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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Effect of three types of liquid compost combined with Avicennia marina leaves on growth and survival of tiger prawns (Penaeus monodon)
Ariyati, Restiana Wisnu ; Rejeki, Sri ; Widowati, Lestari L. ; Elfitasari, Tita ; Bosma, Roel H. - \ 2019
International Aquatic Research (2019). - ISSN 2008-4935
Aquaculture - Fertilizer - LEISA - Mangrove - Shrimp

The sustainability of prawn farming in brackish water ponds is controversial because of low yields and a history of mangrove clearing. Low yields are due largely to insufficient preparation of pond bottoms. Mangrove trees are often planted on pond bunds as window dressing. This study examines the effect of three types of liquid compost from vegetable, fruit, and both vegetable and fruit in tanks to which whole or chopped Avicennia marina leaves have been added to mimic local pond conditions. In a split-plot design, 28 square tanks were each stocked with one hundred 15-day-old post-larvae tiger prawns (Penaeus monodon). Four tanks were used as controls and 24 were assigned to the treatments, 12 with whole and 12 with chopped leaves. Of the treatment tanks, 4 received liquid compost from vegetable, 4 received fruit, and 4 received mixed vegetable and fruit. Shrimp were weighed at the start, halfway point, and the end of the 50-day trial, and fed at 5% of the estimated total weight; survival was counted at the end. The survival rates of treatments and controls (65–76%) were not significantly different. Shrimp in water with vegetable compost grew significantly faster (2.7% day−1) than in both treatments with fruit (2.5% day−1), while all treatments were associated with significantly faster growth than were the controls (2.0% day−1). The lower growth rate of shrimp fed fruit compost may have been due to dinoflagellates, which are known to negatively affect shrimp. Shrimp in tanks with chopped mangrove leaves grew slightly better than shrimp in tanks with whole mangrove leaves.

The effects of decomposing mangrove leaf litter and its tannins on water quality and the growth and survival of tiger prawn (Penaeus monodon) post-larvae
Rejeki, Sri ; Middeljans, Marcel ; Widowati, Lestari L. ; Ariyati, Restiana W. ; Elfitasari, Tita ; Bosma, Roel H. - \ 2019
Biodiversitas 20 (2019)9. - ISSN 1412-033X - p. 2750 - 2757.
Ammonia-N - Avicennia marina - Penaeus monodon - Rhizophora apiculata - Tannin

Shrimp farming in Demak, Indonesia is often practiced in silvo-aquaculture systems in which mangrove trees are planted on pond bunds. As such, mangrove leaves and its substrates may have impact on penaeid shrimp production. In this area, mangrove re-growth proceeded with Avicennia marina while planting is mostly done with Rhizophora apiculata. We compared the effects of decomposing fresh leaves of A. marina and R. apiculata on water quality and on the performance of Penaeus monodon postlarvae (PL). A hundred of PL21 (postlarvae aged 21 days with weight of 0.28 g) were stocked in each of 30 aerated tanks containing 800 liters of brackish water (salinity of 21 ppt) for 37 days. Five treatments with three replicates for each mangrove species were assigned by adding into the tanks of 0.125, 0.25, and 0.5 g L-1 of air-dried leave, 0.125 of g L-1 minced leave and 0.125 g L-1 of leachate of minced leaves. The PLs were fed 3 times daily with pellets at 10 % of initial total body weight. Water quality parameters were recorded daily. Tannin, H2S and NH3-N concentrations were measured every ten days. Prawn’s body weight (BW) was measured and specific growth rate (SGR, % day-1) and survival rate (SR, %) were calculated after the end of experiment. Results were analyzed with ANOVA and Pearson’s correlation. The results showed that tannin in decomposing mangrove leaf litter up to a concentration of 0.5 mg g-1 did not have a significant effect on water quality and on the growth and survival of P. monodon PL. However, increasing leaf litter concentrations showed an increase in NH3-N concentration due to organic matter degradation. The accumulation of NH3-N may have caused the slow growth of shrimp PL in A. marina treatment. Shrimp PL in leaf litter leachates treatment has a higher growth rate than those PL in regular leaf litter in relation to nutritional value. Survival and growth varied from 62 ±14 to 70 ± 8% and 3.1±2.1 to 5.5±1.2% day-1, respectively. Although decomposing mangrove leaves of A. marina and R. apiculata had no toxic effects on P. monodon PL up to a concentration of 1.25 g L-1, but causing severe mortality for shrimp in tanks without water exchange. As a conclusion, the present of mangrove leaves in brackish water ponds with insufficient water exchange can be harmful to shrimps. However, if the water exchange is good, decomposed mangrove leaves can become organic fertilizer that beneficial for the growth of natural food for the shrimps.

