Expression, Enzymatic Activities and Subcellular Localization of Hepatitis E Virus and Semliki Forest Virus Replicase Proteins

Viruses are submicroscopic, infectious agents that are obligate intracellular parasites. They adopt various types of strategies for their parasitic replication and proliferation in infected cells. The nucleic acid genome of a virus contains information that redirects molecular machinery of the cell to the replication and production of new virions. Viruses that replicate in the cytoplasm and are unable to use the nuclear transcription machinery of the host cell have developed their own transcription and capping systems. This thesis describes replication strategies of two distantly related viruses, hepatitis E virus (HEV) and Semliki Forest virus (SFV), which belong to the alphavirus-like superfamily of positive-strand RNA viruses. We have demonstrated that HEV and SFV share a unique cap formation pathway specific for alphavirus-like superfamily. The capping enzyme first acts as a methyltransferase, catalyzing the transfer of a methyl group from S-adenosylmethionine to GTP to yield m7GTP. It then transfers the methylated guanosine to the end of viral mRNA. Both reactions are virus-specific and differ from those described for the host cell. Therefore, these capping reactions offer attractive targets for the development of antiviral drugs. Additionally, it has been shown that replication of SFV and HEV takes place in association with cellular membranes. The origin of these membranes and the intracellular localization of the components of the replication complex were studied by modern microscopy techniques. It was demonstrated that SFV replicates in cytoplasmic membranes that are derived from endosomes and lysosomes. According to our studies, site for HEV replication seems to be the intermediate compartment which mediates the traffic between endoplasmic reticulum and the Golgi complex. As a result of this work, a unique mechanism of cap formation for hepatitis E virus replicase has been characterized. It represents a novel target for the development of specific inhibitors against viral replication.

Prey of the silver-headed antechinus (Antechinus argentus), a new species of Australian dasyurid marsupial

The silver-headed antechinus (Antechinus argentus) is one of Australia’s most recently described mammals, and the single known population at Kroombit Tops in south-east Queensland is threatened. Nothing is known of the species’ ecology, so during 2014 we collected faecal pellets each month (March–September) from a population at the type locality to gather baseline data on diet composition. A total of 38 faecal pellets were collected from 12 individuals (eight females, four males) and microscopic analysis of pellets identified seven invertebrate orders, with 70% combined mean composition of beetles (Coleoptera: 38%) and cockroaches (Blattodea: 32%). Other orders that featured as prey were ants, crickets/grasshoppers, butterflies/moths, spiders, and true bugs. Given that faecal pellets could only be collected from a single habitat type (Eucalyptus montivaga high-altitude open forest) and location, this is best described as a generalist insectivorous diet that is characteristic of other previously studied congeners.

The line transect method for estimating densities of large mammals in a tropical deciduous forest: An evaluation of models and field experiments

We have evaluated techniques of estimating animal density through direct counts using line transects during 1988-92 in the tropical deciduous forests of Mudumalai Sanctuary in southern India for four species of large herbivorous mammals, namely, chital (Axis axis), sambar (Cervus unicolor), Asian elephant (Elephas maximus) and gaur (Bos gauras). Density estimates derived from the Fourier Series and the Half-Normal models consistently had the lowest coefficient of variation. These two models also generated similar mean density estimates. For the Fourier Series estimator, appropriate cut-off widths for analysing line transect data for the four species are suggested. Grouping data into various distance classes did not produce any appreciable differences in estimates of mean density or their variances, although model fit is generally better when data are placed in fewer groups. The sampling effort needed to achieve a desired precision (coefficient of variation) in the density estimate is derived. A sampling effort of 800 km of transects returned a 10% coefficient of variation on estimate for chital; for the other species a higher effort was needed to achieve this level of precision. There was no statistically significant relationship between detectability of a group and the size of the group for any species. Density estimates along roads were generally significantly different from those in the interior af the forest, indicating that road-side counts may not be appropriate for most species.

