3D Genome Reconstruction from Partially Phased Hi-C Data.

The 3-dimensional (3D) structure of the genome is of significant importance for many cellular processes. In this paper, we study the problem of reconstructing the 3D structure of chromosomes from Hi-C data of diploid organisms, which poses additional challenges compared to the better-studied haploid setting. With the help of techniques from algebraic geometry, we prove that a small amount of phased data is sufficient to ensure finite identifiability, both for noiseless and noisy data. In the light of these results, we propose a new 3D reconstruction method based on semidefinite programming, paired with numerical algebraic geometry and local optimization. The performance of this method is tested on several simulated datasets under different noise levels and with different amounts of phased data. We also apply it to a real dataset from mouse X chromosomes, and we are then able to recover previously known structural features

Affordable phenotyping of winter wheat under field and controlled conditions for drought tolerance

Drought stress is one of the key plant stresses reducing grain yield in cereal crops worldwide. Although it is not a breeding target in Northern Europe, the changing climate and the drought of 2018 have increased its significance in the region. A key challenge, therefore, is to identify novel germplasm with higher drought tolerance, a task that will require continuous characterization of a large number of genotypes. The aim of this work was to assess if phenotyping systems with low-cost consumer-grade digital cameras can be used to characterize germplasm for drought tolerance. To achieve this goal, we built a proximal phenotyping cart mounted with digital cameras and evaluated it by characterizing 142 winter wheat genotypes for drought tolerance under field conditions. The same genotypes were additionally characterized for seedling stage traits by imaging under controlled growth conditions. The analysis revealed that under field conditions, plant biomass, relative growth rates, and Normalized Difference Vegetation Index (NDVI) from different growth stages estimated by imaging were significantly correlated to drought tolerance. Under controlled growth conditions, root count at the seedling stage evaluated by imaging was significantly correlated to adult plant drought tolerance observed in the field. Random forest models were trained by integrating measurements from field and controlled conditions and revealed that plant biomass and relative growth rates at key plant growth stages are important predictors of drought tolerance. Thus, based on the results, it can be concluded that the consumer-grade cameras can be key components of affordable automated phenotyping systems to accelerate pre-breeding for drought tolerance

Foderproduktion och metanbildning i våmmen utgör 85-90 % av mjölkens klimatpåverkan

Klimatpåverkan från mjölkproduktionen har varit i fokus de senaste åren, inte minst p g a djurens utsläpp av metan. Mjölkens klimatpåverkan består dock inte enbart av metan från foderomvandling i våmmen. Även foderproduktionen står för en betydande andel av växthusgaserna medan t ex transporter och gårdens elförbrukning utgör små andelar

Genome-Wide Association Analysis and Genomic Prediction for Adult-Plant Resistance to Septoria Tritici Blotch and Powdery Mildew in Winter Wheat

Septoria tritici blotch (STB) caused by the fungal pathogen Zymoseptoria tritici and powdery mildew (PM) caused by Blumeria graminis f.sp tritici (Bgt) are among the forefront foliar diseases of wheat that lead to a significant loss of grain yield and quality. Resistance breeding aimed at developing varieties with inherent resistance to STB and PM diseases has been the most sustainable and environment-friendly approach. In this study, 175 winter wheat landraces and historical cultivars originated from the Nordic region were evaluated for adult-plant resistance (APR) to STB and PM in Denmark, Estonia, Lithuania, and Sweden. Genome-wide association study (GWAS) and genomic prediction (GP) were performed based on the adult-plant response to STB and PM in field conditions using 7,401 single-nucleotide polymorphism (SNP) markers generated by 20K SNP chip. Genotype-by-environment interaction was significant for both disease scores. GWAS detected stable and environment-specific quantitative trait locis (QTLs) on chromosomes 1A, 1B, 1D, 2B, 3B, 4A, 5A, 6A, and 6B for STB and 2A, 2D, 3A, 4B, 5A, 6B, 7A, and 7B for PM adult-plant disease resistance. GP accuracy was improved when assisted with QTL from GWAS as a fixed effect. The GWAS-assisted GP accuracy ranged within 0.53-0.75 and 0.36-0.83 for STB and PM, respectively, across the tested environments. This study highlights that landraces and historical cultivars are a valuable source of APR to STB and PM. Such germplasm could be used to identify and introgress novel resistance genes to modern breeding lines

Hållbar avfallshantering: utvärdering av styrmedel från ett psykologiskt och etnologiskt perspektiv

