively, quercetin decreased high-fat diet-induced body weight gain, hepatic lipid accumulation and serum lipid levels. This was accompanied by regulation of cytochrome P450 2b genes in liver, which are considered to be under transcriptional control of CAR. The quercetin effects are likely dependent on the fat content and composition of the diet.
In chapter 5 we investigated whether flavonoids from other flavonoid subclasses can exert the same effects as we observed for quercetin. Effects of quercetin, hesperetin, epicatechin, apigenin and anthocyanins, in C57BL/6JOlaHsd male adult mice fed a high-fat diet for 12 weeks were compared, relative to a normal-fat diet. High-fat diet-induced body weight gain was significantly lowered by all flavonoids (17-29%), but most by quercetin. Quercetin significantly lowered high-fat diet-induced hepatic lipid accumulation (by 71%). High-fat diet-induced increases of mesenteric adipose tissue weight and serum leptin levels were significantly lowered by quercetin, hesperetin, and anthocyanins. Adipocyte cell size and adipose tissue inflammation were not affected.
The effects on body weight and adiposity could not be explained by individual significant differences in energy intake, energy expenditure, nor by differences in activity. Lipid metabolism was not changed as measured by indirect calorimetry or expression of known lipid metabolic genes in liver and white adipose tissue. Hepatic expression of Cyp2b9 was strongly down-regulated by all flavonoids. Overall, all five flavonoids lowered parameters of high-fat diet-induced adiposity, with quercetin being most effective.
Next to the beneficial health effects of flavonoids, the safety of flavonoids is under discussion, mainly because of potential genotoxic effects found for quercetin in vitro. Therefore, in chapter 6 the in vivo genotoxicity of this flavonoid was studied by transcriptome analyses in two tissues, small intestine and liver, where the highest exposure to quercetin is expected. This is especially of interest in view of high intake by widely available food supplements. Quercetin (0.33%) supplemented to a high-fat diet was administered to C57BL/6JOlaHsd male adult mice during 12 weeks. Serum alanine aminotransferase and aspartate aminotransferase levels revealed no indications for hepatotoxicity. General microarray pathway analysis of liver and small intestinal tissue samples showed no regulation of genotoxicity related pathways. In addition, analysis of DNA damage pathways in these tissues did also not point at genotoxicity. Furthermore, comparison with a published classifier set of transcripts for identifying genotoxic compounds did not reveal any similarities in the regulation of these classifier set by quercetin. Available microarray datasets of known genotoxic liver carcinogens, 2-acetylaminofluorene and aflatoxin B1 in mice were taken along as positive controls for comparison, and indeed showed genotoxic properties (regulation of genotoxic related genes) in the analyses. This transcriptomic analysis showed that supplementation with quercetin at ~350 mg/kg bw/day for 12 weeks did not induce genotoxicity in liver and small intestine.
In conclusion, we have shown in vivo efficacy of flavonoids reflected by effects on metabolic health parameters, including hepatic lipid metabolism. These effects on hepatic lipid metabolism seemed to be related or influenced by the transcription factor CAR. The dietary contexts appeared to modify the health effects. The five studied flavonoids in general showed the same effects, with quercetin being the most effective. No genotoxicity of quercetin was found by transcriptome analyses in liver and small intestine. Overall, we have obtained indications for beneficial health effects of flavonoids in mice, which makes it interesting to study if these effects can be extrapolated to humans to further explore their potential as functional compounds of dietary flavonoid intake.
Muizenschade in Friesland
Roerink, G.J. - \ 2015
Wageningen : Wageningen UR Alterra
graslanden - vegetatiemonitoring - remote sensing - schade - beweidingsschade - monitoring - muizen - friesland - grasslands - vegetation monitoring - damage - browsing damage - mice
Friesland is getroffen door een muizenplaag. Al meer dan 12 duizend ha grasland heeft zodanige schade opgelopen dat het waarneembaar wordt op satellietbeelden. Door de zachte winter en de warme droge zomer van afgelopen jaar is de muizenpopulatie in de loop van 2014 in Friesland geëxplodeerd. De muizenkolonies graven gangen onder de graslandzode en vreten de wortels ervan op zodat het gras afsterft. Alterra brengt via satellietbeelden de schade in kaart.
Metabolic adaptation of white adipose tissue to nutritional and environmental challenges
Hoevenaars, F.P.M. - \ 2014
Wageningen University. Promotor(en): Jaap Keijer, co-promotor(en): Evert van Schothorst. - Wageningen : Wageningen University - ISBN 9789461739162 - 166
muizen - vetweefsel - metabolisme - adaptatiefysiologie - voeding - milieufactoren - obesitas - energieopname - zuurstoftekort - ontsteking - voedingsfysiologie - diermodellen - mice - adipose tissue - metabolism - adaptation physiology - nutrition - environmental factors - obesity - energy intake - oxygen deficiency - inflammation - nutrition physiology - animal models
Summary of main findings
When adipose tissue is present in excessive amounts, as in obesity, it predisposes to a number of pathologies. Obesity is a complex, multifactorial condition as it influences many endogenous genetic, endocrine, and inflammatory pathways. Excess dietary intake is one of the important factors which are responsible for the increasing prevalence of obesity. For the understanding of the reciprocity between
consumed diet and excessive amounts of adipose tissue, it is essential to investigate underlying functioning. In this thesis, I have addressed three important aspects that play a role in the development of diet induced obesity and its pathologies with a focus on adipose tissue metabolism.
