Scoring functions for transcription factor binding site prediction

BACKGROUND: Transcription factor binding site (TFBS) prediction is a difficult problem, which requires a good scoring function to discriminate between real binding sites and background noise. Many scoring functions have been proposed in the literature, but it is difficult to assess their relative performance, because they are implemented in different software tools using different search methods and different TFBS representations. RESULTS: Here we compare how several scoring functions perform on both real and semi-simulated data sets in a common test environment. We have also developed two new scoring functions and included them in the comparison. The data sets are from the yeast (S. cerevisiae) genome. Our new scoring function LLBG (least likely under the background model) performs best in this study. It achieves the best average rank for the correct motifs. Scoring functions based on positional bias performed quite poorly in this study. CONCLUSION: LLBG may provide an interesting alternative to current scoring functions for TFBS prediction

Optical characterization of colloidal CdSe quantum dots in endothelial progenitor cells

We have quantitatively analyzed the confocal spectra of colloidal quantum dots (QDs) in rat endothelial progenitor cells (EPCs) by using Leica TCS SP5 Confocal Microscopy System. Comparison of the confocal spectra of QDs located inside and outside EPCs revealed that the interaction between the QDs and EPCs effectively reduces the radius of the exciton confinement inside the QDs so that the excitonic energy increases and the QD fluorescence peak blueshifts. Furthermore, the EPC environment surrounding the QDs shields the QDs so that the excitation of the QDs inside the cells is relatively weak, whereas the QDs outside the cells can be highly excited. At high excitations, the occupation of the ground excitonic state in the QD outside the cells becomes saturated and high-energy states excited, resulting in a large relaxation energy and a broad fluorescence peak. This permits, in concept, to use QD biomarkers to monitor EPCs by characterizing QD fluorescence spectra

Neonatal ACE inhibition in rats interferes with lung development.

The renin-angiotensin system (RAS) is developmentally up-regulated and it is essential for kidney development in several species. Given the fact that the rat lung undergoes postnatal development, the mammalian lung possesses the highest angiotensin-converting enzyme (ACE) levels and ACE activity increases during the first weeks postpartum, we tested the hypothesis that ACE inhibition influences postnatal lung development. Rats were given the ACE inhibitor enalapril (10 mg kg-1) from 0 to 9 days of age and their lungs were examined at day 4 and 9. Lung structure was evaluated by means of light microscopy, and surface tension of bronchoalveolar lavage fluid was measured by means of a Wilhelmy balance. Neonatal ACE inhibition lowered the surface tension of bronchoalveolar lavage fluid and caused widening of respiratory airspaces and thinning of alveolar septa. Our results suggest that early postnatal ACE inhibition in rats interferes with lung development

High Physiological Omega-3 Fatty Acid Supplementation Affects Muscle Fatty Acid Composition and Glucose and Insulin Homeostasis in Obese Adolescents

Obese adolescents have high concentrations of saturated fatty acids and low omega-3 long-chain polyunsaturated fatty acids (LCUFAs) in plasma phospholipids. We aimed to investigate effects of omega-3 LCPUFA supplementation to obese adolescents on skeletal muscle lipids and glucose and insulin homeostasis. Twenty-five obese adolescents (14–17 years old, 14 females) completed a randomized double-blind crossover study supplying capsules containing either 1.2 g omega-3 LCPUFAs or placebo, for 3 months each with a six-week washout period. Fasting blood glucose, insulin, leptin, adiponectin, and lipids were measured. Intravenous glucose tolerance test (IVGTT) and euglycemic-hyperinsulinemic clamp were performed, and skeletal muscle biopsies were obtained at the end of each period. The concentrations of EPA, DHA, and total omega-3 PUFA in muscle phospholipids increased in both sexes. In the females, omega-3 LCPUFA supplementation improved glucose tolerance by 39% (P = 0.04) and restored insulin concentration by 34% (P = 0.02) during IVGTT. Insulin sensitivity improved 17% (P = 0.07). In males, none of these parameters was influenced by omega-3 supplementation. Thus, three months of supplementation of omega-3 LCPUFA improved glucose and insulin homeostasis in obese girls without influencing body weight

Quantum limits to center-of-mass measurements

We discuss the issue of measuring the mean position (center-of-mass) of a group of bosonic or fermionic quantum particles, including particle number fluctuations. We introduce a standard quantum limit for these measurements at ultra-low temperatures, and discuss this limit in the context of both photons and ultra-cold atoms. In the case of fermions, we present evidence that the Pauli exclusion principle has a strongly beneficial effect, giving rise to a 1/N scaling in the position standard-deviation -- as opposed to a $1/\sqrt{N}$ scaling for bosons. The difference between the actual mean-position fluctuation and this limit is evidence for quantum wave-packet spreading in the center-of-mass. This macroscopic quantum effect cannot be readily observed for non-interacting particles, due to classical pulse broadening. For this reason, we also study the evolution of photonic and matter-wave solitons, where classical dispersion is suppressed. In the photonic case, we show that the intrinsic quantum diffusion of the mean position can contribute significantly to uncertainties in soliton pulse arrival times. We also discuss ways in which the relatively long lifetimes of attractive bosons in matter-wave solitons may be used to demonstrate quantum interference between massive objects composed of thousands of particles.Comment: 12 pages, 6 figures. Submitted to PRA. Revised to include more references as well as a discussion of fermionic center-of-mas

