Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber
Zhang, Z. ; Mao, L. ; Chen, Junshi ; Bu, F. ; Li, G. ; Sun, J. ; Li, S. ; Sun, H. ; Jiao, C. ; Blakely, R. ; Pan, J. ; Cai, R. ; Luo, R. ; Peer, Y. Van de; Jacobsen, E. ; Fei, Z. ; Huang, S. - \ 2015
The Plant Cell 27 (2015)6. - ISSN 1040-4651 - p. 1595 - 1604.
indel-associated mutation - tuberculate fruit gene - false discovery rate - arabidopsis-thaliana - population-scale - functional impact - sequencing data - synthase gene - paired-end - sativus l.
Structural variations (SVs) represent a major source of genetic diversity. However, the functional impact and formation mechanisms of SVs in plant genomes remain largely unexplored. Here, we report a nucleotide-resolution SV map of cucumber (Cucumis sativas) that comprises 26,788 SVs based on deep resequencing of 115 diverse accessions. The largest proportion of cucumber SVs was formed through nonhomologous end-joining rearrangements, and the occurrence of SVs is closely associated with regions of high nucleotide diversity. These SVs affect the coding regions of 1676 genes, some of which are associated with cucumber domestication. Based on the map, we discovered a copy number variation (CNV) involving four genes that defines the Female (F) locus and gives rise to gynoecious cucumber plants, which bear only female flowers and set fruit at almost every node. The CNV arose from a recent 30.2-kb duplication at a meiotically unstable region, likely via microhomology-mediated break-induced replication. The SV set provides a snapshot of structural variations in plants and will serve as an important resource for exploring genes underlying key traits and for facilitating practical breeding in cucumber.
Uncertainties in predicting rice yield by current crop models under a wide range of climatic conditions
Li, T. ; Hasegawa, T. ; Yin, X. ; Zhu, Y. ; Boote, K. ; Adam, M. ; Bregaglio, S. ; Buis, S. ; Confalonieri, R. ; Fumoto, T. ; Gaydon, D. ; Marcaida III, M. ; Nakagawa, H. ; Oriol, P. ; Ruane, A.C. ; Ruget, F. ; Singh, B. ; Singh, U. ; Tang, L. ; Yoshida, H. ; Zhang, Z. ; Bouman, B. - \ 2015
Global Change Biology 21 (2015)3. - ISSN 1354-1013 - p. 1328 - 1341.
air co2 enrichment - high-temperature stress - elevated co2 - spikelet fertility - night temperature - carbon-dioxide - growth - sterility - face - productivity
Predicting rice (Oryza sativa) productivity under future climates is important for global food security. Ecophysiological crop models in combination with climate model outputs are commonly used in yield prediction, but uncertainties associated with crop models remain largely unquantified. We evaluated 13 rice models against multi-year experimental yield data at four sites with diverse climatic conditions in Asia and examined whether different modeling approaches on major physiological processes attribute to the uncertainties of prediction to field measured yields and to the uncertainties of sensitivity to changes in temperature and CO2 concentration [CO2]. We also examined whether a use of an ensemble of crop models can reduce the uncertainties. Individual models did not consistently reproduce both experimental and regional yields well, and uncertainty was larger at the warmest and coolest sites. The variation in yield projections was larger among crop models than variation resulting from 16 global climate model-based scenarios. However, the mean of predictions of all crop models reproduced experimental data, with an uncertainty of less than 10% of measured yields. Using an ensemble of eight models calibrated only for phenology or five models calibrated in detail resulted in the uncertainty equivalent to that of the measured yield in well-controlled agronomic field experiments. Sensitivity analysis indicates the necessity to improve the accuracy in predicting both biomass and harvest index in response to increasing [CO2] and temperature.
