Gene duplication within the Green Lineage: the case of TEL genes

Recent years have witnessed a breathtaking increase in the availability of genome sequence data, providing evidence of the highly duplicate nature of eukaryotic genomes. Plants are exceptional among eukaryotic organisms in that duplicate loci compose a large fraction of their genomes, partly because of the frequent occurrence of polyploidy (or whole-genome duplication) events. Tandem gene duplication and transposition have also contributed to the large number of duplicated genes in plant genomes. Evolutionary analyses allowed the dynamics of duplicate gene evolution to be studied and several models were proposed. It seems that, over time, many duplicated genes were lost and some of those that were retained gained new functions and/or expression patterns (neofunctionalization) or subdivided their functions and/or expression patterns between them (subfunctionalization). Recent studies have provided examples of genes that originated by duplication with successive diversification within plants. In this review, we focused on the TEL (TERMINAL EAR1-like) genes to illustrate such mechanisms. Emerged from the mei2 gene family, these TEL genes are likely to be land plant-specific. Phylogenetic analyses revealed one or two TEL copies per diploid genome. TEL gene degeneration and loss in several Angiosperm species such as in poplar and maize seem to have occurred. In Arabidopsis thaliana, whose genome experienced at least three polyploidy events followed by massive gene loss and genomic reorganization, two TEL genes were retained and two new shorter TEL-like (MCT) genes emerged. Molecular and expression analyses suggest for these genes sub- and neofunctionalization events, but confirmation will come from their functional characterization.     

Shear stress induces cell apoptosis via a c-Src-phospholipase D-mTOR signaling pathway in cultured podocytes

The glomerular capillary wall, composed of endothelial cells, the glomerular basement membrane and the podocytes, is continually subjected to hemodynamic force arising from tractional stress due to blood pressure and shear stress due to blood flow. Exposure of glomeruli to abnormal hemodynamic force such as hyperfiltration is associated with glomerular injury and progressive renal disease, and the conversion of mechanical stimuli to chemical signals in the regulation of the process is poorly understood in podocytes. By examining DNA fragmentation, apoptotic nuclear changes and cytochrome c release, we found that shear stress induced cell apoptosis in cultured podocytes. Meanwhile, podocytes exposed to shear stress also stimulated c-Src phosphorylation, phospholipase D (PLD) activation and mammalian target of rapamycin (mTOR) signaling. Using the antibodies against c-Src, PLD(1), and PLD(2) to perform reciprocal co-immunoprecipitations and in vitro PLD activity assay, our data indicated that c-Src interacted with and activated PLD(1) but not PLD(2). The inhibition of shear stress-induced c-Src phosphorylation by PP(2) (a specific inhibitor of c-Src kinase) resulted in reduced PLD activity. Phosphatidic acid, produced by shear stress-induced PLD activation, stimulated mTOR signaling, and caused podocyte hypertrophy and apoptosis.     

Status of resistance to Bt maize in Spodoptera frugiperda: lessons from Puerto Rico

In 2006, reports of potential Spodoptera frugiperda resistance to TC1507 maize in Puerto Rico were received. Subsequent investigation confirmed that pest populations collected from several sites in Puerto Rico were largely unaffected by the Cry1F protein in bioassays, with resistance ratios likely in excess of 1000. Since then, we have continued monitoring populations in Puerto Rico and in southern areas of the mainland US. The majority of the collections from Puerto Rico continue to show high levels of Cry1F resistance whereas populations collected from the southern US mainland continue to show full susceptibility to Cry1F and TC1507 maize. It does not appear that resistant populations have spread to any measurable extent from Puerto Rico to mainland US, nor that local selection pressure from Cry1F-expressing maize or cotton production in the southern US has caused a measurable change in population susceptibility. Lessons learned from Puerto Rico are being applied in other parts of the Americas where TC1507 maize is grown and additional steps being taken to protect the long-term durability of Cry1F in maize in areas where similar selection pressure may be expected. Tactics include using locally-adapted germplasm that contain native Spodoptera resistance, a robust education program to teach end-users about the potential for resistance to develop appropriate crop stewardship, resistance monitoring, and the use of insecticides under high S. frugiperda pressure. Perhaps most importantly, pyramided trait products that produce two or more different Bt proteins are being introduced to further delay resistance development to Cry1F.     

