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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    Bispecific antibody generated with sortase and click chemistry has broad anti-influenza virus activity
    Wagner, K. ; Kwakkenbos, M.J. ; Claassen, Y.B. ; Maijoor, K. ; Bohne, M. ; Sluijs, K.F. van der; Witte, M.D. ; Zoelen, D.J. van; Cornelissen, A.H.M. ; Beaumont, T. ; Bakker, A.Q. ; Ploegh, H.L. ; Spits, H.G. - \ 2014
    Proceedings of the National Academy of Sciences of the United States of America 111 (2014)47. - ISSN 0027-8424 - p. 16820 - 16825.
    influenza-a-viruses - memory b-cells - staphylococcus-aureus - human igg1 - proteins - site - fab - binding - design - heterodimerization
    Bispecific antibodies have therapeutic potential by expanding the functions of conventional antibodies. Many different formats of bispecific antibodies have meanwhile been developed. Most are genetic modifications of the antibody backbone to facilitate incorporation of two different variable domains into a single molecule. Here, we present a bispecific format where we have fused two full-sized IgG antibodies via their C termini using sortase transpeptidation and click chemistry to create a covalently linked IgG antibody heterodimer. By linking two potent anti-influenza A antibodies together, we have generated a full antibody dimer with bispecific activity that retains the activity and stability of the two fusion partners.
    Trends in Soil, Sediment and Groundwater Quality Management
    Rijnaarts, H. ; Weiss, H. - \ 2014
    Science of the Total Environment 485-486 (2014). - ISSN 0048-9697 - p. 701 - 704.
    site - germany
    Soil, groundwater, surface water and sediment systems play an important role in quality of life. The harmful effects of chemical pollution of such systems have been a concern for politicians, the public and scientists for decades. More than half a century of experience in soil and groundwater quality management gives the opportunity to abstract some interesting trends in societal responses, and how these relate to cost effective research and management approaches.
    Meteorology during the DOMINO campaign and its connection with trace gases and aerols
    Adame, J.A. ; Martinez, M. ; Sorribas, M. ; Hidalgo, P.J. ; Vilà-Guerau de Arellano, J. - \ 2014
    Atmospheric Chemistry and Physics 14 (2014). - ISSN 1680-7316 - p. 2325 - 2342.
    oh reactivity measurements - particulate matter - spain - air - variability - emissions - origin - ozone - pm10 - site
    The DOMINO (Diel Oxidant Mechanisms in relation to Nitrogen Oxides) campaign was carried out from 21 November to 8 December 2008 at the El Arenosillo station (SW of Spain) in a coastal-rural environment. The main weather conditions are analysed using local meteorological variables, meteorological soundings and synoptic maps, as well as back trajectories of the air masses using the HYSPLIT (Hybrid Single-Particle Lagrangian Integrated Trajectory Model) model and a high spatial resolution of meteorological fields. Measurements of the main meteorological parameters were collected both from the surface and from a tall tower. A detailed land use analysis was performed on a 80 km scale showing the main types of vegetation and land use. Also the main anthropogenic atmospheric emission sources – both industrial-urban from Huelva and from the urban Seville area – are shown. A study to identify air mass origins and their variation with height was carried out. In this intensive campaign, air masses coming from different areas with different emission sources were observed: from the NW, with a highly industrial-urban character; continental flows from northerly directions; from the NE, with a pathway starting over the Seville metropolitan area and then continuing over the Doñana National Park; and maritime air masses coming from the Atlantic Ocean. To study the chemistry in the four atmospheric scenarios identified, gas -phase measurements of primary and secondary species such as ozone, NO, NO2 and SO2, biogenic and anthropogenic VOCs (volatile organic compounds) like benzene and isoprene, as well as total particle concentration and chemical composition of the aerosols are compared and discussed. The highest levels for total particle concentration, NO, NO2, SO2, benzene, PM10, PM2.5 and chemical elements such as As or Cu were found under flows associated with industrial-urban emissions from the Huelva–Portugal sector which are transported to the site before significant removal by chemical or deposition mechanism can occur. The air masses from the north were affected mainly by crustal elements and biogenic sources, the latter being exemplified by the biogenic species such as isoprene, particularly in the first part of the campaign. The urban air from the Seville area, before arriving at El Arenosillo, traversed the Doñana National Park and therefore was affected by industrial-urban and biogenic emissions. This aged air parcel can transport low levels of NOx, total particle concentration and SO2 as well as ozone and isoprene. Marine air masses from the Atlantic Ocean influence El Arenosillo frequently. Under these conditions, the lowest levels of almost all the species – with the exception of ozone levels associated to long-range transport – were measured
    Breeding Biology and Diet of the African Swallow-Tailed Kite (Chelictinia riocourii) in Senegal and Cameroon
    Buij, R. ; Cavaillés, S. ; Mullié, W.C. - \ 2013
    Journal of Raptor Research 47 (2013)1. - ISSN 0892-1016 - p. 41 - 53.