Does a body weight set-point exist?
How is the diet-induced metabolic response affected by housing at
Does oxygen restriction induce inflammation in white adipose tissue?
The first aspect investigated was the existence of a body weight set point. A body weight set point is defined as a pre-determined or preferred level of body weight which is preserved by an internal feedback control mechanism. In chapter 2, a dietary intervention with none, one, or two diet alterations of purified diets was performed in C57BL/6J mice to investigate if a long lasting effect on body weight persistence was present. Diets contained equal protein content and source of ingredients but differed in the fat-to-sugar ratio. Therefore, energy content and amount of fat was different for either the low fat diet or the high fat. In the intervention the last consumed diet of the mice determined energy intake, energy expenditure, body weight, body fat stores, circulating hormones and metabolites. These data support the settling point theory as body weight and metabolic parameters ‘settle’ based on current energetic input and output and do not support the set point theory. Next to that it underlines the importance of diet choice in intervention studies focusing on aspects on the crossroads of nutrition and physiology.
In chapter 3adipose tissue physiology and molecular regulation was further investigated by exposure to more metabolic stress in the form of a weight loss challenge with different purified diets. Diet-induced obese C57BL/6J mice were fed a high fat diet restricted to 70% intake of previous ad libitum high fat diet
intake or they were changed to ad libitum low fat diet for 5 weeks. Beneficial effects were seen in both interventions regarding physiological parameters. However, molecular parameters in white adipose tissue differed between the two restriction interventions, with increased activation of mitochondrial carbohydrate and fat metabolism in high fat diet restricted mice. When extrapolated to the human
situation this may suggest that a reduction of portion size is the best method for weight loss.
It is standard practice to house mice at ambient temperature during physiological intervention studies. Unfortunately mice are then exposed to a temperature below their thermal neutral zone. This implies that their metabolism is chronically increased which is known to influence study outcomes. In chapter 4the second question; “how is the diet-induced metabolic response affected by housing at thermoneutrality?”was investigated. A 14-week dietary intervention with two semi-purified diets, a
low fat diet and a moderately high fat diet, was performed at 28°C in C57BL/6J mice. This resulted in a large diet-induced difference in bodyweight, adipose tissue mass, adipocyte size, and serum leptin level. But no differential effects of the diets were seen on serum glucose, free fatty acids, triacylglycerides, insulin, a panel of cardiovascular markers, and a number of (metabolic) parameters in liver and muscle.
Although adipose tissue mass and adipocyte size was increased significantly, there was no sign of inflammation or dysfunction in the adipose tissue. This study suggests that diet-induced obesity of C57BL/6J mice at thermoneutrality results in a suitable model for the metabolically ‘healthy’ obese (people who are significantly overweight but show none of the usual metabolic problems). Next to that, this study emphasizes the importance of consideration and control of housing temperature for mice, as it has profound effects on study outcomes.
The third and last question investigated was if oxygen restriction is able to induce inflammation in white adipose tissue. There is substantial evidence that white adipose tissue becomes hypoxic when excessively enlarged. Due to fast expansion of white adipose tissue the vasculature is not able to keep pace with growth. Next to that, adipocytes are able to increase in size beyond the limit of oxygen diffusion. To investigate if hypoxia was able to induce inflammation in white adipose tissue, the model for healthy obese adipocytes (developed in chapter 4) was used and exposed to ambient oxygen restriction (13%) to challenge adipose tissue metabolism. This resulted in the presence of systemic oxygen restriction as shown by increased levels of hemoglobin and hematocrit. Furthermore a switch to glycolytic metabolism, which is indicative for tissue hypoxia, was present. No differences in adipose tissue macrophage infiltration (as marker for inflammation) were found. But, serum branched chain amino acids and adipokines were affected. Branched chain amino acids were increased in mice exposed to oxygen restriction which shows resemblance with findings in humans where increased levels were found in lean versus obese people. The peptide hormone adiponectin was increased in serum, without differences in WAT expression. On the other hand, the peptide hormones CCDC3 and CCK showed decreased transcript levels in white adipose tissue without significant change in serum levels, although for CCDC3 a trend was seen. Together these results suggest that oxygen restriction does not induce inflammation in adipose tissue. However, it does affect adipokine regulation.
After performing these studies it was clear that composition of the diet has a major influence on outcome parameters of physiological studies as shown in chapter 2. To compare functional effects of different nutrients, it is important to use standardized purified diets. Not only the experimental intervention diet is of importance but also the reference control diet can influence outcomes. For example, when an intervention is performed with a high fat purified diet and the reference diet is chow this will lead to a difficult comparison. The content of chow is variable as it is grain or cereal based (ground corn, ground oats alfalfa meal, soybean meal and ground wheat). Nutritional adequacy is ensured by addition of vitamins, minerals, and fat. However, the exact amount of the various ingredients is frequently kept secret by the manufacturer. Next to that, due to the plant based origin of chow it will contain nutritive (protein, carbohydrate, fat) components but also non-nutritive components (phytochemicals). The content of the chow diet will vary from batch to batch as the nutritive and nonnutritive value will change between harvests. When using a chow reference diet in
comparison to a purified diet you will never know exactly what you are comparing, i.e. difference in amino acids or effects of phytochemicals etc. Therefore, a reference diet for physiology was designed (chapter 6) to improve comparison of study outcomes and to increase efficiency of resources and material. A key feature of the diet is the fixed protein concentration, which allows for an exchange of carbohydrate and fat in a high fat version of the diet.
