Peroxisomal Import Reduces the Proapoptotic Activity of Deubiquitinating Enzyme USP2

The human deubiquitinating enzyme ubiquitin-specific protease 2 (USP2) regulates multiple cellular pathways, including cell proliferation and apoptosis. As a result of alternative splicing four USP2 isoenzymes are expressed in human cells of which all contain a weak peroxisome targeting signal of type 1 (PTS1) at their C-termini. Here, we systematically analyzed apoptotic effects induced by overexpression and intracellular localization for each isoform. All isoforms exhibit proapoptotic activity and are post-translationally imported into the matrix of peroxisomes in a PEX5-dependent manner. However, a significant fraction of the USP2 pool resides in the cytosol due to a weaker PTS1 and thus low affinity to the PTS receptor PEX5. Blocking of peroxisomal import did not interfere with the proapoptotic activity of USP2, suggesting that the enzyme performs its critical function outside of this compartment. Instead, increase of the efficiency of USP2 import into peroxisomes either by optimization of its peroxisomal targeting signal or by overexpression of the PTS1 receptor did result in a reduction of the apoptotic rate of transfected cells. Our studies suggest that peroxisomal import of USP2 provides additional control over the proapoptotic activity of cytosolic USP2 by spatial separation of the deubiquitinating enzymes from their interaction partners in the cytosol and nucleus.     

Patterns of drought tolerance in major European temperate forest trees: climatic drivers and levels of variability

The future performance of native tree species under climate change conditions is frequently discussed, since increasingly severe and more frequent drought events are expected to become a major risk for forest ecosystems. To improve our understanding of the drought tolerance of the three common European temperate forest tree species Norway spruce, silver fir and common beech, we tested the influence of climate and tree‐specific traits on the inter and intrasite variability in drought responses of these species. Basal area increment data from a large tree‐ring network in Southern Germany and Alpine Austria along a climatic cline from warm‐dry to cool‐wet conditions were used to calculate indices of tolerance to drought events and their variability at the level of individual trees and populations. General patterns of tolerance indicated a high vulnerability of Norway spruce in comparison to fir and beech and a strong influence of bioclimatic conditions on drought response for all species. On the level of individual trees, low‐growth rates prior to drought events, high competitive status and low age favored resilience in growth response to drought. Consequently, drought events led to heterogeneous and variable response patterns in forests stands. These findings may support the idea of deliberately using spontaneous selection and adaption effects as a passive strategy of forest management under climate change conditions, especially a strong directional selection for more tolerant individuals when frequency and intensity of summer droughts will increase in the course of global climate change.     

Acetylation of α-tubilin in different bovine cell types: implications for microtubule dynamics in interphase and mitosis.

Previous work on five cell types isolated from the bovine corpus luteum showed that the mass of acetylated microtubules (acet-MTs) in interphase differed. Endothelial cells, termed type 3, showed few acet-MTs, whereas the interphase cytoskeleton of granulosal-like cells, termed type 5, was rich in acet-MTs. In the present study, these cultured cells were used to determine whether the degree of α-tubulin acetylation in interphase had consequences on mitosis. To this end, the distribution of acet-MTs was determined throughout the cell cycle using a monoclonal antibody, 6-11B-1, directed against acetylated α-tubulin. For comparison, tyrosinated MTs were visualized with another monoclonal antibody, YL1/2, detecting tyrosinated α-tubulin. Although the amount of acet-MTs in interphase differed significantly between both cell types, major differences in the appearance of acet-MTs during mitosis were only apparent in prophase and during transition from late telophase to interphase. Thus, irrespective of different α-tubulin acetylation in interphase, spindle structure is uniform. Since acetylation of α-tubulin is believed to indicate the presence of relatively stable MTs, we conclude that MT dynamics is differently controlled in interphase and mitosis. Thereby interphase cells are able to carry out functions which involve stable MTs and the cells progress through mitosis in the presence of more dynamic MTs.     

Environmental effects on fine‐scale spatial genetic structure in four Alpine keystone forest tree species

Genetic responses to environmental changes take place at different spatial scales. While the effect of environment on the distribution of species' genetic diversity at large geographical scales has been the focus of several recent studies, its potential effects on genetic structure at local scales are understudied. Environmental effects on fine‐scale spatial genetic structure (FSGS) were investigated in four Alpine conifer species (five to eight populations per species) from the eastern Italian Alps. Significant FSGS was found for 11 of 25 populations. Interestingly, we found no significant differences in FSGS across species but great variation among populations within species, highlighting the importance of local environmental factors. Interannual variability in spring temperature had a small but significant effect on FSGS of Larix decidua, probably related to species‐specific life history traits. For Abies alba, Picea abies and Pinus cembra, linear models identified spring precipitation as a potentially relevant climate factor associated with differences in FSGS across populations; however, models had low explanatory power and were strongly influenced by a P. cembra outlier population from a very dry site. Overall, the direction of the identified effects is according to expectations, with drier and more variable environments increasing FSGS. Underlying mechanisms may include climate‐related changes in the variance of reproductive success and/or environmental selection of specific families. This study provides new insights on potential changes in local genetic structure of four Alpine conifers in the face of environmental changes, suggesting that new climates, through altering FSGS, may also have relevant impacts on plant microevolution.     

