Process‐based models not always better than empirical models for simulating budburst of Norway spruce and birch in Europe

Budburst models have mainly been developed to capture the processes of individual trees, and vary in their complexity and plant physiological realism. We evaluated how well eleven models capture the variation in budburst of birch and Norway spruce in Germany, Austria, the United Kingdom and Finland. The comparison was based on the models performance in relation to their underlying physiological assumptions with four different calibration schemes. The models were not able to accurately simulate the timing of budburst. In general the models overestimated the temperature effect, thereby the timing of budburst was simulated too early in the United Kingdom and too late in Finland. Among the better performing models were three models based on the growing degree day concept, with or without day length or chilling, and an empirical model based on spring temperatures. These models were also the models least influenced by the calibration data. For birch the best calibration scheme was based on multiple sites in either Germany or Europe, and for Norway spruce the best scheme included multiple sites in Germany or cold years of all sites. Most model and calibration combinations indicated greater bias with higher spring temperatures, mostly simulating earlier than observed budburst.     

A Strategy for Sensitive,Large Scale Quantitative Metabolomics

Metabolite profiling has been a valuable asset in the study of metabolism in health and disease. However, current platforms have different limiting factors, such as labor intensive sample preparations, low detection limits, slow scan speeds, intensive method optimization for each metabolite, and the inability to measure both positively and negatively charged ions in single experiments. Therefore, a novel metabolomics protocol could advance metabolomics studies. Amide-based hydrophilic chromatography enables polar metabolite analysis without any chemical derivatization. High resolution MS using the Q-Exactive (QE-MS) has improved ion optics, increased scan speeds (256 msec at resolution 70,000), and has the capability of carrying out positive/negative switching. Using a cold methanol extraction strategy, and coupling an amide column with QE-MS enables robust detection of 168 targeted polar metabolites and thousands of additional features simultaneously.  Data processing is carried out with commercially available software in a highly efficient way, and unknown features extracted from the mass spectra can be queried in databases.     

Is the instrumented-pointer method of calibrating anatomical landmarks in 3D motion analysis reliable?

Instrumented-pointers are often used to calibrate anatomical landmarks in biomechanical analyses. However, little is known about the effect of altering the orientation of the pointer during calibration on the co-ordinates recorded. Incorrect positioning of a landmark influences the axes created, and thus the kinematic data recorded. This study aimed to investigate the reliability of the pointer method for anatomical calibration. Two points were drawn onto a fixed box to resemble knee joint epicondyles, then a custom-made pointer was used to define the positions of these landmarks in three-dimensions. Twenty different pointer-orientations were chosen, and the position of the pointer in each of these orientations was recorded 8 times. Euclidean distances between single points were calculated for both landmarks and compared statistically (α = 0.05). Average Euclidean distances between all reconstructed points were 3.2±1.4 mm (range: 0.3–7.1 mm) for one landmark and 3.3±1.5 mm (range: 0.3–7.9mm) for the other. The x- and y-co-ordinates recorded differed statistically when the pointer was moved about the X and Y axes (anterior/posterior and superior/inferior to landmark) (p < 0.05). No statistical differences were found between co-ordinates recorded when the pointer was moved around the Z axes (p > 0.05). ICC values for all co-ordinates were excellent, highlighting the reliability of the method (ICC > 0.90). These results support this method of anatomical calibration; however, we recommend that pointers be consistently held in a neutral oriented position (where the handle is not anterior, posterior, superior or inferior to the landmark) during calibration, to reduce the likelihood of calibration errors.     

Calibration of Watermark soil moisture sensors for soil matric potential and temperature

Rapid, accurate, and automated measurement of soil matric potential is desirable. Evidence suggested that the Watermark resistance block might be an appropriate and inexpensive tool, so we conducted an evaluation of its relevant characteristics. A number of these blocks were calibrated under laboratory conditions to determine their individual and aggregate responses to soil matric potential, soil type, and temperature. We found that the temperature response could be expressed as a single equation, valid for all tested blocks, but comparison against matric potential revealed that each block had a characteristic response. Furthermore, block responses were different in two soils and, for a given soil, not necessarily reproducible. Given these limitations, these sensors are probably useful only as relative indicators of soil water status.     

Geometric mouse variation: Implications to the axial ulnar loading protocol and animal specific calibration

Large variations in axial ulnar load strain calibration results suggest that animal-specific calibrations may be necessary. However, the optimal set of geometric measures for performing an animal-specific calibration are not known, potentially as a result of confounding effects associated with experimentally introduced variation. The purpose of this study was to characterize the inherent variability of ulnar geometric measures known to influence periosteal midshaft strain during axial ulnar exogenous loading, and to further quantify the relationship between the variance of those geometric measures and periosteal strain during axial loading. Thirty-nine right mouse forelimbs were scanned with microCT. Seven geometric measures that influence periosteal strain resulting from a combined axial and bending loading were computed and used to estimate animal-specific strains on the periosteal midshaft. Animal specific strains were estimated using a theoretical model based on the generalized flexure formula. The predicted mean and standard deviation of the simulated midshaft strain gauge measurement resulting from the inter-animal geometric differences was −985±148 με/N. The complete beam bending term associated with bending about the I_min axis accounted for 89% of the variance and reduced the residual RMSE to 50.4 με. Eccentricity associated with the axial loading contributed a substantial portion of variation to the computed strain suggesting that calibration procedures to account for animal differences should incorporate that variable. The method developed in this study provides a relatively simple procedure for computing animal-specific strains using microCT scan data, without the need of a load/strain calibration study or computationally intensive finite element models.     

