Skogsbrukets erfarenheter av Poppel Populus sp. i Skåne

In Europe poplar plantations has been planted for more than one hundred years. In the first plantation was made in 1940. The interest for poplars has since then shifted over the years and has for long periods been very low but is now slowly increasing again. The main reasons why poplars are becoming more interesting are because of their great production potential. Nevertheless, the knowledge of how to mange poplars in Sweden are very low and very little research has been done concerning management of the species. The objective for this study was to; 1) investigate and document experience and results obtained in practical Swedish forestry, 2) to give a fair picture of the perceived advantages and disadvantages that the poplars has for the forestry, 3) document what the foresters that has experience and those who has no experience of poplar plantations thinks about the potential of poplars. Together this will hopefully make a rather complete picture of what is known of poplar silviculture in Sweden today. O.P 42 (P. maximowiczii x P. trichocarpa) is today the only poplar clone used in a large scale in Swedish forestry. The result from the field inventory shows that poplar plantation can have a higher survival than 90 % after one growing season, both with and without fencing against deer's and mouse. In Sweden three different seedlings types of poplars have been tested: 1-year rooted cuttings, un-rooted cuttings and half years rooted cuttings in pot plants. Root- and stump shoots regenerations has produced more than 15 000 stems/ha three years after the regenerations felling. Browsing animals have shown little interest of feeding of leafs and branches from poplars. Over a sixteen years long rotation period five poplar stands (O.P 42) showed a mean annual production of 20,5 – 38,5 m3/ha. Other clones in test plantations have a mean annual production of 11,2 – 37,0 m3/ha. The mean annual growth over the six years since the first thinning in four O.P 42 stands have been 30,1 – 39,8 m3/ha/year. In some cases poplar stands have been subject to storm felling but in other cases it withstands wind so experiences do not show a clear picture. The interviewed foresters with experience of poplars were all positive to plant more poplars in the future. The main reason for the foresters to establish poplar plantations where that poplar gives an economic income on a time span that for forestry is very short. Today the goal is the same and the foresters are encouraged by the results that they have seen so far. The recommendations by the interviewed forester about the silviculture of poplar are that the species should be planted on rich soils, with god supply of water without being too wet. The initial spacing should be 2 – 3 meters and the stand should be thinned 0 – 2 times in a rotations period of 15 – 25 years. The rotation length depends on which spacing you starts with and how many thinnings that are planned. The demand of poplar timber has not been high on the timber market but pulpwood has always been an alternative. Sveaskog and Södra skogsägarna are less positive to poplar but agrees that there is a general interest to test new fast growing species like poplars. A small genetic variation, insufficient knowledge, a small timber market and low cultivation security are seen as negative factors for an introduction of poplars.I Europa har poppel planterats i plantager i över hundra år, i Sverige började poppel uppmärksammas på 1940-talet men sedan dess har vi i liten utsträckning använt oss av poppel. Intresset för poppel har under perioder varit mycket lågt i Sverige men sedan några år tillbaka är den återupptäckt, främst är det poppelns stora produktionspotential som har dragit till sig intresset. Kunskaperna är dock ringa om poppel i Sverige och lite forskning har gjorts inom området. Arbetet har till syfte att: 1) kartlägga och dokumentera vilka resultat/erfarenheter som finns i Sverige idag i fråga om poppelskogsburk, 2) inventera vilka för och nackdelar som finns med poppel, 3) dokumentera vad de skogsbrukare som planterat poppel har för erfarenheter och hur skogsbruket i allmänhet ser på poppel. Sammanlagt ska detta ge en samlad bild av kunskaper och erfarenheter om poppel som skogsträd i Sverige. I svenskt skogsbruk används idag endast klonen O.P 42 (P. maximowiczii x P. trichocarpa). Resultatet från fältinventeringen visar att poppelplanteringar kan ha en överlevnad större än 90 % med eller utan hägn efter en växtsäsong. Det har i Sverige testats tre olika planttyper av poppel: 1-åriga rotade sticklingar, orotade sticklingar, samt halvåriga täckrotssticklingar. Rotoch stubbskottsföryngring har visat sig ge upp till 15 000 skott/ha tre år efter avverkning av det gamla beståndet. Vilt verkar inte vara någon större skadegörare på poppel. Över en sextonårig omloppstid har O.P 42 klonen årligen producerat i medeltal 20,5 – 38,5 m3sk/ha i fem olika bestånd. Andra kloner i testplanteringar har gett en medelproduktion på 11,2 – 37,0 m3sk/ha. Medeltillväxt över sex växtsäsonger har också uppmäts till 30,1 – 39,8 m3sk/ha/ för O.P 42 sedan första gallringen. Samtliga skogsförvaltare som har intervjuats om sina erfarenheter av poppel är positiva till att plantera mer poppel i framtiden. Den enda anledningen att samtliga skogsförvaltare planterade poppel en gång i tiden var att de såg det som en möjlighet till en god ekonomisk avkastning inom skogsbruket på kort sikt. Målet är detsamma idag och de resultat skogsförvaltarna har fått har stärkt deras inställning till poppel. Rekommendationerna som ges från skogsförvaltarna är att poppel ska planteras på näringsrika marker med god vattentillgång, utan att för den skull vara blöta. Planteringsförbandet ska vara 2 – 3 meter och gallras 0 – 2 gånger över en omloppstid på 15 – 25 år beroende om gallring/gallringar utförs. Virkesmarknaden anses dock trög, men poppel har ändå kunnat säljas som massaved och energived. Sveaskog och Södra skogsägarna är mindre positiva till poppel men anser att det finns ett intresse att testa snabbväxande träd som poppel. Liten genetisk bredd, dåliga kunskaper, liten marknad för virket och osäker odlingssäkerhet ses som negativa faktorer för poppel

