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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Electrochemically mediated calcium phosphate precipitation from phosphonates: Implications on phosphorus recovery from non-orthophosphate
Lei, Yang ; Saakes, Michel ; Weijden, Renata D. van der; Buisman, Cees J.N. - \ 2020
Water Research 169 (2020). - ISSN 0043-1354
Calcium phosphate - Local high pH - Organic phosphorus - Oxidation - Precipitation

Phosphonates are an important type of phosphorus-containing compounds and have possible eutrophication potential. Therefore, the removal of phosphonates from waste streams is as important as orthophosphate. Herein, we achieved simultaneously removal and recovery of phosphorus from nitrilotris (methylene phosphonic acid) (NTMP) using an electrochemical cell. It was found that the C–N and C–P bonds of NTMP were cleaved at the anode, leading to the formation of orthophosphate and formic acid. Meanwhile, the converted orthophosphate reacted with coexisting calcium ions and precipitated on the cathode as recoverable calcium phosphate solids, due to an electrochemically induced high pH region near the cathode. Electrochemical removal of NTMP (30 mg/L) was more efficient when dosed to effluent of a wastewater treatment plant (89% in 24 h) than dosed to synthetic solutions of 1.0 mM Ca and 50 mM Na2SO4 (43% in 168 h) while applying a current density of 28 A/m2 and using a Pt anode and Ti cathode. The higher removal efficiency of NTMP in real waste water is due to the presence of chloride ions, which resulted in anodic formation of chlorine. This study establishes a one-step approach for simultaneously phosphorus removal and recovery of calcium phosphate from non-orthophosphates.

