Uppsala University

About: Uppsala University is a education organization based out in Uppsala, Sweden. It is known for research contribution in the topics: Population & Gene. The organization has 36485 authors who have published 107509 publications receiving 4220668 citations. The organization is also known as: Uppsala universitet & uu.se.

A simple and universal method for molecular sexing of non-ratite birds

Abstract: Molecular sexing is an attractive means to determine the sex of sexually monomorphic birds, e.g. chicks of most species. A universal approach for molecular sexing of birds would require that a conserved W chromosome-linked sequence could be analysed, but no single gene has previously been known from any avian W chromosome. The recent discovery of the CHD1W gene, apparently W-linked in all non-ratite birds, has opened new possibilities in this direction, although there is a problem in that the gene also exists in a very similar copy on the Z chromosome (CHD1Z). Here we describe a universal method for molecular sexing of non-ratite birds which is based on the detection of a constant size difference between CHD1W and CHD1Z introns. Using highly conserved primers flanking the intron, PCR amplification and agarose electrophoresis, females are characterised by displaying one (CHD1W) or two fragments (CHD1W and CHD1Z), while males only show one fragment (CHD1Z) clearly different in size from the female-specific CHD1W fragment. With one particular pair of primers (2550F and 2718R) we applied this test to 50 bird species from 11 orders throughout the avian phylogeny, successfully sexing 47 of the species. Using an alternative pair of primers, the three failing species could be reliably sexed. This means that a simple, rapid and cheap universal system for molecular sexing of non-ratite birds is now available.

Whole-genome analyses resolve early branches in the tree of life of modern birds

Abstract: To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

On the Generality of the Latitudinal Diversity Gradient

Abstract: The decline of biodiversity with latitude has received great attention, but both the concise pattern and the causes of the gradient are under strong debate. Most studies of the latitudinal gradient comprise only one or few organism types and are often restricted to certain region or habitat types. To test for significant variation in the gradient between organisms, habitats, or regions, a meta-analysis was conducted on nearly 600 latitudinal gradients assembled from the literature. Each gradient was characterized by two effect sizes, strength (correlation coefficient) and slope, and additionally by 14 variables describing organisms, habitats, and regions. The analysis corroborated the high generality of the latitudinal diversity decline. Gradients on regional scales were significantly stronger and steeper than on local scales, and slopes also varied with sampling grain. Both strength and slope increased with organism body mass, and strength increased with trophic level. The body mass-effect size relation varied for ecto- versus homeotherm organisms and for different dispersal types, suggesting allometric effects on energy use and dispersal ability as possible mechanisms for the body mass effect. Latitudinal gradients were weaker and less steep in freshwater than in marine or terrestrial environments and differed significantly between continents and habitat types. The gradient parameters were not affected by hemisphere or the latitudinal range covered. This analysis is the first to describe these general and significant patterns, which have important consequences for models aiming to explain the latitudinal gradient.

Pseudo-halide anion engineering for α-FAPbI3 perovskite solar cells.

Abstract: Metal halide perovskites of the general formula ABX3—where A is a monovalent cation such as caesium, methylammonium or formamidinium; B is divalent lead, tin or germanium; and X is a halide anion—have shown great potential as light harvesters for thin-film photovoltaics1–5. Among a large number of compositions investigated, the cubic α-phase of formamidinium lead triiodide (FAPbI3) has emerged as the most promising semiconductor for highly efficient and stable perovskite solar cells6–9, and maximizing the performance of this material in such devices is of vital importance for the perovskite research community. Here we introduce an anion engineering concept that uses the pseudo-halide anion formate (HCOO−) to suppress anion-vacancy defects that are present at grain boundaries and at the surface of the perovskite films and to augment the crystallinity of the films. The resulting solar cell devices attain a power conversion efficiency of 25.6 per cent (certified 25.2 per cent), have long-term operational stability (450 hours) and show intense electroluminescence with external quantum efficiencies of more than 10 per cent. Our findings provide a direct route to eliminate the most abundant and deleterious lattice defects present in metal halide perovskites, providing a facile access to solution-processable films with improved optoelectronic performance. Incorporation of the pseudo-halide anion formate during the fabrication of α-FAPbI3 perovskite films eliminates deleterious iodide vacancies, yielding solar cell devices with a certified power conversion efficiency of 25.21 per cent and long-term operational stability.

Pan-cancer analysis of whole genomes

Abstract: Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1,2,3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10,11,12,13,14,15,16,17,18.