Options to reuse sludge from striped catfish (Pangasianodon hypophthalmus, Sauvage, 1878) ponds and recirculating systems
Nhut, N. ; Hao, N.V. ; Bosma, R.H. ; Verreth, J.A.V. ; Eding, E.H. ; Verdegem, M.C.J. - \ 2019
Aquacultural Engineering 87 (2019). - ISSN 0144-8609
Biogas - Compost - Energy - Methane - Sludge - Striped catfish

This paper compares the quantity and quality of solid waste obtained from traditional ponds and recirculating aquaculture systems (RAS) for striped catfish and evaluates methane and compost production from these wastes. Striped catfish sludge was collected from four commercial ponds along the Mekong river and from three indoor RAS. The amount of sludge dry matter produced per kilogram of fish in ponds was 6 times higher than that in RAS. However, the concentration of nutrients in solid waste from RAS was much higher, with better compost quality and higher methane yield than that of sludge from ponds. Out of the collected 381 L biogas, the methane yield of striped catfish's solid waste in RAS systems was 201 L per kg chemical oxygen demand (COD). In ponds, the collected 267 L biogas yielded 125 L CH4 per kg COD. The higher methane production from RAS sludge concurred with higher digestibility of COD: 58% for RAS versus 38% for ponds. The quality and quantity of methane from striped catfish sludge were lower than that for other animal manures, and the resulting electricity yield was low. Considering the higher nutrient concentration in RAS-sludge, we recommend the combination RAS and composting in reusing sludge, which is presently the best option for a more sustainable and cleaner striped catfish production system.

Changing opinion, knowledge, skill and behaviour of Vietnamese shrimp farmers by using serious board games
Bosma, Roel H. ; Ha, Tran T.P. ; Hiep, Tong Quoc ; Phuong, Nguyen T.H. ; Ligtenberg, Arend ; Rodela, Romina ; Bregt, Arnold K. - \ 2019
The Journal of Agricultural Education and Extension (2019). - ISSN 1389-224X - 19 p.
Purpose: Mekong Delta's shrimp farming contributes to socio-economic development but tends to reduce the mangrove area. On the one hand, NGOs advocate balancing ecology and economy, while on the other hand, the Vietnamese government supports intensifying shrimp production. The latter strategy increases shrimp diseases and marginalises smallholders. To influence the opinions, knowledge and behaviour of shrimp farmers, we developed and tested a serious board game. Approach: Through several iterations, we designed a realistic board game mimicking local shrimp farming. Then, after conducting three sessions of gameplay with farmers in three sites, we assessed how this gameplay influenced players. We used a semi-experimental set-up by collecting data on the day of the gameplay, and on two further time-points. Findings: After the gameplays, farmers reported to have learned about the risks of monoculture-intensive-shrimp system and the advantages of hybrid systems. Likert ratings showed that players adopted innovations faster and, in case of shrimp diseases, consulted commercial service-providers less, but with other farmers more. They confirmed to have learned that the best strategy for them would be to adopt hybrid systems, i.e. intensify part of the area of mixed-mangrove or improved-extensive shrimp farms. Theoretical implications: Realistic board games can create opportunities for social learning and training of groups which are not always easy to reach. Practical implications: Board games can support transfer of knowledge and skills to farmers, and can develop their critical thinking. Creation: The findings that board games are effective in the context of a top-down extension systems offer value opportunities.
Ode aan haver in Landbouwmuseum
Gilissen, Luud - \ 2019
Is Integrated Multi-Trophic Aquaculture (Imta) Concept An Answer to Abraded Coastal Area? A Stakeholders' Perspective Analysis
Elfitasari, T. ; Klerkx, L. ; Joffrey, O. ; Rejeki, S. ; Widowati, L.L. ; Aryati, R.W. ; Bosma, R.H. - \ 2019
In: 4th International Conference on Tropical and Coastal Region Eco Development. - Semarang, Indonesia : IOP Publishing (IOP Conference Series: Earth and Environmental Science ) - 9 p.

