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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    A collective response from food sovereignty scholars on the EU’s Farm to Fork Strategy
    Alberdi, Goiuri ; Begiristain Zubillaga, Mirene ; Brent, Zoe ; Choplin, Gérard ; Claeys, Priscilla ; Conti, Mauro ; Corrado, Alessandra ; Duncan, Jessica ; Ferrando, Tomaso ; McKeon, Nora ; Marinis, Pietro De; Milgroom, Jessica ; Moeller, Nina I. ; Nicol, Poppy ; Onorati, Antonio ; Plank, Christina ; Ploeg, Jan Douwe van der; Rivera Ferre, Marta G. ; Sharma, Divya ; Sotiropoulou, Irene ; Tornaghi, Chiara ; Dyck, Barbara Van - \ 2020
    - 8
    Microbial–Faunal Interactions in the Rhizosphere
    Geisen, Stefan ; Quist, C.W. - \ 2020
    In: Rhizosphere Biology: Interactions Between Microbes and Plants / Gupta, V.V.S.R., Sharma, A.K., Springer Nature Singapore - ISBN 9789811561245 - p. 237 - 253.
    Soils are home for a huge variety of organisms that are profoundly enriched in the rhizosphere. The most abundant ones, microbial bacteria (and to a lesser extent archaea) and fungi, directly compete for plant-derived nutrients that they use for reproduction. Predators of these minute microorganisms control their abundances, community structure and activity. Microbial protists, faunal nematodes and microarthropods are arguably the main bacterial and fungal predators, but also other groups including enchytraeids and even predatory bacteria, fungi and viruses contribute to microbial mortality. In this chapter, we introduce the major predators of microorganisms, their specific interactions with bacteria and fungi, and how predation on microorganisms affects nutrient cycling and eventually plant performance. We focus on protists and nematodes as the key microbial predators. We exemplify how this knowledge helps at better understanding microbial–faunal interactions, and how interactions among those microbial predators affect soil food webs. Overall, we show that the diversity of microbial predators is key to control rhizosphere microbiomes and, eventually, governs plant performance.
    The global abundance of tree palms
    Muscarella, Robert ; Emilio, Thaise ; Phillips, Oliver L. ; Lewis, Simon L. ; Slik, Ferry ; Baker, William J. ; Couvreur, Thomas L.P. ; Eiserhardt, Wolf L. ; Svenning, Jens Christian ; Affum-Baffoe, Kofi ; Aiba, Shin Ichiro ; Almeida, Everton C. de; Almeida, Samuel S. de; Oliveira, Edmar Almeida de; Álvarez-Dávila, Esteban ; Alves, Luciana F. ; Alvez-Valles, Carlos Mariano ; Carvalho, Fabrício Alvim ; Guarin, Fernando Alzate ; Andrade, Ana ; Aragão, Luis E.O.C. ; Murakami, Alejandro Araujo ; Arroyo, Luzmila ; Ashton, Peter S. ; Corredor, Gerardo A.A. ; Baker, Timothy R. ; Camargo, Plinio Barbosa de; Barlow, Jos ; Bastin, Jean François ; Bengone, Natacha Nssi ; Berenguer, Erika ; Berry, Nicholas ; Blanc, Lilian ; Böhning-Gaese, Katrin ; Bonal, Damien ; Bongers, Frans ; Bradford, Matt ; Brambach, Fabian ; Brearley, Francis Q. ; Brewer, Steven W. ; Camargo, Jose L.C. ; Campbell, David G. ; Castilho, Carolina V. ; Castro, Wendeson ; Catchpole, Damien ; Cerón Martínez, Carlos E. ; Chen, Shengbin ; Chhang, Phourin ; Cho, Percival ; Chutipong, Wanlop ; Clark, Connie ; Collins, Murray ; Comiskey, James A. ; Medina, Massiel Nataly Corrales ; Costa, Flávia R.C. ; Culmsee, Heike ; David-Higuita, Heriberto ; Davidar, Priya ; Aguila-Pasquel, Jhon del; Derroire, Géraldine ; Fiore, Anthony Di; Do, Tran Van; Doucet, Jean Louis ; Dourdain, Aurélie ; Drake, Donald R. ; Ensslin, Andreas ; Erwin, Terry ; Ewango, Corneille E.N. ; Ewers, Robert M. ; Fauset, Sophie ; Feldpausch, Ted R. ; Ferreira, Joice ; Ferreira, Leandro Valle ; Fischer, Markus ; Franklin, Janet ; Fredriksson, Gabriella M. ; Gillespie, Thomas W. ; Gilpin, Martin ; Gonmadje, Christelle ; Gunatilleke, Arachchige Upali Nimal ; Hakeem, Khalid Rehman ; Hall, Jefferson S. ; Hamer, Keith C. ; Harris, David J. ; Harrison, Rhett D. ; Hector, Andrew ; Hemp, Andreas ; Herault, Bruno ; Pizango, Carlos Gabriel Hidalgo ; Honorio Coronado, Eurídice N. ; Hubau, Wannes ; Hussain, Mohammad Shah ; Ibrahim, Faridah Hanum ; Imai, Nobuo ; Joly, Carlos A. ; Joseph, Shijo ; Anitha, K. ; Kartawinata, Kuswata ; Kassi, Justin ; Killeen, Timothy J. ; Kitayama, Kanehiro ; Klitgård, Bente Bang ; Kooyman, Robert ; Labrière, Nicolas ; Larney, Eileen ; Laumonier, Yves ; Laurance, Susan G. ; Laurance, William F. ; Lawes, Michael J. ; Levesley, Aurora ; Lisingo, Janvier ; Lovejoy, Thomas ; Lovett, Jon C. ; Lu, Xinghui ; Lykke, Anne Mette ; Magnusson, William E. ; Mahayani, Ni Putu Diana ; Malhi, Yadvinder ; Mansor, Asyraf ; Peña, Jose Luis Marcelo ; Marimon-Junior, Ben H. ; Marshall, Andrew R. ; Melgaco, Karina ; Bautista, Casimiro Mendoza ; Mihindou, Vianet ; Millet, Jérôme ; Milliken, William ; Mohandass, D. ; Mendoza, Abel Lorenzo Monteagudo ; Mugerwa, Badru ; Nagamasu, Hidetoshi ; Nagy, Laszlo ; Seuaturien, Naret ; Nascimento, Marcelo T. ; Neill, David A. ; Neto, Luiz Menini ; Nilus, Rueben ; Vargas, Mario Percy Núñez ; Nurtjahya, Eddy ; Araújo, R.N.O. de; Onrizal, Onrizal ; Palacios, Walter A. ; Palacios-Ramos, Sonia ; Parren, Marc ; Paudel, Ekananda ; Morandi, Paulo S. ; Pennington, R.T. ; Pickavance, Georgia ; Pipoly, John J. ; Pitman, Nigel C.A. ; Poedjirahajoe, Erny ; Poorter, Lourens ; Poulsen, John R. ; Prasad, P.R.C. ; Prieto, Adriana ; Puyravaud, Jean Philippe ; Qie, Lan ; Quesada, Carlos A. ; Ramírez-Angulo, Hirma ; Razafimahaimodison, Jean Claude ; Reitsma, Jan Meindert ; Requena-Rojas, Edilson J. ; Correa, Zorayda Restrepo ; Rodriguez, Carlos Reynel ; Roopsind, Anand ; Rovero, Francesco ; Rozak, Andes ; Lleras, Agustín Rudas ; Rutishauser, Ervan ; Rutten, Gemma ; Punchi-Manage, Ruwan ; Salomão, Rafael P. ; Sam, Hoang Van; Sarker, Swapan Kumar ; Satdichanh, Manichanh ; Schietti, Juliana ; Schmitt, Christine B. ; Marimon, Beatriz Schwantes ; Senbeta, Feyera ; Nath Sharma, Lila ; Sheil, Douglas ; Sierra, Rodrigo ; Silva-Espejo, Javier E. ; Silveira, Marcos ; Sonké, Bonaventure ; Steininger, Marc K. ; Steinmetz, Robert ; Stévart, Tariq ; Sukumar, Raman ; Sultana, Aisha ; Sunderland, Terry C.H. ; Suresh, Hebbalalu Satyanarayana ; Tang, Jianwei ; Tanner, Edmund ; Steege, Hans ter; Terborgh, John W. ; Theilade, Ida ; Timberlake, Jonathan ; Torres-Lezama, Armando ; Umunay, Peter ; Uriarte, María ; Gamarra, Luis Valenzuela ; Bult, Martin van de; Hout, Peter van der; Martinez, Rodolfo Vasquez ; Vieira, Ima Célia Guimarães ; Vieira, Simone A. ; Vilanova, Emilio ; Cayo, Jeanneth Villalobos ; Wang, Ophelia ; Webb, Campbell O. ; Webb, Edward L. ; White, Lee ; Whitfeld, Timothy J.S. ; Wich, Serge ; Willcock, Simon ; Wiser, Susan K. ; Young, Kenneth R. ; Zakaria, Rahmad ; Zang, Runguo ; Zartman, Charles E. ; Zo-Bi, Irié Casimir ; Balslev, Henrik - \ 2020
    Global Ecology and Biogeography 29 (2020)9. - ISSN 1466-822X - p. 1495 - 1514.
    above-ground biomass - abundance patterns - Arecaceae - local abiotic conditions - Neotropics - pantropical biogeography - tropical rainforest - wood density

    Aim: Palms are an iconic, diverse and often abundant component of tropical ecosystems that provide many ecosystem services. Being monocots, tree palms are evolutionarily, morphologically and physiologically distinct from other trees, and these differences have important consequences for ecosystem services (e.g., carbon sequestration and storage) and in terms of responses to climate change. We quantified global patterns of tree palm relative abundance to help improve understanding of tropical forests and reduce uncertainty about these ecosystems under climate change. Location: Tropical and subtropical moist forests. Time period: Current. Major taxa studied: Palms (Arecaceae). Methods: We assembled a pantropical dataset of 2,548 forest plots (covering 1,191 ha) and quantified tree palm (i.e., ≥10 cm diameter at breast height) abundance relative to co-occurring non-palm trees. We compared the relative abundance of tree palms across biogeographical realms and tested for associations with palaeoclimate stability, current climate, edaphic conditions and metrics of forest structure. Results: On average, the relative abundance of tree palms was more than five times larger between Neotropical locations and other biogeographical realms. Tree palms were absent in most locations outside the Neotropics but present in >80% of Neotropical locations. The relative abundance of tree palms was more strongly associated with local conditions (e.g., higher mean annual precipitation, lower soil fertility, shallower water table and lower plot mean wood density) than metrics of long-term climate stability. Life-form diversity also influenced the patterns; palm assemblages outside the Neotropics comprise many non-tree (e.g., climbing) palms. Finally, we show that tree palms can influence estimates of above-ground biomass, but the magnitude and direction of the effect require additional work. Conclusions: Tree palms are not only quintessentially tropical, but they are also overwhelmingly Neotropical. Future work to understand the contributions of tree palms to biomass estimates and carbon cycling will be particularly crucial in Neotropical forests.

    The Genome of Peronospora belbahrii Reveals High Heterozygosity, a Low Number of Canonical Effectors, and TC-Rich Promoters
    Thines, Marco ; Sharma, Rahul ; Rodenburg, Sander Y.A. ; Gogleva, Anna ; Judelson, Howard S. ; Xia, Xiaojuan ; Hoogen, Johan van den; Kitner, Miloslav ; Klein, Joël ; Neilen, Manon ; Ridder, Dick de; Seidl, Michael F. ; Ackerveken, Guido van den; Govers, Francine ; Schornack, Sebastian ; Studholme, David J. - \ 2020
    Molecular Plant-Microbe Interactions 33 (2020)5. - ISSN 0894-0282 - p. 742 - 753.
    Comparative genomics - Downy mildew - Evolutionary biology - Metabolic pathways - Oomycetes

    Along with Plasmopara destructor, Peronosopora belbahrii has arguably been the economically most important newly emerging downy mildew pathogen of the past two decades. Originating from Africa, it has started devastating basil production throughout the world, most likely due to the distribution of infested seed material. Here, we present the genome of this pathogen and results from comparisons of its genomic features to other oomycetes. The assembly of the nuclear genome was around 35.4 Mbp in length, with an N50 scaffold length of around 248 kbp and an L50 scaffold count of 46. The circular mitochondrial genome consisted of around 40.1 kbp. From the repeat-masked genome, 9,049 protein-coding genes were predicted, out of which 335 were predicted to have extracellular functions, representing the smallest secretome so far found in peronosporalean oomycetes. About 16% of the genome consists of repetitive sequences, and, based on simple sequence repeat regions, we provide a set of microsatellites that could be used for population genetic studies of P. belbahrii. P. belbahrii has undergone a high degree of convergent evolution with other obligate parasitic pathogen groups, reflecting its obligate biotrophic lifestyle. Features of its secretome, signaling networks, and promoters are presented, and some patterns are hypothesized to reflect the high degree of host specificity in Peronospora species. In addition, we suggest the presence of additional virulence factors apart from classical effector classes that are promising candidates for future functional studies.

    Hepatotoxicity of the pesticides imazalil, thiacloprid and clothianidin – Individual and mixture effects in a 28-day study in female Wistar rats
    Alarcan, Jimmy ; Waizenegger, Julia ; Lourdes Marzo Solano, Marize de; Lichtenstein, Dajana ; Luckert, Claudia ; Peijnenburg, Ad ; Stoopen, Geert ; Sharma, Raju Prasad ; Kumar, Vikas ; Marx-Stoelting, Philip ; Lampen, Alfonso ; Braeuning, Albert - \ 2020
    Food and Chemical Toxicology 140 (2020). - ISSN 0278-6915
    EuroMix - Liver hypertrophy - Mixture effects - Pesticides

    Humans are exposed to pesticide residues through various food products. As these residues can occur in mixtures, there is a need to investigate possible mixture effects on human health. Recent exposure studies revealed the preponderance of imazalil, thiacloprid, and clothianidin in food diets. In this study, we assessed their toxicity alone and in binary mixtures in a 28-day gavage study in female Wistar rats. Five dose levels (up to 350 mg/kg bw/day) ranging from a typical toxicological reference value to a clear effect dose were applied. Data show that the liver was a target organ of all pesticides and their mixtures. Increases in liver weight were observed and histopathological examination revealed centrilobular hepatocellular hypertrophy and cytoplasm degeneration for all treatment conditions. No accumulation of hepatic triglycerides was reported. Tissue residue analysis showed altered pesticide residues in the liver and the kidney when being in mixture as compared to the levels of pesticide residues for the single compound treatment, indicating possible toxicokinetic interactions. Overall, all mixtures appeared to follow the additivity concept, even though quantitative analysis was limited for some endpoints due to the semi-quantitative nature of the data, raising no specific concern for the risk assessment of the examined pesticides.

    On the merits and pitfalls of introducing a digital platform to aid conservation management : Volunteer data submission and the mediating role of volunteer coordinators
    Arts, Koen ; Melero, Yolanda ; Webster, Gemma ; Sharma, Nirwan ; Tintarev, Nava ; Tait, Elizabeth ; Mellish, Christopher ; Sripada, Somayajulu ; MacMaster, Ann Marie ; Sutherland, Hollie ; Horrill, Chris ; Lambin, Xavier ; Wal, René van der - \ 2020
    Journal of Environmental Management 265 (2020). - ISSN 0301-4797
    Environmental citizen science - Human-computer interaction - Invasive species control - Technological innovation - Volunteer coordination - Volunteer-based management

    Against a backdrop of accelerating digital innovation in nature conservation and environmental management, a real-world experiment was conducted with the research aims of assessing: 1) the effects of introducing a digital data-entry platform on volunteer data submission; and 2) the extent to which coordinators influence digital platform use by their volunteers. We focussed on a large-scale volunteer-based initiative aimed at eradicating the non-native American mink (Neovison vison) from northern Scotland. This geographically dispersed conservation initiative adopted a digital platform that allowed volunteers to submit records to a central database. We found that the platform had a direct and positive effect on volunteer data submission behaviour, increasing both the number and frequency of submissions. However, our analysis revealed striking differences in coordinator engagement with the platform, which in turn influenced the engagement of volunteers with this centrally introduced digital innovation. As a consequence, the intended organisation-wide rolling out of a digital platform translated into a diversely-implemented innovation, limiting the efficacy of the tool and revealing key challenges for digital innovation in geographically-dispersed conservation initiatives.

    Maternal exposure to mixtures of dienestrol, linuron and flutamide. Part I: Feminization effects on male rat offspring
    Schreiber, Elga ; Garcia, Tània ; González, Neus ; Esplugas, Roser ; Sharma, Raju Prasad ; Torrente, Margarita ; Kumar, Vikas ; Bovee, Toine ; Katsanou, Efrosini S. ; Machera, Kyriaki ; Domingo, José Luis ; Gómez, Mercedes - \ 2020
    Food and Chemical Toxicology 139 (2020). - ISSN 0278-6915
    Dienestrol - Feminization effects - Flutamide - Linuron - Male rats - Mixtures

    Exposure to endocrine-disrupting compounds (EDCs) during pregnancy can result in negative health effects in later generations, including sex changes and feminization. The present study assessed the feminization effects on male offspring rats of three EDCs: Dienestrol (DIES), Linuron (LIN), and Flutamide (FLU). Sexually mature female rats were exposed from gestation day (GD) 6 until postnatal day (PND) 21 to: 0.37, 0.75, 1.5, 3.12 or 6.25 μg/kg/day of DIES, 1.5, 3, 6, 12.5, 25 or 50 mg/kg/day of LIN, 3.5, 6.7, 12.5, 25 or 50 mg/kg/day of FLU, and the following mixtures: FLU + DIES (mg/kg/day+μg/kg/day), 3.5 + 0.37, or 3.5 + 3, 25 + 0.37, or 25 + 3; FLU + LIN (mg/kg/day + mg/kg/day), 3.5 + 12.5, or 25 + 12.5; and DIES + LIN (μg/kg/day + mg/kg/day), 0.37 + 12.5, or 3 + 12.5. Anogenital distance (AGD), nipple retention (NR) and cryptorchidism were evaluated. FLU produced a decrease of AGD, an increase of NR, and an increase of cryptorchidism at the highest dose. None of these three endpoints were significantly affected by LIN or DIES treatments alone. Combinations of FLU + LIN and FLU + DIES increased NR, and decreased AGD, while DIES + LIN did not produce any effects in male pups. Results show that FLU is able to induce feminization in male pups, while binary combinations of LIN and DIES did not modify the effects produced by FLU.