Warming and increased precipitation frequency on the Colorado Plateau: implications for biological soil crusts and soil processes

Aims

Changes in temperature and precipitation are expected to influence ecosystem processes worldwide. Despite their globally large extent, few studies to date have examined the effects of climate change in desert ecosystems, where biological soil crusts are key nutrient cycling components. The goal of this work was to assess how increased temperature and frequency of summertime precipitation affect the contributions of crust organisms to soil processes.

Methods

With a combination of experimental 2°C warming and altered summer precipitation frequency applied over 2?years, we measured soil nutrient cycling and the structure and function of crust communities.

Results

We saw no change in crust cover, composition, or other measures of crust function in response to 2°C warming and no effects on any measure of soil chemistry. In contrast, crust cover and function responded to increased frequency of summer precipitation, shifting from moss to cyanobacteria-dominated crusts; however, in the short timeframe we measured, there was no accompanying change in soil chemistry. Total bacterial and fungal biomass was also reduced in watered plots, while the activity of two enzymes increased, indicating a functional change in the microbial community.

Conclusions

Taken together, our results highlight the limited effects of warming alone on biological soil crust communities and soil chemistry, but demonstrate the substantially larger effects of altered summertime precipitation.     

Mouse large-scale phenotyping initiatives: overview of the European Mouse Disease Clinic (EUMODIC) and of the Wellcome Trust Sanger Institute Mouse Genetics Project

Two large-scale phenotyping efforts, the European Mouse Disease Clinic (EUMODIC) and the Wellcome Trust Sanger Institute Mouse Genetics Project (SANGER-MGP), started during the late 2000s with the aim to deliver a comprehensive assessment of phenotypes or to screen for robust indicators of diseases in mouse mutants. They both took advantage of available mouse mutant lines but predominantly of the embryonic stem (ES) cells resources derived from the European Conditional Mouse Mutagenesis programme (EUCOMM) and the Knockout Mouse Project (KOMP) to produce and study 799 mouse models that were systematically analysed with a comprehensive set of physiological and behavioural paradigms. They captured more than 400 variables and an additional panel of metadata describing the conditions of the tests. All the data are now available through EuroPhenome database (www.europhenome.org) and the WTSI mouse portal (http://www.sanger.ac.uk/mouseportal/), and the corresponding mouse lines are available through the European Mouse Mutant Archive (EMMA), the International Knockout Mouse Consortium (IKMC), or the Knockout Mouse Project (KOMP) Repository. Overall conclusions from both studies converged, with at least one phenotype scored in at least 80?% of the mutant lines. In addition, 57?% of the lines were viable, 13?% subviable, 30?% embryonic lethal, and 7?% displayed fertility impairments. These efforts provide an important underpinning for a future global programme that will undertake the complete functional annotation of the mammalian genome in the mouse model.     

Leaf evolution in Southern Hemisphere conifers tracks the angiosperm ecological radiation

The angiosperm radiation has been linked to sharp declines in gymnosperm diversity and the virtual elimination of conifers from the tropics. The conifer family Podocarpaceae stands as an exception with highest species diversity in wet equatorial forests. It has been hypothesized that efficient light harvesting by the highly flattened leaves of several podocarp genera facilitates persistence with canopy-forming angiosperms, and the angiosperm ecological radiation may have preferentially favoured the diversification of these lineages. To test these ideas, we develop a molecular phylogeny for Podocarpaceae using Bayesian-relaxed clock methods incorporating fossil time constraints. We find several independent origins of flattened foliage types, and that these lineages have diversified predominantly through the Cenozoic and therefore among canopy-forming angiosperms. The onset of sustained foliage flattening podocarp diversification is coincident with a declining diversification rate of scale/needle-leaved lineages and also with ecological and climatic transformations linked to angiosperm foliar evolution. We demonstrate that climatic range evolution is contingent on the underlying state for leaf morphology. Taken together, our findings imply that as angiosperms came to dominate most terrestrial ecosystems, competitive interactions at the foliar level have profoundly shaped podocarp geography and as a consequence, rates of lineage diversification.     

