The plasticity of NBS resistance genes in sorghum is driven by multiple evolutionary processes

Background Increased disease resistance is a key target of cereal breeding programs, with disease outbreaks continuing to threaten global food production, particularly in Africa. Of the disease resistance gene families, the nucleotide-binding site plus leucine-rich repeat (NBS-LRR) family is the most prevalent and ancient and is also one of the largest gene families known in plants. The sequence diversity in NBS-encoding genes was explored in sorghum, a critical food staple in Africa, with comparisons to rice and maize and with comparisons to fungal pathogen resistance QTL. Results In sorghum, NBS-encoding genes had significantly higher diversity in comparison to non NBS-encoding genes and were significantly enriched in regions of the genome under purifying and balancing selection, both through domestication and improvement. Ancestral genes, pre-dating species divergence, were more abundant in regions with signatures of selection than in regions not under selection. Sorghum NBS-encoding genes were also significantly enriched in the regions of the genome containing fungal pathogen disease resistance QTL; with the diversity of the NBS-encoding genes influenced by the type of co-locating biotic stress resistance QTL. Conclusions NBS-encoding genes are under strong selection pressure in sorghum, through the contrasting evolutionary processes of purifying and balancing selection. Such contrasting evolutionary processes have impacted ancestral genes more than species-specific genes. Fungal disease resistance hot-spots in the genome, with resistance against multiple pathogens, provides further insight into the mechanisms that cereals use in the “arms race” with rapidly evolving pathogens in addition to providing plant breeders with selection targets for fast-tracking the development of high performing varieties with more durable pathogen resistance.

Characterization of acyl chain position in unsaturated phosphatidylcholines using differential mobility-mass spectrometry

Glycerophospholipids (GPs) that differ in the relative position of the two fatty acyl chains on the glycerol backbone (i.e., sn-positional isomers) can have distinct physicochemical properties. The unambiguous assignment of acyl chain position to an individual GP represents a significant analytical challenge. Here we describe a workflow where phosphatidylcholines (PCs) are subjected to ESI for characterization by a combination of differential mobility spectrometry and MS (DMS-MS). When infused as a mixture, ions formed from silver adduction of each phospholipid isomer {e.g., [PC (16:0/18:1) + Ag]+ and [PC (18:1/16:0) + Ag]+} are transmitted through the DMS device at discrete compensation voltages. Varying their relative amounts allows facile and unambiguous assignment of the sn-positions of the fatty acyl chains for each isomer. Integration of the well-resolved ion populations provides a rapid method (< 3 min) for relative quantification of these lipid isomers. The DMS-MS results show excellent agreement with established, but time-consuming, enzymatic approaches and also provide superior accuracy to methods that rely on MS alone. The advantages of this DMS-MS method in identification and quantification of GP isomer populations is demonstrated by direct analysis of complex biological extracts without any prior fractionation.

Primary and secondary neural networks of auditory prepulse inhibition: a functional magnetic resonance imaging study of sensorimotor gating of the human acoustic startle response

Feedforward inhibition deficits have been consistently demonstrated in a range of neuropsychiatric conditions using prepulse inhibition (PPI) of the acoustic startle eye-blink reflex when assessing sensorimotor gating. While PPI can be recorded in acutely decerebrated rats, behavioural, pharmacological and psychophysiological studies suggest the involvement of a complex neural network extending from brainstem nuclei to higher order cortical areas. The current functional magnetic resonance imaging study investigated the neural network underlying PPI and its association with electromyographically (EMG) recorded PPI of the acoustic startle eye-blink reflex in 16 healthy volunteers. A sparse imaging design was employed to model signal changes in blood oxygenation level-dependent (BOLD) responses to acoustic startle probes that were preceded by a prepulse at 120 ms or 480 ms stimulus onset asynchrony or without prepulse. Sensorimotor gating was EMG confirmed for the 120-ms prepulse condition, while startle responses in the 480-ms prepulse condition did not differ from startle alone. Multiple regression analysis of BOLD contrasts identified activation in pons, thalamus, caudate nuclei, left angular gyrus and bilaterally in anterior cingulate, associated with EMGrecorded sensorimotor gating. Planned contrasts confirmed increased pons activation for startle alone vs 120-ms prepulse condition, while increased anterior superior frontal gyrus activation was confirmed for the reverse contrast. Our findings are consistent with a primary pontine circuitry of sensorimotor gating that interconnects with inferior parietal, superior temporal, frontal and prefrontal cortices via thalamus and striatum. PPI processes in the prefrontal, frontal and superior temporal cortex were functionally distinct from sensorimotor gating.

