Technologies of the Biology Centre
Diagnosis of viruses, viroids and phytoplasma using Next Generation Sequencing
Dozens of economically significant viruses are known to cause damage to the yield and quality of individual agricultural crops. There is no test capable to identify all the pathogens in one reaction. The use of Next Generation Sequencing (NGS) has the potential to detect all viruses in a plant sample (e.g. 22 viruses in a cherry); not only known viruses but also new disease causing viruses, especially in case of multiple infections. It can be used not only in plant biology, where the current routine diagnosis of plant viruses, viroids and phytoplasma is based on ELISA (viruses) and polymerase chain reaction (viruses, viroids and phytoplasma), but also in agriculture. For example, for a specific area of genetic research aimed at the study of plant and animal genomes with the ultimate goal of generating agronomic enhancements, such as improving crop quality and yield, increasing plant resistance against pathogens, reducing herbicide use, improving plant breeding efficiency and increasing natural tolerance to abiotic stresses, such as drought or frost.
EcoVault – software with database for storing a large volume of biological and ecological data
EcoVault is a database management system – a task researchers standardly delegate to software tools such as MS Excel, MS Access, Biota and others. However, EcoVault, is more intuitive than these other programs, working with it does not require deeper IT knowledge, and data from these programs can be exported to it and imported from it. EcoVault is a modern browserbased application with a user interface known to all who normally fill forms, filter and search for data on websites. The EcoVault interface also allows several users to work on a single dataset simultaneously, both on local networks and the worldwide network. The database has a basic structure for working with taxons, samples, observations of individuals from different trophic levels, as well as for mutual specific interactions. Users can configure the system for individual projects based on their sampling and protocols, which can include adding userdefined variables, setting authentication rules, and setting rules for linking types or other variables.
System for in vitro testing of anti-tick preparations and vaccines
Membrane feeding of ticks allows testing of antitick preparations and vaccines without the use of laboratory and experimental animals and therefore without the associated costs (purchase, breeding, operation). Membrane feeding greatly simplifies the entire testing process, and in addition to manipulation with animals itself, narcotics injections, which may have different effects on the test, and other injections are also avoided when testing organic compounds. In addition, the amount of test substances is lower in in vitro testing and the possibility of simultaneous testing of different preparations is greater than that of in vivo tests. This membrane feeding system allows you to work with all stages of development of ticks, i.e. also nymphs, which represent the stage with a highest risk for the transmission of infectious diseases. The ethical aspect is, however, also important, for example when testing anti-tick repellents, etc., it is possible to apply for a certificate confirming the non-use of experimental animals, such as the Humane Cosmetics Standard – HCS.
Diagnosis of Lyme disease with the help of markers of the early stage of the disease
This is a diagnostic kit for early diagnosis of patients with Lyme disease which is able to detect the disease with higher efficacy than currently used tests. It also allows to diagnose the patient more quickly after tick infestation, especially when the patient is infected with rarer Borrelia pathogens. Although Lyme disease is among the most intensively studied tick-borne diseases, there is no vaccine available for this disease so far. Current tests use markers of later stages of the disease, have an efficacy of about 70%, and are unable to detect the early stages. Lyme borreliosis does not cause death directly, but if the diagnosis is late, the spirochetes are able to settle in the body, for example, in joint fluid, and cause life-threatening health problems in patients, and there is a risk of relapse if the immune system is weakened. This test is ultimately able to save the costs of treating patients, as timely and accurate diagnostics will allow shorter treatment and reduce relapses and chronic disease states.
Transmission model of Lyme disease
A reliable laboratory transmission model is necessary for routine testing of potential vaccines and preparations to prevent Borrelia transmission. At present, the workplaces of BC CAS are the only ones in the world to have a detailed transmission model including the European tick of Ixodes ricinus and the European Borrelia strains (in particular Borrelia afzelii – the most common borreliosis agent in Europe). In the US there is a transmission model for the American tick Ixodes scapularis and the American strain Borrelia burgdorferi sensu stricto. Due to different biology of the two systems, however, the US model cannot be used in European conditions. The transmission model developed at BC CAS worksites therefore has the potential to become sought after in the most important national and international projects on ticks and tick-transmitted pathogens, and at the same time also serves as a platform for applied and contractual research.
