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A regional benthic fauna assessment method for the Southern North Sea using Margalef diversity and reference value modelling
Loon, Willem M.G.M. van; Walvoort, Dennis J.J. ; Hoey, Gert van; Vina-Herbon, Christina ; Blandon, Abigayil ; Pesch, Roland ; Schmitt, Petra ; Scholle, Jörg ; Heyer, Karin ; Lavaleye, Marc ; Phillips, Graham ; Duineveld, Gerard C.A. ; Blomqvist, Mats - \ 2018
Ecological Indicators 89 (2018). - ISSN 1470-160X - p. 667 - 679.
AMBI - Benthic assessment method - Fishing pressure - Index - ITI - Margalef diversity - Marine benthos - MMI - Model - MSFD - Multi-metric index - Organic enrichment - OSPAR - PIE - Reference value estimation - Sedimentation - Shannon index - SN - SNA - Species richness
The aims of this study are to develop an optimized method for regional benthic fauna assessment of the Southern North Sea which (a) is sensitive and precise (quantified as the slope and the R2 value of the pressure-impact relationships, respectively) for the anthropogenic pressures bottom fishing and organic enrichment, (b) is suitable for estimating and modelling reference values, (c) is transparent, (d) can be efficiently applied using dedicated software; and to apply this method to benthic data from the Southern North Sea. Margalef diversity appeared to be the best performing benthic index regarding these criteria, even better than several Multi-Metric Indices (MMIs) containing e.g. AMBI (AZTI Marine Biotic Index) and ITI (Infaunal Trophic Index). Therefore, this relatively simple and very practical index, including a new reference value estimation and modelling method, and BENMMI software were selected as a common OSPAR (Oslo Paris convention) method for the benthic fauna assessment of the Southern North Sea. This method was applied to benthic fauna data from the Southern North Sea collected during the period 2010–2015. The results in general show lower normalized Margalef values in coastal areas, and higher normalized Margalef values in deeper offshore areas. The following benthic indices were compared in this study: species richness, Margalef diversity, SNA index, Shannon index, PIE index, AMBI, ITI. For each assessment area, the least disturbed benthic dataset was selected as an adjacent 6 year period with, on average, the highest Margalef diversity values. For these datasets, the reference values were primarily set as the 99th percentile values of the respective indices. This procedure results in the highest stable reference values that are not outliers. In addition, a variable percentile method was developed, in which the percentile value is adjusted to the average bottom fishing pressure (according to data from the International Council for the Exploration of the Sea, ICES) in the period 2009–2013. The adjusted percentile values were set by expert judgement, at 75th (low fishing pressure), 95th (medium fishing pressure) and 99th (high fishing pressure) percentile. The estimated reference values for Margalef diversity correlate quite well with the median depth of the assessment areas using a sigmoid model (pseudo-R2 = 0.86). This relationship between depth and Margalef diversity was used to estimate reference values in case an assessment area had insufficient benthic data For testing the effects of bottom fishing pressure, normalized index values (NIV; index value divided by reference value) were used. The rationale for using NIVs is the assumption that, although a certain level of bottom fishing pressure will have a larger absolute effect on more biodiverse benthic communities in deeper waters than on more robust and less biodiverse coastal benthic communities, the relative effects (tested using NIVs) are comparable. A clear exponentially decreasing relationship (R2 = 0.26–0.27, p < 0.00001) was found between both bottom surface and subsurface fishing activity (penetration depth <2 cm and >2 cm, respectively) and normalized Margalef diversity values, with an asymptotic normalized Margalef value of 0.45 at a subsurface fishing activity >2.3 sweeps/year. This asymptotic value is predominantly found in coastal waters, and probably shows that the naturally more robust coastal benthic communities have been transformed into resilient benthic communities, which rapidly recover from increasing fishing pressure.
Modeling food logistics networks with emission considerations: the case of an international beef supply chain
Soysal, M. ; Bloemhof, J.M. ; Vorst, J.G.A.J. van der - \ 2014
International Journal of Production Economics 152 (2014). - ISSN 0925-5273 - p. 57 - 70.
life-cycle assessment - operations management - programming approach - green logistics - design - sustainability - challenges - inventory - quality - systems
Intrinsic characteristics of food products and processes along with growing sustainability concerns lead to the need for decision support tools that can integrate economic considerations with quality preservation and environmental protection in food supply chains. In this study, we develop a multi-objective linear programming (MOLP) model for a generic beef logistics network problem. The objectives of the model are (i) minimizing total logistics cost and (ii) minimizing total amount of greenhouse gas emissions from transportation operations. The model is solved with the ee-constraint method. This study breaks away from the literature on logistics network models by simultaneously considering transportation emissions (affected by road structure, vehicle and fuel types, weight loads of vehicles, traveled distances), return hauls and product perishability in a MOLP model. We present computational results and analysis based on an application of the model on a real-life international beef logistics chain operating in Nova Andradina, Mato Grosso do Sul, Brazil and exporting beef to the European Union. Trade-off relationships between multiple objectives are observed by the derived Pareto frontier that presents the cost of being sustainable from the point of reducing transportation emissions. The results from the pie chart analysis indicate the importance of distances between actors in terms of environmental impact. Moreover, sensitivity analysis on practically important parameters shows that export ports' capacities put pressure on the logistics system; decreasing fuel efficiency due to the bad infrastructure has negative effects on cost and emissions; and green tax incentives result in economic and environmental improvement.
