A (green) wave of the future?

During the last years, Sweden has seen the rise of a new green wave (NGV) consisting of people who move to rural areas in a strive for self-sufficiency and alternative ways of living. The point of departure for this thesis is that radical changes in lifestyle is a result of discontent with some aspect(s) of mainstream society. Through unstructured interviews and a discourse analysis inspired by Carol Bacchi’s WPR-approach, I investigate discourses present in the NGV through inquiries into the respondents’ practices and motives. The study shows that the respondents’ daily practices and life choices are motivated by their ideas about our economic system, social change, food production and sustainability. The findings are then placed in the context of ecomodernism, degrowth, the crisis of democracy and an economic system based on growth, consumption and paid labour

Vaxholm (Egentliga Östersjön) 2016–2018

Under de tre år som provfisket i Vaxholm har pågått har fångstsammansättningen varit relativt konstant. Under 2018 fångades 75 fiskar per ansträngning (antal individer per nät och natt) fördelat på 12 arter. Totalfångsten var större än 2016 och 2017. Mört var den vanligaste arten i fångsten (50 procent), följt av abborre, strömming, braxen och gärs. Den totala fångsten av karpfisk i Vaxholm var stor, under 2018 fångades 44 individer per ansträngning vilket var högre än tidigare år. De arter av karpfisk som fångats i Vaxholm är mört, braxen, löja, björkna, id och sutare. Det fångades relativt många stora individer (> 30 centimeter) i Vaxholm och fångsten var något större 2018 än under de två tidigare åren. Av stora fiskar dominerar braxen och abborre, men även individer av gös, sik, mört och sutare över 30 centimeter fångades. I provfiskefångsten utgjorde abborre 98 procent av all rovfisk. Förutom abborre förekom även rovfisken gös i fångsten. Antalet abborrar såväl som antalet rovfiskar var fler under 2018 än tidigare år. Diversitetsindexet och den trofiska medelnivån har varit likartad under de tre år provfisket pågått, och är i nivå med närliggande provfiskeområden. Ett- till fyra-åriga abborrar var efter den varma sommaren 2018 större vid given ålder jämfört med tidigare år. Ett lågt siktdjup i kombination med den stora fångsten av karpfisk antyder att Vaxholm är påverkat av hög näringsbelastning

Classification of microarrays; synergistic effects between normalization, gene selection and machine learning

<p>Abstract</p> <p>Background</p> <p>Machine learning is a powerful approach for describing and predicting classes in microarray data. Although several comparative studies have investigated the relative performance of various machine learning methods, these often do not account for the fact that performance (e.g. error rate) is a result of a series of analysis steps of which the most important are data normalization, gene selection and machine learning.</p> <p>Results</p> <p>In this study, we used seven previously published cancer-related microarray data sets to compare the effects on classification performance of five normalization methods, three gene selection methods with 21 different numbers of selected genes and eight machine learning methods. Performance in term of error rate was rigorously estimated by repeatedly employing a double cross validation approach. Since performance varies greatly between data sets, we devised an analysis method that first compares methods within individual data sets and then visualizes the comparisons across data sets. We discovered both well performing individual methods and synergies between different methods.</p> <p>Conclusion</p> <p>Support Vector Machines with a radial basis kernel, linear kernel or polynomial kernel of degree 2 all performed consistently well across data sets. We show that there is a synergistic relationship between these methods and gene selection based on the T-test and the selection of a relatively high number of genes. Also, we find that these methods benefit significantly from using normalized data, although it is hard to draw general conclusions about the relative performance of different normalization procedures.</p

Immortalization of T-cells is accompanied by gradual changes in CpG methylation resulting in a profile resembling a subset of T-cell leukemias

We have previously described gene expression changes during spontaneous immortalization of T-cells, thereby identifying cellular processes important for cell growth crisis escape and unlimited proliferation. Here, we analyze the same model to investigate the role of genome-wide methylation in the immortalization process at different time points pre-crisis and post-crisis using high-resolution arrays. We show that over time in culture there is an overall accumulation of methylation alterations, with preferential increased methylation close to transcription start sites (TSSs), islands, and shore regions. Methylation and gene expression alterations did not correlate for the majority of genes, but for the fraction that correlated, gain of methylation close to TSS was associated with decreased gene expression. Interestingly, the pattern of CpG site methylation observed in immortal T-cell cultures was similar to clinical T-cell acute lymphoblastic leukemia (T-ALL) samples classified as CpG island methylator phenotype positive. These sites were highly overrepresented by polycomb target genes and involved in developmental, cell adhesion, and cell signaling processes. The presence of non-random methylation events in in vitro immortalized T-cell cultures and diagnostic T-ALL samples indicates altered methylation of CpG sites with a possible role in malignant hematopoiesis

