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.

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    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.

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