Can three incongruence tests predict when data should be combined?

Advocates of conditional combination have argued that testing for incongruence between data partitions is an important step in data exploration. Unless the partitions have had distinct histories, as in horizontal gene transfer, incongruence means that one or more data support the wrong phylogeny. This study examines the relationship between incongruence and phylogenetic accuracy using three tests of incongruence. These tests were applied to pairs of mitochondrial DNA data partitions from two well-corroborated vertebrate phylogenies. Of the three tests, the most useful was the incongruence length difference test (ILD, also called the partition homogeneity test). This test distinguished between cases in which combining the data generally improved phylogenetic accuracy (P > 0.01) and cases in which accuracy of the combined data suffered relative to the individual partitions (P < 0.001). In contrast, in several cases, the Templeton and Rodrigo tests detected highly significant incongruence (P < 0.001) even though combining the incongruent partitions actually increased phylogenetic accuracy. All three tests identified cases in which improving the reconstruction model would improve the phylogenetic accuracy of the individual partitions.      

Which in vitro models could be best used to study hepatocyte polarity?

The correct functioning of the liver is ensured by the setting and the maintenance of hepatocyte polarity. The complex polarity of the hepatocyte is characterized by the existence of several basolateral and apical poles per cell. Many in vitro models are available for studying hepatocyte polarity, but which are the more suitable? To answer this question, we aimed to identify criteria which determine the typical hepatocyte polarity. Therefore, we compiled a range of protein markers of membrane domains in rat hepatocytes and investigated their involvement in hepatocytic functions. Then, we focused on the relationship between hepatic functions and the cytoskeleton, Golgi apparatus and endoplasmic reticulum. Subsequently, we compared different cell lines expressing hepatocyte polarity. Finally, to demonstrate the usefulness of some of these lines, we presented new data on endoplasmic reticulum organization in relation to polarity.     

Which factors influence the ability of a computational model to predict the in vivo deformation behaviour of skeletal muscle?

Deep tissue injury (DTI) is a severe form of pressure ulcer where tissue damage starts in deep tissues underneath intact skin. Tissue deformation may play an important role in the aetiology, which can be investigated using an experimental–numerical approach. Recently, an animal-specific finite element model has been developed to simulate experiments in which muscle tissue was compressed with an indenter. In this study, the material behaviour and boundary conditions were adapted to improve the agreement between model and experiment and to investigate the influence of these adaptations on the predicted strain distribution. The use of a highly nonlinear material law and including friction between the indenter and the muscle both improved the quality of the model and considerably influenced the estimated strain distribution. With the improved model, the required sample size to detect significant differences between loading conditions can be diminished, which is clearly relevant in experiments involving animals.     

Lemur catta in small forest fragments: Which variables best predict population viability?

Habitat fragmentation is an increasingly serious issue affecting primates in most regions where they are found today. Populations of Lemur catta (ring-tailed lemur) in Madagascar's south-central region are increasingly restricted to small, isolated forest fragments, surrounded by grasslands or small-scale agriculture. Our aim was to evaluate the potential for population viability of L. catta in nine forest fragments of varying sizes (2–46 ha, population range: 6–210 animals) in south-central Madagascar, using a set of comparative, quantitative ecological measures. We used Poisson regression models with a log link function to examine the effects of fragment size, within-fragment food availability, and abundance of matrix resources (food and water sources) on L. catta population sizes and juvenile recruitment. We found a strong association between overall population size and (a) fragment size and (b) abundance of key food resources Melia azedarach and Ficus spp. (per 100 m along transect lines). Juvenile recruitment was also associated with fragment size and abundance of the two above-mentioned food resources. When the largest population, an outlier, was removed from the analysis, again, the model containing fragment size and abundance of M. azedarach and Ficus spp. was the best fitting, but the model that best predicted juvenile recruitment contained only fragment size. While our results are useful for predicting population presence and possible persistence in these fragments, both the potential for male dispersal and the extent of human disturbance within most fragments play crucial roles regarding the likelihood of long-term L. catta survival. While seven of the nine fragments were reasonably protected from human disturbance, only three offered the strong potential for male dispersal, thus the long-term viability of many of these populations is highly uncertain.     

How should clinical data be included in experimental studies of cancer immunology?

