UNIGOU REMOTE - AVAILABLE TOPICS
Czech University of Life Sciences Prague, Faculty of Environmental Sciences, Department of Spatial Sciences
Plant Vitality Mapping & Soil/Canopy Moisture Assessments Using Earth Observation Data
Topic Overview:
The objective is to set up a methodical workflow for scaling methods on the example of detailed monitoring of plant stress/vitality and moisture content combining different types of remotely sensed (RS) imagery at various scale levels. The aim is to develop methodology and process data in order to (a) obtain information of the current tree/plant species and health condition (stress); (b) detect and repeatedly map biotic and abiotic disturbances; (c) estimate soil/canopy water content; (d) fuse RS data acquired at various altitude-levels in order to manage imagery scaling to achieve the most effective results; (e) and utilize the benefits arising from the use of multi-sensor recording at various spatial scales (satellites, aircrafts, UAVs, and in-situ measurements).
POSSIBLE DATA (depending on specific deal with student):
Sentinel-2 (VNIR+SWIR)
Sentinel-3 (TIR)
Landsat 8,9 (VNIR+SWIR+TIR)
PlanetScope (VNIR)
UAV-borne and airborne (VNIR+TIR)
In-situ climatic sensors
Field surveys + ground data from forest inventories
A specific topic is possible only after agreement with the student (interview needed in advance). The topic is relatively broad and it is possible to choose different methods, different data, different study scales and different target applications.
Tasks:
Comprehensive literature review. Pre-processing and processing of space-, air-, drone-borne data. Qualitative and quantitative evaluation of given analysis, relevant discussion of the achieved results. Preparation of the scientific manuscript.
Requirements:
Independence, reliability, enthusiasms, critical thinking. Experience with RS data and techniques (image matching, image analysis, statistical evaluation etc.). Skills with software (e.g. ArcGIS, QGIS, ENVI, SNAP, R..).
Outcomes:
Literature review, Data processed, Draft of the manuscript ready for the submission.
References:
Lausch, A., Erasmi, S., King, D.J., Magdon, P., Heurich, M., 2016. Understanding forest health with remote sensing-Part I-A review of spectral traits, processes and remote-sensing characteristics. Remote Sens. 8, 1–44. https://doi.org/10.3390/rs8121029
Lausch, A., Erasmi, S., King, D.J., Magdon, P., Heurich, M., 2017. Understanding forest health with Remote sensing-Part II-A review of approaches and data models. Remote Sens. 9, 1–33. https://doi.org/10.3390/rs9020129
Seidl, R.; Thom, D.; Kautz, M.; Martin-Benito, D.; Peltoniemi, M.; Vacchiano, G.; Wild, J.; Ascoli, D.; Petr, M.; Honkaniemi, J.; et al. Forest disturbances under climate change. Nat. Clim. Chang. 2017, 7, 395–402.
Senf, C.; Seidl, R.; Hostert, P. Remote sensing of forest insect disturbances: Current state and future directions. Int. J. Appl. Earth Obs. Geoinf. 2017, 60, 49–60.
Li, Z. L., Leng, P., Zhou, C., Chen, K. S., Zhou, F. C., & Shang, G. F. (2021). Soil moisture retrieval from remote sensing measurements: Current knowledge and directions for the future. Earth-Science Reviews, 218, 103673.
Babaeian, E., Sadeghi, M., Jones, S. B., Montzka, C., Vereecken, H., & Tuller, M. (2019). Ground, proximal, and satellite remote sensing of soil moisture. Reviews of Geophysics, 57(2), 530-616.
Notes:
Knowledge of neural networks & deep learning methods is welcomed.
The objective is to set up a methodical workflow for scaling methods on the example of detailed monitoring of plant stress/vitality and moisture content combining different types of remotely sensed (RS) imagery at various scale levels. The aim is to develop methodology and process data in order to (a) obtain information of the current tree/plant species and health condition (stress); (b) detect and repeatedly map biotic and abiotic disturbances; (c) estimate soil/canopy water content; (d) fuse RS data acquired at various altitude-levels in order to manage imagery scaling to achieve the most effective results; (e) and utilize the benefits arising from the use of multi-sensor recording at various spatial scales (satellites, aircrafts, UAVs, and in-situ measurements).
POSSIBLE DATA (depending on specific deal with student):
Sentinel-2 (VNIR+SWIR)
Sentinel-3 (TIR)
Landsat 8,9 (VNIR+SWIR+TIR)
PlanetScope (VNIR)
UAV-borne and airborne (VNIR+TIR)
In-situ climatic sensors
Field surveys + ground data from forest inventories
A specific topic is possible only after agreement with the student (interview needed in advance). The topic is relatively broad and it is possible to choose different methods, different data, different study scales and different target applications.