    savanna - raptors - birds - hawk - populations - predation - survival - site
    We studied the breeding biology of the African Swallow-tailed Kite (Chelictinia riocourii) in two study areas located 3400 km apart in the central (Cameroon) and western (Senegal) portions of the species' breeding range. With 110 nests in 2.8 km2 of suitable breeding habitat, Kousmar islet (23 km2) in Senegal supports the largest documented colony of African Swallow-tailed Kites known to date. Breeding kites in Senegal nested in a single large colony near a massive winter roost. In Cameroon, breeding colonies averaged seven pairs/colony, with nest densities of 0.3 nests/km2 in protected woodland and 0.9 nests/km2 in cultivated habitat. Egg-laying coincided with the end of the dry season in Cameroon, but eggs were recorded from the middle of the dry season in Senegal. Eggs hatched between April and June in both study sites in 2010, but from March 2012 in Senegal. The incubation period was estimated at 27–31 d based on two nests, and the fledging period was 32–35 d (n ¿=¿ 3 fledglings). Mean clutch size was 2.5 eggs (n ¿=¿ 32) in Cameroon and 2.1 in Senegal (n ¿=¿ 29); one clutch of four eggs was recorded in Cameroon. Nest success estimated with the Mayfield method was low at 17% in Cameroon and exceptionally low at 4% in Senegal, possibly related to a combination of suboptimal food conditions, high predation pressure, intraspecific aggression, and lack of experience among breeding pairs. Prey items at nests were made up primarily of lizards (30–54% of items) and insects (27–49%), notably grasshoppers, whereas the diet at the winter roost in Senegal was predominantly Orthoptera (55%) and Solifugids (43%). Our study suggested that African Swallow-tailed Kites were able to adapt to moderate land transformation near floodplains.
    Analysis of steady-state Förster resonance energy transfer data by avoiding pitfalls: Interaction of JAK2 tyrosine kinase with N-methylanthraniloyl nucleotides.
    Niranjan, Y. ; Ungureanu, D. ; Hammarén, H. ; Sanz-Sanz, A. ; Westphal, A.H. ; Borst, J.W. ; Silvennoinen, O. ; Hilhorst, M.H. - \ 2013
    Analytical Biochemistry 442 (2013)2. - ISSN 0003-2697 - p. 213 - 222.
    pseudokinase domain - protein-kinase - fluorescence - atp - binding - receptor - analogs - site - autophosphorylation - mechanism
    Förster resonance energy transfer (FRET) between the fluorescent ATP analogue 2'/3'-(N-methyl-anthraniloyl)-adenosine-5'-triphosphate (MANT–ATP) and enzymes is widely used to determine affinities for ATP–protein binding. However, in analysis of FRET fluorescence data, several important parameters are often ignored, resulting in poor accuracy of the calculated dissociation constant (Kd). In this study, we systematically analyze factors that interfere with Kd determination and describe methods for correction of primary and secondary inner filter effects that extend the use of the FRET method to higher MANT nucleotide concentrations. The interactions of the fluorescent nucleotide analogues MANT–ATP, MANT–ADP [2'/3'-O-(N-methylanthraniloyl) adenosine diphosphate], and MANT–AMP [2'/3'-O-(N-methylanthraniloyl) adenosine monophosphate] with the JAK2 tyrosine kinase domain are characterized. Taking all interfering factors into consideration, we found that JAK2 binds MANT–ATP tightly with a Kd of 15 to 25 nM and excluded the presence of a second binding site. The affinity for MANT–ADP is also tight with a Kd of 50 to 80 nM, whereas MANT–AMP does not bind. Titrations of JAK2 JH1 with nonhydrolyzable ATP analogue MANT–ATP-¿-S [2'/3'-O-(N-methylanthraniloyl) adenosine-5'-(thio)- triphosphate] yielded a Kd of 30 to 50 nM. The methods demonstrated here are applicable to other enzyme–fluorophore combinations and are expected to help improve the analysis of steady-state FRET data in MANT nucleotide binding studies and to obtain more accurate results for the affinities of nucleotide binding proteins.
