The functionalization of molecules by cleaving inert carbon-carbon single bonds is regarded as a great synthetic challenge due to their inherent stability. In recent years, significant progress has ...been made in the activation of small rings relying on the release of strain energy. By contrast, the number of catalytic methodologies for the activation of unstrained carbon-carbon single bonds is still limited. This review focuses on the recent developments in transition-metal-catalyzed cleavage of C-C bonds in unstrained alcohols via β-carbon elimination. Emphasis is placed on the mechanistic aspects of the discussed transformations and their applications to the deconstruction and reorganization of molecules.
DNA methylation is an important, heritable epigenetic modification in most eukaryotic organisms that is connected with numerous biological processes. To study the impact of natural epigenetic ...variation in an ecological or evolutionary context, epigenetic studies are increasingly using methylation‐sensitive amplification polymorphism (MSAP) for surveys at the population or species level. However, no consensus exists on how to interpret and score the multistate information obtained from the MSAP banding patterns. Here, we review the previously used scoring approaches for population epigenetic studies and develop new alternatives. To assess effects of the different approaches on parameters of epigenetic diversity and differentiation, we applied eight scoring schemes to a case study of three populations of the plant species Viola elatior. For a total number of 168 detected polymorphic MSAP fragments, the number of ultimately scored polymorphic epiloci ranged between 78 and 286 depending on the particular scoring scheme. Both, estimates of epigenetic diversity and differentiation varied strongly between scoring approaches. However, linear regression and PCoA revealed qualitatively similar patterns, suggesting that the scoring approaches are largely consistent. For single‐locus analyses of MSAP data, for example the search for loci under selection, we advocate a new scoring approach that separately takes into account different methylation types and thus seems appropriate for drawing more detailed conclusions in ecological or evolutionary contexts. An R script (MSAP_score.r) for scoring and basic data analysis is provided.
ABSTRACT
Macrophytes are an important part of freshwater ecosystems and they have direct and indirect roles in keeping the water clear and providing structure and habitats for other aquatic ...organisms. Currently, climate change is posing a major threat to macrophyte communities by altering the many drivers that determine macrophyte abundance and composition. We synthesise current literature to examine the direct effects of climate change (i.e. changes in CO2, temperature, and precipitation patterns) on aquatic macrophytes in lakes as well as indirect effects via invasive species and nutrient dynamics. The combined effects of climate change are likely to lead to an increased abundance and distribution of emergent and floating species, and a decreased abundance and distribution of submerged macrophytes. In small shallow lakes, these processes are likely to be faster than in deep temperate lakes; with lower light levels, water level fluctuations and increases in temperature, the systems will become dominated by algae. In general, specialized macrophyte species in high‐latitude and high‐altitude areas will decrease in number while more competitive invasive species are likely to outcompete native species. Given that the majority of endemic species reside in tropical lakes, climate change, together with other anthropogenic pressures, might cause the extinction of a large number of endemic species. Lakes at higher altitudes in tropical areas could therefore potentially be a hotspot for future conservation efforts for protecting endemic macrophyte species. In response to a combination of climate‐change induced threats, the macrophyte community might collapse, which will change the status of lakes and may initiate a negative feedback loop that will affect entire lake ecosystems.
1. Plant litter is a key component in terrestrial ecosystems. It plays a major role in nutrient cycles and community organization. Land use and climate change may change the accumulation of litter in ...herbaceous ecosystems and affect plant community dynamics. Additionally, the transfer of seeds containing plant material (i.e. litter) is a widespread technique in grassland restoration. 2. Ecosystem responses to litter represent the outcome of interactions, whose sign and strength will depend on many variables (e.g. litter amount, seed size). A previous meta-analysis (from 1999) reported that litter had an overall negative effect on seed germination and seedling establishment in different ecosystems. However, recent studies indicated that this might not be the case in grassland ecosystems. 3. We used 914 data from 46 independent studies to analyse the effects of litter on seedling (i) emergence, (ii) survival and (iii) biomass, employing meta-analytical techniques. Each data set was stratified according to methodology, grassland type, irrigation conditions, litter amount and seed size. 4. We found an overall neutral effect of litter presence on seedling emergence and survival and a positive effect on seedling biomass. However, whereas for field experiments the response remained neutral, it was positive for common garden studies. In glasshouse experiments, litter effects were negative for emergence and positive for biomass. 5. Litter may have a positive effect on seedling recruitment in dry grasslands or under water-limited conditions, or in the presence of low to medium litter amounts (< 500 g m⁻² ). However, high litter amounts ( > 500 g m⁻² ) will inhibit seedling recruitment. Large seeds showed a more positive response to litter presence with respect to seedling emergence and survival, but not concerning biomass. 6. Synthesis. Under dry conditions (e.g. dry grasslands or dry periods) or with low to medium litter amounts, litter presence has a positive effect on seedling establishment. However, climate and land use change may promote litter accumulation and reduce seedling establishment, affecting grasslands composition and ecosystem functions.
