Accessibility as a determinant of opportunities : A case study from Peruvian Amazonia

Accessibility is a crucial factor for interaction between areas in economic, cultural, political and environmental terms. Therefore, information concerning accessibility is relevant for informed decision making, planning and research. The Loreto region in the Peruvian Amazonia provides an interesting scene for an accessibility study. Loreto is sparsely populated and because there are few roads in the region, in practice all movement and transportation happens along the river network. Due to the proximity of the Andes, river dynamics are strong and annual changes in water level combined with these dynamic processes constantly reshape accessibility patterns of the region. Selling non-timber forest products (NTFP) and agricultural products (AP) in regional centres is an important income source for local rain forest dwellers. Thus, accessibility to the centres is crucial for the livelihood of local population. -- In this thesis I studied how accessible the regional centre Iquitos is from other parts of Loreto. In addition, I studied the regional NTFP/AP trade patterns and compared them with patterns of accessibility. Based on GPS-measurements, using GIS, I created a time-distance surface covering Loreto. This surface describes the time-distance to Iquitos, along the river network. Based on interview material, I assessed annual changes to accessibility patterns in the region. The most common regional NTFP/AP were classified according to the amount of time they can be preserved, and based on the accessibility surface, I modelled a catchment area for each of these product classes. -- According to my results, navigation speeds vary considerably in different parts of the river network, depending on river types, vessels, flow direction and season. Navigating downstream is, generally, faster than upstream navigation. Thus, Iquitos is better accessible from areas situated south and south west of the city, like along the rivers Ucayali and Marañon. Differences in accessibility between different seasons are also substantial: during the dry season navigation is slower due to lower water levels and emerging sand bars. Regularly operating boats follow routes only along certain rivers and close to Iquitos transport facilities are more abundant than in more distant areas. Most of the products present in Iquitos market places are agricultural products, and the share of NTFP is significantly smaller. Most of the products were classified in product class 2, and the catchment area for these products is rather small. Many products also belonged to class 5, and the catchment area for these products reaches up to the edges of my study area, following the patterns of the river network. -- The accessibility model created in this study predicts travel times relatively well, although in some cases the modelled time-distances are substantially shorter than observed time-distances. This is partly caused by the fact that real-life navigation routes are more complicated than the modelled routes. Rain forest dwellers having easier access to Iquitos have more opportunities in terms of the products they decide to market. Thus, they can better take advantage of other factors affecting the market potential of different products. -- In all, understanding spatial variation in accessibility is important. In the Amazonian context it is difficult to combine the accessibility-related needs of the local dwellers with conservation purposes and the future challenge lies in finding solution that satisfy both of these needs.

Microbial identification by detection of ligation probes on DNA microarray

Microbes in natural and artificial environments as well as in the human body are a key part of the functional properties of these complex systems. The presence or absence of certain microbial taxa is a correlate of functional status like risk of disease or course of metabolic processes of a microbial community. As microbes are highly diverse and mostly notcultivable, molecular markers like gene sequences are a potential basis for detection and identification of key types. The goal of this thesis was to study molecular methods for identification of microbial DNA in order to develop a tool for analysis of environmental and clinical DNA samples. Particular emphasis was placed on specificity of detection which is a major challenge when analyzing complex microbial communities. The approach taken in this study was the application and optimization of enzymatic ligation of DNA probes coupled with microarray read-out for high-throughput microbial profiling. The results show that fungal phylotypes and human papillomavirus genotypes could be accurately identified from pools of PCR amplicons generated from purified sample DNA. Approximately 1 ng/μl of sample DNA was needed for representative PCR amplification as measured by comparisons between clone sequencing and microarray. A minimum of 0,25 amol/μl of PCR amplicons was detectable from amongst 5 ng/μl of background DNA, suggesting that the detection limit of the test comprising of ligation reaction followed by microarray read-out was approximately 0,04%. Detection from sample DNA directly was shown to be feasible with probes forming a circular molecule upon ligation followed by PCR amplification of the probe. In this approach, the minimum detectable relative amount of target genome was found to be 1% of all genomes in the sample as estimated from 454 deep sequencing results. Signal-to-noise of contact printed microarrays could be improved by using an internal microarray hybridization control oligonucleotide probe together with a computational algorithm. The algorithm was based on identification of a bias in the microarray data and correction of the bias as shown by simulated and real data. The results further suggest semiquantitative detection to be possible by ligation detection, allowing estimation of target abundance in a sample. However, in practise, comprehensive sequence information of full length rRNA genes is needed to support probe design with complex samples. This study shows that DNA microarray has the potential for an accurate microbial diagnostic platform to take advantage of increasing sequence data and to replace traditional, less efficient methods that still dominate routine testing in laboratories. The data suggests that ligation reaction based microarray assay can be optimized to a degree that allows good signal-tonoise and semiquantitative detection.

FGF signaling in neurogenesis and patterning of the developing midbrain and anterior hindbrain