Just a bite: Considerably smaller snack portions satisfy delayed hunger and craving
Kleef, E. van; Shimizu, M. ; Wansink, B. - \ 2013
Food Quality and Preference 27 (2013)1. - ISSN 0950-3293 - p. 96 - 100.
food cravings - energy-intake - size - appetite
Could smaller snack portions be similarly effective in decreasing cravings or feelings of hunger as larger portions? To answer this, three common snack foods – chocolate, apple pie, potato chips – were given to 104 participants as either a small portion (x) or a substantially larger portion (5–10x). Results indicate that smaller portions satisfied one’s ratings of hunger and craving similar to larger portions, but led to a mean intake that was significantly lower than in the large portion condition (with a difference of 103 calories). This suggests that 15 min after eating a considerably smaller snack, people will have eaten much less but will feel equally satisfied.
Eating behaviour and retro-nasal aroma release in normal-weight and overweight adults: a pilot study
Zijlstra, N. ; Bukman, A.J. ; Mars, M. ; Stafleu, A. ; Ruijschop, R.M.A.J. ; Graaf, C. de - \ 2011
The British journal of nutrition 106 (2011)2. - ISSN 0007-1145 - p. 297 - 306.
food-intake curve - bite size - flavor release - energy-intake - appetite control - obesity - women - meals - satiation - humans
Eating rate and bite size are important factors affecting food intake, and we hypothesise the underlying role of oral sensory exposure in this. However, the latter currently lacks objective measuring parameters, but an interesting measure could be the extent of in vivo retronasal aroma release. Second, the literature is ambiguous about overweight subjects differing from normal-weight subjects in eating behaviour. Consequently, we investigated: (1) whether eating behaviour (food intake, eating rate, bite size, number of bites and meal duration) relates to weight status and (2) whether the extent of retro-nasal aroma release relates to eating behaviour and weight status. A matched group (sex, age and dietary restraint) of twenty-seven normal-weight (BMI 21.8 (SD 1.6) kg/m(2)) and twenty-seven overweight/obese subjects (BMI 30.5 (SD 5.8) kg/m(2)) consumed a spiced rice meal and apple pie yogurt on separate test days. The extent of retro-nasal aroma release was measured on a third test day. Mean bite size for spiced rice was significantly (P=0.03) larger in overweight/obese (10.3 (SD 3.2) g) v. normal-weight subjects (8.7 (SD 2.1) g). There were no other significant differences in eating behaviour or retro-nasal aroma release between the groups. Eating behaviours were not correlated with BMI or retro-nasal aroma release. Subjects showed consistent eating behaviour for both test products. Eating behaviour might be a characteristic of an individual but not by definition a characteristic for a group of people based on their weight. Given the large sample sizes, necessary according to a posteriori sample size calculations, one needs to consider the relevance of finding a statistically significant difference in eating behaviour between the weight groups in a laboratory setting.
The Socio-political Use of Environmental Perception, Interpretation and Evaluation Research
Duineveld, M. - \ 2008
In: Landscape, Leisure and Tourism; Socio-spatial Studies in Experiences, Practices and Policies / de Haan, H.J., van der Duim, V.R., Delft : Eburon - ISBN 9789059722996 - p. 245 - 257.
landschap - perceptie - landschapsbeleving - landscape - perception - landscape experience
This chapter outlines a critical, reflexive research agenda for environmental perception, interpretation and evaluation research (PIE). Here, PIE refers to all those studies that explore the ways in which people perceive, interpret and vaue the natural and the cultural environment
|Ze ruimen bomen vanwege een aaltje. (interview met Ferry Pie-kart)
Moraal, Leen - \ 2007
Effects of added fermentable carbohydrates in the diet on intestinal proinflammatory cytokine-specific mRNA content in weaning piglets
Pié, S. ; Awati, A. ; Vida, S. ; Falluel, I. ; Williams, B.A. ; Oswald, I.P. - \ 2007
Journal of Animal Science 85 (2007). - ISSN 0021-8812 - p. 673 - 683.
