Emulators for dynamic vegetation models - Supervised learning in large data sets

The observed and expected changes in the environment due to human actions implies risks that future food production will be insufficient. Pre- dicting the impact these changes have on the agricultural system could be beneficial by allowing for proactive mitigating efforts. The prediction of these impacts often involve large computer programs that simulate the behavior of the environment. By implementing a statistical representation of the simulator, called an emulator, our hope is that these predictions could be obtain at a lower computational cost. This master thesis has implemented and evaluated a Gaussian process emulator for a vegeta- tion model that is used for predicting the annual production of spring wheat based on climate data at different locations around the world. The problem of accurately modeling the simulator using a Gaussian process approach was split into two parts. The first part was to model the average yield at each location given average climate input at that location. The second part was to model the yield at a specific year for a location given the average yield at that location and the climate input anomalies dur- ing that year. The results was far from satisfactory and a more complex approach is probably needed before the emulator can be of any practical use. Based on our findings, possible extensions that might improve results are discussed

Contributions to the Natural History of Aroostook: The Orchis

A pamphlet on some of the most rare and beautiful lady\u27s slipper plants found in Aroostook County in the early 1900s. Includes photographs

Putative cold acclimation pathways in Arabidopsis thaliana identified by a combined analysis of mRNA co-expression patterns, promoter motifs and transcription factors

<p>Abstract</p> <p>Background</p> <p>With the advent of microarray technology, it has become feasible to identify virtually all genes in an organism that are induced by developmental or environmental changes. However, relying solely on gene expression data may be of limited value if the aim is to infer the underlying genetic networks. Development of computational methods to combine microarray data with other information sources is therefore necessary. Here we describe one such method.</p> <p>Results</p> <p>By means of our method, previously published Arabidopsis microarray data from cold acclimated plants at six different time points, promoter motif sequence data extracted from ~24,000 Arabidopsis promoters and known transcription factor binding sites were combined to construct a putative genetic regulatory interaction network. The inferred network includes both previously characterised and hitherto un-described regulatory interactions between transcription factor (TF) genes and genes that encode other TFs or other proteins. Part of the obtained transcription factor regulatory network is presented here. More detailed information is available in the additional files.</p> <p>Conclusion</p> <p>The rule-based method described here can be used to infer genetic networks by combining data from microarrays, promoter sequences and known promoter binding sites. This method should in principle be applicable to any biological system. We tested the method on the cold acclimation process in Arabidopsis and could identify a more complex putative genetic regulatory network than previously described. However, it should be noted that information on specific binding sites for individual TFs were in most cases not available. Thus, gene targets for the entire TF gene families were predicted. In addition, the networks were built solely by a bioinformatics approach and experimental verifications will be necessary for their final validation. On the other hand, since our method highlights putative novel interactions, more directed experiments could now be performed.</p

Evaluation of Combining Several Statistical Methods with a Flexible Cutoff for Identifying Differentially Expressed Genes in Pairwise Comparison of EST Sets

The detection of differentially expressed genes from EST data is of importance for the discovery of potential biological or pharmaceutical targets, especially when studying biological processes in less characterized organisms and where large-scale microarrays are not an option. We present a comparison of five different statistical methods for identifying up-regulated genes through pairwise comparison of EST sets, where one of the sets is generated from a treatment and the other one serves as a control. In addition, we specifically address situations where the sets are relatively small (~2,000–10,000 ESTs) and may differ in size. The methods were tested on both simulated and experimentally derived data, and compared to a collection of cold stress induced genes identified by microarrays. We found that combining the method proposed by Audic and Claverie with Fisher’s exact test and a method based on calculating the difference in relative frequency was the best combination for maximizing the detection of up-regulated genes. We also introduced the use of a flexible cutoff, which takes the size of the EST sets into consideration. This could be considered as an alternative to a static cutoff. Finally, the detected genes showed a low overlap with those identified by microarrays, which indicates, as in previous studies, low overall concordance between the two platforms

Recreation and outdoor education in urban forest : planning for a forest suited for children and analysis of recreation in a part of Gävle

