Karst landscapes and karst aquifers, which are composed of a variety of soluble rocks such as salt, gypsum, anhydrite, limestone, dolomite and quartzite, are fascinating areas of study. As karst rocks are abundant on the Earth's surface, the fast evolution of karst landscapes and the rapid flow of water through karst aquifers present challenges from a number of different perspectives. This collection of 25 papers deals with different aspects of these challenges, including karst geology, geomorphology and speleogenesis, karst hydrogeology, karst modelling, and karst hazards and management. Together these papers provide a state-of-the-art review of the current challenges and solutions in describing karst from a scientific perspective.View less
Identifying and implementing interventions that create co-benefits in terms of food and nutrition security as well as food safety requires an interdisciplinary and intersectoral approach. This study was part of a larger project that applied an integrated framework for combined nutritional, food safety and value chain analysis to assess the dairy value chain in two regions of Tanzania, namely Morogoro and Tanga. Here, we report on the use of participatory rural appraisals (PRAs) with producers and consumers to investigate seasonality, constraints and opportunities in cow milk production and consumption in ten villages in Tanzania and describe attitudes and practices surrounding milk quality and safety. The PRAs allowed identifying strong seasonal milk production and consumption practices reflecting rainfall patterns and a dependence on the natural environment. A wide range of production constraints were described by producers including insufficient technical know-how, poor quality breeds, cattle diseases, lack of capital, feed, water and reliable markets. While milk availability had a strong influence on milk consumption, findings showed that there are a range of other factors such as the consistency of milk, purchasing power and the availability of other foods which also influence consumer choice. A dependence on sensory milk quality attributes in the absence of other systems of certification was described. Both producers and consumers showed little concern regarding potentially contaminated milk despite an awareness of the existence of milkborne disease risks. The results indicate great potential for upscaling dairy production and at the same time highlight that any such interventions should carefully consider mitigation measures for food safety risks.View less
State variables in lake ecosystems are subject to processes that act on different time scales. The relative importance of each of these processes changes over time, e.g., due to varying constraints of physical, biological, and biogeochemical processes. Correspondingly, continuous automatic measurements at high temporal resolution often reveal intriguing patterns that can rarely be directly ascribed to single processes. In light of the rather complex interplay of such processes, disentangling them requires more powerful methods than researchers have applied up to this point. For this reason, we tested the potential of wavelet coherence, based on the assumption that different processes result in correlations between different variables, on different time scales and during different time windows across the seasons. The approach was tested on a set of multivariate hourly data measured between the onset of an ice cover and a cyanobacterial summer bloom in the year 2009 in the Müggelsee, a polymictic eutrophic lake. We found that processes such as photosynthesis and respiration, the growth and decay of phytoplankton biomass, dynamics in the CO2‐carbonate system, wind‐induced resuspension of particles, and vertical mixing all occasionally served as dominant drivers of the variability in our data. We therefore conclude that high‐resolution data and a method capable of analyzing time series in both the time and the frequency domain can help to enhance our understanding of the time scales and processes responsible for the high variability in driver variables and response variables, which in turn can lay the ground for mechanistic analyses.View less
Anatolia was home to some of the earliest farming communities. It has been long debated whether a migration of farming groups introduced agriculture to central Anatolia. Here, we report the first genome-wide data from a 15,000-year-old Anatolian hunter-gatherer and from seven Anatolian and Levantine early farmers. We find high genetic continuity (~80–90%) between the hunter-gatherers and early farmers of Anatolia and detect two distinct incoming ancestries: an early Iranian/Caucasus related one and a later one linked to the ancient Levant. Finally, we observe a genetic link between southern Europe and the Near East predating 15,000 years ago. Our results suggest a limited role of human migration in the emergence of agriculture in central Anatolia.View less
Background Long non-coding RNAs (lncRNAs) play an important role in regulating gene expression and are thus important for determining phenotypes. Most attempts to measure selection in lncRNAs have focused on the primary sequence. The majority of small RNAs and at least some parts of lncRNAs must fold into specific structures to perform their biological function. Comprehensive assessments of selection acting on RNAs therefore must also encompass structure. Selection pressures acting on the structure of non-coding genes can be detected within multiple sequence alignments. Approaches of this type, however, have so far focused on negative selection. Thus, a computational method for identifying ncRNAs under positive selection is needed.