total parenteral-nutrition - lactic-acid bacteria - inflammatory responses - weanling piglets - induced colitis - growing pigs - expression - performance - absorption - prebiotics
There is increasing evidence showing that dietary supplementation with prebiotics can be effective in the treatment of intestinal inflammation. Because weaning time is characterized by rapid intestinal inflammation, this study investigated the effect of a diet supplemented with a combination of 4 fermentable carbohydrates (lactulose, inulin, sugarbeet pulp, and wheat starch) on the mRNA content of proinflammatory cytokines in newly weaned piglets. Cytokines (IL-1ß, IL-6, IL-8, IL-12p40, IL-18, and tumor necrosis factor-) were analyzed using a semiquantitative reverse-transcription PCR technique on d 1, 4, and 10 in the ileum and colon of piglets fed either a test diet (CHO) or a control diet. In addition to the diet, the effect of enforced fasting on cytokine mRNA content was also evaluated. No effect of fasting was observed on the pro-inflammatory cytokine mRNA content. Our results showed that the CHO diet induced an up-regulation of IL-6 mRNA content in the colon of piglets 4 d postweaning. This up-regulation was specific for the animals fed the CHO diet and was not observed in animals fed the control diet. An increase in IL-1ß mRNA content was also observed on d 4 postweaning in all of the piglets. Correlations between proinflammatory cytokines and the end-products of fermentation indicated that the regulation of cytokines may be linked with some of the fermentation end-products such as branched-chain fatty acids, which are in turn end-products of protein fermentation
Quantitative analyses of ß-carotene and retinol in serum and feces in support of clinical bioavalailability studies
Zhu, D. ; Wang, Y. ; Pang, Y. ; Liu, A. ; Guo, Jian ; Bouwman, C.A. ; West, C.E. ; Breemen, R.B. van - \ 2006
Rapid Communications in Mass Spectrometry 20 (2006)16. - ISSN 0951-4198 - p. 2427 - 2432.
chromatography-mass-spectrometry - bioefficacy - children - humans
Among more than 50 provitamin carotenoids, beta-carotene is the most metabolically active source of retinol. Despite diets rich in fruits and vegetables containing beta-carotene, vitamin A deficiency is the leading cause of blindness and childhood mortality in developing countries. In addition, the uncertainty of beta-carotene bioconversion into vitamin A suggests that new data are needed to update the nutritional guidelines in developed countries. Previously, we reported the development of a carotene/retinol plateau isotopic enrichment method (CarRet PIE) for the determination of beta-carotene bioavailability and bioconversion into retinol, which utilizes positive ion atmospheric pressure chemical ionization (APCI) liquid chromatography/mass spectrometry (LC/MS). While seeking to validate the CarRet PIE using a mass balance approach requiring fecal measurements of beta-carotene and retinol, interference was encountered that required substantial modifications of the LC/MS assay. Here we report a new LC/MS assay that is based on the detection of molecular anions of beta-carotene using negative ion APCI with a reversed-phase C-30 column for HPLC separation. Sample preparation required saponification to eliminate interfering triglycerides. The limit of detection (LOD) of beta-carotene was 0.25 pmol calculated on the basis of an injection of 20 mu L of 0.0125 mu M beta-carotene, and the limit of quantitation (LOQ) was 1.0 pmol based on the injection of 20 mu L of 0.050 mu M beta-carotene. The linear range was 1.1 to 2179 pmol on-column. The wide linear range and low LOD and LOQ of this assay facilitated the sensitive and selective quantitative analysis of beta-carotene in both serum and fecal samples in support of an on-going clinical investigation of beta-carotene bioavailability and bioconversion into vitamin A. Copyright (c) 2006 John Wiley & Sons, Ltd.
Identification of quantitative trait loci for carcass composition and meat quality traits in a commercial finishing cross
Wijk, H.J. van; Dibbits, B.W. ; Baron, E.E. ; Brings, A.D. ; Harlizius, B. ; Groenen, M.A.M. ; Knol, E.F. ; Bovenhuis, H. - \ 2006
Journal of Animal Science 84 (2006)4. - ISSN 0021-8812 - p. 789 - 799.
influencing economic traits - large white intercross - genome scan analysis - pig skeletal-muscle - sus-scrofa - meat quality - body-composition - glycogen-content - igf2 locus - qtl
A QTL study for carcass composition and meat quality traits was conducted on finisher pigs of a cross between a synthetic Pie¿train/Large White boar line and a commercial sow cross. The mapping population comprised 715 individuals evaluated for a total of 30 traits related to growth and fatness (4 traits), carcass composition (11 traits), and meat quality (15 traits). Offspring of 8 sires (n = 715) were used for linkage analysis and genotyped for 73 microsatellite markers covering 14 chromosomal regions representing approximately 50% of the pig genome. The regions examined were selected based on previous studies suggesting the presence of QTL affecting carcass composition or meat quality traits. Thirty-two QTL exceeding the 5% chromosome-wise significance level were identified. Among these, 5 QTL affecting 5 different traits were significant at the 1% chromosome-wise level. The greatest significance levels were found for a QTL affecting loin weight on SSC11 and a QTL with an effect on the Japanese color scale score of the loin on SSC4. About one-third of the identified QTL were in agreement with QTL previously reported. Results showed that QTL affecting carcass composition and meat quality traits segregated within commercial lines. Use of these results for marker-assisted selection offers opportunities for improving pork quality by within-line selection
Introduction: Water for Food and Ecosystems: How to Cut which Pie?