The Macroecology of Airborne Pollen in Australian and New Zealand Urban Areas

he composition and relative abundance of airborne pollen in urban areas of Australia and New Zealand are strongly influenced by geographical location, climate and land use. There is mounting evidence that the diversity and quality of airborne pollen is substantially modified by climate change and land-use yet there are insufficient data to project the future nature of these changes. Our study highlights the need for long-term aerobiological monitoring in Australian and New Zealand urban areas in a systematic, standardised, and sustained way, and provides a framework for targeting the most clinically significant taxa in terms of abundance, allergenic effects and public health burden.

Regional and seasonal variation in airborne grass pollen levels between cities of Australia and New Zealand

Although grass pollen is widely regarded as the major outdoor aeroallergen source in Australia and New Zealand (NZ), no assemblage of airborne pollen data for the region has been previously compiled. Grass pollen count data collected at 14 urban sites in Australia and NZ over periods ranging from 1 to 17 years were acquired, assembled and compared, revealing considerable spatiotemporal variability. Although direct comparison between these data is problematic due to methodological differences between monitoring sites, the following patterns are apparent. Grass pollen seasons tended to have more than one peak from tropics to latitudes of 37°S and single peaks at sites south of this latitude. A longer grass pollen season was therefore found at sites below 37°S, driven by later seasonal end dates for grass growth and flowering. Daily pollen counts increased with latitude; subtropical regions had seasons of both high intensity and long duration. At higher latitude sites, the single springtime grass pollen peak is potentially due to a cooler growing season and a predominance of pollen from C3 grasses. The multiple peaks at lower latitude sites may be due to a warmer season and the predominance of pollen from C4 grasses. Prevalence and duration of seasonal allergies may reflect the differing pollen seasons across Australia and NZ. It must be emphasized that these findings are tentative due to limitations in the available data, reinforcing the need to implement standardized pollen-monitoring methods across Australasia. Furthermore, spatiotemporal differences in grass pollen counts indicate that local, current, standardized pollen monitoring would assist with the management of pollen allergen exposure for patients at risk of allergic rhinitis and asthma. © 2015 Springer Science+Business Media Dordrecht

Differences in grass pollen allergen exposure across Australia

Objective Allergic rhinitis and allergic asthma are important chronic diseases posing serious public health issues in Australia with associated medical, economic, and societal burdens. Pollen are significant sources of clinically relevant outdoor aeroallergens, recognised as both a major trigger for, and cause of, allergic respiratory diseases. This study aimed to provide a national, and indeed international, perspective on the state of Australian pollen data using a large representative sample. Methods Atmospheric grass pollen concentration is examined over a number of years within the period 1995 to 2013 for Brisbane, Canberra, Darwin, Hobart, Melbourne, and Sydney, including determination of the clinical' grass pollen season and grass pollen peak. Results The results of this study describe, for the first time, a striking spatial and temporal variability in grass pollen seasons in Australia, with important implications for clinicians and public health professionals, and the Australian grass pollen-allergic community. Conclusions These results demonstrate that static pollen calendars are of limited utility and in some cases misleading. This study also highlights significant deficiencies and limitations in the existing Australian pollen monitoring and data. Implications: Establishment of an Australian national pollen monitoring network would help facilitate advances in the clinical and public health management of the millions of Australians with asthma and allergic rhinitis.