To conclude, the work presented in this thesis provides clear insight in factors that are of importance for improvement of translatability of mouse studies to the human situation. It was shown that when investigating the weight balance many parameters, i.e. genetics, metabolic rate, environmental factors like ambient housing temperature and light and cognitive behavior, besides the diet and its composition are able to influence the outcome parameters. As most mouse experiments are performed
in a fixed environment with no choices of food and a standard temperature set to 22°C. This is clearly not reflective of humans under free living conditions. However, these fixed conditions are able to result in experiments that unravel underlying mechanisms of weight balance, which form the basis for discovering a solution to the obesity epidemic.
RegIII proteins as gatekeepers of the intestinal epithelium
Loonen, L.M.P. - \ 2013
Wageningen University. Promotor(en): Jerry Wells, co-promotor(en): Peter van Baarlen. - S.l. : s.n. - ISBN 9789461736727 - 205
eiwitten - darmen - darmslijmvlies - darmziekten - colitis - bacterieziekten - immuunsysteem - verdedigingsmechanismen - muizen - diermodellen - microbiologie - immuniteit - geneeskunde - proteins - intestines - intestinal mucosa - intestinal diseases - colitis - bacterial diseases - immune system - defence mechanisms - mice - animal models - microbiology - immunity - medicine
Mammalian RegIII proteins are expressed in the intestine and in the pancreas in response to inflammation or infection. In the mouse intestine, expression of RegIIIβ and RegIIIγ is increased by microbial colonization, inflammation and infection. At the outset of this thesis human PAP and mouse RegIIIγ were reported to be bactericidal for Gram-positive bacteria. Additionally, human PAP had been shown to attenuate NF-κbsignallingin human monocytes and epithelial cells and administration of anti-PAP antibodies increased inflammation in an experimental rat model of acute pancreatitis. The overarching goals of this thesis were to find out more about the protective role of mouse RegIIIβ and RegIIIγ in the intestine and explore their protective role in colitis and bacterial infection.
In Chapter 2 we investigated expression of RegIIIβ and RegIIIγ in intestine of Muc2 knockout (-/-) mice, which develop colitis after about 4 weeks, due to the absence of a secreted mucus layer in the small intestine or colon. RegIII proteins were expressed in Paneth cells, enterocytes and goblet cells pointing to a new function for goblet cells in innate immunity. Ang4 expression was confined to Paneth cells and goblet cells. Absence of Muc2 increased expression levels of RegIIIβ, RegIIIγ, and Ang4 and colitis appeared first in the distal colon where the RegIII expression is lowest.
In Chapter 3 we investigated the distinct phases of colitis development in Muc2-/- mice from before weaning to 4 and 8 weeks of age, also taking into account the effect that mucin deficiency has in the ileum. Gene set enrichment approaches showed increased expression of innate and adaptive immune pathways associated with colitis over time, whereas in the ileum many immune signalling pathways were down-regulated. Nevertheless, RegIIIβ and RegIIIγ were significantly upregulated, suggesting their proposed antimicrobial and/or anti-inflammatory activities might be related to the suppression of immune pathways and avoidance of immune-mediated damage. Furthermore, we showed that RegIIIβ could specifically bind to mucin and fucosylated glycans in vitro, which may serve to inhibit bacterial binding to membrane bound mucins on the epithelium, and also enable RegIIIβ to be retained in the secreted mucin.
An in vitro approach was used in Chapter 4, where we investigated the activities of RegIIIγ and RegIIIβby expressing and purifying recombinant proteins. Both proteins were insoluble when expressed in E. coli but RegIIIβ could be expressed and secreted in baculovirus as a soluble protein. As previous work reported that RegIII proteins were bactericidal even when produced as inclusion bodies in E. coli and refolded, we followed similar procedures to obtain soluble RegIII proteins. In our hands both the E. coli and baculovirus produced proteins bound strongly to both Gram-positive and Gram-negative bacteria after processing of an N-terminal pro-peptide by trypsin, but lacked any appreciable bactericidal activity. Furthermore these proteins did not influence the growth of Salmonella enteritidis andListeria monocytogenes. Attempts to crystallize the proteins were unsuccessful but structural models of the protein were generated based on the crystal structure of human PAP. These models were used to dock known ligands of RegIIIγ or RegIIIβ. Only one ligand is known for RegIIIγ, which is peptidoglycan, but for RegIIIβ the ligands include peptidoglycan, lipid A and the fucose-containing glycans identified in chapter 3. RegIIIβ was predicted to have two different binding sites which would allow it to bind to mucins and bacteria simultaneously, thereby preventing penetrating of the mucus.