    Dataset for: Presence of seed-borne pest and pathogens on/in the seed produced by farmers in the province of Cotopaxi
    Navarrete Cueva, Israel ; Andrade, Jorge ; Almekinders, Conny ; Struik, Paul - \ 2019
    Kansas State University
    seed degeneration - nematodes - fungi - viruses - seed tubers - seed damaging insects - Potato - Rhizoctonia - Streptomyces scabies - Fusarium - Silver scurf - Powdery scabs - Andean potato weevil - Potato tuber moth - White grub - Wireworm - Flea beetle - PVS - PVY - PVX - PLRV - APMoV - Globodera pallida - Tylenchus spp. - Pratylenchus spp. - Aphelenchoides spp. - Heterodera spp. - Meloidogyne spp. - Paratylenchus Spp. - Saprophytes - Tylenchorhynchus spp.
    Seed degeneration (PSD) threats potato production in developing countries. PSD is defined as the accumulation of pest and pathogens in/on the seed tuber due to the successive cycles of vegetative propagation leading potentially to a yield and quality reduction (Thomas-Sharma et al., 2016; Pl. Path. [vol 65, issue 1]). However, the understanding of PSD in the Andes is deficient due to the limited comprehension of the spatial distribution of potato seed- and soil- borne pests and pathogens. For this reason, 260 farmers´ seed lots and fields were surveyed in the province of Cotopaxi-Ecuador from September to October 2018. The survey was implemented using a stratified sampling design (stratum = Cantons of Latacunga, Pujilí, Salcedo and Saquisilí). The sample size was defined based on the seed replacement rate reported by farmers in a pilot study previously implemented. In each place, farmers kindly provided a sample of (1 to 10) potato seed tubers depending on their willingness. In addition to it, a soil sample was collected from the closest field to the house after farmers provided oral consent. Symptoms and damages on the seed tubers caused by insects and fungi were visually inspected following the methodology suggested by James (1971, [Canadian pl. dis. survey {vol. 51}]) and the photography guide of the main pests and pathogens of the potato crop in Ecuador (Montesdeoca et al., 2013)(Reported in sheet coined "Insects and Fungi"). Virus identification was carried out on plantlets coming from the tubers assessed previously. This was performed by using the kits and the protocol for DAS-ELISA manufactured and suggested by CIP (2007). Six viruses were identified: PVX, PVS, PVY, APLV, PLRV, and APMoV (Reported in sheet coined "Virus"). Forty three soil samples out of the 260 were selected depending on the farmers’ field altitude and landscape location (Reported in sheet coined "nematodes"). These were sent to the laboratory of Plant Protection of the National Agriculture Research Center (INIAP) for nematodes identification. Nematodes were identified according to the methodologies of Oostenbrink (1960) and Fenwick (1940). It is expected that this database contributes to a deeper knowledge about the presence of seed-borne pests and pathogens in the tropical highlands of Ecuador and to design better seed system interventions.;The dataset contains data about presence of seed-borne pest and pathogens on/in the seed produced by farmers in the province of Cotopaxi.
    Farmers' Knowledge and Practices of Potato Bacterial Wilt Management in Ethiopia
    Gobena, Shiferaw Tafesse ; Damtew, E. ; Mierlo, B.C. van; Lie, R. ; Lemaga, B. ; Sharma, Kalpana ; Leeuwis, C. ; Struik, P.C. - \ 2019
    - 1 p.
    Potato (Solanum tuberosum L.) is an increasingly important crop for food and nutrition security in Ethiopia. It is also a vital source of income and more than 3.7 million smallholder farmers are involved in potato production in the country. However, bacterial wilt is currently causing an overwhelming impact on the country's potato production systems, threatening food and nutrition security initiatives.
    A survey of 261 randomly selected smallholder farmers was carried out in three major potato growing districts in the central highlands of Ethiopia to examine farmers' knowledge and management practices of bacterial wilt, and to analyse the role of relevant knowledge in their practices. Considering their different characteristics, three groups of farmers were distinguished: producers of quality declared seed, producers of normal seed and producers of ware potatoes. The results of the study indicated that most farmers (72%) could recognise symptoms of the disease on infected potato plants. However, they had very limited knowledge of the disease including its causal agent, spreading mechanisms, and management methods. All of the farmers were unaware of the causal agent of the disease and there were significant incongruences between scientific explanations and farmers' understanding of the disease. The farmers provided different explanations and confused a causal agent of the disease with various factors, such as water shortage, insects, planting seed potato with high moisture content, and waterlogging. Further, the majority of the farmers (60%) did not know spreading mechanisms of the disease. There was also no statistically significant association between farmers' knowledge of the disease and the category of the farmers.
    Farmers' knowledge of recommended management methods for bacterial wilt was also limited. The study further showed that practices of farmers have striking implication for spreading of the disease instead of controlling it. Previous agricultural extension efforts did not have the desirable effect on farmers' knowledge and practices. Therefore, to bridge the gap between scientific knowledge and farmers' understanding and practices, farmers need to learn about the disease and how to manage it through appropriate learning approaches that foster innovations in their local context.
    Molecular Epidemiology of Ralstonia solanacearum Species Complex Strains Causing Bacterial Wilt of Potato in Uganda
    Abdurahman, Abdulwahab ; Parker, Monica L. ; Kreuze, Jan ; Elphinstone, John G. ; Struik, Paul C. ; Kigundu, Andrew ; Arengo, Esther ; Sharma, Kalpana - \ 2019
    Phytopathology 109 (2019)11. - ISSN 0031-949X - p. 1922 - 1931.
    bacteriology - etiology - population biology

    Bacterial wilt (BW) caused by the Ralstonia solanacearum species complex (RSSC) is a serious threat to potato production in Uganda. However, little is known about the extent of the disease and the type of the pathogen strains involved. A nationwide survey was conducted to study BW prevalence and incidence in potato, and potato tuber and stem samples of potential alternative hosts were collected for pathogen isolation. DNA was extracted from pure cultures for genetic diversity studies. The pathogen was phylotyped by multiplex PCR; then, a subset of isolates was typed at sequevar level. Isolates of the same sequevar were then haplotyped using multilocus tandem repeat sequence typing (TRST) schemes. BW prevalence and incidence in potato farms were 81.4 and 1.7%, respectively. Three RSSC phylotypes were identified, with the majority of the strains belonging to Phylotype II (80%) followed by Phylotype I (18.5%) and III (1.5%). Phylotype I strains belonged to Sequevar 31, and Phylotype II strains belonged to Sequevar 1. Potato-associated Phylotype II Sequevar 1 strains were more diverse (27 TRST haplotypes) than nonpotato Phylotype I (5 TRST haplotypes). Mapping of TRST haplotypes revealed that three TRST haplotypes of Phylotype II Sequevar 1 strains play an important epidemiological role in BW of potato in Uganda being disseminated via latently infected seed.[Formula: see text]

    The genome of Peronospora belbahrii reveals high heterozygosity, a low number of canonical effectors and CT-rich promoters
    Thines, M. ; Sharma, R. ; Rodenburg, Y.A. ; Gogleva, A. ; Judelson, H.S. ; Xia, X. ; Hoogen, D.J. van den; Kitner, M. ; Klein, J. ; Neilen, M. ; Ridder, D. de; Seidl, M.F. ; Ackerveken, G. van den; Govers, F. ; Schornack, S. ; Studholme, D.J. - \ 2019
    BioRxiv
    Along with Plasmopara destructor, Peronosopora belbahrii has arguably been the economically most important newly emerging downy mildew pathogen of the past two decades. Originating from Africa, it has started devastating basil production throughout the world, most likely due to the distribution of infested seed material. Here we present the genome of this pathogen and results from comparisons of its genomic features to other oomycetes. The assembly of the nuclear genome was ca. 35.4 Mbp in length, with an N50 scaffold length of ca. 248 kbp and an L50 scaffold count of 46. The circular mitochondrial genome consisted of ca. 40.1 kbp. From the repeat-masked genome 9049 protein-coding genes were predicted, out of which 335 were predicted to have extracellular functions, representing the smallest secretome so far found in peronosporalean oomycetes. About 16 % of the genome consists of repetitive sequences, and based on simple sequence repeat regions, we provide a set of microsatellites that could be used for population genetic studies of Pe. belbahrii. Peronospora belbahrii has undergone a high degree of convergent evolution, reflecting its obligate biotrophic lifestyle. Features of its secretome, signalling networks, and promoters are presented, and some patterns are hypothesised to reflect the high degree of host specificity in Peronospora species. In addition, we suggest the presence of additional virulence factors apart from classical effector classes that are promising candidates for future functional studies.
    Validation of an ultra-high-performance liquid chromatography-mass spectrometry method for the quantification of cysteinylated aldehydes and application to malt and beer samples
    Bustillo Trueba, P. ; Jaskula-Goiris, B. ; Clippeleer, J. De; Goiris, K. ; Praet, T. ; Sharma, U.K. ; Eycken, E. Van der; Sanders, M.G. ; Vincken, J.P. ; Brabanter, J. De; Rouck, G. De; Aerts, G. ; Cooman, L. De - \ 2019
    Journal of Chromatography. A, Including electrophoresis and other separation methods 1604 (2019). - ISSN 0021-9673
    2-substituted 1,3-thiazolidine-4-carboxylic acids - Beer - Cysteinylated aldehydes - Liquid chromatography-mass spectrometry - Malt - Method validation

    This paper describes the method validation for the simultaneous determination of seven cysteinylated aldehydes, i.e. 2-substituted 1,3-thiazolidines-4-carboxylic acids, using ultra-high-performance liquid chromatography-mass spectrometry (UHPLC–MS). Authentic reference compounds were first synthesized for identification and quantification purposes. Moreover, nuclear magnetic resonance (1H NMR and 13C NMR) was applied for verification of their structure, while ultra-high-performance liquid chromatography–mass spectrometry (UHPLC–MS) was applied for estimation of the purity. The method for quantification of cysteinylated aldehydes in model solutions has been validated according to the criteria and procedures described in international standards. The synthesized compounds were successfully identified via UHPLC–MS by comparing retention time and MS spectra with the commercial reference compounds. Method validation revealed good linearity (R2 > 0.995) over the range of 0.4–2.2 µg/L to approximately 1000 µg/L, depending on the analyte. The limits of quantification varied from 0.9 to 4.3 µg/L depending on the nature of the compound. Furthermore, evaluation of the method showed good accuracy and stability of the standard solutions. Reported chromatographic recoveries ranged from 112 to 120%. Consequently, the currently described method was applied on malt and beer samples. For the first time, quantification of cysteinylated aldehydes was obtained in malt. In contrast, in fresh beers unambiguous identification of these compounds was not achieved.

    Efficiency of insect-proof net tunnels in reducing virus-related seed degeneration in sweet potato
    Ogero, K.O. ; Kreuze, J.F. ; McEwan, M.A. ; Luambano, N.D. ; Bachwenkizi, H. ; Garrett, K.A. ; Andersen, K.F. ; Thomas-Sharma, S. ; Vlugt, R.A.A. van der - \ 2019
    Plant Pathology 68 (2019)8. - ISSN 0032-0862 - p. 1472 - 1480.
    farmer-multiplier - modelling - net tunnels - seed - sweet potato - virus-related degeneration

    Virus-related degeneration constrains production of quality sweet potato seed, especially under open field conditions. Once in the open, virus-indexed seed is prone to virus infection leading to decline in performance. Insect-proof net tunnels have been proven to reduce virus infection under researcher management. However, their effectiveness under farmer-multiplier management is not known. This study investigated the ability of net tunnels to reduce degeneration in sweet potato under farmer-multiplier management. Infection and degeneration were assessed for two cultivars, Kabode and Polista, grown in net tunnels and open fields at two sites with varying virus pressures. There was zero virus incidence at both sites during the first five generations. Sweet potato feathery mottle virus and sweet potato chlorotic stunt virus were present in the last three generations, occurring singly or in combination to form sweet potato virus disease. Virus infection increased successively, with higher incidences recorded at the high virus pressure site. Seed degeneration modelling illustrated that for both varieties, degeneration was reduced by the maintenance of vines under net tunnel conditions. The time series of likely degeneration based on a generic model of yield loss suggested that, under the conditions experienced during the experimental period, infection and losses within the net tunnels would be limited. By comparison, in the open field most of the yield could be lost after a small number of generations without the input of seed with lower disease incidence. Adopting the technology at the farmer-multiplier level can increase availability of clean seed, particularly in high virus pressure areas.

    Twenty-three unsolved problems in hydrology (UPH)–a community perspective
    Blöschl, Günter ; Bierkens, Marc F.P. ; Chambel, Antonio ; Cudennec, Christophe ; Destouni, Georgia ; Fiori, Aldo ; Kirchner, James W. ; McDonnell, Jeffrey J. ; Savenije, Hubert H.G. ; Sivapalan, Murugesu ; Stumpp, Christine ; Toth, Elena ; Volpi, Elena ; Carr, Gemma ; Lupton, Claire ; Salinas, Josè ; Széles, Borbála ; Viglione, Alberto ; Aksoy, Hafzullah ; Allen, Scott T. ; Amin, Anam ; Andréassian, Vazken ; Arheimer, Berit ; Aryal, Santosh K. ; Baker, Victor ; Bardsley, Earl ; Barendrecht, Marlies H. ; Bartosova, Alena ; Batelaan, Okke ; Berghuijs, Wouter R. ; Beven, Keith ; Blume, Theresa ; Bogaard, Thom ; Borges de Amorim, Pablo ; Böttcher, Michael E. ; Boulet, Gilles ; Breinl, Korbinian ; Brilly, Mitja ; Brocca, Luca ; Buytaert, Wouter ; Castellarin, Attilio ; Castelletti, Andrea ; Chen, Xiaohong ; Chen, Yangbo ; Chen, Yuanfang ; Chifflard, Peter ; Claps, Pierluigi ; Clark, Martyn P. ; Collins, Adrian L. ; Croke, Barry ; Dathe, Annette ; David, Paula C. ; Barros, Felipe P.J. de; Rooij, Gerrit de; Baldassarre, Giuliano Di; Driscoll, Jessica M. ; Duethmann, Doris ; Dwivedi, Ravindra ; Eris, Ebru ; Farmer, William H. ; Feiccabrino, James ; Ferguson, Grant ; Ferrari, Ennio ; Ferraris, Stefano ; Fersch, Benjamin ; Finger, David ; Foglia, Laura ; Fowler, Keirnan ; Gartsman, Boris ; Gascoin, Simon ; Gaume, Eric ; Gelfan, Alexander ; Geris, Josie ; Gharari, Shervan ; Gleeson, Tom ; Glendell, Miriam ; Gonzalez Bevacqua, Alena ; González-Dugo, María P. ; Grimaldi, Salvatore ; Gupta, A.B. ; Guse, Björn ; Han, Dawei ; Hannah, David ; Harpold, Adrian ; Haun, Stefan ; Heal, Kate ; Helfricht, Kay ; Herrnegger, Mathew ; Hipsey, Matthew ; Hlaváčiková, Hana ; Hohmann, Clara ; Holko, Ladislav ; Hopkinson, Christopher ; Hrachowitz, Markus ; Illangasekare, Tissa H. ; Inam, Azhar ; Innocente, Camyla ; Istanbulluoglu, Erkan ; Jarihani, Ben ; Kalantari, Zahra ; Kalvans, Andis ; Khanal, Sonu ; Khatami, Sina ; Kiesel, Jens ; Kirkby, Mike ; Knoben, Wouter ; Kochanek, Krzysztof ; Kohnová, Silvia ; Kolechkina, Alla ; Krause, Stefan ; Kreamer, David ; Kreibich, Heidi ; Kunstmann, Harald ; Lange, Holger ; Liberato, Margarida L.R. ; Lindquist, Eric ; Link, Timothy ; Liu, Junguo ; Loucks, Daniel Peter ; Luce, Charles ; Mahé, Gil ; Makarieva, Olga ; Malard, Julien ; Mashtayeva, Shamshagul ; Maskey, Shreedhar ; Mas-Pla, Josep ; Mavrova-Guirguinova, Maria ; Mazzoleni, Maurizio ; Mernild, Sebastian ; Misstear, Bruce Dudley ; Montanari, Alberto ; Müller-Thomy, Hannes ; Nabizadeh, Alireza ; Nardi, Fernando ; Neale, Christopher ; Nesterova, Nataliia ; Nurtaev, Bakhram ; Odongo, Vincent O. ; Panda, Subhabrata ; Pande, Saket ; Pang, Zhonghe ; Papacharalampous, Georgia ; Perrin, Charles ; Pfister, Laurent ; Pimentel, Rafael ; Polo, María J. ; Post, David ; Prieto Sierra, Cristina ; Ramos, Maria Helena ; Renner, Maik ; Reynolds, José Eduardo ; Ridolfi, Elena ; Rigon, Riccardo ; Riva, Monica ; Robertson, David E. ; Rosso, Renzo ; Roy, Tirthankar ; Sá, João H.M. ; Salvadori, Gianfausto ; Sandells, Mel ; Schaefli, Bettina ; Schumann, Andreas ; Scolobig, Anna ; Seibert, Jan ; Servat, Eric ; Shafiei, Mojtaba ; Sharma, Ashish ; Sidibe, Moussa ; Sidle, Roy C. ; Skaugen, Thomas ; Smith, Hugh ; Spiessl, Sabine M. ; Stein, Lina ; Steinsland, Ingelin ; Strasser, Ulrich ; Su, Bob ; Szolgay, Jan ; Tarboton, David ; Tauro, Flavia ; Thirel, Guillaume ; Tian, Fuqiang ; Tong, Rui ; Tussupova, Kamshat ; Tyralis, Hristos ; Uijlenhoet, Remko ; Beek, Rens van; Ent, Ruud J. van der; Ploeg, Martine van der; Loon, Anne F. Van; Meerveld, Ilja van; Nooijen, Ronald van; Oel, Pieter R. van; Vidal, Jean Philippe ; Freyberg, Jana von; Vorogushyn, Sergiy ; Wachniew, Przemyslaw ; Wade, Andrew J. ; Ward, Philip ; Westerberg, Ida K. ; White, Christopher ; Wood, Eric F. ; Woods, Ross ; Xu, Zongxue ; Yilmaz, Koray K. ; Zhang, Yongqiang - \ 2019
    Hydrological Sciences Journal 64 (2019)10. - ISSN 0262-6667 - p. 1141 - 1158.
    hydrology - interdisciplinary - knowledge gaps - research agenda - science questions

    This paper is the outcome of a community initiative to identify major unsolved scientific problems in hydrology motivated by a need for stronger harmonisation of research efforts. The procedure involved a public consultation through online media, followed by two workshops through which a large number of potential science questions were collated, prioritised, and synthesised. In spite of the diversity of the participants (230 scientists in total), the process revealed much about community priorities and the state of our science: a preference for continuity in research questions rather than radical departures or redirections from past and current work. Questions remain focused on the process-based understanding of hydrological variability and causality at all space and time scales. Increased attention to environmental change drives a new emphasis on understanding how change propagates across interfaces within the hydrological system and across disciplinary boundaries. In particular, the expansion of the human footprint raises a new set of questions related to human interactions with nature and water cycle feedbacks in the context of complex water management problems. We hope that this reflection and synthesis of the 23 unsolved problems in hydrology will help guide research efforts for some years to come.

    Towards the development of a biobased economy in Europe and India
    Pant, Deepak ; Misra, Shilpi ; Nizami, Abdul Sattar ; Rehan, Mohammad ; Leeuwen, Rebecca van; Tabacchioni, Silvia ; Goel, Reeta ; Sarma, Priyangshu ; Bakker, Rob ; Sharma, Neeta ; Kwant, Kees ; Diels, Ludo ; Elst, Kathy - \ 2019
    Critical Reviews in Biotechnology 39 (2019)6. - ISSN 0738-8551 - p. 779 - 799.
    Biobased economy - biomass - biorefineries - European Union (EU) - India - value-added products

    India has emerged as a key player with a high potential to develop a biomass and biobased economy due to its large geographic size and the massive amounts of agricultural and non agricultural biomass produced. India has joined hands with Europe to synchronize its efforts to create and facilitate the development of a biobased economy in this country. This paper aims to examine common research and development actions between the European Union (EU) and India to facilitate the development of these biobased economies. As a base, a thorough study has been performed considering the biomass potential and current status of the bioeconomy in both the EU and India based on the distillation of a series of 80 potential recommendations. The recommendations were grouped into four major categories: (1) biomass production, (2) by-products/waste, (3) biorefineries and (4) policy, market, and value-added products. A questionnaire was designed and distributed to key stakeholders belonging to: academia, industry, and policymakers in both India and the EU. A total of 231 responses were received and analyzed, based on the key recommendations made for the essential research and development topics that are of prime importance to develop biobased economies in both the EU and India. The findings of this study suggest recognizing the value-added contributions made by biobased products such as: food, feed, valuable materials and chemicals in both regions. It is important to reduce the overall process costs and minimize the environmental impacts of such a biobased economy.