This study analyses how indicators of water quality (thirteen physico-chemical variables) and drivers of change (i.e., monthly aggregated air temperature and streamflow, population density, and ...percentage of agricultural land use) coevolve in three large European river basins (i.e., Adige, Ebro, Sava) with different climatic, soil and water use conditions. Spearman rank correlation, Principal Component Analysis, and Mann-Kendall trend tests were applied to long-term time series of water quality data during the period 1990–2015 in order to investigate the relationships between water quality parameters and the main factors controlling them. Results show that air temperature, considered as a proxy of climatic change, has a significant impact, in particular in the Adige and Ebro: positive trends of water temperature and negative of dissolved oxygen are correlated with upward trends of air temperatures. The aquatic ecosystems of these rivers are, therefore, experiencing a reduction in oxygen, which may exacerbate in the future given the projected further increase in temperature. Furthermore, monthly streamflow has been shown to reduce in the Ebro, thereby reducing the beneficial effect of dilution, which appears evident from the observed upward patterns of chloride concentrations and electrical conductivity. Upward trends of chloride and biological oxygen demand in the Adige and Sava, and of phosphate in the Adige appears to be related to increasing human population density, whereas phosphates in the Sava and biological oxygen demand in the Ebro are highly correlated with agricultural land use, considered as a proxy of the impact of agricultural practises.
The present study shows the complex relationships between drivers and observed changes in water quality parameters. Such analysis can represent, complementary to a deep knowledge of the investigated systems, a reliable tool for decision makers in river basin planning by providing an overview of the potential impacts on the aquatic ecosystem of the three basins.
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•Trend analysis of physico-chemical variables in surface waters and their drivers of change•Comparison among surficial water quality in three contrasting European river basins•Highest risk of developing anoxic conditions in Iberian Peninsula•Agriculture as source of organic compounds and phosphate in the Adige basin•Increasing trends of chloride and phosphate in the Sava linked with agriculture
Urine cell-free DNA (cfDNA) is a valuable non-invasive biomarker with broad potential clinical applications, but there is no consensus on its optimal pre-analytical methodology, including the DNA ...extraction step. Due to its short length (majority of fragments <100 bp) and low concentration (ng/mL), urine cfDNA is not efficiently recovered by conventional silica-based extraction methods. To maximize sensitivity of urine cfDNA assays, we developed an ultrasensitive hybridization method that uses sequence-specific oligonucleotide capture probes immobilized on magnetic beads to improve extraction of short cfDNA from large-volume urine samples. Our hybridization method recovers near 100% (95% CI: 82.6-117.6%) of target-specific DNA from 10 mL urine, independent of fragment length (25-150 bp), and has a limit of detection of ≤5 copies of double-stranded DNA (0.5 copies/mL). Pairing hybridization with an ultrashort qPCR design, we can efficiently capture and amplify fragments as short as 25 bp. Our method enables amplification of cfDNA from 10 mL urine in a single qPCR well, tolerates variation in sample composition, and effectively removes non-target DNA. Our hybridization protocol improves upon both existing silica-based urine cfDNA extraction methods and previous hybridization-based sample preparation protocols. Two key innovations contribute to the strong performance of our method: a two-probe system enabling recovery of both strands of double-stranded DNA and dual biotinylated capture probes, which ensure consistent, high recovery by facilitating optimal probe density on the bead surface, improving thermostability of the probe-bead linkage, and eliminating interference by endogenous biotin. We originally designed the hybridization method for tuberculosis diagnosis from urine cfDNA, but expect that it will be versatile across urine cfDNA targets, and may be useful for other cfDNA sample types and applications beyond cfDNA. To make our hybridization method accessible to new users, we present a detailed protocol and straightforward guidelines for designing new capture probes.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Transit time distributions (TTDs) are crucial descriptors of flow and transport processes in catchments, which can be determined from stable water isotope data. Recently, the young water fraction ...(Fyw) has been introduced as an additional metric derivable from seasonal isotope cycles. In this study, we calculated Fyw and TTDs using monthly isotope data from 24 contrasting subcatchments in a mesoscale catchment (3,300 km2) in Germany. Fyw ranged from 0.01 to 0.27 (mean = 0.11) and was smallest in mountainous catchments. Assuming gamma‐shaped TTDs, we determined stationary TTDs with the convolution integral method for each subcatchment. The convolution integral was first calibrated against the isotope data only (i.e., traditional calibration) and, second, using a multiobjective calibration with the Fyw estimates as an additional constraint. This yielded largely differing TTD parameters even for neighboring catchments, with Fyw values below 0.1 generally involving a delayed peak in TTDs (i.e., gamma‐distribution shape parameter > 1). While the traditional calibration resulted in large uncertainties in TTD parameters, these uncertainties were reduced with the multiobjective calibration, thereby improving the assessment of mean transit times (2 years on average, ranging between 9.6 months and 5.6 years). This highlights the need for uncertainty assessment when using simple isotope models and shows that the traditional calibration might not yield an optimum solution in that it may give a TTD nonconsistent with Fyw. Given the robustness of Fyw estimates, isotope models should thus aim at accurately describing both Fyw and measured isotope data in order to improve the description of flow and transport in catchments.