Special growing substrate
Special growing substrate ("smart growing substrate") with increased resistance to diseases and pests. It is a value-added substrate (2 in 1 or 3 in 1), which is pre-colonized with the CCM 8367 strain of the entomopathogenic fungus Isaria fumosorosea, either alone or in combination with other bioagents based on the genus Pythium or Trichoderma, or with organic or mineral fertilizers. The substrate thus offers protection against important plant pests that spend part of their development cycle in the soil (e.g. fungus gnats (Sciaridae), weevils). The use of products based on entomopathogenic fungi, due to their very complex mode of action on pests, prevents the development of resistance and leaves no residues. Strain CCM8367 is highly virulent against both butterflies and beetles and can be expected to be highly effective against a complex of canola pests. The fungus Isaria fumosorosea has fungicidal effects in addition to its insecticidal effects.
Duoeffect - Insecticidal and acaricidal additive for plant growing substrates
The unique soil additive provides protection against important plant pests by combining the action of two bioagents. The complex way of acting on pests prevents the development of resistance and leaves no residues, making it suitable for organic cultivation and bio-dynamic agriculture. A number of chemical insecticides will be banned in the future due to stricter legislative conditions, which is why major chemical concerns are already incorporating biopesticides into their portfolios. Special growing or suppressive substrates are difficult to store and transport in a way that preserves their properties. Due to unsuitable conditions, it loses efficiency significantly. The logistics of high-volume goods such as substrates are quite complicated and costly. The highly concentrated formulation, where the substrate is only a carrier, allows for several times smaller packaging. Soil additive is also not subject to as strict legislative rules as biopesticides. It enriches the soil or growing medium with useful micro and macro organisms and takes advantage of their synergistic effect. Duoeffect works on the basis of two bioagens: the entomopathogenic fungus Isaria fumosorosea strain CCM 8367, the use of which is protected by a patent, and another bioagens, the combination of which achieves extended efficacy on multiple species of insect pests and harmful soil mites. The combination and synergy of both bioagens ensures an immediate effect, e.g. against fungus gnats, as well as long-term survival in the treated soil (substrate). In addition, the entomopathogenic fungus has an inhibitory effect on the growth of some pathogenic microorganisms. It allows to reduce the consumption of chemical pesticides and increase the quality of production with minimal impact on the environment. This soil preparation can be used especially in the cultivation of indoor and outdoor flowers and herbs grown in pots, boxes or beds, to protect greenhouse crops, especially vegetables and fruit and ornamental shrubs and trees and other crops. It is intended for application to soil, for enrichment of growing media and composts and for pickling seeds and seedlings. It is particularly suitable for small growers and organic and bio-dynamic agriculture.
Food for bees
A number of stress factors acting on bees in a so-called cocktail effect can cause colony death. In particular, the low quality and low diversity of pollen and the substitution of sugar for honey is identified as one of the causes of a significant reduction in bee immunity to disease from the larval to the adult stage. In addition, there is virtually no effective and safe agens useful for suppressing the spores and growth of the culture of Paenibacillus larvae, the bacterium causing the bee foulbrood, which is the most important current bee disease. This disease has been controlled for many years with pyrethroids, organophosphates and anti-biotics, which can subsequently contaminate bee products, especially honey. Feed for bees according to this technical solution containing sugar, water and 0.1 to 20% by weight of Chlorella sp. algae in the form of dried algal biomass is an attractive food for bees and represents a varied source of nutritional substances in a period that is poor in natural pollen sources. In addition, it has been shown to have a positive effect on increasing health resistance. Secondary metabolites of algae generally differ from higher plants, fungi and bacteria not only in their chemical structure but also in their spectrum of biological activities, such as antibacterial, allelopathic, antiviral, fungicidal activity or inhibitory effects against a number of enzymes. The composition of the biomass of this algae is varied, very similar to pollen, with a high protein content (up to 40-60%) and also contains a group of substances that have an inhibitory effect on the causative agent of the foulbrood, the bacterium P. larvae.
Smart Hive - a comprehensive system for digital monitoring of beehives
The way bees are kept can affect the health of the colony, thereby increasing or decreasing losses. Similarly, methods of diagnosis and prevention of bee diseases can influence the health of the colony. Therefore, it is important to signal in time the course of key life parameters in the hive and to monitor the manifestations of hive activities in the area of the hive entrance. That is why early signaling is important in the course of key life parameters in the hive and monitoring the manifestations of hive activities in the area of the hive entrance. Monitoring the condition of the colony using modern digital technologies and information on the course of key life parameters in the colony, including the detection of the Varroa mite, are useful not only for remote control of hives, but especially for possible early intervention of beekeepers - beginners, experienced hobby beekeepers, professional beekeepers and all those who need to control hives remotely. The solution aims in particular to contribute to improving the health status of bees, especially by early signaling of the course of key life parameters in the hive, monitoring the manifestations of colony activity in the area of the entrance to the hive and refining the detection of the parasite - Varroa destructor mite - on the hive mat. The technical solution is developed in cooperation with the Institute of Applied Informatics at the University of South Bohemia in Č. Budějovice. The new colony monitoring system uses the latest findings from artificial intelligence, neural networks, deep learning and IOT technologies. Thanks to this, it is possible to automatically monitor variables such as the temperature and humidity in the hive, the temperature in a tuft of bees, the temperature, humidity and barometric pressure outside the hive, bee sounds, hive weight, CO2 concentration in the hive, as well as the visual monitoring of the hives by the camera system - the frequency of bees entering and leaving the hives. Beekeepers can have an overview not only of the condition of the colony, the conditions inside the hive and the surrounding area, but they can also monitor their colonies, for example, using GPS in case of hive theft or using a scale to monitor the growth, to detect honey theft, swarming, etc. Using artificial intelligence, neural networks and deep learning, the detection of a queen bee on a honeycomb or the detection of a pathogen on a hive mat can then be refined.