Tasks:
Comprehensive literature review. Pre-processing and processing of space-, air-, drone-borne data. Qualitative and quantitative evaluation of given analysis, relevant discussion of the achieved results. Preparation of the scientific manuscript.
Requirements:
Independence, reliability, enthusiasms, critical thinking. Experience with RS data and techniques (image matching, image analysis, statistical evaluation etc.). Skills with software (e.g. ArcGIS, QGIS, ENVI, SNAP, R..).
Outcomes:
Literature review, Data processed, Draft of the manuscript ready for the submission.
References:
Lausch, A., Erasmi, S., King, D.J., Magdon, P., Heurich, M., 2016. Understanding forest health with remote sensing-Part I-A review of spectral traits, processes and remote-sensing characteristics. Remote Sens. 8, 1–44. https://doi.org/10.3390/rs8121029
Lausch, A., Erasmi, S., King, D.J., Magdon, P., Heurich, M., 2017. Understanding forest health with Remote sensing-Part II-A review of approaches and data models. Remote Sens. 9, 1–33. https://doi.org/10.3390/rs9020129
Seidl, R.; Thom, D.; Kautz, M.; Martin-Benito, D.; Peltoniemi, M.; Vacchiano, G.; Wild, J.; Ascoli, D.; Petr, M.; Honkaniemi, J.; et al. Forest disturbances under climate change. Nat. Clim. Chang. 2017, 7, 395–402.
Senf, C.; Seidl, R.; Hostert, P. Remote sensing of forest insect disturbances: Current state and future directions. Int. J. Appl. Earth Obs. Geoinf. 2017, 60, 49–60.
Li, Z. L., Leng, P., Zhou, C., Chen, K. S., Zhou, F. C., & Shang, G. F. (2021). Soil moisture retrieval from remote sensing measurements: Current knowledge and directions for the future. Earth-Science Reviews, 218, 103673.
Babaeian, E., Sadeghi, M., Jones, S. B., Montzka, C., Vereecken, H., & Tuller, M. (2019). Ground, proximal, and satellite remote sensing of soil moisture. Reviews of Geophysics, 57(2), 530-616.
Notes:
Knowledge of neural networks & deep learning methods is welcomed.
Czech University of Life Sciences in Prague, Faculty of Tropical AgriSciences, Centre for Infectious Animal Diseases
Genetic Bases of SARS-CoV-2 Adaptation to Animals
Topic Overview:
Since the start of the COVID-19 pandemic, SARS-CoV-2 showed its ability to infect wide spectrum of different animal species including white-tailed deer, minks, hamsters, great ape, felines etc. Despite during the pandemics, SARS-CoV-2 was mostly transmitted from human-to-human, several cases of human-to-animal, animal-to-animal and animal-to-human transmission were also observed. Moreover, in some cases the SARS-CoV-2 infected animals served as an important secondary reservoir of the virus or as a source of SARS-CoV-2 strains coding for important evolutionary innovations in its genome. Nevertheless, the precise mechanism allowing SARS-CoV-2 adaptation to different animal hosts are still not know. The goal of this project is to collect data and help with statistical analyses which would help us to better understand which SARS-CoV-2 strains are able to replicate more efficiently in different animal hosts.
Tasks:
The intern will collect data from GISAID, the world largest database of SARS-CoV-2 sequences. Special attention will be focused on those SARS-CoV-2 isolates which high quality full genome is known and which were extracted from animals. Full genome sequences of these animal-originating SARS-CoV-2 isolates will be downloaded together with important metadata (animal species, locality, date, virus clade, virus lineage etc.). For comparison, data describing human-originating SARS-CoV-2 isolates circulating in the same date at the same locality will be collected. These data will be compared to search for animal-originating SARS-CoV-2 isolates which are present on the selected locality with higher frequency than could be expected based on SARS-CoV-2 strains circulating in humans. Positive hits indicate that these strains could develop some adaptation to successfully replicated in the selected animal species. Full genome sequences of these positive hits will be compared with other related animal and human extracted SARS-CoV-2 isolates to detect possible mutations which could be responsible for this phenotype.
Requirements:
Required skills – MS Excel or similar (at least on the independent user level). Beneficial skills – R or Phyton.
Outcomes:
The intern(s) will produce a database of full genome sequences of the animal-originating SARS-CoV-2 isolates including important metadata (animal species, locality, date, virus clade, virus lineage etc.) and data describing human-originating SARS-CoV-2 isolates circulating in the same date at the same locality. Further he/she can prepare and test R scripts testing overrepresentation of detected SARS-CoV-2 strains in animal hosts.