Relationship between annual rainfall and tree mortality in a tropical dry forest: Results of a 19-year study at Mudumalai, southern India

Variability in rainfall is known to be a major influence on the dynamics of tropical forests, especially rates and patterns of tree mortality. In tropical dry forests a number of contributing factors to tree mortality, including dry season fire and herbivory by large herbivorous mammals, could be related to rainfall patterns, while loss of water potential in trees during the dry season or a wet season drought could also result in enhanced rates of death. While tree mortality as influenced by severe drought has been examined in tropical wet forests there is insufficient understanding of this process in tropical dry forests. We examined these causal factors in relation to inter-annual differences in rainfall in causing tree mortality within a 50-ha Forest Dynamics Plot located in the tropical dry deciduous forests of Mudumalai, southern India, that has been monitored annually since 1988. Over a 19-year period (1988-2007) mean annual mortality rate of all stems >1 cm dbh was 6.9 +/- 4.6% (range = 1.5-17.5%); mortality rates broadly declined from the smaller to the larger size classes with the rates in stems >30 cm dbh being among the lowest recorded in tropical forest globally. Fire was the main agent of mortality in stems 1-5 cm dbh, elephant-herbivory in stems 5-10 cm dbh, and other natural causes in stems > 10 cm dbh. Elephant-related mortality did not show any relationship to rainfall. On the other hand, fire-related mortality was significantly negatively correlated to quantity of rainfall during the preceding year. Mortality due to other causes in the larger stem sizes was significantly negatively correlated to rainfall with a 2-3-year lag, suggesting that water deficit from mild or prolonged drought enhanced the risk of death but only with a time lag that was greater than similar lags in tree mortality observed in other forest types. In this respect, tropical dry forests growing in regions of high rainfall variability may have evolved greater resistance to rainfall deficit as compared to tropical moist or temperate forests but are still vulnerable to drought-related mortality.

Development of biogenic VOC emission inventories for the boreal forest

Luonnosta haihtuvat orgaaniset yhdisteet, joita pääsee ilmaan etenkin metsistä, voivat vaikuttaa paikalliseen ja alueelliseen ilmanlaatuun, koska ne reagoivat ilmakehässä. Niiden reaktiotuotteet voivat myös osallistua uusien hiukkasten muodostumiseen ja kasvuun, millä voi olla vaikutusta ilmakehän säteilytaseeseen ja tätä kautta myös ilmastoon. Hiukkaset absorboivat ja sirottavat auringon säteilyä ja maapallon lämpösäteilyä minkä lisäksi ne vaikuttavat pilvien säteilyominaisuuksiin, määrään ja elinikään. Koko maapallon mittakaavassa luonnosta tulevat hiilivetypäästöt ylittävät ihmistoiminnan aiheuttamat päästöt moninkertaisesti. Tämän vuoksi luonnon päästöjen arviointi on tärkeää kun halutaan kehittää tehokkaita ilmanlaatu- ja ilmastostrategioita. Tämä tutkimus käsittelee boreaalisen metsän hiilivetypäästöjä. Boreaalinen metsä eli pohjoinen havumetsä on suurin maanpäällinen ekosysteemi, ja se ulottuu lähes yhtenäisenä nauhana koko pohjoisen pallonpuoliskon ympäri. Sille on tyypillistä puulajien suhteellisen pieni kirjo sekä olosuhteiden ja kasvun voimakkaat vuodenaikaisvaihtelut. Työssä on tutkittu Suomen yleisimmän boreaalisen puun eli männyn hiilivetypäästöjen vuodenaikaisvaihtelua sekä päästöjen riippuvuutta lämpötilasta ja valosta. Saatuja tuloksia on käytetty yhdessä muiden boreaalisilla puilla tehtyjen päästömittaustulosten kanssa Suomen metsiä varten kehitetyssä päästömallissa. Malli perustuu lisäksi maankäyttötietoihin, suomen metsille kehitettyyn luokitukseen ja meteorologisiin tietoihin, joiden avulla se laskee metsien hiilivetypäästöt kasvukauden aikana. Suomen metsien päästöt koostuvat koko kasvukauden ajan suurelta osin alfa- ja beta-pineenistä sekä delta-kareenista. Kesällä ja syksyllä päästöissä on myös paljon sabineenia, jota tulee etenkin lehtipuista. Päästöt seuraavat lämpötilan keskimääräistä vaihtelua, ovat suurimmillaan maan eteläosissa ja laskevat tasaisesti pohjoiseen siirryttäessä. Metsän isopreenipäästö on suhteellisen pieni – Suomessa tärkein isopreeniä päästävä puu on vähäpäästöinen kuusi, koska runsaspäästöisten pajun ja haavan osuus metsän lehtimassasta on hyvin pieni. Tässä työssä on myös laskettu ensimmäinen arvio metsän seskviterpeenipäästöistä. Seskviterpeenipäästöt alkavat Juhannuksen jälkeen ja ovat kasvukauden aikana samaa suuruusluokkaa kuin isopreenipäästöt. Vuositasolla Suomen metsien hiilivetypäästöt ovat noin kaksinkertaiset ihmistoiminnasta aiheutuviin päästöihin verrattuna.