Warner, J.F. ; Bindraban, P.S. ; Keulen, H. van - \ 2006
International Journal of Water Resources Development 22 (2006)1. - ISSN 0790-0627 - p. 3 - 13.
agriculture - yield - efficiency - rainfall - drought
Two decades of awareness-raising and dialogues have clearly spelled out the water-related challenges the world is facing. Still, not enough concrete improvements have been realized on key issues, such as the coverage of potable water and sanitation services, and an adequate balance between water for food and ecosystems. Addressing these problems remains a continuous challenge that can only be confronted with an integrated approach, comprising knowledge generation, permanent communication between very different stakeholders, adequate capacity-building and continuous learning, and innovative technology development. With a view to the Fourth World Water Forum in Mexico, this contribution reviews such issues, drawing lessons from experience in a program on Water for Food and Ecosystems (funded by Netherlands Partners for Water initiative) and related on-going work in this area carried out by Wageningen University and Research Centre working closely with partner institutions inside and outside the Netherlands. The debate is structured around three key dimensions (i) balancing human and natural values of water, (ii) multiple stakeholder involvement, (iii) technological innovation. Visualized in the Triangle of Sustainability, the study recognizes the advances made in integrating political processes such as multi-stakeholder negotiation in water resource management as a way of achieving a better balance between the values of water, but warn against neglecting the potential for technical advances that can help increasing the size of the `cake¿ as a whole.
Postnatal development of intestinal immune system in piglets: implications for the process of weaning
Stokes, C.R. ; Bailey, M. ; Haverson, K. ; Harris, C. ; Jones, P. ; Inman, C. ; Pie, S. ; Oswald, I.P. ; Williams, B.A. ; Akkermans, A.D.L. ; Sowa, E. ; Rothkotter, H.J. ; Miller, B.G. - \ 2004
Animal Research 53 (2004)4. - ISSN 1627-3583 - p. 325 - 334.
antibody repertoire development - ileal peyers-patches - lamina propria - t-cells - intraepithelial lymphocytes - neonatal piglets - newborn piglets - miniature pig - antigen - gut
European-wide directives are in place to establish a sustainable production of pigs without using production enhancers and chemotherapeutics. Thus, an economically-viable pig production is now only possible when the physiological mechanisms of defense against pathogens and tolerance against nutrients and commensal bacteria in the intestinal immune system are taken into account. During the postnatal period the piglet is facing first the time large amounts of new antigens and at weaning a second wave of nutritional antigens is entering the intestinal tract. The appropriate development of humoral and cellular functions of the intestinal immune system is essential for optimum growth and performance of the piglets. The integrity of the intestinal surfaces is a prerequisite of intestinal immunity and tolerance. Secretory IgA serves to exclude harmful antigens from uptake. The induction of intestinal immune reactions starts with antigen presentation by professional antigen presenting cells of Peyer's patches and mesenteric lymph nodes. In addition, the intestinal lamina propria serves as a mucosal compartment for regulation of immune responses. Here especially T regulatory cells (CD4(+) CD25(+)) have their function for maintaining intestinal homeostasis. The network of mucosal T and B cells develops after birth in a programmed sequence; it is almost completed at week 7 after birth. Weaning is associated with changes in the regulation of the lymphoid cells in the mucosa. In small and large intestine increases in pro- and anti-inflammatory cytokines were observed after weaning in lymphocytes. Epithelial cells were studied both in intestinal samples and in vitro. Here the cytokine patterns provide evidence that weaning is inducing a transient inflammation of the mucosa. Piglets weaned under conventional conditions have a thicker mucosa than pigs weaned from isolators. Cells of isolator-reared pigs show slightly higher levels of activation markers - probably reflecting the interaction of the foreign protein derived from bovine milk. The results presented in this overview demonstrate that further effort is necessary to elucidate the function of the porcine intestinal immune system in the postnatal period and at the time of weaning to provide criteria for porcine intestinal health.
Nutritional composition and flavonoid content of edible wild greens and green pies: a potential rich source and antioxidant nutrients in the Mediterranean diet
Trichopoulou, A. ; Vasilopoulou, E. ; Hollman, P.C.H. ; Chamalides, Ch. ; Foufa, E. - \ 2000
Food Chemistry 70 (2000). - ISSN 0308-8146 - p. 319 - 323.
The traditional Greek diet is dominated by the high consumption of olive oil, fruit and vegetables. Antioxidants represent a common element in these foods and may be important mediators of the beneficial effect of this diet. Wild edible greens are frequently consumed throughout Greece. Seven edible wild greens and traditional Cretan green pies were analyzed for their nutritional composition and flavonoid content, in particular flavonols and flavones. A high nutritional value and a low energy value characterize the wild greens. These wild greens have a very high flavonol content when compared with regular fresh vegetables, fruits and beverages commonly consumed in Europe. Rumex obtusifolius was found to contain twice the amount of quercetin contained in onions. Two pieces of Cretan green pie (100 g) contain approximately 12 times more quercetin than one glass of red wine (100 ml) and three times more quercetin than a cup of black tea (200 ml). Wild greens potentially are a very rich source of antioxidant flavonols and flavones in the Greek diet.