    Soil Salinity Limits Plant Shade Avoidance
    Hayes, Scott ; Pantazopoulou, Chrysoula K. ; Gelderen, Kasper van; Reinen, Emilie ; Tween, Adrian Louis ; Sharma, Ashutosh ; Vries, Michel de; Prat, Salomé ; Schuurink, Robert C. ; Testerink, Christa ; Pierik, Ronald - \ 2019
    Current Biology 29 (2019)10. - ISSN 0960-9822 - p. 1669 - 1676.e4.
    abscisic acid - brassinosteroids - phytochrome - phytohormones - PIF - plant photobiology - salt response - salt stress

    Global food production is set to keep increasing despite a predicted decrease in total arable land [1]. To achieve higher production, denser planting will be required on increasingly degraded soils. When grown in dense stands, crops elongate and raise their leaves in an effort to reach sunlight, a process termed shade avoidance [2]. Shade is perceived by a reduction in the ratio of red (R) to far-red (FR) light and results in the stabilization of a class of transcription factors known as PHYTOCHROME INTERACTING FACTORS (PIFs) [3, 4]. PIFs activate the expression of auxin biosynthesis genes [4, 5] and enhance auxin sensitivity [6], which promotes cell-wall loosening and drives elongation growth. Despite our molecular understanding of shade-induced growth, little is known about how this developmental program is integrated with other environmental factors. Here, we demonstrate that low levels of NaCl in soil strongly impair the ability of plants to respond to shade. This block is dependent upon abscisic acid (ABA) signaling and the canonical ABA signaling pathway. Low R:FR light enhances brassinosteroid (BR) signaling through BRASSINOSTEROID SIGNALING KINASE 5 (BSK5) and leads to the activation of BRI1 EMS SUPPRESSOR 1 (BES1). ABA inhibits BSK5 upregulation and interferes with GSK3-like kinase inactivation by the BR pathway, thus leading to a suppression of BES1:PIF function. By demonstrating a link between light, ABA-, and BR-signaling pathways, this study provides an important step forward in our understanding of how multiple environmental cues are integrated into plant development. Intensively farmed crops often experience multiple stresses simultaneously. Here, Hayes et al. show that low-level soil salinity suppresses shade avoidance in plants. Through investigation of the mechanisms underlying this trait, they uncover a regulatory pathway that converges at the level of brassinosteroid signaling.

    WRF Model Prediction of a Dense Fog Event Occurred During the Winter Fog Experiment (WIFEX)
    Pithani, Prakash ; Ghude, Sachin D. ; Chennu, V.N. ; Kulkarni, Rachana G. ; Steeneveld, Gert Jan ; Sharma, Ashish ; Prabhakaran, Thara ; Chate, D.M. ; Gultepe, Ismail ; Jenamani, R.K. ; Madhavan, Rajeevan - \ 2019
    Pure and Applied Geophysics 176 (2019)4. - ISSN 0033-4553 - p. 1827 - 1846.
    Liquid water content - PBL scheme - vertical level - WIFEX - WRF model

    In this study, the sensitivity of the Weather Research and Forecasting (WRF) model to simulate the life cycle of a dense fog event that occurred on 23–24 January 2016 is evaluated using different model configurations. For the first time, intensive observational periods (IOPs) were made during the unique winter fog experiment (WIFEX) that took place over Delhi, India, where air quality is serious during the winter months. The multiple sensitivity experiments to evaluate the WRF model performance included parameters such as initial model and boundary conditions, vertical resolution in the lower boundary layer (BL), and the planetary BL (PBL) physical parameterizations. In addition, the model sensitivity was tested using various configurations that included domain size and grid resolution. Results showed that simulations with a high number of vertical levels within the lower PBL height (i.e., 10 levels below 300 m) simulated the accurate timing of fog formation, development, and dissipation. On the other hand, simulations with less vertical levels in the PBL captured only the mature physical characteristics of the fog cycle. A comparison of six local PBL schemes showed little variation in the onset of fog life cycle in comparison to observations of visibility. However, comparisons of observations with thermodynamical values such as 2-m temperature and longwave radiation showed poor relationships. Overall, quasi-normal scale elimination (QNSE) and MYNN 2.5 PBL schemes simulated the complete fog life cycle correctly with high liquid water content (LWC; 0.5/0.35 g m −3 ), while other schemes only responded during the mature phase.

    Comparison of Pesticide Exposure in Honey Bees (Hymenoptera : Apidae) and Bumble Bees (Hymenoptera: Apidae): Implications for Risk Assessments
    Gradish, Angela E. ; Steen, Jozef Van Der; Scott-Dupree, Cynthia D. ; Cabrera, Ana R. ; Cutler, G.C. ; Goulson, Dave ; Klein, Olaf ; Lehmann, David M. ; Lückmann, Johannes ; O'Neill, Bridget ; Raine, Nigel E. ; Sharma, Bibek ; Thompson, Helen - \ 2019
    Environmental Entomology 48 (2019)1. - ISSN 0046-225X - p. 12 - 21.
    bumble bee - honey bee - pesticide exposure - risk assessment

    To date, regulatory pesticide risk assessments have relied on the honey bee (Apis mellifera L.) (Hymenoptera: Apidae) as a surrogate test species for estimating the risk of pesticide exposure to all bee species. However, honey bees and non-Apis bees may differ in their susceptibility and exposure to pesticides. In 2017, a workshop ('Pesticide Exposure Assessment Paradigm for Non-Apis Bees') was held to assess if honey bee risk assessment frameworks are reflective of non-Apis bee pesticide exposure. In this article, we summarize the workshop discussions on bumble bees (Bombus spp.). We review the life history and foraging behavior of bumble bees and honey bees and discuss how these traits may influence routes and levels of exposure for both taxa. Overall, the major pesticide exposure routes for bumble bees and honey bees are similar; however, bumble bees face additional exposure routes (direct exposure of foraging queens and exposure of larvae and adults to soil residues). Furthermore, bumble bees may receive comparatively higher pesticide doses via contact or oral exposure. We conclude that honey bee pesticide risk assessments may not always be protective of bumble bees, especially queens, in terms of exposure. Data needed to reliably quantify pesticide exposure for bumble bees (e.g., food consumption rates, soil residue levels) are lacking. Addressing these knowledge gaps will be crucial before bumble bee exposure can be incorporated into the pesticide risk assessment process. Because bumble bees exhibit appreciable interspecific variation in colony and behavioral characteristics, data relevant to pesticide exposure should be generated for multiple species.

    Micro magnetic resonance imaging of murine liver tissue slices on a microfluidic perfusion device
    Sharma, Manvendra ; Patra, Bishnubrata ; Hale, William ; Karsten, Ruby E.H. ; Salentijn, Gert I.J. ; Grajewski, Maciej ; Fuhrer, Erwin ; Zakhurdaeva, Anna ; Mager, Dario ; Korvink, Jan ; Olinga, Peter ; Verpoorte, Elisabeth ; Utz, Marcel - \ 2018
    In: 22nd International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2018. - Chemical and Biological Microsystems Society (22nd International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2018 ) - ISBN 9781510897571 - p. 1722 - 1724.
    Micro-MRI - NMR - PCLS

    Micro-MRI (Magnetic Resonance Imaging) and NMR (Nuclear Magnetic Resonance) spectroscopy are used to image and study metabolic activity of precision-cut liver slices (PCLS) on a microfluidic perfusion device. The imaging experiments were performed under static medium conditions while metabolic activity was monitored under continuous flow of medium. LDH (Lactate dehydrogenase) leakage assay was performed to assess the tissue viability on different days. MR images having ~30 (μm)2 in-plane resolution are recorded. This method could be used to culture and monitor PCLS non-invasively.

    Comparative genomics including the basal pathogen Peronospora belbahrii reveal common evolutionary patterns and the monophyly of downy mildews in a paraphyletic Phytophthora
    Thines, M. ; Sharma, R. ; Rodenburg, Y.A. ; Gogleva, A. ; Judelson, H.S. ; Xia, X. ; Hoogen, D.J. van den; Kitner, M. ; Klein, J. ; Ridder, D. de; Seidl, M.F. ; Ackerveken, G. van den; Govers, F. ; Schornack, S. ; Studholme, D.J. - \ 2018
    IPF
    PRJEB15119 - ERP016822 - Peronospora belbahrii
    The obligate biotrophic downy mildew constitute the most species rich group of oomycetes. So far only handful of genomes of this group of pathogens has been sequenced. Most likely due to low taxon sampling, until now phylogenomic studies with few taxa were in stark contrast to multigene phylogenies with a large number of accessions with respect to the relationships of downy mildews and Phytophthora species. In the current study, we sequenced the whole genome of the economically important basil pathogen Peronospora belbahrii, and performed in-depth comparative genomics and phylogenomics towards clarifying some aspects of downy mildew and Phytophthora evolution.
    Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen
    Pais, Marina ; Yoshida, Kentaro ; Giannakopoulou, Artemis ; Pel, M. ; Cano, Liliana M. ; Oliva, Ricardo F. ; Witek, Kamil ; Lindqvist-Kreuze, Hannele ; Vleeshouwers, V.G.A.A. ; Kamoun, Sophien - \ 2018
    The Sainsbury Laboratory
    asexual reproduction - clonal lineage - Phytophthora infestans - emergent pathogen - evolution - immunity - phenotypic plasticity - expression polymorphism - structural variation - copy number variation - loss of heterozygosity
    Background Outbreaks caused by asexual lineages of fungal and oomycete pathogens are a continuing threat to crops, wild animals and natural ecosystems (Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, Gurr SJ, Nature 484:186–194, 2012; Kupferschmidt K, Science 337:636–638, 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl MF, Thomma BP, BioEssays 36:335–345, 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Goodwin SB, Cohen BA, Fry WE, Proc Natl Acad Sci USA 91:11591–11595, 1994; Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10:e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Cooke DEL, Cano LM, Raffaele S, Bain RA, Cooke LR, Etherington GJ, Deahl KL, Farrer RA, Gilroy EM, Goss EM, et al. PLoS Pathog 8:e1002940, 2012). However, the dynamics of genome evolution within these clonal lineages have not been determined. The objective of this study was to use a comparative genomics and transcriptomics approach to determine the molecular mechanisms that underpin phenotypic variation within a clonal lineage of P. infestans. Results Here, we reveal patterns of genomic and gene expression variation within a P. infestans asexual lineage by comparing strains belonging to the South American EC-1 clone that has dominated Andean populations since the 1990s (Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Delgado RA, Monteros-Altamirano AR, Li Y, Visser RGF, van der Lee TAJ, Vosman B, Plant Pathol 62:1081–1088, 2013; Forbes GA, Escobar XC, Ayala CC, Revelo J, Ordonez ME, Fry BA, Doucett K, Fry WE, Phytopathology 87:375–380, 1997; Oyarzun PJ, Pozo A, Ordonez ME, Doucett K, Forbes GA, Phytopathology 88:265–271, 1998). We detected numerous examples of structural variation, nucleotide polymorphisms and loss of heterozygosity within the EC-1 clone. Remarkably, 17 genes are not expressed in one of the two EC-1 isolates despite apparent absence of sequence polymorphisms. Among these, silencing of an effector gene was associated with evasion of disease resistance conferred by a potato immune receptor. Conclusions Our findings highlight the molecular changes underpinning the exceptional genetic and phenotypic plasticity associated with host adaptation in a pandemic clonal lineage of a eukaryotic plant pathogen. We observed that the asexual P. infestans lineage EC-1 can exhibit phenotypic plasticity in the absence of apparent genetic mutations resulting in virulence on a potato carrying the Rpi-vnt1.1 gene. Such variant alleles may be epialleles that arose through epigenetic changes in the underlying genes.
    Data from: Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses
    Velzen, R. van; Holmer, R. ; Bu, F. ; Rutten, L.J.J. ; Zeijl, A.L. van; Liu, W. ; Santuari, L. ; Cao, Q. ; Sharma, Trupti ; Shen, D. ; Roswanjaya, Yuda ; Wardhani, T. ; Seifi Kalhor, M. ; Jansen, Joelle ; Hoogen, D.J. van den; Gungor, Berivan ; Hartog, M.V. ; Hontelez, Jan ; Verver, J.W.G. ; Yang, Wei-Cai ; Schijlen, E.G.W.M. ; Repin, Rimi ; Schilthuizen, M. ; Schranz, M.E. ; Heidstra, R. ; Miyata, Kana ; Fedorova, E. ; Kohlen, W. ; Bisseling, A.H.J. ; Smit, S. ; Geurts, R. - \ 2018
    Wageningen University & Research
    comparative genomics - copy number variation - evolution - nitrogen fixation - symbiosis - Parasponia andersonii - Parasponia rigada - Parasponia rugosa - Trema levigata - Trema orientalis - Trema tomentosa
    Nodules harboring nitrogen-fixing rhizobia are a well-known trait of legumes, but nodules also occur in other plant lineages, with rhizobia or the actinomycete Frankia as microsymbiont. It is generally assumed that nodulation evolved independently multiple times. However, molecular-genetic support for this hypothesis is lacking, as the genetic changes underlying nodule evolution remain elusive. We conducted genetic and comparative genomics studies by using Parasponia species (Cannabaceae), the only nonlegumes that can establish nitrogen-fixing nodules with rhizobium. Intergeneric crosses between Parasponia andersonii and its nonnodulating relative Trema tomentosa demonstrated that nodule organogenesis, but not intracellular infection, is a dominant genetic trait. Comparative transcriptomics of P. andersonii and the legume Medicago truncatula revealed utilization of at least 290 orthologous symbiosis genes in nodules. Among these are key genes that, in legumes, are essential for nodulation, including NODULE INCEPTION (NIN) and RHIZOBIUM-DIRECTED POLAR GROWTH (RPG). Comparative analysis of genomes from three Parasponia species and related nonnodulating plant species show evidence of parallel loss in nonnodulating species of putative orthologs of NIN, RPG, and NOD FACTOR PERCEPTION. Parallel loss of these symbiosis genes indicates that these nonnodulating lineages lost the potential to nodulate. Taken together, our results challenge the view that nodulation evolved in parallel and raises the possibility that nodulation originated ∼100 Mya in a common ancestor of all nodulating plant species, but was subsequently lost in many descendant lineages. This will have profound implications for translational approaches aimed at engineering nitrogen-fixing nodules in crop plants
    Nonselective Chemical Inhibition of Sec7 Domain-Containing ARF GTPase Exchange Factors
    Mishev, Kiril ; Lu, Qing ; Denoo, Bram ; Peurois, François ; Dejonghe, Wim ; Hullaert, Jan ; Rycke, Riet De; Boeren, Sjef ; Bretou, Marine ; Munck, Steven De; Sharma, Isha ; Goodman, Kaija ; Kalinowska, Kamila ; Storme, Veronique ; Nguyen, Le Son Long ; Drozdzecki, Andrzej ; Martins, Sara ; Nerinckx, Wim ; Audenaert, Dominique ; Vert, Grégory ; Madder, Annemieke ; Otegui, Marisa S. ; Isono, Erika ; Savvides, Savvas N. ; Annaert, Wim ; Vries, Sacco de; Cherfils, Jacqueline ; Winne, Johan ; Russinova, Eugenia - \ 2018
    The Plant Cell 30 (2018)10. - ISSN 1040-4651 - p. 2573 - 2593.

    Small GTP-binding proteins from the ADP-ribosylation factor (ARF) family are important regulators of vesicle formation and cellular trafficking in all eukaryotes. ARF activation is accomplished by a protein family of guanine nucleotide exchange factors (GEFs) that contain a conserved catalytic Sec7 domain. Here, we identified and characterized Secdin, a small-molecule inhibitor of Arabidopsis thaliana ARF-GEFs. Secdin application caused aberrant retention of plasma membrane (PM) proteins in late endosomal compartments, enhanced vacuolar degradation, impaired protein recycling, and delayed secretion and endocytosis. Combined treatments with Secdin and the known ARF-GEF inhibitor Brefeldin A (BFA) prevented the BFA-induced PM stabilization of the ARF-GEF GNOM, impaired its translocation from the Golgi to the trans-Golgi network/early endosomes, and led to the formation of hybrid endomembrane compartments reminiscent of those in ARF-GEF-deficient mutants. Drug affinity-responsive target stability assays revealed that Secdin, unlike BFA, targeted all examined Arabidopsis ARF-GEFs, but that the interaction was probably not mediated by the Sec7 domain because Secdin did not interfere with the Sec7 domain-mediated ARF activation. These results show that Secdin and BFA affect their protein targets through distinct mechanisms, in turn showing the usefulness of Secdin in studies in which ARF-GEF-dependent endomembrane transport cannot be manipulated with BFA.

    Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen
    Pais, Marina ; Yoshida, Kentaro ; Giannakopoulou, Artemis ; Pel, Mathieu A. ; Cano, Liliana M. ; Oliva, Ricardo F. ; Witek, Kamil ; Lindqvist-Kreuze, Hannele ; Vleeshouwers, Vivianne G.A.A. ; Kamoun, Sophien - \ 2018
    BMC Evolutionary Biology 18 (2018)1. - ISSN 1471-2148
    Asexual reproduction - Clonal lineage - Copy number variation - Emergent pathogen - Evolution - Expression polymorphism - Immunity - Loss of heterozygosity - Phenotypic plasticity - Phytophthora infestans - Structural variation

    Background: Outbreaks caused by asexual lineages of fungal and oomycete pathogens are a continuing threat to crops, wild animals and natural ecosystems (Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, Gurr SJ, Nature 484:186-194, 2012; Kupferschmidt K, Science 337:636-638, 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl MF, Thomma BP, BioEssays 36:335-345, 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Goodwin SB, Cohen BA, Fry WE, Proc Natl Acad Sci USA 91:11591-11595, 1994; Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10:e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Cooke DEL, Cano LM, Raffaele S, Bain RA, Cooke LR, Etherington GJ, Deahl KL, Farrer RA, Gilroy EM, Goss EM, et al. PLoS Pathog 8:e1002940, 2012). However, the dynamics of genome evolution within these clonal lineages have not been determined. The objective of this study was to use a comparative genomics and transcriptomics approach to determine the molecular mechanisms that underpin phenotypic variation within a clonal lineage of P. infestans. Results: Here, we reveal patterns of genomic and gene expression variation within a P. infestans asexual lineage by comparing strains belonging to the South American EC-1 clone that has dominated Andean populations since the 1990s (Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Delgado RA, Monteros-Altamirano AR, Li Y, Visser RGF, van der Lee TAJ, Vosman B, Plant Pathol 62:1081-1088, 2013; Forbes GA, Escobar XC, Ayala CC, Revelo J, Ordonez ME, Fry BA, Doucett K, Fry WE, Phytopathology 87:375-380, 1997; Oyarzun PJ, Pozo A, Ordonez ME, Doucett K, Forbes GA, Phytopathology 88:265-271, 1998). We detected numerous examples of structural variation, nucleotide polymorphisms and loss of heterozygosity within the EC-1 clone. Remarkably, 17 genes are not expressed in one of the two EC-1 isolates despite apparent absence of sequence polymorphisms. Among these, silencing of an effector gene was associated with evasion of disease resistance conferred by a potato immune receptor. Conclusions: Our findings highlight the molecular changes underpinning the exceptional genetic and phenotypic plasticity associated with host adaptation in a pandemic clonal lineage of a eukaryotic plant pathogen. We observed that the asexual P. infestans lineage EC-1 can exhibit phenotypic plasticity in the absence of apparent genetic mutations resulting in virulence on a potato carrying the Rpi-vnt1.1 gene. Such variant alleles may be epialleles that arose through epigenetic changes in the underlying genes.