A global perspective on the application of riverine macroinvertebrates as biological indicators in Africa, South-Central America, Mexico and Southern Asia

The aim of this study is to generate a first global overview of pressures and methods used to assess the environmental quality of rivers and streams using macroinvertebrates. In total, 314 peer-review studies were reviewed, published in the period 1997 – 2018, from developing economies in Africa, South-Central America, Mexico and Southern Asia. To establish a global perspective, the results from the literature review were compared to other compiled datasets, biomonitoring manuals, environmental surveys and literature reviews from Europe, North America and Australasia. The literature review from the developing economies showed that sampling was most usual during baseflow, using kick- or Surber sampling, with taxonomical identification levels mostly to genus or family. Assessments were most often done using metrics (singular and multimetrics; > 70% of the applications) and were based on community attributes related to richness and dominance (58% of studies), sensitivity (40%), diversity by heterogeneity (32%) and functional traits (25%). Within each category, the most used metrics were the richness and dominance of Ephemeroptera, Plecoptera and Trichoptera (EPT), Biological Monitoring Working Party scoring systems (BMWP/ASPT), Shannon-Wiener diversity and feeding traits. Overall, 92% of the reviewed studies reported that the use of macroinvertebrates, at least in some of their responses, was successful in detecting degradation of environmental quality in the investigated rivers. Given the many similarities in applied methods worldwide, at present, we consider that a global assessment of riverine environmental quality can be feasible by using family level identifications of macroinvertebrate samples. We propose a global common metric (multimetric), comprising three of the most common river assessment metrics from the reviewed literature, but also elsewhere, namely the BMWP/ASPT, Shannon-Wiener diversity and richness of EPT. Recent concerns regarding the global state of nature and consequences for freshwater communities, as reported by the intergovernmental science-policy platform on biodiversity and ecosystem services (IPBES), emphasize the urgent need for such a synthesis

The battle for COVID-19 vaccines highlights the need for a new global governance mechanism

To the Editor—Although the rapid development of several vaccines against COVID-19 is an unparalleled scientific accomplishment, one made possible through the collaboration of researchers, industry and funding bodies, the absence of a system that secures equitable access to vaccines has uncovered deep fissures in the global governance systems for health, as noted in a recent Nature Medicine Editorial. For example, advance purchase agreements for vaccines against COVID-19 have favored affluent countries, allowing them to secure 150–500% of their predicted needs, while many citizens of low-and middle-income countries (LMICs) will remain unvaccinated until 2024. Additionally, the power of patent-holders and pharmaceutical companies to place conditions on the use of vaccines prices out access for LMICs, and bilateral purchasing deals are rarely disclosed. By affording priority on the basis of economic or political power, today’s discourse clearly deviates from previous ethical and public-health principles of maximizing lives or life-years saved, and the sentiment that “people’s entitlement to lifesaving resources should not depend on nationality”. The COVID-19 pandemic has tested wealthy nations’ commitments to Agenda 2030 and to ‘leaving no one behind’ at the same time that it has revealed democratic deficits, institutional rigidity, weak accountability systems, and inadequate policy space that protects health-governance systems from economic goals. Thus, the as-yet-limited support for the vaccine-sharing and allocation principles of the COVAX initiative may be a sign not only of a moral catastrophe, to quote the director-general of the World Health Organization (WHO), but also of inadequate global accountability mechanisms that exposes the consequences of commercial determinants of health

Stream restoration and ecosystem functioning in lowland streams

Restoration has been increasingly applied over the last decades as a way to improve the ecological conditions in stream ecosystems, but documentation of the impact of restoration on ecosystem functions is sparse. Here, we applied a space-for-time approach to explore effects of stream restoration on metabolism and organic matter decomposition in lowland agricultural streams. We included stream reaches that were restored >10 years ago and compared ecosystem functioning in these streams with those in channelized and naturally meandering stream reaches from the same geographical region. Specifically, we tested the following hypotheses: 1) rates of stream metabolism (gross primary production, GPP, and ecosystem respiration, ER) and organic matter decomposition in restored reaches resemble rates in naturally meandering reaches more than rates in channelized stream reaches and 2) higher resemblance in ecosystem metabolism and organic matter decomposition between restored reaches and meandering reaches can be attributed to the improved physical habitat conditions in the restored stream reaches. Overall, we did not find that stream metabolism or organic matter decomposition differed among restored, channelized and naturally meandering stream reaches even though habitat conditions differed among the three stream types. Instead, we found a large variation in ecosystem function characteristics across all sites. When analyzing all stream types combined, we found that GPP increased with increasing plant coverage and that ER increased with increasing stream size and with the coverage of coarse substratum on the stream bottom. Organic matter decomposition, on the other hand, only slightly increased with the number of plant species and declined with increasing concentrations of nutrients. Overall, our findings suggest that physical habitat improvements in restored stream reaches can affect ecosystem functions, but also that the restoration outcome is context-dependent since many of the physical characteristics playing a role for the measured functions were only to some extent affected by the restoration and/or clouded by interference with factors operating at a larger-scale.publishedVersio