Abrasion in coastal area of northern Central Java is severe, with abraded area exceeding 5,000 hectares which resulted in many aquaculture ponds became submerged and dissapeared. Eventhough physically the ponds are no longer visible, however the water quality is still supporting aquaculture to be carried out in that area. This paper explores the possibility that aquaculture innovation technology using an IMTA concept is suitable for abraded area in the stakeholders' point of view so that can be introduced to local community affected by abrasion to support their livelihood. This study employed rapid appraisal for aquaculture innovation system (RAAIS) to obtain data in two location in Central Java: Demak and Brebes regency and used descriptive for analysis method. Stakeholders from different background were involved representing fish farmers, government, NGOs, private sector and academics. Systemic analysis showed that both areas uncover similar constraints due to adopting the new IMTA technology. Stakeholders believed that constraints were mostly grouped as technological and institutional issues and that most problems rooted in the national level. Issues along value chain were believed by stakeholders from Brebes region may occur mostly in production area while stakeholders from Demak believed that inability to access credit deserves the blame. The possibility of using IMTA for aquaculture activity in abraded coastal area were also dicussed based on the obtained data.

Reductive dechlorination of 1,2-dichloroethane in the presence of chloroethenes and 1,2-dichloropropane as co-contaminants
Peng, Peng ; Schneidewind, Uwe ; Haest, Pieter Jan ; Bosma, Tom N.P. ; Danko, Anthony S. ; Smidt, Hauke ; Atashgahi, Siavash - \ 2019
Applied Microbiology and Biotechnology 103 (2019)16. - ISSN 0175-7598 - p. 6837 - 6849.
1,2-Dichloroethane - Co-contaminants - Dechlorination kinetics - Dehalococcoides - Dehalogenimonas

1,2-Dichloroethane (1,2-DCA) is one of the most abundant manmade chlorinated organic contaminants in the world. Reductive dechlorination of 1,2-DCA by organohalide-respiring bacteria (OHRB) can be impacted by other chlorinated contaminants such as chloroethenes and chloropropanes that can co-exist with 1,2-DCA at contaminated sites. The aim of this study was to evaluate the effect of chloroethenes and 1,2-dichloropropane (1,2-DCP) on 1,2-DCA dechlorination using sediment cultures enriched with 1,2-DCA as the sole chlorinated compound (EA culture) or with 1,2-DCA and tetrachloroethene (PCE) (EB culture), and to model dechlorination kinetics. Both cultures contained Dehalococcoides as most predominated OHRB, and Dehalogenimonas and Geobacter as other known OHRB. In sediment-free enrichments obtained from the EA and EB cultures, dechlorination of 1,2-DCA was inhibited in the presence of the same concentrations of either PCE, vinyl chloride (VC), or 1,2-DCP; however, concurrent dechlorination of dual chlorinated compounds was achieved. In contrast, 1,2-DCA dechlorination completely ceased in the presence of cis-dichloroethene (cDCE) and only occurred after cDCE was fully dechlorinated. In turn, 1,2-DCA did not affect dechlorination of PCE, cDCE, VC, and 1,2-DCP. In sediment-free enrichments obtained from the EA culture, Dehalogenimonas 16S rRNA gene copy numbers decreased 1–3 orders of magnitude likely due to an inhibitory effect of chloroethenes. Dechlorination with and without competitive inhibition fit Michaelis-Menten kinetics and confirmed the inhibitory effect of chloroethenes and 1,2-DCP on 1,2-DCA dechlorination. This study reinforces that the type of chlorinated substrate drives the selection of specific OHRB, and indicates that removal of chloroethenes and in particular cDCE might be necessary before effective removal of 1,2-DCA at sites contaminated with mixed chlorinated solvents.

