A General Approach for the Analysis of Habitat Selection

Investigating habitat selection of animals aims at the detection of preferred and avoided habitat types as well as at the identification of covariates influencing the choice of certain habitat types. The final goal of such analyses is an improvement of the conservation of animals. Usually, habitat selection by larger animals is assessed by radio-tracking or visual observation studies, where the chosen habitat is determined for a number of animals at a set of time points. Hence the resulting data often have the following structure: A categorical variable indicating the habitat type selected by an animal at a specific time point is repeatedly observed and shall be explained by covariates. These may either describe properties of the habitat types currently available and / or properties of the animal. In this paper, we present a general approach for the analysis of such data in a categorical regression setup. The proposed model generalises and improves upon several of the approaches previously discussed in the literature and in particular allows to account for changing habitat availability due to the movement of animals within the observation area. It incorporates both habitat- and animal-specific covariates, and includes individual-specific random effects in order to account for correlations introduced by the repeated measurements on single animals. The methodology is implemented in a freely available software package. We demonstrate the general applicability and the capabilities of the proposed approach in two case studies: The analysis of a songbird in South-America and a study on brown bears in Central Europe

A versatile Cell-free Protein Production Platform for the Synthesis of multifunctional Enzymes

Enzymes are indispensable proteins for all types of organisms, capable of fulfilling various functions by catalyzing diverse chemical reactions. This makes them important tools not only for fundamental research in biochemistry but also for applied research in pharmacology and organic chemistry. However, the recombinant production of enzymes is not trivial, and conventional isolations and expressions from cells are often unsuitable for many applications due to decreased enzyme activity. Cell-free protein synthesis can simplify the synthesis of some enzymes that were previously difficult to produce. Representatives of various enzyme classes were synthesized and subsequently analyzed. Modifications to the established synthesis platforms based on translationally active CHO and Sf21 lysates were made. These modifications allowed for the production of a soluble enzyme, a representative of the hydrolases, GH78 from Xylaria polymorpha. Kinetic analyses after synthesis optimization confirmed the kinetic similarity to the naturally synthesized enzyme. In particular, temperature and synthesis condition adjustments, as well as DNA template modifications, were found to increase enzyme activity. Efforts to adapt a cell-free synthesis platform for the production of further active fungal enzymes, mainly comprising unspecific peroxygenases in active CHO lysates have not yet yielded successful results. However, progress has been made in laying the foundation for future advancements, including the generation of templates, successful synthesis, and the establishment of activity assays. To provide a mammalian enzyme alternative to the unspecific peroxygenases, difficult-to-express monooxygenases comprising members of the cytochrome P450 enzyme family (CYP), the membrane-bound enzymes CYP1A2, CYP2B6, and CYP3A4 from Homo Sapiens, were produced in a eukaryotic translationally active cell lysate. By genetically modifying the CHO cells used for lysate production, an increased amount of CPR, the coenzyme of CYPs, was integrated into the endogenous membrane vesicles of the lysate, thus increasing the activity of the cell-free produced CYPs. Further adaptations of the synthesis, such as synthesis temperature and supplementation with heme, led to further increases in CYP activity in the endogenous membrane vesicles. This allowed for exemplary screening experiments with known CYP substrates.Enzyme sind unverzichtbare Proteine für alle Arten von Organismen, die durch Katalyse verschiedener chemischer Reaktionen verschiedene Funktionen erfüllen können. Dies macht sie nicht nur für die Grundlagenforschung in der Biochemie, sondern auch für die angewandte Forschung in der Pharmakologie und organischen Chemie zu wichtigen Werkzeugen. Die rekombinante Produktion von Enzymen ist jedoch nicht trivial, und herkömmliche Isolations- und Expressionsmethoden aus Zellen sind oft für viele Anwendungen aufgrund verringerte Enzymaktivität ungeeignet. Die zellfreie Proteinsynthese kann die Synthese einiger zuvor schwer herstellbarer Enzyme vereinfachen. Vertreter verschiedener Enzymklassen wurden synthetisiert und anschließend analysiert. Modifikationen an den etablierten Syntheseplattformen basierend auf translationsaktiven CHO- und Sf21-Lysaten wurden vorgenommen. Diese Modifikationen ermöglichten die Produktion eines löslichen Enzyms, eines Vertreters der Hydrolasen, GH78 von Xylaria polymorpha. Kinetische Analysen nach Optimierung der Synthese bestätigten die kinetische Ähnlichkeit zum natürlichen Enzym. Insbesondere Temperatur- und Synthesebedingungsanpassungen sowie Modifikationen der DNS-Vorlage wurden durchgeführt, um die Enzymaktivität zu erhöhen. Die Anpassung einer zellfreien Syntheseplattform zur Produktion weiterer aktiver Pilzenzyme, hauptsächlich von unspezifischen Peroxygenasen in translationsaktiven CHO-Lysaten, hat bisher keine erfolgreichen Ergebnisse erbracht. Es wurden allerdings bereits die ersten Schritte, insbesondere die Generierung von DNS-Template, erfolgreicher erste Synthesen und der Etablierung von Aktivitätsassays durchgeführt. Als Alternative zu den unspezifischen Peroxygenasen, wurden schwer herstellbare Monooxygenasen der Cytochrom-P450-Enzymfamilie (CYP), in einem eukaryotischen translationsaktiven Zelllysat produziert. Durch genetische Modifikation, der für die Lysatproduktion verwendeten CHO-Zellen wurde, eine erhöhte Menge an CPR, dem Coenzym der CYPs, in die endogenen Membranvesikel des Lysats integriert, was die Aktivität der CYPs erhöhte. Weitere Anpassungen der Synthese, wie z.B. die Synthesetemperatur und die Zugabe von Häm, führten zu weiteren Steigerungen der CYP-Aktivität in den endogenen Membranvesikeln. Dies ermöglichte exemplarische Screening-Experimente mit bekannten CYP-Substraten

