The Definition of British Water Beetle Species Pools (Coleoptera) and their Relationship to Altitude, Temperature, Precipitation and Land Cover Variables

Pooled water beetle species lists from 1826 British national grid 10-km squares were analysed using multivariate ordination and classification methods. The relationships of pool groups to the climate, altitude and land cover variables were assessed using constrained and partial ordinations. Ordination of the species pool data indicated a major trend between squares in the north-west of Scotland and those in southern England, illustrating differences in acid and basic water standing water. Secondary variation was from acid standing water to fast-flowing streams and rivers. Classification generated nine species pool groups. These showed a distinct north-west to south-east trend but there was no obvious coastal or brackish water effect on distribution. The climatic and land cover variables were all significantly related to each other, and to north-south variation in grid square location, but the constrained ordination results indicated that that the most important influence on water beetle species pool distribution was mean summer temperature. Although the amount of variation explained by the environmental variables was low, spatial variation in the environmental predictors was almost as important as the environmental variables themselves in determining species pool composition. Mean annual temperature was also strongly correlated with species pool distribution with two land cover variables slightly less important. Altitude and precipitation had the least influence. The water beetle national recording scheme database appears to be of sufficiently high quality for environmental investigations at the British scale. There is considerable potential for the synthesis of invertebrate species distribution, land cover and climate change predictions in the assessment of environmental change. The results, together with previous work on other invertebrate species, indicate that changing summer temperatures may have a considerable influence on the distribution British invertebrate species.     

Human mesenchymal stem cells in contact with their environment: surface characteristics and the integrin system

The identification of mesenchymal stem cells (MSCs) in adult human tissues and the disclosure of their self-renew-al and multi-lineage differentiation capabilities have provided exciting prospects for cell-based regeneration and tis-sue engineering. Although a considerable amount of data is available describing MSCs, there is still lack of information regarding the molecular mechanisms that govern their adhesion and migration. In this work, we will review the current state of knowledge on integrins and other adhesion molecules found to be expressed on MSCs. The discussed topics include the characteristics of MSCs and their clinical applications, integrins and their central role in cell-matrix attachment and migration, and comments on mobilization, differentiation and contribution to tumour development. Finally, by understanding the complex and fundamental pathways by which MSCs attach and migrate, it might be possible to fine-tune the strategies for effective and safe use of MSCs in regenerative therapies.     

Trypsin cleaves exclusively C-terminal to arginine and lysine residues

Almost all large-scale projects in mass spectrometry-based proteomics use trypsin to convert protein mixtures into more readily analyzable peptide populations. When searching peptide fragmentation spectra against sequence databases, potentially matching peptide sequences can be required to conform to tryptic specificity, namely, cleavage exclusively C-terminal to arginine or lysine. In many published reports, however, significant numbers of proteins are identified by non-tryptic peptides. Here we use the sub-parts per million mass accuracy of a new ion trap Fourier transform mass spectrometer to achieve more than a 100-fold increased confidence in peptide identification compared with typical ion trap experiments and show that trypsin cleaves solely C-terminal to arginine and lysine. We find that non-tryptic peptides occur only as the C-terminal peptides of proteins and as breakup products of fully tryptic peptides N-terminal to an internal proline. Simulating lower mass accuracy led to a large number of proteins erroneously identified with non-tryptic peptide hits. Our results indicate that such peptide hits in previous studies should be re-examined and that peptide identification should be based on strict trypsin specificity.     

Neighboring plant influences on arbuscular mycorrhizal fungal community composition as assessed by T-RFLP analysis

Controls on root colonization by arbuscular mycorrhizal fungi (AMF) include host nutrient status, identity of symbionts and soil physico-chemical properties. Here we show, in the field, that the subset of the AMF community colonizing the roots of a common grass species, Dactylis glomerata, was strongly controlled by neighboring roots of a different plant species, Centaurea maculosa, an invasive forb, thus adding a biological spatial component to controls on root colonization. Using an AMF-specific, 18s rDNA-based terminal restriction fragment length polymorphism (T-RFLP) analysis method, significant differences were found between AMF community fingerprints of samples derived from roots of grasses with (G_Cm) and without (G₀) neighboring C. maculosa. There were also significant differences between samples derived from C. maculosa roots (C_mac) and both G_Cm and G₀ roots. Sample ordination indicated three generally distinct groups consisting of C_mac, G_Cm and G₀, with G_Cm samples being of intermediate distance between G₀and C_mac. Our results indicate that, with the presence of C. maculosa, AMF communities of D. glomerata shift to reflect community composition associated with C. maculosa roots. These results highlight the importance of complex spatial distributions of AMF communities at the scale of a root system. An additional dimension to our study is that C. maculosa is an aggressively invasive plant in the intermountain West. Viewed in this light, these results suggest that pervasive influences of this plant on AMF communities, specifically in roots of its competitors, may represent a mechanism contributing to its invasive success. However, further work is clearly required to determine the extent to which AMF genotypic alteration by neighboring plants influences competitive relationships.     