Localization of type 1 diabetes susceptibility to the MHC class I genes HLA-B and HLA-A

The major histocompatibility complex (MHC) on chromosome 6 is associated with susceptibility to more common diseases than any other region of the human genome, including almost all disorders classified as autoimmune. In type 1 diabetes the major genetic susceptibility determinants have been mapped to the MHC class II genes HLA-DQB1 and HLA-DRB1 (refs 1–3), but these genes cannot completely explain the association between type 1 diabetes and the MHC region4, 5, 6, 7, 8, 9, 10, 11. Owing to the region's extreme gene density, the multiplicity of disease-associated alleles, strong associations between alleles, limited genotyping capability, and inadequate statistical approaches and sample sizes, which, and how many, loci within the MHC determine susceptibility remains unclear. Here, in several large type 1 diabetes data sets, we analyse a combined total of 1,729 polymorphisms, and apply statistical methods—recursive partitioning and regression...

Mediapolulla - Kasvatustieteellistä ja teknisen alan osaamista yhdistämässä : Opiskelijoiden yhteistyö ja oppiminen tieto- ja viestintätekniikkaprojektissa

The study concentrated on interdisciplinary teamwork of students in Helsinki University Department of Education and Helsinki University of Technology. Students worked in small interdisciplinary groups (n 12) to plan and teach in an information- and communication technology (ICT) club in elementary schools. The focus of the study was co-operation in the student groups and students learning experiences. Theoretical background of the study consists of theories of collaboration and socially shared cognition. Study was an qualitative case study and the data was collected with individual focus interviews and learning diaries. The data was categorised and the connections between categories were analysed with a table. Shared cognition appeared as a form of distribution of tasks and in the actual processes of shared expertise. The tasks were shared according to students expertise. Processes of shared expertise were joint knowledge building, integration of interests, awareness and exploitation of others expertise and allowing freedom for others to use their expertise. Additionally expression of ones own views and setting an example to others were one sided sharing of expertise. Students of technology were responsible of technical issues and the responsibility sphere of educational science students was more fragmented. For instance they concentrated in taking children s abilities into consideration. The sphere of shared cognition included also the need for tutoring and learning from others. Usually students did not directly learn from representative of other discipline, instead the learning for instance of social skills happened indirectly. Learning was fostered if learning was set as a goal and prevented if the differences in expertise were too minor. Sharing of cognition was prevented if co-operation was too problematic. Co-operation was usually successful. Good planning, good person chemistry and appreciation of expertise of others promoted success. Problems caused by different backgrounds were usually slight. Successful interaction was complementary and equal. Groups were usually able to circumvent problems in communication and use of justification in discussion promoted co-operation. When comparing the groups in the scope of the study, two were found to be notably opposed and the other groups located between these extreme cases, but the elements of success prevailed. Learning experiences concentrated on social skills, project management, school world and ICT. Essential was achieved field experience and observation of ones own capabilities. In organisation of student interdisciplinary co-operation is important to ensure sufficient differences in expertise and guide students to gain complementary interaction and appropriate setting of goals. Interdisciplinary field project prepared students to face the demands of

Yliopiston oppimis- ja opetuskäsitykset murroksessa : Teknillistieteellisen alan opettajien käsityksiä ja lähestymistapoja alan oppimiseen ja opetukseen

