Colonization of a host tree by herbivorous insects under a changing climate

Climate warming has been predicted to increase the abundance of herbivorous insects. Together with concurrent poleward shifts in many insect species this may increase herbivore pressure on plants. However, the manner in which plants at higher latitudes become colonized by herbivorous insects in the future is unknown. We established a translocation experiment using 26 micropropagated silver birch Betula pendula genotypes from six populations originating from 60°N to 67°N, to study the susceptibility of the translocated birches to local herbivores. The birches were planted at three different latitudes in Finland (60°N, 62°N and 67°N). We studied the effect of source population and latitudinal translocation on herbivore density, species richness, and community composition among the genotypes growing in the same environmental conditions in two years; 2011 and 2012. The source population explained the variation in the herbivore density only in 2012, whereas latitudinal translocation did not affect herbivore density. Variation in species richness was not explained by the source population or by the latitudinal translocation. At two of the study sites, the similarity of the herbivore communities among the populations decreased with increasing latitudinal distance of the source populations, possibly because birch populations that grow geographically closer to each other are genetically more similar, and therefore support a more similar composition of the arthropod community. All birch genotypes were colonized by local herbivores, suggesting that as herbivores shift their ranges polewards, they are able to colonize novel host‐plant genotypes. This enables compositional changes in insect communities on their host plants in the future, which in turn, might affect total herbivory and eventually, plant growth.     

Terrestrial isopods (Crustacea: Isopoda: Oniscidea) from Brazilian caves

To date, six species of terrestrial isopods were known from Brazilian caves, but only four could be classified as troglobites. This article deals with material of Oniscidea collected in many Brazilian karst caves in the states of Pará, Bahia, Minas Gerais, Mato Grosso do Sul, and São Paulo, and deposited in the collections of the Museu de Zoologia, Universidade de São Paulo, the Coleção de Carcinologia do Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, and the collection of the Natural History Museum, Section of Zoology ‘La Specola’, Florence. Three new genera have been recognized: Spelunconiscus gen. nov. and Xangoniscus gen. nov. (Styloniscidae), and Leonardoscia gen. nov. (Philosciidae). Twenty‐two species have been identified, 11 of which in the families Styloniscidae, Philosciidae, Scleropactidae, Plathyartridae, Dubioniscidae, and Armadillidae are new to science: Leonardoscia hassalli sp. nov., Metaprosekia quadriocellata sp. nov. , Metaprosekia caupe sp. nov. , Amazoniscus leistikowi sp. nov. , Novamundoniscus altamiraensis sp. nov. , Trichorhina yiara sp. nov. , Trichorhina curupira sp. nov. , and Ctenorillo ferrarai sp. nov. from Pará; Xangoniscus aganju sp. nov. from Bahia; and Spelunconiscus castroi sp. nov. and Trichorhina anhanguera sp. nov. from Minas Gerais. Four new species in the families Styloniscidae ( Spelunconiscus castroi sp. nov. and Xangoniscus aganju sp. nov. ), Philosciidae ( Leonardoscia hassalli sp. nov. ), and Scleropactidae ( Amazoniscus leistikowi sp. nov. ) with highly troglomorphic traits can be considered as troglobitic, whereas all the remaining species are either troglophilic or accidentals. Brazilian caves are now under potential threat because of recent legislation, and the knowledge of the subterranean biodiversity of the country is thus of primary importance. © 2014 The Linnean Society of London     

Persistence length of fascin-cross-linked actin filament bundles in solution and the in vitro motility assay

Background

Bundles of unipolar actin filaments (F-actin), cross-linked via the actin-binding protein fascin, are important in filopodia of motile cells and stereocilia of inner ear sensory cells. However, such bundles are also useful as shuttles in myosin-driven nanotechnological applications. Therefore, and for elucidating aspects of biological function, we investigate if the bundle tendency to follow straight paths (quantified by path persistence length) when propelled by myosin motors is directly determined by material properties quantified by persistence length of thermally fluctuating bundles.

Methods

Fluorescent bundles, labeled with rhodamine-phalloidin, were studied at fascin:actin molar ratios: 0:1 (F-actin), 1:7, 1:4 and 1:2. Persistence lengths (Lp) were obtained by fitting the cosine correlation function (CCF) to a single exponential function: < cos(θ(0) − θ(s)) > = exp(−s / (2Lp)) where θ(s) is tangent angle; s: path or contour lengths. < > denotes averaging over filaments.