Mumame: A software tool for quantifying gene-specific point-mutations in shotgun metagenomic data

Metagenomics has emerged as a central technique for studying the structure and function of microbial communities. Often the functional analysis is restricted to classification into broad functional categories. However, important phenotypic differences, such as resistance to antibiotics, are often the result of just one or a few point mutations in otherwise identical sequences. Bioinformatic methods for metagenomic analysis have generally been poor at accounting for this fact, resulting in a somewhat limited picture of important aspects of microbial communities. Here, we address this problem by providing a software tool called Mumame, which can distinguish between wildtype and mutated sequences in shotgun metagenomic data and quantify their relative abundances. We demonstrate the utility of the tool by quantifying antibiotic resistance mutations in several publicly available metagenomic data sets. We also identified that sequencing depth is a key factor to detect rare mutations. Therefore, much larger numbers of sequences may be required for reliable detection of mutations than for most other applications of shotgun metagenomics. Mumame is freely available online (http://microbiology.se/software/mumame)

Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomics

Background: Metagenomics is the study of microbial communities by sequencing of genetic material directly from environmental or clinical samples. The genes present in the metagenomes are quantified by annotating and counting the generated DNA fragments. Identification of differentially abundant genes between metagenomes can provide important information about differences in community structure, diversity and biological function. Metagenomic data is however high-dimensional, contain high levels of biological and technical noise and have typically few biological replicates. The statistical analysis is therefore challenging and many approaches have been suggested to date. Results: In this article we perform a comprehensive evaluation of 14 methods for identification of differentially abundant genes between metagenomes. The methods are compared based on the power to detect differentially abundant genes and their ability to correctly estimate the type I error rate and the false discovery rate. We show that sample size, effect size, and gene abundance greatly affect the performance of all methods. Several of the methods also show non-optimal model assumptions and biased false discovery rate estimates, which can result in too large numbers of false positives. We also demonstrate that the performance of several of the methods differs substantially between metagenomic data sequenced by different technologies. Conclusions: Two methods, primarily designed for the analysis of RNA sequencing data (edgeR and DESeq2) together with a generalized linear model based on an overdispersed Poisson distribution were found to have best overall performance. The results presented in this study may serve as a guide for selecting suitable statistical methods for identification of differentially abundant genes in metagenomes

Les exposicions del Guernica de Picasso

Aproximació al procés de creació del Guernica de Pablo Picasso i a la seva presentació pública, a través de les exposicions de caràcter temporal i les corresponents a les col·leccions dels museus en les quals es va dipositar, per a poder reconstruir la història d’una de les icones mundials de l’art modern universal. El treball atent a la creació, contingut simbòlic i característiques principals de l’obra, a les circumstàncies històriques que la van envoltar, als itineraris expositius, els discursos museogràfics i les condicions de la seva presentació pública: al Pavelló espanyol de l’Exposició Internacional de París de 1937, al Museu d’Art Modern de New York (MoMA), al Museo Nacional del Prado i al Museu Nacional Centre de Artes Reina Sofía de Madrid, institució que acull actualment l’obra. Al llarg del treball es descriu el procés de transformació de la seva significació en funció del context en el qual s’insereix en cada moment, des d’un instrument de propaganda política, icona de l’art modern occidental, fins a la seva consideració com a obra mestra en la articulació de l’art espanyol modern i contemporani

Comparison of normalization methods for the analysis of metagenomic gene abundance data