In Chapter 5 a RegIIIβ-/- mouse was used to study the role of the protein during infection with Gram-negative Salmonella enteritidis or Gram-positive Listeria monocytogenes. Whereas recovery of S. enteritidis orL. monocytogenes from faeces was similar in RegIIIβ-/- and wild type (WT) mice, significantly higher numbers of viable S. enteritidis, but not L. monocytogenes, were recovered from the colon, mesenteric lymph nodes, spleen, and liver of the RegIIIβ-/- than the WT mice. The results suggest that mouse RegIIIβ plays a protective role against intestinal translocation of the Gram-negative bacterium S. enteritidis but not against the Gram-positive bacterium L. monocytogenes.
In Chapter 6, the generation of a RegIIIγ-/- mouse is described. One of the main phenotypic differences between the RegIIIγ-/- and WT was an altered distribution of the ileal mucus and increased bacterial contact with the epithelium. Additionally, measurement of innate immune markers in the mucosa suggested heightened inflammation in the RegIIIγ-/- mice. Compared to WT mice, RegIIIγ-/- mice infected with S. enteritidis and L. monocytogenes showed an increase of mucosal inflammatory markers indicating protective, anti-microbial roles of RegIIIγ in defense against both Gram-positive and Gram-negative bacteria.
Chapter 7summarizes and discusses the key results of the thesis in the context of the wider literature and possible directions for future research
The diet of the garden dormouse (Eliomys quercinus) in the Netherlands in summer and autumn
Kuipers, L. ; Scholten, J. ; Thissen, J.B.M. ; Bekkers, L. ; Geertsma, M. ; Pulles, C.A.T. ; Siepel, H. ; Turnhout, L.J.E.A. van - \ 2012
Lutra 55 (2012)1. - ISSN 0024-7634 - p. 17 - 27.
muizen - voedingsgedrag - monitoring - bodemecologie - bosecologie - zuid-limburg - mice - feeding behaviour - soil ecology - forest ecology
The food of the last remaining population of garden dormouse (Eliomys quercinus) in the Netherlands is studied by means of analysing faecal samples, collected in the summer and autumn of the year 2010. In total 139 scat samples were collected from 51 different nest boxes. The samples were visually analysed for the presence (or absence) of different animal and vegetable food items using a stereo microscope. Millipedes (Diplopoda), beetles (Coleoptera) and snails (Gastropoda) were found to be the main animal food sources. Important vegetable food remains were the fruit pulp of apples, pears and seeds. The identified seeds were the remains of blackberries (Rubus ssp.) and elderberries (Sambucus nigra). The results were skewed by someone feeding the garden dormice with apples and pears. All the other food items were collected by the garden dormice themselves. These animal and vegetable food sources were present in more than 20% of the samples. Hymnopterans (Hymenoptera), earthworms (Lumbricidae), spiders (Araneae), harvestmen (Opiliones) and wood mice (Apodemus sylvaticus) were present in 5% to 20% of the samples. Flies (Diptera), true bugs (Heteroptera), woodlice (Isopoda), pseudoscorpions
(Pseudoscorpiones), butterfly larvae (caterpillars) (Lepidoaptera), songbirds (Passeriformes) and flowers were occasionally found. Invertebrates, especially millipedes, are the staple food during the entire active feeding period.
In spring and early summer the garden dormouse eats relatively more vertebrates (possibly mainly the nestlings of birds and mice), gastropods, beetles and flowers, than in August-November. The first seeds of berries were identified in the beginning of August. The occurrence of seeds increased rapidly to 90% at the end of August and then decreased to 30% in September and 0% by the end of October. Garden dormice in woods seem to depend on the rich invertebrate fauna within the litter layer. Mesotrophic mull soils have a rich fauna of medium-sized to large invertebrates and these soils are disappearing from the Savelsbos as a result of traditional management practices being abandoned. Re-establishment of species-rich wood types that produce mesotrophic mull soils could be of benefit to the remnant population of garden dormouse in the Savelsbos.
Waterberging De Run en knaagdieren: een risico?
Meerburg, B.G. - \ 2012
Lelystad : Wageningen UR Livestock Research (Rapport / Wageningen UR Livestock Research 583) - 7
inundatie - wateropslag - bodemwater - verzadiging - habitats - ongedierte - ratten - muizen - nadelige gevolgen - milieueffectrapportage - landbouwbedrijven - noord-brabant - flooding - water storage - soil water - saturation - vermin - rats - mice - adverse effects - environmental impact reporting - farms
Waterschap De Dommel heeft voor het milieueffect-rapport van waterberging De Run advies gevraagd omtrent de mogelijke effecten van ongedierte (ratten en muizen) in relatie tot de agrarische bedrijven. Het betreft het beekherstel- en waterbergingsgebied De Run in de buurt van Veldhoven.
