Two distinct cytoplasmic regions of the beta2 integrin chain regulate RhoA function during phagocytosis

AlphaMbeta2 integrins mediate phagocytosis of opsonized particles in a process controlled by RhoA, Rho kinase, myosin II, Arp2/3, and actin polymerization. AlphaMbeta2, Rho, Arp2/3, and F-actin accumulate underneath bound particles; however, the mechanism regulating Rho function during alphaMbeta2-mediated phagocytosis is poorly understood. We report that the binding of C3bi-opsonized sheep red blood cells (RBCs) to alphaMbeta2 increases Rho-GTP, but not Rac-GTP, levels. Deletion of the cytoplasmic domain of beta2, but not of alphaM, abolished Rho recruitment and activation, as well as phagocytic uptake. Interestingly, a 16-amino acid (aa) region in the membrane-proximal half of the beta2 cytoplasmic domain was necessary for activating Rho. Three COOH-terminal residues (aa 758-760) were essential for beta2-induced accumulation of Rho at complement receptor 3 (CR3) phagosomes. Activation of Rho was necessary, but not sufficient, for its stable recruitment underneath bound particles or for uptake. However, recruitment of active Rho was sufficient for phagocytosis. Our data shed light on the mechanism of outside-in signaling, from ligated integrins to the activation of Rho GTPase signaling.     

Behavioural and population responses to changing availability of <Emphasis Type="Italic">Artemia</Emphasis> prey by moulting black-necked grebes, <Emphasis Type="Italic">Podiceps nigricollis</Emphasis>

Chemical communication may inform about the location of prey, predators, co-specifics, and mate partners in zooplankton. In this study, we evaluated several life-history traits of the rotifer, Brachionus calyciflorus, exposed to conditioned media by a rotifer predator (Asplanchna brightwelli) and a cladocera competitor (Daphnia similis), quantifying population growth and life-table demography at two algal food levels (2.0 and 0.5 × 10⁶ cells ml⁻¹ of Chlorella pyrenoidosa). At both food levels, B. calyciflorus grown in predator-conditioned media had lower population abundance and slower population growth rate than controls. Conversely, the competitor-conditioned media treatments produced both higher rotifer population abundance and faster population growth rate than controls. Life-history parameters varied significantly depending on the presence of predator and competitor-conditioned media. The Asplanchna-conditioned media significantly decreased gross reproductive rate (GRR): 8–9 offsprings per female; net reproductive rate (R ₀): 6–7 offsprings per female; population growth rate (r): 0.34–0.37 day⁻¹; and increased generation time (T): 5.5–5.6 days. On the other hand, The Daphnia-conditioned media significantly increased the GRR (13–14 offsprings per female); net reproductive rate (8–9 offsprings per female); population growth rate (0.42–0.43 day⁻¹); and decreased generation time (4.9–5.0 days). However, the effects of food level on the life-history characteristic were not significant in both treatments. Maximum values of the population abundance and the population growth rate are significantly influenced by the predator densities and pre-culture time. This study suggests that rotifers use variable life-history strategies (low reproduction and high survivorship versus high reproduction and low survivorship) based on the presence of predators and competitors.     

Calling sample mix-ups in cancer population studies

Sample tracking errors have been and always will be a part of the practical implementation of large experiments. It has recently been proposed that expression quantitative trait loci (eQTLs) and their associated effects could be used to identify sample mix-ups and this approach has been applied to a number of large population genomics studies to illustrate the prevalence of the problem. We had adopted a similar approach, termed 'BADGER', in the METABRIC project. METABRIC is a large breast cancer study that may have been the first in which eQTL-based detection of mismatches was used during the study, rather than after the event, to aid quality assurance. We report here on the particular issues associated with large cancer studies performed using historical samples, which complicate the interpretation of such approaches. In particular we identify the complications of using tumour samples, of considering cellularity and RNA quality, of distinct subgroups existing in the study population (including family structures), and of choosing eQTLs to use. We also present some results regarding the design of experiments given consideration of these matters. The eQTL-based approach to identifying sample tracking errors is seen to be of value to these studies, but requiring care in its implementation.     