Evaluierung von sechs Fotofallenmodellen hinsichtlich der Eignung für Fang-Wiederfang Methoden beim Eurasischen Luchs (Lynx lynx)

Digital outdoor cameras are increasingly used in wildlife research because they allow species inventories, population estimates, and behavior or activity observations. Which camera model is suitable and practical depends on environmental conditions, focus species and specific scientific questions posed. Here we focused on testing cameras appropriate for elusive species that can be identified visually owing to individual coat patterns. Specifically the camera should be adequate for calculating the minimum population of Eurasian Lynx (Lynx lynx) during a systematic monitoring with camera traps. Therefore we tested six digital camera models with regard to trigger speed and the image quality necessary for visual identification of pacing lynx on trails. The decision if a camera model is adequate for the scientific goal was regulated due to priority levels under laboratory conditions. Only one camera model proved to be suitable for camera-trap monitoring. Our practical camera test can be used to evaluate newer models of digital cameras as they become available. This application opens an avenue for a non-invasive population monitoring of rare and elusive species in a low mountain range area.Digitale Fotofallen werden weltweit in der Wildtierforschung eingesetzt. Die Einsatzgebiete sind vielfältig, sie reichen von Artenbestandsaufnahmen und Populationsschätzungen über die Verhaltensforschung bis hin zu Aktivitätsanalysen. Das jeweilig eingesetzte Kameramodell muss an die Aufnahmesituation und die Zielsetzung der Analyse angepasst sein. Das Ziel unseres Fotofallentests war es, ein Modell zu finden, welches für die visuelle Identifizierung von Fellmustern des Eurasischen Luchses geeignet ist. Die Fotofalle soll in einem systematischen Monitoring für die minimale Anzahl der im Gebiet vorkommenden Luchse und deren Populationsschätzung mit Fang-Wiederfang Methoden eingesetzt werden können. Bei dem Test von sechs Fotofallenmodellen, fiel das Hauptaugenmerk auf die Auslösegeschwindigkeit und die Bildqualität welche die nötigen Faktoren für die Sicherstellung der visuellen Identifikation von schreitenden Luchsen am Wildwechsel darstellen. Zur Entscheidungsfindung der Eignung eines Fotofallenmodells für die Fragestellung definierten wir Prioritätslevel unter Laborbedingungen. Es stellte sich heraus, dass nur ein Fotofallenmodell die Ansprüche erfüllte. Der praktische Fotofallentest kann für neuerscheinende Fotofallenmodelle adaptiert werden. Diese Anwendung eröffnet die Möglichkeit für ein nicht invasives Monitoring in Mittelgebirgslandschaften