An integrated catalog of reference genes in the human gut microbiome
Li, J. ; Jia, H. ; Cai, X. ; Zhong, H. ; Feng, Q. ; Sunagawa, S. ; Arumugam, M. ; Kultima, J.R. ; Prifti, E. ; Nielsen, T. ; Juncker, A.S. ; Manichanh, C. ; Chen, B. ; Zhang, W. ; Levenez, F. ; Xu, X. ; Xiao, L. ; Liang, S. ; Zhang, D. ; Zhang, Z. ; Chen, W. ; Zhao, H. ; Al-Aama, J.Y. ; Edris, S. ; Yang, H. ; Hansen, H. ; Nielsen, H.B. ; Brunak, S. ; Kristiansen, K. ; Guarner, F. ; Pedersen, O. ; Doré, J. ; Ehrlich, S.D. ; Bork, P. ; Wang, J. ; Vos, W.M. de; Tims, S. ; Zoetendal, E.G. ; Kleerebezem, M. - \ 2014
Nature Biotechnology 32 (2014)8. - ISSN 1087-0156 - p. 834 - 841.
eukaryotic diversity - fecal microbiota - population-size - metagenome - sequences - genomes - tool - alignment - impact - twins
Many analyses of the human gut microbiome depend on a catalog of reference genes. Existing catalogs for the human gut microbiome are based on samples from single cohorts or on reference genomes or protein sequences, which limits coverage of global microbiome diversity. Here we combined 249 newly sequenced samples of the Metagenomics of the Human Intestinal Tract (MetaHit) project with 1,018 previously sequenced samples to create a cohort from three continents that is at least threefold larger than cohorts used for previous gene catalogs. From this we established the integrated gene catalog (IGC) comprising 9,879,896 genes. The catalog includes close-to-complete sets of genes for most gut microbes, which are also of considerably higher quality than in previous catalogs. Analyses of a group of samples from Chinese and Danish individuals using the catalog revealed country-specific gut microbial signatures. This expanded catalog should facilitate quantitative characterization of metagenomic, metatranscriptomic and metaproteomic data from the gut microbiome to understand its variation across populations in human health and disease.
Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus
Lin, K. ; Limpens, E.H.M. ; Zhang, Z. ; Ivanov, S. ; Saunders, D.G.O. ; Mu, D. ; Pang, E. ; Cao, H. ; Cha, H. ; Lin, T. ; Zhou, Q. ; Shang, Y. ; Li, Y. ; Sharma, T.C. ; Velzen, R. van; Ruijter, N.C.A. de; Aanen, D.K. ; Win, J. ; Kamoun, S. ; Bisseling, T. ; Geurts, R. ; Huang, S.W. - \ 2014
Plos Genetics 10 (2014)1. - ISSN 1553-7404 - 13 p.
arbuscular mycorrhizal fungi - pathogen phytophthora-infestans - glomus-intraradices - sexual reproduction - protein families - cdna sequences - kingdom fungi - gene - identification - efficient
Nuclei of arbuscular endomycorrhizal fungi have been described as highly diverse due to their asexual nature and absence of a single cell stage with only one nucleus. This has raised fundamental questions concerning speciation, selection and transmission of the genetic make-up to next generations. Although this concept has become textbook knowledge, it is only based on studying a few loci, including 45S rDNA. To provide a more comprehensive insight into the genetic makeup of arbuscular endomycorrhizal fungi, we applied de novo genome sequencing of individual nuclei of Rhizophagus irregularis. This revealed a surprisingly low level of polymorphism between nuclei. In contrast, within a nucleus, the 45S rDNA repeat unit turned out to be highly diverged. This finding demystifies a long-lasting hypothesis on the complex genetic makeup of arbuscular endomycorrhizal fungi. Subsequent genome assembly resulted in the first draft reference genome sequence of an arbuscular endomycorrhizal fungus. Its length is 141 Mbps, representing over 27,000 protein-coding gene models. We used the genomic sequence to reinvestigate the phylogenetic relationships of Rhizophagus irregularis with other fungal phyla. This unambiguously demonstrated that Glomeromycota are more closely related to Mucoromycotina than to its postulated sister Dikarya.