Fokusprojekt Raps och avbrottsgrödor

Fokusgruppen Raps och avbrottsgrödor inriktades på förväntade utmaningar för växtskyddet mot patogener, skadedjur och ogräs i avbrotts- och mellangrödor. Avbrottsgrödor odlas som omväxlingsgrödor till huvudgrödorna i en växtföljd, för att bryta uppförökningen av skadeorganismer eller bidra med andra positiva effekter som till exempel jordförbättring och näringsämnen. Fokusgruppen innehöll representanter för myndigheter, näringsliv och forskare. På den första workshopen beslutade gruppen att det fortsatta arbetet skulle fokuseras på på grödor från kål- och ärtväxter. I en fördjupad kunskapssammanställning fokuserade vi specifikt på de största växtskyddsutmaningarna för tre grödor: raps, åkerböna och ärter. De viktigaste slutsatserna fokusgruppen har kommit fram till är: • Ökad odling av många avbrotts- och mellangrödor kan förväntas ge högre risk för uppförökning av skadeorganismer. Förväntad minskad tillgång på verksamma och godkända bekämpningsmedel mot insekter, sjukdomar och ogräs gör det till en stor utmaning att möta dessa förväntade hot. • Resistensutveckling hos skadegörare bör motverkas med väl genomtänkt användning av kemiska bekämpningsmedel, bl a genom bättre tillämpat integrerat växtskydd med fokus på växtföljdsplanering, utarbetande och uppdatering av bekämpningströsklar och andra sammanhållna bekämpningsstrategier. • Det finns stora kunskapsluckor vad gäller den grundläggande biologin hos flera viktiga skadegörare som angriper kål- och ärtväxter. Det gäller till exempel vissa patogener, för vilka faktiska kunskaper om diagnos, verklig förekomst och förorsakade skördeförluster är eftersatta, men även insektsskadegörare som till exempel bönsmygen. • Skadeorganismers spridningsmönster och möjligheter att angripa olika värdar är en grundläggande biologisk egenskap som bör studeras noggrannare för att förstå bekämpningsbehovet och ge möjligheter att minimera spridning och uppförökning. Lantbrukares faktiska möjligheter till fysisk planering för att minska uppförökning kan dock vara begränsade och lösningar bör undersökas och anpassas till rådande förhållanden. • Odlingssystemens utformning för att minska påverkan av ogräs behöver studeras. Kemisk bekämpning kan reduceras eller kompletteras genom integrerat växtskydd med konkurrensstarka grödor, växtföljder och jordbearbetning som långsiktigt minskar biomassan och frösättningen hos ogräs. • Betydelsen av och möjligheten att aktivt gynna biologisk mångfald bör studeras mer. Till exempel, bör effekter av naturliga fiender studeras ytterligare, då predation har betydelse för skadedjur såväl som ogräsfröer. En ökad biologisk mångfald påverkar också pollinering av viktiga grödor. Det gäller både studier av faktiska näringsvävar och landskapsutformningens och odlingssystemens betydelse för att gynna naturliga fiender. • Resistensförädling har stor potential inom hållbart växtskydd framför allt mot olika patogener men även mot insekter. Resistensegenskaper hos olika grödor behöver kartläggas. Resistensförädling är tids- och resurskrävande, vilket gör att koordinering och samordningsmöjligheter är nödvändiga

Intercomparison of in-situ aircraft and satellite aerosol measurements in the stratosphere

Aerosol composition and optical scattering from particles in the lowermost stratosphere (LMS) have been studied by comparing in-situ aerosol samples from the IAGOS-CARIBIC passenger aircraft with vertical profiles of aerosol backscattering obtained from the CALIOP lidar aboard the CALIPSO satellite. Concentrations of the dominating fractions of the stratospheric aerosol, being sulphur and carbon, have been obtained from post-flight analysis of IAGOS-CARIBIC aerosol samples. This information together with literature data on black carbon concentrations were used to calculate the aerosol backscattering which subsequently is compared with measurements by CALIOP. Vertical optical profiles were taken in an altitude range of several kilometres from and above the northern hemispheric extratropical tropopause for the years 2006-2014. We find that the two vastly different measurement platforms yield different aerosol backscattering, especially close to the tropopause where the influence from tropospheric aerosol is strong. The best agreement is found when the LMS is affected by volcanism, i.e., at elevated aerosol loadings. At background conditions, best agreement is obtained some distance (>2 km) above the tropopause in winter and spring, i.e., at likewise elevated aerosol loadings from subsiding aerosol-rich stratospheric air. This is to our knowledge the first time the CALIPSO lidar measurements have been compared to in-situ long-term aerosol measurements. © 2019, The Author(s)