•Three common sap flow measuring techniques were compared and calibrated.•Thermal dissipation probes underestimated gravimetric flow by 23–45%.•Species-independent re-parameterization significantly ...improved accuracy.•Heat field deformation system overestimated flux density by ∼11%.•At low to medium flow rates, heat ratio method showed highest accuracy.
Sap flow probes are routinely used in forest and horticulture hydrology for estimating tree water use. This requires unbiased measurements when upscaling from tree to stand level, but accuracy and comparability of different thermometric methods have been questioned. Three sap flow measuring techniques were compared against gravimetric flow measurement in cut stem segments: ‘Granier-type’ thermal dissipation probes (TDP; three different sensor types), the heat field deformation method (HFD), and the heat ratio method (HRM). For the empirical methods (TDP and HFD), new calibration parameters were estimated using a nonlinear hierarchical modelling approach. 66 stem segments from five temperate, diffuse-porous tree species (9–16cm stem diameter, 100cm stem length) were exposed to a wide range of flux densities by applying subatmospheric pressure (−50 to −650hPa) analogous to natural flow conditions in the field.
All TDP probes underestimated flux density by 23–45% when calculated with Granier's original calibration parameters, with the deviation increasing with flux rate. The accuracy was significantly improved by estimating new calibration parameters, especially for probes differing from Granier's original sensor design. Species-specific parameters further improved accuracy, although the species differences might partially be explained by variation in the observed ranges of sap flux. The HFD sensor overestimated gravimetric flow by ∼11%; empirical calibration did not improve its accuracy compared to the manufacturer's equation. At low to medium flow rates, the HRM system achieved higher accuracy than the other probes (0.8% underestimation), while performing poorly at high flux rates under our measurement settings (energy input of 25J). Both for TDP and HFD sensors, we observed a surprisingly large variability in calibration parameters between different stems of the same species.
We conclude that (i) TDP and HFD sensors require species-specific calibration to measure sap flux with high accuracy, (ii) the original Granier equation cannot be used for TDP probes with deviating design, and (iii), at low to medium flow rates, the highest accuracy can be achieved with HRM sensors. Our results help to increase the accuracy of tree sap flow measurements with thermal dissipation probes, and to assess various levels of errors related to the different thermometric methods. This is important when synthesizing forest transpiration data on regional and global scales.
Expansions of short tandem repeats are genetic variants that have been implicated in several neuropsychiatric and other disorders, but their assessment remains challenging with current ...polymerase-based methods
. Here we introduce a CRISPR-Cas-based enrichment strategy for nanopore sequencing combined with an algorithm for raw signal analysis. Our method, termed STRique for short tandem repeat identification, quantification and evaluation, integrates conventional sequence mapping of nanopore reads with raw signal alignment for the localization of repeat boundaries and a hidden Markov model-based repeat counting mechanism. We demonstrate the precise quantification of repeat numbers in conjunction with the determination of CpG methylation states in the repeat expansion and in adjacent regions at the single-molecule level without amplification. Our method enables the study of previously inaccessible genomic regions and their epigenetic marks.
Pluripotent stem cells (PSCs) are defined by their potential to generate all cell types of an organism. The standard assay for pluripotency of mouse PSCs is cell transmission through the germline, ...but for human PSCs researchers depend on indirect methods such as differentiation into teratomas in immunodeficient mice. Here we report PluriTest, a robust open-access bioinformatic assay of pluripotency in human cells based on their gene expression profiles.