The dynamic interplay of microbiota and mucosa drives establishment of homeostasis in conventionalized mice
Aidy, S.F. El - \ 2012
Wageningen University. Promotor(en): Michiel Kleerebezem, co-promotor(en): Peter van Baarlen; Erwin Zoetendal. - S.l. : s.n. - ISBN 9789461731951 - 168
kiemvrije dieren - muizen - darmmicro-organismen - homeostase - slijmvlies van het spijsverteringskanaal - transcriptomica - metabolomica - germfree animals - mice - intestinal microorganisms - homeostasis - digestive tract mucosa - transcriptomics - metabolomics
The intimate interplay between gut microbiota, host, and nutrient flow is crucial in defining the health status of the host. During microbial conventionalization of germfree mice, tightly regulated molecular responses assure the establishment of homeostasis and immune tolerance towards the microbiota. To decipher the temporal and regional dynamics of host-microbiota communication during the process of conventionalization, a combination of transcriptomics, (immune-)histology, metabonomics (tissue, urine, and plasma), as well as MITchip (Mouse Intestinal Tract chip) based microbiota profiling was employed. To this end, C57/B6 J germfree mice were conventionalized with mouse fecal microbiota and responses were followed in a time-resolved manner for thirty days. The colonizing microbiota was characterized by a shift from low towards higher diversity of its composition, over the period of conventionalization. Microbial colonization was rapidly (after one day) reflected by increased concentrations of specific urine and jejunal metabolites as well as by biologically relevant changes in jejunal tissue transcriptome profiles. Conversely, ileal and colonic transcriptome responses could be measured later, after four days post-conventionalization, and led towards stable molecular profiles at sixteen and thirty days of conventionalization, albeit with region-specific differences. The major molecular responses included strong induction of innate immune response followed by stimulation of adaptive and regulatory immune functions, as well as modulation of metabolic pathways involved in lipid, carbohydrate, and anabolic metabolism. Conventionalization was characterized by two stages separated by one stage of a single day which, particularly in the colon, resembled a transient stage of inflammation, based on transcriptomes, histology and transiently elevated levels of specific plasma markers. This state coincided with temporal domination of specific microbial groups that have previously been identified as “pathobionts”, suggestive of a transient state of dysbiosis. Extensive transcriptome profile analyses throughout the GI tract enabled the identification of central gene regulatory networks that govern the molecular responses during conventionalization and are proposed to serve as genetic signatures for the control of intestinal homeostasis in mice. Nearly all genes in these regulatory networks have human orthologues, suggesting that the biological findings of this study is also relevant for human intestinal biology. In support of this hypothesis, in the jejunum, the identified gene regulatory network appeared to be strongly associated with human metabolic disorders. This notion also suggests that at least in mice, possibly also in human, there is a prominent role of the proximal small intestine in systemic metabolic control.
This thesis exemplifies the pivotal role of the dynamic molecular interactions between the microbiota and the intestinal mucosa, in the establishment and maintenance of mucosal homeostasis in healthy mice. The molecular signatures obtained from these studies in mice may provide novel diagnostic tools and/or therapeutic targets in humans for specific disorders associated with intestinal dysbiosis and loss of mucosal homeostasis.
Keywords: C57/BL6 J mice, conventionalization, transcriptomics, (immune-)histology, metabonomics, microbiota
PPARa: master regulator of lipid metabolism im mouse and human : identification of hepatic PPARa target genes by expression profiling
Rakhshandehroo, M. - \ 2010
Wageningen University. Promotor(en): Michael Muller, co-promotor(en): Sander Kersten. - [S.l. : S.n. - ISBN 9789085857716 - 238
lipidenmetabolisme - transcriptiefactoren - genexpressie - muizen - mens - nutrigenomica - lipid metabolism - transcription factors - gene expression - mice - man - nutrigenomics
The peroxisome proliferator activated receptor alpha (PPARα) is a ligand activated tran- scription factor involved in the regulation of a variety of processes, ranging from inflam- mation and immunity to nutrient metabolism and energy homeostasis. PPARα serves as a molecular target for hypolipidemic fibrates drugs which bind the receptor with high affinity. Furthermore, PPARα binds and is activated by numerous fatty acids and fatty acid derived compounds. PPARα governs biological processes by altering the expression of large number of target genes. Although the role of PPARα as a gene regulator in liver has been well estab- lished, a comprehensive overview of its target genes has been missing so far. Additionally, it is not very clear whether PPARα has a similar role in mice and humans and to what extent target genes are shared between the two species. The aim of the research presented in this thesis was to identify PPARα-regulated genes in mouse and human liver and thereby further elucidate hepatic PPARα function. The applied nutrigenomics approaches are mainly expression microarrays combined with knockout mouse models and in vitro cell culture systems. By combining several independent nutrigenomics studies, we generated a comprehensive overview of PPARα-regulated genes in liver with the focus on lipid metabolism. We identi- fied a large number of PPARα target genes involved in different aspects of lipid metabolism. Furthermore, a major role of PPARα in lipogenesis was detected. Our data pointed to several novel putative PPARα target genes. Next, we compared PPARα-regulated genes in primary mouse and human hepatocytes treated with the PPARα agonist Wy14643 and generated an overview of overlapping and species specific PPARα target genes. A large number of genes were found to be regulated by PPARα activation in human primary hepatocytes, which iden- tified a major role for PPARα in human liver. Interestingly, we could characterize mannose binding lectin 2 (Mbl2) as a novel human specific PPARα target gene. Plasma Mbl2 levels were found to be changed in subjects receiving fenofibrate treatment or upon fasting. Regula- tion of Mbl2 by PPARα suggests that it may play a role in regulation of energy metabolism, although additional research is needed. We also compared the PPARα-induced transcriptome in HepG2 cells versus primary human hepatocytes to investigate the suitability of HepG2 cells in PPARα research. The results re- vealed that the HepG2 cell line poorly reflects the established PPARα target genes and func- tion, specifically with respect to lipid metabolism. Finally, we characterized the transcription factors Klf10 and Klf11 as novel PPARα target genes. Our preliminary findings using in vitro transfection assays and in vivo tail vein injection of plasmid DNA suggested a potential metabolic role of Klf10 and Klf11 in liver. In conclusion, this thesis has extended our understanding of PPARα-regulated genes and function in liver, and has specifically highlightened a major role of PPARα in human hepa- tocytes. This research has also given birth to a possible biomarker of hepatic PPARα activity which is of great interest for future studies. Considering the need for proper biomarkers in the field of nutrigenomics and beyond, the properties of Mbl2 as a biomarker should be further investigated. The identification of other novel putative PPARα target genes offers ample op- portunities for continued research.