Pollinator limitation and the effect of breeding systems on plant reproduction in forest fragments

Reproduction of plants in fragmented habitats may be limited because of lower diversity or abundance of pollinators, and/or variation in local plant density. We assessed natural fruit set and pollinator limitation in ten species of woody plants in natural and restored fragments in the Pondicherry region of southern India, to see whether breeding system of plants (self-compatible and self-incompatible) affected fruit set. We tested whether the number of flowering individuals in the fragments affected the fruit set and further examined the adult and sapling densities of self-compatible (SC) and self-incompatible (SI) species. We measured the natural level of fruit set and pollinator limitation (calculated as the difference in fruit set between hand cross-pollinated and naturally pollinated flowers). Our results demonstrate that there was a higher level of pollinator limitation and hence lower levels of natural fruit set in self-incompatible species as compared to self-compatible species. However, the hand cross-pollinated flowers in SC and SI species produced similar levels of fruit set,further indicating that lower fruit set was due to pollinator limitation and not due to lack of cross-compatible individuals in the fragments. There was no significant relation between number of flowering individuals and the levels of natural fruit set, except for two species Derris ovalifolia, Ixora pavetta. In these species the natural fruit set decreased with increasing population size, again indicating pollinator limitation. The adult and sapling densities in self-compatible species were significantly higher than inself-incompatible species. These findings indicate that the low reproductive output in self-incompatible species may eventually lead to lower population sizes. Restoration of pollinator services along with plant species in fragmented habitats is important for the long-term conservation of biodiversity. (C) 2009 Elsevier Masson SAS. All rights reserved.

Evaluation of methods to estimate foliage density in the understorey of a tropical evergreen forest

Foliage density and leaf area index are important vegetation structure variables. They can be measured by several methods but few have been tested in tropical forests which have high structural heterogeneity. In this study, foliage density estimates by two indirect methods, the point quadrat and photographic methods, were compared with those obtained by direct leaf counts in the understorey of a wet evergreen forest in southern India. The point quadrat method has a tendency to overestimate, whereas the photographic method consistently and ignificantly underestimates foliage density. There was stratification within the understorey, with areas close to the ground having higher foliage densities.

Regeneration ecology and woody species diversity in the remnant natural forest at Wondo Genet, Ethiopia – Potential for landscape restoration