    Biodegradation of aged diesel in diverse soil matrixes: impact of environmental conditions and bioavailability on microbial remediation capacity
    Sutton, N.B. ; Gaans, P. van; Langenhoff, A.A.M. ; Maphosa, F. ; Smidt, H. ; Grotenhuis, J.T.C. ; Rijnaarts, H.H.M. - \ 2013
    Biodegradation 24 (2013)4. - ISSN 0923-9820 - p. 487 - 498.
    oil-contaminated soil - real-time pcr - crude-oil - bioremediation - community - sediments - hydrocarbons - degradation - scale - site
    While bioremediation of total petroleum hydrocarbons (TPH) is in general a robust technique, heterogeneity in terms of contaminant and environmental characteristics can impact the extent of biodegradation. The current study investigates the implications of different soil matrix types (anthropogenic fill layer, peat, clay, and sand) and bioavailability on bioremediation of an aged diesel contamination from a heterogeneous site. In addition to an uncontaminated sample for each soil type, samples representing two levels of contamination (high and low) were also used; initial TPH concentrations varied between 1.6 and 26.6 g TPH/kg and bioavailability between 36 and 100 %. While significant biodegradation occurred during 100 days of incubation under biostimulating conditions (64.4-100 % remediation efficiency), low bioavailability restricted full biodegradation, yielding a residual TPH concentration. Respiration levels, as well as the abundance of alkB, encoding mono-oxygenases pivotal for hydrocarbon metabolism, were positively correlated with TPH degradation, demonstrating their usefulness as a proxy for hydrocarbon biodegradation. However, absolute respiration and alkB presence were dependent on soil matrix type, indicating the sensitivity of results to initial environmental conditions. Through investigating biodegradation potential across a heterogeneous site, this research illuminates the interplay between soil matrix type, bioavailability, and bioremediation and the implications of these parameters for the effectiveness of an in situ treatment
    Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DLT)
    Spring, S. ; Visser, M. ; Lu, M. ; Copeland, A. ; Lapidus, A. ; Lucas, S. ; Cheng, J.F. ; Han, C. ; Tapia, R. ; Goodwin, L.A. ; Pitluck, S. ; Ivanova, N. ; Land, M. ; Hauser, L. ; Larimer, F. ; Rohde, M. ; Göker, M. ; Detter, J.C. ; Kyrpides, N. ; Woyke, T. ; Schaap, P.J. ; Plugge, C.M. ; Muyzer, G. ; Kuever, J. ; Pereira, I.A.C. ; Parshina, S.N. ; Bernier-Latmani, R. ; Stams, A.J.M. ; Klenk, H.P. - \ 2012
    Standards in Genomic Sciences 7 (2012). - ISSN 1944-3277 - p. 304 - 319.
    bacterial names - classification - hydrogenases - database - archaea - system - site - tool
    Strain DLT (= DSM 2154 = ATCC 23193 = NCIMB 8452) is the type strain of the species Desulfotomaculum ruminis [1], one out of current-ly 30 species with validly published names in the paraphyletic genus Desulfotomaculum [2,3]. Strain DLT was initially isolated by G. S. Coleman in the 1950s from the rumen of hay-fed sheep [4]. Dissimilatory reduction of sulfate to sulfide in the rumen was first demonstrated by Lewis [5], who dosed fistulated sheep with sulfate and deter-mined the amount of sulfide produced. As high amounts of sulfide may be toxic to animals, bacte-rial sulfate-reduction in ruminants was a concern due to the presence of sulfate in grass and hay. D. ruminis represented the first pure culture of a sul-fate-reducing bacterium isolated from the rumen. The genus name was derived from the Latin words 'de', from, ‘sulfur’, sulfur, and 'tomaculum', a kind of sausage, meaning 'a sausage-shaped sul-fate reducer' [2,6]. The species epithet is derived from the Latin word 'rumen', throat, first stomach (rumen) of a ruminant, meaning of a rumen [1,2]. Here, we present a summary classification and a set of features for D. ruminis strain DLT, together with the description of the complete genomic se-quencing and annotation. The complete genome sequence of strain DLT will provide valuable in-formation for defining a more adequate descrip-tion of the currently paraphyletic genus Desulfotomaculum
    Effect of feeding a reduced-starch diet with or without amylase addition on lactation performance in dairy cows
    Gencoglu, H. ; Shaver, R.D. ; Steinberg, W. ; Ensink, J. ; Ferraretto, L.F. ; Bertics, S.J. ; Lopes, J.C. ; Akins, M.S. - \ 2010
    Journal of Dairy Science 93 (2010)2. - ISSN 0022-0302 - p. 723 - 732.