Terrestrial Laser Scanning International Interest Group (TLSIIG): Brisbane Instrument Intercomparison
Armston, J. ; Newnham, G. ; Strahler, A. ; Schaaf, C. ; Danson, M. ; Gaulton, R. ; Zhang, Z. ; Burt, A. ; Calders, K. ; Disney, M. ; Goodwin, N. ; Hancock, S. ; Hero, J. ; Herold, M. ; Howe, G. ; Johansen, K. ; Jupp, D. ; Li, Z. ; Muir, J. ; Paynter, I. ; Phinn, S. ; Saenz, E. ; Schaefer, M. ; Walker, L. - \ 2013
Carbon sequestration - methodology and measurement of CPRWRP impact
Arets, E.J.M.M. ; Zhang, Z. - \ 2012
Wuhan, China : EU China River Basin Management Programme (Technical Report 071)
Catching carbon and how to measure it.
Arets, E.J.M.M. ; Zhang, Z. - \ 2012
Wuhan, China : Chiangjiang Water Resources Commission (Changjiang and pearl river watershed rehabilitation project booklet no. 6)
Application of satellite remote sensing for mapping wind erosion risk and dusk emission-deposition in Inner Mongolia grassland, China
Reiche, M. ; Funk, R. ; Zhang, Z. ; Hoffmann, C. ; Reiche, J. ; Wehrhan, M. ; Li, Y. ; Sommer, M. - \ 2012
Grassland Science 58 (2012)1. - ISSN 1744-6961 - p. 8 - 19.
vegetation indexes - northern china - landsat tm - degradation - variability - topography - forest - cover - hills - aster
Intensive grazing leads to land degradation and desertification of grassland ecosystems followed by serious environmental and social problems. The Xilingol steppe grassland in Inner Mongolia, China, which has been a sink area for dust for centuries, is strongly affected by the negative effects of overgrazing and wind erosion. The aim of this study is the provision of a wind erosion risk map with a spatial high resolution of 25 m to identify actual source and sink areas. In an integrative approach, field measurements of vegetation features and surface roughness length z0 were combined with Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) image data for a land use classification. To determine the characteristics of the different land use classes, a field observation (ground truth) was performed in April 2009. The correlation of vegetation height and z0 (R2 = 0.8, n = 55) provided the basis for a separation of three main classes, “grassland”, “non-vegetation” and “other”. The integration of the soil-adjusted vegetation index (SAVI) and the spectral information from the atmospheric corrected ASTER bands 1, 2 and 3 (visible to near-infrared) led to a classification of the overall accuracy (OA) of 0.79 with a kappa () statistic of 0.74, respectively. Additionally, a digital elevation model (DEM) was used to identify topographical effects in relation to the main wind direction, which enabled a qualitative estimation of potential dust deposition areas. The generated maps result in a significantly higher description of the spatial variability in the Xilingol steppe grassland reflecting the different land use intensities on the current state of the grassland – less, moderately and highly degraded. The wind erosion risk map enables the identification of characteristic mineral dust sources, sinks and transition zones.
Genetic diversity and population structure of cucumber (Cucumis sativus L.)