Regeneration ecology, diversity of native woody species and its potential for landscape restoration was studied in the remnant natural forest at the College of Forestry and Natural Resources at Wondo Genet, Ethiopia. The type of forest is Afromontane rainforest , with many valuable tree species like Aningeria adolfi-friederici, and it is an important provider of ecological, social and economical services for the population that lives in this area. The study contains two parts, natural regeneration studies (at the natural forest) and interviews with farmers in the nearby village of the remnant patch. The objective of the first part was to investigate the floristic composition, densitiy and regeneration profiles of native woody species in the forest, paying special attention to woody species that are considered the most relevant (socio-economic). The second part provided information on woody species preferred by the farmers and on multiple uses of the adjacent natural forest, it also provided information and analysed perceptions on forest degradation. Systematic plot sampling was used in the forest inventory. Twenty square plots of 20 x 20 m were assessed, with 38 identified woody species (the total number of species was 45), representing 26 families. Of these species 61% were trees, 13% shrubs, 11% lianas and 16% species that could have both life forms. An analysis of natural regeneration of five important tree species in the natural forest showed that Aningeria adolfi-friederici had the best regeneration results. An analysis of population structure (as determined by height classes) of two commercially important woody species in the forest, Aningeria adolfi-friederici and Podocarpus falcatus, showed a marked difference: Aningeria had a typical “reversed J” frequency distribution, while Podocarpus showed very low values in all height classes. Multi dimensional scaling (MDS) was used to map the sample plots according to their similarity in species composition, using the Sørensen quantitative index, coupled with indicator species analysis .Three groups were identified with respective indicator species: Group 1 – Adhatoda schimperiana, Group 2 – Olea hochstetteri , Group 3 – Acacia senegal and Aningeria adolfi-friederici. Thirty questionnaire interviews were conducted with farmers in the village of Gotu Onoma that use the nearby remant forest patch. Their tree preferences were exotic species such as Eucalyptus globulus for construction and fuelwood and Grevillea robusta for shade and fertility. Considering forest land degradation farmers were aware of the problem and suggested that the governmental institutions address the problem by planting more Eucalyptus globulus. The natural forest seemed to have moderate levels of disturbance and it was still floristically diverse. However, the low rate of natural regeneration of Podocarpus falcatus suggested that this species is threatened and must be a priority in conservation actions. Plantations and agroforestry seem to be possible solutions for rehabilitation of the surrounding degraded lands, thereby decreasing the existent pressure in the remnant natural forest.

The role of selected non-timber forest products for rural areas in Laos: Case studies in Ban Napo and Ban Kouay communities

Non-timber forest products (NTFPs) are one of the major income sources for the rural population of Laos. An exploratory study was conducted to determine the role of non-timber forest products for rural communities of the study area. The study was carried out in two villages viz. Ban Napo and Ban Kouay of Sangthong district between January and March 2010. A semi-structured questionnaire was used to gather data from the respondents. Twenty-five respondents from each village were chosen based on their involvement in NTFPs collection and marketing activities. Statistically significant NTFPs income differences were not found between the villages and age groups of the respondents, however, significant differences were found in the annual incomes between farms size of the respondents. This study also analyzed the value chain structure of the three (See khai’ ton, Bamboo mats and Incense sticks) important non-timber forest products and the interactions between the actors in the case study areas. Barriers to entry the market, governance and upgrading possibilities have been discussed for each of the value chains. Comparison of unit prices at different levels of the value chains indicated uneven income distribution in favour of the intermediaries, factories and foreign buyers. The lack of capital, marketing information and negotiation skills restricted the villagers to increase their income. However, all the respondents have shown their satisfaction with their income from NTFPs.

Juvenile diversity of tree species in Theobroma cacao L. agroforestry and primary forest – Central Sulawesi, Indonesia