Results We introduce the SSS-test (test for Selection on Secondary Structure) to identify positive selection and thus adaptive evolution. Benchmarks with biological as well as synthetic controls yield coherent signals for both negative and positive selection, demonstrating the functionality of the test. A survey of a lncRNA collection comprising 15,443 families resulted in 110 candidates that appear to be under positive selection in human. In 26 lncRNAs that have been associated with psychiatric disorders we identified local structures that have signs of positive selection in the human lineage.
Conclusions It is feasible to assay positive selection acting on RNA secondary structures on a genome-wide scale. The detection of human-specific positive selection in lncRNAs associated with cognitive disorder provides a set of candidate genes for further experimental testing and may provide insights into the evolution of cognitive abilities in humans.
Availability The SSS-test and related software is available at: https://github.com/waltercostamb/SSS-test. The databases used in this work are available at: http://www.bioinf.uni-leipzig.de/Software/SSS-test/.View less
C6H9F3N2, monoclinic, P21/n (no. 14), a = 10.6224(9) Å, b = 11.8639(9) Å, c = 13.3139(11) Å, β = 105.903(3)°, V = 1613.6(2) Å3, Z = 8, Rgt(F) = 0.0618, wRref(F2) = 0.1629, T = 102(2) K [1–3].
Viola beati, a hitherto unknown species of V. sect. Andinium (Violaceae) is described and illustrated. It is an inconspicuous, diminutive, perennial forb currently known from only one locality in NW Argentina. We draw attention to its morphology, ecology, rarity and endemism. The differences between V. beati and its apparently only close relative, V. singularis J. M. Watson & A. R. Flores, are defined.
Virtual Observatory tools are specifically designed for astronomical data, but they can be adapted to work with geospatial data by providing existing Geographical Information System tools with Simple Application Messaging Protocol interface. Open source QGIS package was chosen as a platform for this. The Simple Application Messaging Protocol interface was made with Python plug‐ins. Geospatial data were exposed to Virtual European Solar and Planetary Access via a dedicated German Astronomical Virtual Observatory Data Center Helper Suite server and several tables exposing existing Open Geospatial Consortium—compliant planetary services were published to Virtual European Solar and Planetary Access providing a variety of geospatial data types: vector data and spectral cube rasters, as well as Open Geospatial Consortium Web Map Service of planetary maps.View less
This study examined the association between job characteristics, namely job demands and job resources, and mental health outcomes in terms of emotional exhaustion and well-being among police officers. Eight hundred forty-three German police officers participated in a cross-sectional online survey. Structural equation modeling was used to examine the validity of the dual process model of the Job Demands-Resources (JD-R) framework in the context of police work. Job demands (verbal assaults by citizens, workload, and administrative stressors) predicted emotional exhaustion whereas job resources (team support, shared values, and perceived fairness) predicted well-being. Moreover, job resources were directly and negatively associated with emotional exhaustion. The findings confirm the capacity of job resources to simultaneously promote well-being and reduce emotional exhaustion. Work place interventions should thus not merely decrease job demands. To improve and protect police officers’ well-being, it is advisable to promote job resources. A supportive and fair organizational climate based on shared values is required to foster mental health in the context of police work.View less
In this work we provide a proof of principle for a theoretical methodology to identify functionalisation patterns in oxidised carbon 2D nanomaterials. The methodology is based on calculating a large number of X-ray absorption spectra of individually excited carbon atoms in different chemical environments using density functional theory. Since each resulting spectrum gives a fingerprint of the local electronic structure surrounding the excited atom, we may relate each spectrum to the functionalisation pattern of that excited atom up to a desired neighbourhood radius. These functionalisation pattern-specific spectra are collected in a database, that allows fast composition of X-ray absorption spectra for arbitrary structures in density functional theory quality. Finally, we present an exemplary application of the database approach to estimate the relative amount of functional groups in two different experimental samples of carbon nanomaterials.View less