A standardized assessment of forest mammal communities reveals consistent functional composition and vulnerability across the tropics
Rovero, Francesco ; Ahumada, Jorge ; Jansen, Patrick A. ; Sheil, Douglas ; Alvarez, Patricia ; Boekee, Kelly ; Espinosa, Santiago ; Lima, Marcela Guimarães Moreira ; Martin, Emanuel H. ; O'Brien, Timothy G. ; Salvador, Julia ; Santos, Fernanda ; Rosa, Melissa ; Zvoleff, Alexander ; Sutherland, Chris ; Tenan, Simone - \ 2019
Ecography (2019). - ISSN 0906-7590
The understanding of global diversity patterns has benefitted from a focus on functional traits and how they relate to variation in environmental conditions among assemblages. Distant communities in similar environments often share characteristics, and for tropical forest mammals, this functional trait convergence has been demonstrated at coarse scales (110–200 km resolution), but less is known about how these patterns manifest at fine scales, where local processes (e.g. habitat features and anthropogenic activities) and biotic interactions occur. Here, we used standardized camera trapping data and a novel analytical method that accounts for imperfect detection to assess how the functional composition of terrestrial mammal communities for two traits – trophic guild and body mass – varies across 16 protected areas in tropical forests and three continents, in relation to the extent of protected habitat and anthropogenic pressures. We found that despite their taxonomic differences, communities generally have a consistent trophic guild composition, and respond similarly to these factors. Insectivores were found to be sensitive to the size of protected habitat and surrounding human population density. Body mass distribution varied little among communities both in terms of central tendency and spread, and interestingly, community average body mass declined with proximity to human settlements. Results indicate predicted trait convergence among assemblages at the coarse scale reflects consistent functional composition among communities at the local scale, suggesting that broadly similar habitats and selective pressures shaped communities with similar trophic strategies and responses to drivers of change. These similarities provide a foundation for assessing assemblages under anthropogenic threats and sharing conservation measures.
Metabarcoding of nematode communities for soil quality evaluation
Bongiorno, Giulia ; Bodenhausen, Natacha ; Bünemann, Else K. ; Brussaard, Lijbert ; Geisen, Stefan ; Mäder, Paul ; Quist, Casper ; Walser, Jean-Claude ; Goede, Ron de - \ 2019
Wageningen University
PRJEB32262 - ERP114920 - nematodes - nematode community - soil quality
Nematodes are abundant and diverse in nearly any soil, and directly and indirectly contribute to important soil functions such as nutrient cycling, decomposition, and pest and pathogen regulation. In addition, nematode communities have been shown to be sensitive to agricultural management such as tillage and organic matter additions. As such, soil nematode are promising indicators for soil quality. Morphological assessment of nematode communities and indices such as the maturity index (MI), enrichment index (EI), structure index (SI) and channel index (CI) have been used for soil quality evaluations. Molecular methods to study community composition and diversity offer advantages compared to traditional methods in terms of cost, time, resolution and throughput. Thus far, the use of molecular data to calculate indices has not received much attention. In the present study we used molecular methods to: i) assess the effects of soil management on nematode qPCR counts, alpha- and beta- diversity, and food web indices; ii) identify nematode taxa specific to certain soil management, and iii) investigate the relationship between nematode community parameters with soil chemical, physical and biological parameters. We assessed nematodes communities with metabarcoding in 10 European long-term field experiments to study the effect of tillage (conventional vs reduced) and organic matter addition (low vs high).
Reduced tillage, but not organic matter input, increased nematode diversity and food web stability in European long‐term field experiments
Bongiorno, Giulia ; Bodenhausen, Natacha ; Bünemann, Else K. ; Brussaard, Lijbert ; Geisen, Stefan ; Mäder, Paul ; Quist, Casper W. ; Walser, Jean-Claude ; Goede, Ron G.M. de - \ 2019
Molecular Ecology (2019). - ISSN 0962-1083
Soil nematode communities and food web indices can inform about the complexity, nutrient flows and decomposition pathways of soil food webs, reflecting soil quality. Relative abundance of nematode feeding and life‐history groups are used for calculating food web indices, i.e., maturity index (MI), enrichment index (EI), structure index (SI) and channel index (CI). Molecular methods to study nematode communities potentially offer advantages compared to traditional methods in terms of resolution, throughput, cost and time. In spite of such advantages, molecular data have not often been adopted so far to assess the effects of soil management on nematode communities and to calculate these food web indices. Here, we used high‐throughput amplicon sequencing to investigate the effects of tillage (conventional vs. reduced) and organic matter addition (low vs. high) on nematode communities and food web indices in 10 European long‐term field experiments and we assessed the relationship between nematode communities and soil parameters. We found that nematode communities were more strongly affected by tillage than by organic matter addition. Compared to conventional tillage, reduced tillage increased nematode diversity (23% higher Shannon diversity index), nematode community stability (12% higher MI), structure (24% higher SI), and the fungal decomposition channel (59% higher CI), and also the number of herbivorous nematodes (70% higher). Total and labile organic carbon, available K and microbial parameters explained nematode community structure. Our findings show that nematode communities are sensitive indicators of soil quality and that molecular profiling of nematode communities has the potential to reveal the effects of soil management on soil quality.
Soft dendritic microparticles with unusual adhesion and structuring properties
Roh, Sangchul ; Williams, Austin H. ; Bang, Rachel S. ; Stoyanov, Simeon D. ; Velev, Orlin D. - \ 2019
Nature Materials (2019). - ISSN 1476-1122

The interplay between morphology, excluded volume and adhesivity of particles critically determines the physical properties of numerous soft materials and coatings1–6. Branched particles2 or nanofibres3, nanofibrillated cellulose4 or fumed silica5 can enhance the structure-building abilities of colloids, whose adhesion may also be increased by capillarity or binding agents6. Nonetheless, alternative mechanisms of strong adhesion found in nature involve fibrillar mats with numerous subcontacts (contact splitting)7–11 as seen in the feet of gecko lizards and spider webs12–17. Here, we describe the fabrication of hierarchically structured polymeric microparticles having branched nanofibre coronas with a dendritic morphology. Polymer precipitation in highly turbulent flow results in microparticles with fractal branching and nanofibrillar contact splitting that exhibit gelation at very low volume fractions, strong interparticle adhesion and binding into coatings and non-woven sheets. These soft dendritic particles also have potential advantages for food, personal care or pharmaceutical product formulations.

