Histopathology reveals correlative and unique phenotypes in a high-throughput mouse phenotyping screen

The Mouse Genetics Project (MGP) at the Wellcome Trust Sanger Institute aims to generate and phenotype over 800 genetically modified mouse lines over the next 5 years to gain a better understanding of mammalian gene function and provide an invaluable resource to the scientific community for follow-up studies. Phenotyping includes the generation of a standardized biobank of paraffin-embedded tissues for each mouse line, but histopathology is not routinely performed. In collaboration with the Pathology Core of the Centre for Modeling Human Disease (CMHD) we report the utility of histopathology in a high-throughput primary phenotyping screen. Histopathology was assessed in an unbiased selection of 50 mouse lines with (n=30) or without (n=20) clinical phenotypes detected by the standard MGP primary phenotyping screen. Our findings revealed that histopathology added correlating morphological data in 19 of 30 lines (63.3%) in which the primary screen detected a phenotype. In addition, seven of the 50 lines (14%) presented significant histopathology findings that were not associated with or predicted by the standard primary screen. Three of these seven lines had no clinical phenotype detected by the standard primary screen. Incidental and strain-associated background lesions were present in all mutant lines with good concordance to wild-type controls. These findings demonstrate the complementary and unique contribution of histopathology to high-throughput primary phenotyping of mutant mice.KEY WORDS: Histopathology, High-throughput phenotyping, Mouse, Pathology     

Leginon: New features and applications

Leginon is a system for automated data acquisition from a transmission electron microscope. Here we provide an updated summary of the overall Leginon architecture and an update of the current state of the package. We also highlight a few recent developments to provide some concrete examples and use cases.     

Deconvolution of pigment and physiologically related photochemical reflectance index variability at the canopy scale over an entire growing season

The sensitivity of the photochemical reflectance index (PRI) to leaf pigmentation and its impacts on its potential as a proxy for light‐use efficiency (LUE) have recently been shown to be problematic at the leaf scale. Most leaf‐to‐leaf and seasonal variability can be explained by such a confounding effect. This study relies on the analysis of PRI light curves that were generated at the canopy scale under natural conditions to derive a precise deconvolution of pigment‐related and physiologically related variability in the PRI. These sources of variability were explained by measured or estimated physiologically relevant variables, such as soil water content, that can be used as indicators of water availability and canopy chlorophyll content. The PRI mainly reflected the variability in the pigment content of the canopy. However, the corrected PRI, which was obtained by subtracting the pigment‐related seasonal variability from the PRI measurement, was highly correlated with the upscaled LUE measurements. Moreover, the sensitivity of the PRI to the leaf pigment content may mask the PRI versus LUE relationship or result in an artificial relationship that reflects the relationship of chlorophyll versus LUE, depending on the species phenology.     

Genomic and functional analysis of Vibrio phage SIO-2 reveals novel insights into ecology and evolution of marine siphoviruses

We report on a genomic and functional analysis of a novel marine siphovirus, the Vibrio phage SIO-2. This phage is lytic for related Vibrio species of great ecological interest including the broadly antagonistic bacterium Vibrio sp. SWAT3 as well as notable members of the Harveyi clade (V.harveyi ATTC BAA-1116 and V.campbellii ATCC 25920). Vibrio phage SIO-2 has a circularly permuted genome of 80598 bp, which displays unusual features. This genome is larger than that of most known siphoviruses and only 38 of the 116 predicted proteins had homologues in databases. Another divergence is manifest by the origin of core genes, most of which share robust similarities with unrelated viruses and bacteria spanning a wide range of phyla. These core genes are arranged in the same order as in most bacteriophages but they are unusually interspaced at two places with insertions of DNA comprising a high density of uncharacterized genes. The acquisition of these DNA inserts is associated with morphological variation of SIO-2 capsid, which assembles as a large (80 nm) shell with a novel T=12 symmetry. These atypical structural features confer on SIO-2 a remarkable stability to a variety of physical, chemical and environmental factors. Given this high level of functional and genomic novelty, SIO-2 emerges as a model of considerable interest in ecological and evolutionary studies.     

Sediment accumulation predicts the distribution of a unionid mussel (Elliptio complanata) in nearshore areas of a Canadian Shield lake

