Shared Ancestry and Signatures of Recent Selection in Gotland Sheep

Gotland sheep, a breed native to Gotland, Sweden (an island in the Baltic Sea), split from the Gute sheep breed approximately 100 years ago, and since, has probably been crossed with other breeds. This breed has recently gained popularity, due to its pelt quality. This study estimates the shared ancestors and identifies recent selection signatures in Gotland sheep using 600 K single nucleotide polymorphism (SNP) genotype data. Admixture analysis shows that the Gotland sheep is a distinct breed, but also has shared ancestral genomic components with Gute (similar to 50%), Karakul (similar to 30%), Romanov (similar to 20%), and Fjallnas (similar to 10%) sheep breeds. Two complementary methods were applied to detect selection signatures: A Bayesian population differentiation F-ST and an integrated haplotype homozygosity score (iHS). Our results find that seven significant SNPs (q-value < 0.05) using the F-ST analysis and 55 significant SNPs (p-value < 0.0001) using the iHS analysis. Of the candidate genes that contain significant markers, or are in proximity to them, we identify several belongings to the keratin genes, RXFP2, ADCY1, ENOX1, USF2, COX7A1, ARHGAP28, CRYBB2, CAPNS1, FMO3, and GREB1. These genes are involved in wool quality, polled and horned phenotypes, fertility, twining rate, meat quality, and growth traits. In summary, our results provide shared founders of Gotland sheep and insight into genomic regions maintained under selection after the breed was formed. These results contribute to the detection of candidate genes and QTLs underlying economic traits in sheep

High-yield production of a super-soluble miniature spidroin for biomimetic high-performance materials

The mechanical properties of artificial spider silks are approaching a stage where commercial applications become realistic. However, the yields of recombinant silk proteins that can be used to produce fibers with good mechanical properties are typically very low and many purification and spinning protocols still require the use of urea, hexafluoroisopropanol, and/or methanol. Thus, improved production and spinning methods with a minimal environmental impact are needed. We have previously developed a miniature spider silk protein that is characterized by high solubility in aqueous buffers and spinnability in biomimetic set-ups. In this study, we developed a production protocol that resulted in an expression level of >20 g target protein per liter in an Escherichia coli fedbatch culture, and subsequent purification under native conditions yielded 14.5 g/l. This corresponds to a nearly six-fold increase in expression levels, and a 10-fold increase in yield after purification compared to reports for recombinant spider silk proteins. Biomimetic spinning using only aqueous buffers resulted in fibers with a toughness modulus of 74 MJ/m(3), which is the highest reported for biomimetically as-spun artificial silk fibers. Thus, the process described herein represents a milestone for the economic production of biomimetic silk fibers for industrial applications

Impact of physio-chemical spinning conditions on the mechanical properties of biomimetic spider silk fibers

Artificial spider silk has emerged as a biobased fiber that could replace some petroleum-based materials that are on the market today. Recent progress made it possible to produce the recombinant spider silk protein NT2RepCT at levels that would make the commercialization of fibers spun from this protein economically feasible. However, for most applications, the mechanical properties of the artificial silk fibers need to be improved. This could potentially be achieved by redesigning the spidroin, and/or by changing spinning conditions. Here, we show that several spinning parameters have a significant impact on the fibers' mechanical properties by tensile testing more than 1000 fibers produced under 92 different conditions. The most important factors that contribute to increasing the tensile strength are fast reeling speeds and/or employing post-spin stretching. Stretching in combination with optimized spinning conditions results in fibers with a strength of >250 MPa, which is the highest reported value for fibers spun using natively folded recombinant spidroins that polymerize in response to shear forces and lowered pH.The mechanical properties of spider silk are known to be dependent on spinning conditions. Here, the tensile behavior of over 1000 biomimetic spider silk fibers spun under 92 different conditions are tested, resulting in a yield strength of more than 250 MPa

Oscillatory Instabilities of Standing Waves in One-Dimensional Nonlinear Lattices