State paternalism and institutional degradation at Treesleeper Eco-camp: Community-based tourism and the loss of sovereignty among Bushmen in Namibia
Koot, Stasja ; Ingram, Verina Jane ; Bijsterbosch, Mariska - \ 2019
Development Southern Africa (2019). - ISSN 0376-835X
Bushmen - Community-based tourism - institutional design principles - Namibia - state paternalism

The Namibian government promotes community-based tourism (CBT) as market-based development. At Treesleeper Eco-camp, a CBT-project among marginalised Hai//om and !Xun Bushmen (San), we investigate how Bushmen's historically developed paternalist relations shape contemporary local institutional processes. Institutional design principles, seen as prerequisites for stable and robust institutions (norms, rules and regulations), and thus successful CBT, are used to analyse local changes of the project in relation to a government grant. Ironically, after the grant, Treesleeper generated less income and the consequent ‘upgrade’ intensified conflicts. This study shows that community control, ownership and participation are key factors for successful CBT-projects, but currently the state has obstructed these, just as various other ‘superior’ actors have also done (throughout history) in relation to ‘inferior’ Bushmen. We argue that paternalist ideologies perpetuate today in the Bushmen's relation with the state, leading to weaker institutions locally through dispossession of their sovereignty.

Workshopbericht: Das Erbe der Gewalt in Französisch-Äquatorialafrika
Vries, Lotje de; Mangarella, Joseph - \ 2019
Afrika Spectrum (2019). - ISSN 0002-0397
French Equatorial Africa - history - instability - marginality - violence

This report offers an account of an international workshop held at the Omar Bongo University in Libreville, Gabon, from 23 November to 27 November 2018. Bringing together specialists on and from Cameroon, Central African Republic, Chad, Congo, Equatorial Guinea, and Gabon, participants reflected on the ways in which different forms of violence have historically had – and continue to have – an impact on social fabrics and several dimensions of politics. The workshop also sought to relate these legacies of violence to the region’s economies of extraction. The region is confronted with social and political turmoil that receives little international attention. The combination of simmering and open instability and the relatively marginal position of the region vis-à-vis the wider continent risks propelling several countries into outright political strife with regional repercussions. The debates concluded that further thinking on how violence permeates every aspect of social and political life is much needed.

Relaxation Behavior and Nonlinear Surface Rheology of PEO-PPO-PEO Triblock Copolymers at the Air-Water Interface
Moghimikheirabadi, Ahmad ; Fischer, Peter ; Kröger, Martin ; Sagis, Leonard M.C. - \ 2019
Langmuir 35 (2019)44. - ISSN 0743-7463 - p. 14388 - 14396.

Surface dilatational viscoelasticity of adsorbed layers of pluronics triblock copolymers at the air-water interface was measured using the oscillating barrier technique. The effect of molecular architecture and concentration on surface viscoelasticity was explored for two different types of pluronics with different degrees of hydrophobicity, Pluronic F-108 (Mw ≈ 14600 g/mol) and Pluronic P-123 (Mw ≈ 5800 g/mol), the former exhibiting a larger hydrophilic to hydrophobic block length ratio. Frequency sweeps in the linear regime suggested that interfacial films of F-108 have higher surface limiting elasticity and larger in-plane and out-of-plane relaxation times at the same bulk concentration (the former possibly related to in-plane microstructure rearrangements, the latter to surface/bulk diffusion). Increasing the bulk concentration of pluronics from 1 to 100 μM led to a decrease in both in- and out-of-plane relaxation times. Large amplitude oscillatory dilatation (LAOD) tests were performed to capture nonlinear behavior of these interfacial films by means of elastic and viscous Lissajous plots. Nonlinearities in elastic responses were quantified through calculation of the strain-stiffening indices in extension SE and compression SC. Both pluronics exhibited strain softening in extension. In compression, P-123 showed strain-hardening and F-108 displayed a relatively linear response. Apparent strain hardening in extension was observed for the P-123 adsorbed film, at high strain, at a bulk concentration of 100 μM. However, at these strains, the response was dominated by the viscous contribution and calculation of strain rate-thickening factors in extension and compression showed that the overall response was strain rate-thinning in extension and strain rate-thickening in compression.