Finding the missing link between landscape structure and population dynamics: a spatially explicit perspective

We construct and explore a general modeling framework that allows for a systematic investigation of the impact of changes in landscape structure on population dynamics. The essential parts of the framework are a landscape generator with independent control over landscape composition and physiognomy, an individual-based spatially explicit population model that simulates population dynamics within heterogeneous landscapes, and scale-dependent landscape indices that depict the essential aspects of landscape that interact with dispersal and demographic processes. Landscape maps are represented by a grid of 50#50 cells and consist of good-quality, poorquality, or uninhabitable matrix habitat cells. The population model was shaped in accordance to the biology of European brown bears (Ursus arctos), and demographic parameters were adjusted to yield a source-sink configuration. Results obtained with the spatially explicit model do not confirm results of earlier nonspatial source-sink models where addition of sink habitat resulted in a decrease of total population size because of dilution of high-quality habitat. Our landscape indices, which describe scale-dependent correlation between and within habitat types, were able to explain variations in variables of population dynamics (mean number of females with sink home ranges, mean number of females with source home ranges, and mean dispersal distance) caused by different landscape structure. When landscape structure changed, changes in these variables generally followed the corresponding change of an appropriate landscape index in a linear way. Our general approach incorporates source-sink dynamics as well as metapopulation dynamics, and the population model can easily be modified for other species groups

Songbirds use scent cues to relocate to feeding sites after displacement: An experiment in great tits (Parus major)

Air-borne chemicals are highly abundant sensory cues and their use in navigation might be one of the major evolutionary mechanisms explaining the development of olfaction in animals. Despite solid evidence for the importance of olfaction in avian life (e.g., foraging or mating), the importance of chemical cues in avian orientation remains controversial. In particular, songbirds are sorely neglected models, despite their remarkable orientation skills. Here we show that great tits (Parus major) require olfactory cues to orientate toward winter-feeding sites within their home range after displacement. Birds that received an olfaction-depriving treatment were impaired in homing. However, the return rates between olfaction-deprived and control individuals did not differ. Birds with decreased perception of olfactory cues required more time to return to the winter feeding sites. This effect became apparent when the distance between the releasing and capture sites was greater. Our results indicate that even in a familiar environment with possible visual landmarks, scent cues might serve as an important source of information for orientation

Synthesis of mono Cytochrome P450 in a modified CHO-CPR cell-free protein production platform

Cytochromes P450 (CYPs) are a group of monooxygenases that can be found in almost all kinds of organisms. For CYPs to receive electrons from co-substrate NADPH, the activity of NADPH-Cytochrome-P450-oxidoreductase (CPR) is required as well. In humans, CYPs are an integral part of liver-based phase-1 biotransformation, which is essential for the metabolization of multiple xenobiotics and drugs. Consequently, CYPs are important players during drug development and therefore these enzymes are implemented in diverse screening applications. For these applications it is usually advantageous to use mono CYP microsomes containing only the CYP of interest. The generation of mono-CYP containing mammalian cells and vesicles is difficult since endogenous CYPs are present in many cell types that contain the necessary co-factors. By obtaining translationally active lysates from a modified CHO-CPR cell line, it is now possible to generate mono CYPs in a cell-free protein synthesis process in a straightforward manner. As a proof of principle, the synthesis of active human CYPs from three different CYP450 gene families (CYP1A2, CYP2B6 and CYP3A4), which are of outstanding interest in industry and academia was demonstrated. Luciferase based activity assays confirm the activity of the produced CYPs and enable the individual adaptation of the synthesis process for efficient cell-free enzyme production. Furthermore, they allow for substrate and inhibitor screenings not only for wild-type CYPs but also for mutants and further CYP isoforms and variants. As an example, the turnover of selected CYP substrates by cell-free synthesized CYPs was demonstrated via an indirect luciferase assay-based screening setup

