Taxonomy and phylogeny of the manna lichens and allied species (Megasporaceae)

This dissertation is focused on the taxonomy, phylogeny, and ecology of the vagrant, erratic and allied terricolous and saxicolous species of the genera Aspicilia A. Massal. and Circinaria Link (Megasporaceae), particularly those traditionally referred to as manna lichens . The group has previously been defined on the basis of few morphological characters. The phylogeny of the family Megasporaceae is inferred from the combined dataset of nuLSU and mtSSU sequences. Five genera Aspicilia, Circinaria, Lobothallia, Megaspora, and Sagedia are recognized. Lobothallia is sister of the four other genera, while Aspicilia and Sagedia form the next clade. All these genera have small asci with eight spores. Circinaria is a sister genus of Megaspora, and these two have in common asci with (1 4) 6 8 large spores. Circinaria forms a monophyletic group and sphaerothallioid species form a monophyletic group within Circinaria. The presence of certain morphological characters such as pseudocyphellae, thickness of cortex and medulla layers, as well as ecological differences in sphaerothallioid species distinguish it from some other crustose species, especially those containing aspicilin and characterised by thin cortex and medulla layers, conidium length c. 6 12 µm and absence of pseudocyphellae. If sphaerothallioid species are accepted as a distinct genus, the rest of the Circinaria species would remain as a paraphyletic assemblage. Currently, the genus Circinaria includes all the sphaerothallioid species and its generic position is confirmed and accepted. Thus, it is proposed as a correct generic name also for the manna lichens described originally in other genera. Phylogeny at the species level was studied using nrITS sequence data. Traditionally, morphological characters have been used for the recognition of species. They were re-evaluated in the light of molecular data. Since characters such as vagrant, erratic and crustose growth forms proved to be misleading for the recognition of some species, a combination of several characters (including molecular data) is recommended. Vagrant growth form seems to have evolved several times among the distantly related lineages and even within a single population. The reasons behind the high plasticity in the external morphology of the sphaerothallioid Circinaria remain, however, unknown. Six new species are recognized: Aspicilia tibetica, Circinaria arida, C. digitata nom provis., C. gyrosa nom. provis., C. rogeri nom. provis., and C. rostamii nom. provis. Based on an analysis of nrITS dataset, three new erratic, vagrant and crustose species were also recognized, but these require additional study. The results also reveal that C. elmorei and C. hispida are not monophyletic as currently understood. In addition, 13 new combinations in the genus Circinaria are proposed.

Demi-glace-kastikepohjan valmistuksen optimointi ylipainekeittomenetelmälle

Tämän tutkimuksen kirjallisuusosan tavoitteena oli selvittää perinteisen kastikepohjan valmistukseen ja valmistuksen kokonaisvaltaiseen onnistumiseen vaikuttavia seikkoja. Lisäksi käsiteltiin kastikepohjan valmistukseen liittyviä ympäristö- ja energia-asioita, kuten eläinperäisten sivutuotteiden kierrätysmahdollisuuksia. Kokeellisessa osassa tutkimuksen keskeinen lähtökohta oli pyrkiä löytämään ratkaisu ylipainekeittomenetelmään liittyvään kastikepohjan liemiaineksen sameutumisongelmaan. Tutkimuksessa haluttiin löytää syyt sameuden muodostumiseen luiden painekeitossa (max. 1,5 bar). Näin pyrittiin selvittämään keinot sameuden syntymisen estämiseen tai tuotteesta poistamiseen. Ratkaisua etsittiin sekä keittoaika-paine-kombinaatiosta että proteolyyttisen entsyymivalmisteen käytöstä. Tavoitteena oli ulkonäöltään kirkas ja kuiva-ainepitoisuudeltaan mahdollisimman korkea naudanmakuinen demi-glace-kastikepohjaliemi. Liemiaineksista tarkasteltiin kuiva-aine-, kokonaisproteiini- ja sidekudosproteiinipitoisuuksia, pH-arvoja sekä sameutta, ja vertailtiin näitä tuloksia käytettyihin valmistusmenetelmiin ja -olosuhteisiin. Lisäksi otettiin selvää lämmöntalteenoton parantamis-mahdollisuuksista. Tutkimuksessa valmistetun kastikepohjaliemen kuiva-aine koostui pääasiassa proteiineista. Liemen valmistuksessa suuremmalla paineella päästiin hieman nopeammin samoihin kuiva-ainepitoisuuksiin kuin matalammalla paineella. Samoin tapahtui entsyymiä käytettäessä kuin käyttämättä jätettäessä. Tämän tutkimuksen perusteella korkeaa kuiva-ainepitoisuutta tavoiteltaessa kastikepohjaliemen valmistuksessa on valittava korkean sidekudosproteiinin tai sameuden väliltä. Ylipainekeitolla luista saatiin irti lähes pelkästään sidekudosproteiinia, koska luita kuumennettaessa vain kollageeni liukeni veteen muiden proteiinien saostuessa. Lämmöntalteenottojärjestelmien rakentaminen pieneen elintarviketeollisuusyritykseen voi olla kannattamatonta, koska investointikustannuksia ei välttämättä pystytä maksamaan takaisin. Energiatehokkuuden parantaminen pienessä elintarviketeollisuusyrityksessä on haastavaa, mutta kuitenkin mahdollista ammattilaisten tekemien tarkkojen laskelmien ja arviointien avulla.