    ruminal digestion kinetics - neutral detergent fiber - fed varying amounts - high-moisture corn - milk-production - nutrient digestibility - fermentation - soyhulls - grain - site
    The objective of this study was to determine lactation performance responses of high-producing dairy cows to a reduced-starch diet compared with a normal-starch diet and to the addition of exogenous amylase to the reduced-starch diet. Thirty-six multiparous Holstein cows (51 +/- 22 DIM and 643 +/- 49 kg of body weight at trial initiation) were randomly assigned to I of 3 treatments in a completely randomized design: a 3-wk covariate adjustment period during which the cows were fed the normal-starch diet, followed by a 12-wk treatment period during which the cows were fed their assigned treatment diets. The normal-starch TMR did not contain exogenous amylase (NS-). The reduced-starch diets, formulated by partially replacing corn grain with soy hulls, were fed without (RS-) and with (RS+) exogenous amylase added to the TMR. Starch and NDF concentrations averaged 27.1 and 30.6%, 21.8 and 36.6%, and 20.7 and 36.6% (dry matter basis) for the NS-, RS-, and RS+ diets, respectively. Dry matter intake for cows fed the RS- diet was 2.4 and 3.2 kg/d greater than for cows fed the NS- and RS+ diets, respectively. Intake of NDF ranged from 1.19 to 1.52% of body weight among the treatments, with the RS- diet being 28% greater than the NS- diet and 13% greater than the RS+ diet. Milk yield averaged 50.4 kg/d and was unaffected by treatment. Fat-corrected milk yield was 2.9 kg/d greater for cows fed the RS- diet than for cows fed the NS- diet. Body weight and body condition score measurements were unaffected by treatment. Fat, solids-, and energy-corrected milk feed conversions (kilograms/kilogram of DMI) were 12 to 13% greater for cows fed the RS+ diet than for cows fed the RS-diet. Dry matter and nutrient digestibilities were lowest for cows fed the NS- diet and greatest for cows fed the RS+ diet, and were greater for cows fed the RS+ diet than for cows fed the RS- diet, with the exception of starch digestibility, which was similar. Greater conversion of feed to milk for dairy cows fed reduced-starch diets that include exogenous amylase may offer potential for improving economic performance.
    Viruses: incredible nanomachines. New advances with filamentous phages
    Hemminga, M.A. ; Vos, W.L. ; Nazarov, P.V. ; Koehorst, R.B.M. ; Wolfs, C.J.A.M. ; Spruijt, R.B. ; Stopar, D. - \ 2010
    European Biophysics Journal 39 (2010)4. - ISSN 0175-7571 - p. 541 - 550.
    major coat protein - transmembrane alpha-helix - membrane-protein - bacteriophage m13 - nmr-spectroscopy - ff fd - site - dynamics - display - domain
    During recent decades, bacteriophages have been at the cutting edge of new developments in molecular biology, biophysics, and, more recently, bionanotechnology. In particular filamentous viruses, for example bacteriophage M13, have a virion architecture that enables precision building of ordered and defect-free two and three-dimensional structures on a nanometre scale. This could not have been possible without detailed knowledge of coat protein structure and dynamics during the virus reproduction cycle. The results of the spectroscopic studies conducted in our group compellingly demonstrate a critical role of membrane embedment of the protein both during infectious entry of the virus into the host cell and during assembly of the new virion in the host membrane. The protein is effectively embedded in the membrane by a strong C-terminal interfacial anchor, which together with a simple tilt mechanism and a subtle structural adjustment of the extreme end of its N terminus provides favourable thermodynamical association of the protein in the lipid bilayer. This basic physicochemical rule cannot be violated and any new bionanotechnology that will emerge from bacteriophage M13 should take this into accou
    Mutation of His465 Alters the pH-dependent Spectroscopic Properties of Escherichia coli Glutamate Decarboxylase and Broadens the Range of Its Activity toward More Alkaline pH
    Pennacchietti, E. ; Lammens, T.M. ; Capitani, G. ; Franssen, M.C.R. ; John, R.A. ; Bossa, F. ; Biase, D. De - \ 2009
    Journal of Biological Chemistry 284 (2009)46. - ISSN 0021-9258 - p. 31587 - 31596.
    pyridoxal 5'-phosphate - acid decarboxylase - amino-acids - phosphorylase - resistance - binding - enzyme - site - aminotransferase - activation
    Glutamate decarboxylase (GadB) from Escherichia coli is a hexameric, pyridoxal 5'-phosphate-dependent enzyme catalyzing CO2 release from the a-carboxyl group of l-glutamate to yield ¿-aminobutyrate. GadB exhibits an acidic pH optimum and undergoes a spectroscopically detectable and strongly cooperative pH-dependent conformational change involving at least six protons. Crystallographic studies showed that at mildly alkaline pH GadB is inactive because all active sites are locked by the C termini and that the 340 nm absorbance is an aldamine formed by the pyridoxal 5'-phosphate-Lys276 Schiff base with the distal nitrogen of His465, the penultimate residue in the GadB sequence. Herein we show that His465 has a massive influence on the equilibrium between active and inactive forms, the former being favored when this residue is absent. His465 contributes with n ˜ 2.5 to the overall cooperativity of the system. The residual cooperativity (n ˜ 3) is associated with the conformational changes still occurring at the N-terminal ends regardless of the mutation. His465, dispensable for the cooperativity that affects enzyme activity, is essential to include the conformational change of the N termini into the cooperativity of the whole system. In the absence of His465, a 330-nm absorbing species appears, with fluorescence emission spectra more complex than model compounds and consisting of two maxima at 390 and 510 nm. Because His465 mutants are active at pH well above 5.7, they appear to be suitable for biotechnological applications
    Quantitative forest canopy structure assessment using an inverted geometric-optical model and up-scaling
    Zeng, Y. ; Schaepman, M.E. ; Wu, B. ; Clevers, J.G.P.W. ; Bregt, A.K. - \ 2009
    International Journal of Remote Sensing 30 (2009)6. - ISSN 0143-1161 - p. 1385 - 1406.
