Genetic and phenotypic population divergence on a microgeographic scale in brown trout.

Salmonid populations of many rivers are rapidly declining. One possible explanation is that habitat fragmentation increases genetic drift and reduces the populations' potential to adapt to changing environmental conditions. We measured the genetic and eco-morphological diversity of brown trout (Salmo trutta) in a Swiss stream system, using multivariate statistics and Bayesian clustering. We found large genetic and phenotypic variation within only 40 km of stream length. Eighty-eight percent of all pairwise F(ST) comparisons and 50% of the population comparisons in body shape were significant. High success rates of population assignment tests confirmed the distinctiveness of populations in both genotype and phenotype. Spatial analysis revealed that divergence increased with waterway distance, the number of weirs, and stretches of poor habitat between sampling locations, but effects of isolation-by-distance and habitat fragmentation could not be fully disentangled. Stocking intensity varied between streams but did not appear to erode genetic diversity within populations. A lack of association between phenotypic and genetic divergence points to a role of local adaptation or phenotypically plastic responses to habitat heterogeneity. Indeed, body shape could be largely explained by topographic stream slope, and variation in overall phenotype matched the flow regimes of the respective habitats.

Adaptive divergence of ancient gene duplicates in the avian MHC class II beta.

Gene duplication and neofunctionalization are known to be important processes in the evolution of phenotypic complexity. They account for important evolutionary novelties that confer ecological adaptation, such as the major histocompatibility complex (MHC), a multigene family crucial to the vertebrate immune system. In birds, two MHC class II β (MHCIIβ) exon 3 lineages have been recently characterized, and two hypotheses for the evolutionary history of MHCIIβ lineages were proposed. These lineages could have arisen either by 1) an ancient duplication and subsequent divergence of one paralog or by 2) recent parallel duplications followed by functional convergence. Here, we compiled a data set consisting of 63 MHCIIβ exon 3 sequences from six avian orders to distinguish between these hypotheses and to understand the role of selection in the divergent evolution of the two avian MHCIIβ lineages. Based on phylogenetic reconstructions and simulations, we show that a unique duplication event preceding the major avian radiations gave rise to two ancestral MHCIIβ lineages that were each likely lost once later during avian evolution. Maximum likelihood estimation shows that following the ancestral duplication, positive selection drove a radical shift from basic to acidic amino acid composition of a protein domain facing the α-chain in the MHCII α β-heterodimer. Structural analyses of the MHCII α β-heterodimer highlight that three of these residues are potentially involved in direct interactions with the α-chain, suggesting that the shift following duplication may have been accompanied by coevolution of the interacting α- and β-chains. These results provide new insights into the long-term evolutionary relationships among avian MHC genes and open interesting perspectives for comparative and population genomic studies of avian MHC evolution.

Dual-wavelength digital holographic microscopy with sub-nanometer axial accuracy

We present dual-wavelength Digital Holographic Microscopy (DHM) measurements on a certified 8.9 nm high Chromium thin step sample and demonstrate sub-nanometer axial accuracy. We introduce a modified DHM Reference Calibrated Hologram (RCH) reconstruction algorithm taking into account amplitude contributions. By combining this with a temporal averaging procedure and a specific dual-wavelength DHM arrangement, it is shown that specimen topography can be measured with an accuracy, defined as the axial standard deviation, reduced to at least 0.9 nm. Indeed, it is reported that averaging each of the two wavefronts recorded with real-time dual-wavelength DHM can provide up to 30% spatial noise reduction for the given configuration, thanks to their non-correlated nature. ©2008 COPYRIGHT SPIE

Post-axial polydactyly type A2, overgrowth and autistic traits associated with a chromosome 13q31.3 microduplication encompassing miR-17-92 and GPC5.

Genomic rearrangements at chromosome 13q31.3q32.1 have been associated with digital anomalies, dysmorphic features, and variable degree of mental disability. Microdeletions leading to haploinsufficiency of miR17∼92, a cluster of micro RNA genes closely linked to GPC5 in both mouse and human genomes, has recently been associated with digital anomalies in the Feingold like syndrome. Here, we report on a boy with familial dominant post-axial polydactyly (PAP) type A, overgrowth, significant facial dysmorphisms and autistic traits who carries the smallest germline microduplication known so far in that region. The microduplication encompasses the whole miR17∼92 cluster and the first 5 exons of GPC5. This report supports the newly recognized role of miR17∼92 gene dosage in digital developmental anomalies, and suggests a possible role of GPC5 in growth regulation and in cognitive development.

De novo characterization of the Timema cristinae transcriptome facilitates marker discovery and inference of genetic divergence.

Adaptation to different ecological environments can promote speciation. Although numerous examples of such 'ecological speciation' now exist, the genomic basis of the process, and the role of gene flow in it, remains less understood. This is, at least in part, because systems that are well characterized in terms of their ecology often lack genomic resources. In this study, we characterize the transcriptome of Timema cristinae stick insects, a system that has been researched intensively in terms of ecological speciation, but for which genomic resources have not been previously developed. Specifically, we obtained >1 million 454 sequencing reads that assembled into 84,937 contigs representing approximately 18,282 unique genes and tens of thousands of potential molecular markers. Second, as an illustration of their utility, we used these genomic resources to assess multilocus genetic divergence within both an ecotype pair and a species pair of Timema stick insects. The results suggest variable levels of genetic divergence and gene flow among taxon pairs and genes and illustrate a first step towards future genomic work in Timema.

Direct MR arthrography of the shoulder under axial traction: Feasibility study to evaluate the superior labrum-biceps tendon complex and articular cartilage.