Results

Bundle-Lp (bundles < 15 μm long) increased from ~ 10 to 150 μm with increased fascin:actin ratio. The increase was similar for path-Lp (path < 15 μm), with highly linear correlation. For longer bundle paths, the CCF-decay deviated from a single exponential, consistent with superimposition of the random path with a circular path as suggested by theoretical analysis.

Conclusions

Fascin–actin bundles have similar path-Lp and bundle-Lp, both increasing with fascin:actin ratio. Path-Lp is determined by the flexural rigidity of the bundle.

General significance

The findings give general insight into mechanics of cytoskeletal polymers that interact with molecular motors, aid rational development of nanotechnological applications and have implications for structure and in vivo functions of fascin–actin bundles.     

Isolation and characterization of phage–host systems from the Baltic Sea ice

In search for sea ice bacteria and their phages from the Baltic Sea ice, two ice samples were collected from land-fast ice in a south-west Finland coastal site in February and March 2011. Bacteria were isolated from the melted sea ice samples and phages were screened from the same samples for 43 purified isolates. Plaque-producing phages were found for 15 bacterial isolates at 3 °C. Ten phage isolates were successfully plaque purified and eight of them were chosen for particle purification to analyze their morphology and structural proteins. Phage 1/32 infecting an isolate affiliated to phylum Bacteroidetes (Flavobacterium sp.) is a siphovirus and six phages infecting isolates affiliated to γ-Proteobacteria (Shewanella sp.) hosts were myoviruses. Cross titrations between the hosts showed that all studied phages are host specific. Phage solutions, host growth and phage infection were tested in different temperatures revealing phage temperature tolerance up to 45 °C, whereas phage infection was in most of the cases retarded above 15 °C. This study is the first to report isolation and cultivation of ice bacteria and cold-active phages from the Baltic Sea ice.     

Allergic diseases and asthma in the family predict the persistence and onset-age of asthma: a prospective cohort study

BackgroundFamily history of asthma and other allergic diseases have been linked to the risk of childhood asthma previously, but little is known about their effect on the age-of-onset and persistency of asthma until young adulthood.MethodsWe assessed the effect of the family history of asthma and allergic diseases on persistent vs. transient, and early- vs. late-onset persistent asthma in The Espoo Cohort Study 1991–2011, a population-based cohort study of 1623 subjects (follow-up rate 63.2%). The determinants were any family history (any parent or sibling); maternal; paternal; siblings only; parents only; and both siblings and parents. Analyses were conducted separately for asthma and allergic diseases while taking the other disease into account as a confounding factor. The outcomes were persistent, transient, early-onset persistent (<13 years) and late-onset persistent asthma. Adjusted risk ratios (RR) were calculated applying Poisson regression. Q-statistics were used to assess heterogeneity between RRs.ResultsFamily history was associated with the different subtypes but the magnitude of effect varied quantitatively. Any family history of asthma was a stronger determinant of persistent (adjusted RR = 2.82, 95% CI 1.99-4.00) than transient asthma (1.65, 1.03-2.65) (heterogeneity: P = 0.07) and on early-onset than late-onset persistent asthma. Also any family history of allergic diseases was a stronger determinant of persistent and early-onset asthma. The impact of paternal asthma continued to young adulthood (early-onset: 3.33, 1.57-7.06 vs. late-onset 2.04, 0.75-5.52) while the influence of maternal asthma decreased with age (Early-onset 3.94, 2.11-7.36 vs. Late-onset 0.88, 0.28-2.81). Paternal allergic diseases did not follow the pattern of paternal asthma, since they showed no association with late-onset asthma. Also the effect estimates for other subtypes were lower than in other hereditary groups (persistent 1.29, 0.75-2.22 vs. transient 1.20, 0.67-2.15 and early-onset 1.86, 0.95-3.64 vs. late-onset 0.64, 0.22-1.80).ConclusionsFamily history of asthma and allergic diseases are strong determinants of asthma, but the magnitude of effect varies according to the hereditary group so that some subtypes have a stronger hereditary component, and others may be more strongly related to environmental exposures. Our results provide useful information for assessing the prognosis of asthma based on a thorough family history.     