Lv, J. ; Qi, J. ; Shi, Q. ; Shen, D. ; Zhang, S. ; Shao, G. ; Li, H. ; Sun, Z. ; Weng, Y. ; Shang, Y. ; Gu, X. ; Li, X. ; Zhu, X. ; Zhang, J. ; Treuren, R. van; Dooijeweert, W. van; Zhang, Z. ; Huang, S. - \ 2012
PLoS ONE 7 (2012)10. - ISSN 1932-6203 - 9
genetische diversiteit - cucumis sativus - komkommers - populatiegenetica - genenbanken - dna-fingerprinting - germplasm - genetische merkers - vruchtgroenten - groenten - genetic diversity - cucumbers - population genetics - gene banks - dna fingerprinting - genetic markers - fruit vegetables - vegetables - genome - map
Knowing the extent and structure of genetic variation in germplasm collections is essential for the conservation and utilization of biodiversity in cultivated plants. Cucumber is the fourth most important vegetable crop worldwide and is a model system for other Cucurbitaceae, a family that also includes melon, watermelon, pumpkin and squash. Previous isozyme studies revealed a low genetic diversity in cucumber, but detailed insights into the crop's genetic structure and diversity are largely missing. We have fingerprinted 3,342 accessions from the Chinese, Dutch and U.S. cucumber collections with 23 highly polymorphic Simple Sequence Repeat (SSR) markers evenly distributed in the genome. The data reveal three distinct populations, largely corresponding to three geographic regions. Population 1 corresponds to germplasm from China, except for the unique semi-wild landraces found in Xishuangbanna in Southwest China and East Asia; population 2 to Europe, America, and Central and West Asia; and population 3 to India and Xishuangbanna. Admixtures were also detected, reflecting hybridization and migration events between the populations. The genetic background of the Indian germplasm is heterogeneous, indicating that the Indian cucumbers maintain a large proportion of the genetic diversity and that only a small fraction was introduced to other parts of the world. Subsequently, we defined a core collection consisting of 115 accessions and capturing over 77% of the SSR alleles. Insight into the genetic structure of cucumber will help developing appropriate conservation strategies and provides a basis for population-level genome sequencing in cucumber.
Serial translocation by means of circular intermediates underlies colour sidedness in cattle
Durkin, K. ; Coppieters, W. ; Drogemuller, C. ; Ahariz, N. ; Cambisano, N. ; Druet, T. ; Fasquelle, C. ; Haile, A. ; Horin, P. ; Huang, L. ; Kamatani, Y. ; Karim, L. ; Lathrop, M. ; Moser, S. ; Oldenbroek, J.K. ; Rieder, S. ; Sartelet, A. ; Sölkner, J. ; Stalhammer, H. ; Zelenika, D. ; Zhang, Z. ; Leeb, T. ; Georges, M. ; Charlier, C. - \ 2012
Nature 482 (2012). - ISSN 0028-0836 - p. 81 - 84.
copy number - gene - expression - pattern - genome
Colour sidedness is a dominantly inherited phenotype of cattle characterized by the polarization of pigmented sectors on the flanks, snout and ear tips1. It is also referred to as ‘lineback’ or ‘witrik’ (which means white back), as colour-sided animals typically display a white band along their spine. Colour sidedness is documented at least since the Middle Ages and is presently segregating in several cattle breeds around the globe, including in Belgian blue and brown Swiss1, 2. Here we report that colour sidedness is determined by a first allele on chromosome 29 (Cs29), which results from the translocation of a 492-kilobase chromosome 6 segment encompassing KIT to chromosome 29, and a second allele on chromosome 6 (Cs6), derived from the first by repatriation of fused 575-kilobase chromosome 6 and 29 sequences to the KIT locus. We provide evidence that both translocation events involved circular intermediates. This is the first example, to our knowledge, of a phenotype determined by homologous yet non-syntenic alleles that result from a novel copy-number-variant-generating mechanism
Uptake and release kinetics of lysozyme in and from an oxidized starch polymer microgel
Li, Y. ; Zhang, Z. ; Leeuwen, H.P. van; Cohen Stuart, M.A. ; Norde, W. ; Kleijn, J.M. - \ 2011
Soft Matter 7 (2011). - ISSN 1744-683X - p. 10377 - 10385.