PURPOSE: To assess the value of adding axial traction to direct MR arthrography of the shoulder, in terms of subacromial and glenohumeral joint space widths, and coverage of the superior labrum-biceps tendon complex and articular cartilage by contrast material. MATERIALS AND METHODS: Twenty-one patients investigated by direct MR arthrography of the shoulder were prospectively included. Studies were performed with a 3 Tesla (T) unit and included a three-dimensional isotropic fat-suppressed T1-weighted gradient-recalled echo sequence, without and with axial traction (4 kg). Two radiologists independently measured the width of the subacromial, superior, and inferior glenohumeral joint spaces. They subsequently rated the amount of contrast material around the superior labrum-biceps tendon complex and between glenohumeral cartilage surfaces, using a three-point scale: 0 = no, 1 = partial, 2 = full. RESULTS: Under traction, the subacromial (Δ = 2.0 mm, P = 0.0003), superior (Δ = 0.7 mm, P = 0.0001) and inferior (Δ = 1.4 mm, P = 0.0006) glenohumeral joint space widths were all significantly increased, and both readers noted significantly more contrast material around the superior labrum-biceps tendon complex (P = 0.014), and between the superior (P = 0.001) and inferior (P = 0.025) glenohumeral cartilage surfaces. CONCLUSION: Direct MR arthrography of the shoulder under axial traction increases subacromial and glenohumeral joint space widths, and prompts better coverage of the superior labrum-biceps tendon complex and articular cartilage by contrast material. J. Magn. Reson. Imaging 2013;37:1228-1233. © 2012 Wiley Periodicals, Inc.

Direct magnetic resonance arthrography of the knee: utility of axial traction.

The purpose of this study was to determine the impact of axial traction during acquisition of direct magnetic resonance (MR) arthrography examination of the knee in terms of joint space width and amount of contrast material between the cartilage surfaces. Direct knee MR arthrography was performed in 11 patients on a 3-T MR imaging unit using a T1-weighted isotropic gradient echo sequence in a coronal plane with and without axial traction of 15 kg. Joint space widths were measured at the level of the medial and the lateral femorotibial joint with and without traction. The amount of contrast material in the medial and lateral femorotibial joint was assessed independently by two musculoskeletal radiologists in a semiquantitative manner using three grades ('absence of surface visualization, 'partial surface visualization or 'complete surface visualization'). With traction, joint space width increased significantly at the lateral femorotibial compartment (mean = 0.55 mm, p = 0.0105) and at the medial femorotibial compartment (mean = 0.4 mm, p = 0.0124). There was a trend towards an increased amount of contrast material in the femorotibial compartment with axial traction. Direct MR arthrography of the knee with axial traction showed a slight and significant increase of the width of the femorotibial compartment with a trend towards more contrast material between the articular cartilage surfaces.

Developmental and Environmental Regulation of Aquaporin Gene Expression across Populus Species: Divergence or Redundancy?

Aquaporins (AQPs) are membrane channels belonging to the major intrinsic proteins family and are known for their ability to facilitate water movement. While in Populus trichocarpa, AQP proteins form a large family encompassing fifty-five genes, most of the experimental work focused on a few genes or subfamilies. The current work was undertaken to develop a comprehensive picture of the whole AQP gene family in Populus species by delineating gene expression domain and distinguishing responsiveness to developmental and environmental cues. Since duplication events amplified the poplar AQP family, we addressed the question of expression redundancy between gene duplicates. On these purposes, we carried a meta-analysis of all publicly available Affymetrix experiments. Our in-silico strategy controlled for previously identified biases in cross-species transcriptomics, a necessary step for any comparative transcriptomics based on multispecies design chips. Three poplar AQPs were not supported by any expression data, even in a large collection of situations (abiotic and biotic constraints, temporal oscillations and mutants). The expression of 11 AQPs was never or poorly regulated whatever the wideness of their expression domain and their expression level. Our work highlighted that PtTIP1;4 was the most responsive gene of the AQP family. A high functional divergence between gene duplicates was detected across species and in response to tested cues, except for the root-expressed PtTIP2;3/PtTIP2;4 pair exhibiting 80% convergent responses. Our meta-analysis assessed key features of aquaporin expression which had remained hidden in single experiments, such as expression wideness, response specificity and genotype and environment interactions. By consolidating expression profiles using independent experimental series, we showed that the large expansion of AQP family in poplar was accompanied with a strong divergence of gene expression, even if some cases of functional redundancy could be suspected.

Digital holographic microscopy: a noninvasive contrast imaging technique allowing quantitative visualization of living cells with subwavelength axial accuracy.

We have developed a digital holographic microscope (DHM), in a transmission mode, especially dedicated to the quantitative visualization of phase objects such as living cells. The method is based on an original numerical algorithm presented in detail elsewhere [Cuche et al., Appl. Opt. 38, 6994 (1999)]. DHM images of living cells in culture are shown for what is to our knowledge the first time. They represent the distribution of the optical path length over the cell, which has been measured with subwavelength accuracy. These DHM images are compared with those obtained by use of the widely used phase contrast and Nomarski differential interference contrast techniques.

Axial sub-nanometer accuracy in digital holographic microscopy

We present state-of-the-art dual-wavelength digital holographic microscopy (DHM) measurement on a calibrated 8.9 nm high chromium thin step sample and demonstrate sub-nanometer axial accuracy. By using a modified DHM reference calibrated hologram (RCH) reconstruction method, a temporal averaging procedure and a specific dual-wavelength DHM arrangement, it is shown that specimen topography can be measured with an accuracy, defined as the axial standard deviation, reduced to at least 0.9 nm. Indeed for the first time to the best of our knowledge, it is reported that averaging each of the two wavefronts recorded with real-time dual-wavelength DHM can provide up to 30% spatial noise reduction for the given configuration. Moreover, the presented experimental configuration achieves a temporal stability below 0.8 nm, thus paving the way to Angström range for dual-wavelength DHM.