In one-dimensional anharmonic lattices, we construct nonlinear standing waves (SWs) reducing to harmonic SWs at small amplitude. For SWs with spatial periodicity incommensurate with the lattice period, a transition by breaking of analyticity versus wave amplitude is observed. As a consequence of the discreteness, oscillatory linear instabilities, persisting for arbitrarily small amplitude in infinite lattices, appear for all wave numbers Q not equal to zero or \pi. Incommensurate analytic SWs with |Q|>\pi/2 may however appear as 'quasi-stable', as their instability growth rate is of higher order.Comment: 4 pages, 6 figures, to appear in Phys. Rev. Let

Quinolone resistance mutations in the faecal microbiota of Swedish travellers to India

Background: International travel contributes to the spread of antibiotic resistant bacteria over the world. Most studies addressing travel-related changes in the faecal flora have focused on specific mobile resistance genes, or depended on culturing of individual bacterial isolates. Antibiotic resistance can, however, also spread via travellers colonized by bacteria carrying chromosomal antibiotic resistance mutations, but this has received little attention so far. Here we aimed at exploring the abundance of chromosomal quinolone resistance mutations in Escherichia communities residing in the gut of Swedish travellers, and to determine potential changes after visiting India. Sweden is a country with a comparably low degree of quinolone use and quinolone resistance, whereas the opposite is true for India. Methods: Massively parallel amplicon sequencing targeting the quinolone-resistance determining region of gyrA and parC was applied to total DNA extracted from faecal samples. Paired samples were collected from 12 Swedish medical students before and after a 4-15 week visit to India. Twelve Indian residents were included for additional comparisons. Methods known resistance mutations were common in Swedes before travel as well as in Indians, with a trend for all mutations to be more common in the Indian sub group. There was a significant increase in the abundance of the most common amino acid substitution in GyrA (S83L, from 44 to 72 %, p = 0.036) in the samples collected after return to Sweden. No other substitution, including others commonly associated with quinolone resistance (D87N in GyrA, S80I in ParC) changed significantly. The number of distinct genotypes encoded in each traveller was significantly reduced after their visit to India for both GyrA (p = 0.0020) and ParC (p = 0.0051), indicating a reduced genetic diversity, similar to that found in the Indians. Conclusions: International travel can alter the composition of the Escherichia communities in the faecal flora, favouring bacteria carrying certain resistance mutations, and, thereby, contributes to the global spread of antibiotic resistance. A high abundance of specific mutations in Swedish travellers before visiting India is consistent with the hypothesis that these mutation have no fitness cost even in the absence of an antibiotic selection pressure

RED, PEF, and EPD: Conflicting rules for determining the carbon footprint of biofuels give unclear signals to fuel producers and customers

Biofuel producers and other commodity suppliers are increasingly affected by conflicting rules for life cycle assessment (LCA). They may get multiple requests for LCAs to be used in various contexts, which require the application of different methodological approaches that vary in scope, system boundaries, data demand, and more. This results in increased cost and competence requirements for producers, as well as confusion among other actors including their customers. Differences in methodologies might also lead to various outcomes, conclusions and conflicting guidance regarding which fuels to prioritize or develop. We have analyzed the actual differences when applying three different frameworks: the EU Renewable Energy Directive (RED), the EU framework for Product Environmental Footprints (PEF), and the framework of Environmental Product Declarations (EPD), which have different modeling requirements. We analyzed the methods from a conceptual point of view and also applied the methods to estimate the carbon footprint on a wide range of biofuel production pathways: (i) ethanol from corn, (ii) fatty acid methyl ester (FAME) from rapeseed oil, (iii) biogas from food waste, (iv) hydrogenated vegetable oil (HVO) from rapeseed oil, and (v) HVO from used cooking oil. Results obtained for a specific fuel could differ substantially depending on the framework applied and the assumptions and interpretations made when applying the different frameworks. Particularly, the results are very sensitive to the modeling of waste management when biofuel is produced from waste. Our results indicate a much higher climate impact for, e.g., biogas and HVO produced from used cooking oil when assessed with the PEF framework compared to the other frameworks. This is because PEF assigns at least part of the production of primary materials and energy to the use of recycled material and recovered energy. Developing Category Rules for biofuels for PEF and EPD ought to help clarifying remaining ambiguities

