Baby Grain Passport

Det är utmanande att producera tillräckliga volymer spannmål som uppfyller kvalitetskriterierna för barnmatsråvara, främst på grund av strikta gränsvärden för tungmetaller och mykotoxiner. Med bättre underlag i form av digitala kartor och väderbaserade riskmodeller, som tillgängliggörs i ändamålsenliga beslutssystem, kan man arbeta mer effektivt med sourcing (råvaruförsörjning), spårbarhet och kvalitetssäkring. Det ger möjlighet att öka kapaciteten att producera svensk spannmålsråvara med barnmatskvalitet, både för inhemsk konsumtion och export, och samtidigt ställa hållbarhetskrav på odlingen. Med förbättrade modeller i digitala beslutsstöd för växtodlare kan man lättare optimera resurseffektiviteten, vilket bidrar till förverkligandet av nationella och internationella miljö- och klimatmål. T.ex. kan satellitbaserade kartunderlag användas för att med högre rumslig upplösning anpassa gödselgivor till lokala behov (s.k. precisionsodling). I projektet Baby Grain Passport har vi arbetat med följande frågor i fyra arbetspaket:1) Till vilka områden bör man styra barnmatsodlingen för att säkerställa att kadmiumhalten i grödan är så låg som möjligt?2) Hur kan man kartera – och ta hänsyn till – varierande skördenivåer inom fält när man anpassar gödselgivor?3) Hur kan man undvika mykotoxiner som kan bildas vid odling och lagring?4) Hur kan man ta kombinera statiska och dynamiska beslutsunderlag för effektivare sourcing och logistik av spannmål med specialkvalitet?Markinformation från miljöövervakning och mätkampanjer som Mark- och grödoinventeringen samt Jordbruksverkets åkermarksprovtagning, utgör en värdefull grund för att kunna kartlägga och undvika risk för höga kadmiumhalter i spannmålspartier. Genom att kombinera punktobservationer med högupplöst bakgrundsinformation enligt principer för digital markkartering togs detaljerade riskkartor för höga kadmiumhalter i matjord fram. I samverkan med SLUs miljöövervakning har sedan metoden generaliserats till ett ramverk för digital åkermarkskartering (Åkermarksdatakuben, ÅMDK), som kan användas för att förhållandevis snabbt ta fram nya eller uppdaterade kartprodukter även över flera andra tungmetaller – i projektet gjordes en test med kartläggning av nickelhalter i mark och i havre. I kartläggningsarbetet blev det tydligt att vissa geografiska områden är särskilt lämpade för produktion av spannmål till barnmat. Risken för att påträffa kadmiumhalter (och nickelhalter) över gränsen för barnmat i havre och vete är liten i t.ex. stora delar av Västsverige (Halland, Västra Götaland och Värmland). Resultat från kadmiumkarteringen i marken finns tillgänglig här: https://bit.ly/sannolika_kadmiumhalter.. Precisionsstyrning av växtnäring tillämpas idag ganska brett men det finns utrymme till ytterligare förbättring, t.ex. genom att hänsyn tas till varierande skördepotential inom fält. För att kunna göra det behövs effektiva metoder att generera underlag i form av detaljerade skördekartor. Fritt tillgängliga satellitdata kan nyttjas för förenklad skördekartering, utan krav på egen utrustning. När det gäller satellitbaserad skördekartering är det lämpligt att arbeta på en något grövre upplösning än den ursprungliga upplösningen hos satellitbilderna, t.ex. 40 m eller ett antal homogena zoner inom fält. Modellerna blir mer tillförlitliga om de bygger på ett vegetationsindex som är känsligt får grödans vattenstatus (NDWI) och om man använder satellitdata från ett relativt sent utvecklingsstadium (nära mjölkmognad), alternativt tidsserier av data från uppkomst fram till detta stadium.  Prognossystem och mätprogram för mykotoxinerna DON och T2+HT2 är nödvändiga för att under pågående säsong informera inköpsprocessen samt för fortsatt kunskapsuppbyggnad kring biologi och utbredning av de fusariumsvampar som bildar toxinerna. För att säkert komma under det nya gränsvärde för T2+HT2, som från och med 2024 gäller för skalad havre till barnmat, bör man ha halter Inköp av spannmål med särskilda kvalitetskrav är en kritisk process som i grova drag innebär att man utifrån ställda krav hittar de volymer som är bäst lämpade. Lantmännen utvecklar nu sina interna strategier och system för inköp och logistik av spannmål med specialkvaliteter. Genom att nyttja bl.a. framtagna riskkartor och riskmodeller från projektet som underlag, kan man få en säkrare urvalsbas och bli effektivare. I processen kan man samtidigt ställa krav på att råvaran är hållbart odlad. Det är denna levande infrastuktur av data, metoder och rutiner som utgör Baby Grain Passport