drug-delivery applications - encapsulation - diffusion - gels
The kinetics of uptake and release of fluorescently labeled lysozyme by/from spherical oxidized starch polymer microgel particles (diameter 10–20 µm) was investigated using confocal laser scanning microscopy. Both the protein and the microgel have a pH dependent charge; in the pH range 3–9, the protein (pI ˜ 10) is positive and the gel is negative. Uptake was monitored at different protein concentrations, pH values and ionic strengths. Lysozyme release was triggered by changing the pH and salt concentration and measured during enzymatic degradation of the gel by a-amylase. The release is of importance for potential use of the microgel in gastro-intestine drug delivery applications, while amylase-induced protein release is relevant for antimicrobial applications. To analyze the uptake and release kinetics we used a model based on diffusion, taking into account equilibrium exchange between protein bound to the gel matrix and free protein in the gel. For the uptake process the time-dependent evolution of the protein concentration profile in the gel phase and the medium was computed numerically. The calculated concentration profiles closely resemble the experimentally found profiles. In the case of high affinity between protein and the gel network (at low pH and low ionic strength), the initial uptake rate equals the limiting flux of protein at the gel–solution interface, completely determined by the rate of diffusion in the medium. The diffusion coefficient of free protein in the gel, Dp,g, was found to be on the order of 10-11 m2 s-1, about one order of magnitude lower than the diffusion coefficient of lysozyme in bulk solution. Release experiments were carried out with zero protein concentration in the medium, for which approximate analytic release equations are available. The experimental release curves obtained at pH 7 yielded estimated values for the concentration ratio R of bound and free protein in the gel and, related to this ratio, the effective diffusion coefficient of lysozyme in the gel, Deff. These values are extremely dependent on the ionic strength, ranging from ca. 1000 and 10-14 m2 s-1 at 0.025 M NaCl to 50 and 2 × 10-12 m2 s-1 at 0.05 M, respectively. The results are in line with our earlier absorption and FRAP (fluorescence recovery after photobleaching) studies, showing a sharply decreasing affinity and increasing overall exchange rate with increasing ionic strength. Amylase completely breaks down the oxidized starch microgel, while releasing the embedded protein into solution.
Identification of Components of the Female Sex Pheromone of the Simao pine caterpillar moth, Dendrolimus kikuchii Matsumura
Kong, X.B. ; Sun, X.L. ; Wang, H.B. ; Zhang, Z. ; Booij, C.J.H. - \ 2011
Journal of Chemical Ecology 37 (2011)4. - ISSN 0098-0331 - p. 412 - 419.
mass-spectrometry - lasiocampidae - lepidoptera - acetates - superans - china
The pine caterpillar moth, Dendrolimus kikuchii Matsumura (Lepidoptera: Lasiocampidae), is a pest of economic importance on pine in southwest China. Three active compounds were detected during analyses of solvent extracts and effluvia sampled by solid phase microextraction (SPME) from virgin female D. kikuchii using gas chromatography (GC) coupled with electroantennographic (EAG) recording with antennae from a male moth. The compounds were identified as (5Z,7E)-5,7-dodecadien-1-yl acetate (Z5,E7-12:OAc), (5Z,7E)-5,7-dodecadien-1-ol (Z5,E7-12:OH), and (5Z)-5-dodecenyl acetate (Z5-12:OAc) by comparison of their GC retention indices, mass spectra, and EAG activities with those of synthetic standards. Microchemical reactions of gland extracts provided further information confirming the identifications of the three components. Solvent extractions and SPME samples of pheromone effluvia from virgin calling females provided 100:18:0.6 and 100:7:1 ratios of Z5,E7-12:OAc:Z5,E7-12:OH:Z5-12:OAc, respectively. Field behavioral assays showed that Z5,E7-12:OAc and Z5,E7-12:OH were essential for attraction of male D. kikuchii moths. However, the most attractive blend contained these three components in a 100:20:25 ratio in a gray rubber septa. Our results demonstrated that the blend of Z5,E7-12:OAc, Z5,E7-12:OH, and Z5-12:OAc comprise the sex pheromone of D. kikuchii. The optimized three-component lure blend is recommended for monitoring D. kikuchii infestations
Population genetic analysis of Fusarium asiaticum populations from barley suggest a recent shift favoring 3ADON producers in southern Chin
Zhang, H. ; Zhang, Z. ; Lee, T.A.J. van der; Xu, J. ; Xu, J.S. ; Yang, L. ; Yu, D. ; Waalwijk, C. ; Feng, J. - \ 2010
Phytopathology 100 (2010)4. - ISSN 0031-949X - p. 328 - 336.