Cell-free production of the bifunctional glycoside hydrolase GH78 from Xylaria polymorpha

The ability to catalyze diverse reactions with relevance for chemical and pharmaceutical research and industry has led to an increasing interest in fungal enzymes. There is still an enormous potential considering the sheer amount of new enzymes from the huge diversity of fungi. Most of these fungal enzymes have not been characterized yet due to the lack of high throughput synthesis and analysis methods. This bottleneck could be overcome by means of cell-free protein synthesis. In this study, cell-free protein synthesis based on eukaryotic cell lysates was utilized to produce a functional glycoside hydrolase (GH78) from the soft-rot fungus Xylaria polymorpha (Ascomycota). The enzyme was successfully synthesized under different reaction conditions. We characterized its enzymatic activities and immobilized the protein via FLAG-Tag interaction. Alteration of several conditions including reaction temperature, template design and lysate supplementation had an influence on the activity of cell-free synthesized GH78. Consequently this led to a production of purified GH78 with a specific activity of 15.4 U mg− 1. The results of this study may be foundational for future high throughput fungal enzyme screenings, including substrate spectra analysis and mutant screenings

Action A3 : analysis of spatial connectivity and preparation of environmental impact assessment guidelines : prepared within A3 action of LIFE DINALP BEAR Project (LIFE13 NAT/SI/0005)