Water quality estimation by optical remote sensing in boreal lakes

In lake-rich regions, the gathering of information about water quality is challenging because only a small proportion of the lakes can be assessed each year by conventional methods. One of the techniques for improving the spatial and temporal representativeness of lake monitoring is remote sensing from satellites and aircrafts. The experimental material included detailed optical measurements in 11 lakes, air- and spaceborne remote sensing measurements with concurrent field sampling, automatic raft measurements and a national dataset of routine water quality measurements from over 1100 lakes. The analyses of the spatially high-resolution airborne remote sensing data from eutrophic and mesotrophic lakes showed that one or a few discrete water quality observations using conventional monitoring can yield a clear over- or underestimation of the overall water quality in a lake. The use of TM-type satellite instruments in addition to routine monitoring results substantially increases the number of lakes for which water quality information can be obtained. The preliminary results indicated that coloured dissolved organic matter (CDOM) can be estimated with TM-type satellite instruments, which could possibly be utilised as an aid in estimating the role of lakes in global carbon budgets. Based on the results of reflectance modelling and experimental data, MERIS satellite instrument has optimal or near-optimal channels for the estimation of turbidity, chlorophyll a and CDOM in Finnish lakes. MERIS images with a 300 m spatial resolution can provide water quality information in different parts of large and medium-sized lakes, and in filling in the gaps resulting from conventional monitoring. Algorithms that would not require simultaneous field data for algorithm training would increase the amount of remote sensing-based information available for lake monitoring. The MERIS Boreal Lakes processor, trained with the optical data and concentration ranges provided by this study, enabled turbidity estimations with good accuracy without the need for algorithm correction with field measurements, while chlorophyll a and CDOM estimations require further development of the processor. The accuracy of interpreting chlorophyll a via semi empirical algorithms can be improved by classifying lakes prior to interpretation according to their CDOM level and trophic status. Optical modelling indicated that the spectral diffuse attenuation coefficient can be estimated with reasonable accuracy from the measured water quality concentrations. This provides more detailed information on light attenuation from routine monitoring measurements than is available through the Secchi disk transparency. The results of this study improve the interpretation of lake water quality by remote sensing and encourage the use of remote sensing in lake monitoring.

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.

Heraproteiinivalmisteen vaikutus laihdutukseen ja laihdutustuloksen pysyvyyteen ylipainoisilla aikuisilla