head blight pathogen - gibberella-zeae - graminearum clade - united-states - wheat scab - chemotypes - diversity - deoxynivalenol - culmorum - markers
Fusarium asiaticum is the predominant causal agent of Fusarium head blight (FHB) in southern China. The genetic diversity was assessed by analyzing 448 single-spore F. asiaticum isolates from 18 sampling sites that were 10 to 2,000 km apart, using seven highly informative variable number of tandem repeat (VNTR) markers. This analysis showed a significant degree of population subdivision (P <0.001) among populations from upper, middle, and lower valleys of the Yangtze River, with little gene flow (Nm = 1.210). We observed a strong association between this genetic population subdivision and the mycotoxin produced. Our results show that the dramatic cline in trichothecene chemotypes may be explained by a recent and significant invasion of 3-acetyldeoxynivalenol (3ADON) producers in FHB pathogen composition in the middle valley. Using Bayesian statistics, we found a biased gene flow from 3ADON to nivalenol (NIV) populations. In addition, we observed significant genetic differentiation and linkage disequilibrium between NIV- and 3ADON-producing isolates at the same sampling sites. The impact of the changed agronomy and trade of cereal commodities on the spread of the new Fusarium population and the consequent increase of FHB observed in southern China are discussed.
Genetic diversity studies on Fusarium asiaticum isolates collected from barley in China show a clear substructure associated with their geographic origin
Zhang, Z. ; Zhang, H. ; Lee, T.A.J. van der; Li, C. ; Arens, P. ; Xu, J. ; Xu, J.S. ; Yang, L.J. ; Yu, D.Z. ; Waalwijk, C. ; Feng, J. - \ 2010
European Journal of Plant Pathology 127 (2010)2. - ISSN 0929-1873 - p. 239 - 248.
head blight pathogen - graminearum clade - genetic diversity - wheat fields - populations - scab - deoxynivalenol - mycotoxins
Abstract Fusarium head blight (FHB) can affect wheat and barley and is a devastating disease caused by a complex of Fusarium species. Here we report on a large-scale survey on the genetic diversity of isolates collected from barley in China. Ten VNTR markers were tested on a representative set of 40 isolates covering 14 sampling areas along the Yangtze River. VNTR4 and VNTR7, with 13 and 6 alleles, each were applied to a total of 1106 single-spore isolates to reveal the population structure of F. asiaticum. The F. asiaticum population showed high genetic diversity and a clear genotypic substructure within China. Pairwise comparisons of allele frequencies between the mountainous provinces of Sichuan and Chongqing in Western China, Hubei Province in the centre or the eastern provinces of Zhejiang, Jiangsu and Shanghai showed significant differences. Even between counties of the same province, significant differences between allele frequencies were found (P
Genotyping panels available in cattle and their properties
Druet, T. ; Zhang, Z. ; Coppieters, W. ; Mulder, H.A. ; Calus, M.P.L. ; Mullaart, E. ; Schrooten, C. ; Roos, S. de; Georges, M. - \ 2010
In: Book of Abstracts 61th Annual Meeting of the European Association for Animal Production, Heraklion, Crete, Greece, 23-27 August 2010. - Wageningen : Wageningen Academic Publishers - ISBN 9789086861521 - p. 356 - 356.
Metal Flux in ligand mixtures. 2. Flux enhancement due to kinetic interplay: Comparison of the reaction layer approximation with a rigorous approach
Zhang, Z. ; Buffle, J. ; Town, R.M. ; Puy, J. ; Leeuwen, H.P. van - \ 2009
The Journal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment, & General Theory 113 (2009)24. - ISSN 1089-5639 - p. 6572 - 6580.