This thesis studies the tree species’ juvenile diversity in cacao (Theobroma cacao L.) based agroforestry and in primary forest in a natural conservation forest environment of Lore Lindu National Park, Sulawesi, Indonesia. Species’ adult composition in Lore Lindu National Park is relatively well studied, less is known about tree species’ diversity in seedling communities particularly in frequently disturbed cacao agroforestry field environment. Cacao production forms a potentially serious thread for maintaining the conservation areas pristine and forested in Sulawesi. The impacts of cacao production on natural environment are directly linked to the diversity and abundance of shade tree usage. The study aims at comparing differences between cacao agroforestry and natural forest in the surrounding area in their species composition in seedling and sapling size categories. The study was carried out in two parts. Biodiversity inventory of seedlings and saplings was combined with social survey with farmer interviews. Aim of the survey was to gain knowledge of the cacao fields, and farmers’ observations and choices regarding tree species associated with cacao. Data was collected in summer 2008. The assessment of the impact of environmental factors of solar radiation, weeding frequency, cacao tree planting density, distance to forest and distance to main park road, and type of habitat on seedling and sapling compositions was done with Non-metric Multidimensional Scaling (NMS). Outlier analysis was used to assess distorting variables for NMS, and Multi-Response Permutation Procedures (MRPP) analysis to differentiate the impact of categorical variables. Sampling success was estimated with rarefaction curves and jackknife estimate of species richness. In the inventory 135 species of trees and shrubs were found. Only some agroforestry related species were dominating. The most species rich were sapling communities in forest habitat. NMS was showing generally low linear correlation between variation of species composition and environmental variables. Solar radiation was having most significance as explaining variable. The most clearly separated in ordination were cacao and forest habitats. The results of seedling and sapling inventory were only partly coinciding with farmers’ knowledge of the tree species occurring on their fields. More research with frequent assessment of seedling cohorts is needed due to natural variability of cohorts and high mortality rate of seedlings.

Forest governance and climate change adaptation : Case studies of four African countries

Africa is threatened by climate change. The adaptive capacity of local communities continues to be weakened by ineffective and inefficient livelihood strategies and inappropriate development interventions. One of the greatest challenges for climate change adaptation in Africa is related to the governance of natural resources used by vulnerable poor groups as assets for adaptation. Practical and good governance activities for adaptation in Africa is urgently and much needed to support adaptation actions, interventions and planning. The adaptation role of forests has not been as prominent in the international discourse and actions as their mitigation role. This study therefore focused on the forest as one of the natural resources used for adaptation. The general objective of this research was to assess the extent to which cases of current forest governance practices in four African countries Burkina Faso, The Democratic Republic of Congo (DRC), Ghana and Sudan are supportive to the adaptation of vulnerable societies and ecosystems to impacts of climate change. Qualitative and quantitative analyses from surveys, expert consultations and group discussions were used in analysing the case studies. The entire research was guided by three conceptual sets of thinking forest governance, climate change vulnerability and ecosystem services. Data for the research were collected from selected ongoing forestry activities and programmes. The study mainly dealt with forest management policies and practices that can improve the adaptation of forest ecosystems (Study I) and the adaptive capacity through the management of forest resources by vulnerable farmers (Studies II, III, IV and V). It was found that adaptation is not part of current forest policies, but, instead, policies contain elements of risk management practices, which are also relevant to the adaptation of forest ecosystems. These practices include, among others, the management of forest fires, forest genetic resources, non-timber resources and silvicultural practices. Better livelihood opportunities emerged as the priority for the farmers. These vulnerable farmers had different forms of forest management. They have a wide range of experience and practical knowledge relevant to ensure and achieve livelihood improvement alongside sustainable management and good governance of natural resources. The contributions of traded non-timber forest products to climate change adaptation appear limited for local communities, based on their distribution among the stakeholders in the market chain. Plantation (agro)forestry, if well implemented and managed by communities, has a high potential in reducing socio-ecological vulnerability by increasing the food production and restocking degraded forest lands. Integration of legal arrangements with continuous monitoring, evaluation and improvement may drive this activity to support short, medium and long term expectations related to adaptation processes. The study concludes that effective forest governance initiatives led by vulnerable poor groups represent one practical way to improve the adaptive capacities of socio-ecological systems against the impacts of climate change in Africa.

Markov random fields and spatial smoothing in improving of forest inventory estimates

Markov random fields (MRF) are popular in image processing applications to describe spatial dependencies between image units. Here, we take a look at the theory and the models of MRFs with an application to improve forest inventory estimates. Typically, autocorrelation between study units is a nuisance in statistical inference, but we take an advantage of the dependencies to smooth noisy measurements by borrowing information from the neighbouring units. We build a stochastic spatial model, which we estimate with a Markov chain Monte Carlo simulation method. The smooth values are validated against another data set increasing our confidence that the estimates are more accurate than the originals.