Recognition and separation of single particles with size variation by statistical analysis of their images

Macromolecules may occupy conformations with structural differences that cannot be resolved biochemically. The separation of mixed molecular populations is a pressing problem in single-particle analysis. Until recently, the task of distinguishing small structural variations was intractable, but developments in cryo-electron microscopy hardware and software now make it possible to address this problem. We have developed a general strategy for recognizing and separating structures of variable size from cryo-electron micrographs of single particles. The method uses a combination of statistical analysis and projection matching to multiple models. Identification of size variations by multivariate statistical analysis was used to do an initial separation of the data and generate starting models by angular reconstitution. Refinement was performed using alternate projection matching to models and angular reconstitution of the separated subsets. The approach has been successful at intermediate resolution, taking it within range of resolving secondary structure elements of proteins. Analysis of simulated and real data sets is used to illustrate the problems encountered and possible solutions. The strategy developed was used to resolve the structures of two forms of a small heat shock protein (Hsp26) that vary slightly in diameter and subunit packing.     

Three-dimensional chromatin ensemble reconstruction via stochastic embedding

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Responses of radial growth and stable carbon isotopes to climate in the northern Tianshan Mountains

Climate change has profound effects on forest ecosystems. Schrenk spruce (P. schrenkiana) is a natural conifer species endemic to the arid inland areas of Asia. In this study, the relationship between tree-ring parameters of P. schrenkiana and major meteorological factors were analyzed, and the main limiting factors for tree radial growth and stable carbon isotope fractionation were explored. Our results indicate that moisture stress before and during the growing season have an important influence on radial growth of P. schrenkiana, especially, the correlation coefficient between tree-ring width and vapor pressure deficit (VPD) from previous August to current July is as high as −0.622 (n = 51, p < 0.01). Collinearity analysis further supports the conclusion that the limiting factor for the radial growth of P. schrenkiana is moisture. Although the correlation analysis results show that the tree-ring δ¹³C_corr is significantly positively correlated with sunshine duration (SD), additional analysis based on first order difference variables suggests that the climate factor may not be the only limiting factor for the stable carbon isotope fractionation of tree rings in the Sayram Lake Basin. This lays the foundation for the assessment of forest management practices and carbon sink capacity in light of future climate change.     

Provenance selection and site conditions determine growth performance of pedunculate oak

Forests of the future need to cope with adverse climatic conditions, in particular drought, to ensure forest stability and productivity. Given the usually long rotation period of forests, forest managers need to select appropriate, i.e. productive and climate-change resilient tree species and/or provenances, to lower tree-mortality risks and sustain current wood production rates at the end of the 21^st century. A frequent means of assessing which provenances of a given species are adapted to anticipated climate conditions is common garden experiments, where trees from different provenances are planted under similar climate conditions. However, in this context soil conditions also play an important role, since they govern how climate translates into plant-available water and hence plant’s ability to cope with extreme drought events. Here, we examine the effects of soil conditions on pedunculate oak (Quercus robur L.), by studying 10 different Dutch oak provenances that were planted in three provenance trials on different soil types in 1988 in the Netherlands. Using dendroecological methods, we quantified provenance-specific productivity and assessed provenance- and site-specific growth patterns. Our results indicated clear differences in productivity among provenances as well as soil-type specific growth patterns. Consequently, our study highlights the importance of incorporating soil characteristics when evaluating the growth performance of provenances within common garden experiments.     

The effect of drought stress on heterozygosity–fitness correlations in pedunculate oak (Quercus robur)

Background and Aims

The interaction between forest fragmentation and predicted climate change may pose a serious threat to tree populations. In small and spatially isolated forest fragments, increased homozygosity may directly affect individual tree fitness through the expression of deleterious alleles. Climate change-induced drought stress may exacerbate these detrimental genetic consequences of forest fragmentation, as the fitness response to low levels of individual heterozygosity is generally thought to be stronger under environmental stress than under optimal conditions.

Methods

To test this hypothesis, a greenhouse experiment was performed in which various transpiration and growth traits of 6-month-old seedlings of Quercus robur differing in multilocus heterozygosity (MLH) were recorded for 3 months under a well-watered and a drought stress treatment. Heterozygosity–fitness correlations (HFC) were examined by correlating the recorded traits of individual seedlings to their MLH and by studying their response to drought stress.

Key Results

Weak, but significant, effects of MLH on several fitness traits were obtained, which were stronger for transpiration variables than for the recorded growth traits. High atmospheric stress (measured as vapour pressure deficit) influenced the strength of the HFCs of the transpiration variables, whereas only a limited effect of the irrigation treatment on the HFCs was observed.

Conclusions

Under ongoing climate change, increased atmospheric stress in the future may strengthen the negative fitness responses of trees to low MLH. This indicates the necessity to maximize individual multilocus heterozygosity in forest tree breeding programmes.     