References:
https://www.nature.com/articles/s41467-023-39782-x;
https://www.nature.com/articles/s41586-020-2342-5;
https://www.science.org/content/article/captive-gorillas-test-positive-coronavirus
Since the start of the COVID-19 pandemic, SARS-CoV-2 showed its ability to infect wide spectrum of different animal species including white-tailed deer, minks, hamsters, great ape, felines etc. Despite during the pandemics, SARS-CoV-2 was mostly transmitted from human-to-human, several cases of human-to-animal, animal-to-animal and animal-to-human transmission were also observed. Moreover, in some cases the SARS-CoV-2 infected animals served as an important secondary reservoir of the virus or as a source of SARS-CoV-2 strains coding for important evolutionary innovations in its genome. Nevertheless, the precise mechanism allowing SARS-CoV-2 adaptation to different animal hosts are still not know. The goal of this project is to collect data and help with statistical analyses which would help us to better understand which SARS-CoV-2 strains are able to replicate more efficiently in different animal hosts.
Tasks:
The intern will collect data from GISAID, the world largest database of SARS-CoV-2 sequences. Special attention will be focused on those SARS-CoV-2 isolates which high quality full genome is known and which were extracted from animals. Full genome sequences of these animal-originating SARS-CoV-2 isolates will be downloaded together with important metadata (animal species, locality, date, virus clade, virus lineage etc.). For comparison, data describing human-originating SARS-CoV-2 isolates circulating in the same date at the same locality will be collected. These data will be compared to search for animal-originating SARS-CoV-2 isolates which are present on the selected locality with higher frequency than could be expected based on SARS-CoV-2 strains circulating in humans. Positive hits indicate that these strains could develop some adaptation to successfully replicated in the selected animal species. Full genome sequences of these positive hits will be compared with other related animal and human extracted SARS-CoV-2 isolates to detect possible mutations which could be responsible for this phenotype.
Requirements:
Required skills – MS Excel or similar (at least on the independent user level). Beneficial skills – R or Phyton.
Outcomes:
The intern(s) will produce a database of full genome sequences of the animal-originating SARS-CoV-2 isolates including important metadata (animal species, locality, date, virus clade, virus lineage etc.) and data describing human-originating SARS-CoV-2 isolates circulating in the same date at the same locality. Further he/she can prepare and test R scripts testing overrepresentation of detected SARS-CoV-2 strains in animal hosts.
References:
https://www.nature.com/articles/s41467-023-39782-x;
https://www.nature.com/articles/s41586-020-2342-5;
https://www.science.org/content/article/captive-gorillas-test-positive-coronavirus
Czech University of Life Sciences in Prague, Faculty of Tropical AgriSciences, Centre for Infectious Animal Diseases
Building a Prediction Model of Dengue Outbreaks in Sao Paulo, Brazil
Topic Overview:
Mosquito-borne diseases are among the most dangerous threats for all people living in tropical areas. Seasons associated with a particular type of weather (usually wet and hot) are also typical for the highest incidence of mosquito-borne diseases. This association is logical as mosquitos’ activity and development highly depend on meteorological conditions. We expect that these associations can be found also on small scale (weather in past few days or weeks) allowing us to predict actual risk of mosquito-borne diseases based on actual weather and not only the general risks associated with the season. Brazil (at least some of the federal states) has a very good system for monitoring of mosquito-borne diseases incidence, therefore it seems to be an ideal country for collection of data allowing such type of research.
Since last year, we have collected data on the incidence of Dengue and Zika on a municipality level in Sao Paulo, Brazil, covering the period 2016-2022. In addition, we have extracted data on temperature, humidity, wind and precipitation from the ERA5 reanalysis.
Tasks:
The intern(s) will i) analyze spatio-temporal links between weather variables and Dengue incidence in Sao Paolo and/or ii) help with the collection of socioeconomic data from the study area.
Requirements:
Required skills:
1) data processing in MS Excel and/or R Studio or similar.
2) basic experience with statistical analysis and/or programming (R, Python, Matlab etc.)
Outcomes:
The intern(s) will analyze the links between weather variability and Dengue/Zika dynamisc in Sao Paulo, Brazil Further he/she/they can help with further data collection.
References:
https://www.thelancet.com/journals/lanplh/article/PIIS2542-5196(22)00073-0/fulltext; https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(21)01787-6/fulltext#seccestitle70 (part 1.3); https://www.nature.com/articles/s41598-019-56650-1; http://www.saude.sp.gov.br/cve-centro-de-vigilancia-epidemiologica-prof.-alexandre-vranjac/areas-de-vigilancia/doencas-de-transmissao-por-vetores-e-zoonoses/agravos/febre-amarela/boletim-epidemiologico
Mosquito-borne diseases are among the most dangerous threats for all people living in tropical areas. Seasons associated with a particular type of weather (usually wet and hot) are also typical for the highest incidence of mosquito-borne diseases. This association is logical as mosquitos’ activity and development highly depend on meteorological conditions. We expect that these associations can be found also on small scale (weather in past few days or weeks) allowing us to predict actual risk of mosquito-borne diseases based on actual weather and not only the general risks associated with the season. Brazil (at least some of the federal states) has a very good system for monitoring of mosquito-borne diseases incidence, therefore it seems to be an ideal country for collection of data allowing such type of research.