Quantitative PCR shows propagation of Plasmodiophora brassicae in Swedish long term field trials

Clubroot (Plasmodiophora brassicae) is a serious soil-borne disease in brassica crops world-wide. We report on a time series of soil samples from Swedish long-term fertility trials started in 1957, 1963 and 1966, which were analyzed for the amount ofP. brassicaeDNA. The crop rotations included a brassica crop every 4 or 6years. All experimental sites with a 4-year rotation of oilseed rape, except one with calcium carbonate in the soil profile, showed high (>1000fg DNA g−1soil) levels ofP. brassicaeDNA after 9, 11 and 12 rotations. In contrast, detectable levels (>5fg DNA g−1soil) ofP. brassicaewere found only at one of five sites with a 6-year rotation of spring oilseed rape. In years with high levels ofP. brassicaeDNA, low yield was reported and a subsequent decline inP. brassicaeDNA in soil was observed. Different NPK (nitrogen/phosphorus/potassium) fertiliser regimes resulted in similarP. brassicaeDNA levels. The robustness and reliability of the method applied was verified by analyses of soil from individual plots compared with a mixture of plots and by repeated analyses of selected samples, which showed thatP. brassicaeDNA remained stable during dry storage

Country-Wide qPCR Based Assessment of Plasmodiophora brassicae Spread in Agricultural Soils and Recommendations for the Cultivation of Brassicaceae Crops in Poland

Clubroot is a damaging disease of oilseed rape and vegetable brassicas worldwide, caused by the soil-borne protist Plasmodiophora brassicae Wor. Due to the long life of resting spores, the assessment of the pathogen abundance in agricultural fields can serve as a guideline for disease control at the country-wide level or the regional scale. Between 2013 and 2019, we collected 431 soil samples from fields cultivated with Brassicaceae crops throughout 16 provinces of Poland. The samples were subjected to qPCR based analysis of P. brassicae DNA concentration. From these data, the spore loads and gene copies g−1 soil were calculated and used to produce an assessment of the current clubroot risk potential at a country-wide and regional scale. The country-wide map, showing the spread of the pathogen in agricultural soils, was made using ArcGis software package implementing the interpolation with the Inverse Distance Weight method. The calculation of gene copies specific to P. brassicae helped to formulate the recommendations for farmers in respect to the cultivation guidelines. It showed a high risk of yield losses in defined regions of north, south-west and central Poland and an urgent need to undertake intensive preventative measures

Artificial Intelligence Supports Automated Characterization of Differentiated Human Pluripotent Stem Cells

Revolutionary advances in AI and deep learning in recent years have resulted in an upsurge of papers exploring applications within the biomedical field. Within stem cell research, promising results have been reported from analyses of microscopy images to, that is, distinguish between pluripotent stem cells and differentiated cell types derived from stem cells. In this work, we investigated the possibility of using a deep learning model to predict the differentiation stage of pluripotent stem cells undergoing differentiation toward hepatocytes, based on morphological features of cell cultures. We were able to achieve close to perfect classification of images from early and late time points during differentiation, and this aligned very well with the experimental validation of cell identity and function. Our results suggest that deep learning models can distinguish between different cell morphologies, and provide alternative means of semi-automated functional characterization of stem cell cultures