A comparison of the optical probe HGP and the ultrasonic devices Renco and Pie Medical for estimation of the lean meat proportion in pig carcasses
Hulsegge, B. ; Merkus, G.S.M. - \ 1997
Animal Science 64 (1997)2. - ISSN 1357-7298 - p. 379 - 383.
Characterization of genes expressed during mesoderm formation and anteroposterior patterning in carp (Cyprinus carpio)
Stevens, C.J.M. - \ 1997
Agricultural University. Promotor(en): L.P.M. Timmermans; H.W.J. Stroband; G. te Kronnie. - S.l. : Stevens - ISBN 9789054857549 - 130
cyprinidae - karper - moleculaire genetica - genexpressie - pleiotropie - methodologie - technieken - moleculaire biologie - cyprinidae - carp - molecular genetics - gene expression - pleiotropy - methodology - techniques - molecular biology
The formation of germ layers during gastrulation and the specification and patterning of the body axes are important events in the development of the embryo. The investigations described in this thesis aimed to isolate and characterize the distribution of transcripts of genes, in particular novel genes, that are expressed during the formation of mesoderm and the patterning of the anteroposterior axis in the carp (Cyprinus carpio), a cyprinid teleost fish. Such studies may contribute to a better insight in the molecular mechanisms underlying the above processes, in two respects. Firstly, the characterization of a gene's expression pattern is one of the first steps towards the elucidation of its function. Especially the characterization of novel genes may provide a key to new insights in development. Furthermore, in studies of development, it is of importance to have markers that identify specific cell types, for example early mesodermal precursor cells. The isolation of genes that are specifically expressed in certain cell types provides such markers.
Two molecular approaches were chosen for gene isolation. Firstly, we specifically searched for homeobox genes, which encode transcription factors with important regulatory functions during development. A particular class of homeobox genes, the Hox genes, provides cells along the anteroposterior axis with positional information and the expression patterns of members of this class are excellent markers of position on this axis. Our second approach was a subtractive hybridization strategy. It was applied to isolate genes that are differentially expressed between the oocyte and the early segmentation stage, a period during which mesoderm is induced.
For the identification of homeobox-containing sequences in a carp early segmentation stage cDNA library, we used a probe that was composed of a mixture of homeobox fragments, produced by PCR. The PCR primers were designed against the most conserved regions of the homeobox. This approach yielded a number of different genes of which two are described in this thesis. The gene cdx1(Chapter 2) is a member of the caudal class of homeobox genes and is expressed in ventrolateral cells of the embryo prior to gastrulation. During gastrulation, transcripts of this gene accumulate in the posterior half of the embryo. The functions of caudal class genes of Drosophila, mouse and Xenopus indicate that genes of this class mediate the specification of posterior positional values in the embryo. Because of their characteristic distribution, cdx1 transcripts are useful markers of (ventro) posterior position in the embryo and have been used as such in the studies of mesoderm formation and anteroposterior patterning in blastoderm explants, performed in our laboratory.
A second gene isolated in the search for homeobox genes was the Hoxb-1 gene, described in Chapter 3. This gene belongs to the class of Hox genes, whose members are organized into clusters in the genome of many species. With expression reaching into the hindbrain, the Hoxb-1 gene is one of the most anteriorly expressed Hox genes. Its most prominent expression, especially during segmentation, is found in rhombomere 4. In the late segmentation stage embryo, Hoxb-1 expression is a valuable marker of this rhombomere and the neural crest cells at that level of the hindbrain.
Chapter 4 describes the cloning of genes on the basis of their differential gene expression between the oocyte and the early segmentation stage, using a subtractive hybridization strategy. Fifteen genes, identified from the oocyte stage cDNA library, are expressed in early development, when mesoderm induction occurs, and their expression disappears before the beginning of segmentation. From the early segmentation stage cDNA library, 26 genes were selected whose expression was activated during segmentation but not yet in early development, coinciding with the differentiation of the mesoderm and the patterning of the anteroposterior axis. In total 27 genes appeared to code for novel proteins and are therefore candidates for further studies and may provide a better insight into molecular mechanisms underlying developmental processes. Also in light of the large scale mutagenesis screens of zebrafish that have recently been undertaken in a number of laboratories and for which the affected genes yet need to be molecularly identified, it is important that the search for novel genes continues for only few candidate sequences are available so far. The subtractive hybridization strategy described in this thesis appears a worthwhile technique to obtain such candidate sequences.