Four insect oils as food ingredient: Physical and chemical characterisation of insect oils obtained by an aqueous oil extraction
Tzompa-Sosa, D.A. ; Yi, L. ; Valenberg, H.J.F. van; Lakemond, C.M.M. - \ 2019
Journal of Insects as Food and Feed 5 (2019)4. - ISSN 2352-4588 - p. 279 - 292.
Acheta domesticus - Alphitobius diaperinus - Aroma - Blaptica dubia - Insect oils - Novel food - Tenebrio molitor

Insect fractionation and insect ingredient characterisation is of relevance in view of the increase in insect production and demand of insect ingredients worldwide. This study aims to contribute to the knowledge of insect oils that were extracted from insects commercially reared in Europe. Oil was extracted from yellow mealworm, lesser mealworm, house cricket and Dubia cockroach by an aqueous based oil extraction method. These insect oils were physicochemically characterised on the most important parameters for food applications, namely thermal behaviour (differential scanning calorimeter), colour (spectrophotometry) and aroma compounds (gas chromatography-mass spectrometry). The amount and the composition of the un-extracted lipid fraction was determined by means of fatty acid (FA) profiling (gas chromatography with flame ionisation detector). Although no distinctive pattern was seen in all four species, it becomes clear from its FA profile that the extracted fat is more similar to the residue and cream fractions than to the pellet and supernatant. The amount of lipids that was not extracted was species dependent ranging from 40 to up to 82% of the total lipid content. Further work is needed to reduce the oil loss in this extraction. The extracted insect oil presented a wide range of melting peaks, from -30.7 to 22.7 °C, which makes them liquid-like at room temperature. Its thermal profile shows separated peaks showing that fat fractionation is feasible. Oil colour was bright yellow-reddish. Most oils had compounds related to pleasant aromas, except for Dubia cockroach. In the latter oil several acid compounds related to unpleasant aromas were identified. This study shows that yellow meal worm oil, lesser mealworm oil and cricket oil have characteristics desirable for table oils and for oils use as food ingredients.

Rhizosphere and litter feedbacks to range-expanding plant species and related natives
Manrubia, Marta ; Putten, Wim H. van der; Weser, Carolin ; Veen, Ciska G.F. - \ 2019
Journal of Ecology (2019). - ISSN 0022-0477
litter feedback - novel communities - plant range expansion - plant–soil feedback - rhizosphere feedback

Plant–soil feedback (PSF) results from the net legacy effect that plants leave in the composition of soil communities and abiotic soil properties. PSF is induced by the rhizosphere and by litter inputs into the soil, however, we have little understanding of their individual contributions. Here, we examine feedback effects from the rhizosphere of living plants, decomposing litter and their combination. We used four pairs of climate warming-induced range-expanding plant species and congeneric natives, and examined PSF effects on plant biomass production, as well as on decomposition in their new range. We tested the hypothesis that the plant rhizosphere provides less negative feedback to range-expanders than to the congeneric natives, and that feedback mediated by litter decomposition does not provide such a difference because decomposers might be less specialized than pathogens. To determine PSF, we used soil from the congener species within each pair as an ‘away’ soil to indicate whether range-expanders may have lost their specialized soil biota upon arrival in the novel range. Our results show that although range-expanding plant species and their congeneric natives developed neutral PSF in both rhizosphere- and litter-conditioned soils, two of the four range-expanders produced more biomass than natives in soils conditioned by litter, that is, soils with high nutrient content. Shoot litter from two out of four range-expanding species decomposed more than that of natives, but decomposition was unaffected by soil conditioning. Synthesis. We compared PSF effects of range-expanders and congeneric natives mediated via both the rhizosphere and litter using the congeneric species as a control. Under those conditions, PSF effects were neutral and not affected by plant origin. Therefore, we conclude that studies not comparing within plant genera may overestimate the impact of plant origin on PSF. Still, even under those conditions range-expanders appeared to benefit more from high soil nutrient availability than natives, thus providing a possible advantage over congeneric natives.