Patients diagnosed with the same malignant disease are often heterogeneous with regard to age, complications, malignant cell morphology and tumor histology, disease stage, prognostic parameters, and previous therapy. Many of these factors can affect immunocompetent cells or influence the malignant cell susceptibility to immunotherapy. Summaries of relevant clinical information should therefore be included in cancer immunology studies to increase the present as well as the future scientific impact. Guidelines for selection of relevant information are suggested in the article.     

When should a DDH experiment be mandatory in microbial taxonomy?

DNA–DNA hybridizations (DDH) play a key role in microbial species discrimination in cases when 16S rRNA gene sequence similarities are 97 % or higher. Using real-world 16S rRNA gene sequences and DDH data, we here re-investigate whether or not, and in which situations, this threshold value might be too conservative. Statistical estimates of these thresholds are calculated in general as well as more specifically for a number of phyla that are frequently subjected to DDH. Among several methods to infer 16S gene sequence similarities investigated, most of those routinely applied by taxonomists appear well suited for the task. The effects of using distinct DDH methods also seem to be insignificant. Depending on the investigated taxonomic group, a threshold between 98.2 and 99.0 % appears reasonable. In that way, up to half of the currently conducted DDH experiments could safely be omitted without a significant risk for wrongly differentiated species.     

Which fields under a coverslip should one assess to estimate sperm motility?

Under field conditions the motility of bull semen often has to be estimated under a coverslip on a microscope slide. This study was aimed at determining which combination of fields under coverslips provides measurements of sperm motility that best represent the motility in semen specimens as measured in a specially designed chamber for use in a computer-assisted sperm analyzer (CASA). We measured the motility (percentages motile, progressively motile, and aberrantly motile spermatozoa) in each of four straws of frozen-thawed semen from each of 10 bulls five times, ranging from 5 to 120 minutes after thawing with each bull by straw by time combination yielding one semen specimen. Motility was measured in duplicate in a Hamilton, Thorne IVOS CASA; once in each of 12 fields equally spaced along the equatorial radius of a coverslip (Field 0 at the edge and Field 11 at the center) and once in each of eight equally spaced fields along the equator of a Leja 4 chamber designed for use in a CASA. We used the weighted average motility of all fields in a chamber as gold standard and compared it to the average motility of each the following combinations of fields under the coverslip: all 12 fields, Fields 2 to 4, Fields 2 and four, Field 3 and the center three fields. The concordance correlation coefficient (CCC) was determined between the motility in each combination of fields under coverslips and the chambers as a reproducibility index, which evaluates the agreement between the readings under the coverslips and the gold standard readings in the chambers (n = 187 for each CCC). We performed pairwise comparisons of the CCCs (P < 0.005 for each comparison) and established that the average motility under all 12 fields better reproduced the motility in the chamber than the center three fields or Field 3. The averages of Fields 2 to 4 and Fields 2 and 4 reproduced chamber motility as well as the average of all 12 fields, except for the percentage motile sperm, where the average of all 12 fields was better. Using the average motility of Fields 2 and 4, 50% of estimates fell within 6%, 4% and 3% above or below the percentages motile, progressively motile and aberrantly motile spermatozoa in the Leja 4 chamber, 80% of estimates fell within 12%, 8% and 7% thereof and 95% fell within 23%, 13% and 12% thereof. In conclusion, for the method of spreading semen under a coverslip and the range in motility values used, this study shows that the average of the motility over the 12 fields along the equatorial radius under a coverslip provides the best estimate of the motility of a semen specimen, while the average of Fields 2 and 4 is also suitable for the subjective estimation of motility under field conditions, although the estimated motility is expected to fall within 6% above or below the motility of the specimen in only 50% of semen specimens.     

How much data are needed to resolve a difficult phylogeny?: case study in Lamiales

Reconstructing phylogeny is a crucial target of contemporary biology, now commonly approached through computerized analysis of genetic sequence data. In angiosperms, despite recent progress at the ordinal level, many relationships between families remain unclear. Here we take a case study from Lamiales, an angiosperm order in which interfamilial relationships have so far proved particularly problematic. We examine the effect of changing one factor-the quantity of sequence data analyzed-on phylogeny reconstruction in this group. We use simulation to estimate a priori the sequence data that would be needed to resolve an accurate, supported phylogeny of Lamiales. We investigate the effect of increasing the length of sequence data analyzed, the rate of substitution in the sequences used, and of combining gene partitions. This method could be a valuable technique for planning systematic investigations in other problematic groups. Our results suggest that increasing sequence length is a better way to improve support, resolution, and accuracy than employing sequences with a faster substitution rate. Indeed, the latter may in some cases have detrimental effects on phylogeny reconstruction. Further molecular sequencing-of at least 10,000 bp-should result in a fully resolved and supported phylogeny of Lamiales, but at present the problematic aspects of this tree model remain.     

