Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations

Background: A number of the deeper divergences in the placental mammal tree are still inconclusively resolved despite extensive phylogenomic analyses. A recent analysis of 200 kbp of protein coding sequences yielded only limited support for the relationships among Laurasiatheria (cow, dog, bat and shrew), probably because the divergences occurred only within a few million years from each other. It is generally expected that increasing the amount of data and improving the taxon sampling enhance the resolution of narrow divergences. Therefore these and other difficult splits were examined by phylogenomic analysis of the hitherto largest sequence alignment. The increasingly complete genome data of placental mammals also allowed developing a novel and stringent data search method. Results: The rigorous data handling, recursive BLAST, successfully removed the sequences from gene families, including those from well-known families hemoglobin, olfactory, myosin and HOX genes, thus avoiding alignment of possibly paralogous sequences. The current phylogenomic analysis of 3,012 genes (2,844,615 nucleotides) from a total of 22 species yielded statistically significant support for most relationships. While some major clades were confirmed using genomic sequence data, the placement of the treeshrew, bat and the relationship between Boreoeutheria, Xenarthra and Afrotheria remained problematic to resolve despite the size of the alignment. Phylogenomic analysis of divergence times dated the basal placental mammal splits at 95–100 million years ago. Many of the following divergences occurred only a few (2–4) million years later. Relationships with narrow divergence time intervals received unexpectedly limited support even from the phylogenomic analyses. Conclusion: The narrow temporal window within which some placental divergences took place suggests that inconsistencies and limited resolution of the mammalian tree may have their natural explanation in speciation processes such as lineage sorting, introgression from species hybridization or hybrid speciation. These processes obscure phylogenetic analysis, making some parts of the tree difficult to resolve even with genome data

A genomic approach to examine the complex evolution of laurasiatherian mammals

Recent phylogenomic studies have failed to conclusively resolve certain branches of the placental mammalian tree, despite the evolutionary analysis of genomic data from 32 species. Previous analyses of single genes and retroposon insertion data yielded support for different phylogenetic scenarios for the most basal divergences. The results indicated that some mammalian divergences were best interpreted not as a single bifurcating tree, but as an evolutionary network. In these studies the relationships among some orders of the super-clade Laurasiatheria were poorly supported, albeit not studied in detail. Therefore, 4775 protein-coding genes (6,196,263 nucleotides) were collected and aligned in order to analyze the evolution of this clade. Additionally, over 200,000 introns were screened in silico, resulting in 32 phylogenetically informative long interspersed nuclear elements (LINE) insertion events. The present study shows that the genome evolution of Laurasiatheria may best be understood as an evolutionary network. Thus, contrary to the common expectation to resolve major evolutionary events as a bifurcating tree, genome analyses unveil complex speciation processes even in deep mammalian divergences. We exemplify this on a subset of 1159 suitable genes that have individual histories, most likely due to incomplete lineage sorting or introgression, processes that can make the genealogy of mammalian genomes complex. These unexpected results have major implications for the understanding of evolution in general, because the evolution of even some higher level taxa such as mammalian orders may sometimes not be interpreted as a simple bifurcating pattern

Finding the physiological function of the enzyme GPCAT.

The aim of this project was to study the enzyme Glycerophosphocholine Acyltransferase (GPCAT) and try to find its physiological function. The biochemical reaction that the enzyme GPCAT catalyses is known, but its physiological function, e.g. why and when plants need the enzyme GPCAT, is unknown. To investigate the physiological function, Arabidopsis plants with (wild type) and without (knockout 19) the gene encoding for the enzyme GPCAT were cultivated and then exposed to abiotic stresses. The gene expression of six genes were studied by Q-RT-PCR and differences in gene expression was calculated by the Pfaffl method. The three genes that were associated with Sphingolipids (delta-9 acyl-lipid desaturase 2, very-long-chain 3-oxoacyl-CoA synthase and sphinganine C4-monooxygenase 1) showed higher gene expression in the knockout 19 plants than the wild type in the cold treatments. This implies that the silencing of GPCAT gene influences the genes in sphingolipids synthesis in the cold treated plants. Therefore, GPCAT might be involved in the regulation of lipids, with focus on sphingolipids, in cold stress

Dietary change for sustainable food systems: Effects on climate, land use and health