Integrin cytoplasmic domain-associated protein-1 (ICAP-1) interacts with the ROCK-I kinase at the plasma membrane

The integrin cytoplasmic domain-associated protein-1 (ICAP-1) binds via its C-terminal PTB (phosphotyrosine-binding) domain to the cytoplasmic tails of beta1 but not other integrins. Using the yeast two-hybrid assay, we found that ICAP-1 binds the ROCK-I kinase, an effector of the RhoA GTPase. By coimmunoprecipitation we show that ICAP-1 and ROCK form complexes in cells and that ICAP-1 contains two binding sites for ROCK. In cells transfected with both ICAP-1 and ROCK, the proteins colocalized at the cell membrane predominantly in lamellipodia and membrane ruffles, but also in retraction fibers. ROCK was not found at these sites when ICAP-1 was not co-transfected, indicating that ICAP-1 translocated ROCK. In lamellipodia ICAP-1 and ROCK colocalized with endogenous beta1 integrins and this colocalization was also observed with the isolated ICAP-1 PTB domain. The plasma membrane localization of ROCK did not depend on beta1 integrin ligation or ROCK kinase activity, and in truncated ROCK proteins it required the presence of the ICAP-1-binding domain. To show that the interaction was direct, we measured fluorescence resonance energy transfer (FRET) between cyan fluorescent protein (CFP) fused to ICAP-1 and yellow fluorescent protein (YFP) fused to ROCK. FRET was observed in lamellipodia in cells that were induced to spread. These results indicate that ICAP-1-mediated binding of ROCK to beta1 integrin serves to localize the ROCK-I kinase to both the leading edge and the trailing edge where ROCK affects cell migration.     

The cellular basis for enhanced volume-modulated cardiac output in fish hearts

During vertebrate evolution there has been a shift in the way in which the heart varies cardiac output (the product of heart rate and stroke volume). While mammals, birds, and amphibians increase cardiac output through large increases in heart rate and only modest increases (approximately 30%) in stroke volume, fish and some reptiles use modest increases in heart rate and very large increases in stroke volume (up to 300%). The cellular mechanisms underlying these fundamentally different approaches to cardiac output modulation are unknown. We hypothesized that the divergence between volume modulation and frequency modulation lies in the response of different vertebrate myocardium to stretch. We tested this by progressively stretching individual cardiac myocytes from the fish heart while measuring sarcomere length (SL), developed tension, and intracellular Ca2+ ([Ca2+]i) transients. We show that in fish cardiac myocytes, active tension increases at SLs greater than those previously demonstrated for intact mammalian myocytes, representing a twofold increase in the functional ascending limb of the length-tension relationship. The mechanism of action is a length-dependent increase in myofilament Ca2+ sensitivity, rather than changes in the [Ca2+]i transient or actin filament length in the fish cell. The capacity for greater sarcomere extension in fish myocardium may be linked to the low resting tension that is developed during stretch. These adaptations allow the fish heart to volume modulate and thus underpin the fundamental difference between the way fish and higher vertebrates vary cardiac output.     

An in vitro model for analysing neutrophil migration into and away from the sub-endothelial space: Roles of flow and CD31

To model the later stages of neutrophil migration into tissue, we developed an assay in which human umbilical vein endothelial cells (HUVEC) were cultured on porous filters, treated with the inflammatory cytokine tumour necrosis factor-alpha (TNF), and then incorporated in a flow chamber. Video-microscopic observations were made of neutrophils as they were perfused over the HUVEC. When 3 microm pore filters were used (as opposed to 0.4 microm pore filters), neutrophils could be observed to migrate not only through the endothelial monolayer but also through the filter within minutes. The proportion of adherent neutrophils migrating through the endothelial monolayer and velocity of migration underneath it, were similar on the different filters, and also when neutrophils were perfused over cultures in glass capillaries, or settled on HUVEC cultured in standard plastic dishes. However, neutrophils migrated through HUVEC/filter constructs more rapidly in the flow chamber than in a standard, static, Transwell system, even though the velocities of migration under HUVEC were similar when directly observed under flow or static conditions. A function-blocking antibody against CD31 did not alter movement through the endothelial monolayer or the filter in the new flow system, but did reduce the migration velocity of neutrophils underneath the HUVEC (by 24%). Thus, we have developed a method for following each stage of neutrophil migration, including exit from the sub-endothelial space, and shown how they may be modified by applied fluid shear stress and blockade of a regulatory adhesion molecule.