FeedCalculator, een app om rantsoenen voor vis te berekenen
Bosma, R.H. ; Veluw, S. van; Meijer, P. - \ 2019
Aquacultuur 34 (2019)1. - ISSN 1382-2764 - p. 20 - 23.
De Nederlandse sociale onderneming Single Spark heeft een smartphone app ontwikkeld waarmee kleine boeren en bedrijven zelf rantsoenen voor hun dieren kunnen berekenen (zie foto’s onder). Dat geeft hen de mogelijkheid goedkopere grondstoffen, zoals hun eigen oogstresten, te gebruiken en toch een optimaal rantsoen te voeren. Nadat het wereldwijd voor kippen en varkens was uitgerold, is de app in 2018 getest voor meerval en tilapia in resp. Nigeria en Benin.
Effects of long-term chlorpyrifos exposure on mortality and reproductive tissues of Banded Gourami (Trichogaster fasciata)
Sumon, Kizar Ahmed ; Yesmin, Most Farzana ; Brink, Paul J. Van den; Bosma, Roel H. ; Peeters, Edwin T.H.M. ; Rashid, Harunur - \ 2019
Journal of Environmental Science and Health. Part B, Pesticides Food Contaminants, and agricultural wastes 54 (2019)7. - ISSN 0360-1234 - p. 549 - 559.
Aquatic environment - fish - histopathology - organophosphate pesticide - reproductive toxicity

This study assessed the long-term toxicity of chlorpyrifos on survival and reproduction of Banded Gourami by using mortality, gonado-somatic index (GSI) and histopathological observations as endpoints. Adult fish were exposed to five different concentrations of chlorpyrifos (0, 15, 50, 150, 500 µg/L) in 15 PVC tanks for 15, 30, 45, 60 and 75 days. Results showed that all male and female fish died after 15 days of 500 µg/L chlorpyrifos exposure. No consistent significant effect was observed for both male and female GSI. Furthermore, results showed dose- and time-dependent histopathological alterations for both ovary and testes. The 60-d No Observed Effect Concentration (NOEC) for most histopathological alterations of Banded Gourami ovary and testes was 50 μg/L, while 60-d NOEC for mortality of both male and female fish was < 15 μg/L. The results show that the long-term exposure to chlorpyrifos not only affect the reproductive tissues of Banded Gourami at exposure concentrations but also cause their mortality. Future studies should evaluate effects at lower concentrations.

Thermostable Cas9 nucleases with reduced off-target activity
Oost, J. van der; Kranenburg, R. van; Bosma, E.F. ; Mougiakos, I. ; Mohanraju, P. - \ 2019
Octrooinummer: WO2019072596, verleend: 2019-04-18.
ThermoCas9 is identified and characterized from the thermophilic bacterium Geobacillus thermodenitrificans T12. Experiments show how in vitro ThermoCas9 is active between 20 and 70 °C, has stringent PAM-preference at lower temperatures, tolerates fewer spacer-protospacer mismatches than SpCas9 and its activity at elevated temperatures depends on the sgRNA-structure. Described are ThermoCas9-based engineering tools for gene deletion and transcriptional silencing at 5 °C in Bacillus smithii and for gene deletion at 37 °C in Pseudomonas putida
A Low-Power MEMS IDE Capacitor with Integrated Microhotplate : Application as Methanol Sensor using a Metal-Organic Framework Coating as Affinity Layer
Venkatesh, Manjunath R. ; Sachdeva, Sumit ; Mansouri, Brahim El; Wei, Jia ; Bossche, Andre ; Bosma, Duco ; Smet, Louis C.P.M. de; Sudhölter, Ernst J.R. ; Zhang, Guo Qi - \ 2019
Sensors 19 (2019)4. - ISSN 1424-8220
Capacitor interdigitated electrodes - MEMS microhotplate - ZIF-8

Capacitors made of interdigitated electrodes (IDEs) as a transducer platform for the sensing of volatile organic compounds (VOCs) have advantages due to their lower power operation and fabrication using standard micro-fabrication techniques. Integrating a micro-electromechanical system (MEMS), such as a microhotplate with IDE capacitor, further allows study of the temperature- dependent sensing response of VOCs. In this paper, the design, fabrication, and characterization of a low-power MEMS microhotplate with IDE capacitor to study the temperature-dependent sensing response to methanol using Zeolitic imidazolate framework (ZIF-8), a class of metal-organic framework (MOF), is presented. A Titanium nitride (TiN) microhotplate with aluminum IDEs suspended on a silicon nitride membrane is fabricated and characterized. The power consumption of the ZIF-8 MOF-coated device at an operating temperature of 50 ∘ C is 4.5 mW and at 200 ∘ C it is 26 mW. A calibration methodology for the effects of temperature of the isolation layer between the microhotplate electrodes and the capacitor IDEs is developed. The device coated with ZIF-8 MOF shows a response to methanol in the concentration range of 500 ppm to 7000 ppm. The detection limit of the sensor for methanol vapor at 20 ∘ C is 100 ppm. In situ study of sensing properties of ZIF-8 MOF to methanol in the temperature range from 20 ∘ C to 50 ∘ C using the integrated microhotplate and IDE capacitor is presented. The kinetics of temperature-dependent adsorption and desorption of methanol by ZIF-8 MOF are fitted with double-exponential models. With the increase in temperature from 20 ∘ C to 50 ∘ C, the response time for sensing of methanol vapor concentration of 5000 ppm decreases by 28%, whereas the recovery time decreases by 70%.