Synaptonemal complexes , transverse filaments and interference in mouse meiotic recombination; an immunocytological study = Synaptonemale complexen, transversale filamenten en interferentie bij de meiotsche recombinatie bij de muis; een immuuncytologische studie
Boer, E. de - \ 2007
Wageningen University. Promotor(en): C. Heyting. - [S.l.] : S.n. - ISBN 9789085045854 - 123
immunocytochemie - synaptonemal complex - meiose - muizen - moleculaire genetica - immunocytochemistry - synaptonemal complex - meiosis - mice - molecular genetics
During the prophase of the first meiotic division, homologous chromosomes (homologs} recognize each other and form stable pairs (bivalents). Subsequently non-sister chromatids of homologous chromosomes exchange corresponding parts (crossing over). These events are accompanied by the formation of a ladder like protein structure, the synaptonemal complex (SC), between the paired homologs. First, the two sister chromatids of each chromosome form a common axis, the axial element (AE)1 and subsequently the AEs of homologous chromosomes are connected by numerous transverse filaments (TFs), a process called "synapsis". AEs and TFs together form the SC.
In addition, protein complexes are formed during meiotic prophase that are involved both in homologous chromosome pairing and in crossover formation. These protein complexes can be visualized at the light microscope level as foci by immunofluorescence labeling. Previous research has shown that the composition of these foci changes during the course of meiotic prophase, which reflects the order of proteins that are involved in successive steps in meiotic recombination. Initially, one finds only RAD51/DMC1 foci; subsequently, the recombination proteins RPA and MSH4 become components of the foci, while RAD51 and DMCl disappear; finally MLHl appears, whereas RPA and MSH4 are lost. In the mouse, foci are initially formed in much greater numbers per nucleus than the number of crossovers (COs) that is eventually formed. Accordingly, most foci in early meiotic prophase are not involved in CO formation, but in recombinational interactions that promote homologous chromosome pairing. However, at the transition from RPA/MSH4 to MLHl foci, the number of foci per nucleus decreases drastically, so that eventually the number of MLHl nucleus fits closely with the number of COs per nucleus. Also, the spatial distribution of MLH1 foci along the bivalents closely corresponds to the spatial distribution of COs along the bivalents.
Early in meiosis, the RAD51/DMC1 foci associate already with the AEs and the SCs that are being formed, and this association persists in subsequent stages. This elicited various questions regarding the relation between foci and the SC: do the recombination protein complexes that are marked by the foci have a role in homologous chromosome pairing and the assembly of the SC, and/or is the SC involved in meiotic recombination? In this thesis I focused mainly on the second question: Is the SC involved in meiotic recombination, and if yes, how? Following a primarily immunocytological approach, I analyzed this question in the mouse, because foci can be analyzed well in this species, whereas antibodies against most known components of foci and SCs were already available.
In chapter 1 I summarize the course of meiosis, and provide an overview of the roles of various recombination proteins and SC components, as far as these were known when I started my thesis investigation. Although most information has been obtained by research in yeast, it seems likely that many recombination proteins fulfill similar roles in yeast and mouse meiosis. However, there are also some differences. For instance, mouse meiocytes form far more MSH4 foci than COs, while this is not so in yeast. Furthermore, yeast can form two types of meiotic COs, class I and class U COs, whereas the mouse forms (almost) exclusively class 1 COs. Class I COs display interference, i.e., they are more evenly spaced along the bivalents was to be expected if they would be placed randomly along the bivalents. One important question is, whether SCs have a role in the formation of COs and the positioning of COs along the bivalents.
In chapter 2 we focus on the role of the TFs. The gene encoding TF protein SYCPl is disrupted, and the effects of the mutation on meiotic recombination and chromosome behavior are analyzed. Mice that are homozygous for the SYCPI disruption (Sycpl" mice) were infertile. Sycpl'" spermatocytes formed morphologically normal axial elements (AEs), and homologous AEs were properly aligned, but, as expected, no SC was formed. Most SycpI' ~ spermatocytes were blocked in the pachytene stage of meiotic prophase, and subsequently entered apoptosis. A small proportion, however, reached a later stage of meiotic prophase, diplotene, or, exceptionally, the metaphase of the first meiotic division (metaphase I). However, we found almost no chiasmata in these Sycpl~'~ metaphase I cells. Chiasmata are the cytological manifestations of crossing over. In wild type metaphase I cells one finds the same number of chiasmata as the number of COs that is formed. The absence of chiasmata from Sycpl~'~ spermatocytes might indicate that intact SCs are required for CO formation; alternatively, the SYCPl protein is involved in CO formation besides its role in the assembly of TFs and SCs.