Quantification of visits of wild fauna to a commercial free-range layer farm in the Netherlands located in an avian influenza hot-spot area assessed by video-camera monitoring
Elbers, Armin R.W. ; Gonzales, José L. - \ 2019
Transboundary and Emerging Diseases (2019). - ISSN 1865-1674
avian influenza - ducks - free-range poultry - gulls - water pools - wild fauna

Free-range poultry farms have a high risk of introduction of avian influenza viruses (AIV), and it is presumed that wild (water) birds are the source of introduction. There is very scarce quantitative data on wild fauna visiting free-range poultry farms. We quantified visits of wild fauna to a free-range area of a layer farm, situated in an AIV hot-spot area, assessed by video-camera monitoring. A total of 5,016 hr (209 days) of video recordings, covering all 12 months of a year, were analysed. A total of 16 families of wild birds and five families of mammals visited the free-range area of the layer farm. Wild birds, except for the dabbling ducks, visited the free-range area almost exclusively in the period between sunrise and the moment the chickens entered the free-range area. Known carriers of AIV visited the outdoor facility regularly: species of gulls almost daily in the period January–August; dabbling ducks only in the night in the period November–May, with a distinct peak in the period December–February. Only a small fraction of visits of wild fauna had overlap with the presence of chickens at the same time in the free-range area. No direct contact between chickens and wild birds was observed. It is hypothesized that AIV transmission to poultry on free-range poultry farms will predominantly take place via indirect contact: taking up AIV by chickens via wild-bird-faeces-contaminated water or soil in the free-range area. The free-range poultry farmer has several possibilities to potentially lower the attractiveness of the free-range area for wild (bird) fauna: daily inspection of the free-range area and removal of carcasses and eggs; prevention of forming of water pools in the free-range facility. Furthermore, there are ways to scare-off wild birds, for example use of laser equipment or trained dogs.

Gel Trapping Enables Optical Spectroscopy of Single Solvated Conjugated Polymers in Equilibrium
De Laar, Ties Van; Hooiveld, Ellard ; Higler, Ruben ; Scheer, Pieter Van Der; Sprakel, Joris - \ 2019
ACS Nano (2019). - ISSN 1936-0851
conjugated polymers - gel entrapment - photodynamics - single-molecule fluorescent lifetime imaging - single-molecule spectroscopy

Single-molecule studies have provided a wealth of insight into the photophysics of conjugated polymers in the solid and desolvated state. Desolvating conjugated chains, e.g., by their embedding in inert solid matrices, invariably leads to chain collapse and the formation of intermolecular aggregates, which have a pronounced effect on their properties. By contrast, the luminescent properties of individual semiconducting polymers in their solvated and thermodynamic state remain largely unexplored. In this paper, we demonstrate a versatile gel trapping technique that enables the chemistry-free immobilization and interrogation of individual conjugated macromolecules, which retain a fully equilibrated conformation by contrast to conventional solid-state immobilization methods. We show how the technique can be used to record full luminescence spectra of single chains, to evaluate their time-resolved fluorescence, and to probe their photodynamics. Finally, we explore how the photophysics of different conjugated polymers is strongly affected by desolvation and chain collapse.

An alternative bioassay for Synchytrium endobioticum demonstrates the expression of potato wart resistance in aboveground plant parts
Vossenberg, Bart van de; Gent-Pelzer, Marga van; Boerma, M. ; Gouw, Lucas P. van der; Lee, Theo van der; Vossen, Jack - \ 2019
Wageningen University and Research
PRJEB30662 - ERP113139 - Synchytrium endobioticum
The obligate biotrophic chytrid species Synchytrium endobioticum is the causal agent of potato wart disease. Currently 39 pathotypes have been described based on their interaction with a differential set of potato varieties. Wart resistance and pathotyping is performed using bioassays in which etiolated tuber sprouts are inoculated. Here we describe an alternative method in which aboveground plant parts are inoculated. Susceptible plants produced typical wart symptoms in developing, but not in fully expanded, aboveground organs. Colonization of the host by S endobioticum was verified by screening for resting spores by microscopy and by molecular techniques using TaqMan PCR and RNAseq analysis. When applied to resistant plants, none of these symptoms were detectable. Recognition of S. endobioticum pathotypes by differentially resistant potato varieties was identical in aboveground plant parts and the tuber-based bioassays. This suggests that S. endobioticum resistance genes are expressed both in etiolated “belowground” sprouts and green aboveground organs. RNAseq analysis demonstrated that the symptomatic aboveground materials contain less contaminants compared to resting spores extracted from tuber-based assays. This reduced microbial contamination in the aboveground bioassay could be an important advantage to study this obligate biotrophic plant-pathogen interaction. As wart resistance is active in both below and above ground organs, the aboveground bioassay can potentially speed up screening for S. endobioticum resistance in potato breeding programs as it omits the requirement for tuber formation. In addition, possibilities arise to express S. endobioticum effectors in potato leaves through agroinfiltration, thereby providing additional phenotyping tools for research and breeding.
Edible insects: The value chain
Lakemond, C.M.M. ; Veldkamp, T. ; Huis, A. van - \ 2019
Journal of Insects as Food and Feed 5 (2019)4. - ISSN 2352-4588 - p. 245 - 246.