测定叶片蒸腾系数的封闭系统

光合测定系统内附装一控制定温的定量吸湿装置,使这系统在测定叶片光合(或呼吸)过程中,湿度保持恒定,可以测得蒸腾量及蒸腾速率,从而得到蒸腾系数。文中还介绍CO_2的标定方法。     

New evidence for the recent divergence of Devil's Hole pupfish and the plausibility of elevated mutation rates in endangered taxa

Sa?lam et al. recently argued that the Devil's Hole pupfish (Cyprinodon diabolis), a conservation icon with the smallest known species range, was isolated 60 kya based on a new genomic data set. If true, this would be a radically long timescale for any species to persist at population sizes <500 individuals, in contrast to conservation genetics theory. However, here we argue that their analyses and interpretation are inappropriate. They placed highly restrictive prior distributions on divergence times, which do not appropriately model the large uncertainty and result in removing nearly all uncertainty from their analyses, and chose among models by assuming that pupfishes exhibit human mutation rates. We reanalysed their data with their same methods, only using an informative prior for the plausible range of mutation rates observed across vertebrates, including an estimate of the genomewide mutation rate from a pedigree analysis of cichlid fishes. In fact, Saglam et al.'s phylogenetic data support much younger median divergence times for C. diabolis, ranging from 6.2 to 19.9 kya, overlapping with our previous phylogenetic divergence time estimates of 2.5–6.5 kya. There are many reasons to suspect an even younger age and higher mutation rate in C. diabolis, as we previously estimated, due to their high metabolism, small adult size, small population size and severe environmental stressors. In conclusion, our results highlight the need for measuring mutation rate in this fascinating species and suggest that the ages of endangered taxa present in small, isolated populations may frequently be overestimated.     

Evolutionary Relationships Among the Eukaryotic Crown Taxa Taking into Account Site-to-Site Rate Variation in 18S rRNA

In this study we constructed a bootstrapped distance tree of 500 small subunit ribosomal RNA sequences from organisms belonging to the so-called crown of eukaryote evolution. Taking into account the substitution rate of the individual nucleotides of the rRNA sequence alignment, our results suggest that (1) animals, true fungi, and choanoflagellates share a common origin: The branch joining these taxa is highly supported by bootstrap analysis (bootstrap support [BS] > 90%), (2) stramenopiles and alveolates are sister groups (BS = 75%), (3) within the alveolates, dinoflagellates and apicomplexans share a common ancestor BS > 95%), while in turn they both share a common origin with the ciliates (BS > 80%), and (4) within the stramenopiles, heterokont algae, hyphochytriomycetes, and oomycetes form a monophyletic grouping well supported by bootstrap analysis (BS > 85%), preceded by the well-supported successive divergence of labyrinthulomycetes and bicosoecids. On the other hand, many evolutionary relationships between crown taxa are still obscure on the basis of 18S rRNA. The branching order between the animal-fungal-choanoflagellates clade and the chlorobionts, the alveolates and stramenopiles, red algae, and several smaller groups of organisms remains largely unresolved. When among-site rate variation is not considered, the inferred tree topologies are inferior to those where the substitution rate spectrum for the 18S rRNA is taken into account. This is primarily indicated by the erroneous branching of fast-evolving sequences. Moreover, when different substitution rates among sites are not considered, the animals no longer appear as a monophyletic grouping in most distance trees. Received: 11 June 1997 / Accepted: 21 July 1997     

The relationship between diatoms and surface water quality in the Høylandet area of Nord-Trøndelag, Norway

Although the ecological effects of surface wateracidification are now well researched, factorscontrolling the abundance and occurrence of aquaticorganisms in unpolluted acid-sensitive systems arepoorly known. The Høylandet region in central Norwayexperiences relatively low levels of atmosphericpollution and its surface waters, although acid, arenot significantly acidified. Hence lakes and streamsin this region were selected to study the influence ofwater chemistry on diatom algae. Relationships betweenthe two were explored using the multivariate techniqueof canonical correspondence analysis (CCA). Theprincipal water chemistry variables influencingspecies composition of periphytic diatoms were foundto be pH and water colour. Furthermore, therelationship between species abundance and pH wassufficiently strong to enable reconstruction of wateracidity from diatom data. Establishing the nature ofaquatic communities in atmospherically clean butgeologically sensitive regions is an important meansof identifying control systems against which therecovery of acidified lakes in polluted regions can beassessed. The Høylandet region has the potential toprovide a Europe-wide control system of this naturebut much further work is required to follow up andextend the results of this preliminary study.