Decreased telomere length in children with cartilage-hair hypoplasia

Background Cartilage-hair hypoplasia (CHH) is an autosomal recessive chondrodysplasia caused by RMRP (RNA component of mitochondrial RNA processing endoribonuclease) gene mutations. Manifestations include short stature, variable immunodeficiency, anaemia and increased risk of malignancies, all of which have been described also in telomere biology disorders. RMRP interacts with the telomerase RT (TERT) subunit, but the influence of RMRP mutations on telomere length is unknown. We measured relative telomere length (RTL) in patients with CHH, their first-degree relatives and healthy controls and correlated RTL with clinical and laboratory features. Methods The study cohort included 48 patients with CHH with homozygous (n=36) or compound heterozygous RMRP mutations (median age 38.2 years, range 6.0-70.8 years), 86 relatives (74 with a heterozygous RMRP mutation) and 94 unrelated healthy controls. We extracted DNA from peripheral blood, sequenced the RMRP gene and measured RTL by qPCR. Results Compared with age-matched and sex-matched healthy controls, median RTL was significantly shorter in patients with CHH (n=40 pairs, 1.05 vs 1.21, p=0.017), but not in mutation carriers (n=48 pairs, 1.16 vs 1.10, p=0.224). RTL correlated significantly with age in RMRP mutation carriers (r=-0.482, p <0.001) and non-carriers (r=-0.498, p Conclusions Telomere length was decreased in children with CHH. We found no correlation between RTL and clinical or laboratory parameters.Peer reviewe

Beståndsstatus för torsk i Ålands hav 2022

Jämförelser mellan torsk i Ålands hav och i södra Östersjön för 2021 och 2022 visar att torsken i Ålands hav växer snabbare, har bättre kondition och blir större och äldre än torsken i södra Östersjön. Journalföringen visar att fångst per ansträngning för 2022 under april–juni är den näst högsta under hela tidsserien 2000–2022. Trots förekomst av parasiter i levern, påverkas inte torskens konditionsindex (Fulton K) i Ålands hav, men antalet levermaskar ökar med ålder, längd, vikt och levervikt. Endast ett fåtal torskar var angripna av muskelparasiter. Analys av maginnehållet visade att torsken i Ålands hav främst äter ishavsgråsugga men även sillartade fiskar och pungräkor

An integrated transcriptome analysis in T-cell acute lymphoblastic leukemia links DNA methylation subgroups to dysregulated TAL1 and ANTP homeobox gene expression

Classification of pediatric T-cell acute lymphoblastic leukemia (T-ALL) patients into CIMP (CpG Island Methylator Phenotype) subgroups has the potential to improve current risk stratification. To investigate the biology behind these CIMP subgroups, diagnostic samples from Nordic pediatric T-ALL patients were characterized by genome-wide methylation arrays, followed by targeted exome sequencing, telomere length measurement, and RNA sequencing. The CIMP subgroups did not correlate significantly with variations in epigenetic regulators. However, the CIMP+ subgroup, associated with better prognosis, showed indicators of longer replicative history, including shorter telomere length (P = 0.015) and older epigenetic (P <0.001) and mitotic age (P <0.001). Moreover, the CIMP+ subgroup had significantly higher expression of ANTP homeobox oncogenes, namely TLX3, HOXA9, HOXA10, and NKX2-1, and novel genes in T-ALL biology including PLCB4, PLXND1, and MYO18B. The CIMP- subgroup, with worse prognosis, was associated with higher expression of TAL1 along with frequent STIL-TAL1 fusions (2/40 in CIMP+ vs 11/24 in CIMP-), as well as stronger expression of BEX1. Altogether, our findings suggest different routes for leukemogenic transformation in the T-ALL CIMP subgroups, indicated by different replicative histories and distinct methylomic and transcriptomic profiles. These novel findings can lead to new therapeutic strategies.Peer reviewe