Plain Language Summary
Information on the age of river water is crucial for assessing the vulnerability of rivers to weather extremes and pollution. The age of river water is defined as the time that water has spent underground after rainfall infiltration and before ending up in the river. The probability distribution of river water age can be determined using environmental tracers, which are tracers that naturally occur in the system such as stable water isotopes. In this study, we used isotope models to analyze time series of stable water isotopes in rainfall and streamwater measured in 24 subcatchments of the Bode catchment in central Germany. We found that the mean age of river water ranges between 9.6 months and 5.6 years depending on catchment characteristics such as climate and soil type. Moreover, river water with an age of below 2 to 3 months accounts for between 1% and 27% of the entire age distribution. We demonstrate how to use this information on young river water to constrain other metrics such as the mean water age. We suggest that this method is valuable for future studies using environmental tracers and models to determine water age in catchments.
Key Points
Calculation of young water fractions and transit time distributions in 24 contrasting subcatchments of a mesoscale catchment
Climate is a key control on young water fractions and transit time distributions in the study catchments
Information on young water fractions largely reduces uncertainty in calibrated transit time distributions and mean transit times
Due to anthropogenic pressures, African lion (Panthera leo) populations in Kenya and Tanzania are increasingly limited to fragmented populations. Lions living on isolated habitat patches exist in a ...matrix of less-preferred habitat. A framework of habitat patches within a less-suitable matrix describes a metapopulation. Metapopulation analysis can provide insight into the dynamics of each population patch in reference to the system as a whole, and these analyses often guide conservation planning. We present the first metapopulation analysis of African lions. We use a spatially-realistic model to investigate how sex-biased dispersal abilities of lions affect patch occupancy and also examine whether human densities surrounding the remaining lion populations affect the metapopulation as a whole. Our results indicate that male lion dispersal ability strongly contributes to population connectivity while the lesser dispersal ability of females could be a limiting factor. When populations go extinct, recolonization will not occur if distances between patches exceed female dispersal ability or if females are not able to survive moving across the matrix. This has profound implications for the overall metapopulation; the female models showed an intrinsic extinction rate from five-fold to a hundred-fold higher than the male models. Patch isolation is a consideration for even the largest lion populations. As lion populations continue to decline and with local extinctions occurring, female dispersal ability and the proximity to the nearest lion population are serious considerations for the recolonization of individual populations and for broader conservation efforts.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Here, we describe a multiplexed immunohistochemical platform with computational image processing workflows, including image cytometry, enabling simultaneous evaluation of 12 biomarkers in one ...formalin-fixed paraffin-embedded tissue section. To validate this platform, we used tissue microarrays containing 38 archival head and neck squamous cell carcinomas and revealed differential immune profiles based on lymphoid and myeloid cell densities, correlating with human papilloma virus status and prognosis. Based on these results, we investigated 24 pancreatic ductal adenocarcinomas from patients who received neoadjuvant GVAX vaccination and revealed that response to therapy correlated with degree of mono-myelocytic cell density and percentages of CD8+ T cells expressing T cell exhaustion markers. These data highlight the utility of in situ immune monitoring for patient stratification and provide digital image processing pipelines to the community for examining immune complexity in precious tissue sections, where phenotype and tissue architecture are preserved to improve biomarker discovery and assessment.
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•Multiplex IHC and computational image analysis phenotypes tumor-immune complexity•In situ leukocyte density correlates with subclassification and prognosis in HNSCC•Immune complexity stratifies response to vaccination therapy in PDAC•CD8+ T cell and PD-L1 status correlate with outcomes of vaccinated PDAC patients
Tsujikawa et al. develop a multiplex immunohistochemistry and image cytometry platform to reveal immune-based metrics for patient stratification and response monitoring. In HNSCC and PDAC, prognosis correlates with mono-myelocytic cell density. In PDAC, percentages of PD-1, Eomes, Ki67, and granzyme B in CD8+ T cells correlate with response to vaccine therapy.
A microdose cocktail containing midazolam, dabigatran etexilate, pitavastatin, rosuvastatin, and atorvastatin has been established to allow simultaneous assessment of a perpetrator impact on the most ...common drug metabolizing enzyme, cytochrome P450 (CYP)3A, and the major transporters organic anion‐transporting polypeptides (OATP)1B, breast cancer resistance protein (BCRP), and MDR1 P‐glycoprotein (P‐gp). The clinical utility of these microdose cocktail probe substrates was qualified by conducting clinical drug interaction studies with three inhibitors with different in vitro inhibitory profiles (rifampin, itraconazole, and clarithromycin). Generally, the pharmacokinetic profiles of the probe substrates, in the absence and presence of the inhibitors, were comparable to their reported corresponding pharmacological doses, and/or in agreement with theoretical expectations. The exception was dabigatran, which resulted in an approximately twofold higher magnitude for microdose compared to conventional dosing, and, thus, can be used to flag a worst‐case scenario for P‐gp. Broader application of the microdose cocktail will facilitate a more comprehensive understanding of the roles of drug transporters in drug disposition and drug interactions.
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