Inom psykologi och etnologi studeras företeelser ur perspektiv som återfinns hos den enskilda individen samt i det lokala eller sociala sammanhanget. I studien har olika styrmedel bedömts från ett etnologiskt och psykologiskt perspektiv. Studien har därvid inneburit nya arbetsmetoder – i varken psykologi eller etnologi brukar man arbeta med att förutsäga hur olika medel (t.ex. styrmedel) påverkar människan, normalt arbetar man efter att beskriva hur människan upplever ett befintligt styrmedel. Nytt i arbetssättet är också att utvärdera styrmedlen i olika framtidsscenarier. De viktigaste slutsatserna om de studerade styrmedlen är enligt följande. Information är ett viktigt styrmedel, men bör främst ses i kombination med andra styrmedel. Information bör utformas så att den är anpassad för olika grupper, hellre än massutskick och glättiga kampanjer. Informationen bör vara både deklarativ (ge information om effekter och konsekvenser) och procedurell (beskriva hur man ska göra). Information är viktigast som styrmedel i de hållbara scenarierna, men är av betydelse i samtliga scenarier. Vad gäller verksamheter kan man skilja på information till företagsledningen och information till anställda. Styrmedlet ”Reklam ja tack” förväntas leda till minskad mängd pappersavfall och är lätt att förstå för hushållen. Styrmedlet är mest effektivt i de hållbara scenarierna. Styrmedlet bedöms verksamt även i scenariot regional marknad eftersom det då är större tryck på verksamheterna att föra ut sitt budskap. Negativ kemikaliemärkning bedöms vara ett effektivt styrmedel, och framför allt effektivare än positiv märkning. Negativ kemikaliemärkning bedöms också vara effektivt i alla scenarier. I styrmedlet viktbaserad avfallstaxa kan storleken på den rörliga delen av avfallstaxan påverka styrmedlets genomslagskraft. Viktbaserad avfallstaxa bedöms fungera bäst i de marknadsdrivna scenarierna där individen tar ett stort ansvar själv. I de hållbara scenarierna kan styrmedlet komma att upplevas negativ eftersom ansvaret för miljöfrågorna är mer överflyttade till staten från medborgarna. Miljödifferentierad avfallstaxa bedöms ge ytterst små styreffekter eftersom det med den givna utformningen kan vara svår att kommunicera med människorna. Med vissa ändringar skulle det däremot kunna bli kraftfullt. Utvecklade insamlingssystem bedöms leda till ökad källsortering i alla scenarier. Detta gäller både ökad fastighetsnära insamling och insamling i materialströmmar

A transnational and holistic breeding approach is needed for sustainable wheat production in the Baltic Sea region

The Baltic Sea is one of the largest brackish water bodies in the world. Eutrophication is a major concern in the Baltic Sea due to the leakage of nutrients to the sea with agriculture being the primary source. Wheat (Triticum aestivum L.) is the most widely grown crop in the countries surrounding the Baltic Sea and thus promoting sustainable agriculture practices for wheat cultivation will have a major impact on reducing pollution in the Baltic Sea. This approach requires identifying and addressing key challenges for sustainable wheat production in the region. Implementing new technologies for climate-friendly breeding and digital farming across all surrounding countries should promote sustainable intensification of agriculture in the region. In this review, we highlight major challenges for wheat cultivation in the Baltic Sea region and discuss various solutions integrating transnational collaboration for pre-breeding and technology sharing to accelerate development of low input wheat cultivars with improved host plant resistance to pathogen and enhanced adaptability to the changing climate.Peer reviewe

High-cycle thermal fatigue in mixing tees. Large-eddy simulations compared to a new validation experiment

ABSTRACT The present paper describes new experimental data of thermal mixing in a T-junction compared with results from Large-Eddy Simulations (LES) and Detached Eddy Simulations (DES). The experimental setup was designed in order to provide data suitable for validation of CFD-calculations. The data is obtained from temperature measurements with thermocouples located near the pipe wall, velocity measurements with Laser Doppler Velocimetry (LDV) as well as single-point concentration measurements with Laser Induced Fluorescence (LIF). The LES showed good agreement with the experimental data also when fairly coarse computational meshes were used. However, grid refinement studies revealed a fairly strong sensitivity to the grid resolution, and a simulation using a fine mesh with nearly 10 million cells significantly improved the results in the entire flow domain. The sensitivity to different unsteady inlet boundary conditions was however small, which shows that the strong large-scale instabilities that are present in the mixing region are triggered independent of the applied inlet perturbations. A shortcoming in the performed simulations is insufficient near-wall resolution, which resulted in poor predictions of the near-wall mean velocity profiles and the wall-shear stress. Simulations using DES improved the near-wall velocity predictions, but failed to predict the temperature fluctuations due to high levels of modeled turbulent viscosity that restrained the formation of small scale turbulence