Structural Characterization by Cross-linking Reveals the Detailed Architecture of a Coatomer-related Heptameric Module from the Nuclear Pore Complex

Most cellular processes are orchestrated by macromolecular complexes. However, structural elucidation of these endogenous complexes can be challenging because they frequently contain large numbers of proteins, are compositionally and morphologically heterogeneous, can be dynamic, and are often of low abundance in the cell. Here, we present a strategy for the structural characterization of such complexes that has at its center chemical cross-linking with mass spectrometric readout. In this strategy, we isolate the endogenous complexes using a highly optimized sample preparation protocol and generate a comprehensive, high-quality cross-linking dataset using two complementary cross-linking reagents. We then determine the structure of the complex using a refined integrative method that combines the cross-linking data with information generated from other sources, including electron microscopy, X-ray crystallography, and comparative protein structure modeling. We applied this integrative strategy to determine the structure of the native Nup84 complex, a stable hetero-heptameric assembly (∼600 kDa), 16 copies of which form the outer rings of the 50-MDa nuclear pore complex (NPC) in budding yeast. The unprecedented detail of the Nup84 complex structure reveals previously unseen features in its pentameric structural hub and provides information on the conformational flexibility of the assembly. These additional details further support and augment the protocoatomer hypothesis, which proposes an evolutionary relationship between vesicle coating complexes and the NPC, and indicates a conserved mechanism by which the NPC is anchored in the nuclear envelope.Macromolecular complexes are the building blocks that drive virtually all cellular and biological processes. In each eukaryotic cell, there exist many hundreds of these protein complexes (1–3), the majority of which are still poorly understood in terms of their structures, dynamics, and functions. The classical structure determination approaches of nuclear magnetic resonance, X-ray crystallography, and electron microscopy (EM)¹ remain challenged in attempts to determine the high-resolution structures of large, dynamic, and flexible complexes in a living cell (4). Thus, additional robust and rapid methods are needed, ideally working in concert with these classical approaches, to allow the greatest structural and functional detail in characterizations of macromolecular assemblies.Integrative modeling approaches help address this need, providing powerful tools for determining the structures of endogenous protein complexes (5, 6) by relying on the collection of an extensive experimental dataset, preferably coming from diverse sources (both classical and new) and different levels of resolution. These data are translated into spatial restraints that are used to calculate an ensemble of structures by satisfying the restraints, which in turn can be analyzed and assessed to determine precision and estimate accuracy (5, 7). A major advantage of this approach is that it readily integrates structural data from different methods and a wide range of resolutions, spanning from a few angstroms to dozens of nanometers. This strategy has been successfully applied to a number of protein complexes (8–16). However, it has proven difficult and time-consuming to generate a sufficient number of accurate spatial restraints to enable high-resolution structural characterization; thus, the determination of spatial restraints currently presents a major bottleneck for widespread application of this integrative approach. An important step forward is therefore the development of technologies for collecting high-resolution and information-rich spatial restraints in a rapid and efficient manner, ideally from endogenous complexes isolated directly from living cells.Chemical cross-linking with mass spectrometric readout (CX-MS) (17, 18) has recently emerged as an enabling approach for obtaining residue-specific restraints on the structures of proteins and protein complexes (19–25). In a CX-MS experiment, the purified protein complex is chemically conjugated by a functional group-specific cross-linker, and this is followed by proteolytic digestion and analysis of the resulting peptide mixture by mass spectrometry (MS). However, because of the complexity of the peptide mixtures and low abundance of most of the informative cross-linked species, comprehensive detection of these cross-linked peptides has proven challenging. This challenge increases substantially in studies of endogenous complexes of modest to low abundance, which encompass the great majority of assemblies in any cell (26, 27). In addition, because most cross-linkers used for CX-MS target primary amines, comprehensive detection of cross-links is further limited by the occurrence of lysine, which constitutes only ∼6% of protein sequences, although these lysine residues are generally present on protein surfaces. The use of cross-linkers with different chemistries and reactive groups, especially toward abundant residues, would increase the cross-linking coverage and could be of great help for downstream structural analysis (28).The nuclear pore complex (NPC) is one of the largest protein assemblies in the cell and is the sole mediator of macromolecular transport between the nucleus and the cytoplasm. The NPC is formed by multiple copies of ∼30 different proteins termed nucleoporins (Nups) that are assembled into discrete subcomplexes (8, 29). These building blocks are arranged into eight symmetrical units called spokes that are radially connected to form several concentric rings. The outer rings of the NPC are mainly formed by the Nup84 complex (a conserved complex, termed the Nup107–Nup160 complex in vertebrates). In budding yeast, the Nup84 complex is an essential, Y-shaped assembly of ∼600 kDa that is formed by seven nucleoporins (Nup133, Nup120, Nup145c, Nup85, Nup84, Seh1, and Sec13 in Saccharomyces cerevisiae) (30). The Nup84 complex has been shown to have a common evolutionary origin with vesicle coating complexes (VCCs), such as COPII, COPI, and clathrin (31, 32), but the evolutionary relationships between these VCCs have not been fully delineated. The Nup84 complex has been extensively characterized; several of its components have been analyzed via X-ray crystallography (33, 34), its overall shape has been defined by means of negative-stain electron microscopy (14, 30, 35, 36), and recently efforts were made to define the protein contacts in the Nup84 complex via CX-MS in humans (35) and a thermophilic fungus (37). Finally, we recently used an integrative modeling approach combining domain mapping, negative-stain electron microscopy (38), and publicly available crystal structures to generate a medium-resolution map of the native Nup84 complex (14). However, despite all these efforts, the fine features of the complex, and in particular the intricate domain orientations and contacts within the complex''s hub, remain poorly described.To address these issues, we present here an optimized CX-MS strategy for robust and in-depth structural characterization of endogenous protein complexes. To test the strategy, we generated a comprehensive high-quality CX-MS dataset on the endogenous Nup84 complex using two complementary cross-linkers, disuccinimidyl suberate (DSS) and 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC). Using the resulting cross-linking restraints together with other sources of information (including electron microscopy, X-ray crystallography, and comparative modeling), we computed a detailed structure of the endogenous Nup84 complex. In addition to providing the overall architecture of the yeast Nup84 complex, the resulting structure reveals the previously unknown architecture of its pentameric structural hub. Our results demonstrate that the present approach provides a robust framework for the standardized generation and use of CX-MS spatial restraints toward the structural characterization of endogenous protein complexes.     