The starting point for this study was university teaching and teachers and specifically their changing role when confronting the Finnish University Reform and the student-focused theories of learning. Teachers’ pedagogical thinking and pedagogical content knowledge were also part of the theoretical framework. In the research of conceptions of and approaches to learning and teaching, the qualitative classifications of Säljö and Marton (1976; 1997), Ramsden (1992), Kember (1997) and Trigwell and Prosser (1999) were utilised. Two study questions were raised (1) What kind of conceptions of and approaches to learning do engineering science teachers have? and (2) What kind of conceptions of and approaches to teaching do engineering science teachers have? The relationship between teachers’ conceptions and teaching was also examined. The research material was collected in autumn 2008 by interviewing teachers and by observing teaching in the Department of Energy Technology at Helsinki University of Technology. Altogether two tutorials and ten lectures were observed. Each teacher of the observed lectures was interviewed once. The interviews were carried out as semi-structured theme interviews. In the analysis of the research material phenomenographical approach was adapted. The study revealed many kinds of conceptions of and approaches to learning and teaching in the teachers’ speech. On the basis of the research material, the conceptions and approaches that the teachers declare do not always reflect their actions in the teaching situation. The surface approaches to learning and teacher-focused approaches to teaching and conceptions of receiving and transmission of knowledge were parallel. Instead the teachers’ declarations of the deep approaches to learning and student-focused approaches to teaching were partly in conflict with how the teacher taught. When striving towards student-centered teaching culture attention should be paid to the development of teachers’ pedagogical thinking and pedagogical content knowledge. The culture and the structures of the educational institution should also be considered.

Matkalla suomalaiseksi ja hoiva-alan ammattilaiseksi? : Venäläis- ja virolaistaustaisten naisten ja suomalaisuuden kohtaamiset kuulumista rakentamassa

The research examines the process by which a sense of belonging to Finnish society is constructed among women of Russian and Estonian background who are multiply marginalised in Finnish society. It does so by analysing the encounters between their nationality and 'being Finnis'. Attention is focused on the question of what kind of "journey" they take after moving to Finland, how a sense of belonging is constructed especially along the paths followed in education and at work, and what kind of agency is available to them. The thesis is connected with post-colonial research and also draws from studies on citizenship and nationality as well as the social structures of interaction, when analysing careers. As the educational system forms the most central context of the research, the work is also focused on educational sociology. The research methodology includes life history and a narrative approach. The raw data is from thematic interviews concerning the life experiences of women of immigrant backgrounds. They were studying in Finland to be practical nurses or to complete Bachelor of Social Service degree. According to the study, the women had been encountered as alien, strange, and carrying a shade of "otherness". The experience of inclusion in Finnish communities and society turned out to be conditional, an inclusion based on the notion of a citizen worker, which is defined by national needs. The person from abroad is placed in the position of someone who fills gaps in the services of the welfare state. The choice of education in the care sector and the overall necessity of obtaining Finnish education turned out to be socially directed. Gendered structures of education and working life were found to act as a frame in which the decisions of the immigrant women were made. Although national education policy emphasis as an orientation to global labour markets, the immigrant student is placed above all in the position of an object to be made suitable for the Finnish labour market. Citizenship, a goal of education, requires consent to being "socialised" into Finnish society as well as learning to be Finnish. One s only option to negotiate appearing suitable as a member is to construct oneself into someone who adopts Finnish and Western cultural values, values which favour individuality. However, Finnish education is a resource to Finnishness. Finnish education enables a sense of being Finnish, and empowers the job applicant for example, and in addition to providing cultural, human and social capital strengthen inclusion as well. The study confirms the view that the encounter of an immigrant is still characterised by its colonial nature. It shows that encounters with Finns and Finnish society place the person of immigrant background, even one receiving a Finnish education, in the position of "the other". The journey as an immigrant continues. The immigrant has access only to certain predefined subject positions, which limits agency. When categorised as an immigrant, one becomes a per-son who is different and "other", while the sense of belonging as a member of Finnish society without conditions appears to be somewhat unreachable. Yet, new arrivals are capable of acting change. An immigrant woman can challenge the positions offered to her and present herself as strong. Her life story has often included struggle, and she has the fortitude strength to change her circumstances. Key words: life story, post-colonial encounter, nationality, citizenship, the career of immi-grant, position, agency

New genetic loci link adipose and insulin biology to body fat distribution

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10−8). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms.