How can we face the challenge of future nutrition security? Insects offer a high quality, efficient and sustainable alternative to the common protein sources, and have the capacity to valorise organic side streams. As such, insects can close the loop in a circular economy. The current issue of Journal of Insects as Food and Feed is related to the international conference 'Edible insects: the value chain'. The papers presented link to research related to rearing, processing, nutrition and health, and consumer behaviour. Future chain development would benefit from further multi- and interdisciplinary knowledge gain. Also, other factors are important, like business development, enabling regulation, increased marketing and promotion, and fostering industrial partnership. These activities require collaboration among the actors within the insect chain.

Development of a landslide early warning system in Indonesia
Hidayat, Rokhmat ; Sutanto, Samuel Jonson ; Hidayah, Alidina ; Ridwan, Banata ; Mulyana, Arif - \ 2019
Geosciences 9 (2019)10. - ISSN 2076-3263
Early warning system - Landslides - Precipitation forecasts - Rainfall threshold - Slope stability model

Landslides are one of the most disastrous natural hazards in Indonesia, in terms of number of fatalities and economic losses. Therefore, Balai Litbang Sabo (BLS) has developed a Landslide Early Warning System (LEWS) for Indonesia, based on a Delft–FEWS (Flood Early Warning System) platform. This system utilizes daily precipitation data, a rainfall threshold method, and a Transient Rainfall Infiltration and Grid-based Regional Slope-stability model (TRIGRS) to predict landslide occurrences. For precipitation data, we use a combination of 1-day and 3-day cumulative observed and forecasted precipitation data, obtained from the Tropical Rainfall Measuring Mission (TRMM) and the Indonesian Meteorological Climatological and Geophysical Agency (BMKG). The TRIGRS model is used to simulate the slope stability in regions that are predicted to have a high probability of landslide occurrence. Our results show that the landslides, which occurred in Pacitan (28 November 2017) and Brebes regions (22 February 2018), could be detected by the LEWS from one to three days in advance. The TRIGRS model supports the warning signals issued by the LEWS, with a simulated factor of safety values lower than 1 in these locations. The ability of the Indonesian LEWS to detect landslide occurrences in Pacitan and Brebes indicates that the LEWS shows good potential to detect landslide occurrences a few days in advance. However, this system is still undergoing further developments for better landslide prediction.

Efficient photosynthesis in dynamic light environments: A chloroplast's perspective
Kaiser, Elias ; Galvis, Viviana Correa ; Armbruster, Ute - \ 2019
Biochemical Journal 476 (2019)19. - ISSN 0264-6021 - p. 2725 - 2741.

In nature, light availability for photosynthesis can undergo massive changes on a very short timescale. Photosynthesis in such dynamic light environments requires that plants can respond swiftly. Expanding our knowledge of the rapid responses that underlie dynamic photosynthesis is an important endeavor: It provides insights into nature's design of a highly dynamic energy conversion system and hereby can open up new strategies for improving photosynthesis in the field. The present review focuses on three processes that have previously been identified as promising engineering targets for enhancing crop yield by accelerating dynamic photosynthesis, all three of them involving or being linked to processes in the chloroplast, i.e. relaxation of non-photochemical quenching, Calvin-Benson-Bassham cycle enzyme activation/deactivation and dynamics of stomatal conductance. We dissect these three processes on the functional and molecular level to reveal gaps in our understanding and critically discuss current strategies to improve photosynthesis in the field.