The apicomplexan parasite Sarcocystis calchasi (Coccidia: Eimeriorina: Sarcocystidae) is the causative agent of Pigeon Protozoal Encephalitis (PPE) and infects birds of the orders Columbiformes, Piciformes and Psittaciformes. Accipiter hawks (Aves: Accipitriformes) are the definitive hosts of this parasite. Infections of S. calchasi have been detected in Germany, the United States and Japan. However, the prevalence of the parasite in racing pigeon flocks has not yet been determined. Here, the first cross-sectional prevalence study to investigate S. calchasi in pigeon racing flocks was accomplished including 245 pigeon flocks across Germany. A total of 1,225 muscle biopsies, were taken between 2012 and 2016 and examined by semi-nested PCR for S. calchasi DNA targeting the ITS gene. Additionally, a questionnaire on construction of the aviary as well as management and health status of the flock was conducted. In 27.8% (95% C.I. = 22.3–33.8%) of the flocks, S. calchasi DNA was detected in at least one pigeon. Positive flocks were located in 15 out of 16 federal states. A significant increase of infected racing pigeons was seen in spring. Half-covered or open aviary constructions showed a trend of increase of the prevalence rate, while anti-coccidian treatment and acidified drinking water had no effects. The high prevalence and the geographical distribution of S. calchasi suggest a long-standing occurrence of the parasite in the German racing pigeon population. For pigeons presented with neurological signs or other symptoms possibly related to PPE, S. calchasi should be considered as a potential cause throughout Germany.View less
AlienScenarios, a three-year project starting in March 2019, will evaluate for the first time the range of plausible futures of biological invasions for the 21st century. AlienScenarios consists of seven project partners and seven integrated complementary subprojects. We will develop the qualitative narratives for plausible futures of global alien species richness and impacts in the 21st century – the Alien Species Narratives (ASNs). The ASNs further serve as overarching concept to parameterize quantitative models of global, continental and regional futures of biological invasions. We will also establish the first global mechanistic invasion model considering major processes of biological invasions such as source pools, driver dynamics and establishment rates. Further, we will assess the impacts of invasive alien species (IAS) in terms of economic costs according to the different ASNs. In addition, we will assess the consequences of different levels of implementation of the European Union Regulation on IAS. Providing some more detailed regional information, we will analyse changes of the functional composition of communities in mountain regions under different scenario storylines and will extend the analyses to the Global South using Panama as a country-level case study. Finally, the results of the other WPs will be synthesized, and the approach and results of AlienScenarios will be discussed with and communicated to stakeholders and the wider community. AlienScenarios will provide crucially needed insights for pro-active alien species management and policy. It will thus make an important contribution to global assessments and projections of biodiversity and ecosystem services, as well as regional policies (e.g. EU regulation on IAS).View less
The autophagy cargo receptor p62 facilitates the condensation of misfolded, ubiquitin-positive proteins and their degradation by autophagy, but the molecular mechanism of p62 signaling to the core autophagy machinery is unclear. Here, we show that disordered residues 326–380 of p62 directly interact with the C-terminal region (CTR) of FIP200. Crystal structure determination shows that the FIP200 CTR contains a dimeric globular domain that we designated the “Claw” for its shape. The interaction of p62 with FIP200 is mediated by a positively charged pocket in the Claw, enhanced by p62 phosphorylation, mutually exclusive with the binding of p62 to LC3B, and it promotes degradation of ubiquitinated cargo by autophagy. Furthermore, the recruitment of the FIP200 CTR slows the phase separation of ubiquitinated proteins by p62 in a reconstituted system. Our data provide the molecular basis for a crosstalk between cargo condensation and autophagosome formation.View less
Mucins are of great interest in intestinal research and histochemical methods are often employed to identify them. Since it is in the nature of mucins that they are “hard to hold onto” once they come into contact with water, a frequently used medium in histochemistry, there are a number of challenges that may decrease diagnostic accuracy. As the outcome of methods published for microscopic detection of mucosubstances proved to be unsatisfactory in our hands, the aim was the establishment of a reliable and reproducible protocol. Tissue samples were available from pig feeding experiments. In the present study, we focus on a fixation / staining procedure without making comparisons between differently fed pigs. Several fixation and staining procedures were evaluated for their use in semiautomatic quantification and quality assessment of different mucus fractions simultaneous on one tissue section. Cryostat sectioning, subsequent fixation steps with heat, ethanol and modified Bouin’s solution, followed by triple staining with high iron diamine, alcian blue and periodic acid-Schiff turned out to be the best method to identify sulfomucin, sialomucin and neutral mucin simultaneous on one tissue section. This methodology resulted in very good morphology of goblet cells with intact mucin containing vesicles within the cells, which was comparable to ultrastructural electron microscopical observations. Semiautomatic quantification of different mucins was possible. In conclusion, reliable mucus quantification and assessment of mucus quality requires strictly tested procedures. According to our experience, the most important aim after cryosectioning is fast fixation of the mucosubstances, which requires a combination of different fixation steps.View less