Further investigations of these novel genes were restricted to a detailed characterization of the expression of one gene: cth1.Chapter 5 gives a description of the distribution of the mRNA transcripts of this gene during cleavage, blastula and gastrula stages. Whereas maternal cth1 mRNA is ubiquitously distributed in the blastomeres, the embryonically transcribed cth1 mRNA is expressed after the late blastula stage, in cells at the blastoderm margin which have mesodermal and endodermal fates. The cth1 transcripts disappear around midgastrulation, coinciding with the commitment of cells to the mesodermal (or endodermal) fate. In the cth1 protein, motifs containing three cysteines and one histidine (C3H) are present that are most likely zinc fingers, structures involved in the regulation of expression of target genes. The cth1 mRNA expression pattern and the gene's homology to the TIS11 family, a family of primary response genes whose expression is activated after treatment with for example growth factors, suggest a function for the cth1 gene of maintenance of the cellular potential in cells with mesodermal (and endodermal) fates, and in cells of cleavage stages. By inhibiting the expression of certain target genes, cth1 could prevent or delay the selection of certain differentiation pathways, such as for example the commitment to a mesodermal fate before midgastrulation.
Proteins containing C3H motifs are expressed in a number of species.For example in C.elegans, the PIE-1 protein is required to keep germlineblastomeres totipotent during early development, most likely by suppressing the transcription in these blastomeres. In Chapter 6 the literature on the C3H class of proteins is shortly reviewed and the hypothesis is proposed that they may be widely involved in preserving cellular potency in specification events during development.
In Chapter 7 the results presented in previous chapters are discussed, with emphasis on the proposed role for cth1 and how its activity could affect the fate of the cells expressing this gene.
A molecular analysis of L-arabinan degradation in Aspergillus niger and Aspergillus nidulans
Flipphi, M.J.A. - \ 1995
Agricultural University. Promotor(en): A.J.J. van Ooyen; J. Visser. - S.l. : Flipphi - ISBN 9789054853923 - 165
aspergillus - celwanden - koolhydraten - cellulose - celmembranen - fermentatie - voedselbiotechnologie - glycosidasen - polysacchariden - genexpressie - pleiotropie - moleculaire genetica - aspergillus - cell walls - carbohydrates - cellulose - cell membranes - fermentation - food biotechnology - glycosidases - polysaccharides - gene expression - pleiotropy - molecular genetics
This thesis describes a molecular study of the genetics ofL-arabinan degradation in Aspergillus niger and Aspergillus nidulans. These saprophytic hyphal fungi produce an extracellular hydrolytic enzyme system to depolymerize the plant cell wall polysaccharideL-arabinan. Chapter 1 surveys the occurrence, properties and applications ofL-arabinanolytic enzymes (arabinases). The A.niger system, which constitutes an endolytic endo-1,5-α-L-arabinase (ABN A) and two distinct α-L-arabinofuranosidases (ABF A and ABF B), has been a frequent subject of investigation in the past and represents the best characterizedL-arabinanolytic system to date. These three enzymes are all glycosylated. Current knowledge on the induction of fungal arabinase expression is summarized in this Chapter. Furthermore, the structure of the polysaccharide substrate and its function in the plant cell wall matrix are introduced.
In Chapters 2 to 5, the cloning and characterization of the structural genes coding for the three glycosyl hydrolases from the A. nigerL-arabinan-degrading complex are described. A. niger abf A and abf B ar e the first eukaryotic ABF-encoding genes to be isolated and sequenced, abn A is the first ABN-encoding gene published. Chapter 2 reports on the isolation of the abf A gene encoding ABF A, the minor extracellular ABF. This gene could be cloned by utilizing ABF Aspecific cDNA as the probe. This cDNA was immunochemically identified from a cDNA library generated fromL-arabitol-induced myceliurn of an A. nigerD-xylulose kinase mutant. This mutant is unable to grow onL-arabitol and features enhanced expression of all three arabinases when transferred to medium containing this pentitol as sole carbon source. In Chapter 3 , the cloning of the ABN A-encoding gene (abn A) is described. This gene was isolated following the same strategy as with abf A, although a second cDNA library had to be generated first. The induction process was immunochemically monitored in order to establish the proper induction conditions for the new library. The abn A gene and the gene product were characterized by DNA sequence analyses of the cloned genomic DNA and the cDN A. The N-terminal amino acid sequences of ABN A and a CNBr-derived peptide were determined. Several transcription initiation sites and one polyadenylation site could be identified. The structural region codes for a protein of 321 amino acids and is interrupted by three introns. Extracellular ABN A consists of 302 amino acid residues with a deduced molecular weight of 32.5 kDa and a theoretical pl of 3.5. For the protein, an apparent pl of 3.0 and an apparent molecular weight of 43 kDa, determined upon SDS-PAGE, were previously reported. Chapter 4 documents the isolation and characterization of the abf B gene, coding for the major extracellular ABF. The determination of N-terminal amino acid sequences from ABF B and CNBr-generated peptides allowed the design of deoxyoligonucleotide mixtures which enabled the cloning of abf B. When utilized as primers in a polymerase chain reaction (PCR), ABF B-specific amplification products emerged, one of which was used to probe the gene. The abf B gene and the gene product were characterized by DNA sequence analyses of the cloned genomic DNA and of ABF B- specific cDNA isolated from the library described in Chapter 3. Several transcription initiation sites and one polyadenylation site could be identified. The structural region is a single open reading frame and codes for a protein of 499 amino acids. The mature enzyme consists of 481 amino acid residues with a deduced molecular weight of 50.7 kDa and a theoretical pl of 3.8. An apparent pl of 3.5 and an apparent molecular weight of 67 kDa, determined upon SDS-PAGE, were previously reported. The abf B gene product was suggested to be identical to the ABF purified and characterized by Kaji and Tagawa (Biochim Biophys Acta 207 : 456-464 (1970)). Considering the non-amino acid content of the latter protein, a molecular weight of 64 kDa could be deduced for ABF B. In Chapter 5 , the abf A gene and its gene product were characterized by DNA sequence analyses of the genomic DNA and of the cDNA for which the isolation was described in Chapter 2. The N-terminal amino acid sequences of ABF A and a CNBr-derived peptide were determined. One transcription initiation site and two polyadenylation sites could be identified. The structural region is interrupted by seven introns and codes for a protein of 628 amino acids. Mature ABF A consists of 603 amino acid residues with a deduced molecular weight of 65.4 kDa and a theoretical pl of 3.7. For this ABF, an apparent pi of 3.3 and an apparent molecular weight of 83 kDa, determined upon SDS-PAGE, were previously documented.