To analyze the CO defect in Sycpl~'' metaphase E spermatocytes in more detail, we performed an imunocytochemical analysis of a series of proteins that are involved in successive steps in meiotic recombination. Foci of proteins that are involved in early and intermediate steps in meiotic recombination, such as RAD51 and MSH4 foci, were formed in normal numbers, and were positioned normally relative to the AEs. However, they persisted much longer than in wild type spermatocytes, and MLHl foci were not formed. Apparently, the first steps in meiotic recombination occur normally in Sycpl' spermatocytes, but subsequently the SYCPl protein is required for the resolution of the recombination intermediates, either by formation of COs, or in other ways that do not yield COs.
One of the first markers for the presence of a meiotic recombination intermediate is ??2??, a phosphorylated form of histone H2A variant H2AX. Ear!y in meiotic prophase of SycpI" spermatocytes, ??2?? appeared throughout the nucleus, as in wild type. However, subsequently yH2AX disappeared much more slowly from the nuclei of SycpI" spermatocytes than from wild type spermatocyte nuclei, whereas in later stages of meiotic prophase, a limited number of distinct yH2AX domains persisted on each bivalent, presumably at sites of unrepaired, blocked recombination intermediates. The ATR protein, which phosphorylates H2AX to generate vH2AX, displayed a similar aberrant localization pattern as ??2??. Notably, the XY bivalent also displayed a limited number of distinct yH2AX domains, whereas in wild type, yH2AX was present throughout the XY bivalent from pachytene on. In other respects the XY bivalent also behaved aberrantly in Sycpl~'~ spermatocytes: whereas the XY bivalent in wild type formed a compact, condensed chromatin domain (the sex vesicle), this did not happen in Sycpl' spermatocytes. We suppose that in wild type, synapsis is accompanied by repair of recombination intermediates, and that ATR disappears from the synapsed portions of AEs as soon as repair has been completed. The ATR that has been released from the synapsed portions of AEs might subsequently relocate to the remaining asynaptic portions of AEs, including those of the XY bivalent, and it might phosphorylate H2AX at these sites. On the XY bivalent, this might result in the formation of a compact chromatin structure, the sex vesicle. In Sycpl' ~ spermatocytes, there is no synapsis, and most recombination intermediates are presumably not repaired. Possibly, ATR is sequestered at the sites of unrepaired DNA, so that insufficient ATR can relocate to the XY bivalent, and no sex vesicle is formed.
In chapter 3 we focus on the spatial distribution of recombination complexes along the bivalents in wild type and Sycpl' spermatocytes and oocytes. Whi!e characterizing the Sycpl' mutant, we noticed that the distinct yH2AX domains, which persisted in Sycpl~ ~ spermatocytes, were more evenly spaced along the bivalents than was to be expected if they were placed randomly, in other words, they displayed (positive) interference. This was remarkable for two reasons: firstly, interference had only been described for COs, and secondly, particularly in older models for the interference mechanism, an important role was ascribed to the SCs and/or synapsis. Therefore, we decided to analyze systematically in wild type and Sycpl' spermatocytes when interference is first detectable, and whether interference manifests itself at a constant level during the course of meiotic prophase. In pachytene of wild type, we found strong interference among MLHl foci, which mark virtually all meiotic COs in the mouse. However, in an earlier stage of meiotic prophase, late zygotene, interference was already detectable among MSH4 foci, which mark intermediate steps in the recombination process. RPA foci, which represent slightly earlier steps in recombination than MSH4 foci, also displayed already interference in late zygotene. Thus, the phenomenon of interference is not limited to COs. The level of interference among RPA or MSH4 foci was lower than the level of interference among MLHl foci. In SycpI''' mutants, interference among MSH4 or RPA foci was as strong as interference among these foci in wild type, which shows that interference can occur without synapsis and without SC. Because the Sycpl^^ mutant does not make MLHl foci, we could not analyze whether the SYCPl protein is required for the strong interference among MLHl foci.
In chapter 4 we consider the question whether the weak interference among MSH4 foci is imposed by the same mechanism that causes the strong interference among MLHlfoci. In particular, we wondered which metric applies to the regulation of the distances between foci, and whether the same metric applies to the regulation of the distances between MSH4 foci (the inter-MSH4 distances) as to the regulation of the inter~MLHl distances: are the interfocus distances regulated in terms of micrometers SC length (?m SC), percentage of the entire SC or chromosome (% SC), or does another metric apply? We assumed that the average length of the interfocus distances and the strength of interference among foci (i.e., the evenness of spacing of foci along the SCs) are regulated by one single mechanism, which we will denote as "the interference mechanism". The question was therefore whether the interference mechanisms for MSH4 and MLHl foci were the same, or at least employed the same interference metric. From comparisons of inter-MSH4 distances on long chromosomes with those on short chromosomes we inferred that within spermatocytes, the proportion of "??? SC length" to the interference metric for MSH4 foci was constant, whereas this did not hold true for the proportion of"% SC length" to the interference metric MSH4 foci; within oocytes we found the same. "%SC" was therefore not the interference metric for MSH4 foci. Furthermore, we concluded, based on comparisons of inter-MSH4 distances in spermatocytes with those in oocytes, that the proportion ??"??? SC length" and the interference metric for MSH4 foci in spermatocytes differs from the corresponding proportion in oocytes. Therefore, "?m SC" also dropped out as possible interference metric for MSH4 foci. We argue that the number of chromatin loops between adjacent MSH4 foci could be the interference metric for MSH4 foci.