Successful Host Adaptation of IncK2 Plasmids
Rozwandowicz, Marta ; Brouwer, Michael S.M. ; Mughini-Gras, Lapo ; Wagenaar, Jaap A. ; Gonzalez-Zorn, Bruno ; Mevius, Dik J. ; Hordijk, Joost - \ 2019
Frontiers in Microbiology 10 (2019). - ISSN 1664-302X
chicken - conjugation - IncK2 - plasmid - sigma-32

The IncK plasmid group can be divided into two separate lineages named IncK1 and IncK2. IncK2 is found predominantly in poultry while IncK1 was reported in various mammals, including animals and humans. The physiological basis of this distinction is not known. In this manuscript we examined fitness cost of IncK1 and IncK2 plasmids at 37 and 42°C, which resembles mammalian and chicken body temperatures, respectively. We analyzed conjugation frequency, plasmid copy number and plasmid fitness cost in direct competition. Additionally, we measured levels of σ-32 in Escherichia coli carrying either wild type or conjugation-deficient IncK plasmids. The results show that IncK2 plasmids have a higher conjugation frequency and lower copy number at 42°C compared to IncK1. While the overall fitness cost to the host bacterium of IncK2 plasmids was higher than that of IncK1, it was not affected by the temperature while the fitness cost of IncK1 was shown to increase at 42°C compared to 37°C. These differences correlate with an increased expression of σ-32, a regulator of heat-shock protein expression, in E. coli with IncK2 compared to cells containing IncK1. This effect was not seen in cells containing conjugation deficient plasmids. Therefore, it is hypothesized that the assembly of the functional T4S may lead to these increased levels of σ–32. Increased activation of CpxR at 42°C may explain why IncK2 plasmids, and not IncK1, are predominantly found in chicken isolates.

Seine Plastic Debris Transport Tenfolded During Increased River Discharge
Emmerik, Tim van; Tramoy, Romain ; Calcar, Caroline van; Alligant, Soline ; Treilles, Robin ; Tassin, Bruno ; Gasperi, Johnny - \ 2019
Frontiers in Marine Science 6 (2019). - ISSN 2296-7745
France - hydrology - marine plastic debris - plastic pollution - plastic pollution monitoring - river plastic - Seine

Rivers transport land-based plastic waste into the ocean. Current efforts to quantify riverine plastic emission come with uncertainty as field observations are scarce. One of the challenging aspects is the lack of consistent measurement methods that allow for comparing rivers over space and time. Recent studies have shown that simple visual observations provide a robust first-order characterization of floating and superficially suspended plastic transport, both in quantity, spatiotemporal distribution and composition. For this study, we applied this method to the river Seine, France, to provide new insights in the spatiotemporal variation in riverine plastic transport. First, we studied the response of plastic flow to increased river discharge by comparing measurements taken during low flow and high flow periods. Second, we investigated the variation of riverine plastic transport over the river length to improve our understanding of the origin and fate of riverine plastics. We demonstrate that during a period with higher river discharge, plastic transport increased up to a factor ten at the observation point closest to the river mouth. This suggests that the plastic emission into the ocean from the Seine may also be considerably higher during increased discharge. Upstream of Paris plastic transport increased only with a factor 1.5, suggesting that most plastics originate from Paris or areas further downstream. With this paper we aim to shed additional light on the seasonal variation in riverine plastic transport and its distribution along the river length, which may benefit future long-term monitoring efforts and plastic pollution mitigation strategies.