Climate warming will increase the drought exposure of many forests world‐wide. It is not well understood how trees adapt their hydraulic architecture to a long‐term decrease in water availability. We ...examined 23 traits characterizing the hydraulic architecture and growth rate of branches and the dependent foliage of mature European beech (Fagus sylvatica) trees along a precipitation gradient (855–594 mm yr⁻¹) on uniform soil. A main goal was to identify traits that are associated with xylem efficiency, safety and growth. Our data demonstrate for the first time a linear increase in embolism resistance with climatic aridity (by 10%) across populations within a species. Simultaneously, vessel diameter declined by 7% and pit membrane thickness (Tₘ) increased by 15%. Although specific conductivity did not change, leaf‐specific conductivity declined by 40% with decreasing precipitation. Of eight plant traits commonly associated with embolism resistance, only vessel density in combination with pathway redundancy and Tₘ were related. We did not confirm the widely assumed trade‐off between xylem safety and efficiency but obtained evidence in support of a positive relationship between hydraulic efficiency and growth. We conclude that the branch hydraulic system of beech has a distinct adaptive potential to respond to a precipitation reduction as a result of the environmental control of embolism resistance.
The International Stem Cell Initiative compared several commonly used approaches to assess human pluripotent stem cells (PSC). PluriTest predicts pluripotency through bioinformatic analysis of the ...transcriptomes of undifferentiated cells, whereas, embryoid body (EB) formation in vitro and teratoma formation in vivo provide direct tests of differentiation. Here we report that EB assays, analyzed after differentiation under neutral conditions and under conditions promoting differentiation to ectoderm, mesoderm, or endoderm lineages, are sufficient to assess the differentiation potential of PSCs. However, teratoma analysis by histologic examination and by TeratoScore, which estimates differential gene expression in each tumor, not only measures differentiation but also allows insight into a PSC's malignant potential. Each of the assays can be used to predict pluripotent differentiation potential but, at this stage of assay development, only the teratoma assay provides an assessment of pluripotency and malignant potential, which are both relevant to the pre-clinical safety assessment of PSCs.
1. Forest dieback caused by drought-induced tree mortality has been observed world-wide. Forecasting which trees in which locations are vulnerable to drought-induced mortality is important to predict ...the consequences of drought on forest structure, biodiversity and ecosystem function. 2. In this paper, our central aim was to compile a synthesis of tree traits and associated abiotic variables that can be used to predict drought-induced mortality. 3. We reviewed the literature that specifically links drought mortality to functional traits and site conditions (i.e. edaphic variables and biotic conditions), targeting studies that show clear use of tree traits in drought analysis. We separated the review into five climatic zones to determine global vs. regionally restricted relationships between traits and mortality. 4. Our synthesis identifies a number of traits that have clear relationships with droughtinduced mortality (e.g. wood density at the species level and tree size and growth at the individual level). However, the lack of direct relationships between most traits and droughtinduced mortality highlights areas where future research should focus to broaden our understanding. 5. Synthesis and applications. Our synthesis highlights established relationships between traits and drought-induced mortality, presents knowledge gaps for future research focus and suggests monitoring and research avenues for improving our understanding of drought-induced mortality. It is intended to assist ecologists and natural resource managers choose appropriate and measurable parameters for predicting local and regional scale tree mortality risk in different climatic zones within constraints of time and funding availability.
In angiosperms, many studies have described the inter-specific variability of hydraulic-related traits and little is known at the intra-specific level. This information is however mandatory to assess ...the adaptive capacities of tree populations in the context of increasing drought frequency and severity. Ten 20-year old European beech (Fagus sylvatica L.) provenances representing the entire distribution range throughout Europe and differing significantly in aboveground biomass increment (ABI) by a factor of up to four were investigated for branch wood anatomical, hydraulic, and foliar traits in a provenance trial located in Northern Europe. We quantified to which extend xylem hydraulic and leaf traits are under genetic control and tested whether the xylem hydraulic properties (hydraulic efficiency and safety) trades off with yield and wood anatomical and leaf traits. Our results showed that only three out of 22 investigated ecophysiological traits showed significant genetic differentiations between provenances, namely vessel density (VD), the xylem pressure causing 88% loss of hydraulic conductance and mean leaf size. Depending of the ecophysiological traits measured, genetic differentiation between populations explained 0-14% of total phenotypic variation, while intra-population variability was higher than inter-population variability. Most wood anatomical traits and some foliar traits were additionally related to the climate of provenance origin. The lumen to sapwood area ratio, vessel diameter, theoretical specific conductivity and theoretical leaf-specific conductivity as well as the C:N-ratio increased with climatic aridity at the place of origin while the carbon isotope signature (δ(13)C) decreased. Contrary to our assumption, none of the wood anatomical traits were related to embolism resistance but were strong determinants of hydraulic efficiency. Although ABI was associated with both VD and δ(13)C, both hydraulic efficiency and embolism resistance were unrelated, disproving the assumed trade-off between hydraulic efficiency and safety. European beech seems to compensate increasing water stress with growing size mainly by adjusting vessel number and not vessel diameter. In conclusion, European beech has a high potential capacity to cope with climate change due to the high degree of intra-population genetic variability.