Genetic studies of body mass index yield new insights for obesity biology

Obesity is heritable and predisposes to many diseases. To understand the genetic basis of obesity better, here we conduct a genome-wide association study and Metabochip meta-analysis of body mass index (BMI), a measure commonly used to define obesity and assess adiposity, in up to 339,224 individuals. This analysis identifies 97 BMI-associated loci (P < 5 × 10−8), 56 of which are novel. Five loci demonstrate clear evidence of several independent association signals, and many loci have significant effects on other metabolic phenotypes. The 97 loci account for ~2.7% of BMI variation, and genome-wide estimates suggest that common variation accounts for >20% of BMI variation. Pathway analyses provide strong support for a role of the central nervous system in obesity susceptibility and implicate new genes and pathways, including those related to synaptic function, glutamate signalling, insulin secretion/action, energy metabolism, lipid biology and adipogenesis.

FTO genotype is associated with phenotypic variability of body mass index

There is evidence across several species for genetic control of phenotypic variation of complex traits1, 2, 3, 4, such that the variance among phenotypes is genotype dependent. Understanding genetic control of variability is important in evolutionary biology, agricultural selection programmes and human medicine, yet for complex traits, no individual genetic variants associated with variance, as opposed to the mean, have been identified. Here we perform a meta-analysis of genome-wide association studies of phenotypic variation using ~170,000 samples on height and body mass index (BMI) in human populations. We report evidence that the single nucleotide polymorphism (SNP) rs7202116 at the FTO gene locus, which is known to be associated with obesity (as measured by mean BMI for each rs7202116 genotype)5, 6, 7, is also associated with phenotypic variability. We show that the results are not due to scale effects or other artefacts, and find no other experiment-wise significant evidence for effects on variability, either at loci other than FTO for BMI or at any locus for height. The difference in variance for BMI among individuals with opposite homozygous genotypes at the FTO locus is approximately 7%, corresponding to a difference of ~0.5 kilograms in the standard deviation of weight. Our results indicate that genetic variants can be discovered that are associated with variability, and that between-person variability in obesity can partly be explained by the genotype at the FTO locus. The results are consistent with reported FTO by environment interactions for BMI8, possibly mediated by DNA methylation9, 10. Our BMI results for other SNPs and our height results for all SNPs suggest that most genetic variants, including those that influence mean height or mean BMI, are not associated with phenotypic variance, or that their effects on variability are too small to detect even with samples sizes greater than 100,000.

Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution

Waist-hip ratio (WHR) is a measure of body fat distribution and a predictor of metabolic consequences independent of overall adiposity. WHR is heritable, but few genetic variants influencing this trait have been identified. We conducted a meta-analysis of 32 genome-wide association studies for WHR adjusted for body mass index (comprising up to 77,167 participants), following up 16 loci in an additional 29 studies (comprising up to 113,636 subjects). We identified 13 new loci in or near RSPO3, VEGFA, TBX15-WARS2, NFE2L3, GRB14, DNM3-PIGC, ITPR2-SSPN, LY86, HOXC13, ADAMTS9, ZNRF3-KREMEN1, NISCH-STAB1 and CPEB4 (P = 1.9 × 10−9 to P = 1.8 × 10−40) and the known signal at LYPLAL1. Seven of these loci exhibited marked sexual dimorphism, all with a stronger effect on WHR in women than men (P for sex difference = 1.9 × 10−3 to P = 1.2 × 10−13). These findings provide evidence for multiple loci that modulate body fat distribution independent of overall adiposity and reveal strong gene-by-sex interactions.

Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum

Sorghum is a food and feed cereal crop adapted to heat and drought and a staple for 500 million of the world’s poorest people. Its small diploid genome and phenotypic diversity make it an ideal C4 grass model as a complement to C3 rice. Here we present high coverage (16-45 × ) resequenced genomes of 44 sorghum lines representing the primary gene pool and spanning dimensions of geographic origin, end-use and taxonomic group. We also report the first resequenced genome of S. propinquum, identifying 8 M high-quality SNPs, 1.9 M indels and specific gene loss and gain events in S. bicolor. We observe strong racial structure and a complex domestication history involving at least two distinct domestication events. These assembled genomes enable the leveraging of existing cereal functional genomics data against the novel diversity available in sorghum, providing an unmatched resource for the genetic improvement of sorghum and other grass species.