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Cassava mosaic disease, one of the ten most economically important crop viral diseases in the world, was first reported in Southeast Asia from a single plantation in Cambodia in 2015. To determine the presence and incidence of Sri Lankan cassava mosaic virus (SLCMV) one year after first detection, a total of 6,480 samples from 419 fields were systematically collected from cassava production areas across Cambodia (3,840 samples; 240 fields) and Vietnam (2,640samples; 179 fields) in the 2016 cropping season. Using PCR-based diagnostics, we identified 49 SLCMV-infected plants from nine fields, representing 2% of the total number of fields sampled. Infected fields were geographically restricted to two provinces of Eastern Cambodia, while no infection was detected from any of the other sampled sites in either country. Symptom expression patterns in infected plants suggested that SLCMV may have been transmitted both through infected planting materials, and by Bemisia tabaci, the known whitefly vector of SLCMV. In addition, 14% of virus infected plants did not express typical symptoms of cassava mosaic disease on their leaves, highlighting that molecular-based validation is needed to confirm the presence of SLCMV in the field. None of the owners of the SLCMV-infected fields indicated acquired planting materials from the plantation in Ratanakiri where SLCMV was first reported. The surveillance baseline data generated for both countries is discussed in light of future options to control and manage cassava mosaic disease.

Biological control, a globally-important ecosystem service, can provide long-term and broad-scale suppression of invasive pests, weeds and pathogens in natural, urban and agricultural environments. Following (few) historic cases that led to sizeable environmental up-sets, the discipline of arthropod biological control has—over the past decades—evolved and matured. Now, by deliberately taking into account the ecological risks associated with the planned introduction of insect natural enemies, immense environmental and societal benefits can be gained. In this study, we document and analyze a successful case of biological control against the cassava mealybug, Phenacoccus manihoti (Hemiptera: Pseudococcidae) which invaded Southeast Asia in 2008, where it caused substantial crop losses and triggered two- to three-fold surges in agricultural commodity prices. In 2009, the host-specific parasitoid Anagyrus lopezi (Hymenoptera: Encyrtidae) was released in Thailand and subsequently introduced into neighboring Asian countries. Drawing upon continental-scale insect surveys, multi-year population studies and (field-level) experimental assays, we show how A. lopezi attained intermediate to high parasitism rates across diverse agro-ecological contexts. Driving mealybug populations below non-damaging levels over a broad geographical area, A. lopezi allowed yield recoveries up to 10.0 t/ha and provided biological control services worth several hundred dollars per ha (at local farm-gate prices) in Asia’s four-million ha cassava crop. Our work provides lessons to invasion science and crop protection worldwide. Furthermore, it accentuates the importance of scientifically-guided biological control for insect pest management, and highlights its potentially large socio-economic benefits to agricultural sustainability in the face of a debilitating invasive pest. In times of unrelenting insect invasions, surging pesticide use and accelerating biodiversity loss across the globe, this study demonstrates how biological control—as a pure public good endeavor—constitutes a powerful, cost-effective and environmentally-responsible solution for invasive species mitigation.

Initiation of transcription is essential for most of the cellular responses to environmental conditions and for cell and tissue specificity. This process is regulated through numerous proteins, their ligands and mutual interactions, as well as interactions with DNA. The key such regulatory proteins are transcription factors (TFs) and transcription co-factors (TcoFs). TcoFs are important since they modulate the transcription initiation process through interaction with TFs. In eukaryotes, transcription requires that TFs form different protein complexes with various nuclear proteins. To better understand transcription regulation, it is important to know the functional class of proteins interacting with TFs during transcription initiation. Such information is not fully available, since not all proteins that act as TFs or TcoFs are yet annotated as such, due to generally partial functional annotation of proteins. In this study we have developed a method to predict, using only sequence composition of the interacting proteins, the functional class of human TF binding partners to be (i) TF, (ii) TcoF, or (iii) other nuclear protein. This allows for complementing the annotation of the currently known pool of nuclear proteins. Since only the knowledge of protein sequences is required in addition to protein interaction, the method should be easily applicable to many species. Based on experimentally validated interactions between human TFs with different TFs, TcoFs and other nuclear proteins, our two classification systems (implemented as a web-based application) achieve high accuracies in distinguishing TFs and TcoFs from other nuclear proteins, and TFs from TcoFs respectively. As demonstrated, given the fact that two proteins are capable of forming direct physical interactions and using only information about their sequence composition, we have developed a completely new method for predicting a functional class of TF interacting protein partners with high precision and accuracy.