Embryonic midbrain and hindbrain are structures which will give rise to brain stem and cerebellum in the adult vertebrates. Brain stem contains several nuclei which are essential for the regulation of movements and behavior. They include serotonin-producing neurons, which develop in the hindbrain, and dopamine-producing neurons in the ventral midbrain. Degeneration and malfunction of these neurons leads to various neurological disorders, including schizophrenia, depression, Alzheimer s, and Parkinson s disease. Thus, understanding their development is of high interest. During embryogenesis, a local signaling center called isthmic organizer regulates the development of midbrain and anterior hindbrain. It secretes peptides belonging to fibroblast growth factor (FGF) and Wingless/Int (Wnt) families. These factors bind to their receptors in the surrounding tissues, and activate various downstream signaling pathways which lead to alterations in gene expression. This in turn affects the various developmental processes in this region, such as proliferation, survival, patterning, and neuronal differentiation. In this study we have analyzed the role of FGFs in the development of midbrain and anterior hindbrain, by using mouse as a model organism. We show that FGF receptors cooperate to receive isthmic signals, and cell-autonomously promote cell survival, proliferation, and maintenance of neuronal progenitors. FGF signaling is required for the maintenance of Sox3 and Hes1 expression in progenitors, and Hes1 in turn suppresses the activity of proneural genes. Loss of Hes1 is correlated with increased cell cycle exit and premature neuronal differentiation. We further demonstrate that FGF8 protein forms an antero-posterior gradient in the basal lamina, and might enter the neuronal progenitors via their basal processes. We also analyze the impact of FGF signaling on the various neuronal nuclei in midbrain and hindbrain. Rostral serotonergic neurons appear to require high levels of FGF signaling in order to develop. In the absence of FGF signaling, these neurons are absent. We also show that embryonic meso-diencephalic dopaminergic domain consists of two populations in the anterior-posterior direction, and that these populations display different molecular profiles. The anterior diencephalic domain appears less dependent on isthmic FGFs, and lack several genes typical of midbrain dopaminergic neurons, such as Pitx3 and DAT. In Fgfr compound mutants, midbrain dopaminergic neurons begin to develop but soon adopt characteristics which highly resemble those of diencephalic dopaminergic precursors. Our results indicate that FGF signaling regulates patterning of these two domains cell-autonomously.

Linguistic and perceptual processing of communicative cues in Asperger Syndrome

Asperger Syndrome (AS) belongs to autism spectrum disorders where both verbal and non-verbal communication difficulties are at the core of the impairment. Social communication requires a complex use of affective, linguistic-cognitive and perceptual processes. In the four studies included in the current thesis, some of the linguistic and perceptual factors that are important for face-to-face communication were studied using behavioural methods. In all four studies the results obtained from individuals with AS were compared with typically developed age, gender and IQ matched controls. First, the language skills of school-aged children were characterized in detail with standardized tests that measured different aspects of receptive and expressive language (Study I). The children with AS were found to be worse than the controls in following complex verbal instructions. Next, the visual perception of facial expressions of emotion with varying degrees of visual detail was examined (Study II). Adults with AS were found to have impaired recognition of facial expressions on the basis of very low spatial frequencies which are important for processing global information. Following that, multisensory perception was investigated by looking at audiovisual speech perception (Studies III and IV). Adults with AS were found to perceive audiovisual speech qualitatively differently from typically developed adults, although both groups were equally accurate in recognizing auditory and visual speech presented alone. Finally, the effect of attention on audiovisual speech perception was studied by registering eye gaze behaviour (Study III) and by studying the voluntary control of visual attention (Study IV). The groups did not differ in eye gaze behaviour or in the voluntary control of visual attention. The results of the study series demonstrate that many factors underpinning face-to-face social communication are atypical in AS. In contrast with previous assumptions about intact language abilities, the current results show that children with AS have difficulties in understanding complex verbal instructions. Furthermore, the study makes clear that deviations in the perception of global features in faces expressing emotions as well as in the multisensory perception of speech are likely to harm face-to-face social communication.

Periglasiaalisten ilmiöiden alueellinen mallintaminen subarktisessa ympäristössä

Periglacial processes act on cold, non-glacial regions where the landscape deveploment is mainly controlled by frost activity. Circa 25 percent of Earth's surface can be considered as periglacial. Geographical Information System combined with advanced statistical modeling methods, provides an efficient tool and new theoretical perspective for study of cold environments. The aim of this study was to: 1) model and predict the abundance of periglacial phenomena in subarctic environment with statistical modeling, 2) investigate the most import factors affecting the occurence of these phenomena with hierarchical partitioning, 3) compare two widely used statistical modeling methods: Generalized Linear Models and Generalized Additive Models, 4) study modeling resolution's effect on prediction and 5) study how spatially continous prediction can be obtained from point data. The observational data of this study consist of 369 points that were collected during the summers of 2009 and 2010 at the study area in Kilpisjärvi northern Lapland. The periglacial phenomena of interest were cryoturbations, slope processes, weathering, deflation, nivation and fluvial processes. The features were modeled using Generalized Linear Models (GLM) and Generalized Additive Models (GAM) based on Poisson-errors. The abundance of periglacial features were predicted based on these models to a spatial grid with a resolution of one hectare. The most important environmental factors were examined with hierarchical partitioning. The effect of modeling resolution was investigated with in a small independent study area with a spatial resolution of 0,01 hectare. The models explained 45-70 % of the occurence of periglacial phenomena. When spatial variables were added to the models the amount of explained deviance was considerably higher, which signalled a geographical trend structure. The ability of the models to predict periglacial phenomena were assessed with independent evaluation data. Spearman's correlation varied 0,258 - 0,754 between the observed and predicted values. Based on explained deviance, and the results of hierarchical partitioning, the most important environmental variables were mean altitude, vegetation and mean slope angle. The effect of modeling resolution was clear, too coarse resolution caused a loss of information, while finer resolution brought out more localized variation. The models ability to explain and predict periglacial phenomena in the study area were mostly good and moderate respectively. Differences between modeling methods were small, although the explained deviance was higher with GLM-models than GAMs. In turn, GAMs produced more realistic spatial predictions. The single most important environmental variable controlling the occurence of periglacial phenomena was mean altitude, which had strong correlations with many other explanatory variables. The ongoing global warming will have great impact especially in cold environments on high latitudes, and for this reason, an important research topic in the near future will be the response of periglacial environments to a warming climate.