A combined morphological and molecular phylogeny of the genus Chironius Fitzinger, 1826 (Serpentes: Colubridae)

Chironius is one of the most speciose genera of the South American colubrid snakes. Although the genus represents a well‐known radiation of diurnal racers, its monophyly, affinities with other Neotropical colubrid genera, and intrageneric relationships are open questions. Here, we present a phylogenetic analysis of Chironius based on a data matrix that combines one nuclear (c‐mos) and two mitochondrial (12S and 16S rRNA) genes with 37 morphological characters derived from scutellation, skull, and hemipenial features. Phylogenetic relationships were inferred using maximum parsimony (MP) and maximum likelihood (ML). Our combined morphological and molecular analyses strongly support the monophyly of the genus Chironius and its sister‐group relationship with a clade formed by the genera Dendrophidion and Drymobius. Phylogenetic relationships within the genus Chironius is still controversial, although five clades are retrieved with medium to strong support. © 2014 The Linnean Society of London     

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.     

Mating and the inferred function of the genital system of the nudibranch, Aeolidiella glauca (Gastropoda: Opisthobranchia: Aeolidioidea)

Abstract. We describe the genital system of the aeolid nudibranch gastropod Aeolidiella glauca as a basis for our ongoing analysis of the mating system of this hermaphroditic species. In addition we give a short account of its mating behavior. A. glauca has an androdiaulic genital system with a proximally situated semiserial seminal receptacle. There is no bursa copulatrix. After fertilization, eggs pass through six glands, i.e., the capsule gland and the female gland mass which is comprised of five histologically differentiated parts. The prostate is a long, glandular tube. The everted, unarmed penis is very large and bears a series of 3–4 hook-shaped lobes consisting only of a simple, ciliated epithelium on its ventral side. Their function is unknown. After courtship, which involves moving in circles followed by resting in a head-to-head position, reciprocally touching each other with the tentacles, the slugs glide into a position where the everted genital atria are in contact. The huge penes are protruded simultaneously shortly after this contact occurs. Each animal strokes its partner's back with the penis and deposits a spermatophore of undetermined shape onto the partner's notum. Sperm enter the recipient through histolysis. How the sperm find their way to the seminal receptacle is not known.     

Limnology of a Warm Hypertrophic Wastewater Reservoir in Israel. II. Changes in Water Quality

Factor analysis was used to identify the processes responsible for the changes in water quality in a stratified wastewater reservoir. These reservoirs are well suited to study hypertrophic conditions. In the epilimnion, the main source of variablility was the external loading due to variations in wastewater inputs and water level (volume) of the reservoir. The second source was the seasonal climatic changes affecting photosynthesis. The third source was differences between night and day processes affecting REDOX potential. In the hypolimnion, the main source of variability was organic loading but due to both external loading (wastewater inputs) and internal loading (compounds released from the sediments). The second source was related to the input of chlorophyll into the hypolimnion, which were external (entry of chlorophyll rich inflow from a waste stabilization pond) and/or internal (input of chlorophyll from upper layers due to water column mixing).     

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.     

VARIATION IN THE OCCURRENCE OF EXTERNAL CARBONIC ANHYDRASE AMONG STRAINS OF THE MARINE DIATOM PHAEODACTYLUM TRICORNUTUM (BACILLARIOPHYCEAE)1

Eleven different strains of Phaeodactylum tricornutum Bohlin were obtained from three culture collections and were examined for the presence of external and internal carbonic anhydrase (CA). Cells of all strains, grown in standing culture at alkaline pH and low, dissolved inorganic carbon had internal CA, but only eight were found to have external CA. External CA activity was reduced when cultures were bubbled with air and was completely repressed when they were grown on 5% CO₂. Expression of external CA activity appears to be regulated by CO₂ concentration in the growth medium, but within one species, there appears to be a variation in occurrence of external CA and consequently in the mode of inorganic carbon acquisition.     

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.