Johdanto: Lihavuus on maailmalaajuisesti merkittävä kansanterveydellinen ja –taloudellinen ongelma. Lihavuuden ehkäisemiseksi ja epidemian leviämisen hillitsemiseksi on tärkeää tuntea lihavuuteen vaikuttavat tekijät. Yksittäisistä ruoka-aineista maidon käytön on havaittu monissa epidemiologisissa ja kokeellisissa tutkimuksissa olevan yhteydessä alhaisempaan painoon, ehkäisevän lihomista ja edistävän laihtumista. Maidon sisältämistä yhdisteistä kalsiumin vaikutuksia on tutkittu eniten. Myös heraproteiinin on esitetty olevan yksi mahdollinen painoon vaikuttava komponentti, ja näyttöä tästä on saatu eläinkokeista. Tavoitteet: Tutkimuksessa tavoitteena oli selvittää, vaikuttaako päivittäin nautittu heraproteiinia sisältävä välipalajuoma laihtumiseen tai saavutetun laihdutustuloksen pysyvyyteen ylipainoisilla aikuisilla. Aineisto ja menetelmät: Tutkimus toteutettiin osana Valio Oy:n OMPPU2-tutkimusta, joka oli satunnaistettu, lumekontrolloitu ja kaksoissokkoutettu kahden rinnakkaisen ryhmän tutkimus. Tutkimus alkoi rekrytoinneilla alkuvuodesta 2010, joissa tutkimukseen valittiin 105 ylipainoista (BMI 27–35), tervettä, 20–50-vuotiasta naista ja miestä. Tutkimushenkilöt satunnaistettiin tutkimus- ja verrokkiryhmiin, ja molemmat ryhmät nauttivat tutkimusvalmisteensa päivittäin hedelmätäysmehuun sekoitettuna (tutkimusryhmä heraproteiinijauheen ja verrokkiryhmä maltodekstriinijauheen). Tutkimus koostui kahdesta jaksosta: viiden kuukauden laihdutusjaksosta ja tätä seuranneesta kolmen kuukauden painonhallintajaksosta. Tutkimuskäynneillä tutkimuksen alussa, laihdutusjakson lopussa ja painonhallintajakson lopussa mitattiin tutkimushenkilöiden paino ja vyötärönympärys sekä määritettiin kehonkoostumus bioimpedanssilaitteella. Tutkimushenkilöiden ruoankäyttö ja ravinnonsaanti laskettiin samoissa aikapisteissä kerättyjen kolmen päivän ruokapäiväkirjojen perusteella. Tutkimushenkilöitä, joilla tutkimusvalmisteen käyttö oli alle 50 %, ei otettu huomioon tilastoanalyyseissä. Tilastollinen analyysi tehtiin käyttäen kahden riippumattoman otoksen t-testiä ja kaksisuuntaista parittaista t-testiä normaalijakautuneilla muuttujilla, ja Mann-Whitneyn U-testiä ja Wilcoxonin ttestiä ei-normaalijakautuneilla muuttujilla. Tutkimusvalmisteen ja painonmuutosten välinen korrelaatio laskettiin käyttäen Pearsonin korrelaatiokertoimia. Tulokset on ilmaistu keskiarvoina (keskihajonta). Tulokset: Molemmat ryhmät laihtuivat laihdutusjakson aikana. Heraproteiiniryhmässä painonpudotus oli 2,4 (3,8) kg (p=0,002) ja verrokkiryhmässä 3,4 (4,1) kg (p<0,001). Ryhmien välinen ero ei ollut merkitsevä. Rasvamassa väheni verrokkiryhmässä 2,4 (3,8) kg (p<0,001), mikä oli viiteellisesti enemmän (p=0,054) kuin heraproteiiniryhmässä 1,1 (3,1) kg (p=0,129). Rasvaprosentti ja viskeraalirasvan määrä pienenivät verrokkiryhmässä heraproteiiniryhmää enemmän (p<0,025). Vyötärönympärys pieneni heraproteiiniryhmässä 1,9 (3,0) cm (p=0,001) ja verrokkiryhmässä 3,8 (3,8) cm (p<0,001) ryhmien välisen eron ollessa merkitsevä (p=0,017). Maltodekstriinin käyttö korreloi käänteisesti painonmuutosten kanssa laihdutusjaksolla (r=-0,389, p=0,013). Painonhallintajaksolla painossa ei tapahtunut merkitseviä muutoksia kummassakaan ryhmässä. Heraproteiinin käytön ja painonmuutosten välisestä negatiivisesta korrelaatiosta oli viitteitä tällä jaksolla (r=-0,344, p=0,063). Kun tarkasteltiin koko tutkimuksen aikana tapahtuneita muutoksia (laihdutusjakson alusta painonhallintajakson loppuun), ei ryhmien välillä ollut merkitseviä eroja painon tai kehonkoostumuksen muutoksissa. Energiansaanti väheni molemmissa ryhmissä merkitsevästi laihdutusjakson aikana (p<0,01), mutta muutos ei eronnut ryhmien välillä. Ravintoaineista rasvan saanti väheni (p<0,001) ja C-vitamiinin saanti lisääntyi (p<0,001) molemmissa ryhmissä laihdutusjaksolla. Alkoholin saanti väheni verrokkiryhmässä (p=0,017). Proteiinin saanti lisääntyi heraproteiiniryhmässä merkitsevästi enemmän kuin verrokkiryhmässä (p=0,002). Painonhallintajaksolla energiansaanti ei muuttunut kummassakaan ryhmässä laihdutusjakson loppuun verrattuna. Fyysisessä aktiivisuudessa tutkimuksen aikana ei ollut eroa ryhmien välillä. Johtopäätökset: Heraproteiinin ei havaittu tehostavan laihdutusta maltodekstriiniin verrattuna tässä tutkimuksessa. Sen sijaan maltodekstriiniä nauttineessa ryhmässä rasvaprosentti ja erityisesti vatsan alueen rasva pienenivät heraproteiiniryhmää enemmän laihdutusjaksolla. Tulos oli lähes täysin vastakkainen tutkimushypoteesin kanssa, eikä vaikuttaisi selittyvän eroilla energiansaannissa tai fyysisessä aktiivisuudessa. Tämä tutkimus ei siis tue olettamusta, että heraproteiini osana laihdutusruokavaliota auttaisi laihdutuksessa. Painonhallintajaksolla heraproteiinin ja painonmuutosten välinen lähes merkitsevä käänteinen korrelaatio saattaa viitata heraproteiinin merkitykseen painonhallinnassa. Vapaasti elävien ihmisten kohdalla sekoittavia tekijöitä on kuitenkin vaikea vakioida, mikä vaikeuttaa johtopäätösten tekemistä.