Kinetics of PKCε activating and inhibiting llama single chain antibodies and their effect on PKCε translocation in HeLa cells

Dysregulation of PKCε is involved in several serious diseases such as cancer, type II diabetes and Alzheimer's disease. Therefore, specific activators and inhibitors of PKCε hold promise as future therapeutics, in addition to being useful in research into PKCε regulated pathways. We have previously described llama single chain antibodies (VHHs) that specifically activate (A10, C1 and D1) or inhibit (E6 and G8) human recombinant PKCε. Here we report a thorough kinetic analysis of these VHHs. The inhibiting VHHs act as non-competitive inhibitors of PKCε activity, whereas the activating VHHs have several different modes of action, either increasing V(max) and/or decreasing K(m) values. We also show that the binding of the VHHs to PKCε is conformation-dependent, rendering the determination of affinities difficult. Apparent affinities are in the micromolar range based on surface plasmon resonance studies. Furthermore, the VHHs have no effect on the activity of rat PKCε nor can they bind the rat form of the protein in immunoprecipitation studies despite the 98% identity between the human and rat PKCε proteins. Finally, we show for the first time that the VHHs can influence PKCε function also in cells, since an activating VHH increases the rate of PKCε translocation in response to PMA in HeLa cells, whereas an inhibiting VHH slows down the translocation. These results give insight into the mechanisms of PKCε activity modulation and highlight the importance of protein conformation on VHH binding.     

Tracking Sphingosine Metabolism and Transport in Sphingolipidoses: NPC1 Deficiency as a Test Case

The late endosomal/lysosomal compartment (LE/LY) plays a key role in sphingolipid breakdown, with the last degradative step catalyzed by acid ceramidase. The released sphingosine can be converted to ceramide in the ER and transported by ceramide transfer protein (CERT) to the Golgi for conversion to sphingomyelin. The mechanism by which sphingosine exits LE/LY is unknown but Niemann-Pick C1 protein (NPC1) has been suggested to be involved. Here, we used sphingomyelin, ceramide and sphingosine labeled with [(3) H] in carbon-3 of the sphingosine backbone and targeted them to LE/LY in low-density lipoprotein (LDL) particles. These probes traced LE/LY sphingolipid degradation and recycling as suggested by (1) accumulation of [(3) H]-sphingomyelin-derived [(3) H]-ceramide and depletion of [(3) H]-sphingosine upon acid ceramidase depletion, and (2) accumulation of [(3) H]-sphingosine-derived [(3) H]-ceramide and attenuation of [(3) H]-sphingomyelin synthesis upon CERT depletion. NPC1 silencing did not result in the accumulation of [(3) H]-sphingosine derived from [(3) H]-sphingomyelin/LDL or [(3) H]-ceramide/LDL. Additional evidence against NPC1 playing a significant role in LE/LY sphingosine export was obtained in experiments using the [(3) H]-sphingolipids or a fluorescent sphingosine derivative in NPC1 knock-out cells. Instead, NPC1-deficient cells displayed an increased affinity for sphingosine independently of protein-mediated lipid transport. This likely contributes to the increased sphingosine content of NPC1 cells.