Deep convolutional neural networks accurately predict the differentiation status of human induced pluripotent stem cells

Rapid progress of AI technology in the life science area is observed in recent years. Convolutionalneural network (CNN) models were successfully applied for the localization and classification of cellson microscopic images. Induced pluripotent stem cells are one of the most important innovations inbiomedical research and are widely used, e.g. in regenerative medicine, drug screening, and diseasemodeling. However, assessment of cell cultures’ quality requires trained personnel, is timeconsumingand hence expensive. Fluorescence microscope images of human induced pluripotentstem‐hepatocytes (hiPS‐HEPs) derived from three human induced pluripotent stem cell (hiPSC) lineswere taken daily from day 1 until day 22 of differentiation. The cells from day 1 to 14 were classifiedas ´Early differentiation´, and above day 16 as ´Late differentiation´. In this study, it wasdemonstrated that a CNN‐based model can be trained with simple fluorescence microscope imagesof human induced pluripotent stem‐hepatocytes, and then used to predict with high accuracy(96.4%) the differentiation stage of an independent new set of images

Deep convolutional neural networks accurately predict the differentiation status of human induced pluripotent stem cells

Rapid progress of AI technology in the life science area is observed in recent years. Convolutionalneural network (CNN) models were successfully applied for the localization and classification of cellson microscopic images. Induced pluripotent stem cells are one of the most important innovations inbiomedical research and are widely used, e.g. in regenerative medicine, drug screening, and diseasemodeling. However, assessment of cell cultures’ quality requires trained personnel, is timeconsumingand hence expensive. Fluorescence microscope images of human induced pluripotentstem‐hepatocytes (hiPS‐HEPs) derived from three human induced pluripotent stem cell (hiPSC) lineswere taken daily from day 1 until day 22 of differentiation. The cells from day 1 to 14 were classifiedas ´Early differentiation´, and above day 16 as ´Late differentiation´. In this study, it wasdemonstrated that a CNN‐based model can be trained with simple fluorescence microscope imagesof human induced pluripotent stem‐hepatocytes, and then used to predict with high accuracy(96.4%) the differentiation stage of an independent new set of images

Modelling the Effects of Weather Conditions on Cereal Grain Contamination with Deoxynivalenol in the Baltic Sea Region

Fusarium head blight (FHB) is one of the most serious diseases of small-grain cereals worldwide, resulting in yield reduction and an accumulation of the mycotoxin deoxynivalenol (DON) in grain. Weather conditions are known to have a significant effect on the ability of fusaria to infect cereals and produce toxins. In the past 10 years, severe outbreaks of FHB, and grain DON contamination exceeding the EU health safety limits, have occurred in countries in the Baltic Sea region. In this study, extensive data from field trials in Sweden, Poland and Lithuania were analysed to identify the most crucial weather variables for the ability of Fusarium to produce DON. Models were developed for the prediction of DON contamination levels in harvested grain exceeding 200 µg kg−1 for oats, spring barley and spring wheat in Sweden and winter wheat in Poland, and 1250 µg kg−1 for spring wheat in Lithuania. These models were able to predict high DON levels with an accuracy of 70–81%. Relative humidity (RH) and precipitation (PREC) were identified as the weather factors with the greatest influence on DON accumulation in grain, with high RH and PREC around flowering and later in grain development and ripening correlated with high DON levels. High temperatures during grain development and senescence reduced the risk of DON accumulation. The performance of the models, based only on weather variables, was relatively accurate. In future studies, it might be of interest to determine whether inclusion of variables such as pre-crop, agronomic factors and crop resistance to FHB could further improve the performance of the models