Cassava mosaic disease, one of the ten most economically important crop viral diseases in the world, was first reported in Southeast Asia from a single plantation in Cambodia in 2015. To determine the presence and incidence of Sri Lankan cassava mosaic virus (SLCMV) one year after first detection, a total of 6,480 samples from 419 fields were systematically collected from cassava production areas across Cambodia (3,840 samples; 240 fields) and Vietnam (2,640samples; 179 fields) in the 2016 cropping season. Using PCR-based diagnostics, we identified 49 SLCMV-infected plants from nine fields, representing 2% of the total number of fields sampled. Infected fields were geographically restricted to two provinces of Eastern Cambodia, while no infection was detected from any of the other sampled sites in either country. Symptom expression patterns in infected plants suggested that SLCMV may have been transmitted both through infected planting materials, and by Bemisia tabaci, the known whitefly vector of SLCMV. In addition, 14% of virus infected plants did not express typical symptoms of cassava mosaic disease on their leaves, highlighting that molecular-based validation is needed to confirm the presence of SLCMV in the field. None of the owners of the SLCMV-infected fields indicated acquired planting materials from the plantation in Ratanakiri where SLCMV was first reported. The surveillance baseline data generated for both countries is discussed in light of future options to control and manage cassava mosaic disease.

Farmers’ knowledge, attitudes, and beliefs are of paramount importance in shaping the on-farm adoption and diffusion of integrated pest management (IPM). In particular, for invasive pests, this (gendered) knowledge base can dictate how fast and effective farmers respond to emerging threats. In this study, we employ qualitative and quantitative methods to assess agro-ecological knowledge and pest management behavior of small-scale cassava growers in rural Vietnam and Laos, when faced with two new biotic threats, i.e., the invasive cassava mealybug Phenacoccus manihoti and cassava witches broom disease. Despite their pronounced impact on crop yields, farmers overall had limited knowledge of recent invaders and regularly ascribed their appearance to “climate change\". Growers were largely unaware of preventative tactics for pest control, and resorted to curative measures (e.g., unguided pesticide sprays) at the P. manihoti invasion front. Farmers’ attitudes toward invasive pests were highly context- and locality-dependent, and knowledge scores differed between households positioned along a gender continuum. Though women assumed a minor role in IPM decision-making and possessed comparatively deficient knowledge, they favored agro-ecological approaches and took on key tasks in the selection of propagation material. Gender roles in cassava crop protection are equally context-dependent, yet women may be well-positioned to promote IPM practices such as the use of disease-free planting material. Future extension should thus pay attention to (a) strengthening (women) farmers’ knowledge base, to empower them as change agents and drive IPM adoption, and (b) transferring local innovations between sites, eventually through visual educational aids. Given the increasing importance of invasive pests in many developing countries, our work emphasizes how adult education and (adaptive) co-learning should become core components of mitigation programs.