Technical Note: Calcium and carbon stable isotope ratios as paleodietary indicators

Calcium stable isotope ratios are hypothesized to vary as a function of trophic level. This premise raises the possibility of using calcium stable isotope ratios to study the dietary behaviors of fossil taxa and to test competing hypotheses on the adaptive origins of euprimates. To explore this concept, we measured the stable isotope composition of contemporary mammals in northern Borneo and northwestern Costa Rica, two communities with functional or phylogenetic relevance to primate origins. We found that bone collagen δ¹³C and δ¹⁵N values could differentiate trophic levels in each assemblage, a result that justifies the use of these systems to test the predicted inverse relationship between bioapatite δ¹³C and δ⁴⁴Ca values. As expected, taxonomic carnivores (felids) showed a combination of high δ¹³C and low δ⁴⁴Ca values; however, the δ⁴⁴Ca values of other faunivores were indistinguishable from those of primary consumers. We suggest that the trophic insensitivity of most bioapatite δ⁴⁴Ca values is attributable to the negligible calcium content of arthropod prey. Although the present results are inconclusive, the tandem analysis of δ⁴⁴Ca and δ¹³C values in fossils continues to hold promise for informing paleodietary studies and we highlight this potential by drawing attention to the stable isotope composition of the Early Eocene primate Cantius. Am J Phys Anthropol 154:633–643, 2014. © 2014 Wiley Periodicals, Inc.     

Diversity of Saxicolous Lichens along an Aridity Gradient in Central México

Lichens are symbiotic organisms that comprise a fungus and a photosynthetic partner wich are recognized as a good indicator of climate change. However, our understanding of how aridity affects the diversity of saxicolous lichens in drylands is still limited. To evaluate the relationship between saxicolous lichen diversity and aridity in a central México dryland, a geographical transect was established of 100 km to build an aridity gradient in the semiarid zone of the State of Querétaro, Mexico, comprising ten sampling sites with a 10 km separation. Species richness, abundance and diversity of soil lichen species were recorded using two sampling methods: the quadrat-intercept and the line-intercept method, to compare their performance in assessing soil lichen diversity in drylands. The number of species and Shannon diversity of saxicolous lichens were higher at intermediate values of the aridity index (AI = 0.10–0.34). Quadrat intercept and point intercept methods gave quite similar results, which means that the selected method does not influence the results in a significant way. This study confirms the role of saxicolous lichens as climate change indicators and reveals the importance of the sampling method selection in the evaluation of different parameters of soil lichen diversity in drylands.     

Air humidity as key determinant of morphogenesis and productivity of the rare temperate woodland fern Polystichum braunii

(1) Most ferns are restricted to moist and shady habitats, but it is not known whether soil moisture or atmospheric water status are decisive limiting factors, or if both are equally important. (2) Using the rare temperate woodland fern Polystichum braunii, we conducted a three‐factorial climate chamber experiment (soil moisture (SM) × air humidity (RH) × air temperature (T)) to test the hypotheses that: (i) atmospheric water status (RH) exerts a similarly large influence on the fern's biology as soil moisture, and (ii) both a reduction in RH and an increase in air temperature reduce vigour and growth. (3) Nine of 11 morphological, physiological and growth‐related traits were significantly influenced by an increase in RH from 65% to 95%, leading to higher leaf conductance, increased above‐ and belowground productivity, higher fertility, more epidermal trichomes and fewer leaf deformities under high air humidity. In contrast, soil moisture variation (from 66% to 70% in the moist to ca. 42% in the dry treatment) influenced only one trait (specific leaf area), and temperature variation (15 °C versus 19 °C during daytime) only three traits (leaf conductance, root/shoot ratio, specific leaf area); RH was the only factor affecting productivity. (4) This study is the first experimental proof for a soil moisture‐independent air humidity effect on the growth of terrestrial woodland ferns. P. braunii appears to be an air humidity hygrophyte that, whithin the range of realistic environmental conditions set in this study, suffers more from a reduction in RH than in soil moisture. A climate warming‐related increase in summer temperatures, however, seems not to directly threaten this endangered species.     

Dynamical systems analysis of arterial blood pressure signals in relation to heart rate fluctuations in chick embryos

We attempted a new approach based on a modern dynamical system theory to reconstruct the arterial blood pressure signals in relation to heart rate fluctuations of developing chick embryos. The dynamical systems approach in general is to model a phenomenon that is presented by a single time series record and approximate the dynamical property (e.g. heart rate fluctuations) of a system based only on information contained in a single-variable (arterial blood pressure) of the system. The time-series data of the arterial blood pressure was reconstructed in 3-dimensional space to draw characteristic orbits. Since the reconstructed orbits of the blood pressure should retain information contained in the pressure signals, we attempted to derive instantaneous heart rate (IHR) from the reconstructed orbits. The derived IHR presenting HR fluctuations coincided well with the IHR obtained conventionally from the peak-to-peak time intervals of the maximum blood pressure. Movements of the reconstructed orbits of the arterial blood pressure in 3-dimensional space reflected HR fluctuations (i.e. transient decelerations and accelerations).