Referendums provide citizens with more control over policy. At the same time, they often entail choices over highly complex policies and are politicised along partisan lines, suggesting that partisan rather than policy considerations will guide voters’ choices. I look to the 2016 Italian constitutional referendum, which was particularly complex and polarised, as an opportunity to test for mechanisms of government accountability in a referendum. Using a national survey of voters, I show that the more negative a respondent’s evaluation of the state of the economy, the lower their likelihood to vote ‘yes’ on the government’s reform proposal. This relationship is remarkably strong: an average respondent with a very positive evaluation of the state of the economy has an 88% probability of supporting the government’s reform proposal compared to only 12% for a respondent with a very negative evaluation. The fact that economic evaluations are a strong determinant of vote choice provides evidence for the existence of an economic vote in a referendum. This further suggests that voters may treat referendums as a sort of second-order election.View less
Pre-exposure prophylaxis (PrEP) is considered one of the five “pillars” by UNAIDS to reduce HIV transmission. Moreover, it is a tool for female self-protection against HIV, making it highly relevant to sub-Saharan regions, where women have the highest infection burden. To date, Truvada is the only medication for PrEP. However, the cost of Truvada limits its uptake in resource-constrained countries. Similarly, several currently investigated, patent-protected compounds may be unaffordable in these regions. We set out to explore the potential of the patent-expired antiviral efavirenz (EFV) as a cost-efficient PrEP alternative. A population pharmacokinetic model utilizing data from the ENCORE1 study was developed. The model was refined for metabolic autoinduction. We then explored EFV cellular uptake mechanisms, finding that it is largely determined by plasma protein binding. Next, we predicted the prophylactic efficacy of various EFV dosing schemes after exposure to HIV using a stochastic simulation framework. We predicted that plasma concentrations of 11, 36, 1287 and 1486ng/mL prevent 90% sexual transmissions with wild type and Y181C, K103N and G190S mutants, respectively. Trough concentrations achieved after 600 mg once daily dosing (median: 2017 ng/mL, 95% CI:445–9830) and after reduced dose (400 mg) efavirenz (median: 1349ng/mL, 95% CI: 297–6553) provided complete protection against wild-type virus and the Y181C mutant, and median trough concentrations provided about 90% protection against the K103N and G190S mutants. As reduced dose EFV has a lower toxicity profile, we predicted the reduction in HIV infection when 400 mg EFV-PrEP was poorly adhered to, when it was taken “on demand” and as post-exposure prophylaxis (PEP). Once daily EFV-PrEP provided 99% protection against wild-type virus, if ≥50% of doses were taken. PrEP “on demand” provided complete protection against wild-type virus and prevented ≥81% infections in the mutants. PEP could prevent >98% infection with susceptible virus when initiated within 24 h after virus exposure and continued for at least 9 days. We predict that 400 mg oral EFV may provide superior protection against wild-type HIV. However, further studies are warranted to evaluate EFV as a cost-efficient alternative to Truvada. Predicted prophylactic concentrations may guide release kinetics of EFV long-acting formulations for clinical trial design.View less
The transition of skotomorphogenesis to photomorphogenesis is induced by the perception of light, and is characterized by the inhibition of hypocotyl elongation and opening of cotyledons. Although it is known that the plant hormone cytokinin inhibits hypocotyl elongation in dark-grown Arabidopsis plants when applied in high concentrations, it is unclear to what extent this response is the result of cytokinin alone or cytokinin-induced ethylene production. Here, we show that cytokinin-induced inhibition of hypocotyl elongation is largely independent of ethylene and suggest a close connection between the cytokinin two-component system and the light-signaling networks. We show that this cytokinin signal is mainly mediated through the cytokinin receptor ARABIDOPSIS HISTIDINE KINASE3 and the ARABIDOPSIS RESPONSE REGULATOR1 in combination with ARR12. Interestingly, mutation of CONSTITUTIVELY PHOTOMORPOGENIC1 (COP1), DE-ETIOLATED1, and CYTOKININ INSENSITIVE4/COP10 renders plants insensitive to cytokinin, and these factors are indispensable for the transcriptional response during cytokinin-induced de-etiolation, indicating that a functional light-signaling pathway is essential for this cytokinin response. In addition, the effect of cytokinin on hypocotyl elongation is strongly dependent on the light conditions, with higher light intensities causing a switch in the response to cytokinin from an inhibitor to a promoter of hypocotyl elongation.View less