    Preparation of antinutrients-reduced dhokla using response surface process optimisation
    Sharma, Anand ; Kumari, Sarita ; Nout, Martinus J.R. ; Sarkar, Prabir K. - \ 2018
    Journal of Food Science and Technology-Mysore 55 (2018)6. - ISSN 0022-1155 - p. 2048 - 2058.
    Antinutrient - Bengalgram - Dhokla - Process optimisation - Response surface methodology - Rice
    Dhokla, a popular indigenous savoury dish of India, is prepared by soaking bengalgram dal and rice, grinding separately, mixing the batters, and spontaneously fermenting and steaming of mixed batter. Central composite rotatable response surface designs for soaking, fermentation and steaming at five-level combinations were used for optimising preparation of dhokla to achieve reduced contents of antinutrients. Optimum soaking of bengalgram dal (dal–water ratio of 1:5 w/w, pH 7.0, 23 °C, 20 h) and rice (rice–water ratio of 1:5 w/w, pH 5.6, 16 °C, 18 h) resulted in reduced levels of all the antinutrients, except total biogenic amines in rice. Fermentation of dal–rice (3:1 v/v) mixed batter under optimum condition (added NaCl of 8 g/kg, 32 °C, 18 h) further reduced their levels, but total biogenic amines content was enhanced. However, optimum steaming of dal–rice mixed fermented batter for 20 min was effective in reducing all the tested antinutrients. In dhokla, the content of tannins, phytic acid and total biogenic amines reduced by 100, 94 and 20%, respectively; trypsin inhibitor and haemagglutinating activities reduced by 92 and 100%, respectively, over raw ingredients. The optimally prepared product (dhokla) ranked “excellent” in terms of overall sensory quality.
    Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses
    Velzen, R. van; Holmer, R. ; Bu, F. ; Rutten, L.J.J. ; Zeijl, A.L. van; Liu, W. ; Santuari, L. ; Cao, Q. ; Sharma, Trupti ; Shen, Defeng ; Purwana Roswanjaya, Yuda ; Wardhani, T. ; Seifi Kalhor, M. ; Jansen, Joelle ; Hoogen, D.J. van den; Güngör, Berivan ; Hartog, M.V. ; Hontelez, J. ; Verver, Jan ; Yang, Wei-Cai ; Schijlen, E.G.W.M. ; Repin, Rimi ; Schilthuizen, M. ; Schranz, M.E. ; Heidstra, R. ; Miyata, Kana ; Fedorova, E. ; Kohlen, W. ; Bisseling, A.H.J. ; Smit, S. ; Geurts, R. - \ 2018
    Proceedings of the National Academy of Sciences of the United States of America 115 (2018)20. - ISSN 0027-8424 - p. E4700 - E4709.
    Nodules harboring nitrogen-fixing rhizobia are a well-known trait of legumes, but nodules also occur in other plant lineages, with rhizobia or the actinomycete Frankia as microsymbiont. It is generally assumed that nodulation evolved independently multiple times. However, molecular-genetic support for this hypothesis is lacking, as the genetic changes underlying nodule evolution remain elusive. We conducted genetic and comparative genomics studies by using Parasponia species (Cannabaceae), the only nonlegumes that can establish nitrogen-fixing nodules with rhizobium. Intergeneric crosses between Parasponia andersonii and its nonnodulating relative Trema tomentosa demonstrated that nodule organogenesis, but not intracellular infection, is a dominant genetic trait. Comparative transcriptomics of P. andersonii and the legume Medicago truncatula revealed utilization of at least 290 orthologous symbiosis genes in nodules. Among these are key genes that, in legumes, are essential for nodulation, including NODULE INCEPTION (NIN) and RHIZOBIUM-DIRECTED POLAR GROWTH (RPG). Comparative analysis of genomes from three Parasponia species and related nonnodulating plant species show evidence of parallel loss in nonnodulating species of putative orthologs of NIN, RPG, and NOD FACTOR PERCEPTION. Parallel loss of these symbiosis genes indicates that these nonnodulating lineages lost the potential to nodulate. Taken together, our results challenge the view that nodulation evolved in parallel and raises the possibility that nodulation originated ∼100 Mya in a common ancestor of all nodulating plant species, but was subsequently lost in many descendant lineages. This will have profound implications for translational approaches aimed at engineering nitrogen-fixing nodules in crop plants.
    Genomic and physiological analyses of an indigenous strain, Enterococcus faecium 17OM39
    Ghattargi, Vikas C. ; Nimonkar, Yogesh S. ; Burse, Shaunak A. ; Davray, Dimple ; Kumbhare, Shreyas V. ; Shetty, Sudarshan A. ; Gaikwad, Meghana A. ; Suryavanshi, Mangesh V. ; Doijad, Swapnil P. ; Utage, Bhimashankar ; Sharma, Om Prakash ; Shouche, Yogesh S. ; Meti, Bharati S. ; Pawar, Shrikant P. - \ 2018
    Functional and Integrative Genomics 18 (2018)4. - ISSN 1438-793X - p. 385 - 399.
    Bile salt hydrolysis - Genome analysis - Indigenous probiotic - Probiotic genes - Serum resistance
    The human gut microbiome plays a crucial role in human health and efforts need to be done for cultivation and characterisation of bacteria with potential health benefits. Here, we isolated a bacterium from a healthy Indian adult faeces and investigated its potential as probiotic. The cultured bacterial strain 17OM39 was identified as Enterococcus faecium by 16S rRNA gene sequencing. The strain 17OM39 exhibited tolerance to acidic pH, showed antimicrobial activity and displayed strong cell surface traits such as hydrophobicity and autoaggregation capacity. The strain was able to tolerate bile salts and showed bile salt hydrolytic (BSH) activity, exopolysaccharide production and adherence to human HT-29 cell line. Importantly, partial haemolytic activity was detected and the strain was susceptible to the human serum. Genomics investigation of strain 17OM39 revealed the presence of diverse genes encoding for proteolytic enzymes, stress response systems and the ability to produce essential amino acids, vitamins and antimicrobial compound Bacteriocin-A. No virulence factors and plasmids were found in this genome of the strain 17OM39. Collectively, these physiological and genomic features of 17OM39 confirm the potential of this strain as a candidate probiotic.
    Diagnosis of management of bacterial wilt and late blight in potato in Ethiopia : A systems thinking perspective
    Damtew, E. ; Tafesse, Shiferaw ; Lie, R. ; Mierlo, B. van; Lemaga, B. ; Sharma, K. ; Struik, P.C. ; Leeuwis, C. - \ 2018
    NJAS Wageningen Journal of Life Sciences 86-87 (2018). - ISSN 1573-5214 - p. 12 - 24.
    Bacterial wilt - Complex problems - Disease management - Late blight - Potato - Systems thinking
    Potato is one of the most important food crops for smallholder farmers in the Ethiopian highlands. Diseases, particularly bacterial wilt (caused by Ralstonia solanacearum) and late blight (caused by Phytophthora infestans), are among the major constraints of potato production, despite continuous efforts to control them. Bacterial wilt and late blight are complex problems with multiple technical and institutional features, involving multiple actors with different perceptions and understanding, not only of the problem but also of possible solutions. Appreciating such complexity, this study adopted a systems thinking perspective. It aimed to explore actors’ understanding of the complex problem situation and its implication for the management of the diseases at a collective level. Using a multi-stakeholder workshop and in-depth interviews, a qualitative study was conducted with actors that are directly or indirectly involved in the management of the two diseases. Results showed that actors essentially overlooked key systemic problems in the management of the two diseases. This is mainly reflected in actors’ tendency to give event-level responses, shift responsibilities and engage in a mutual blaming to the problem of bacterial wilt and late blight. Lack of a preventive disease management culture, limited recognition of interdependencies among activities of actors, power inequalities, and top-down and linear approaches in information and knowledge sharing are identified as key structural problems that are underrated by the actors. We contend that the most appropriate way forward towards the management of both diseases is designing and implementing management strategies that, on the one hand, are preventive of disease epidemics, and, on the other hand, foster horizontal information sharing, learning and collective action among the local actors in the system. Digital platforms, particularly mobile-based technologies, can play a role in catalyzing new forms of information sharing, broader learning, and collaboration among farmers and local actors.
    Farmers’ knowledge and practices of potato disease management in Ethiopia
    Tafesse, Shiferaw ; Damtew, E. ; Mierlo, B. van; Lie, R. ; Lemaga, B. ; Sharma, K. ; Leeuwis, C. ; Struik, P.C. - \ 2018
    NJAS Wageningen Journal of Life Sciences 86–87 (2018). - ISSN 1573-5214 - p. 25 - 38.
    Bacterial wilt - Disease management - Farmers’ knowledge - Farmers’ practices - Late blight - Phytophthora infestans - Potato diseases - Ralstonia solanacearum
    Effective management of potato diseases such as bacterial wilt and late blight depends to a large extent on farmers’ knowledge of the diseases as well as on the integration of recommended management methods in their daily practices. Late blight has continued to be a dominant potato disease for many decades in Ethiopia, whereas bacterial wilt has emerged more recently with a devastating impact on the country's potato production systems. A survey of 261 randomly selected farmers was carried out in three major potato growing districts in the central highlands of Ethiopia to examine farmers’ knowledge and management practices of the two diseases, and to analyze the role of relevant knowledge in their practices. Considering their different characteristics, three groups of farmers were distinguished: producers of quality declared seed, producers of normal seed and producers of ware. The study shed light on the vital role the lack of knowledge about the diseases plays in shaping farmers’ daily potato production practices. Most farmers could recognize symptoms of the diseases on infected leaves and stems. However, they had very limited knowledge of the diseases including their causal agents, spreading mechanisms, and effective management methods, although they knew a little bit more about late blight than about bacterial wilt. Therefore, to effectively manage the diseases, farmers need to learn about the diseases and how to manage them in their local context applying a feasible combination of management options through a community-based approach. The effectivity of such an approach could be enhanced by stipulating operational standards in bylaws and through continuous monitoring of changes in farmers’ practices and environmental monitoring for disease occurrence by leveraging an interactive mobile-based platform.
    Effect of peste des petits ruminants virus (PPRV) infection on the host immune response in naturally infected goats
    Das, S. ; Choudhury, R. ; Balamurugan, V. ; Chakravarty, I. ; Devi, M. ; Bora, M. ; Sharma, K. - \ 2017
    The Indian Journal of Animal Sciences 87 (2017). - ISSN 0367-8318
    Toll like receptors (TLRs) expressed by various immune cells and tissues are known to play an important role in recognising the pathogens by the host. The study was carried out to envisage the expression of virus-recognising-TLRs like TLR-3, TLR-7 and TLR-8 as well as the Th1 and Th2 cytokines in the serum of naturally Peste des petits ruminants virus (PPRV) infected goats. Goat serum samples, collected from three districts of Asom (Kamrup, Nalbari, Darrang), were screened for Peste des petits ruminants virus (PPRV) antibody by Complementary-ELISA. Out of 227 samples screened, 72 samples showed presence of PPR viral antibody with a percentage prevalence of 31.72%. Out of the positive samples, 39 were selected randomly for testing the TLR and cytokine response after PPRV infection. The study indicated TLR-8 to have an enhanced expression in serum of PPRV infected goats along
    with IL-12 and IFN-γ of the Th1 pathway. Further, in infected group, a significant correlation was registered between IL-12 and IFN-γ. The present study showed the involvement of the Th-1 pathway in host immune response after PPRV natural infection which may help in proper disease management and control strategies.
    Parallel loss of symbiosis genes in relatives of nitrogen-fixing non-legume Parasponia
    Velzen, R. van; Holmer, R. ; Bu, F. ; Rutten, L.J.J. ; Zeijl, A.L. van; Liu, W. ; Santuari, L. ; Cao, Q. ; Sharma, Trupti ; Shen, D. ; Purwana Roswanjaya, Yuda ; Wardhani, T. ; Seifi Kalhor, M. ; Jansen, Joelle ; Hoogen, D.J. van den; Gungor, Berivan ; Hartog, M.V. ; Hontelez, J. ; Verver, J.W.G. ; Yang, W.C. ; Schijlen, E.G.W.M. ; Repin, Rimi ; Schilthuizen, M. ; Schranz, M.E. ; Heidstra, R. ; Miyata, Kana ; Fedorova, E. ; Kohlen, W. ; Bisseling, A.H.J. ; Smit, S. ; Geurts, R. - \ 2017
    BioRxiv - 88 p.
    Rhizobium nitrogen-fixing nodules are a well-known trait of legumes, but nodules also occur in other plant lineages either with rhizobium or the actinomycete Frankia as microsymbiont. The widely accepted hypothesis is that nodulation evolved independently multiple times, with only a few losses. However, insight in the evolutionary trajectory of nodulation is lacking. We conducted comparative studies using Parasponia (Cannabaceae), the only non-legume able to establish nitrogen fixing nodules with rhizobium. This revealed that Parasponia and legumes utilize a large set of orthologous symbiosis genes. Comparing genomes of Parasponia and its non-nodulating relative Trema did not reveal specific gene duplications that could explain a recent gain of nodulation in Parasponia. Rather, Trema and other non-nodulating species in the order Rosales show evidence of pseudogenization or loss of key symbiosis genes. This demonstrates that these species have lost the potential to nodulate. This finding challenges a long-standing hypothesis on evolution of nitrogen-fixing symbioses, and has profound implications for translational approaches aimed at engineering nitrogen-fixing nodules in crop plants.
    Minimization of Antinutrients in Idli by Using Response Surface Process Optimization
    Sharma, Anand ; Kumari, Sarita ; Nout, Martinus J.R. ; Sarkar, Prabir K. - \ 2017
    Journal of Food Processing and Preservation 41 (2017)5. - ISSN 0145-8892 - 13 p.

    Deploying response surface methodology, the stages of idli preparation were optimized for minimizing the level of antinutrients. Under optimum conditions of soaking blackgram dal (1:5 of dal and water at 16C, and pH 4.0 for 18 h) and rice (1:5 of rice and water at 16C, and pH 5.6 for 18 h), the tannins content, trypsin inhibitor activity and hemagglutinating activity reduced, while phytic acid content remained unchanged. The optimum conditions for fermentation of dal-rice (1:2) mixed batter were 16 g/kg common salt supplementation and 19 h at 35C, resulting in a decrease in all the antinutrient levels, except amines. Steaming for an optimized period of 20 min further reduced the phytic acid content and trypsin inhibitor activity. In idli, while total biogenic amines content increased by 339% over raw ingredients, tannins content, phytic acid content, trypsin inhibitor activity and hemagglutinating activity decreased by 100, 89, 58 and 100%, respectively. Practical Applications: For idli preparation, the optimization of processing stages using response surface methodology significantly minimized the level of antinutrients from both blackgram dal and rice without affecting the organoleptic attributes of the product. The optimized process parameters can be applied to household level and are also useful in scaling up idli production with a minimum level of antinutrients and better consumer acceptability. The outcome of this research can be exploited to other legume-based foods as well, particularly in developing regions where the consequences of antinutrients may exacerbate malnutrition and disease, thus effectively utilizing full potential of the legumes as human and animal foods.

    Increasing farmer's income and reducing soil erosion using intercropping in rainfed maize-wheat rotation of Himalaya, India
    Sharma, N.K. ; Singh, Raman Jeet ; Mandal, D. ; Kumar, Ambrish ; Alam, N.M. ; Keesstra, Saskia - \ 2017
    Agriculture, Ecosystems and Environment 247 (2017). - ISSN 0167-8809 - p. 43 - 53.
    Crop canopy of maize - Crop diversification - Runoff - Slope - Soil loss

    Humankind faces the need to achieve sustainable agriculture production, meanwhile increasing crop yields and reducing soil and water losses. Soil conservation through intercropping or crop canopy management is widely accepted as one of the ways of diversifying crop yields in rainfed agriculture in sloping landscapes. Field experiments were conducted between 2009 and 2014 to evaluate the effects of one or two rows of cowpea/okra intercropped with maize (planted either in 90 or 150 cm row spacing) on productivity, profitability, and resource conservation on 4% sloping crop land in the Himalayas. During five years of experimentation, a total of 110 runoff events were observed in the maize crop grown in rainy months of June to September. The results showed that by growing one row of cowpea in between two rows of maize (90 × 20 cm), no effect was observed on the productivity of rainfed maize. Productivity of the succeeding wheat crop was enhanced by 13% which resulted in a higher net return (117 US$ ha−1) than in a maize-wheat system. This system also reduced runoff and soil loss by 26% and 43%, respectively, compared to only a maize cropping system. Regression analysis revealed as runoff in maize crop increases, grain yield of succeeding rainfed wheat crop decreases due to the less availability of soil moisture.

    Molecular characterization of Ralstonia solanacearum strains from Ethiopia and tracing potential source of bacterial wilt disease outbreak in seed potatoes
    Abdurahman, A. ; Griffin, D. ; Elphinstone, J. ; Struik, P.C. ; Schulz, S. ; Schulte-Geldermann, E. ; Sharma, K. - \ 2017
    Plant Pathology 66 (2017)5. - ISSN 0032-0862 - p. 826 - 834.
    Ralstonia solanacearum - Molecular epidemiology - Multilocus VNTR - Seed potato
    Bacterial wilt, caused by Ralstonia solanacearum, is emerging as a major threat to potato production in Ethiopia, reaching epidemic proportions in the Chencha district recently, with a prevalence of 97% of potato fields in 2015. The recent disease outbreak in the district coincided with a significant introduction of seed potatoes. This research was therefore initiated to genetically characterize the pathogen so as to trace its source, identify its relationship with outbreaks in the rest of the country, and make intervention recommendations. Ralstonia solanacearum isolates were sampled both from seed and ware potato fields in Chencha and from seed potato fields in production regions suspected of being potential sources of the pathogen. Multiplex PCR and phylogenetic analysis of partial endoglucanase gene sequences identified all of the isolates as phylotype IIB sequevar 1. VNTR sequence analysis distinguished 11 different haplotypes, nine of which were unique to the Chencha district. However, one of the haplotypes was common to all seed potato producer regions of Ethiopia except for the Shashemene area. The unique and diverse VNTR haplotypes of the pathogen in Chencha indicates that it is well established in the district. When a geographical map of the VNTR haplotypes was superimposed with the main cross-regional seed potato distribution pattern of the country, it became evident that the pathogen was being disseminated via latently infected seed from the Holeta-Jeldu area in the Central Highlands of Ethiopia. Identification of largely uninfected highland districts and multiplication of high-grade seed potato exclusively in those districts should be given priority.
    An overview on emerging bioelectrochemical systems (BESs): Technology for sustainable electricity, waste remediation, resource recovery, chemical production and beyond
    Bajracharya, S. ; Sharma, M. ; Mohanakrishna, Gunda ; Benneton, Xochitl Dominguez ; Strik, D.P.B.T.B. ; Sarma, Priyangshu M. ; Pant, Deepak - \ 2016
    Renewable Energy 98 (2016). - ISSN 0960-1481 - p. 153 - 170.
    Recalcitrant removal - Microbial electrocatalysis - CO2 sequestration - Biosensors - Value-added chemicals production
    Bioelectrochemical systems (BESs) are unique systems capable of converting chemical energy into electrical energy (and vice-versa) while employing microbes as catalysts. Such organic wastes including low-strength wastewaters and lignocellulosic biomass were converted into electricity with microbial fuel cells (MFCs). Likewise, electrical energy was used to produce hydrogen in microbial electrolysis cells (MECs) or other products including caustic and peroxide. BES were also designed to recover nutrients, metals or removal of recalcitrant compounds. Moreover, photosynthetic micro-organisms as well as higher plants were implemented to use solar energy for electricity generation. The diversity on microbial and enzymatic catalysts offered by nature allows a plurality of potential applications. As compared to conventional fuel cells, BESs operate under relatively mild conditions and do not use expensive precious metals as catalysts. The recently discovered microbial electrosynthesis (MES) of high-value chemicals has greatly expanded the horizon for BES. Newer concepts in application as well as development of alternative materials for electrodes, separators, catalysts along with innovative designs have made BES very promising technology. This article discusses the recent developments that have been made in BESs so far, with the emphasis on their various applications beyond electricity generation and resulting performances as well as existing limitations.
    Using phenomics and genomics to unlock landrace and wild relative diversity for crop improvement
    Vosman, B. ; Pelgrom, K.T.B. ; Sharma, G. ; Voorrips, R.E. ; Broekgaarden, C. ; Pritchard, J. ; May, S. ; Adobor, S. ; Castellanos-Uribe, M. ; Kaauwen, M.P.W. van; Finkers, H.J. ; Janssen, B. ; Workum, W.T. van; Ford-Lloyd, B.V. - \ 2016
    In: Enhancing crop genepool use: capturing wild relative and landrace diversity for crop improvement / Maxted, N., Dulloo, M.E., Ford-Lloyd, B.V., CABI - ISBN 9781780646138 - p. 1 - 9.
    This chapter discusses some of the activities and achievements of the Plant Genetic Resources (PGR) Secure project, which aims to: (i) identify host plant resistance to the cabbage whitefly (Aleyrodes proletella) and cabbage aphid (Brevicoryne brassicae) via a germplasm screen where both are specialist phloem-feeding insects that feed only on members of the Brassicaceae family; (ii) elucidate the resistance mechanism; and (iii) provide tools to breeders that will facilitate resistance breeding. It is shown that the PGR Secure project has delivered valuable information on the extent of whitefly and aphid resistance in landrace accessions of Brassica oleracea var. capitata, as well as in wild relatives of B. oleracea. The whitefly resistance present in Brassica villosa, B. incana and B. montana is expressed both in 6- and 12-week-old plants, which indicates that this form of resistance is probably different from that already present in B. oleracea. These sources can be used in breeding resistant varieties. By combining novel phenomics, genomics and transcriptomics technologies, resistance breeding can be speeded up significantly. The developed and publicly available 90 k Affymetrix Axiom Brassica array can play an important role in this. The single nucleotide polymorphism markers linked to the resistance quantitative trait loci (QTLs) will facilitate an efficient introgression of the QTLs into high-yielding varieties.
    RNA interference for functional genomics and improvement of cotton (Gossypium sp.)
    Abdurakhmonov, Ibrokhim Y. ; Ayubov, Mirzakamol S. ; Ubaydullaeva, Khurshida A. ; Buriev, Zabardast T. ; Shermatov, Shukhrat E. ; Ruziboev, Haydarali S. ; Shapulatov, Umidjon ; Saha, Sukumar ; Ulloa, Mauricio ; Yu, John Z. ; Percy, Richard G. ; Devor, Eric J. ; Sharma, Govind C. ; Sripathi, Venkateswara R. ; Kumpatla, Siva P. ; Krol, Sander van der; Kater, Hake D. ; Khamidov, Khakimdjan ; Salikhov, Shavkat I. ; Jenkins, Johnie N. ; Abdukarimov, Abdusattor ; Pepper, Alan E. - \ 2016
    Frontiers in Plant Science 7 (2016)FEB2016. - ISSN 1664-462X
    Antisense - Cotton pest control - Disease resistance - Fiber quality - Gene silencing - Gossypium

    RNA interference (RNAi), is a powerful new technology in the discovery of genetic sequence functions, and has become a valuable tool for functional genomics of cotton (Gossypium sp.). The rapid adoption of RNAi has replaced previous antisense technology. RNAi has aided in the discovery of function and biological roles of many key cotton genes involved in fiber development, fertility and somatic embryogenesis, resistance to important biotic and abiotic stresses, and oil and seed quality improvements as well as the key agronomic traits including yield and maturity. Here, we have comparatively reviewed seminal research efforts in previously used antisense approaches and currently applied breakthrough RNAi studies in cotton, analyzing developed RNAi methodologies, achievements, limitations, and future needs in functional characterizations of cotton genes. We also highlighted needed efforts in the development of RNAi-based cotton cultivars, and their safety and risk assessment, small and large-scale field trials, and commercialization.