Background Potato late blight caused by the oomycete pathogen Phytophthora infestans can lead to immense yield loss. We investigated the transcriptome of Solanum tubersoum (cv. Desiree) and characterized the secretome by quantitative proteomics after foliar application of the protective agent phosphite. We also studied the distribution of phosphite in planta after application and tested transgenic potato lines with impaired in salicylic and jasmonic acid signaling. Results Phosphite had a rapid and transient effect on the transcriptome, with a clear response 3 h after treatment. Strikingly this effect lasted less than 24 h, whereas protection was observed throughout all time points tested. In contrast, 67 secretome proteins predominantly associated with cell-wall processes and defense changed in abundance at 48 h after treatment. Transcripts associated with defense, wounding, and oxidative stress constituted the core of the phosphite response. We also observed changes in primary metabolism and cell wall-related processes. These changes were shown not to be due to phosphate depletion or acidification caused by phosphite treatment. Of the phosphite-regulated transcripts 40% also changed with β-aminobutyric acid (BABA) as an elicitor, while the defence gene PR1 was only up-regulated by BABA. Although phosphite was shown to be distributed in planta to parts not directly exposed to phosphite, no protection in leaves without direct foliar application was observed. Furthermore, the analysis of transgenic potato lines indicated that the phosphite-mediated resistance was independent of the plant hormones salicylic and jasmonic acid. Conclusions Our study suggests that a rapid phosphite-triggered response is important to confer long-lasting resistance against P. infestans and gives molecular understanding of its successful field applications.

Background Induced resistance (IR) can be part of a sustainable plant protection strategy against important plant diseases. β-aminobutyric acid (BABA) can induce resistance in a wide range of plants against several types of pathogens, including potato infected with Phytophthora infestans . However, the molecular mechanisms behind this are unclear and seem to be dependent on the system studied. To elucidate the defence responses activated by BABA in potato, a genome-wide transcript microarray analysis in combination with label-free quantitative proteomics analysis of the apoplast secretome were performed two days after treatment of the leaf canopy with BABA at two concentrations, 1 and 10 mM. Results Over 5000 transcripts were differentially expressed and over 90 secretome proteins changed in abundance indicating a massive activation of defence mechanisms with 10 mM BABA, the concentration effective against late blight disease. To aid analysis, we present a more comprehensive functional annotation of the microarray probes and gene models by retrieving information from orthologous gene families across 26 sequenced plant genomes. The new annotation provided GO terms to 8616 previously un-annotated probes. Conclusions BABA at 10 mM affected several processes related to plant hormones and amino acid metabolism. A major accumulation of PR proteins was also evident, and in the mevalonate pathway, genes involved in sterol biosynthesis were down-regulated, whereas several enzymes involved in the sesquiterpene phytoalexin biosynthesis were up-regulated. Interestingly, abscisic acid (ABA) responsive genes were not as clearly regulated by BABA in potato as previously reported in Arabidopsis. Together these findings provide candidates and markers for improved resistance in potato, one of the most important crops in the world.

Biological control constitutes one of the world’s prime ecosystems services, and can provide long-term and broad-scale suppression of invasive pests, weeds and pathogens in both natural and agricultural environments. Following (very few) widely-documented historic cases that led to sizeable environmental up-sets, the discipline of insect biological control has -over the past three decades- gone through much-needed reform. Now, by deliberately taking into account the ecological risks associated with insect biological control, immense environmental and societal benefits can be gained. In this study, we document and analyze a rare, successful case of biological control against the invasive mealybug, Phenacoccus manihoti (Hemiptera: Pseudococcidae) which invaded Southeast Asia in 2008, where it caused substantial crop losses and triggered 2- to 3-fold surges in agricultural commodity prices. In 2009, the host-specific parasitoid Anagyrus lopezi (Hymenoptera: Encyrtidae) was released in Thailand and subsequently introduced into neighboring Asian countries. Drawing upon continental-scale insect surveys, multi-year population studies and (field-level) experimental assays, we show how A. lopezi attained intermediate to high parasitism rates across diverse agro-ecological contexts. Driving mealybug populations below non-damaging levels at a continental scale, A. lopezi allowed yield recoveries up to 10.0 t/ha and provided biological control services worth several hundred dollars per ha (at local farm-gate prices) in Asia’s 4-million ha cassava crop. Our work provides lessons to invasion science and crop protection worldwide, heralds a new era for insect biological control, and highlights its potentially large socio-economic benefits to agricultural sustainability in the face of a debilitating invasive pest. In times of unrelenting insect invasions, surging pesticide use and accelerating (invertebrate) biodiversity loss across the globe, this study unequivocally demonstrates how biological control – as a pure public good – constitutes a powerful, cost-effective and environmentally-responsible solution for invasive species mitigation.