Since last year, we have collected data on the incidence of Dengue and Zika on a municipality level in Sao Paulo, Brazil, covering the period 2016-2022. In addition, we have extracted data on temperature, humidity, wind and precipitation from the ERA5 reanalysis.
Tasks:
The intern(s) will i) analyze spatio-temporal links between weather variables and Dengue incidence in Sao Paolo and/or ii) help with the collection of socioeconomic data from the study area.
Requirements:
Required skills:
1) data processing in MS Excel and/or R Studio or similar.
2) basic experience with statistical analysis and/or programming (R, Python, Matlab etc.)
Outcomes:
The intern(s) will analyze the links between weather variability and Dengue/Zika dynamisc in Sao Paulo, Brazil Further he/she/they can help with further data collection.
References:
https://www.thelancet.com/journals/lanplh/article/PIIS2542-5196(22)00073-0/fulltext; https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(21)01787-6/fulltext#seccestitle70 (part 1.3); https://www.nature.com/articles/s41598-019-56650-1; http://www.saude.sp.gov.br/cve-centro-de-vigilancia-epidemiologica-prof.-alexandre-vranjac/areas-de-vigilancia/doencas-de-transmissao-por-vetores-e-zoonoses/agravos/febre-amarela/boletim-epidemiologico
Czech University of Life Sciences in Prague, Faculty of Agrobiology, Food and Natural Resources, Department of Botany and Plant Physiology
Combustion Calorimetry and Its Application in Ecosystem Assessment
Topic Overview:
The destructive combustion calorimetry method is one of the methodological possibilities in biological sciences. Using calorimetry, interspecies and interorgan organ differences in the rate of primary and secondary metabolism can be determined. Generally, the lower energy content is usually that of vegetative organs in comparison with the generative organs, whereas stems or leaves have a similar composition of organic matter and a relatively high proportion of ash matter; therefore, their calorific content fluctuates less than in the reproductive organs. This is also suitable for utilizing solar energy of plant leaves, harmful thermometers utilizing sunlight, water, and other natural resources by plants. The use of natural resources affects the composition of plants in ecosystems, which are always affected by convergence or divergence of ecological strategies between species and functional plants. Functional properties of plants may be weakened/enhanced ue to external conditions, and therefore, it is likely that from a physiological point of view it is likely to predict them, but the combustion temperature values are compromised. he combustion calorimetry method is therefore a suitable method for monitoring the development and stability of natural but also agroforestry ecosystems.
Tasks:
The intern will collect plant material at the selected location according to their interest and prepare a sample for analysis in the laboratory. The subsequent analysis of combustion heat will take place at the workplace in Prague. Processing of literary research.
Requirements:
No special skill are needed, except enthusiasm for work and sense of duty. Knowledge of botany, work in the field is an advantage.
Outcomes:
Report and presentation. Sampling in the field, Findings will contribute to the laboratory's publication.
References:
https://link.springer.com/article/10.1007/s10973-020-09961-9,
https://link.springer.com/article/10.1007/s10973-014-3716-4
Recommended for:
Students of ecology and botany programmes.
The destructive combustion calorimetry method is one of the methodological possibilities in biological sciences. Using calorimetry, interspecies and interorgan organ differences in the rate of primary and secondary metabolism can be determined. Generally, the lower energy content is usually that of vegetative organs in comparison with the generative organs, whereas stems or leaves have a similar composition of organic matter and a relatively high proportion of ash matter; therefore, their calorific content fluctuates less than in the reproductive organs. This is also suitable for utilizing solar energy of plant leaves, harmful thermometers utilizing sunlight, water, and other natural resources by plants. The use of natural resources affects the composition of plants in ecosystems, which are always affected by convergence or divergence of ecological strategies between species and functional plants. Functional properties of plants may be weakened/enhanced ue to external conditions, and therefore, it is likely that from a physiological point of view it is likely to predict them, but the combustion temperature values are compromised. he combustion calorimetry method is therefore a suitable method for monitoring the development and stability of natural but also agroforestry ecosystems.
Tasks:
The intern will collect plant material at the selected location according to their interest and prepare a sample for analysis in the laboratory. The subsequent analysis of combustion heat will take place at the workplace in Prague. Processing of literary research.
Requirements:
No special skill are needed, except enthusiasm for work and sense of duty. Knowledge of botany, work in the field is an advantage.