Phylogeography of an estuarine mysid, Neomysis integer (Crustacea, Mysida), along the north-east Atlantic coasts

Aim The brackish water mysid, Neomysis integer, is one of the most common mysid species along the coasts of the north‐east Atlantic. In the present study, the phylogeographical patterns were examined throughout the distribution range of N. integer. In particular, the latitudinal trends in genetic diversity and the distribution of genetic variation were examined in order to elucidate the imprints of the Pleistocene glaciations. Location North‐east Atlantic coasts from the Baltic Sea to the south of Spain. Methods A total of 461 specimens from 11 populations were analysed by means of single‐stranded conformation polymorphism analysis combined with DNA sequencing of a fragment of the mitochondrial cytochrome c oxidase I gene. The genetic structure was examined by using a progression of phylogenetic, demographic and population genetic analyses to elucidate not only the geographical structure, but also the evolutionary history producing that structure. Results The levels of genetic diversity were relatively uniform throughout the distribution range, with the exception of a decline at the northern and southern edges of distribution. A high heterogeneity was observed between the populations analysed (global Φ_ST = 0.787). This is caused by the disparate distribution of the cytochrome oxidase I haplotypes, with several population‐specific haplotypes. A clear genetic break (2.4% sequence divergence) occurred between the southernmost Guadalquivir population and all other populations. Main conclusions The present study corroborates the expectations of the genetic patterns typically observed in an estuarine species. The within‐population variability was low, whereas a significant (moderate to high) divergence was observed between populations. Phylogeographical analysis revealed that northern populations within the English Channel, North Sea and Baltic Sea are characterized by several widespread haplotypes, while the Irish population and all sites south of the Bay of Biscay consist solely of unique haplotypes. This pattern, combined with the relative high levels of genetic diversity, could be indicative for the presence of a glacial refugium in the English Channel region. Under this scenario N. integer must have survived the Last Glacial Maximum in the palaeoriver system present in that region.     

Molecular mechanisms and kinetics between DNA and DNA binding ligands

Mechanical properties of single double-stranded DNA (dsDNA) in the presence of different binding ligands were analyzed in optical-tweezers experiments with subpiconewton force resolution. The binding of ligands to DNA changes the overall mechanic response of the dsDNA molecule. This fundamental property can be used for discrimination and identification of different binding modes and, furthermore, may be relevant for various processes like nucleosome packing or applications like cancer therapy. We compared the effects of the minor groove binder distamycin-A, a major groove binding alpha-helical peptide, the intercalators ethidium bromide, YO-1, and daunomycin as well as the bisintercalator YOYO-1 on lambda-DNA. Binding of molecules to the minor and major groove of dsDNA induces distinct changes in the molecular elasticity compared to the free dsDNA detectable as a shift of the overstretching transition to higher forces. Intercalating molecules affect the molecular mechanics by a complete disappearance of the B-S transition and an associated increase in molecular contour length. Significant force hysteresis effects occurring during stretching/relaxation cycles with velocities >10 nm/s for YOYO-1 and >1000 nm/s for daunomycin. These indicate structural changes in the timescale of minutes for the YOYO-DNA and of seconds for the daunomycin-DNA complexes, respectively.     

Immunity of the ox to the brown ear tickRhipicephalus appendiculatus

Controlled repeated infestation ofBos taurus andBos indicus cattle resulted in a decline in the recovery of allR. appendiculatus instars. Resistance to infestation varied between individuals although all individuals manifested severe hypersensitivity at the attachment site, which was reflected in the grooming reflex.     