Denitrification in the River Estuaries of the Northern Baltic Sea

Estuaries have been suggested to have an important role in reducing the nitrogen load transported to the sea. We measured denitrification rates in six estuaries of the northern Baltic Sea. Four of them were river mouths in the Bothnian Bay (northern Gulf of Bothnia), and two were estuary bays, one in the Archipelago Sea (southern Gulf of Bothnia) and the other in the Gulf of Finland. Denitrification rates in the four river mouths varied between 330 and 905 mu mol N m(-2) d(-1). The estuary bays at the Archipelago Sea and the Gulf of Bothnia had denitrification rates from 90 mu mol N m(-2) d(-1) to 910 mu mol N m(-2) d(-1) and from 230 mu mol N m(-2) d(-1) to 320 mu mol N m(-2) d(-1), respectively. Denitrification removed 3.6-9.0% of the total nitrogen loading in the river mouths and in the estuary bay in the Gulf of Finland, where the residence times were short. In the estuary bay with a long residence time, in the Archipelago Sea, up to 4.5% of nitrate loading and 19% of nitrogen loading were removed before entering the sea. According to our results, the sediments of the fast-flowing rivers and them estuary areas with short residence times have a limited capacity to reduce the nitrogen load to the Baltic Sea.

Anaerobic ammonium oxidation (anammox) in sediments of the Gulf of Finland

Anaerobic ammonium oxidation (anammox) and denitrification were measured in the open sea and coastal accumulation basins of the Gulf of Finland. The different methods used gave conflicting results on the importance of the anammox process in the sediments. Anammox generally contributed less than 20 % to the total N-2 production, and no anammox was found in a shallow inner estuary basin. However, the discovery of the anammox process in the open sea sediments challenges the denitrification measurements made in the area, as the coexistence of anammox and denitrification compromises the central assumptions behind the method used in denitrification measurements and causes overestimates of the N-2 production. The high (NO3-)-N-15 incubation concentration used in Baltic Sea denitrification measurements exacerbates this overestimation, which is likely to have been substantial.

Seasonal and short-term variation in denitrification and anammox at a coastal station on the Gulf of Finland, Baltic Sea

Benthic processes were measured at a coastal deposition area in the northern Baltic Sea, covering all seasons. The N-2 production rates, 90-400 mu mol N m(-2) d(-1), were highest in autumn-early winter and lowest in spring. Heterotrophic bacterial production peaked unexpectedly late in the year, indicating that in addition to the temperature, the availability of carbon compounds suitable for the heterotrophic bacteria also plays a major role in regulating the denitrification rate. Anaerobic ammonium oxidation (anammox) was measured in spring and autumn and contributed 10% and 15%, respectively, to the total N-2 production. The low percentage did, however, result in a significant error in the total N-2 production rate estimate, calculated using the isotope pairing technique. Anammox must be taken into account in the Gulf of Finland in future sediment nitrogen cycling research.

Geographical Information System Approach for Regional Biogas Potential Assessment

The economic prosperity and quality of life in a region are closely linked to the level of its per capita energy consumption. In India more than 70% of the total population inhabits rural areas and 85-90% of energy requirement is being met by bioresources. With dwindling resources, attention of planners is diverted to viable energy alternatives to meet the rural energy demand. Biogas as fuel is one such alternative, which can be obtained by anaerobic digestion of animal residues and domestic and farm wastes, abundantly available in the countryside. Study presents the techniques to assess biogas potential spatially using GIS in Kolar district, Karnataka State, India. This would help decision makers in selecting villages for implementing biogas programmes based on resource availability. Analyses reveal that the domestic energy requirement of more than 60% population can be met by biogas option. This is based on the estimation of the per capita requirement of gas for domestic purposes and availability of livestock residues.

Not just another pretty reef: the Gainesville Florida Reef, a satellite of the worldwide Hyperbolic Crochet Coral Reef project: poster presentation

The Gainesville Florida Reef, a satellite of the Worldwide Hyperbolic Crochet Coral Reef, project not only shows the beauty of reefs but serves to: • Foster scientific communication through the visual arts • Raise awareness of the fragility of our coral reefs and the entire ecosystem • Support learning by creating physical models of geometric principles • Connect several areas on campus, including fine arts, mathematics and ecology and environmental sciences through collaboration and mutual interest • Encourage local community and alumni involvement through creating, observing and learning