Outcomes:
Report and presentation. Sampling in the field, Findings will contribute to the laboratory's publication.
References:
https://link.springer.com/article/10.1007/s10973-020-09961-9,
https://link.springer.com/article/10.1007/s10973-014-3716-4
Recommended for:
Students of ecology and botany programmes.
Czech University of Life Sciences in Prague, Faculty of Agrobiology, Food and Natural Resources, Department of Botany and Plant Physiology
The Effect of Hazardous Substances on the Germination and Emergence of Selected Plants
Topic Overview:
Heavy metal, pharmaceutical or other organic pollutants is a challenging task due to its non-degradable nature, which allows it to persist in the soil much longer than other components of the biosphere. Rapid industrialization and poor management of industrial wastewater lead to increased pollution of metals and pharmaceuticals in all components of the environment. Crops have shown varying tolerance to metal or drug stress based on their biochemical and genetic composition. Seed germination and seedling growth are important growth stages in the plant life cycle, as the number of healthy seedlings ensures greater crop growth in the field and thus higher production.
Tasks:
The intern will conduct an experiment with the germination of a selected crop in an environment contaminated with hazardous substances (e.g., hazardous metals, pharmaceuticals). It evaluates the parameters of germination and emergence of plants.
Requirements:
Basic laboratory practice. Ability to maintain and operate short-term laboratory experiments, basic knowledge of data manipulation in spreadsheets. Evaluation of the experiment.
Outcomes:
Report and presentation. Tabular data of measured germination and emergence parameters.
References:
https://link.springer.com/article/10.1007/s11756-021-00952-1,
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3783763/,
https://link.springer.com/article/10.1007/s11270-019-4329-
Recommended for:
Students of plant physiology, biology, and plant cultivation programmes.
Heavy metal, pharmaceutical or other organic pollutants is a challenging task due to its non-degradable nature, which allows it to persist in the soil much longer than other components of the biosphere. Rapid industrialization and poor management of industrial wastewater lead to increased pollution of metals and pharmaceuticals in all components of the environment. Crops have shown varying tolerance to metal or drug stress based on their biochemical and genetic composition. Seed germination and seedling growth are important growth stages in the plant life cycle, as the number of healthy seedlings ensures greater crop growth in the field and thus higher production.
Tasks:
The intern will conduct an experiment with the germination of a selected crop in an environment contaminated with hazardous substances (e.g., hazardous metals, pharmaceuticals). It evaluates the parameters of germination and emergence of plants.
Requirements:
Basic laboratory practice. Ability to maintain and operate short-term laboratory experiments, basic knowledge of data manipulation in spreadsheets. Evaluation of the experiment.
Outcomes:
Report and presentation. Tabular data of measured germination and emergence parameters.
References:
https://link.springer.com/article/10.1007/s11756-021-00952-1,
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3783763/,
https://link.springer.com/article/10.1007/s11270-019-4329-
Recommended for:
Students of plant physiology, biology, and plant cultivation programmes.
Czech University of Life Sciences in Prague, Faculty of Agrobiology, Food and Natural Resources, Department of Botany and Plant Physiology
Effect of Climate Change on Plant Properties
Topic Overview:
In field conditions, individual stressors do not act on plants separately, but always in combination, e.g. high temperature, higher intensity of sunlight and lack of water. According to some projected reports, agriculture is considered to be the most threatened activity adversely affected by climate change. Abiotic stress factors cause morphological, physiological and biochemical changes. Ultimately, they can affect product yield and quality, as well as alter visual appearance and/or nutritional value. Plant adaptation and stress mitigation are essential to increase agricultural system resilience, crop yields and quality assurance. Environmental conditions cannot be controlled and therefore there are several strategies such as agronomic techniques or breeding more tolerant cultivars. Another way to eliminate the impact of abiotic stressors is to increase the yield potential of new cultivars. The storage capacity of the spike, which stimulates the influx of assimilates into the grain in the period after anthesis, plays an important role in yield formation. Therefore, sources of genes are sought to increase the number of reproductive organs, such as the number of spikelets in an ear, the number of grains in an ear, or the number of embryos in a flower.
Tasks:
The intern will focus primarily on the processing of literature research on the given topic. An option is to set up a short-term experiment to monitor the effect of abiotic stressors (water deficit, high temperature, salinity) on the selected crop.
Requirements:
No special skills are needed, except enthusiasm for work and a sense of duty.
Outcomes:
Report and presentation. The findings will contribute to the laboratory's publication.
References:
https://iks.ukzn.ac.za/sites/default/files/61.pdf,
https://www.sciencedirect.com/science/article/pii/S2589004220310129 https://mdpi-res.com/d_attachment/agronomy/agronomy-12-00078/article_deploy/agronomy-12-00078-v2.pdf?version=164189530
Recommended for:
Students of plant physiology, biology, and plant cultivation programmes.