    spectral mixture analysis - resolution image data - reflectance model - bidirectional reflectance - biophysical structure - solar-radiation - ground cover - inversion - site
    The physical-based geometric-optical Li-Strahler model can be inverted to retrieve forest canopy structural variables. One of the main input variables of the inverted model is the fractional component of sunlit background (K g). K g is calculated by using pure reflectance spectra (endmembers) of the viewed surface components. In this paper, the feasibility of up-scaling from high (Quickbird) to medium (Hyperion) spatial resolution data for extracting the required endmembers is demonstrated. Furthermore, the sensitivity of the endmembers used as input for inverting Li-Strahler model is evaluated. After validating the inverted model results, namely spatially explicit forest mean crown closure and crown diameter using field measurements, it can be concluded that the regional scaling-based endmembers derived from the linear unmixing model are the best ones to be used in combination with the inverted Li-Strahler model for quantitatively monitoring disturbance in forest canopy structure
    On inferring isoprene emission surface flux from atmospheric boundary layer concentration measurements
    Vilà-Guerau de Arellano, J. ; Dries, K. van den; Pino, D. - \ 2009
    Atmospheric Chemistry and Physics 9 (2009). - ISSN 1680-7316 - p. 3629 - 3640.
    model - hydrocarbons - entrainment - inversion - forest - parameterization - dynamics - cumulus - amazon - site
    We examine the dependence of the inferred isoprene surface emission flux from atmospheric concentration on the diurnal variability of the convective boundary layer (CBL). A series of systematic numerical experiments carried out using the mixed-layer technique enabled us to study the sensitivity of isoprene fluxes to the entrainment process, the partition of surface fluxes, the horizontal advection of warm/cold air masses and subsidence. Our findings demonstrate the key role played by the evolution of boundary layer height in modulating the retrieved isoprene flux. More specifically, inaccurate values of the potential temperature lapse rate lead to changes in the dilution capacity of the CBL and as a result the isoprene flux may be overestimated or underestimated by as much as 20%. The inferred emission flux estimated in the early morning hours is highly dependent on the accurate estimation of the discontinuity of the thermodynamic values between the residual layer and the rapidly forming CBL. Uncertainties associated with the partition of the sensible and latent heat flux also yield large deviations in the calculation of the isoprene surface flux. Similar results are obtained if we neglect the influence of warm or cold advection in the development of the CBL.We show that all the above-mentioned processes are non-linear, for which reason the dynamic and chemical evolutions of the CBL must be solved simultaneously. Based on the discussion of our results, we suggest the measurements needed to correctly apply the mixed-layer technique in order to minimize the uncertainties associated with the diurnal variability of the convective boundary layer.
    Lactobacillus plantarum WCFS1 Electron Transport Chains
    Brooijmans, R.J.W. ; Vos, W.M. de; Hugenholtz, J. - \ 2009
    Applied and Environmental Microbiology 75 (2009)11. - ISSN 0099-2240 - p. 3580 - 3585.