The Versatility of Helicobacter pylori CagA Effector Protein Functions: The Master Key Hypothesis

Several bacterial pathogens inject virulence proteins into host target cells that are substrates of eukaryotic tyrosine kinases. One of the key examples is the Helicobacter pylori CagA effector protein which is translocated by a type‐IV secretion system. Injected CagA becomes tyrosine‐phosphorylated on EPIYA sequence motifs by Src and Abl family kinases. CagA then binds to and activates/inactivates multiple signaling proteins in a phosphorylation‐dependent and phosphorylation‐independent manner. A recent proteomic screen systematically identified eukaryotic binding partners of the EPIYA phosphorylation sites of CagA and similar sites in other bacterial effectors by high‐resolution mass spectrometry. Individual phosphorylation sites recruited a surprisingly high number of interaction partners suggesting that each phosphorylation site can interfere with many downstream pathways. We now count 20 reported cellular binding partners of CagA, which represents the highest quantitiy among all yet known virulence‐associated effector proteins in the microbial world. This complexity generates a highly remarkable and puzzling scenario. In addition, the first crystal structure of CagA provided us with new information on the function of this important virulence determinant. Here we review the recent advances in characterizing the multiple binding signaling activities of CagA. Injected CagA can act as a ‘master key’ that evolved the ability to highjack multiple host cell signalling cascades, which include the induction of membrane dynamics, actin‐cytoskeletal rearrangements and the disruption of cell‐to‐cell junctions as well as proliferative, pro‐inflammatory and anti‐apoptotic nuclear responses. The discovery that different pathogens use this common strategy to subvert host cell functions suggests that more examples will emerge soon.     

High‐Throughput DNA sequencing of ancient wood

Reconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA molecules preserved in wooden tree archaeological and subfossil remains. Here, we advance such analyses by applying high‐throughput (HTS) DNA sequencing to wood archaeological and subfossil material for the first time, using a comprehensive sample of 167 European white oak waterlogged remains spanning a large temporal (from 550 to 9,800 years) and geographical range across Europe. The successful characterization of the endogenous DNA and exogenous microbial DNA of 140 (~83%) samples helped the identification of environmental conditions favouring long‐term DNA preservation in wood remains, and started to unveil the first trends in the DNA decay process in wood material. Additionally, the maternally inherited chloroplast haplotypes of 21 samples from three periods of forest human‐induced use (Neolithic, Bronze Age and Middle Ages) were found to be consistent with those of modern populations growing in the same geographic areas. Our work paves the way for further studies aiming at using ancient DNA preserved in wood to reconstruct the micro‐evolutionary response of trees to climate change and human forest management.     

The Net Landscape Carbon Balance—Integrating terrestrial and aquatic carbon fluxes in a managed boreal forest landscape in Sweden

The boreal biome exchanges large amounts of carbon (C) and greenhouse gases (GHGs) with the atmosphere and thus significantly affects the global climate. A managed boreal landscape consists of various sinks and sources of carbon dioxide (CO₂), methane (CH₄), and dissolved organic and inorganic carbon (DOC and DIC) across forests, mires, lakes, and streams. Due to the spatial heterogeneity, large uncertainties exist regarding the net landscape carbon balance (NLCB). In this study, we compiled terrestrial and aquatic fluxes of CO₂, CH₄, DOC, DIC, and harvested C obtained from tall‐tower eddy covariance measurements, stream monitoring, and remote sensing of biomass stocks for an entire boreal catchment (~68 km²) in Sweden to estimate the NLCB across the land–water–atmosphere continuum. Our results showed that this managed boreal forest landscape was a net C sink (NLCB = 39 g C m^?2 year^?1) with the landscape–atmosphere CO₂ exchange being the dominant component, followed by the C export via harvest and streams. Accounting for the global warming potential of CH₄, the landscape was a GHG sink of 237 g CO₂‐eq m^?2 year^?1, thus providing a climate‐cooling effect. The CH₄ flux contribution to the annual GHG budget increased from 0.6% during spring to 3.2% during winter. The aquatic C loss was most significant during spring contributing 8% to the annual NLCB. We further found that abiotic controls (e.g., air temperature and incoming radiation) regulated the temporal variability of the NLCB whereas land cover types (e.g., mire vs. forest) and management practices (e.g., clear‐cutting) determined their spatial variability. Our study advocates the need for integrating terrestrial and aquatic fluxes at the landscape scale based on tall‐tower eddy covariance measurements combined with biomass stock and stream monitoring to develop a holistic understanding of the NLCB of managed boreal forest landscapes and to better evaluate their potential for mitigating climate change.