Although the three enzymes are all active against (1->5)-α-glycosidic bonds betweenL-arabinofuranosides, ABF A, ABF B and ABN A are genetically unrelated. ABF A was found to be N -glycosylated whereas ABF B and ABN A were not - these enzymes are only O -glycosylated. For each gene, arabinaseoverproducing strains were generated by introducing multiple gene copies in A.niger or in A.nidulans uridine auxotrophic strains through co-transformation. Transformants were isolated upon primary selection for uridine prototrophy. Subsequent overproduction of the genes introduced was demonstrated in these recombinant strains upon growth on sugar beet pulp, both immunochemically and by assaying enzyme activity. abf A was shown to be expressed in the heterologous host A.nidulans, despite the absence of an abf A gene equivalent in this organism. High-copy number A.niger abf B transformants featured impaired secretion of other extracellular proteins upon growth on sugar beet pulp. ABN A overproduction was found to be limited to approximately five times the wild-type level in A.niger abn A transformants, but not in A.nidulans transformants. Such a limitation was not observed in case of the ABFs.
In Chapters 5 and 6, the regulation ofL-arabinan degradation is addressed. The structural genes seem to be regulated mainly at the transcriptional level. Additional copies of either A13F-encoding gene in A.niger were shown to result in a reduction, but not in total silencing of the expression of the wild-type ABN Aencoding gene upon induction with either sugar beet pulp orL-arabitol ( Chapter 5 ). The reduction of the expression level of abn A correlated with the abf gene dosage. The repression effected by extra abf B gene copies was more stringent and more persistent than that elicited by additional abf A copies. Although observed with both inducers, these phenomena were more outspoken and more persistent on sugar beet pulp. Similar, but more moderate effects were observed towards the expression of the other abf gene in multiple copy abf A- and abf B-transformants. It was proposed that the abf genes titrate two distinct gene activators both involved in coordination of arabinase gene expression. However, the three genes were shown to respond differently upon a mycelial transfer toL-arabitol-containing medium, indicating that gene-specific factors are also involved. Four distinct sequence motifs were found in common in the promoter regions of the three genes. One of these elements is identical to the A.nidulans CREA-motif, which has been shown to mediate carbon catabolite repression on several A.nidulans enzyme systems. Arabinase expression in A.niger is known to be repressed in the presence ofD-glucose. Two other motifs are highly homologous to cAMP-responsive elements described in other organisms. For the fourth motif no functional analogues could be found, but the element was found to be present in several other fungal genes which are not involved inL-arabinan degradation at all. It is therefore likely that none of these common elements confer system-specific regulation.
The presumed involvement ofL-arabitol in the induction process of fungal arabinases was further emphasized by the induction characteristics of an A. nidulans mutant unable to grow on the end-product ofL-arabinan degradation,L-arabinose, nor onL-arabitol ( Chapter 6).L-Arabitol is an intermediate ofL-arabinose catabolism in Aspergilli. This mutant was shown to lack NAD +-dependentL-arabitol dehydrogenase activity resulting inL-arabitol accumulation, both intracellularly and in the culture medium, wheneverL-arabinose is present. Upon submerged growth on various carbon sources in the presence ofL-arabinose, the mutant featured enhanced expression of the enzymes involved in extracellularL-arabinan degradation, and of those of the intracellularL-arabinose catabolism. The co-substrates on which the mutant secreted large amounts of arabitol simultaneously exhibited high arabinase expression and featured reduced growth.L-Arabitol secretion and enzyme production were also observed on a mixed carbon source ofD-glucose andL-arabinose, resulting in normal growth. Hence, in the presence ofL- arabinose, the carbon catabolite repression conferred byD-glucose in the wild-type, is overruled in the mutant.