Background Initiation of transcription is essential for most of the cellular responses to environmental conditions and for cell and tissue specificity. This process is regulated through numerous proteins, their ligands and mutual interactions, as well as interactions with DNA. The key such regulatory proteins are transcription factors (TFs) and transcription co-factors (TcoFs). TcoFs are important since they modulate the transcription initiation process through interaction with TFs. In eukaryotes, transcription requires that TFs form different protein complexes with various nuclear proteins. To better understand transcription regulation, it is important to know the functional class of proteins interacting with TFs during transcription initiation. Such information is not fully available, since not all proteins that act as TFs or TcoFs are yet annotated as such, due to generally partial functional annotation of proteins. In this study we have developed a method to predict, using only sequence composition of the interacting proteins, the functional class of human TF binding partners to be (i) TF, (ii) TcoF, or (iii) other nuclear protein. This allows for complementing the annotation of the currently known pool of nuclear proteins. Since only the knowledge of protein sequences is required in addition to protein interaction, the method should be easily applicable to many species. Results Based on experimentally validated interactions between human TFs with different TFs, TcoFs and other nuclear proteins, our two classification systems (implemented as a web-based application) achieve high accuracies in distinguishing TFs and TcoFs from other nuclear proteins, and TFs from TcoFs respectively. Conclusion As demonstrated, given the fact that two proteins are capable of forming direct physical interactions and using only information about their sequence composition, we have developed a completely new method for predicting a functional class of TF interacting protein partners with high precision and accuracy.

PurposeSustainable diets are an environmental, economic, and public health imperative, but identifying clear intervention points is challenging. Decision-making will require descriptive analyses from a variety of perspectives, even under the inevitable uncertainty introduced by limited data. This study uses existing data to provide a diet-level perspective on environmental impact from food production in the case study countries of Vietnam and Kenya.MethodsFAO food supply data at decadal time steps were used as a proxy for national average diets in Vietnam and Kenya. We combined these data with estimates of the greenhouse gas emissions (GHGE) and water use impact associated with producing food commodities. Generic GHGE factors were derived from a survey of the life cycle assessment literature. Country- and commodity-specific blue water use estimates were used, reflecting country-of-origin for import-dominated commodities. The AWARE characterization model was used to offer a diet-associated water scarcity footprint. Trends in diet-associated environmental impacts were interpreted in light of diet shifts, economic development trends, and other factors.Results and discussionIncreasing per capita food supply in Vietnam, and in particular increases in meat, have led to rising diet-associated per capita GHGE. While supply of beef remains 5.2 times smaller than pork—the dominant meat—increases in beef demand in the past decade have resulted in it becoming second only to rice in contribution to diet GHGE. The water use and water scarcity footprint in Vietnam follow an increasing trend comparable to food supply. On the other hand, historically consistent levels of dairy and beef in Kenya dominate diet-level GHGE. Water use associated with the Kenyan diet shows marked increases between the 1990s and 2000s due to imports of wheat and rice from water-stressed regions. Environmental performance data for characteristic food production systems in these and other developing countries are needed to improve the representativeness and reliability of such assessments.ConclusionsDespite data limitations, the methods and results presented here may offer a fresh perspective in sustainable development policy deliberations, as they offer an entry point to linking environmental impact and consumption behaviors and can elucidate otherwise obscure or unexpected outcomes. A clear need emerges for further environmental analysis of dominant production systems within both Vietnam and Kenya.