Robotic station category BSL-3 for complete automatized processing of biological samples allowing further measurements in combination with different types of analytical instruments (without limitation to a particular manufacturer). Universally usable station for commercial and research bioanalytical laboratories, primarily for the analysis of xenobiotics (exogenous substances entering the organism from the environment, including drugs, pharmaceuticals, their metabolites, food, etc.), including analysis of endogenous metabolites. The construction, programming and debugging of the automatic operation of the robotic station allows for the preparation and processing of biological samples of various types (body fluids such as urine, serum, cell extract, etc.) without supervision by the operator 24 hours a day. For the analysis of bioactive substances and toxic substances, the device can be placed directly in the fume cupboard or other suitable space for handling such substances.
Multi-user platform for analytics and data services
A software tool developed on BC, called Metabolite Mapper, and associated metabolite profile database. Metabolite Mapper is designed for automatic processing of data from analytical files that are generated by mass spectrometers. Because modern methods allow the detection of hundreds of substances, the deployment of such tool is necessary in research and in the implementation of complex diagnostic methods in medicine, food industry, etc. The commercial use of the software and the associated metabolomics database is offered in the form of a so-called cloud.
Testing parasiticidal and immunomodulatory substances to combat myxozoan infections in aquaculture using in vitro and in vivo models
Myxozoa are microscopic fish parasites whose spread can have a devastating effect on fish stocks in the wild, but especially in aquaculture. In addition, no legalized treatment of this disease is currently available. The parallel process of direct control of infection with parasiticides and simultaneous improvement of the host immune system, so-called immunomodulation, is a very effective approach to fighting this disease. However, a fully functional system for testing substances with parasiticide or immunostimulating properties is necessary for that purpose. The in vitro model with a focus on the blood stage is the key one for testing because most species of myxozoan dwell for at least a short time in their blood before attacking the target’s organs. For immunostimulant testing, companies engaged in fish farming, nutrition for artificially reared fish and aquaculture in general, require an in vivo diagnostic system and the evelopment of such a test model is a response to that need.
Use of a soil Actinomycetes collection to obtain therapeutically active substances
The resistance of many pathogens to antibiotics requires the search for new therapeutically active substances. An effective way to search for substances similar to known antibiotics is genomic analysis aimed at the presence of genes necessary for the synthesis of antibiotics. Institute of Soil Biology BC has created an extensive collection of actinomycetes, which is a potential source of previously unknown active substances. Most cultures belong to the family Streptomycetaceae (Streptomyces and Kitasatospora), however some other families are also represented (Pseudonocardiaceae: the genera Letznea, Amycolatopsis, Saccharothrix, and Nocardiaceae: the genus Nocardia). Streptomyces are known to produce many bioactive metabolites, which can be used in medicine as antifungal, antiviral, anticoagulant, immunomodification, antitumor drugs or as enzyme inhibitors. Furthermore, also in agriculture as insecticides, herbicides, fungicides or growth-promoting agent for plants and animals.
Use of a soil Micromycetes collection to obtain biotechnologically useful substances
Soil microscopic fungi (micromycetes) produce a number of industrially useful substances - enzymes, unsaturated (omega) fatty acids, antibiotics, pigments. Collections of soil micromycetes are potentially the source of such specific types of fungi, which can be more effective as producers of known substances or as producers completely new substances. The collection of microscopic fungi contains over 2000 strains of predominantly filamentous fungi (ascomycetes, zygomycetes, and anamorphic stages of asko- and basidiomycetes) isolated from a variety of environments (soil, compost, air, cave environment or invertebrate digestive tracts and excrements etc.). The collection is currently a highly unique collection containing specific isolates that are not located in any other collection in the world.