The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals

Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced by integrating multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). It is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of normal gene expression. Curation includes very large datasets such as GTEx (re-annotation of samples as ‘healthy’ or not) as well as many small ones. Data are integrated and made comparable between species thanks to consistent data annotation and processing, and to calls of presence/absence of expression, along with expression scores. As a result, Bgee is capable of detecting the conditions of expression of any single gene, accommodating any data type and species. Bgee provides several tools for analyses, allowing, e.g., automated comparisons of gene expression patterns within and between species, retrieval of the prefered conditions of expression of any gene, or enrichment analyses of conditions with expression of sets of genes. Bgee release 14.1 includes 29 animal species, and is available at https://bgee.org/ and through its Bioconductor R package BgeeDB.

Sensory and Behavioral Components of Neocortical Signal Flow in Discrimination Tasks with Short-Term Memory

In the neocortex, each sensory modality engages distinct sensory areas that route information to association areas. Where signal flow converges for maintaining information in short-term memory and how behavior may influence signal routing remain open questions. Using wide-field calcium imaging, we compared cortex-wide neuronal activity in layer 2/3 for mice trained in auditory and tactile tasks with delayed response. In both tasks, mice were either active or passive during stimulus presentation, moving their body or sitting quietly. Irrespective of behavioral strategy, auditory and tactile stimulation activated distinct subdivisions of the posterior parietal cortex, anterior area A and rostrolateral area RL, which held stimulus-related information necessary for the respective tasks. In the delay period, in contrast, behavioral strategy rather than sensory modality determined short-term memory location, with activity converging frontomedially in active trials and posterolaterally in passive trials. Our results suggest behavior-dependent routing of sensory-driven cortical signals flow from modality-specific posterior parietal cortex (PPC) subdivisions to higher association areas.

Layer-Specific Refinement of Sensory Coding in Developing Mouse Barrel Cortex

Rodent rhythmic whisking behavior matures during a critical period around 2 weeks after birth. The functional adaptations of neocortical circuitry during this developmental period remain poorly understood. Here, we characterized stimulus-evoked neuronal activity across all layers of mouse barrel cortex before, during, and after the onset of whisking behavior. Employing multi-electrode recordings and 2-photon calcium imaging in anesthetized mice, we tested responses to rostro-caudal whisker deflections, axial "tapping" stimuli, and their combination from postnatal day 10 (P10) to P28. Within this period, whisker-evoked activity of neurons displayed a general decrease in layer 2/3 (L2/3) and L4, but increased in L5 and L6. Distinct alterations in neuronal response adaptation during the 2-s period of stimulation at ~5 Hz accompanied these changes. Moreover, single-unit analysis revealed that response selectivity in favor of either lateral deflection or axial tapping emerges in deeper layers within the critical period around P14. For superficial layers we confirmed this finding using calcium imaging of L2/3 neurons, which also exhibited emergence of response selectivity as well as progressive sparsification and decorrelation of evoked responses around P14. Our results demonstrate layer-specific development of sensory responsiveness and response selectivity in mouse somatosensory cortex coinciding with the onset of exploratory behavior.

Accuracy of a smartphone pedometer application according to different speeds and mobile phone locations in a laboratory context

Background

The purpose of this study was to compare the accuracy of a smartphone application and a mechanical pedometer for step counting at different walking speeds and mobile phone locations in a laboratory context.

Methods

Seventeen adults wore an iPphone6© with Runtastic Pedometer© application (RUN), at 3 different locations (belt, arm, jacket) and a pedometer (YAM) at the waist. They were asked to walk on an instrumented treadmill (reference) at various speeds (2, 4 and 6 km/h).

Results

RUN was more accurate than YAM at 2 km/h (p < 0.05) and at 4 km/h (p = 0.03). At 6 km/h the two devices were equally accurate. The precision of YAM increased with speed (p < 0.05), while for RUN, the results were not significant but showed a trend (p = 0.051). Surprisingly, YAM underestimates the number of step by 60.5% at 2 km/h. The best accurate step counting (0.7% mean error) was observed when RUN is attached to the arm and at the highest speed.

Conclusions

RUN pedometer application could be recommended mainly for walking sessions even for low walking speed. Moreover, our results confirm that the smartphone should be strapped close to the body to discriminate steps from noise by the accelerometers (particularly at low speed).

Selectome update: quality control and computational improvements to a database of positive selection

Selectome (http://selectome.unil.ch/) is a database of positive selection, based on a branch-site likelihood test. This model estimates the number of nonsynonymous substitutions (dN) and synonymous substitutions (dS) to evaluate the variation in selective pressure (dN/dS ratio) over branches and over sites. Since the original release of Selectome, we have benchmarked and implemented a thorough quality control procedure on multiple sequence alignments, aiming to provide minimum false-positive results. We have also improved the computational efficiency of the branch-site test implementation, allowing larger data sets and more frequent updates. Release 6 of Selectome includes all gene trees from Ensembl for Primates and Glires, as well as a large set of vertebrate gene trees. A total of 6810 gene trees have some evidence of positive selection. Finally, the web interface has been improved to be more responsive and to facilitate searches and browsing.