Relating expression signatures from different sources such as cell lines, in vitro cultures from primary cells and biopsy material is an important task in drug development and translational medicine ...as well as for tracking of cell fate and disease progression. Especially the comparison of large scale gene expression changes to tissue or cell type specific signatures is of high interest for the tracking of cell fate in (trans-) differentiation experiments and for cancer research, which increasingly focuses on shared processes and the involvement of the microenvironment. These signature relation approaches require robust statistical methods to account for the high biological heterogeneity in clinical data and must cope with small sample sizes in lab experiments and common patterns of co-expression in ubiquitous cellular processes. We describe a novel method, called PhysioSpace, to position dynamics of time series data derived from cellular differentiation and disease progression in a genome-wide expression space. The PhysioSpace is defined by a compendium of publicly available gene expression signatures representing a large set of biological phenotypes. The mapping of gene expression changes onto the PhysioSpace leads to a robust ranking of physiologically relevant signatures, as rigorously evaluated via sample-label permutations. A spherical transformation of the data improves the performance, leading to stable results even in case of small sample sizes. Using PhysioSpace with clinical cancer datasets reveals that such data exhibits large heterogeneity in the number of significant signature associations. This behavior was closely associated with the classification endpoint and cancer type under consideration, indicating shared biological functionalities in disease associated processes. Even though the time series data of cell line differentiation exhibited responses in larger clusters covering several biologically related patterns, top scoring patterns were highly consistent with a priory known biological information and separated from the rest of response patterns.
•Lack of ecophysiological knowledge on native tree species envisaged for reforestation.•Inter-relation between hydraulic traits and tree size, wood density and growth rates.•Evidence for ...environmental limitations in defining general physiological trade-offs.•Hydraulic traits and wood density can be used as diagnostic tools to predict growth.
Understanding how tropical trees coordinate fast growth with water consumption and carbon investment is of high relevance because climate warming may expose tropical forests to increasing stress. Thus, foresters require more information of native tree species envisaged for reforestation. This study examines the relationship between productivity and possibly growth-determining functional traits of xylem anatomy, hydraulic conductivity, foliar morphology and nutrient status in eight tree species in semi-dry Costa Rica; we further assessed the indicative value of wood density for growth rate and hydraulic efficiency. We tested the hypotheses that (i) wood density is related to both growth rate and hydraulic efficiency contrary to findings from moist tropical forests, and (ii) productivity is closely related to branch xylem properties as well as empirically determined hydraulic conductivity in these drought-adapted species. Growth rate was positively related to tree size, foliar nitrogen content, vessel diameter, specific conductivity and leaf water potential, and negatively to vessel density, wood density and δ13C, indicating that fast-growing tree species with light wood possessed a more efficient hydraulic system but closed their stomata relatively early to prevent xylem dysfunction. We conclude, that in tropical semi-dry climates, productivity is closely associated not only with foliar nitrogen but also with wood anatomical and hydraulic properties. Wood density proved to be a reliable indicator for growth-related, wood anatomical and hydraulic traits in these drought-adapted species.
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