Effect of dietary viscosity on digesta characteristics and progression of digestion in different segments of the gastrointestinal tract of striped catfish (Pangasionodon hypophthalmus)
Tran-Tu, L.C. ; Bosma, R.H. ; Verstegen, M.W.A. ; Schrama, J.W. - \ 2019
Aquaculture 504 (2019). - ISSN 0044-8486 - p. 114 - 120.
Chyme characteristics - Digestibility - Striped catfish - Viscosity

The physical and chemical characteristics of chyme have been shown to relate to apparent faecal nutrient digestibility, also in fish. This study assessed the effect of dietary viscosity on chyme characteristics in different segments of the gastrointestinal tract (GIT) of striped catfish (Pangasianodon hypophthalmus, Sauvage, 1878). Moreover, its effect on the progression of nutrient digestion throughout the GIT was studied. Six diets were produced, that had moderate differences in dietary viscosity by exchanging carboxymethylcellulose for guar gum (0, 0.25, 0.5, 1, 2, or 3 g kg−1 of diet). Eighteen tanks, each stocked with 20 fish of 95 g, were used (three replicate tanks per diet). Diets were randomly assigned to tanks and fed for 29 days. Thereafter fish were euthanized for the collection of chyme from four different segments of the GIT: stomach, proximal, mid and distal intestine. The chyme characteristics, dry matter content, viscosity and osmolarity were affected by the interaction effect of diet and GIT-segment. This implies that the impact of dietary viscosity on chyme characteristics differs between GIT-segments. Chyme viscosity increased with increasing dietary viscosity, but this mainly occurred in the stomach and distal intestine. Dry matter content of chyme was mainly affected (increased with rising dietary viscosity) in the stomach. The digestibility of both dry matter and crude protein was different between GIT-segments and increased from stomach towards distal intestine. Moreover, these nutrient digestibilities were influenced by dietary viscosity being negatively related. Already in the stomach increased dietary viscosity reduced the disappearance of nutrients (i.e., digestibility). These differences in digestibility were persistent and constant throughout the total GIT. In conclusion, moderate increases in dietary viscosity: alter predominantly stomach and distal chyme viscosity; increases chyme DM content in distal intestine; and reduces protein and DM digestibility, which are already different between diets from the stomach onward.