    coli nitrate reductase - aerobic respiratory-chain - escherichia-coli - lactococcus-lactis - terminal oxidase - site - nitrite - heme - translocation - metabolism
    Lactobacillus plantarum WCFS1 requires both heme and menaquinone to induce a respiration-like behavior under aerobic conditions. Addition of these compounds enhanced both biomass production, without progressive acidification, and the oxygen consumption rate. When both heme- and menaquinone were present, L. plantarum WCFS1 was also able to reduce nitrate. The ability to reduce nitrate was severely inhibited by the glucose levels that are typically found in L. plantarum growth media (1-2% v/v glucose). In contrast, comparable mannitol levels did not inhibit the reduction of nitrate. L. plantarum reduced nitrate with concomitant formation of nitrite and ammonia. Genes that encode a bd-type cytochrome (cydABCD) and a nitrate reductase (narGHJI) were identified in the genome of L. plantarum. The narGHJI-operon is part of a cluster of genes that include the molybdopterin cofactor biosynthesis genes and narK. Besides a menaquinone source, isogenic mutants revealed that cydA and ndh1 are required for the aerobic respiration-like response, and narG for nitrate reduction. The ndh1 mutant was still able to reduce nitrate. The existence of a non-redundant branched electron transport chain in L. plantarum WCFS1 is proposed that is capable of using oxygen or nitrate as terminal electron acceptor
    ps2, the gene responsible for functional sterility in tomato, due to non-dehiscent anthers, is the result of a mutation in a novel polygalacturonase gene
    Gorguet, B.J.M. ; Schipper, E.H. ; Lammeren, A.A.M. van; Visser, R.G.F. ; Heusden, A.W. van - \ 2009
    Theoretical and Applied Genetics 118 (2009)6. - ISSN 0040-5752 - p. 1199 - 1209.
    arabidopsis-thaliana - endo-polygalacturonase - plant - expression - mechanism - resource - site
    The recessive mutation ps-2, which appeared spontaneously in tomato, confers functional male sterility due to non-dehiscent anthers. In this study, we isolated and characterized the PS-2 gene. A single nucleotide mutation in a novel tomato polygalacturonase gene is responsible for the ps-2 phenotype. The mutation in ps-2 is responsible for an alternative splicing during maturation of the pre-mRNA, which leads to an aberrant mRNA. Differentiation between ps-2 and wild type (PS-2) anthers only appears in the final developmental stage in which the stomium remains closed in the mutant. To our knowledge, this is the first functional sterility gene isolated in the Solanaceae family. The specific expression of the Arabidopsis homolog of PS-2 in the anther dehiscence zone suggests a conserved mode of action over the plant kingdom, which means that the repression of PS-2 homologs may be a potential way to introduce functional sterility in other species
    A functional F analogue of AcMNPV GP64 is from the Agrotis segetum granulovirus
    Yin, F. ; Wang, M. ; Tan, Y. ; Deng, F. ; Vlak, J.M. ; Hu, Z.H. ; Wang, H. - \ 2008
    Journal of Virology 82 (2008)17. - ISSN 0022-538X - p. 8922 - 8926.
    envelope fusion protein - baculovirus gp64 - multicapsid nucleopolyhedrovirus - genome - sequence - site
    The envelope fusion protein F of Plutella xylostella granulovirus is a computational analogue of the GP64 envelope fusion protein of Autographa californica nucleopolyhedrovirus (AcMNPV). Granulovirus (GV) F proteins were thought to be unable to functionally replace GP64 in the AcMNPV pseudotyping system. In the present study the F protein of Agrotis segetum GV (AgseGV) was identified experimentally as the first functional GP64 analogue from GVs. AgseF can rescue virion propagation and infectivity of gp64-null AcMNPV. The AgseF-pseudotyped AcMNPV also induced syncytium formation as a consequence of low-pH-induced membrane fusion.
    Scaling-based forest structural change detection using an inverted geometric-optical model in the Three Gorges region of China
    Zeng, Y. ; Schaepman, M.E. ; Wu, B. ; Clevers, J.G.P.W. ; Bregt, A.K. - \ 2008
    Remote Sensing of Environment 112 (2008)12. - ISSN 0034-4257 - p. 4261 - 4271.
    spectral mixture analysis - canopy reflectance model - resolution image data - bidirectional reflectance - biophysical structure - cover - inversion - support - site
    We use the Li-Strahler geometric-optical model combined with a scaling-based approach to detect forest structural changes in the Three Gorges region of China. The physical-based Li-Strahler model can be inverted to retrieve forest structural properties. One of the main input variables for the inverted model is the fractional component of sunlit background, which is calculated by using pure reflectance spectra (endmembers) of surface components. In this study, we extract these endmembers from moderate spatial resolution MODIS data using two scaling-based methods (namely, a regional based linear unmixing and a purest-pixel approach) relying on corresponding high spatial resolution Landsat TM images. Then, the forest structural property crown closure (CC) is estimated by inverting the Li-Strahler model based on the extracted endmembers. Changes in CC are mapped using MODIS mosaics dated 2002 and 2004 for the whole Three Gorges region. Validation of the estimated CC using 25 sample sites indicates that the regional scaling-based endmembers extracted using linear unmixing are more suitable to be used in combination with the inverted Li-Strahler model for monitoring the forest CC than the purest-pixel approach, and results in significantly better estimates in both years (R-2002(2)=0.614, RMSE2002=6%, R-2004(2)=0.631 and RMSE2004=5.2%). A change detection map of the model derived CC in 2002 and 2004 shows a decrease in CC in the eastern counties of the Three Gorges region located close to the Three Gorges Dam. An increase in CC has been observed in other counties of the Three Gorges region, implying a preliminary positive feedback on certain policy measures taken safeguarding forest structure. (C) 2008 Elsevier Inc. All rights reserved.