Low molecular weight (LMW) thiols play an important role as thiol-cofactors for many enzymes and are crucial to maintain the reduced state of the cytoplasm. Most Gram-negative bacteria utilize glutathione (GSH) as major LMW thiol. However, in Gram-positive Actinomycetes and Firmicutes alternative LMW thiols, such as mycothiol (MSH) and bacillithiol (BSH) play related roles as GSH surrogates, respectively. Under conditions of hypochlorite stress, MSH and BSH are known to form mixed disulfides with protein thiols, termed as S-mycothiolation or S-bacillithiolation that function in thiol-protection and redox regulation. Protein S-thiolations are widespread redox-modifications discovered in different Gram-positive bacteria, such as Bacillus and Staphylococcus species, Mycobacterium smegmatis, Corynebacterium glutamicum and Corynebacterium diphtheriae. S-thiolated proteins are mainly involved in cellular metabolism, protein translation, redox regulation and antioxidant functions with some conserved targets across bacteria. The reduction of protein S-mycothiolations and S-bacillithiolations requires glutaredoxin-related mycoredoxin and bacilliredoxin pathways to regenerate protein functions. In this review, we present an overview of the functions of mycothiol and bacillithiol and their physiological roles in protein S-bacillithiolations and S-mycothiolations in Gram-positive bacteria. Significant progress has been made to characterize the role of protein S-thiolation in redox-regulation and thiol protection of main metabolic and antioxidant enzymes. However, the physiological roles of the pathways for regeneration are only beginning to emerge as well as their interactions with other cellular redox systems. Future studies should be also directed to explore the roles of protein S-thiolations and their redox pathways in pathogenic bacteria under infection conditions to discover new drug targets and treatment options against multiple antibiotic resistant bacteria.View less
We report a strong correlation between the calculated broadband circular differential optical absorption (CDOA) and the geometric chirality of plasmonic meta-atoms with two-dimensional chirality. We investigate this correlation using three common gold meta-atom geometries: L-shapes, triangles, and nanorod dimers, over a broad range of geometric parameters. We show that this correlation holds for both contiguous plasmonic meta-atoms and non-contiguous structures which support plasmonic coupling effects. A potential application for this correlation is the rapid optimization of plasmonic nanostructure for maximum broadband CDOA.View less
Human herpesvirus-6A (HHV-6A) and 6B (HHV-6B) are two closely related betaherpesviruses that are associated with various diseases including seizures and encephalitis. The HHV-6A/B genomes have been shown to be present in an integrated state in the telomeres of latently infected cells. In addition, integration of HHV-6A/B in germ cells has resulted in individuals harboring this inherited chromosomally integrated HHV-6A/B (iciHHV-6) in every cell of their body. Until now, the viral transcriptome and the epigenetic modifications that contribute to the silencing of the integrated virus genome remain elusive. In the current study, we used a patient-derived iciHHV-6A cell line to assess the global viral gene expression profile by RNA-seq, and the chromatin profiles by MNase-seq and ChIP-seq analyses. In addition, we investigated an in vitro generated cell line (293-HHV-6A) that expresses GFP upon the addition of agents commonly used to induce herpesvirus reactivation such as TPA. No viral gene expression including miRNAs was detected from the HHV-6A genomes, indicating that the integrated virus is transcriptionally silent. Intriguingly, upon stimulation of the 293-HHV-6A cell line with TPA, only foreign promoters in the virus genome were activated, while all HHV-6A promoters remained completely silenced. The transcriptional silencing of latent HHV-6A was further supported by MNase-seq results, which demonstrate that the latent viral genome resides in a highly condensed nucleosome-associated state. We further explored the enrichment profiles of histone modifications via ChIP-seq analysis. Our results indicated that the HHV-6 genome is modestly enriched with the repressive histone marks H3K9me3/H3K27me3 and does not possess the active histone modifications H3K27ac/H3K4me3. Overall, these results indicate that HHV-6 genomes reside in a condensed chromatin state, providing insight into the epigenetic mechanisms associated with the silencing of the integrated HHV-6A genome.View less