In Chapter 7 , ABN A is shown to have remote sequence similarity with four bacterial xylanolytic glycosyl hydrolases (three β-D-xylosidases and an endo-1,4-β-D-xylanase), three of which feature activity against para -nitrophenyl-α-L-arabinofuranoside. This synthetic compound is commonly utilized to assay potential ABF activity, whereas it is known to be an inhibitor of the fourth enzyme. The homology became evident only after multi pie-sequence alignments and hydrophobic cluster analysis. It was proposed that these enzymes share a binding site for a terminal non-reducing α-linkedL-arabinofuranosyl residue and that they all belong to glycosyl hydrolase family 43. Implications from these suggestions were discussed. The ABFs could not be assigned to an established glycosyl hydrolase family.
Based on theL-arabinolytic system of the brown-rot fungus Monilinia fructigena, the sequence similarity found amongst ABF A and bacterial pullulan-degrading enzymes, and ABF expression levels under carbon starvation conditions and onD-glucose as the carbon source, distinct functions inL-arabinan and plant cell-wall degradation were proposed for ABF A and ABF B. ABF A would be essentially cell-wall associated and act to degradeL-arabinan fragments generated by ABN A. ABF B activity would be important for the primary release of small amounts ofL-arabinose which initiate induction of various endolytic systems to degrade plant cell walls, and thus function in substrate sensing. In line with these considerations, the involvement of other, not yet identified glycosyl hydrolases inL-arabinan degradation by A.niger was suggested.
Induction and repression of arabinase gene expression are further discussed in Chapter 7 . The results of the studies in A.niger (Chapter 5) and A.nidulans (Chapter 6) were interpreted in a mutual context. The identity of the lowmolecular-weight compound directly responsible for induction of arabinase gene expression, was addressed. BothL-arabinose andL-arabitol are likely candidates to fulfil such a role. However, it was not possible to weigh the actual inductive capacities ofL-arabinose andL-arabitol due to their in vivo convertibility and the carbon catabolite repression elicited by the pentose. Competition for such a compound provides an alternative explanation for the phenomena observed in Chapter 5. The involvement of the transcriptional repressor CREA in arabinase gene expression is not limited to the direct repression of structural and regulatory genes of theL-arabinan-degrading system. It also plays a role in inducer exclusion and end-product repression, two processes shown to be eminently involved in the regulation ofL-arabinan degradation in wild-type A.nidulans. Fungal growth rate was suggested to be related to derepression of theL-arabinan-degrading system. The possible involvement of cAMP in arabinase gene expression, as suggested by the presence of potential cis -acting cAMP-responsive elements in the structural genes, was considered. Various ways by which cAMP might modulate arabinase synthesis were surveyed.
Bloemen en bollen: onderzoek van houdbaarheid, transport, logistiek en kwaliteit 9 januari 1991
Drent, P.J. ; Schoot, C. van der; Kooten, O. van; Mensink, M.G.J. ; Otma, E.C. ; Harbinson, J. ; Harkema, H. ; Tijskens, L.M.M. ; Woltering, E.J. ; Berg-Somhorst, B.P.M. van de; Vrije, G.J. de; Halaba, J. ; Gorin, N. ; Rudolphij, J.W. ; Pie, K. ; Peppelenbos, H.W. ; Hoogerwerf, A. ; Reinders, M.P. ; Timmermans, A.J.M. - \ 1991
Wageningen : ATO-Agrotechnologie - 33
Vleesproduktie met Piemontese x zwartbont kruislingvaarzen
Hanekamp, W.J.A. - \ 1991
Lelystad : Proefstation voor de Rundveehouderij, Schapenhouderij enPaardenhouderij (Publikatie / Proefstation voor de Rundveehouderij, Schapenhouderij en Paardenhouderij 69) - 23
vleesvee - karkaskwaliteit - kruisingsfokkerij - ontwikkeling - groei - slacht - beef cattle - carcass quality - crossbreeding - development - growth - slaughter
Uit literatuur en modelberekeningen blijkt dat het éénmaal laten afkalven van kruislingvaarzen en deze daarna snel te slachten een aantrekkelijke tweede tak voor de melkveehouderij kan zijn. Voor onderzoek naar de praktische haalbaarheid van dit systeem is er een uitgebreide proef met Pie-montese X zwartbonte kruislingvaarzen gedaan.
|Antifungal modes of action of metalaxyl, cyprofuram, benalaxyl and oxadixyl in phenylamide-sensitive and phenylamide-resistant strains of Phytophthora megasperma f. sp. medicaginis and Phytophthora infestans
Davidse, L.C. ; Gerritsma, O.C.M. ; Ideler, J. ; Pie, K. ; Velthuis, G.C.M. - \ 1988
Crop Protection 7 (1988). - ISSN 0261-2194 - p. 347 - 355.