This Masters Thesis includes a survey of recreational habits and the attitudes towards forests of the people of Sätra, a suburb of the city of Gävle. The study also includes the planning and design of a forest suited for education in the same part of the city. The thesis is a part of a project called Tätortsnära skog, commissioned by the Swedish forest agency. The project aims to survey the recreational habits of the general public in the regions of Dalarna and Gävleborg. Tätortsnära skog is focused on cities with a population of more than 20 000 inhabitants, of which Gävle, Sandviken, Falun and Borlänge all fall within the category. For this thesis Gävle was chosen with a concentration on Sätra. Sätra was chosen as some local schools had expressed interest the amenity of a local forest suited to education of the local children. The particular suburb is also of interest due to the surrounding forests and the planning of the residential areas close to the nature. The methods used for the study behind this thesis were a mail survey and interviews. The questionnaire was sent to 400 randomly selected inhabitants of Sätra in early summer-time 2005. The response rate was 221, or 56 %. The questions in the survey were mostly conclusive and dealt with the subjects of background, recreational habits and values of the citizens, both in general and specific for Sätra. The interviews were held at four schools in the neighbourhood. The individuals interviewed were both teachers and children and the meetings were held both out in the forest as well as inside the school. The aim of the interviews was to create a clear view of how to form and shape a forest suited for education. The project also aimed to show and find suitable activities for learning and playing in the forests, from information obtained in the interviews and the literature. The forest areas of Sätra are classified as neighbourhood recreational areas with a high and frequent rate of visits by the citizens. The survey in this study showed that typical visitors of the forests are mostly alone, or in company of a family member or friend, and the typical visit lasts between 30 minutes and one hour. They usually walk to the forest as all local people of Sätra live close to the nature. The most frequent activity of visitors is walking, mostly on paths, jogging tracks or bicycle lanes. The most popular place to visit is the forest area located northeast of Sätra containing several paths and jogging tracks. This type of easy accessible nature is in great demand from people living in Sätra. They also want more information about activities and possibilities of the forest areas in the neighbourhood. The citizens of Sätra also further value the experience of calmness and privacy in the forests. With the results of the mail survey it was possible to make a recreation opportunity spectrum analysis concerning Sätra. This involves planning and adjusting the forests and forestry activities for the visitors. In particular it is important to adapt the areas of the forest close to buildings, while in more distant or randomly visited areas a more conventional forestry is sufficient. More signs showing information and directions in Sätra. These signs are an easy way to inform the people of Sätra about which opportunities there is, concerning recreation and nature locally. A forest suited for education should be of a simple and basic structure. In this thesis a path with a distance of about 2,5 km was created with the intended use as an educational tool. The track is located in the forest area west of Sätra. Along the track there are several stations, each with a special question or task. These consider subjects such as forestry, different species of trees or plants, animals, nature conservation, soils and mathematics. The forest area has also been modified to satisfy the need of play and movement of the children.Detta examensarbete omfattar en kartläggning av rekreationsvanor och attityder gentemot skogen hos befolkningen i stadsdelen Sätra i Gävle. Studien omfattar också planeringen och utformningen av en skolskog i samma stadsdel. Arbetet utförs inom Skogsstyrelsens projekt Tätortsnära skog, där en kartläggning av skogens sociala värden sker. Aktuella områden för studien var de tätorter inom Dalarnas och Gävleborgs län med en befolkning över 20 000 invånare. I området blev då städerna Gävle, Sandviken, Falun och Borlänge aktuella. I detta fall valdes Gävle och för att inte göra studien alltför generell fokuserades arbetet på stadsdelen Sätra. Valet av Sätra grundades främst på förfrågningar av en skog tillämpad för barn och undervisning från några av stadsdelens skolor. Sätra är också ett intressant område när det gäller rekreation. Hela området omges av skogsmark och bostadsområdena är planerade för en närhet till naturen. Som metod för arbetet användes en enkät och en intervjuundersökning. Enkäten adresserades till 400 av Sätras invånare. Utskick skedde under tidig sommar 2005 och av de slumpmässigt utvalda adressaterna svarade 221 stycken, eller 56 %. Frågorna i enkätformuläret hade främst fasta svarsalternativ och behandlade respondenternas bakgrund, rekreationsvanor, allmänt och specifikt i stadsdelen samt värderingar och åsikter angående skogen. I intervjuundersökningen besöktes fyra av Sätras skolor och förskolor där lärare och barn intervjuades såväl ute i skogen som i klassrummet. Mötena med klasserna och deras lärare syftade till att skapa en bild över hur en skog anpassad för undervisning bör se ut. De skulle också visa vilka aktiviteter som är lämpliga för lek och lärande i skogen samt att kartlägga vilka önskemål barn och lärare har angående en skog anpassad för undervisning. Sätras skogsområden kan betecknas som närrekreationsområden där besöksfrekvensen bland de boende är hög och vardaglig. Allmänt kan sägas om Sätrabornas skogsbesök att de varar mellan en halv och en timme, de sker oftast i ensamhet eller tillsammans med en vän eller familjemedlem, de flesta tar sig till fots till skogen och alla invånare har nära till naturen. Den överlägset vanligaste aktiviteten vid skogsbesöken är promenad, vilken ofta sker på någon av skogsområdenas stigar, motionsspår eller cykelvägar. Populäraste besöksmålet är skogen nordost om Sätra där många stigar och motionsspår finns. Denna typ av lättframkomlig natur är något Sätraborna efterfrågar. Generellt vill de ha mer information om vad stadsdelens skogsområden kan erbjuda. Dessutom är känslorna av avskildhet och lugn viktiga. Med enkätsvaren och fältstudier som grund utfördes en så kallad ROS-analys över Sätra. Detta innebär en analys av de rekreationsmöjligheter som finns i stadsdelen och hur skogarnas skötsel bör anpassas för besökarna. Skogarna närmast bebyggelsen bör helt anpassas efter befolkningens önskemål och behov, för att sedan skötas mer konventionellt med ökande avstånd från stadsdelen. Som rekommendation bör informationsskyltar och enkla hänvisningsskyltar sättas upp på olika ställen i stadsdelen för att underlätta för Sätraborna samt att upplysa dem om vilka rekreationsmöjligheter som finns i området. För en skolskog efterfrågar lärare och barn en enkel och grundläggande uppbyggnad, vilket ledde till valet av en ca 2,5 km lång skolskogsstig. Tillämpad för stigens naturliga betingelser formulerades en frågehandledning vilken behandlar ämnen som trädslag, skogsbruk, naturvård, djur, växter, mark samt matematik. Skolskogen är också anpassad för att tillgodose barnens lek och rörelsebehov