We followed the same approach to learn more about the interference metric for MLHl foci. We found that within oocytes and within spermatocytes, the proportion of"% SC" to the interference metric for MLHl foci was fixed, whereas this did not hold true for the proportion of "?m SC" to the interference metric for MLHl foci. Apparently, "?m SC" is not the interference metric for MLHl foci, and in addition, the interference metric for MLHl differs from that for MSH4 foci. That would imply that the interference mechanism for MLHl foci differs from that for MSH4 foci.
In chapter 5 we analyze whether intact SCs and/or intact AEs are required for the strong interference among MLHl foci. For this purpose we used the mouse Sycp3" mutant, which lacks a protein component of the axial element (AE), SYCP3. We performed the analysis in Sycp3';' oocytes, because spermatocytes of this mutant enter apoptosis, presumably before the stage of meiolic prophase when MLHl foci are assembled. During meiotic prophase of Sycp3' mutants, the two sister chromatids of each chromosome form a common axial structure, which lacks besides SYCP3 another AE protein, SYCP2. Like the AEs in wildtype, the axial structures in Sycp3~'~ mutants contain the proteins that keep the sister chromatids together: the cohesins. Therefore we denote the axial structures in Sycp3~" meiocytes as "cohesin axes". In spread preparations of Sycp3~" spermatocytes or oocytes, the cohesin axes, as visualized by immunofluorescence labeling of cohesins. had a stretched and fragmented appearance. The cohesin axes in Sycp3" mutants displayed synapsis, albeit incomplete and discontinuous.Sycp3~'~ oocytes formed MLHl foci in slightly smaller numbers than wildtype oocytes; the MLHl foci usually occurred al sites where the two cohesin axes were connected by synapsis, but in some instances also at sites where two cohesin axes converged, but were not connected by synapsis. Interference among MLHl foci was as strong in Sycp3'' oocytes as it was in wild type, so intact AEs are not required for wildtype levels of interference among MLHl foci. Furthermore, interference among MLHl foci that were separated by stretches of asynapsis or discontinuous synapsis of the cohesin axes was as strong as interference among MLHl foci that were separated by stretches of continuous synapsis of the cohesin axes, so intact SCs and continuous synapsis are not required either for wildtype levels of interference among MLHl foci.
In chapter 6 we provide an overview of the possible functions of transverse filaments (TFs) of SCs. Evidence is accumulating that TFs and SCs have no role in CO interference, and the work described in this thesis indicates the same. However, TFs appear to enhance the formation of class I COs, and appear to be important for homologous pairing of chromosomes along their entire length. Perhaps, TFs were originally important for the formation of stable chromosome pairs during meiosis I. Later in evolution, homologous recombination might have become more important for the recognition of homologous chromosomes and the formation of stable bivalents; the function of TFs might then have been reduced to a supporting role in these processes.
Presence of Salmonella and Campylobacter spp. in Wild Small Mammals on Organic Farms
Meerburg, B.G. ; Jacobs-Reitsma, W.F. ; Wagenaar, J.A. ; Kijlstra, A. - \ 2006
Applied and Environmental Microbiology 72 (2006)1. - ISSN 0099-2240 - p. 960 - 962.
biologische landbouw - kleine zoogdieren - ratten - muizen - salmonella - campylobacter - organic farming - small mammals - rats - mice - salmonella - campylobacter - poultry - infection - strains - jejuni
The presence of Salmonella and Campylobacter spp. in rodents and insectivores (n = 282) was investigated on organic farms. Infections were encountered in house mice (8 of 83 Campylobacter positive and 1 of 83 Salmonella sp. strain Livingstone positive) and brown rats (1 of 8 Campylobacter positive) but not in other species. No shared Campylobacter genotypes were found between rodent and pig manure isolates. Effective on-farm rodent management is recommended
Veterinaire risico's van ongedierte op biologische varkensbedrijven
Meerburg, B.G. ; Kijlstra, A. - \ 2005
V-focus 2 (2005)6. - ISSN 1574-1575 - p. 36 - 37.
varkenshouderij - biologische landbouw - ongediertebestrijding - knaagdierenbestrijding - ratten - muizen - hygiëne - agrarische bedrijfsvoering - veterinaire hygiëne - dierziektepreventie - pig farming - organic farming - vermin control - rodent control - rats - mice - hygiene - farm management - veterinary hygiene - animal disease prevention
Presentatie van de eerste resultaten van een onderzoek door Animal Sciences Group van Wageningen UR naar de ziekterisico's bij ratten en muizen. Hiervoor zijn ratten en muizen op 10 biologische varkensbedrijven met vallen gevangen en op ziektes onderzocht.