In field conditions, individual stressors do not act on plants separately, but always in combination, e.g. high temperature, higher intensity of sunlight and lack of water. According to some projected reports, agriculture is considered to be the most threatened activity adversely affected by climate change. Abiotic stress factors cause morphological, physiological and biochemical changes. Ultimately, they can affect product yield and quality, as well as alter visual appearance and/or nutritional value. Plant adaptation and stress mitigation are essential to increase agricultural system resilience, crop yields and quality assurance. Environmental conditions cannot be controlled and therefore there are several strategies such as agronomic techniques or breeding more tolerant cultivars. Another way to eliminate the impact of abiotic stressors is to increase the yield potential of new cultivars. The storage capacity of the spike, which stimulates the influx of assimilates into the grain in the period after anthesis, plays an important role in yield formation. Therefore, sources of genes are sought to increase the number of reproductive organs, such as the number of spikelets in an ear, the number of grains in an ear, or the number of embryos in a flower.
Tasks:
The intern will focus primarily on the processing of literature research on the given topic. An option is to set up a short-term experiment to monitor the effect of abiotic stressors (water deficit, high temperature, salinity) on the selected crop.
Requirements:
No special skills are needed, except enthusiasm for work and a sense of duty.
Outcomes:
Report and presentation. The findings will contribute to the laboratory's publication.
References:
https://iks.ukzn.ac.za/sites/default/files/61.pdf,
https://www.sciencedirect.com/science/article/pii/S2589004220310129 https://mdpi-res.com/d_attachment/agronomy/agronomy-12-00078/article_deploy/agronomy-12-00078-v2.pdf?version=164189530
Recommended for:
Students of plant physiology, biology, and plant cultivation programmes.
Topic Overview:
As remote sensing (RS) is a crucial source of Earth spatial data at various scales, the ongoing climate change brings novel challenges for RS utilisation. Early detection of biotic infestation at individual trees is crucial; however, calibration and validation protocols of Unmanned Aerial Vehicles (UAVs) are still not fully utilised. Satellites are invaluable for delineating the core areas of infestation and studying the spatiotemporal dynamics across large extents. A multi-source approach integrates various platforms (satellites, aircraft, UAVs) and sensors (visible, multispectral, hyperspectral, radar, thermal and even chlorophyll fluorescence) at different scale levels and allows the most reliable complex evaluation. Therefore, the synergy of UAVs and field measurements with satellite data carries a potential for mapping and predicting the ever-increasing biotic outbreaks that have not been fully discovered. The project aims to develop an innovative RS solution linking different data types, which can contribute to more effective detection and monitoring of forest disturbances. The project aims to fill the knowledge gap in remote sensing (RS) data (i) preprocessing and its calibration for the tasks connected with forest disturbances, (ii) detection of bark beetle infestation using close-range RS, and (iii) long-term monitoring of bark beetle spreading using satellites.
REMOTE SENSING DATA:
Sentinel-1 (radar, C-band)
Sentinel-2 (VNIR+SWIR)
Landsat 8,9 (VNIR+SWIR+TIR)
PlanetScope (VNIR)
SkySat (VNIR)
Prisma (VNIR+SWIR+TIR)
UAV-borne and airborne (VNIR+TIR, lidar)
In-situ climatic sensors
Field surveys + ground data from forest inventories
A specific topic is possible only after agreement with the student (interview needed in advance). The topic is relatively broad and it is possible to choose different methods, different data, different study scales and different target applications.
Tasks:
Comprehensive literature review. pre-processing and processing input remote sensing data. Species classification and stress detection using multispectral/hyperspectral/thermal data (to be specified). Qualitative and quantitative evaluation of given analysis, relevant discussion of the achieved results. Preparation of the scientific manuscript.
Requirements:
Independence, reliability, enthusiasms, critical thinking. Experience with remote sensing data and techniques (image matching, image analysis, image spectroscopy, statistical evaluation etc.). Skills with GIS software (e.g., ArcGIS, QGIS) and image processing software (e.g., ENVI, eCognition, SNAP). Experience with programming (e.g., Java, R, and python) is an advantage.
Outcomes:
Literature review, data processing, help with manuscript preparation.
References:
Klouček, T., Komárek, J., Surový, P., Hrach, K., Janata, P., Vašíček, B. 2019. The Use of UAV Mounted Sensors for Precise Detection of Bark Beetle Infestation. Remote Sensing, 11, 1561, doi:10.3390/rs11131561.