reaction-diffusion processes - complex-systems - dynamic speciation - alga chlamydomonas - phytoplankton - interfaces - lability - code
The revisited reaction layer approximation (RLA) of metal flux at consuming interfaces in ligand mixtures, discussed in the previous paper (part 1 of this series15) is systematically validated by comparison with the results of rigorous numerical simulations. The current paper focuses on conditions under which the total metal flux is enhanced in the ligand (and complex) mixture compared to the case where the individual fluxes of metal complexes are independent of each other. Such an effect is exhibited only in ligand mixtures and results from the kinetic interplay between the various complexes with different labilities. It is exemplified by the Cu/NTA/N-(2-carboxyphenyl)glycine system (see part 1 paper), in which we show that the flux due to the less labile complex (CuNTA) is increased in the presence of a ligand (2-carboxyphenyl)glycine) that forms labile Cu complexes, even when the latter is in negligible proportion in the bulk solution. This paper first explains how the so-called composite and equivalent reaction layer thicknesses computed by RLA can be determined graphically from the concentration profiles of free metal and its complexes, as obtained by rigorous calculations. This approach allows comparison between the latter and RLA predictions. Comparison between these reaction layer thicknesses is then done using the chemical system mentioned above. The mechanism of flux enhancement with this system is studied in detail by following the change of the concentration profiles and reaction layer thicknesses with the increase of concentration of the ligand forming labile complexes. The mechanism of flux enhancement is well explained by the RLA and is validated by the concentration profiles obtained by rigorous numerical simulations. Based on this validation, the RLA is used to predict the conditions of the individual complex labilities and degree of complexation required to get flux enhancement in a two-ligand system. Due to compensation effects between kinetic and thermodynamic factors, a maximum flux enhancement is observed in a specific range of ratios of the lability indices of the two complexes. Flux enhancement might play a significant role in metal uptake in environmental or biological systems and should be considered in data interpretation
Determination of organic acids evolution during apple cider fermentation using an improved HPLC analysis method
Zhang, H. ; Zhou, F. ; Ji, B. ; Nout, M.J.R. ; Fang, Q. ; Zhang, Z. - \ 2008
European Food Research and Technology 227 (2008)4. - ISSN 1438-2377 - p. 1183 - 1190.
ion chromatography - inhibition - wine
An efficient method for analyzing ten organic acids in food, namely citric, pyruvic, malic, lactic, succinic, formic, acetic, adipic, propionic and butyric acids, using HPLC was developed. Boric acid was added into the mobile phase to separate lactic and succinic acids, and a post-column buffer solution [5 mmol/L p-toluensulfonic acid (p-TSA) + 20 mmol/L bis (2-hydroxyethyl) iminotris (hydroxymethyl) methane (bis¿tris) + 100 ¿mol/L sodium ethylenediaminetetraacetic (EDTA-2Na)] was used to improve the sensitivity of detection. The average spiked recoveries for the ten organic acids ranged from 82.9 to 127.9% with relative standard deviations of 1.44¿4.71%. The linear ranges of determination were from 15 to 1,000 mg/L with correlation coefficients of 0.9995¿0.9999. The metabolism of organic acids in cider, and the effect of nutrients including diammonium phosphate (DAP), thiamine, biotin, niacinamide and pantothenic acid on their metabolism, were studied using this method of analysis. We found that before cider brewing, additions of 200 mg/L DAP and 0.3 mg/L thiamine to apple juice concentrate results in a high quality cider.
A Phytophthora sojae G protein alpha subunit is involved in chemotaxis to soybean isoflavones
Hua, C. ; Wang, Y. ; Zheng, X. ; Dou, D. ; Zhang, Z. ; Govers, F. - \ 2008
Eukaryotic Cell 7 (2008)12. - ISSN 1535-9778 - p. 2133 - 2140.