Petrol Pumps and the Making of Modernity Along the Shores of Lake Victoria, Kenya
Hebinck, P.G.M. ; Bosma, Luwieke ; Veldwisch, G.J.A. - \ 2019
Water Alternatives 12 (2019)1. - ISSN 1965-0175 - p. 13 - 29.
This paper explores how pump irrigation has evolved along the Kenyan shores of Lake Victoria. Over the past two decades access to petrol pumps has allowed small-scale horticultural enterprises to start up and then transform the size, intensity and nature of their production. We analyse the spread of petrol pumps as the assimilation and wider use of a modern device along a mutated trajectory of change. We argue that itwas not led by external actors but is a local and self-organised process driven by actors who negotiated interfaces between themselves and those operating at the macro level. The assimilation unfolded not as a temporally and spatially linear process but through its embeddedness in complex and dynamic social relationships that structure access to the key resources required for vegetable production. This in turn has given rise to a range of strategies in which the pumps' performance is adjusted to fit with various socially differentiated contexts.
Conceptualizing Serious Games as a Learning-Based Intervention in the Context of Natural Resources and Environmental Governance
Rodela, Romina ; Ligtenberg, Arend ; Bosma, Roel - \ 2019
Water 11 (2019)2. - ISSN 2073-4441
The use of serious games in the governance of natural resources and the environment is progressively increasing and includes games used for research and data collection, teaching and training, and fostering a change of practices. However, this diversity remains underexplored and underreported. In view of a growing interest in the use of serious games in natural resource and environmental governance, the absence of discussions about how differences in intended use and delivery influence the performance, assessment, and outcomes of games is problematic. Here we present an inventory, and a description, of such different uses then, by focusing on serious games used as interventions, we discuss when, and how, games could be used to generate learning and social learning. To that end we use a narrative review of selected literature, and insight from research on social learning, to develop an inventory of game use, and within that inventory we conceptualize the use of serious games as a social learning intervention. Also, by means of an illustrative case of a serious game (developed as part of the Assessing the Learning Effects of Games on Attitude of Stakeholders toward Sustainable Shrimp Farming – ALEGAMS research project) we reflect on a few key aspects of game use. We suggest that developing a serious game needs several iterations and, although the learning outcomes can be assessed, the impact of games aiming at changes in current practice and policy will likely fall beyond the timespan of usual project periods. This is something future research should consider as it has implications for the research design and methodology.
"Farmer Field-school" en LEISA: ook goed voor aquacultuur
Bosma, R.H. - \ 2018
Aquacultuur (2018)4. - ISSN 1382-2764 - p. 28 - 33.
De Indonesische boeren die melkvis en garnalen produceren in hun vijvers langs de kust zijn zelden goed getraind in de aquacultuur. De overheidsdiensten proberen de productie met gratis pootgoed en summiere instructies op te krikken. Maar goede training en aangepaste teeltmethoden maken groot verschil, ook in Indonesië. Bodemdaling blijft een bedreiging voor de vijvers van de boeren die weer hoop krijgen na een degelijke training. Het Ecoshape project Bouwen met Natuur stimuleert ze ook om de mangrove in het landschap terug te brengen.
Thermostable Cas9 nucleases
Oost, J. van der; Kranenburg, R. van; Bosma, E.F. ; Mougiakos, I. ; Mohanraju, P. - \ 2018
Octrooinummer: WO2018108339, verleend: 2018-06-21.
The present invention relates to the field of genetic engineering and more particularly to nucleic acid editing and genome modification. The present invention provides an isolated Cas protein or polypeptide fragment thereof having an amino acid sequence of SEQ ID NO: 1 or a sequence of at least 77% identity therewith. The Cas protein or polypeptide is capable of binding, cleaving, marking or modifying a double stranded target polynucleotide at a temperature in the range 20°C and 100°C inclusive. The invention further provides isolated nucleic acid molecules encoding said Cas9 nucleases, expression vectors and host cells. The invention also provides PAM sequences recognized by the Cas protein or polypeptide, The Cas9 nucleases disclosed herein provide novel tools for genetic engineering in general, in particular at elevated temperatures.
Thermostable Cas9 nucleases
Oost, J. van der; Kranenburg, R. van; Bosma, E.F. ; Mougiakos, I. ; Mohanraju, P. - \ 2018
Octrooinummer: WO2018109101, verleend: 2018-06-21.
A polynucleotide encoding a ThermoCas9protein from Geobacillus thermodenitrificans and a constitutive promoter are used to engineer eukaryotic cells, e.g. fungi, yeast or algae, so that the ThermoCas9 endonuclease is integrated and expressed from the genome of the cell. Then, a second expression plasmid is used to transfect these ThermoCas9 expressing cells, the second plasmid containing an inducible promoter and a polynucleotide encoding a guide RNA. The guide RNA combines with the ThermoCas9 to provide the targeted endonuclease activity to cleave the cell DNA at a desired locus or gene of interest. A repair-oligo is also provided to the cell whereby following DNA cleavage, homologous recombination takes place in the cell with the repair-oligo so that either a deletion or substitution of nucleotides in the locus or gene of interest is achieved. Expression vectors and methods of using the vectors to achieve ThermoCas9 mediated gene editing are described whereby higher temperatures, e.g. greater than 30 °C, are used.