Abscisic Acid and Jasmonate Metabolisms Are Jointly Regulated During Senescence in Roots and Leaves of Populus trichocarpa

Plant senescence is a highly regulated process that allows nutrients to be mobilized from dying tissues to other organs. Despite that senescence has been extensively studied in leaves, the senescence of ephemeral organs located underground is still poorly understood, especially in the context of phytohormone engagement. The present study focused on filling this knowledge gap by examining the roles of abscisic acid (ABA) and jasmonate in the regulation of senescence of fine, absorptive roots and leaves of Populus trichocarpa. Immunohistochemical (IHC), chromatographic, and molecular methods were utilized to achieve this objective. A transcriptomic analysis identified significant changes in gene expression that were associated with the metabolism and signal transduction of phytohormones, especially ABA and jasmonate. The increased level of these phytohormones during senescence was detected in both organs and was confirmed by IHC. Based on the obtained data, we suggest that phytohormonal regulation of senescence in roots and leaves is organ-specific. We have shown that the regulation of ABA and JA metabolism is tightly regulated during senescence processes in both leaves and roots. The results were discussed with respect to the role of ABA in cold tolerance and the role of JA in resistance to pathogens

Allies or Enemies: The Role of Reactive Oxygen Species in Developmental Processes of Black Cottonwood (Populus trichocarpa)

In contrast to aboveground organs (stems and leaves), developmental events and their regulation in underground organs, such as pioneer and fine roots, are quite poorly understood. The objective of the current study was to achieve a better understanding of the physiological and molecular role of reactive oxygen species (ROS) and ROS-related enzymes in the process of stem and pioneer root development in black cottonwood (Populus trichocarpa), as well as in the senescence of leaves and fine roots. Results of a transcriptomic analysis revealed that primary/secondary growth and senescence are accompanied by substantial changes in the expression of genes related to oxidative stress metabolism. We observed that some mechanisms common for above- and under-ground organs, e.g., the expression of superoxide dismutase (SOD) genes and SOD activity, declined during stems’ and pioneer roots’ development. Moreover, the localization of hydrogen peroxide (H2O2) and superoxide (O2•–) in the primary and secondary xylem of stems and pioneer roots confirms their involvement in xylem cell wall lignification and the induction of programmed cell death (PCD). H2O2 and O2•– in senescing fine roots were present in the same locations as demonstrated previously for ATG8 (AuTophaGy-related) proteins, implying their participation in cell degradation during senescence, while O2•– in older leaves was also localized similarly to ATG8 in chloroplasts, suggesting their role in chlorophagy. ROS and ROS-related enzymes play an integral role in the lignification of xylem cell walls in Populus trichocarpa, as well as the induction of PCD during xylogenesis and senescence

Country-Wide qPCR Based Assessment of Plasmodiophora brassicae Spread in Agricultural Soils and Recommendations for the Cultivation of Brassicaceae Crops in Poland

Clubroot is a damaging disease of oilseed rape and vegetable brassicas worldwide, caused by the soil-borne protist Plasmodiophora brassicae Wor. Due to the long life of resting spores, the assessment of the pathogen abundance in agricultural fields can serve as a guideline for disease control at the country-wide level or the regional scale. Between 2013 and 2019, we collected 431 soil samples from fields cultivated with Brassicaceae crops throughout 16 provinces of Poland. The samples were subjected to qPCR based analysis of P. brassicae DNA concentration. From these data, the spore loads and gene copies g−1 soil were calculated and used to produce an assessment of the current clubroot risk potential at a country-wide and regional scale. The country-wide map, showing the spread of the pathogen in agricultural soils, was made using ArcGis software package implementing the interpolation with the Inverse Distance Weight method. The calculation of gene copies specific to P. brassicae helped to formulate the recommendations for farmers in respect to the cultivation guidelines. It showed a high risk of yield losses in defined regions of north, south-west and central Poland and an urgent need to undertake intensive preventative measures