    Seed degeneration in potato: the need for an integrated seed health strategy to mitigate the problem in developing countries
    Thomas-Sharma, S. ; Abdurahman, A.A. ; Ali, S. ; Andrade-Piedra, J.L. ; Bao, S. ; Charkowski, A.O. ; Crook, D. ; Kadian, M. ; Kromann, P. ; Struik, P.C. ; Torrance, L. ; Garrett, K.A. ; Forbes, G.A. - \ 2016
    Plant Pathology 65 (2016)1. - ISSN 0032-0862 - p. 3 - 16.
    Seed potato degeneration, the reduction in yield or quality caused by an accumulation of pathogens and pests in planting material due to successive cycles of vegetative propagation, has been a long-standing production challenge for potato growers around the world. In developed countries this problem has been overcome by general access to and frequent use of seed, produced by specialized growers, that has been certified to have pathogen and pest incidence below established thresholds, often referred to as certified seed. The success of certified seed in developed countries has concentrated the research and development agenda on the establishment of similar systems in developing countries. Despite these efforts, certified seed has had little penetration into the informal seed systems currently in place in most developing countries. Small-scale farmers in these countries continue to plant seed tubers acquired through the informal seed system, i.e. produced on-farm or acquired from neighbours or local markets. Informal seed tubers frequently have poor health status, leading to significant reductions in yield and/or market value. This review emphasizes the need to refocus management efforts in developing countries on improving the health status of seed tubers in the informal system by integrating disease resistance and on-farm management tools with strategic seed replacement. This ‘integrated seed health strategy’ can also prolong the good health status of plants derived from certified seed, which would otherwise be diminished due to potential rapid infection from neighbouring fields. Knowledge gaps, development challenges and impacts of this integrated seed health strategy are discussed.
    Data from: Sex-specific effects of natural and sexual selection on the evolution of life span and ageing in Drosophila simulans
    Archer, C.R. ; Duffy, E. ; Hosken, D.J. ; Mokkonen, M. ; Okada, K. ; Oku, K. ; Sharma, M.D. ; Hunt, J. - \ 2015
    University of Exeter
    senescence - drosophila simulans - Experimental evolution - sexual conflict - evolutionary response - ageing rates - longevity
    1. Variation in the strength of age-dependent natural selection shapes differences in ageing rates across species and populations. Likewise, sexual selection can promote divergent patterns of senescence across the sexes. However, the effects of these processes on the evolution of ageing have largely been considered independently, and interactions between them are poorly understood. 2. We use experimental evolution to investigate how natural and sexual selection affect life span and ageing in Drosophila simulans. 3. Replicate populations were evolved under lifetime monogamy (relaxed sexual selection) or lifetime polyandry (elevated sexual selection) and at one of two temperatures, 25 °C (relaxed natural selection) or 27 °C (enhanced natural selection), in a fully factorial design. We measured longevity in 150 individually housed flies taken from each of three replicate populations per selection regime. 4. We found that natural and sexual selection affected the evolution of life span via sex-specific effects on different ageing parameters (ageing rate vs. baseline mortality): natural selection reduced the rate of ageing in both sexes but increased male baseline mortality, while sexual selection elevated baseline mortality in both sexes but particularly in males. 5. This means that sexual and natural selection interacted to reduce male life span but acted on female life span by independently affecting particular ageing parameters. Sex-specific effects of sexual and natural selection may help explain the diverse patterns of ageing seen in nature but complicate predictions about how ageing and life span evolve across the sexes.
    Analysis of protein-RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry
    Sharma, Kundan ; Hrle, Ajla ; Kramer, Katharina ; Sachsenberg, Timo ; Staals, Raymond H.J. ; Randau, Lennart ; Marchfelder, Anita ; Oost, John van der; Kohlbacher, Oliver ; Conti, Elena ; Urlaub, Henning - \ 2015
    Methods : a companion to Methods in enzymology 89 (2015). - ISSN 1046-2023 - p. 138 - 148.
    Cas7 - CRISPR-Cas - Mass spectrometry - Protein-RNA interactions - UV cross-linking

    Ribonucleoprotein (RNP) complexes play important roles in the cell by mediating basic cellular processes, including gene expression and its regulation. Understanding the molecular details of these processes requires the identification and characterization of protein-RNA interactions. Over the years various approaches have been used to investigate these interactions, including computational analyses to look for RNA binding domains, gel-shift mobility assays on recombinant and mutant proteins as well as co-crystallization and NMR studies for structure elucidation. Here we report a more specialized and direct approach using UV-induced cross-linking coupled with mass spectrometry. This approach permits the identification of cross-linked peptides and RNA moieties and can also pin-point exact RNA contact sites within the protein. The power of this method is illustrated by the application to different single- and multi-subunit RNP complexes belonging to the prokaryotic adaptive immune system, CRISPR-Cas (CRISPR: clustered regularly interspaced short palindromic repeats; Cas: CRISPR associated). In particular, we identified the RNA-binding sites within three Cas7 protein homologs and mapped the cross-linking results to reveal structurally conserved Cas7 - RNA binding interfaces. These results demonstrate the strong potential of UV-induced cross-linking coupled with mass spectrometry analysis to identify RNA interaction sites on the RNA binding proteins.

    Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora
    Sharma, R. ; Xia, X. ; Cano, L.M. ; Evangelisti, E. ; Kemen, E. ; Judelson, H. ; Oome, S. ; Sambles, C. ; Hoogen, D.J. van den; Kitner, M. ; Klein, J. ; Meijer, H.J.G. ; Spring, O. ; Win, J. ; Zipper, R. ; Bode, H.B. ; Govers, F. ; Kamoun, S. ; Schornack, S. ; Studholme, D.J. ; Ackerveken, G. van den; Thines, M. - \ 2015
    BMC Genomics 16 (2015). - ISSN 1471-2164 - 23 p.
    Background Downy mildews are the most speciose group of oomycetes and affect crops of great economic importance. So far, there is only a single deeply-sequenced downy mildew genome available, from Hyaloperonospora arabidopsidis. Further genomic resources for downy mildews are required to study their evolution, including pathogenicity effector proteins, such as RxLR effectors. Plasmopara halstedii is a devastating pathogen of sunflower and a potential pathosystem model to study downy mildews, as several Avr-genes and R-genes have been predicted and unlike Arabidopsis downy mildew, large quantities of almost contamination-free material can be obtained easily. Results Here a high-quality draft genome of Plasmopara halstedii is reported and analysed with respect to various aspects, including genome organisation, secondary metabolism, effector proteins and comparative genomics with other sequenced oomycetes. Interestingly, the present analyses revealed further variation of the RxLR motif, suggesting an important role of the conservation of the dEER-motif. Orthology analyses revealed the conservation of 28 RxLR-like core effectors among Phytophthora species. Only six putative RxLR-like effectors were shared by the two sequenced downy mildews, highlighting the fast and largely independent evolution of two of the three major downy mildew lineages. This is seemingly supported by phylogenomic results, in which downy mildews did not appear to be monophyletic. Conclusions The genome resource will be useful for developing markers for monitoring the pathogen population and might provide the basis for new approaches to fight Phytophthora and downy mildew pathogens by targeting core pathogenicity effectors.
    Country report INDIA - MFS II EVALUATIONS
    Lensink, R. ; Bedi, A. ; Gangopadhyay, S. ; Ghosh, N. ; Goderis, B. ; Kumar Yadav, B. ; Meesters, A. ; Prasad Mohapatra, B. ; Rao Sahib, P. ; Sethi, S. ; Sharma, P. ; Srinivasan, S. ; Klaver, D.C. ; Desalos, C.B. ; Hofstede, M. ; Wadhwa, S. ; Pandey, R. ; Madaan, A. ; Kalra, A. ; Kusters, C.S.L. ; Bhargava, S. ; Buizer, N.N. ; Kishore Das, A. ; Wilson Bhatra, R. ; Sen, P. ; Bulte, E. ; Pradhan, M. - \ 2015
    Wageningen : Centre for Development Innovation, Wageningen UR (CDI Rapporten ) - 1860
    This report on India is one of a series of evaluation reports, consisting of ten reports in total, reflecting the results of the jointly-organised MFS II evaluation: - Eight country reports (India, Bangladesh, Ethiopia, Uganda, Indonesia, DR Congo, Liberia, Pakistan); - A synthesis report (covering the eight country studies); and - A report with the results of the international lobbying and advocacy programmes. This series of reports assessed the 2011-2015 contribution of the Dutch Co-Financing System (MFS II) towards achieving the Millennium Development Goals, strengthening international civil society, setting the international agenda and changing decision-makers’ policy and practice, with the ultimate goal of reducing structural poverty. On July 2nd, 2015, the reports were approved by the independent steering committee (see below), which concluded that they meet the quality standards of validity, reliability and usefulness set by the Ministry of Foreign Affairs.
    Optimization of soybean processing into kinema, a Bacillus-fermented alkaline food, with respect to a minimum level of antinutrients
    Sharma, A. ; Kumari, S. ; Wongputtisin, P. ; Nout, M.J.R. ; Sarkar, P.K. - \ 2015
    Journal of Applied Microbiology 119 (2015)1. - ISSN 1364-5072 - p. 162 - 176.
    vitro protein digestibility - histamine-forming bacteria - unguiculata l. walp - cicer-arietinum l. - biogenic-amines - trypsin-inhibitor - phytic acid - antinutritional factors - chemical-composition - nutritional quality
    Aims Optimization of traditional processing of soybeans using response surface methodology (RSM) to achieve a minimum level of antinutritional factors (ANFs) in kinema. Methods and Results Central composite rotatable designs were used to optimize the processing stages of kinema preparation. In each stage, the linear or quadratic effects of independent variables were significant in minimizing ANF levels. The predicted optimum condition for soaking was when the raw beans–water ratio was 1 : 10, and the soaking temperature, time and pH were 10°C, 20 h and 8·0 respectively. Here, tannins content (TC), phytic acid content (PAC) and trypsin inhibitor activity (TIA) decreased (P <0·05). While haemagglutinating activity (HA) level remained unchanged (P <0·05), total biogenic amines content (TBAC) increased. The optimum condition for cooking was optimally soaked beans–water ratio of 1 : 5, and cooking pressure and time were 1·10 kg cm-2 and 20 min respectively. Here, TC, PAC, TIA and HA decreased (P <0·05), but TBAC remained unchanged compared to optimally soaked beans. TC and HA went below the level of detection. The optimum condition for fermentation was obtained when inoculum load was 103 total cells g-1 grits, and fermentation temperature and time were 37°C and 48 h respectively. Fermentation of optimally cooked beans caused a reduction (P <0·05) of PAC. While TIA remained unchanged (P <0·05), TBAC increased. In kinema, TC, PAC, TIA and HA decreased (P <0·05) over raw beans by 100, 61, 71 and 100% respectively. Good agreement was observed between predicted values and experimental values. Conclusions The processing treatments significantly minimized the level of ANFs in soybeans. Significance and Impact of the Study RSM was successfully deployed to obtain the optimum condition for kinema-making with a minimum level of ANFs without impairing sensory attributes of the product. The results are useful for commercial production of kinema.
    Sex-specific effects of natural and sexual selection on the evolution of life span and ageing in Drosophila simulans
    Archer, C.R. ; Duffy, E. ; Hosken, D.J. ; Mokkonen, M. ; Okada, K. ; Oku, K. ; Sharma, M.D. ; Hunt, J. - \ 2015
    Functional Ecology 29 (2015)4. - ISSN 0269-8463 - p. 562 - 569.
    extrinsic mortality - oxidative stress - female fitness - history traits - male-sterility - seed beetle - senescence - melanogaster - age - populations
    1. Variation in the strength of age-dependent natural selection shapes differences in ageing rates across species and populations. Likewise, sexual selection can promote divergent patterns of senescence across the sexes. However, the effects of these processes on the evolution of ageing have largely been considered independently, and interactions between them are poorly understood. 2. We use experimental evolution to investigate how natural and sexual selection affect life span and ageing in Drosophila simulans. 3. Replicate populations were evolved under lifetime monogamy (relaxed sexual selection) or lifetime polyandry (elevated sexual selection) and at one of two temperatures, 25 °C (relaxed natural selection) or 27 °C (enhanced natural selection), in a fully factorial design. We measured longevity in 150 individually housed flies taken from each of three replicate populations per selection regime. 4. We found that natural and sexual selection affected the evolution of life span via sex-specific effects on different ageing parameters (ageing rate vs. baseline mortality): natural selection reduced the rate of ageing in both sexes but increased male baseline mortality, while sexual selection elevated baseline mortality in both sexes but particularly in males. 5. This means that sexual and natural selection interacted to reduce male life span but acted on female life span by independently affecting particular ageing parameters. Sex-specific effects of sexual and natural selection may help explain the diverse patterns of ageing seen in nature but complicate predictions about how ageing and life span evolve across the sexes.
    Phenomics and genomics tools for facilitating brassica crop improvement
    Vosman, B.J. ; Pelgrom, K.T.B. ; Sharma, G. ; Voorrips, R.E. ; Broekgaarden, C. ; Pritchard, J. ; May, S. ; Adobor, S. ; Castellanos-Uribe, M. ; Kaauwen, M.P.W. van; Janssen, B. ; Workum, W. van; Ford-Lloyd, B. - \ 2015
    Crop Wild Relative 10 (2015). - ISSN 1742-3627 - p. 12 - 14.
    Soil health indicators and Fusarium wilt suppression in organically managed greenhouse soils
    Bruggen, A.H.C. van; Sharma, K. ; Kaku, E. ; Karfopoulos, S. ; Zelenev, V.V. ; Blok, W.J. - \ 2015
    Applied Soil Ecology 86 (2015). - ISSN 0929-1393 - p. 192 - 201.
    gradient gel-electrophoresis - escherichia-coli o157-h7 - wave-like dynamics - 16s ribosomal-rna - bacterial-populations - microbial-populations - pythium-ultimum - nutrient input - wheat roots - corky root
    Soil health has been associated with internal cycling of nutrients, microbial activity and diversity as well as root disease suppression, which are frequently greater in organically than in conventionally managed soils. Resistance and resilience, measured as amplitude and frequency of oscillations in bacterial communities after a disturbance, were suggested as integral indicators of soil health, but until now there is little proof for this hypothesis. In this study, resistance and resilience of microbial communities and 24 soil chemical and biological parameters were analyzed and correlated to suppression of flax wilt (caused by Fusarium oxysporum f.sp. lini) in three experiments. Soil samples were collected on three different dates from a recently converted organic greenhouse and a similar, neighboring greenhouse under conventional management. The dynamics of copiotrophic and oligotrophic bacteria after a disturbance were monitored, and the resistance and resilience were calculated. The organic soil showed significantly higher water-holding capacity, organic matter content, total C and N contents, C: N ratio of the small particulate organic matter fraction, microbial biomass carbon, oxygen uptake rate, copiotrophic and oligotrophic bacterial communities and suppression of flax wilt incidence. After incorporation of a grass-clover mixture in both soils, the densities of copiotrophic and oligotrophic bacteria oscillated over time. The relative amplitudes of the oscillations (in grass-clover amended over non- amended soil) and the frequencies of the oscillations of both trophic groups were lower for the organic soil, indicating that the resistance and resilience of the microbial community were greater in this soil. These results support the hypothesis that the bacterial response to a disturbance can serve as an integral indicator for soil health, including disease suppressiveness. (C) 2014 Elsevier B.V. All rights reserved.
    Interpreting characteristic drainage timescale variability across Kilombero Valley, Tanzania
    Lyon, S.W. ; Koutsouris, A. ; Scheibler, F. ; Jarsjö, J. ; Mbanguka, R. ; Tumbo, M. ; Robert, K.K. ; Sharma, A.N. ; Velde, Y. van der - \ 2015
    Hydrological Processes 29 (2015)8. - ISSN 0885-6087 - p. 1912 - 1924.
    blue nile - base-flow - ethiopia - soil - runoff - event - model
    We explore seasonal variability and spatiotemporal patterns in characteristic drainage timescale (K) estimated from river discharge records across the Kilombero Valley in central Tanzania. K values were determined using streamflow recession analysis with a Brutsaert–Nieber solution to the linearized Boussinesq equation. Estimated K values were variable, comparing between wet and dry seasons for the relatively small catchments draining upland positions. For the larger catchments draining through valley bottoms, K values were typically longer and more consistent across seasons. Variations in K were compared with long-term averaged, Moderate-resolution Imaging Spectroradiometer-derived monthly evapotranspiration. Although the variations in K were potentially related to evapotranspiration, the influence of data quality and analysis procedure could not be discounted. As such, even though recession analysis offers a potential approach to explore aquifer release timescales and thereby gain insight to a region's hydrology to inform water resources management, care must be taken when interpreting spatiotemporal shifts in K in connection with process representation in regions like the Kilombero Valley.
    The iodized salt programme in Bangalore, India provides adequate iodine intakes in pregnant women and more-than-adequate iodine intakes in their children
    Jaiswal, N. ; Boonstra, A. ; Sharma, S.K. ; Srinivasan, K. ; Zimmerman, M.B. - \ 2015
    Public Health Nutrition 18 (2015)3. - ISSN 1368-9800 - p. 403 - 413.
    school-aged children - urinary iodine - dietary iodine - deficiency - iodization - fortification - excretion - bread - nutrition - rajasthan
    Objective To compare the iodine status of pregnant women and their children who were sharing all meals in Bangalore, India. Design A cross-sectional study evaluating demographic characteristics, household salt iodine concentration and salt usage patterns, urinary iodine concentrations (UIC) in women and children, and maternal thyroid volume (ultrasound). Setting Antenatal clinic of an urban tertiary-care hospital, which serves a low-income population. Subjects Healthy pregnant women in all trimesters, aged 18–35 years, who had healthy children aged 3–15 years. Results Median (range) iodine concentrations of household powdered and crystal salt were 55·9 (17·2–65·9) ppm and 18·9 (2·2–68·2) ppm, respectively. The contribution of iodine-containing supplements and multi-micronutrient powders to iodine intake in the families was negligible. Adequately iodized salt, together with small amounts of iodine in local foods, were providing adequate iodine during pregnancy: (i) the overall median (range) UIC in women was 172 (5–1024) µg/l; (ii) the median UIC was >150 µg/l in all trimesters; and (iii) thyroid size was not significantly different across trimesters. At the same time, the median (range) UIC in children was 220 (10–782) µg/l, indicating more-than-adequate iodine intake at this age. Median UIC was significantly higher in children than in their mothers (P=0·008). Conclusions In this selected urban population of southern India, the iodized salt programme provides adequate iodine to women throughout pregnancy, at the expense of higher iodine intake in their children. Thus we suggest that the current cut-off for median UIC in children indicating more-than-adequate intake, recommended by the WHO/UNICEF/International Council for the Control of Iodine Deficiency Disorders may, need to be reconsidered.
    RNA-targeting by the Type III-A CRISPR-Cas complex of Thermus thermophilus
    Staals, R.H.J. ; Zhu, Y. ; Taylor, D.W. ; Kornfeld, J.E. ; Sharma, K. ; Barendregt, A. ; Koehorst, J.J. ; Vlot, M. ; Neupane, N. ; Varossieau, K. ; Sakamoto, K. ; Suzuki, T. ; Schaap, P.J. ; Urlaub, H. ; Heck, A.J.R. ; Nogales, E. ; Doudna, J.A. ; Shinkai, A. ; Oost, J. van der - \ 2014
    Wageningen University
    PRJEB7461 - ERP007191
    crRNAs from the Thermus thermophilus CRISPR-Cas Csm complex
    A critical revisit of the key parameters used to describe microbial electrochemical systems
    Sharma, M. ; Bajracharya, S. ; Gildemyn, S. ; Patil, S.A. ; Alvarez-Gallego, Y. ; Pant, D. ; Rabaey, K. ; Dominguez-Benetton, X. - \ 2014
    Electrochimica Acta 140 (2014). - ISSN 0013-4686 - p. 191 - 208.
    extracellular electron-transfer - cathodic oxygen reduction - stainless-steel cathodes - waste-water treatment - fuel-cells - geobacter-sulfurreducens - bioelectrochemical systems - electricity-generation - power-generation - hydrogen-production
    Many microorganisms have the innate capability to discharge and/or receive electrons to and from solid state materials such as electrodes. This ability is now used towards innovative processes in wastewater treatment, power generation, production of fuels and biochemicals, bioremediation, desalination and resource recovery, among others. Despite being a dynamic field in science and technology, significant challenges remain towards industrial implementation which include representation of judicious performance indicators. This critical review outlines the progress in current density evaluated per projected surface area of electrodes, the most wide-spread performance indicator. It also proposes guidelines to correct current and exchange current per porous surface area, biofilm covered area, electrochemically- or bioelectrochemically- active surface area, of the electrodes. Recommendations for indicators to describe the environmental and electrochemical robustness of electrochemically-active biofilms are portrayed, including preservation of the predominant functionality as well as electrochemical mechanistic and phenomenological features. A few additional key elements for industrial processing are depicted. Whereas Microbial Fuel Cells (MFCs) are the main focus, some important parameters for reporting on cathodic bioproduction performance are also discussed. This critical revision aims to provide key parameters to compare the whole spectrum of microbial electrochemical systems in a consistent way. (C) 2014 Elsevier Ltd. All rights reserved.
    High Prevalence of Maternal Hypothyroidism Despite Adequate Iodine Status in Indian Pregnant Woman in the First Trimester
    Jaiswal, N. ; Boonstra, A. ; Thomas, T. ; Basavaraj, C. ; Sharma, S.K. ; Srinivasan, K. ; Zimmerman, M.B. - \ 2014
    Thyroid 24 (2014)9. - ISSN 1050-7256 - p. 1419 - 1429.
    school-age-children - thyroid-function - free-thyroxine - subclinical hypothyroidism - urinary iodine - deficiency - risk - postpartum - iron - dysfunction
    Background: Iodine requirements are increased during pregnancy to maintain maternal and fetal euthyroidism. There have been recent improvements in iodized salt coverage in India, but whether iodized salt is sufficient to sustain iodine requirements during pregnancy remains uncertain. Our aims were to measure thyroid status in first trimester pregnant women in southern India and assess potential determinants of thyroid function, including iodine status, thyroid autoimmunity, dietary patterns, body weight, and anemia. Methods: This was a cross-sectional study among 334 pregnant women of =14 weeks' gestation, in Bangalore, India. We measured anthropometrics, urinary iodine concentration (UIC), maternal thyroid volume (by ultrasound), and thyroid function. We applied a thyrotropin (TSH) upper limit of 2.5¿mIU/L to classify thyroid insufficiency. Using a questionnaire, we obtained sociodemographic and dietary data, obstetric history, and use of iodized salt and iodine supplements. Results: Among the women, the mean (standard deviation) gestational age was 10.3 (2.5) weeks, 67% were nulliparous, 21% were vegetarian, 19% were anemic, and 23% were overweight or obese. Iodized salt was used by 98% of women, and they were iodine sufficient: median UIC (range) was 184.2¿µg/L (8.1–1152¿µg/L) and all had a normal thyroid volume. However, 18% of the women had thyroid insufficiency: 3.7% had overt hypothyroidism (83% with positive TPO-Ab), 9.2% had subclinical hypothyroidism, and 5.2% had hypothyroxinemia. Women consuming vegetarian diets did not have significantly lower iodine intakes or higher risk of hypothyroidism than those consuming mixed diets, but overweight/obesity and anemia predicted thyroid insufficiency. Conclusion: In this urban population of southern India, pregnant women have adequate iodine status in the first trimester. Despite this, many have thyroid insufficiency, and the prevalence of overt hypothyroidism is more than fivefold higher than reported in other iodine sufficient populations of pregnant women.
    RNA Targeting by the Type III-A CRISPR-Cas Csm Complex of Thermus thermophilus
    Staals, R.H.J. ; Zhu, Y. ; Taylor, D.W. ; Kornfeld, J.E. ; Sharma, K. ; Barendregt, A. ; Koehorst, J.J. ; Vlot, M. ; Neupane, N. ; Varossieau, K. ; Sakamoto, K. ; Suzuki, T. ; Schaap, P.J. ; Urlaub, H. ; Heck, A.J.R. ; Nogales, E. ; Doudna, J.A. ; Shinkai, A. ; Oost, J. van der - \ 2014
    Molecular Cell 56 (2014)4. - ISSN 1097-2765 - p. 518 - 530.
    guided surveillance complex - bacterial immune-system - adaptive immunity - mass-spectrometry - crystal-structure - escherichia-coli - haloferax-volcanii - antiviral defense - seed sequence - protein
    CRISPR-Cas is a prokaryotic adaptive immune system that provides sequence-specific defense against foreign nucleic acids. Here we report the structure and function of the effector complex of the Type III-A CRISPR-Cas system of Thermus thermophilus: the Csm complex (TtCsm). TtCsm is composed of five different protein subunits (Csm1–Csm5) with an uneven stoichiometry and a single crRNA of variable size (35–53 nt). The TtCsm crRNA content is similar to the Type III-B Cmr complex, indicating that crRNAs are shared among different subtypes. A negative stain EM structure of the TtCsm complex exhibits the characteristic architecture of Type I and Type III CRISPR-associated ribonucleoprotein complexes. crRNA-protein crosslinking studies show extensive contacts between the Csm3 backbone and the bound crRNA. We show that, like TtCmr, TtCsm cleaves complementary target RNAs at multiple sites. Unlike Type I complexes, interference by TtCsm does not proceed via initial base pairing by a seed sequence.
    Citizen science in hydrology and waterresources: opportunities for knowledge generation, ecosystem service management, and sustainable development
    Buytaert, W. ; Zulkafi, Z. ; Grainger, S. ; Acosta, L. ; Alemie, T.C. ; Bastiaensen, J. ; Bièvre, B. de; Bhusal, J. ; Clark, J. ; Dewulf, A.R.P.J. ; Foggin, M. ; Hannah, D.M. ; Hergarten, C. ; Isaeva, A. ; Karpouzoglou, T.D. ; Pandeya, B. ; Paudel, D. ; Sharma, K. ; Steenhuis, T.S. ; Tilahun, S. ; Hecken, G. van; Zhumanova, M. - \ 2014
    Frontiers in Earth Science 2 (2014). - ISSN 2296-6463 - 21
    klimaatverandering - gegevensverwerking - gegevensanalyse - burgers - publieke participatie - climatic change - data processing - data analysis - citizens - public participation
    The participation of the general public in the research design, data collection and interpretation process together with scientists is often referred to as citizen science. While citizen science itself has existed since the start of scientific practice, developments in sensing technology, data processing and visualization, and communication of ideas and results, are creating a wide range of new opportunities for public participation in scientific research. This paper reviews the state of citizen science in a hydrological context and explores the potential of citizen science to complement more traditional ways of scientific data collection and knowledge generation for hydrological sciences and water resources management. Although hydrological data collection often involves advanced technology, the advent of robust, cheap, and low-maintenance sensing equipment provides unprecedented opportunities for data collection in a citizen science context. These data have a significant potential to create new hydrological knowledge, especially in relation to the characterization of process heterogeneity, remote regions, and human impacts on the water cycle. However, the nature and quality of data collected in citizen science experiments is potentially very different from those of traditional monitoring networks. This poses challenges in terms of their processing, interpretation, and use, especially with regard to assimilation of traditional knowledge, the quantification of uncertainties, and their role in decision support. It also requires care in designing citizen science projects such that the generated data complement optimally other available knowledge. Lastly, using 4 case studies from remote mountain regions we reflect on the challenges and opportunities in the integration of hydrologically-oriented citizen science in water resources management, the role of scientific knowledge in the decision-making process, and the potential contestation to established community institutions posed by co-generation of new knowledge.
    Induction and suppression of tick cell antiviral RNAi responses by tick-borne flaviviruses
    Schnettler, E. ; Tykalova, H. ; Watson, M. ; Sharma, M. ; Sterken, M.G. ; Obbard, D.J. ; Lewis, S.H. ; McFarlane, M. ; Bell-Sakyi, L. ; Barry, G. ; Weisheit, S. ; Best, S.M. ; Kuhn, R.J. ; Pijlman, G.P. ; Chase-Topping, M.E. ; Gould, E.A. ; Grubhoffer, L. ; Fazakerley, J.K. ; Kohl, A. - \ 2014
    Nucleic acids research 42 (2014)14. - ISSN 0305-1048 - p. 9436 - 9446.
    forest-virus replicon - interferon antagonist - arbovirus infection - immunity - replication - drosophila - identification - alphavirus - mosquitos - origin
    Arboviruses are transmitted by distantly related arthropod vectors such as mosquitoes (class Insecta) and ticks (class Arachnida). RNA interference (RNAi) is the major antiviral mechanism in arthropods against arboviruses. Unlike in mosquitoes, tick antiviral RNAi is not understood, although this information is important to compare arbovirus/host interactions in different classes of arbovirus vectos. Using an Ixodes scapularis-derived cell line, key Argonaute proteins involved in RNAi and the response against tick-borne Langat virus (Flaviviridae) replication were identified and phylogenetic relationships characterized. Analysis of small RNAs in infected cells showed the production of virus-derived small interfering RNAs (viRNAs), which are key molecules of the antiviral RNAi response. Importantly, viRNAs were longer (22 nucleotides) than those from other arbovirus vectors and mapped at highest frequency to the termini of the viral genome, as opposed to mosquito-borne flaviviruses. Moreover, tick-borne flaviviruses expressed subgenomic flavivirus RNAs that interfere with tick RNAi. Our results characterize the antiviral RNAi response in tick cells including phylogenetic analysis of genes encoding antiviral proteins, and viral interference with this pathway. This shows important differences in antiviral RNAi between the two major classes of arbovirus vectors, and our data broadens our understanding of arthropod antiviral RNAi.
    Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus
    Lin, K. ; Limpens, E.H.M. ; Zhang, Z. ; Ivanov, S. ; Saunders, D.G.O. ; Mu, D. ; Pang, E. ; Cao, H. ; Cha, H. ; Lin, T. ; Zhou, Q. ; Shang, Y. ; Li, Y. ; Sharma, T.C. ; Velzen, R. van; Ruijter, N.C.A. de; Aanen, D.K. ; Win, J. ; Kamoun, S. ; Bisseling, T. ; Geurts, R. ; Huang, S.W. - \ 2014
    Plos Genetics 10 (2014)1. - ISSN 1553-7404 - 13 p.
    arbuscular mycorrhizal fungi - pathogen phytophthora-infestans - glomus-intraradices - sexual reproduction - protein families - cdna sequences - kingdom fungi - gene - identification - efficient
    Nuclei of arbuscular endomycorrhizal fungi have been described as highly diverse due to their asexual nature and absence of a single cell stage with only one nucleus. This has raised fundamental questions concerning speciation, selection and transmission of the genetic make-up to next generations. Although this concept has become textbook knowledge, it is only based on studying a few loci, including 45S rDNA. To provide a more comprehensive insight into the genetic makeup of arbuscular endomycorrhizal fungi, we applied de novo genome sequencing of individual nuclei of Rhizophagus irregularis. This revealed a surprisingly low level of polymorphism between nuclei. In contrast, within a nucleus, the 45S rDNA repeat unit turned out to be highly diverged. This finding demystifies a long-lasting hypothesis on the complex genetic makeup of arbuscular endomycorrhizal fungi. Subsequent genome assembly resulted in the first draft reference genome sequence of an arbuscular endomycorrhizal fungus. Its length is 141 Mbps, representing over 27,000 protein-coding gene models. We used the genomic sequence to reinvestigate the phylogenetic relationships of Rhizophagus irregularis with other fungal phyla. This unambiguously demonstrated that Glomeromycota are more closely related to Mucoromycotina than to its postulated sister Dikarya.
    Diversity of Global Rice Markets and the Science Required for Consumer-Targeted Rice Breeding
    Calingacion, M.N. ; Laborte, A.G. ; Nelson, A. ; Resurreccion, A. ; Chrystal Concepcion, J. ; Dara Daygon, V. ; Mumm, R. ; Reinke, R. ; Dipti, S. ; Zaczuk Bassinello, P. ; Manful, J. ; Sophany, S. ; Cordero Lara, K. ; Bao, J. ; Xie, L. ; Loaiza, K. ; El-hissewy, A. ; Gayin, J. ; Sharma, N. ; Rajeswari, S. ; Manonmani, S. ; Shobha Rani, N. ; Kota, S. ; Dewi Indrasari, S. ; Habibi, F. ; Hosseini, M. ; Tavasoli, F. ; Suzuki, K. ; Umemoto, T. ; Boualaphanh, C. ; Hong Lee, H. ; Pang Hung, Y. ; Ramli, A. ; Pa Aung, P. ; Ahmad, R. ; Iqbal Wattoo, J. ; Bandonill, E. ; Romero, M. ; Moita Brites, C. ; Hafeel, R. ; Sheng Lur, H. ; Cheaupun, K. ; Jongdee, S. ; Blanco, P. ; Bryant, R. ; Thi Lang, N. ; Hall, R.D. - \ 2014
    PLoS ONE 9 (2014)1. - ISSN 1932-6203 - 12 p.
    single-nucleotide polymorphisms - oryza-sativa l. - starch-synthase-iia - grain length - gelatinization temperature - gel consistency - eating quality - gene - gs3 - association
    With the ever-increasing global demand for high quality rice in both local production regions and with Western consumers, we have a strong desire to understand better the importance of the different traits that make up the quality of the rice grain and obtain a full picture of rice quality demographics. Rice is by no means a ‘one size fits all’ crop. Regional preferences are not only striking, they drive the market and hence are of major economic importance in any rice breeding / improvement strategy. In this analysis, we have engaged local experts across the world to perform a full assessment of all the major rice quality trait characteristics and importantly, to determine how these are combined in the most preferred varieties for each of their regions. Physical as well as biochemical characteristics have been monitored and this has resulted in the identification of no less than 18 quality trait combinations. This complexity immediately reveals the extent of the specificity of consumer preference. Nevertheless, further assessment of these combinations at the variety level reveals that several groups still comprise varieties which consumers can readily identify as being different. This emphasises the shortcomings in the current tools we have available to assess rice quality and raises the issue of how we might correct for this in the future. Only with additional tools and research will we be able to define directed strategies for rice breeding which are able to combine important agronomic features with the demands of local consumers for specific quality attributes and hence, design new, improved crop varieties which will be awarded success in the global market.
    The role of the potato (Solanum tuberosum) CCD8 gene in stolon and tuber development
    Pasare, S.A. ; Ducreux, L.J.M. ; Morris, W.L. ; Campbell, R. ; Sharma, S.K. ; Roumeliotis, E. ; Kohlen, W. ; Krol, A.R. van der; Bramley, P.M. ; Roberts, A.G. ; Fraser, P.D. ; Taylor, M.A. - \ 2013
    New Phytologist 198 (2013)4. - ISSN 0028-646X - p. 1108 - 1120.
    striga-lutea lour - apical-dominance - strigolactone biosynthesis - pisum-sativum - germination stimulants - plant architecture - acts downstream - auxin transport - bud outgrowth - beta-carotene
    Strigolactones (SLs) are a class of phytohormones controlling shoot branching. In potato (Solanum tuberosum), tubers develop from underground stolons, diageotropic stems which originate from basal stem nodes. As the degree of stolon branching influences the number and size distribution of tubers, it was considered timely to investigate the effects of SL production on potato development and tuber life cycle. Transgenic potato plants were generated in which the CAROTENOID CLEAVAGE DIOXYGENASE8 (CCD8) gene, key in the SL biosynthetic pathway, was silenced by RNA interference (RNAi). The resulting CCD8-RNAi potato plants showed significantly more lateral and main branches than control plants, reduced stolon formation, together with a dwarfing phenotype and a lack of flowering in the most severely affected lines. New tubers were formed from sessile buds of the mother tubers. The apical buds of newly formed transgenic tubers grew out as shoots when exposed to light. In addition, we found that CCD8 transcript levels were rapidly downregulated in tuber buds by the application of sprout-inducing treatments. These results suggest that SLs could have an effect, solely or in combination with other phytohormones, in the morphology of potato plants and also in controlling stolon development and maintaining tuber dormancy.
    Local differentiation amidst extensive allele sharing in Oryza nivara and O. rufipogon
    Banaticla-Hilario, M.C.N. ; Berg, R.G. van den; Hamilton, N.R.S. ; McNally, K.L. - \ 2013
    Ecology and Evolution 3 (2013)9. - ISSN 2045-7758 - p. 3047 - 3062.
    asian wild-rice - multilocus genotype data - cultivated rice - population-structure - genetic-structure - phylogenetic analysis - evolutionary relationships - insertion-polymorphism - island populations - species cohesion
    Genetic variation patterns within and between species may change along geographic gradients and at different spatial scales. This was revealed by microsatellite data at 29 loci obtained from 119 accessions of three Oryza series Sativae species in Asia Pacific: Oryza nivara Sharma and Shastry, O. rufipogon Griff., and O. meridionalis Ng. Genetic similarities between O. nivara and O. rufipogon across their distribution are evident in the clustering and ordination results and in the large proportion of shared alleles between these taxa. However, local-level species separation is recognized by Bayesian clustering and neighbor-joining analyses. At the regional scale, the two species seem more differentiated in South Asia than in Southeast Asia as revealed by F-ST analysis. The presence of strong gene flow barriers in smaller spatial units is also suggested in the analysis of molecular variance (AMOVA) results where 64% of the genetic variation is contained among populations (as compared to 26% within populations and 10% among species). Oryza nivara (H-E = 0.67) exhibits slightly lower diversity and greater population differentiation than O. rufipogon (H-E = 0.70). Bayesian inference identified four, and at a finer structural level eight, genetically distinct population groups that correspond to geographic populations within the three taxa. Oryza meridionalis and the Nepalese O. nivara seemed diverged from all the population groups of the series, whereas the Australasian O. rufipogon appeared distinct from the rest of the species.
    Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps
    Sharma, S.K. ; Bolser, D. ; Boer, J.M. de; Visser, R.G.F. ; Bachem, C.W.B. - \ 2013
    G3 : Genes Genomes Genetics 3 (2013)11. - ISSN 2160-1836 - p. 2031 - 2047.
    tomato genome - sequence - dna - microsatellites - identification - centromeres - solanaceae - evolution
    The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new STS marker based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished using a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new ~936 cM linkage map comprising 2,469 marker loci. In silico anchoring approaches employed genetic and physical maps from the diploid potato genotype RH and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (~93%) of the 723 Mb genome assembly and 37,482 (~96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules is closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal 'pseudomolecules'.