Microbial genome editing
Oost, J. van der; Kranenburg, R. van; Bosma, E.F. ; Mougiakos, I. - \ 2018
Octrooinummer: WO2018083128, verleend: 2018-05-11.
In an absence of efficient non-homologous end joining (NHEJ) repair mechanisms in the majority of microbes, double stranded DNA break (DSDB) typically leads to cell death. In methods of microbial gene editing using plasmid transformation, both homologous recombination and Cas9 site-specific gene editing events can be used together. Single or multiple plasmid approaches are used. In a method of counter-selection of microbes for a desired genetic change, a two-phase approach is used whereby a switch is made from a higher growth temperature phase favouring homologous recombination (HR) - as opposed to a Cas9 site-directed nuclease activity- to a lower growth temperature phase at which the Cas9 site directed nuclease activity takes place. This has the effect whereby the Cas9 site-directed nuclease activity has counter selecting activity, removing microbes which do not have a desired modification introduced beforehand by HR. The population of microbes surviving after the temperature switch counter selection is thereby enhanced for the desired modification.
Modeling the Effect of Nutritional Strategies for Dairy Cows on the Composition of Excreta Nitrogen
Dijkstra, J. ; Bannink, A. ; Bosma, Pieter M. ; Lantinga, E.A. ; Reijs, J.W. - \ 2018
Frontiers in Sustainable Food Systems 2 (2018). - ISSN 2571-581X
models - Dairy cattle - Feces - Urine - diet composition - Manure composition
For an integrated evaluation of the effect of nutritional strategies on the utilization and losses of N at dairy farms, reliable estimates of excreta production and composition are indispensable. An extant, dynamic, mechanistic model of rumen functioning was extended with static equations that describe intestinal digestion to simulate the composition of dairy cow feces and urine as a function of diet composition. The extended model predicts organic matter (OM), carbon (C), and nitrogen (N) output of both feces and urine, classified in different components. Total N excretion was partitioned in three fractions based on the C:N ratio of individual components representing their availability of N following manure application to crops, viz. NM (immediately available), NE (easily decomposable), and NR (resistant). Forty nutritional strategies for stall-fed dairy cows, covering diets with a wide range in protein content and OM digestibility, were evaluated. The simulated ranges in fecal and urinary composition were largely in line with values reported in literature. Diet intake and composition had a substantial effect on simulated total N excretion and excreta composition, mainly because of differences in the level of NM excretion and the C:N ratio of the NR fraction. Furthermore, it was shown that the type of OM excreted varies considerably between different diets. A simplified simulation of degradation processes during the first 4 months of excreta storage produced average values and ranges of slurry characteristics that were in line with values reported in literature. The simulated variation in slurry characteristics suggested a strong variability in ammonia N losses from the slurry pit and a moderate variability in plant availability of slurry N. Further efforts are required to integrate effects of manure storage conditions on the storage processes. In conclusion, the model can be a tool to predict fecal and urinary composition of cattle, and ultimately to improve the utilization of N from field applied manure as well as to evaluate the effects of different nutritional strategies on the whole-farm N balance.
Gender action plans in the aquaculture value chain : what's missing?
Bosma, Roel H. ; Nguyen, Thi Dien ; Calumpang, Lorna M. ; Carandang, Sef Alba - \ 2018
Reviews in Aquaculture (2018). - ISSN 1753-5123
farmed seafood - gender mainstreaming - inequality - patriarchy - poverty - women

Gender equality has been a political issue in view of human rights and welfare since several decades. Therefore, many countries have developed Gender Action Plans (GAPs) that support equal access of both sexes to education, employment and finance. Two workshops on GAPs in aquaculture and a literature review brought about the question: what's missing in Asian sectoral GAPs. Not all reviewed Asian countries have GAPs for fishery/ aquaculture, but all encountered constraints to achieve their goals regarding equal access for women. Women's contribution in aquaculture tends to go beyond the traditional gender divide. For example, women may lead in the area of production because they can combine aquaculture with their homebound tasks and own vertically integrated companies. However, skewed perceptions on the role, status and perception of women and men, more so in strong than weak patriarchies (the former accept the subservient role, while the latter exercise the dominant role) limit women's access to training opportunities on new aquaculture technologies. Women are also left out in policy- and decision-making processes; and in the value chain, women receive lower wages than men. Their role is underestimated by lack of disaggregated data, as reflected in post-disaster interventions and industrial development programs. To be effective sectoral GAPs, based on disaggregated data, should have budgets, plans and target indicators for which leaders could be held accountable. These GAPs, however, can't address the required radical change in attitude toward women; unless deliberately planned educational media campaigns are embedded into the national GAPs.

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