    Effect of Nylon Bag and Protozoa on In Vitro Corn Starch Disappearance
    Zwieten, J.T. van; Vuuren, A.M. van; Dijkstra, J. - \ 2008
    Journal of Dairy Science 91 (2008)3. - ISSN 0022-0302 - p. 1133 - 1139.
    ruminal fermentation - dairy-cattle - rumen - degradation - digestion - maize - site - bacteria - extent - degradability
    An in vitro experiment was carried out to study whether the presence of protozoa in nylon bags can explain the underestimation of the in situ degradation of slowly degradable starch. Corn of a high (flint) and a low (dent) vitreousness variety was ground over a 3-mm screen, weighed in nylon bags with a pore size of 37 µ m, and washed in cold water. Samples of washed cornstarch were incubated in 40-mL tubes with faunated and defaunated ruminal fluid. An additional amount of washed corn, in nylon bags, was inserted in each incubation tube. Incubations were carried out for 0, 2, 4, 6, 12, and 24 h, and starch residue in tube and nylon bag was determined. In general, starch disappearance from the nylon bag was less than from the tube, and was less with faunated than defaunated rumen fluid, but corn variety did not affect starch disappearance. When no protozoa were present, the disappearance of starch from the bags was higher after 6 and 12 h incubation compared with presence of protozoa. However, in the tubes, there was no difference in starch disappearance due to presence or absence of protozoa. Estimated lag time was higher in presence (4.6 h) then absence (3.6 h) of protozoa. It was concluded that the effect of presence or absence of protozoa on starch disappearance differs within or outside nylon bags. The reduced disappearance rate of starch inside the nylon bags in the presence of protozoa helps to explain the underestimation of starch degradation based on the in sacco procedure when compared with in vivo data upon incubation of slowly degradable starch sources.
    Isoprene and monoterpene fluxes from Central Amazonian rainforest inferred from tower-based and airborne measurements, and implications on the atmospheric chemistry and the local carbon budget
    Kuhn, U. ; Andreae, M.O. ; Ammann, C. ; Araújo, A.C. ; Brancaleoni, E. ; Ciccioli, P. ; Dindorf, T. ; Frattoni, M. ; Gatti, L.V. ; Ganzeveld, L.N. ; Kruijt, B. ; Lelieveld, J. ; Lloyd, J. ; Meixner, F.X. ; Nobre, A.D. ; Pöschl, U. ; Spirig, C. ; Stefani, P. ; Thielmann, A. ; Valentini, R. ; Kesselmeier, J. - \ 2007
    Atmospheric Chemistry and Physics 7 (2007)11. - ISSN 1680-7316 - p. 2855 - 2879.
    volatile organic-compounds - boundary-layer - art. - emissions - aerosols - dependence - exchange - biomass - site - nox
    We estimated the isoprene and monoterpene source strengths of a pristine tropical forest north of Manaus in the central Amazon Basin using three different micrometeorological flux measurement approaches. During the early dry season campaign of the Cooperative LBA Airborne Regional Experiment (LBA-CLAIRE-2001), a tower-based surface layer gradient (SLG) technique was applied simultaneously with a relaxed eddy accumulation (REA) system. Airborne measurements of vertical profiles within and above the convective boundary layer (CBL) were used to estimate fluxes on a landscape scale by application of the mixed layer gradient (MLG) technique. The mean daytime fluxes of organic carbon measured by REA were 2.1 mg C m¿2 h¿1 for isoprene, 0.20 mg C m¿2 h¿1 for ¿-pinene, and 0.39 mg C m¿2 h¿1 for the sum of monoterpenes. These values are in reasonable agreement with fluxes determined with the SLG approach, which exhibited a higher scatter, as expected for the complex terrain investigated. The observed VOC fluxes are in good agreement with simulations using a single-column chemistry and climate model (SCM). In contrast, the model-derived mixing ratios of VOCs were by far higher than observed, indicating that chemical processes may not be adequately represented in the model. The observed vertical gradients of isoprene and its primary degradation products methyl vinyl ketone (MVK) and methacrolein (MACR) suggest that the oxidation capacity in the tropical CBL is much higher than previously assumed. A simple chemical kinetics model was used to infer OH radical concentrations from the vertical gradients of (MVK+MACR)/isoprene. The estimated range of OH concentrations during the daytime was 3¿8×106 molecules cm¿3, i.e., an order of magnitude higher than is estimated for the tropical CBL by current state-of-the-art atmospheric chemistry and transport models. The remarkably high OH concentrations were also supported by results of a simple budget analysis, based on the flux-to-lifetime relationship of isoprene within the CBL. Furthermore, VOC fluxes determined with the airborne MLG approach were only in reasonable agreement with those of the tower-based REA and SLG approaches after correction for chemical decay by OH radicals, applying a best estimate OH concentration of 5.5×106 molecules cm¿3. The SCM model calculations support relatively high OH concentration estimates after specifically being constrained by the mixing ratios of chemical constituents observed during the campaign. The relevance of the VOC fluxes for the local carbon budget of the tropical rainforest site during the measurements campaign was assessed by comparison with the concurrent CO2 fluxes, estimated by three different methods (eddy correlation, Lagrangian dispersion, and mass budget approach). Depending on the CO2 flux estimate, 1¿6% or more of the carbon gained by net ecosystem productivity appeared to be re-emitted through VOC emissions
    Regeneration after 8 years in artificial canopy gaps in mountain ash (Eucalyptus regnans F. Muell.) forest in south-eastern Australia
    Meer, P.J. van der; Dignan, P. - \ 2007
    Forest Ecology and Management 244 (2007)1-3. - ISSN 0378-1127 - p. 102 - 111.