    Comparative analysis of ESBL-positive Escherichia coli isolates from animals and humans from the UK, The Netherlands and Germany
    Wu, G. ; Day, M.J. ; Mafura, T. ; Nunez-Garcia, J. ; Fenner, J.J. ; Sharma, M. ; Essen-Zandbergen, A. van; Rodriguez, I. ; Dierikx, C.M. ; Mevius, D.J. - \ 2013
    PLoS ONE 8 (2013)9. - ISSN 1932-6203 - 10 p.
    spectrum-beta-lactamase - calgary health region - extended-spectrum - ctx-m - companion animals - poultry products - public-health - resistance - strains - genes
    The putative virulence and antimicrobial resistance gene contents of extended spectrum ß-lactamase (ESBL)-positive E. coli (n=629) isolated between 2005 and 2009 from humans, animals and animal food products in Germany, The Netherlands and the UK were compared using a microarray approach to test the suitability of this approach with regard to determining their similarities. A selection of isolates (n=313) were also analysed by multilocus sequence typing (MLST). Isolates harbouring blaCTX-M-group-1 dominated (66%, n=418) and originated from both animals and cases of human infections in all three countries; 23% (n=144) of all isolates contained both blaCTX-M-group-1 and blaOXA-1-like genes, predominantly from humans (n=127) and UK cattle (n=15). The antimicrobial resistance and virulence gene profiles of this collection of isolates were highly diverse. A substantial number of human isolates (32%, n=87) did not share more than 40% similarity (based on the Jaccard coefficient) with animal isolates. A further 43% of human isolates from the three countries (n=117) were at least 40% similar to each other and to five isolates from UK cattle and one each from Dutch chicken meat and a German dog; the members of this group usually harboured genes such as mph(A), mrx, aac(6’)-Ib, catB3, blaOXA-1-like and blaCTX-M-group-1. forty-four per cent of the MLST-typed isolates in this group belonged to ST131 (n=18) and 22% to ST405 (n=9), all from humans. Among animal isolates subjected to MLST (n=258), only 1.2% (n=3) were more than 70% similar to human isolates in gene profiles and shared the same MLST clonal complex with the corresponding human isolates. The results suggest that minimising human-to-human transmission is essential to control the spread of ESBL-positive E. coli in humans.
    Crossability patterns in Asia Pacific Oryza series Sativae
    Banaticla-Hilario, M.C.N. ; Sackville Hamilton, R. ; Berg, R.G. van den; McNally, K.L. - \ 2013
    Genetic Resources and Crop Evolution 60 (2013)6. - ISSN 0925-9864 - p. 1899 - 1914.
    reproductive isolation - rice oryza - wild-rice - genome - hybridization - evolution - speciation - diversity - rufipogon - differentiation
    Reproductive barriers are thought to intensify with increasing genetic distance between species. To assess the extent of post-pollination reproductive isolation within and among the Asia Pacific species of Oryza series Sativae, crossing experiments using 15 accessions of O. meridionalis Ng, O. nivara Sharma et Shastry, and O. rufipogon Griff. were conducted. Intra- and interspecific crosses of the selfing species O. meridionalis and O. nivara had very low seed set and produced inviable F1 seeds indicative of strong pre- and post-zygotic barriers. Contrastingly, the outcrossing O. rufipogon exhibited high intraspecific crossability and modest compatibility with O. nivara and O. meridionalis in terms of seed set suggesting substantial pre-zygotic reproductive isolation of the species. O. rufipogon was asymmetrically compatible with O. meridionalis and symmetrically with O. nivara. The two inbreeding species manifested comparable degrees of isolation from O. rufipogon despite differences in strength of several post-zygotic barriers. Mating compatibility within and between the Asia Pacific species of Oryza series Sativae is not strongly spatially influenced, but some resistance to gene flow under sympatric conditions was observed. Intraspecific O. rufipogon F1s were more vegetatively robust and more late-flowering than their parents. Intra- and interspecific hybrids of Australasian O. rufipogon differed phenotypically from crosses with non-Australasian populations. Interspecific hybrids displayed both intermediate and parental character traits. O. nivara and O. rufipogon generated early-flowering F1s that are more similar to the former. O. meridionalis and O. rufipogon produced F1s that varied in phenology and morphology depending on the maternal and paternal species.
    Looking for resistance to phloem feeders in Brassica olerace
    Pelgrom, K.T.B. ; Sharma, G. ; Broekgaarden, C. ; Voorrips, R. ; Bas, N. ; Pritchard, J. ; Ford-Lloyd, B. ; Vosman, B. - \ 2012
    Crop Wild Relative 8 (2012). - ISSN 1742-3627 - p. 12 - 14.
    Genome-wide association studies for Agronomical Traits in a world wide Spring Barley Collection
    Pasam, R.K. ; Sharma, R. ; Malosetti, M. ; Eeuwijk, F.A. van; Haseneyer, G. ; Kilian, B. ; Graner, A. - \ 2012
    BMC Plant Biology 12 (2012). - ISSN 1471-2229
    multilocus genotype data - hordeum-vulgare l. - linkage disequilibrium - population-structure - complex traits - flowering time - qtl analysis - missing heritability - haplotype structure - genetic diversity
    Background Genome-wide association studies (GWAS) based on linkage disequilibrium (LD) provide a promising tool for the detection and fine mapping of quantitative trait loci (QTL) underlying complex agronomic traits. In this study we explored the genetic basis of variation for the traits heading date, plant height, thousand grain weight, starch content and crude protein content in a diverse collection of 224 spring barleys of worldwide origin. The whole panel was genotyped with a customized oligonucleotide pool assay containing 1536 SNPs using Illumina's GoldenGate technology resulting in 957 successful SNPs covering all chromosomes. The morphological trait "row type" (two-rowed spike vs. six-rowed spike) was used to confirm the high level of selectivity and sensitivity of the approach. This study describes the detection of QTL for the above mentioned agronomic traits by GWAS. Results Population structure in the panel was investigated by various methods and six subgroups that are mainly based on their spike morphology and region of origin. We explored the patterns of linkage disequilibrium (LD) among the whole panel for all seven barley chromosomes. Average LD was observed to decay below a critical level (r2-value 0.2) within a map distance of 5-10 cM. Phenotypic variation within the panel was reasonably large for all the traits. The heritabilities calculated for each trait over multi-environment experiments ranged between 0.90-0.95. Different statistical models were tested to control spurious LD caused by population structure and to calculate the P-value of marker-trait associations. Using a mixed linear model with kinship for controlling spurious LD effects, we found a total of 171 significant marker trait associations, which delineate into 107 QTL regions. Across all traits these can be grouped into 57 novel QTL and 50 QTL that are congruent with previously mapped QTL positions. Conclusions Our results demonstrate that the described diverse barley panel can be efficiently used for GWAS of various quantitative traits, provided that population structure is appropriately taken into account. The observed significant marker trait associations provide a refined insight into the genetic architecture of important agronomic traits in barley. However, individual QTL account only for a small portion of phenotypic variation, which may be due to insufficient marker coverage and/or the elimination of rare alleles prior to analysis. The fact that the combined SNP effects fall short of explaining the complete phenotypic variance may support the hypothesis that the expression of a quantitative trait is caused by a large number of very small effects that escape detection. Notwithstanding these limitations, the integration of GWAS with biparental linkage mapping and an ever increasing body of genomic sequence information will facilitate the systematic isolation of agronomically important genes and subsequent analysis of their allelic diversity
    Modeling for conjuctive use irrigation planning in sodic groundwater areas
    Kaledhonkar, M.J. ; Sharma, D.R. ; Tyagi, N.K. ; Kumar, A. ; Zee, S.E.A.T.M. van der - \ 2012
    Agricultural Water Management 107 (2012). - ISSN 0378-3774 - p. 14 - 22.
    water-use - soils - saline - wheat
    Prevalent irrigation water quality guidelines for use of sodic groundwater on sandy loam soils of Haryana for kharif (monsoon) fallow–rabi (winter) wheat crop rotation were investigated through modeling with UNSATCHEM. Three sandy loam soils that vary with respect to soil CEC (Cation Exchange Capacity) and Ks (Saturated Hydraulic Conductivity) were considered in the modeling. A procedure was developed to identify safe SAR value for sodic groundwater at a constant RSC for individual farm/soil considering soil CEC and proportions of sodic and fresh waters used for irrigation as variables. The criterion was that if the SAR of available sodic groundwater exceeded the safe SAR-value for irrigation water, a reduction in crop yield occurs. With this assumption, the procedure was tested with published data and the specific data collected from farmers’ fields. If SAR of groundwater exceeds the safe SAR-value, rice–wheat rotation is assumed to be not sustainable in the long-term. The sustainability of rice–wheat crop rotation in sodic groundwater areas in the Assandh and Nissang blocks of the Karnal district of Haryana was assessed. The described procedure of identifying the safe SAR-values for individual farm/soil is more appropriate and flexible than already existing guidelines and could be easily used for efficient conjunctive water use planning of sodic and fresh water
    Yield comparison between switchgrass and miscanthus based on multi-year side by side comparison in Europe
    Lasorella, M.V. ; Monti, A. ; Alexopoulou, E. ; Riche, A. ; Sharma, N. ; Cadoux, S. ; Diepen, C.A. van; Elbersen, B.S. ; Atzema, A.J. ; Elbersen, H.W. - \ 2011
    In: Proceedings of the 19th European Biomass Conference and Exhibition, 6-10 June 2011, Berlin, Germany. - - p. 729 - 733.
    Energy crops are expected to provide a significant amount of biomass to achieve the European targets on renewable energy. Here we focus on switchgrass (Panicum virgatum L.) and Miscanthus (Miscanthus x giganteus Greef & Deuter) two rhizomatous perennial grasses which have received particular interest during the last decade as bioenergy crops. Although the two grasses have been recently investigated deeply in U.S.A. and Europe, a significant uncertainty still exists in literature on measured or predicted potential yields. In order to understand the role these species can play, a study was carried out aimed at collecting measured side by side data on Miscanthus and switchgrass yields across Europe. Biomass productivity of the two crops significantly varied depending on location, however the relative yield (RY), i.e. Miscanthus to switchgrass yields ratio, was rather constant across Europe (78% ± 9.2), thus indicating parallel yield variation by switchgrass and Miscanthus at different locations. By assessing RY a more reliable economic and LCA comparison and then choice among crops could be provided.
    Sources, distribution, and acidity of sulfate–ammonium aerosol in the Arctic in winter–spring
    Fisher, J.A. ; Jacob, D.J. ; Wang, Q. ; Bahreini, R. ; Carouge, C.C. ; Cubison, M.J. ; Dibb, J.E. ; Diehl, T. ; Jiminez, J.L. ; Leibensperger, E.M. ; Lu, Z. ; Meinders, M.B.J. ; Pye, H.O.T. ; Quinn, P.K. ; Sharma, S. ; Streets, D.G. ; Donkelaar, A. van; Yantosca, R.M. - \ 2011
    Atmospheric Environment 45 (2011)39. - ISSN 1352-2310 - p. 7301 - 7318.
    circulation model assessment - cloud resolving simulations - dry deposition - chemical-composition - asian pollution - ice nucleation - air-pollution - intex-b - atmospheric transport - ozone depletion
    We use GEOS-Chem chemical transport model simulations of sulfate–ammonium aerosol data from the NASA ARCTAS and NOAA ARCPAC aircraft campaigns in the North American Arctic in April 2008, together with longer-term data from surface sites, to better understand aerosol sources in the Arctic in winter–spring and the implications for aerosol acidity. Arctic pollution is dominated by transport from mid-latitudes, and we test the relevant ammonia and sulfur dioxide emission inventories in the model by comparison with wet deposition flux data over the source continents. We find that a complicated mix of natural and anthropogenic sources with different vertical signatures is responsible for sulfate concentrations in the Arctic. East Asian pollution influence is weak in winter but becomes important in spring through transport in the free troposphere. European influence is important at all altitudes but never dominant. West Asia (non-Arctic Russia and Kazakhstan) is the largest contributor to Arctic sulfate in surface air in winter, reflecting a southward extension of the Arctic front over that region. Ammonium in Arctic spring mostly originates from anthropogenic sources in East Asia and Europe, with added contribution from boreal fires, resulting in a more neutralized aerosol in the free troposphere than at the surface. The ARCTAS and ARCPAC data indicate a median aerosol neutralization fraction [NH4+]/(2[SO42-] + [NO3-]) of 0.5 mol mol-1 below 2 km and 0.7 mol mol-1 above. We find that East Asian and European aerosol transported to the Arctic is mostly neutralized, whereas West Asian and North American aerosol is highly acidic. Growth of sulfur emissions in West Asia may be responsible for the observed increase in aerosol acidity at Barrow over the past decade. As global sulfur emissions decline over the next decades, increasing aerosol neutralization in the Arctic is expected, potentially accelerating Arctic warming through indirect radiative forcing and feedbacks.
    The Success of the WUA of Pauwe Sartap irrigation System: Strong Leadership and External Funds
    Liebrand, J. ; Yakami, S. - \ 2011
    In: Participatory irrigation and examples of practices of Water User Associations in Nepal / Paudel, T., Sijapati, S., Sharma Neupane, R., Nepal, Baisakh : INPIM/N - p. 53 - 56.
    Pauwa Sartapp sichaai pranali jaal upawakta sansthako saphalata: baliyo nitrito ra bahiya shrotko upyaga
    Liebrand, J. ; Yakami, S. - \ 2011
    In: Sahabhagitamulak sichaaika aadharstambhaharu ra Nepalka sichaai jal Upawakta sansthaharuka udaharaniya prayasharu / Paudel, T., Sijapati, S., Sharma Neupane, R., Nepal, Baisakh : INPIM/N - p. 53 - 56.
    Interfacial re-arrangement in initial microbial adhesion to surfaces
    Busscher, H.J. ; Norde, W. ; Sharma, P.K. ; Mei, H.C. van der - \ 2010
    Current Opinion in Colloid and Interface Science 15 (2010)6. - ISSN 1359-0294 - p. 510 - 517.
    quartz-crystal microbalance - atomic-force microscopy - fibronectin-binding proteins - plate flow chamber - escherichia-coli - ionic-strength - staphylococcus-epidermidis - bacterial adhesion - streptococcus-mutans - parallel-plate
    Upon initial microbial adhesion to a surface multiple events occur that include interfacial re-arrangements in the region between an adhering organism and a surface Application of physico-chemical mechanisms to explain microbial adhesion to surfaces requires better knowledge of the interfacial re arrangement occurring immediately after adhesion than hitherto available
    In-field measurement of soil nitrate using an ion-selective electrode
    Sibley, K.J. ; Brewster, G.R. ; Astatkie, T. ; Adsett, J.F. ; Struik, P.C. - \ 2010
    In: Advances in Measurement Systems / Sharma, Milind Kr, InTech - ISBN 9789533070612 - 28 p.
    LIBS-Based Detection of Antioxidant Elements in Seeds of Emblica officinalis
    Mehta, S. ; Rai, P.K. ; Rai, D.K. ; Rai, N.K. ; Rai, A.K. ; Bicanic, D.D. ; Sharma, B. ; Watal, G. - \ 2010
    Food Biophysics 5 (2010)3. - ISSN 1557-1858 - p. 186 - 192.
    antidiabetic activity - medicinal-plants - psidium-guajava - rat - assay - acid
    The aim of the study was to determine the effect of the elements of the extract of seed from Emblica officinalis on antioxidant enzymes and osmotic fragility of erythrocytes membrane in normal as well as streptozotocin-induced severely diabetic albino Wister rats. The results revealed that the untreated diabetic rats exhibited increase in oxidative stress as indicated by significantly diminished activities of free radical scavenging enzymes such as catalase (CAT) and superoxide dismutase (SOD) by 37.5% (p¿
    Adsorption of Pluronic F-127 on Surfaces with Different Hydrophobicities Probed by Quartz Crystal Microbalance with Dissipation
    Nejadnik, M.R. ; Olsson, A.L.J. ; Sharma, P.K. ; Mei, H.C. van der; Norde, W. ; Busscher, H.J. - \ 2009
    Langmuir 25 (2009)11. - ISSN 0743-7463 - p. 6245 - 6249.
    protein adsorption - vesicle adsorption - adhesion - copolymers - brushes - temperature - surfactants - dependence - kinetics - systems
    Triblock copolymers of polyethylene oxide (PEO) and polypropylene oxide (PPO), that is, PEOn-PPOm-PEOn, better known as Pluronic can adsorb to surfaces in either a pancake or a brushlike configuration. The brushlike configuration is advantageous in numerous applications, since it constitutes a surface repellent to proteins and microorganisms. The conformation of the adsorbed Pluronic layer depends on the hydrophobicity of the substratum surface, but the hydrophobicity threshold above which a brushlike conformation is adopted is unknown. Therefore, the aim of this study is to investigate Pluronic F-127 adsorption on surfaces with different hydrophobicities using a quartz crystal microbalance with dissipation. Adsorption in a brushlike conformation occurred on surfaces with a water contact angle above 80 degrees, as inferred from the thickness, viscosity, and elasticity of the adsorbed layer. The concentration of Pluronic F-127 in solution affected only the kinetics of adsorption and not the final layer thickness or conformation of adsorbed Pluronic molecules.
    Mapping quantitative trait loci (QTLs) for fatty acid composition in an interspecific cross of oil palm
    Singh, R. ; Tan, S.G. ; Panandam, L.M. ; Rahman, R.A. ; Ooi, L.C.L. ; Low, E.T.L. ; Sharma, M. ; Jansen, J. ; Cheah, S.C. - \ 2009
    BMC Plant Biology 9 (2009). - ISSN 1471-2229
    elaeis-guineensis jacq. - genetic-linkage map - marker-assisted selection - brassica-napus - rapd markers - eucalyptus-grandis - pseudo-testcross - seed oil - microsatellite - identification
    Marker Assisted Selection (MAS) is well suited to a perennial crop like oil palm, in which the economic products are not produced until several years after planting. The use of DNA markers for selection in such crops can greatly reduce the number of breeding cycles needed. With the use of DNA markers, informed decisions can be made at the nursery stage, regarding which individuals should be retained as breeding stock, which are satisfactory for agricultural production, and which should be culled. The trait associated with oil quality, measured in terms of its fatty acid composition, is an important agronomic trait that can eventually be tracked using molecular markers. This will speed up the production of new and improved oil palm planting materials. Result: A map was constructed using AFLP, RFLP and SSR markers for an interspecific cross involving a Colombian Elaeis oleifera (UP1026) and a Nigerian E. guinneensis (T128). A framework map was generated for the male parent, T128, using Joinmap ver. 4.0. In the paternal (E.guineensis) map, 252 markers (199 AFLP, 38 RFLP and 15 SSR) could be ordered in 21 linkage groups (1815cM). Interval mapping and multiple-QTL model (MQM) mapping (also known as composite interval mapping, CIM) were used to detect quantitative trait loci (QTLs) controlling oil quality (measured in terms of iodine value and fatty acid composition). At a 5% genome-wide significance threshold level, QTLs associated with iodine value (IV), myristic acid (C14:0), palmitic acid (C16:0), palmitoleic acid (C16:1), stearic acid (C18:0), oleic acid (C18:1) and linoleic acid (C18:2) content were detected. One genomic region on Group 1 appears to be influencing IV, C14:0, C16:0, C18:0 and C18:1 content. Significant QTL for C14:0, C16:1, C18:0 and C18:1 content was detected around the same locus on Group 15, thus revealing another major locus influencing fatty acid composition in oil palm. Additional QTL for C18:0 was detected on Group 3. A minor QTL for C18:2 was detected on Group 2. CONCLUSION: This study describes the first successful detection of QTLs for fatty acid composition in oil palm. These QTLs constitute useful tools for application in breeding programmes
    Yield stability in barley-wheat mixed cropping in Central Highlands of Eritrea
    Woldeamlak, A. ; Struik, P.C. ; Sharma, J.K. - \ 2008
    Indian Journal of Crop Science 3 (2008)1. - ISSN 0973-4880 - p. 14 - 14.
    Yield data of a large set of experiments with barley and wheat were analysed in order to assess whether yield stability was greater in mixed cropping than in sole cropping, and to identify which varietal mixture showed most stable grain yields. Stable cropping system were those having reasonably high mean yield, a regression coefficient b=1.0 of the relation between grain yield of the location and the mean yield of each genotype combination/crop ratio or cropping system and a deviation from regression (S2di) of the mean yield as small as possible. Mixed cropping with a mean grain yield of 1744 kg ha-1, regression coefficient (b) of 0.995 and a deviation from regression (S2di) of 0.277 was more stable in grain yield than either barley or wheat sole cropping. This stability test confirmed that mixed cropping was more stable than wheat or barley mono cropping and that some varietal mixtures were more stable than others
    Quality evaluation of gamma irradiated cereal grains for spawn production
    Sharma, H.S.S. ; Cunha, B. ; Kilpatrick, M. ; Lyons, G. ; Wichers, H.J. ; Hoozee, J. - \ 2008
    Effect of intercropping barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.) landraces under rainfed conditions in the central highlands of Eritrea: productivity, growth and yield attributes
    Woldeamlak, A. ; Sharma, J.K. ; Struik, P.C. ; Dagnew, G. - \ 2007
    Indian Journal of Crop Science 2 (2007)1. - ISSN 0973-4880 - p. 145 - 150.
    Spatial analysis of ecosystem functions of planted forests - A methodology
    Eupen, M. van; Sharma, S.D. ; Vijayanand, T. ; Puchol, S. - \ 2007
    In: Proceedings of the International Congress of Cultivated Forests, Bilbao, Spain, 3 - 7 October, 2006. - Derio : Unión de Selvicultores del Sur de España - p. 367 - 368.
    Taxonomy of the genus Cicer revisited
    Maesen, L.J.G. van der; Maxted, N. ; Javadi, F. ; Coles, S. ; Davies, A.M.R. - \ 2007
    In: Chickpea Breeding & Management / Yadav, S.S., Redden, R., Chen, W., Sharma, B., Oxfordshire : CABI - ISBN 9781845932138 - p. 14 - 46.
    This chapter focuses on the collection and conservation as well as molecular phylogeny of the genus Cicer. Short descriptions with ecogeographic notes are given for 44 Cicer species.
    Rainfall, Soil Moisture Content and Runoff in a Small Catchment in the Indian Himalayas
    Hessel, R. ; Gupta, M.K. ; Singh Datta, P. ; Elsen, E. van den; Sharma, S.D. - \ 2007
    International Journal of Ecology and Environmental Sciences 33 (2007). - ISSN 0377-015X - p. 115 - 128.
    Groundwater: a global assessment of scale and significance
    Shah, T. ; Bruke, J. ; Vullholth, K. ; Angelica, M. ; Custodio, E. ; Daibes, F. ; Hoogesteger van Dijk, J.D. ; Giordano, M. ; Girman, J. ; Gun, J. van der; Kendy, E. ; Kijne, J. ; Llamas, R. ; Masiyandama, M. ; Margat, J. ; Marin, L. ; Peck, J. ; Rozelle, S. ; Sharma, B. ; Vincent, L.F. ; Wang, J. - \ 2007
    In: Water for food Water for life : a comprehensive Assessment of Water Management in Agriculture / Molden, D., London : Earthscan - ISBN 9781844073962 - p. 395 - 423.
    Analysis of agricultural drought in Iiuni, Eastern Kenya: Application of a Markov model
    Biamah, E.K. ; Sterk, G. ; Sharma, T.C. - \ 2005
    Hydrological Processes 19 (2005)6. - ISSN 0885-6087 - p. 1307 - 1322.
    time-series - sums
    In semi-arid Kenya, episodes of agricultural droughts of varying severity and duration occur. The occurrence of these agricultural droughts is associated with seasonal rainfall variability and can be reflected by seasonal soil moisture deficits that significantly affect crop performance and yield. The objective of this study was to stochastically simulate the behaviour of dry and wet spells and rainfall amounts in Iiuni watershed, Kenya. The stochastic behaviour of the longest dry and wet spells (runs) and largest rainfall amounts were simulated using a Markov (order 1) model. There were eight raingauge stations within the watershed. The entire analysis was carried out using probability parameters, i.e. mean, variance, simple and conditional probabilities of dry and rain days. An analysis of variance test (ANOVA) was used to establish significant differences in rainfall characteristics between the eight stations. An analysis of the number of rain days and rainfall amount per rain day was done on a monthly basis to establish the distribution and reliability of seasonal rainfall. The graphic comparison of simulated cumulative distribution functions (Cdfs) of the longest spells and largest rainfall amounts showed Markovian dependence or persistence. The longest dry spells could extend to 24 days in the long rainy season and 12 in the short rainy season. At 50% (median) probability level, the largest rainfall amounts were 91 mm for the long rainy season and 136 mm for the short rainy season. The short rains were more reliable for crop production than the long rains. The Markov model performed well and gave adequate simulations of the spells and rainfall amounts under semi-arid conditions
    Transgenic rice and food safety
    Kleter, G.A. ; Kuiper, H.A. - \ 2005
    In: Biosafety of transgenic rice / Chopra, V.L., Shantharam, S., Sharma, R.P., New Delhi : National Academy of Agricultural Sciences - p. 46 - 64.
    The Tomato Sequencing Project, the first cornerstone of the International Solanaceae Project (SOL)
    Mueller, L.A. ; Tanksley, S.D. ; Giovannoni, J.J. ; Eck, J. van; Stack, S. ; Choi, D. ; Dong Kim, B. ; Chen, M. ; Cheng, Z. ; Li, C. ; Ling, H. ; Xue, Y. ; Seymour, G.B. ; Bishop, G. ; Bryan, G.J. ; Sharma, R. ; Khurana, J. ; Tyagi, A. ; Chattopadhyay, D. ; Singh, N.K. ; Stiekema, W. ; Lindhout, P. ; Jesse, T. ; Klein Lankhorst, R.M. ; Bouzayen, M. ; Shibata, D. ; Tabata, S. ; Granell, A. ; Botella, M.A. ; Giuliano, G. ; Frusciante, L. ; Causse, M. ; Zamir, D. - \ 2005
    Comparative and Functional Genomics 6 (2005)3. - ISSN 1531-6912 - p. 153 - 158.
    maize genome - tuber development - fruit - genes - evolution - plants - hybridization - manipulation - organization - resistance
    The genome of tomato (Solanum lycopersicum) is being sequenced by an international consortium of 10 countries (Korea, China, the United Kingdom, India, The Netherlands, France, Japan, Spain, Italy and the United States) as part of a larger initiative called the International Solanaceae Genome Project (SOL): Systems Approach to Diversity and Adaptation. The goal of this grassroots initiative, launched in November 2003, is to establish a network of information, resources and scientists to ultimately tackle two of the most significant questions in plant biology and agriculture: (1) How can a common set of genes/proteins give rise to a wide range of morphologically and ecologically distinct organisms that occupy our planet? (2) How can a deeper understanding of the genetic basis of plant diversity be harnessed to better meet the needs of society in an environmentally friendly and sustainable manner? The Solanaceae and closely related species such as coffee, which are included in the scope of the SOL project, are ideally suited to address both of these questions. The first step of the SOL project is to use an ordered BAC approach to generate a high quality sequence for the euchromatic portions of the tomato as a reference for the Solanaceae. Due to the high level of macro and micro-synteny in the Solanaceae the BAC-by-BAC tomato sequence will form the framework for shotgun sequencing of other species. The starting point for sequencing the genome is BACs anchored to the genetic map by overgo hybridization and AFLP technology. The overgos are derived from approximately 1500 markers from the tomato high density F2-2000 genetic map (http://sgn.cornell.edu/). These seed BACs will be used as anchors from which to radiate the tiling path using BAC end sequence data. Annotation will be performed according to SOL project guidelines. All the information generated under the SOL umbrella will be made available in a comprehensive website. The information will be interlinked with the ultimate goal that the comparative biology of the Solanaceae - and beyond - achieves a context that will facilitate a systems biology approach.
    A management guide for planting and production of switchgrass as a biomass crop in Europe
    Elbersen, H.W. ; Christian, D.G. ; Bassam, N.E. ; Sauerbeck, G. ; Alexopoulou, E. ; Sharma, N. ; Piscioneri, I. - \ 2004
    panicum virgatum - brandstofgewassen - akkerbouw - vezelgewassen - biomassa productie - teelthandleidingen - biobased economy - panicum virgatum - fuel crops - arable farming - fibre plants - biomass production - cultivation manuals - biobased economy
    Switchgrass is a perennial C4 grass native to North America, where it occurs naturally from 55º N latitude to deep into Mexico. It is used for soil conservation, forage production, as an ornamental grass and more recently as a biomass crop for ethanol, fibre, electricity and heat production. As biomass increases in importance in Europe it is expected that switchgrass can play an important role in supplying sustainably produced lignocellulosic biomass. One of the main attractive features being low establishment costs and high productivity under low input conditions. Recent European research has led to sufficient results to merit publication of a management guide. In this guide all aspects necessary to produce switchgrass from variety choice, site selection, establishment, nutritional requirements, pest management, economics, harvest options, to application for energy or fibre are discussed.
    Simulation of watershed peak runoff rate using the Nash model
    Biamah, E.K. ; Sharma, T.C. ; Stroosnijder, L. - \ 2004
    - 16 p.
    Mapping Equus kiang (Tibetan Wild Ass) Habitat in Surkhang, Upper Mustang, Nepal
    Sharma, B.D. ; Clevers, J.G.P.W. ; Graaf, N.R. de; Chapagain, N.R. - \ 2004
    Mountain Research and Development 24 (2004)2. - ISSN 0276-4741 - p. 149 - 156.
    The present paper describes land cover classification and habitat mapping for the Tibetan wild ass (Equus kiang), also commonly known as kiang, in the Surkhang VDC, Upper Mustang, Nepal. Remote sensing techniques were applied for this classification, employing an ASTER satellite image from October 2002. The whole region was classified into 6 land cover types, relevant to the application of habitat mapping for the kiang. The classes are: grassland, shrubland, bar water bodies, snow cover, and agriculture and settlement. The area of each land cover type was tabulated to give a general picture of the land cover situation. Habitat information was collected mostly from the literature and partially from a field visit. GIS tools for spatial analysis were used to identify the suitability of the habitat in the region. The whole region was classified into 3 different suitability levels, ie primary, secondary, and non-suitable, based on use and potential use by the species in the particular area. The region with suitable habitats was delineated so that any further conservation activities related to kiang habitat can be concentrated within this boundary a : a management implication.
    Assessing the land cover situation in Surkhang, Upper Mustang, Nepal, using an ASTER image
    Sharma, B.D. ; Clevers, J.G.P.W. ; Graaf, N.R. de; Chapagain, N.R. - \ 2003
    Himalayan journal of sciences 1 (2003)2. - ISSN 1727-5210 - p. 93 - 98.
    This paper describes the remote sensing technique used to prepare a land cover map of Surkhang, Upper Mustang Nepal. The latest ASTER image (October 2002) and an ASTER DEM were used for the land cover classification. The study was carried out in Surkhang Village Development Committee (area 799 km2) of Upper Mustang region. The study area falls within the Annapurna Conservation Area. Field surveys for training data, ground truthing and spectral signature collection were carried out during May-June 2002. Various image classification algorithms were tested, and the one that yielded the best result was used for image classification. The land cover situations with their aerial extents were identified and topographic analysis was carried out to study the variations of different land covers types in the region. Various species of grasses covered about 36 %; shrubs covered about 32%; bare land, which includes area from completely bare to less than 10% vegetation, constituted about 20% of the land resources of the study area. Grassland was found abundant in east- to south-facing slopes, while shrub species were abundant in flat regions and west- to north-facing slopes.
    Simulation of Watershed Peak Runoff Rate using the Nash Model
    Biamah, E.K. ; Sharma, T.C. ; Stroosnijder, L. - \ 2002
    Journal of Engineering in Agriculture and the Environment 2 (2002)1. - ISSN 1562-6946 - p. 49 - 56.
    Ectopic expression of BABY BOOM triggers a conversion from vegetative to embryonic growth
    Boutilier, K. ; Offringa, R. ; Sharma, V.K. ; Kieft, H. ; Ouellet, T. ; Zhang, L. ; Hattori, J. ; Liu, C.M. ; Lammeren, A.A.M. van; Miki, B.L.A. ; Custers, J.B.M. ; Lookeren Campagne, M.M. van - \ 2002
    The Plant Cell 14 (2002). - ISSN 1040-4651 - p. 1737 - 1749.
    The molecular mechanisms underlying the initiation and maintenance of the embryonic pathway in plants are largely unknown. To obtain more insight into these processes, we used subtractive hybridization to identify genes that are upregulated during the in vitro induction of embryo development from immature pollen grains of Brassica napus (microspore embryogenesis). One of the genes identified, BABY BOOM (BBM), shows similarity to the AP2/ERF family of transcription factors and is expressed preferentially in developing embryos and seeds. Ectopic expression of BBM in Arabidopsis and Brassica led to the spontaneous formation of somatic embryos and cotyledon-like structures on seedlings. Ectopic BBM expression induced additional pleiotropic phenotypes, including neoplastic growth, hormone-free regeneration of explants, and alterations in leaf and flower morphology. The expression pattern of BBM in developing seeds combined with the BBM overexpression phenotype suggests a role for this gene in promoting cell proliferation and morphogenesis during embryogenesis.
    Cross-reacting lymphocyte antigens of domestic fowl and goose (Anser anser domesticus)
    Tovari, J. ; Nemteth, I. ; Jeurissen, S.H.M. ; Sharma, J.M. ; Davison, T.F. ; Kaiser, P. ; Raso, E. ; Salomonsen, J. ; Bocsi, J. ; Dren, C.N. - \ 2001
    In: 'Current progress on avian immunology research' / Schat, K.A.,
    Adsorptive iron removal from groundwater
    Sharma, S.K. - \ 2001
    Wageningen University. Promotor(en): J.C. Schippers. - S.l. : S.n. - ISBN 9789054104308 - 202
    grondwaterverontreiniging - adsorptie - verwijdering - ijzer - drinkwater - groundwater pollution - adsorption - removal - iron - drinking water