Genomic relatedness and diversity of Swedish native cattle breeds

International audienceAbstractBackgroundNative cattle breeds are important genetic resources given their adaptation to the local environment in which they are bred. However, the widespread use of commercial cattle breeds has resulted in a marked reduction in population size of several native cattle breeds worldwide. Therefore, conservation management of native cattle breeds requires urgent attention to avoid their extinction. To this end, we genotyped nine Swedish native cattle breeds with genome-wide 150 K single nucleotide polymorphisms (SNPs) to investigate the level of genetic diversity and relatedness between these breeds.ResultsWe used various SNP-based approaches on this dataset to connect the demographic history with the genetic diversity and population structure of these Swedish cattle breeds. Our results suggest that the Väne and Ringamåla breeds originating from southern Sweden have experienced population isolation and have a low genetic diversity, whereas the Fjäll breed has a large founder population and a relatively high genetic diversity. Based on the shared ancestry and the constructed phylogenetic trees, we identified two major clusters in Swedish native cattle. In the first cluster, which includes Swedish mountain cattle breeds, there was little differentiation among the Fjäll, Fjällnära, Swedish Polled, and Bohus Polled breeds. The second cluster consists of breeds from southern Sweden: Väne, Ringamåla and Swedish Red. Interestingly, we also identified sub-structuring in the Fjällnära breed, which indicates different breeding practices on the farms that maintain this breed.ConclusionsThis study represents the first comprehensive genome-wide analysis of the genetic relatedness and diversity in Swedish native cattle breeds. Our results show that different demographic patterns such as genetic isolation and cross-breeding have shaped the genomic diversity of Swedish native cattle breeds and that the Swedish mountain breeds have retained their authentic distinct gene pool without significant contribution from any of the other European cattle breeds that were included in this study

Measuring the quality of inpatient specialist consultation in the intensive care unit: Nursing and family experiences of communication

Rationale: Critically ill patients in the intensive care unit (ICU) often require the care of specialist physicians for clinical or procedural expertise. The current state of communication between specialist physicians and families and nurses has not been explored. Objectives: To document the receipt of communication by nurses and family members regarding consultations performed on their patient or loved one, and to quantify how this impacts their overall perceptions of the quality of specialty care. Methods: Prospective survey of 60 adult family members and 90 nurses of 189 ICU patients who received a specialist consultation between March and October of 2015 in a single academic medical center in the United States. Surveys measured the prevalence of direct communication—defined as communication conducted in person, via telephone, or via text-page in which the specialist team gathered information about the patient from the nurse/family member and/or shared recommendations for care—and perceived quality of care. Results: In about two-thirds of family surveys (40/60) and one-half of nurse surveys (75/160), respondents had no direct communication with the specialist team that performed the consultation. Compared to nurses who had no direct communication with the specialists, those who did were 1.5 times more likely to rate the consultation as “excellent” (RR 1.48, 95% CI 1.2–1.8, p Conclusions: Most ICU families and nurses have no interaction with specialist providers. Nurses’ frequent exclusion from conversations about specialty care may pose safety risks and increase the likelihood of mixed messages for patients and families, most of whom desire some interaction with specialists. Future research is needed to identify effective mechanisms for information sharing that keep nurses and families aware of consultation requests, delivery, and outcomes without increasing the risk of mixed messages.</p

Financing essential HIV services: a new economic agenda.

Anna Vassall and colleagues discuss the need for, and challenges facing, innovative and sustainable financing of the HIV response. Please see later in the article for the Editors' Summary

Resolution of the type material of the Asian elephant, Elephas maximus Linnaeus, 1758 (Proboscidea, Elephantidae)

The understanding of Earth’s biodiversity depends critically on the accurate identification and nomenclature of species. Many species were described centuries ago, and in a surprising number of cases their nomenclature or type material remain unclear or inconsistent. A prime example is provided by Elephas maximus, one of the most iconic and well-known mammalian species, described and named by Linnaeus (1758) and today designating the Asian elephant. We used morphological, ancient DNA (aDNA), and high-throughput ancient proteomic analyses to demonstrate that a widely discussed syntype specimen of E. maximus, a complete foetus preserved in ethanol, is actually an African elephant, genus Loxodonta. We further discovered that an additional E. maximus syntype, mentioned in a description by John Ray (1693) cited by Linnaeus, has been preserved as an almost complete skeleton at the Natural History Museum of the University of Florence. Having confirmed its identity as an Asian elephant through both morphological and ancient DNA analyses, we designate this specimen as the lectotype of E. maximus