1. The importance of native freshwater mussels for ecosystem processes depends on their density, size distribution and activity. In lakes, many of the factors that affect mussels (fish hosts, habitat, food) could be directly or indirectly related to wind‐driven physical processes. 2. We tested whether the abundance and size of Elliptio complanata in the shallow, nearshore areas of a medium‐sized lake were related to site exposure, substratum type and fish distribution. To disentangle some of the correlated variables known to affect mussel distribution, we used paired exposed and sheltered sampling sites along the 7‐km fetch of the lake basin. 3. The distribution of sediment characteristics in nearshore areas was highly predictable. The mean depth of accumulated soft sediments decreased with increasing fetch at wind‐exposed sites, but increased with increasing fetch at sheltered sites. Sediments were deeper along the main shoreline than around islands. Deeper sediments tended to be finer and higher in silt content and organic fraction. 4. The density and proportion of juvenile mussels along the main shoreline varied in a unimodal way with sediment depth. These results suggest that wind‐driven physical forces affect the transport of young juveniles to sediment depositional areas and create sediment conditions that influence their growth and survival. In contrast, the proportion of juvenile mussels around islands was not related to sediment characteristics, but decreased with remoteness of the island, suggesting that the distribution of juvenile mussels may be limited by fish movements. These results are tentative since they do not include buried juvenile mussels. 5. We also found a unimodal relationship between total mussel density (juveniles and adults) and sediment depth but, in contrast to the relationship for juveniles only, it applied to all sites with soft sediments, including islands. We conclude that factors related to sediment depth affect the growth and survival of adult mussels around islands and that these factors are strong enough to modify the pattern of distribution established via dispersal during earlier life stages. 6. The mean shell length of adults at different sites within the lake basin ranged from 60 to 85 mm. Mussel shell length decreased with increasing fetch at sites exposed to the prevalent winds, but was relatively constant on the sheltered side of peninsulas and islands. The size of unionid mussels in different parts of the lake seems to be determined both by their exposure to physical forces and by sediments. 7. The local distribution of E. complanata is determined, directly and indirectly, by wind‐driven forces. These processes are likely to be important for other benthic organisms affected by similar habitat conditions (e.g. sediment characteristics, physical disturbance).     

The Leeds Evaluation of Efficacy of Detoxification Study (LEEDS) Prisons Project Study: protocol for a randomised controlled trial comparing methadone and buprenorphine for opiate detoxification

Many research-funding agencies now require open access to the results of research they have funded, and some also require that researchers make available the raw data generated from that research. Similarly, the journal Trials aims to address inadequate reporting in randomised controlled trials, and in order to fulfil this objective, the journal is working with the scientific and publishing communities to try to establish best practice for publishing raw data from clinical trials in peer-reviewed biomedical journals. Common issues encountered when considering raw data for publication include patient privacy – unless explicit consent for publication is obtained – and ownership, but agreed-upon policies for tackling these concerns do not appear to be addressed in the guidance or mandates currently established. Potential next steps for journal editors and publishers, ethics committees, research-funding agencies, and researchers are proposed, and alternatives to journal publication, such as restricted access repositories, are outlined.     

Automated three-dimensional reconstruction of keyhole limpet hemocyanin type 1

We have reconstructed a three-dimensional map of keyhole limpet hemocyanin isoform 1 (KLH1), using our automated data collection software, Leginon, integrated with particle selection algorithms, and the SPIDER reconstruction package. KLH1, a 7.9 MDa macromolecule, is an extracellular respiratory pigment composed of two asymmetric decamers, and presents an overall D(5) point-group symmetry. The reconstruction is in agreement with previous data published on molluscan hemocyanins. The reconstructed map (11.3A resolution, 3sigma criterion) was used to fit an available X-ray crystallography structure of Octopus dofleini Odg, solved at 2.3A [J. Mol. Biol. 278 (4) (1998) 855], with satisfactory results. The results validate the approach of automating the cryoEM process and demonstrate that the quality of the images acquired and the particles selected is comparable to those obtained using manual methods. Several problems remain to be solved however before these results can be generalized.     

v-Src's hold over actin and cell adhesions

The oncoprotein v-Src and its cellular homologue (c-Src) are tyrosine kinases that modulate the actin cytoskeleton and cell adhesions. Through the concerted action of their protein-interaction and kinase domains, they are targeted to cell matrix integrin adhesions or cadherin-dependent junctions between epithelial cells, where they phosphorylate substrates that induce adhesion turnover and actin re-modelling. Recent experiments have defined some of the key targets and effector pathways that mediate the pleiotropic oncogenic effects of v-Src.     

Cleavage of focal adhesion kinase by different proteases during SRC-regulated transformation and apoptosis. Distinct roles for calpain and caspases

Integrin-associated focal adhesion complexes provide the main adhesive links between the cellular actin cytoskeleton and the surrounding extracellular matrix. In vitro, cells utilize a complex temporal and spatially regulated mechanism of focal adhesion assembly and disassembly required for cell migration. Recent studies indicate that members of both calpain and caspase protease families can promote limited proteolytic cleavage of several components of focal adhesions leading to disassembly of these complexes. Such mechanisms that influence cell adhesion may be deregulated under pathological conditions characterized by increased cell motility, such as tumor invasion. v-Src-induced oncogenic transformation is associated with loss of focal adhesion structures and transition to a less adherent, more motile phenotype, while inactivating temperature-sensitive v-Src in serum-deprived transformed cells leads to detachment and apoptosis. In this report, we demonstrate that v-Src-induced disassembly of focal adhesions is accompanied by calpain-dependent proteolysis of focal adhesion kinase. Furthermore, inhibitors of calpain repress v-Src-induced focal adhesion disruption, loss of substrate adhesion, and cell migration. In contrast, focal adhesion loss during detachment and apoptosis induced after switching off temperature-sensitive v-Src in serum-deprived transformed cells is accompanied by caspase-mediated proteolysis of focal adhesion kinase. Thus, calpain and caspase differentially regulate focal adhesion turnover during Src-regulated cell transformation, motility, and apoptosis.