Food production and consumption are key drivers of environmental pressures and essential factors in the promotion and maintenance of health. Production of food occupies more than 1/3 of global land areas and is estimated to be responsible for some 30% of global greenhouse gas emissions. At the same time, we live in a world where nearly one billion people go hungry and even more people suffer from health problems related to overweight and obesity. This raises the question about sustainability of the current food systems. In this thesis the potential of dietary change as a measure to reduce environmental impact and increase health is analyzed with special attention to uncertainty aspects in used data and methods. The results illustrate that awareness of the variability and uncertainty in used data and methods may be crucial for a proper use and interpretation of results in sustainability studies of food and diets. It is further suggested that dietary change, in areas with affluent diet, could play an important role in reaching environmental and health goals, with up to 50% potential to reduce GHG emissions and land use change. The potential to improve sustainability of the food system through dietary change can be substantial and mainly depends on the amount and type of meat included in the diet. Further understanding of dietary change as measure for more sustainable food systems requires interdisciplinary and holistic assessments of the diet including more sustainability aspects. There is also need for improved knowledge of the environmental impact of substitutes and complements to meat, of the effect of dietary change in different geographical regions, of the uncertainties in dietary scenario studies and of policy instruments that can facilitate the transition towards more sustainable diets

Presidential Succession and Disability

Background: Recent research in a large cohort of women showed that coffee consumption is not associated with increased risk of fracture. Whether this is the case also among men is less clear. Methods: In the Cohort of Swedish Men (COSM) study, 42,978 men aged 45-79 years old at baseline in 1997 answered a self-administered food frequency questionnaire covering coffee consumption and a medical and lifestyle questionnaire covering potential confounders. Our main outcomes first fracture at any site and first hip fracture were collected from the National Patient Registry in Sweden. The association between coffee consumption and fracture risk was investigated using Cox's proportional hazards regression. Results: During a mean follow-up of 11.2 years, 5,066 men had a first fracture at any site and of these, 1,186 (23%) were hip fractures. There was no association between increasing coffee consumption (per 200 ml) and rate of any fracture (hazard ratio [HR] 1.00; 95% confidence interval [CI] 0.99-1.02) or hip fracture (HR 1.02; 95% CI 0.99-1.06) after adjustment for potential confounders. For men consuming >= 4 cups of coffee/day compared to those consuming <1 cup of coffee/day, HR for any type of fracture was 0.91 (95% CI 0.80-1.02) and for hip fracture: 0.89 (95% CI 0.70-1.14). Conclusions: High coffee consumption was not associated with an increased risk of fractures in this large cohort of Swedish men

Expansion of CORE-SINEs in the genome of the Tasmanian devil

Background: The genome of the carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii, Order: Dasyuromorphia), was sequenced in the hopes of finding a cure for or gaining a better understanding of the contagious devil facial tumor disease that is threatening the species’ survival. To better understand the Tasmanian devil genome, we screened it for transposable elements and investigated the dynamics of short interspersed element (SINE) retroposons. Results: The temporal history of Tasmanian devil SINEs, elucidated using a transposition in transposition analysis, indicates that WSINE1, a CORE-SINE present in around 200,000 copies, is the most recently active element. Moreover, we discovered a new subtype of WSINE1 (WSINE1b) that comprises at least 90% of all Tasmanian devil WSINE1s. The frequencies of WSINE1 subtypes differ in the genomes of two of the other Australian marsupial orders. A co-segregation analysis indicated that at least 66 subfamilies of WSINE1 evolved during the evolution of Dasyuromorphia. Using a substitution rate derived from WSINE1 insertions, the ages of the subfamilies were estimated and correlated with a newly established phylogeny of Dasyuromorphia. Phylogenetic analyses and divergence time estimates of mitochondrial genome data indicate a rapid radiation of the Tasmanian devil and the closest relative the quolls (Dasyurus) around 14 million years ago. Conclusions: The radiation and abundance of CORE-SINEs in marsupial genomes indicates that they may be a major player in the evolution of marsupials. It is evident that the early phases of evolution of the carnivorous marsupial order Dasyuromorphia was characterized by a burst of SINE activity. A correlation between a speciation event and a major burst of retroposon activity is for the first time shown in a marsupial genome

Laying down the “T” and “E” in STEM education : design as the basis of an integrated STEM philosophy

Abstract: STEM – science, technology, engineering, and mathematics – has become ubiquitous in education. How STEM and STEM education are to be defined is still a matter of debate, however, and it is only just recently that STEM education has been probed from a philosophical point of view. The need for a philosophical basis for STEM education is therefore fundamental. The aim of this study is thus to investigate specifically the role of the “T” and “E” in STEM, and how they not only may be fruitfully integrated with the “S” and “M”, as part of a philosophy of STEM education, but also potentially form a methodological backbone of such a philosophy when it comes to design. The research question that underpinned the study is: What are the affordances of Mitcham’s (1994) fourfold philosophical framework of technology for unifying the STEM subjects, with particular consideration of the “T” and “E”? The research methodology consisted of a qualitative meta-synthesis of the literature regarding the philosophy of technology and engineering, technology education, and the current issues of integrating the various STEM subjects. We conclude that from a methodological point of view – Mitcham’s “activity” – the design in technology (“T”) and engineering (“E”) holds the most promising affordances for unifying the four STEM subjects. Design as part of particular design projects may require the “design” of applicable scientific experiments as well as the design of applicable mathematics expressions and formulae specifically when modelling in “E” (and “T”)