Lausch, A., Erasmi, S., King, D.J., Magdon, P., Heurich, M., 2016. Understanding forest health with remote sensing-Part I-A review of spectral traits, processes and remote-sensing characteristics. Remote Sens. 8, 1–44. https://doi.org/10.3390/rs8121029
Lausch, A., Erasmi, S., King, D.J., Magdon, P., Heurich, M., 2017. Understanding forest health with Remote sensing-Part II-A review of approaches and data models. Remote Sens. 9, 1–33. https://doi.org/10.3390/rs9020129
Seidl, R.; Thom, D.; Kautz, M.; Martin-Benito, D.; Peltoniemi, M.; Vacchiano, G.; Wild, J.; Ascoli, D.; Petr, M.; Honkaniemi, J.; et al. Forest disturbances under climate change. Nat. Clim. Chang. 2017, 7, 395–402.
Senf, C.; Seidl, R.; Hostert, P. Remote sensing of forest insect disturbances: Current state and future directions. Int. J. Appl. Earth Obs. Geoinf. 2017, 60, 49–60.
As remote sensing (RS) is a crucial source of Earth spatial data at various scales, the ongoing climate change brings novel challenges for RS utilisation. Early detection of biotic infestation at individual trees is crucial; however, calibration and validation protocols of Unmanned Aerial Vehicles (UAVs) are still not fully utilised. Satellites are invaluable for delineating the core areas of infestation and studying the spatiotemporal dynamics across large extents. A multi-source approach integrates various platforms (satellites, aircraft, UAVs) and sensors (visible, multispectral, hyperspectral, radar, thermal and even chlorophyll fluorescence) at different scale levels and allows the most reliable complex evaluation. Therefore, the synergy of UAVs and field measurements with satellite data carries a potential for mapping and predicting the ever-increasing biotic outbreaks that have not been fully discovered. The project aims to develop an innovative RS solution linking different data types, which can contribute to more effective detection and monitoring of forest disturbances. The project aims to fill the knowledge gap in remote sensing (RS) data (i) preprocessing and its calibration for the tasks connected with forest disturbances, (ii) detection of bark beetle infestation using close-range RS, and (iii) long-term monitoring of bark beetle spreading using satellites.
REMOTE SENSING DATA:
Sentinel-1 (radar, C-band)
Sentinel-2 (VNIR+SWIR)
Landsat 8,9 (VNIR+SWIR+TIR)
PlanetScope (VNIR)
SkySat (VNIR)
Prisma (VNIR+SWIR+TIR)
UAV-borne and airborne (VNIR+TIR, lidar)
In-situ climatic sensors
Field surveys + ground data from forest inventories
A specific topic is possible only after agreement with the student (interview needed in advance). The topic is relatively broad and it is possible to choose different methods, different data, different study scales and different target applications.
Tasks:
Comprehensive literature review. pre-processing and processing input remote sensing data. Species classification and stress detection using multispectral/hyperspectral/thermal data (to be specified). Qualitative and quantitative evaluation of given analysis, relevant discussion of the achieved results. Preparation of the scientific manuscript.
Requirements:
Independence, reliability, enthusiasms, critical thinking. Experience with remote sensing data and techniques (image matching, image analysis, image spectroscopy, statistical evaluation etc.). Skills with GIS software (e.g., ArcGIS, QGIS) and image processing software (e.g., ENVI, eCognition, SNAP). Experience with programming (e.g., Java, R, and python) is an advantage.
Outcomes:
Literature review, data processing, help with manuscript preparation.
References:
Klouček, T., Komárek, J., Surový, P., Hrach, K., Janata, P., Vašíček, B. 2019. The Use of UAV Mounted Sensors for Precise Detection of Bark Beetle Infestation. Remote Sensing, 11, 1561, doi:10.3390/rs11131561.
Lausch, A., Erasmi, S., King, D.J., Magdon, P., Heurich, M., 2016. Understanding forest health with remote sensing-Part I-A review of spectral traits, processes and remote-sensing characteristics. Remote Sens. 8, 1–44. https://doi.org/10.3390/rs8121029
Lausch, A., Erasmi, S., King, D.J., Magdon, P., Heurich, M., 2017. Understanding forest health with Remote sensing-Part II-A review of approaches and data models. Remote Sens. 9, 1–33. https://doi.org/10.3390/rs9020129
Seidl, R.; Thom, D.; Kautz, M.; Martin-Benito, D.; Peltoniemi, M.; Vacchiano, G.; Wild, J.; Ascoli, D.; Petr, M.; Honkaniemi, J.; et al. Forest disturbances under climate change. Nat. Clim. Chang. 2017, 7, 395–402.
Senf, C.; Seidl, R.; Hostert, P. Remote sensing of forest insect disturbances: Current state and future directions. Int. J. Appl. Earth Obs. Geoinf. 2017, 60, 49–60.