Influence of elevation on bark beetle (Coleoptera: Curculionidae, Scolytinae) community structure and flight periodicity in ponderosa pine forests of Arizona

We examined abundance and flight periodicity of five Ips and six Dendroctonus species (Coleoptera: Curculionidae, Scolytinae) among three different elevation bands in ponderosa pine (Pinus ponderosa Douglas ex. Lawson) forests of northcentral Arizona. Bark beetle populations were monitored at 10 sites in each of three elevation bands (low: 1,600-1,736 m; middle: 2,058-2,230 m; high: 2,505-2,651 m) for 3 yr (2004-2006) using pheromone-baited Lindgren funnel traps. Trap contents were collected weekly from March to December. We also studied temperature differences among the elevation bands and what role this may play in beetle flight behavior. Bark beetles, regardless of species, showed no consistent elevational trend in abundance among the three bands. The higher abundances of Ips lecontei Swaine, I. calligraphus ponderosae Swaine, Dendroctonus frontalis Zimmerman, and D. brevicomis LeConte at low and middle elevations offset the greater abundance of I. knausi Swaine, D. adjunctus Blandford, D. approximatus Dietz, and D. valens LeConte at high elevations. I. pini (Say) and I. latidens LeConte were found in similar numbers across the three bands. Flight periodicity of several species varied among elevation bands. In general, the flight period shortened as elevation increased; flight initiated later and terminated earlier in the year. The timing, number, and magnitude of peaks in flight activity also varied among the elevation bands. These results suggest that abundance and flight seasonality of several bark beetles are related to elevation and the associated temperature differences. The implications of these results are discussed in relation to bark beetle management and population dynamics.     

The shape of mammalian phylogeny: patterns, processes and scales

Mammalian phylogeny is far too asymmetric for all contemporaneous lineages to have had equal chances of diversifying. We consider this asymmetry or imbalance from four perspectives. First, we infer a minimal set of 'regime changes'-points at which net diversification rate has changed-identifying 15 significant radiations and 12 clades that may be 'downshifts'. We next show that mammalian phylogeny is similar in shape to a large set of published phylogenies of other vertebrate, arthropod and plant groups, suggesting that many clades may diversify under a largely shared set of 'rules'. Third, we simulate six simple macroevolutionary models, showing that those where speciation slows down as geographical or niche space is filled, produce more realistic phylogenies than do models involving key innovations. Lastly, an analysis of the spatial scaling of imbalance shows that the phylogeny of species within an assemblage, ecoregion or larger area always tends to be more unbalanced than expected from the phylogeny of species at the next more inclusive spatial scale. We conclude with a verbal model of mammalian macroevolution, which emphasizes the importance to diversification of accessing new regions of geographical or niche space.     

Population Analysis of Large Copy Number Variants and Hotspots of Human Genetic Disease

Copy number variants (CNVs) contribute to human genetic and phenotypic diversity. However, the distribution of larger CNVs in the general population remains largely unexplored. We identify large variants in ~2500 individuals by using Illumina SNP data, with an emphasis on “hotspots” prone to recurrent mutations. We find variants larger than 500 kb in 5%–10% of individuals and variants greater than 1 Mb in 1%–2%. In contrast to previous studies, we find limited evidence for stratification of CNVs in geographically distinct human populations. Importantly, our sample size permits a robust distinction between truly rare and polymorphic but low-frequency copy number variation. We find that a significant fraction of individual CNVs larger than 100 kb are rare and that both gene density and size are strongly anticorrelated with allele frequency. Thus, although large CNVs commonly exist in normal individuals, which suggests that size alone can not be used as a predictor of pathogenicity, such variation is generally deleterious. Considering these observations, we combine our data with published CNVs from more than 12,000 individuals contrasting control and neurological disease collections. This analysis identifies known disease loci and highlights additional CNVs (e.g., 3q29, 16p12, and 15q25.2) for further investigation. This study provides one of the first analyses of large, rare (0.1%–1%) CNVs in the general population, with insights relevant to future analyses of genetic disease.