Background: In shotgun metagenomics, microbial communities are studied through direct sequencing of DNA without any prior cultivation. By comparing gene abundances estimated from the generated sequencing reads, functional differences between the communities can be identified. However, gene abundance data is affected by high levels of systematic variability, which can greatly reduce the statistical power and introduce false positives. Normalization, which is the process where systematic variability is identified and removed, is therefore a vital part of the data analysis. A wide range of normalization methods for high-dimensional count data has been proposed but their performance on the analysis of shotgun metagenomic data has not been evaluated. Results: Here, we present a systematic evaluation of nine normalization methods for gene abundance data. The methods were evaluated through resampling of three comprehensive datasets, creating a realistic setting that preserved the unique characteristics of metagenomic data. Performance was measured in terms of the methods ability to identify differentially abundant genes (DAGs), correctly calculate unbiased p-values and control the false discovery rate (FDR). Our results showed that the choice of normalization method has a large impact on the end results. When the DAGs were asymmetrically present between the experimental conditions, many normalization methods had a reduced true positive rate (TPR) and a high false positive rate (FPR). The methods trimmed mean of M-values (TMM) and relative log expression (RLE) had the overall highest performance and are therefore recommended for the analysis of gene abundance data. For larger sample sizes, CSS also showed satisfactory performance. Conclusions: This study emphasizes the importance of selecting a suitable normalization methods in the analysis of data from shotgun metagenomics. Our results also demonstrate that improper methods may result in unacceptably high levels of false positives, which in turn may lead to incorrect or obfuscated biological interpretation

Mitochondrial dysfunction in adult midbrain dopamine neurons triggers an early immune response

Dopamine (DA) neurons of the midbrain are at risk to become affected by mitochondrial damage over time and mitochondrial defects have been frequently reported in Parkinson\u27s disease (PD) patients. However, the causal contribution of adult-onset mitochondrial dysfunction to PD remains uncertain. Here, we developed a mouse model lacking Mitofusin 2 (MFN2), a key regulator of mitochondrial network homeostasis, in adult midbrain DA neurons. The knockout mice develop severe and progressive DA neuron-specific mitochondrial dysfunction resulting in neurodegeneration and parkinsonism. To gain further insights into pathophysiological events, we performed transcriptomic analyses of isolated DA neurons and found that mitochondrial dysfunction triggers an early onset immune response, which precedes mitochondrial swelling, mtDNA depletion, respiratory chain deficiency and cell death. Our experiments show that the immune response is an early pathological event when mitochondrial dysfunction is induced in adult midbrain DA neurons and that neuronal death may be promoted non-cell autonomously by the cross-talk and activation of surrounding glial cells

Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing

The impact of the microenvironment on innate lymphoid cell (ILC)-mediated immunity in humans remains largely unknown. Here we used full-length Smart-seq2 single-cell RNA-sequencing to unravel tissue-specific transcriptional profiles and heterogeneity of CD127+ ILCs across four human tissues. Correlation analysis identified gene modules characterizing the migratory properties of tonsil and blood ILCs, and signatures of tissue-residency, activation and modified metabolism in colon and lung ILCs. Trajectory analysis revealed potential differentiation pathways from circulating and tissue-resident na\uefve ILCs to a spectrum of mature ILC subsets. In the lung we identified both CRTH2+ and CRTH2− ILC2 with lung-specific signatures, which could be recapitulated by alarmin-exposure of circulating ILC2. Finally, we describe unique TCR-V(D)J-rearrangement patterns of blood ILC1-like cells, revealing a subset of potentially immature ILCs with TCR-δ rearrangement. Our study provides a useful resource for in-depth understanding of ILC-mediated immunity in humans, with implications for disease

Är belöningar ett effektivt styrmedel? –En kvalitativ studie om belöningssystem och dess effekt på motivation

Inledning: Belöningar i form av monetära och icke-monetära används som ett styrningsverktyg till att motivera medarbetarens och dess egenintresse samt att få medarbetarna att handla utefter företagets mål. För att åstadkomma ett samspel mellan medarbetarens egenintresse och organisationens mål krävs en förståelse för hur belöningar bidrar till motivation. Eftersom vad i grunden motiverar medarbetaren skiljs åt blir det således av intresse att studera hur olika typer av belöningar leder till motivation. Syfte: Syftet är att undersöka hur ett belöningssystems olika belöningsformer verkar för att motivera medarbetarna med hänsyn till tidigare motivationsforskning. Även belöningssystemets struktur kommer att undersökas vilket ter sig antingen individ- eller lagbaserat. Metod: Studien är baserad på en kvalitativ studie med en induktiv ansats. Empiriska insamlingen av data utgörs av fem intervjuobjekt från olika företag. Insamlad data analyseras sedan utifrån studiens teoretiska referensram. Slutsats: Monetära lagbaserade belöningar är det mest effektiva styrmedlet, ur ett långsiktigt företagsperspektiv, för att motivera medarbetare. Vidare når företagen i denna studie sina mål och intressekonflikten minimeras, förutsatt att lagen är av rimlig storlek. Författarna kan dock inte dra en generell slutsats baserat på studiens resultat då urvalet är för litet