    Iron is commonly present in groundwater worldwide. The presence of iron in the water supply is not harmful to human health, however it is undesirable. Bad taste, discoloration, staining, deposition in the distribution system leading to aftergrowth, and incidences of high turbidity are some of the aesthetic and operational problems associated with iron in water supplies. Iron removal from groundwater is, therefore, a major concern for water supply companies using groundwater sources. The WHO recommended guideline value of iron in drinking water is 0.3 mg/l and the EC directive has set a parametric value of 0.2 mg/1. In the Netherlands, the guideline value of iron in drinking water is≤0.05mg/1 and several Dutch water supply companies are aiming at iron concentrations below 0.03 mg/1 to minimise distribution network maintenance costs. Of the different methods available to control iron in water supplies (oxidation-filtration, ion exchange, lime softening, sub-surface iron removal, and sequestration), aeration followed by rapid sand filtration is the most commonly used.

     

    Different mechanisms (physical, chemical, and biological) may contribute to the removal of iron in filters and the dominant mechanism depends on water quality and process conditions applied. Fig. 8. 1 summarises the different mechanisms of iron removal in filters and the steps involved. Under anoxic conditions, adsorption is the only mechanism of iron removal from groundwater. In the presence of oxygen, iron removal can take place via three different mechanisms, namely i) oxidation-floe formation (floe filtration), ii) biological oxidation, and iii) adsorption-oxidation (adsorptive filtration). Under the commonly applied treatment conditions in iron removal plants, the oxidation-floe formation mechanism is commonly believed to be dominant. The adsorptionoxidation mechanism (adsorptive iron removal), however, has several potential advantages over the oxidation-floe formation mechanism, namely longer filter run, shorter filter ripening time, and less backwash water use and sludge production.

    Simulation and validation studies for reuse of drainage effluents
    Sharma, D.K. ; Dam, J.C. van; Feddes, R.A. - \ 2000
    In: Role of drainage and challenges in 21st century. Vol. III : Proceedings of the Eighth ICID International , New Delhi, India, 31 January - 4 February 2000 New Delhi : Int. Commission on Irrigation and Drainage - p. 317 - 328.
    hergebruik van water - drainagewater - ondergrondse drainage - zoutgehalte - water reuse - drainage water - subsurface drainage - salinity
    Ectopic expression of Baby Boom converts vegetative organs into embryos and cotyledons
    Boutilier, K. ; Offringa, R. ; Sharma, V. ; Kieft, H. ; Lammeren, A.A.M. van; Ouellet, T. ; Zhang, L. - \ 2000
    In: Abstr. XVIth. Int. Congr. on Sexual Plant Reprod., Banff, Alberta, 2000 Banff, Alberta : - p. 42 - 42.
    The use of mutant and transgenetics in understanding photomorphogenesis
    Sharma, R.P. ; Kendrick, R.E. - \ 1999
    In: Concepts in Photosynthesis and Photomorphogenesis / ed. by G.S. Singhal, G. Renger, S.K. Sopory, K.D. Irrgang and Govindjee. - New Delhi, Narosa Publishing House, 1999 - p. 900 - 931.
    Transposon tagging for the isolation of apomixis mutants and the corresponding genes in Petunia
    Ramulu, K.S. ; Dijkhuis, P. ; Sharma, V.K. ; Boutilier, K. ; Naumova, T.N. ; Angenent, G.C. ; Lookeren Campagne, M.M. van - \ 1998
    Apomixis Newsletter 10 (1998). - p. 19 - 20.
    Effect of conservation tillage on watershed hydrology in semi-arid Kenya.
    Biamah, E.K. ; Stroosnijder, L. ; Sharma, T.C. ; Cherogony, R.K.K. - \ 1998
    In: Proceedings 13th International Congress on Agricultural Engineering. - - p. 335 - 357.
    erosiebestrijding - waterbescherming - bodembescherming - afvoer - oppervlakkige afvoer - hydrologie - modellen - onderzoek - kenya - erosion control - water conservation - soil conservation - discharge - runoff - hydrology - models - research - kenya
    Temporal and spatial features of agricultural drought in semi-arid Kenya.
    Biamah, E.K. ; Stroosnijder, L. ; Sharma, T.C. ; Cherogony, R.K.K. - \ 1998
    In: Proceedings 13th International Congress on Agricultural Engineering, Rabat, Morocco - p. 403 - 508.
    Soil Salinity - Wheat Yield Relationship on Farmers' Fields
    Sharma, D.P. ; Rao, K.V.G.K. ; Oosterbaan, R.J. - \ 1997
    Journal of the Indian Society for Soil Science 45 (1997)2. - p. 406 - 409.
    Runoff and sediment transport in the arid regions of Argentina and India - a case study in comparative hydrology
    Sharma, K.D. ; Menenti, M. ; Huygen, J. ; Fernandez, P.C. ; Vich, A. - \ 1996
    Annals of Arid Zone 35 (1996)1. - ISSN 0570-1791 - p. 17 - 28.
    argentinië - woestijnen - economische impact - economie - india - regen - relaties - oppervlakkige afvoer - gebruikswaarde - aride klimaatzones - argentina - deserts - economic impact - economics - india - rain - relationships - runoff - use value - arid zones
    The arid zones of Argentina and India have been compared. In both regions run-off is often generated by the Hortonian infiltration surplus overland flow, and run-off response to precipitation input tends to be rapid. The sediment transport is governedby the transport capacity of run-off rather than by the availability of erodible material. The magnitude of hydrological processes is different in response to the different rainfall regimes.
    Distributed numerical rainfall-runoff modelling in an arid region using Thematic Mapper data and a geographical information system
    Sharma, K.D. ; Menenti, M. ; Huygen, J. ; Fernandez, P.C. - \ 1996
    Hydrological Processes 10 (1996)9. - ISSN 0885-6087 - p. 1229 - 1242.
    A transient one-dimensional finite-difference model describing the partitioning of precipitation between surface run-off, soil moisture storage and deep percolation, through the coupling of saturated and unsaturated zones, has been implemented in a geographical information system including data on vegetation cover derived from the Landsat Thematic Mapper. The model was used to simulate both the rainfall excess and the resultant outflow hydrographs for a small arid zone drainage basin in the Andean regions of Argentina. The overall hydrograph shape, peak discharge, run-off volume and flow duration are predicted within a relative squared error of 13.2%.
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