As for other large carnivores in Europe, the brown bear shows a trend of recovering under different management scenarios. However, this recovery comes with specific biological and conservation requirements at individual and population levels often followed by conflicts in a highly humanized continent. To foresee conflicts with humans and to facilitate decisionmaking, spatially-explicit research is required to identify potential habitats and the connectivity of fragmented bear populations. First, we conducted multiscale modeling based on scale-integrated resource selection functions (SRSFs) to identify drivers shaping the spaceuse of three bear populations/demographic units (Trentino-Swiss, pre-Alps, and Dinaric), and across 3 scales of space (population distribution, home range establishment, and use of individual home range). Secondly, we also conducted an analysis of the connectivity patterns of suitable habitat patches (nodes) to identify the potential importance of each node to contribute to individual mobility, survival, and population connectivity. Lastly, to support further environmental impact assessment analyses, we identified the most plausible least-cost paths connecting different areas of the same large patch with itself and surrounding patches. Using topographic, landcover, and anthropogenic predictors, our analytical approach transcended from scale dependence bias to produce a predictive map on habitat suitability while delivered information on habitat selection trends for each population. Bears mostly selected forest habitats in all the populationshowever, habitat selection differed for the other variables among populations and scales, especially in the Trentino area where the species selected the most intricate topography. Predictive maps revealed a broad range of suitable but fragmented patches of bear habitat. The largest and most important patches for connectivity occurred in the current distribution range of the species, with the most suitable habitat lying in the pre-Alpine and Dinaric populations. Connecting viable patches to host female homeranges is possible through stepping-stone patches of corridors reachable within the estimated dispersal distance of females. Unified transnational decision-making is required for the conservation of stepping-stone patches, facilitate bear mobility, and ultimately connect bear populations.Podobno kot pri drugih vrstah velikih zveri se tudi pri rjavemu medvedu njegovo območje razširjenosti in številčnost povečujeta v več delih Evrope, in to ob različnih upravljavskih pristopih. Vendar uspešno širjenje vrste vselej zahteva specifične biološke in varstvene pogoje na individualni in populacijski ravni. V gosto poseljeni Evropi širjenje medveda pogosto spremljajo tudi konflikti s človekom. Za pravočasno napovedovanje in racionalno preprečevanje konfliktnih situacij s človekom in s tem lajšanja procesa odločanja so ključne zanesljive prostorske raziskave. Te nam omogočajo prepoznavanje potencialnih habitatov za medveda in območij/koridorjev, ki so ključna za ohranjanje povezljivosti populacije. V prvi fazi pričujoče raziskave smo zato izvedli večstopenjsko hierarhično prostorsko eksplicitno napovedno modeliranje habitatne ustreznosti prostora (scale integrated RSF), s katerim smo lahko prepoznali glavne omejitvene dejavnike rabe prostora za tri obravnavane medvedje populacije oz demografske enote (Trentino-Švicarske, pred-Alpska in Dinarska) na treh prostorskih nivojih (populacijski nivo, nivo območja aktivnosti in nivo notranje rabe znotraj območij aktivnosti). Izvedli smo tudi analizo povezljivosti prostora med osnovnimi zaplatami habitata in opredelili prispevek vsake zaplate k %vitalnosti% celotne medvedje populacije v raziskovalnem območju. Končno smo z namenom lažjega prepoznavanja potreb po prihodnjih presojah vplivov posegov na okolje (PVO) opredelili še najbolj verjetne prehode med habitatnimi krpami (least-cost paths). Na osnovi napovednih spremenljivk, ki opisujejo rabo tal, reliefne značilnosti in prisotnost človeka (npr. ceste, naselja) smo pripravili modele habitatne ustreznosti prostora za medveda in prepoznali tudi razlike v habitatnem izboru med 3 obravnavanimi populacijami in prostorskimi merili. V vseh treh populacijah so medvedi primarno izbirali gozdnata območja, so pa med populacijami in prostorskimi merili opazne razlike v rabi/pomenu ostalih okoljskih spremenljivk. Zlasti odstopa skupina medvedov v Trentinu, za katere je značilna izbira bolj nedostopnih območij (težji, topografsko bolj razgiban teren). Naš prostorsko eksplicitni model kaže, da je v obravnavanem območju veliko habitata, ki je primeren za medveda, vendar pa je zanj značilna močna fragmentiranost. Največje in najbolj pomembne zaplate habitata za povezljivost populacije se nahajajo na območju trenutne razširjenosti vrste, z najbolj primernim habitatom na območju pred-Alpske in Dinarske populacije. Zadostno povezanost najprimernejših zaplat (ki so dovolj velike, da v njih lahko žive samice % medvedke), bi bilo mogoče vzdrževati preko ohranjanja dovolj povezanih habitatnih krp v koridorjih (step-stones). Za ohranjanje zadostne povezanosti prostora/habitatov, zagotavljanja povezav med deli populacij in populacijami medvedov ter za dolgoročno viabilnost medveda v območju Alp in Dinaridov je ključna poenotena % med državami usklajena - politika odločanja in rabe prostora

Blühstreifen für Bestäuber und andere Nützlinge - Wertvolle Nahrungsquellen im Ackerbau

Das Merkblatt hilft Beratungskräften, Landwirtinnen und Landwirten sowie weiteren landwirtschaftlichen Akteuren bei der Umsetzung der neuen Biodiversitätsförderfläche Blühstreifen für Bestäuber und andere Nützlinge. Das Dokument beschreibt den kulturspezifischen Nutzen der Flächen, deren Anlage, Pflege und Aufhebung. Zudem werden Empfehlungen zur optimalen Umsetzung formuliert, damit die erwartete Leistung der Bestäuber und Nützlinge auch langfristig erbracht werden kann