transcription factor - zoospore encystment - hyphal growth - saccharomyces-cerevisiae - signal-transduction - cyst germination - botrytis-cinerea - beta-subunit - infestans - oomycete
For the soybean pathogen Phytophthora sojae, chemotaxis of zoospores to isoflavones is believed to be critical for recognition of the host and for initiating infection. However, the molecular mechanisms underlying this chemotaxis are largely unknown. To investigate the role of G-protein and calcium signaling in chemotaxis, we analyzed the expression of several genes known to be involved in these pathways and selected one that was specifically expressed in sporangia and zoospores but not in mycelium. This gene, named PsGPA1, is a single-copy gene in P. sojae and encodes a G-protein subunit that shares 96% identity in amino acid sequence with that of Phytophthora infestans. To elucidate the function, expression of PsGPA1 was silenced by introducing antisense constructs into P. sojae. PsGPA1 silencing did not disturb hyphal growth or sporulation but severely affected zoospore behavior, including chemotaxis to the soybean isoflavone daidzein. Zoospore encystment and cyst germination were also altered, resulting in the inability of the PsGPA1-silenced mutants to infect soybean. In addition, the expressions of a calmodulin gene, PsCAM1, and two calcium- and calmodulin-dependent protein kinase genes, PsCMK3 and PsCMK4, were increased in the mutant zoospores, suggesting that PsGPA1 negatively regulates the calcium signaling pathways that are likely involved in zoospore chemotaxis
Using seed-tagging methods for assessing post-dispersal seed fate in rodent-dispersed trees.
Xiao, Z. ; Jansen, P.A. ; Zhang, Z. - \ 2006
Forest Ecology and Management 223 (2006)1-3. - ISSN 0378-1127 - p. 18 - 23.
yellow pine chipmunks - rain-forest - acorn dispersal - predation - recruitment - jeffreyi - behavior - tamias - size - nuts
Seed tagging is widely used for tracking seeds during dispersal by seed-caching animals. No studies, however, have fully examined the effects of seed tagging on post-dispersal seed fate. We studied how two seed tagging techniques – thread-marking and wire tin-tagging – affected seed fate by placing tagged and untagged seeds in simulated seed sources and caches and comparing removal rates and fates, and by comparing seedling establishment between tagged and untagged seeds. Tagging had little effect on whether seeds were eaten or dispersed, though both marking methods significantly delayed seed removal by rodents. Both marking methods proved effective for retrieving removed seeds and their fates, but because rodents bit off thread not wire, wire tin-tagging yielded a much higher recovery rate and more accurate estimation of seed fate. We found little difference in dispersal distance between the tagging methods. Piercing of the cotyledons negatively affected seedling emergence in one of two seed species tested. Wire tin tags are a suitable alternative for tracking seeds where seed-caching rodents tend to cut or detach thread marks and yield results comparable to thread-marking. However, both seed tagging methods may underestimate seed dispersal and survival due to delayed removal and damage of the cotyledons by piercing.
Roles of metal ion complexation and membrane permeability in the metal flux through lipophilic membranes. Labile complexes at permeation liquid membranes
Zhang, Z. ; Buffle, J. ; Leeuwen, H.P. van; Wojciechowski, K. - \ 2006
Analytical Chemistry 78 (2006)16. - ISSN 0003-2700 - p. 5693 - 5703.
copper speciation - natural-waters - trace-metals - fatty-acid - separation - voltammetry - system - enrichment - transport - as(iii)
The various physicochemical factors that influence the flux of carrier-transported metal ions through permeation liquid membranes (PLM) are studied systematically. Understanding PLM behavior is important (i) to optimize the application of PLM as metal speciation sensors in environmental media and (ii) because PLM may serve as bioanalogical devices that help to elucidate the environmental physicochemical processes occurring at the surface of biological membranes. Diffusion of free and complexed metal ions in solution, as well as diffusion of the metal carrier complex in the membrane, is considered. The respective roles of diffusion layer thickness, ligand concentration, complex stability, carrier concentration, and membrane thickness are studied experimentally in detail and compared with theory, using various labile complexes, namely, Pb(II)-diglycolate, Cu(II)-diglycolate, and Cu(II)-N-(2-carboxyphenyl)glycine. Conditions where either membrane diffusion or solution diffusion is rate limiting are clearly discriminated. It is shown in particular, that, by tuning the carrier concentration or membrane thickness, either the free metal ion concentration or the total labile metal species are measured. PLM can thus be used to determine whether models based on the free ion activity in solution (such as BLM or FIAM models) are applicable to metal uptake by microorganisms in a real natural medium
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