Do relevant shear forces appear in isokinetic shoulder testing to be implemented in biomechanical models?

Isokinetic dynamometers measure joint torques about a single fixed rotational axis. Previous studies yet suggested that muscles produce both tangential and radial forces during a movement, so that the contact forces exerted to perform this movement are multidirectional. Then, isokinetic dynamometers might neglect the torque components about the two other Euclidean space axes. Our objective was to experimentally quantify the shear forces impact on the overall shoulder torque, by comparing the dynamometer torque to the torque computed from the contact forces at the hand and elbow. Ten healthy women performed isokinetic maximal internal/external concentric/eccentric shoulder rotation movements. The hand and elbow contact forces were measured using two six-axis force sensors. The main finding is that the contact forces at the hand were not purely tangential to the direction of the movement (effectiveness indexes from 0.26 ± 0.25 to 0.54 ± 0.20), such that the resulting shoulder torque computed from the two force sensors was three-dimensional. Therefore, the flexion and abduction components of the shoulder torque measured by the isokinetic dynamometer were significantly underestimated (up to 94.9%). These findings suggest that musculoskeletal models parameters should not be estimated without accounting for the torques about the three space axes.     

Can a reduction approach predict reliable joint contact and musculo-tendon forces?

Musculoskeletal models generally solve the muscular redundancy by numerical optimisation. They have been extensively validated using instrumented implants. Conversely, a reduction approach considers only one flexor or extensor muscle group at the time to equilibrate the inter-segmental joint moment. It is not clear if such models can still predict reliable joint contact and musculo-tendon forces during gait.Tibiofemoral contact force and gastrocnemii, quadriceps, and hamstrings musculo-tendon forces were estimated using a reduction approach for five subjects walking with an instrumented prosthesis. The errors in the proximal-distal tibiofemoral contact force fell in the range (0.3–0.9 body weight) reported in the literature for musculoskeletal models using numerical optimisation. The musculo-tendon forces were in agreement with the EMG envelops and appeared comparable to the ones reported in the literature with generic musculoskeletal models.Although evident simplifications and limitations, it seems that the reduction approach can provided quite reliable results. It can be a useful pedagogical tool in biomechanics, e.g. to illustrate the theoretical differences between inter-segmental and contact forces, and can provide a first estimate of the joint loadings in subjects with limited musculoskeletal deformities and neurological disorders.     

Can root electrical capacitance be used to predict root mass in soil?

Background

Electrical capacitance, measured between an electrode inserted at the base of a plant and an electrode in the rooting substrate, is often linearly correlated with root mass. Electrical capacitance has often been used as an assay for root mass, and is conventionally interpreted using an electrical model in which roots behave as cylindrical capacitors wired in parallel. Recent experiments in hydroponics show that this interpretation is incorrect and a new model has been proposed. Here, the new model is tested in solid substrates.

Methods

The capacitances of compost and soil were determined as a function of water content, and the capacitances of cereal plants growing in sand or potting compost in the glasshouse, or in the field, were measured under contrasting irrigation regimes.

Key Results

Capacitances of compost and soil increased with increasing water content. At water contents approaching field capacity, compost and soil had capacitances at least an order of magnitude greater than those of plant tissues. For plants growing in solid substrates, wetting the substrate locally around the stem base was both necessary and sufficient to record maximum capacitance, which was correlated with stem cross-sectional area: capacitance of excised stem tissue equalled that of the plant in wet soil. Capacitance measured between two electrodes could be modelled as an electrical circuit in which component capacitors (plant tissue or rooting substrate) are wired in series.

Conclusions

The results were consistent with the new physical interpretation of plant capacitance. Substrate capacitance and plant capacitance combine according to standard physical laws. For plants growing in wet substrate, the capacitance measured is largely determined by the tissue between the surface of the substrate and the electrode attached to the plant. Whilst the measured capacitance can, in some circumstances, be correlated with root mass, it is not a direct assay of root mass.     

Scientific discovery as a combinatorial optimisation problem: How best to navigate the landscape of possible experiments?