Mutagenesis as a Tool in Plant Genetics, Functional Genomics, and Breeding

Plant mutagenesis is rapidly coming of age in the aftermath of recent developments in high-resolution molecular and biochemical techniques. By combining the high variation of mutagenised populations with novel screening methods, traits that are almost impossible to identify by conventional breeding are now being developed and characterised at the molecular level. This paper provides a comprehensive overview of the various techniques and workflows available to researchers today in the field of molecular breeding, and how these tools complement the ones already used in traditional breeding. Both genetic (Targeting Induced Local Lesions in Genomes; TILLING) and phenotypic screens are evaluated. Finally, different ways of bridging the gap between genotype and phenotype are discussed

Foraging behaviour of common murres in the Baltic Sea, recorded by simultaneous attachment of GPS and time-depth recorder devices

Global positioning system and time-depth recorders were deployed in combination to investigate the foraging behaviour of common murres Uria aalge breeding at Stora Karlsö Island, Baltic Sea, during the chick-rearing period. In the pre-breeding period the main prey species of murres, sprat Sprattus sprattus, is targeted by commercial fisheries, likely reducing prey availability during the breeding season. Foraging trips typically consisted of a short flight followed by a period sitting on the sea surface (0.39 ± 0.48 h), followed by several (5.3 ± 3.8) diving bouts interspersed by flights and water surface activity. Following the final diving bout, murres returned directly to the colony. Overnight foraging trips lasted longer than daytime trips, and that result corresponded with greater diving activity and reduced dive depths around dawn and dusk, likely times of high prey accessibility. High outward flight groundspeeds (20.0 ± 2.8 m s-1) were aided by tailwinds, and lower inward flight groundspeeds (15.1 ± 2.5 m s-1) were impeded by headwinds. Flights following the wind direction may reflect a strategy to reduce crosswind drift. Foraging intensity was lower than reported by most other studies of murres, suggesting more abundant or aggregated prey