Czech University of Life Sciences Prague, Faculty of Environmental Sciences, Department of Spatial Sciences
Fusion of Remote Sensing Data and Techniques for Detection of Forest Disturbances: From Satellites to Needles
Topic Overview:
Air dried hams are very popular and worldwide spread comodity. Different conditions, such as high temperature, heavy rainfall, and humidity, promote fungal growth leading to increased occurrence of mycotoxins.
Ochratoxin A is one of the most serious contaminant of natural origin, is produced by toxigenic microfungi Aspergillus and Penicillium genera as their secondary metabolite.
The aim of this work is a literature review of the occurrence of ochratoxin A in air dried hams spices from North and South America market, their producers, legislation, and potential ways of mitigation.
References:
Chen, Yuanshan, Jiang Chen, Qiujin Zhu, and Jing Wan. 2022. "Ochratoxin A in Dry-Cured Ham: OTA-Producing Fungi, Prevalence, Detection Methods, and Biocontrol Strategies—A Review" Toxins 14, no. 10: 693. https://doi.org/10.3390/toxins14100693
FAOSTAT. Food and Agriculture Organization of the United Nations. Available online: http://www.fao.org/faostat/en/#data/QC/visualize
Francisco Pizzolato Montanha, Amanda Anater, Javier Felipe Burchard, Fernando Bittencourt Luciano, Giuseppe Meca, Lara Manyes, Cláudia Turra Pimpão, Mycotoxins in dry-cured meats: A review, Food and Chemical Toxicology, Volume 111, 2018, Pages 494-502, ISSN 0278-6915,
https://doi.org/10.1016/j.fct.2017.12.008.
IARC, 1993. International Agency for Research on Cancer. IARC Monographs on the evaluation of
carcinogenic risks to humans: Some naturally occuring substances: Food items and
costituents, heterocyclic aromatic amines and mycotoxins. IARC Press, Lyon, France.
IARC, 2012. International Agency for Research on Cancer. Chemical agents and related occupations: A review of human carcinogens. IARC Press, Lyon, France.
Lešić T, Vulić A, Vahčić N, Šarkanj B, Hengl B, Kos I, Polak T, Kudumija N, Pleadin J. The Occurrence of Five Unregulated Mycotoxins Most Important for Traditional Dry-Cured Meat Products. Toxins (Basel). 2022 Jul 12;14(7):476. doi: 10.3390/toxins14070476. PMID: 35878214; PMCID: PMC9315684.
Air dried hams are very popular and worldwide spread comodity. Different conditions, such as high temperature, heavy rainfall, and humidity, promote fungal growth leading to increased occurrence of mycotoxins.
Ochratoxin A is one of the most serious contaminant of natural origin, is produced by toxigenic microfungi Aspergillus and Penicillium genera as their secondary metabolite.
The aim of this work is a literature review of the occurrence of ochratoxin A in air dried hams spices from North and South America market, their producers, legislation, and potential ways of mitigation.
References:
Chen, Yuanshan, Jiang Chen, Qiujin Zhu, and Jing Wan. 2022. "Ochratoxin A in Dry-Cured Ham: OTA-Producing Fungi, Prevalence, Detection Methods, and Biocontrol Strategies—A Review" Toxins 14, no. 10: 693. https://doi.org/10.3390/toxins14100693
FAOSTAT. Food and Agriculture Organization of the United Nations. Available online: http://www.fao.org/faostat/en/#data/QC/visualize
Francisco Pizzolato Montanha, Amanda Anater, Javier Felipe Burchard, Fernando Bittencourt Luciano, Giuseppe Meca, Lara Manyes, Cláudia Turra Pimpão, Mycotoxins in dry-cured meats: A review, Food and Chemical Toxicology, Volume 111, 2018, Pages 494-502, ISSN 0278-6915,
https://doi.org/10.1016/j.fct.2017.12.008.
IARC, 1993. International Agency for Research on Cancer. IARC Monographs on the evaluation of
carcinogenic risks to humans: Some naturally occuring substances: Food items and
costituents, heterocyclic aromatic amines and mycotoxins. IARC Press, Lyon, France.
IARC, 2012. International Agency for Research on Cancer. Chemical agents and related occupations: A review of human carcinogens. IARC Press, Lyon, France.
Lešić T, Vulić A, Vahčić N, Šarkanj B, Hengl B, Kos I, Polak T, Kudumija N, Pleadin J. The Occurrence of Five Unregulated Mycotoxins Most Important for Traditional Dry-Cured Meat Products. Toxins (Basel). 2022 Jul 12;14(7):476. doi: 10.3390/toxins14070476. PMID: 35878214; PMCID: PMC9315684.
University of Hradec Králové, Faculty of Science, Department of Biology
A Review on Mycotoxins with Focus on Ochratoxin A in Air Dried Hams from North and South America Market in the Light of the Last Ten Years