Sustainable bioenergy for climate mitigation: developing drought-tolerant trees and grasses
Taylor, G. ; Donnison, I.S. ; Murphy-Bokern, D. ; Morgante, M. ; Bogeat-Triboulot, M.B. ; Bhalerao, R. ; Hertzberg, M. ; Polle, A. ; Harfouche, A. ; Alasia, F. ; Petoussi, V. ; Trebbi, D. ; Schwarz, K. ; Keurentjes, J.J.B. ; Centritto, M. ; Genty, B. ; Flexas, J. ; Grill, E. ; Salvi, S. ; Davies, W.J. - \ 2019
Annals of Botany 124 (2019)4. - ISSN 0305-7364 - p. 513 - 520.
Arundo - Miscanthus - Populus - lignocellulosic crop - marginal land - molecular breeding - next-generation sequencing

BACKGROUND AND AIMS: Bioenergy crops are central to climate mitigation strategies that utilize biogenic carbon, such as BECCS (bioenergy with carbon capture and storage), alongside the use of biomass for heat, power, liquid fuels and, in the future, biorefining to chemicals. Several promising lignocellulosic crops are emerging that have no food role - fast-growing trees and grasses - but are well suited as bioenergy feedstocks, including Populus, Salix, Arundo, Miscanthus, Panicum and Sorghum. SCOPE: These promising crops remain largely undomesticated and, until recently, have had limited germplasm resources. In order to avoid competition with food crops for land and nature conservation, it is likely that future bioenergy crops will be grown on marginal land that is not needed for food production and is of poor quality and subject to drought stress. Thus, here we define an ideotype for drought tolerance that will enable biomass production to be maintained in the face of moderate drought stress. This includes traits that can readily be measured in wide populations of several hundred unique genotypes for genome-wide association studies, alongside traits that are informative but can only easily be assessed in limited numbers or training populations that may be more suitable for genomic selection. Phenotyping, not genotyping, is now the major bottleneck for progress, since in all lignocellulosic crops studied extensive use has been made of next-generation sequencing such that several thousand markers are now available and populations are emerging that will enable rapid progress for drought-tolerance breeding. The emergence of novel technologies for targeted genotyping by sequencing are particularly welcome. Genome editing has already been demonstrated for Populus and offers significant potential for rapid deployment of drought-tolerant crops through manipulation of ABA receptors, as demonstrated in Arabidopsis, with other gene targets yet to be tested. CONCLUSIONS: Bioenergy is predicted to be the fastest-developing renewable energy over the coming decade and significant investment over the past decade has been made in developing genomic resources and in collecting wild germplasm from within the natural ranges of several tree and grass crops. Harnessing these resources for climate-resilient crops for the future remains a challenge but one that is likely to be successful.

Making the cut(s): how Cas12a cleaves target and non-target DNA
Swarts, Daan C. - \ 2019
Biochemical Society Transactions 47 (2019)5. - ISSN 0300-5127 - p. 1499 - 1510.
cis-cleavage - trans-cleavage - Cas12a - Cpf1 - CRISPR–Cas - genome editing

CRISPR-Cas12a (previously named Cpf1) is a prokaryotic deoxyribonuclease that can be programmed with an RNA guide to target complementary DNA sequences. Upon binding of the target DNA, Cas12a induces a nick in each of the target DNA strands, yielding a double-stranded DNA break. In addition to inducing cis-cleavage of the targeted DNA, target DNA binding induces trans-cleavage of non-target DNA. As such, Cas12a-RNA guide complexes can provide sequence-specific immunity against invading nucleic acids such as bacteriophages and plasmids. Akin to CRISPR-Cas9, Cas12a has been repurposed as a genetic tool for programmable genome editing and transcriptional control in both prokaryotic and eukaryotic cells. In addition, its trans-cleavage activity has been applied for high-sensitivity nucleic acid detection. Despite the demonstrated value of Cas12a for these applications, the exact molecular mechanisms of both cis- and trans-cleavage of DNA were not completely understood. Recent studies have revealed mechanistic details of Cas12a-mediates DNA cleavage: base pairing of the RNA guide and the target DNA induces major conformational changes in Cas12a. These conformational changes render Cas12a in a catalytically activated state in which it acts as deoxyribonuclease. This deoxyribonuclease activity mediates cis-cleavage of the displaced target DNA strand first, and the RNA guide-bound target DNA strand second. As Cas12a remains in the catalytically activated state after cis-cleavage, it subsequently demonstrates trans-cleavage of non-target DNA. Here, I review the mechanistic details of Cas12a-mediated cis- and trans-cleavage of DNA. In addition, I discuss how bacteriophage-derived anti-CRISPR proteins can inhibit Cas12a activity.

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