    seedling establishment - acacia-mearnsii - f muell. - growth - management - victoria - site - size - tree - disturbance
    We report on a study of regeneration of Mountain Ash (Eucalyptus regnans) forest in S.E. Australia in artificially created canopy gaps (0.01¿2 ha) and clearfelled coupes (4¿27 ha) with different seedbed treatments. Treatments were applied in 1988, 1989, and 1990. Our results are based on measurements 8 years after harvesting. Gap size had a significant influence on sapling height and diameter growth. The effect was substantial for the canopy openings larger than 2 ha, but inconsistent across the smaller gap sizes. Mean height of the largest diameter saplings was significantly greater in the clearfells (13.2 m) than in the 2 ha gaps (10.7 m), while mean heights in the smaller gaps ranged from 6 to 8.8 m. Mean sapling diameters (at 1.3 m) in clearfells and 2 ha gaps were 9.6 and 7.9 cm respectively compared with 3.8¿5.8 cm for the smaller gaps. There was lower stocking in all treatments for the third regeneration year (1990), when regeneration operations were delayed by high summer and autumn rainfall. Stocking ranged from 12 to 33% for the smallest gaps, increasing with increasing gap size to 34¿64% for 2 ha gaps and 48¿76% for clearfells. Results were consistent with a previous study 3 years after treatment, indicating that stocking at 8 years is still dominated by initial stand establishment rather than by stand development processes. There was no significant influence of seedbed preparation on any of the variables tested at year 8; this was in contrast with earlier findings at year 3 when seedling height was significantly higher on burnt sites compared with mechanically disturbed sites. The growth of non-eucalypt competitors was also influenced by gap size and year of regeneration treatment. The main competitor species differed between larger and smaller clearings and between sites. Results indicate that using a silvicultural system based on smaller gaps (
    Binding assays of inhibitors towards selected V-ATPase domains
    Fernandes, F. ; Loura, L.M.S. ; Fedorov, A. ; Dixon, N. ; Kee, T.P. ; Prieto, M. ; Hemminga, M.A. - \ 2006
    Biochimica et Biophysica Acta. Biomembranes 1758 (2006)11. - ISSN 0005-2736 - p. 1777 - 1786.
    vacuolar h+-atpase - membrane penetration depth - acetylcholine-receptor - proteolipid subunit - alpha-subunit - high-affinity - peptides - site - bacteriorhodopsin - concanamycin
    The macrolide antibiotic bafilomycin and the related synthetic compound SB 242784 are potent inhibitors of the vacuolar H+-ATPases (VATPase). It is currently believed that the site of action of these inhibitors is located on the membrane bound c-subunits of V-ATPases. To address the identification of the critical inhibitors binding domain, their specific binding to a synthetic peptide corresponding to the putative 4th transmembrane segment of the c-subunit was investigated using fluorescence resonance energy transfer (FRET), and for this purpose a specific formalism was derived. Another peptide of the corresponding domain of the c' isoform, was checked for binding of bafilomycin, since it is not clear if V-ATPase inhibition can also be achieved by interaction of the inhibitor with the c'-subunit. It was concluded that bafilomycin binds to the selected peptides, whereas SB 242784 was unable to interact, and in addition for bafilomycin, its interaction with the peptides either corresponding to the c- or the c'-subunit isoforms is identical. Since the observed interactions are however much weaker as compared to the very efficient binding of both bafilomycin and SB 242784 to the whole protein, it can be concluded that assembly of all V-ATPase transmembrane segments is required for an efficient interaction.
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