A considerable number of areas of bioscience, including gene and drug discovery, metabolic engineering for the biotechnological improvement of organisms, and the processes of natural and directed evolution, are best viewed in terms of a 'landscape' representing a large search space of possible solutions or experiments populated by a considerably smaller number of actual solutions that then emerge. This is what makes these problems 'hard', but as such these are to be seen as combinatorial optimisation problems that are best attacked by heuristic methods known from that field. Such landscapes, which may also represent or include multiple objectives, are effectively modelled in silico, with modern active learning algorithms such as those based on Darwinian evolution providing guidance, using existing knowledge, as to what is the 'best' experiment to do next. An awareness, and the application, of these methods can thereby enhance the scientific discovery process considerably. This analysis fits comfortably with an emerging epistemology that sees scientific reasoning, the search for solutions, and scientific discovery as Bayesian processes.     

Can occupancy patterns be used to predict distributions in widely separated geographic regions?

Occupancy models, that describe the presence and absence patterns of a species in a given area, are increasingly being used to predict the occurrence of the species in unsurveyed sites, as an aid to conservation planning. In this paper, we consider whether conclusions about local distributions derived from one landscape can be extrapolated to others. We found that habitat patchiness influenced the distribution and abundance of the host-specific moth Wheeleria spilodactylus in a similar way in two landscapes widely separated geographically. In both geographic regions, the spatial location (positive effect of connectivity), and quantity of resource (positive effect of host plant density) increased the likelihood that the moth would be present, consistent with the expectations of metapopulation dynamics. Though some biological attributes of the species appeared to be slightly different, including population density and the timing of the life cycle (phenology), occupancy patterns in one landscape accurately predict occupancy in the other landscape. Our results suggest that it maybe possible to make predictions from one landscape to another, even when the landscapes are widely separated.     

Combining multiple data sets in a likelihood analysis: which models are the best?

Until recently, phylogenetic analyses have been routinely based on homologous sequences of a single gene. Given the vast number of gene sequences now available, phylogenetic studies are now based on the analysis of multiple genes. Thus, it has become necessary to devise statistical methods to combine multiple molecular data sets. Here, we compare several models for combining different genes for the purpose of evaluating the likelihood of tree topologies. Three methods of branch length estimation were studied: assuming all genes have the same branch lengths (concatenate model), assuming that branch lengths are proportional among genes (proportional model), or assuming that each gene has a separate set of branch lengths (separate model). We also compared three models of among-site rate variation: the homogenous model, a model that assumes one gamma parameter for all genes, and a model that assumes one gamma parameter for each gene. On the basis of two nuclear and one mitochondrial amino acid data sets, our results suggest that, depending on the data set chosen, either the separate model or the proportional model represents the most appropriate method for branch length analysis. For all the data sets examined, one gamma parameter for each gene represents the best model for among-site rate variation. Using these models we analyzed alternative mammalian tree topologies, and we describe the effect of the assumed model on the maximum likelihood tree. We show that the choice of the model has an impact on the best phylogeny obtained.     

Remote-sensing of benthic chlorophyll: should ground-truth data be expressed in units of area or mass?

During low tide, field spectrometric data (350-1050 nm) were acquired from intertidal mudflats in the upper reaches of Sydney Harbour, after which samples of sediment were taken using a small contact core. A total of 103 spectra/sediment pairs of samples were acquired. In the laboratory, amounts of chlorophyll in the contact cores were determined spectrophotometrically. The proportion of fine sediment (<63 μm), a major factor influencing bulk-density of sediment, was measured.The relationship between the remotely sensed observations and the amounts of chlorophyll was investigated by comparing chlorophyll expressed as a mass per unit area (area-normalised values) and as a mass per unit mass (content or weight-normalised values) with: (i) reflectance between 350 and 1050 nm and (ii) a ratio of reflectance at 562 and 647 nm (R562/R647). The reflectance at wavelengths >400 nm were found to be more tightly correlated with area-normalised chlorophyll (maximal correlation=−0.51 at 666 nm) than with weight-normalised chlorophyll (maximal correlation=−0.41 at 664 nm). The relationship between R562/R647 and area-normalised chlorophyll was stronger (R²=0.66) than for weight-normalised chlorophyll (R²=0.47). The residuals from the regression of weight-normalised chlorophyll on R562/R647 were strongly correlated with the mass per unit mass of sediment that was <63 μm. There was no such relationship for residuals from the regression of area-normalised chlorophyll on R562/R647. The results demonstrate conclusively that chlorophyll measured as mass per unit mass of sediment, is inappropriate for ground-truthing remotely sensed observations of chlorophyll in intertidal benthic sediments.