Array-assisted Characterization of a Fucosyltransferase Required for the Biosynthesis of Complex Core Modifications of Nematode N-Glycans

Fucose is a common monosaccharide component of cell surfaces and is involved in many biological recognition events. Therefore, definition and exploitation of the specificity of the enzymes (fucosyltransferases) involved in fucosylation is a recurrent theme in modern glycosciences. Despite various studies, the specificities of many fucosyltransferases are still unknown, so new approaches are required to study these. The model nematode Caenorhabditis elegans expresses a wide range of fucosylated glycans, including N-linked oligosaccharides with unusual complex core modifications. Up to three fucose residues can be present on the standard N,N′-diacetylchitobiose unit of these N-glycans, but only the fucosyltransferases responsible for transfer of two of these (the core α1,3-fucosyltransferase FUT-1 and the core α1,6-fucosyltransferase FUT-8) were previously characterized. By use of a glycan library in both array and solution formats, we were able to reveal that FUT-6, another C. elegans α1,3-fucosyltransferase, modifies nematode glycan cores, specifically the distal N-acetylglucosamine residue; this result is in accordance with glycomic analysis of fut-6 mutant worms. This core-modifying activity of FUT-6 in vitro and in vivo is in addition to its previously determined ability to synthesize Lewis X epitopes in vitro. A larger scale synthesis of a nematode N-glycan core in vitro using all three fucosyltransferases was performed, and the nature of the glycosidic linkages was determined by NMR. FUT-6 is probably the first eukaryotic glycosyltransferase whose specificity has been redefined with the aid of glycan microarrays and so is a paradigm for the study of other unusual glycosidic linkages in model and parasitic organisms.     

How a measure of tree structural complexity relates to architectural benefit‐to‐cost ratio,light availability,and growth of trees

Aboveground tree architecture is neither fully deterministic nor random. It is likely the result of mechanisms that balance static requirements and light‐capturing efficiency. Here, we used terrestrial laser scanning data to investigate the relationship between tree architecture, here addressed using the box‐dimension (D_b), and the architectural benefit‐to‐cost ratio, the light availability, and the growth of trees. We detected a clear relationship between D_b and the benefit‐to‐cost ratio for the tested three temperate forest tree species (Fagus sylvatica L., Fraxinus excelsior L., and Acer pseudoplatanus L.). In addition, we could also show that D_b is positively related to the growth performance of several tropical tree species. Finally, we observed a negative relationship between the strength of competition enforced on red oak (Quercus rubra L.) trees and their D_b. We therefore argue that D_b is a meaningful and integrative measure that describes the structural complexity of the aboveground compartments of a plant as well as its relation to structural efficiency (benefit‐to‐cost ratio), productivity, and growing conditions (competition or availability of light).     

Non-HLA genes PTPN22, CDK6 and PADI4 are associated with specific autoantibodies in HLA-defined subgroups of rheumatoid arthritis

Introduction

Genetic susceptibility to complex diseases has been intensively studied during the last decade, yet only signals with small effect have been found leaving open the possibility that subgroups within complex traits show stronger association signals. In rheumatoid arthritis (RA), autoantibody production serves as a helpful discriminator in genetic studies and today anti-citrullinated cyclic peptide (anti-CCP) antibody positivity is employed for diagnosis of disease. The HLA-DRB1 locus is known as the most important genetic contributor for the risk of RA, but is not sufficient to drive autoimmunity and additional genetic and environmental factors are involved. Hence, we addressed the association of previously discovered RA loci with disease-specific autoantibody responses in RA patients stratified by HLA-DRB1*04.

Methods

We investigated 2178 patients from three RA cohorts from Sweden and Spain for 41 genetic variants and four autoantibodies, including the generic anti-CCP as well as specific responses towards citrullinated peptides from vimentin, alpha-enolase and type II collagen.

Results

Our data demonstrated different genetic associations of autoantibody-positive disease subgroups in relation to the presence of DRB1*04. Two specific subgroups of autoantibody-positive RA were identified. The SNP in PTPN22 was associated with presence of anti-citrullinated enolase peptide antibodies in carriers of HLA-DRB1*04 (Cochran-Mantel-Haenszel test P = 0.0001, P_corrected <0.05), whereas SNPs in CDK6 and PADI4 were associated with anti-CCP status in DRB1*04 negative patients (Cochran-Mantel-Haenszel test P = 0.0004, P_corrected <0.05 for both markers). Additionally we see allelic correlation with autoantibody titers for PTPN22 SNP rs2476601 and anti-citrullinated enolase peptide antibodies in carriers of HLA-DRB1*04 (Mann Whitney test P = 0.02) and between CDK6 SNP rs42041 and anti-CCP in non-carriers of HLA-DRB1*04 (Mann Whitney test P = 0.02).

Conclusion

These data point to alternative pathways for disease development in clinically similar RA subgroups and suggest an approach for study of genetic complexity of disease with strong contribution of HLA.

Electronic supplementary material

The online version of this article (doi:10.1186/s13075-014-0414-3) contains supplementary material, which is available to authorized users.     

Flame Experiments at the Advanced Light Source: New Insights into Soot Formation Processes

The following experimental protocols and the accompanying video are concerned with the flame experiments that are performed at the Chemical Dynamics Beamline of the Advanced Light Source (ALS) of the Lawrence Berkeley National Laboratory^1-4. This video demonstrates how the complex chemical structures of laboratory-based model flames are analyzed using flame-sampling mass spectrometry with tunable synchrotron-generated vacuum-ultraviolet (VUV) radiation. This experimental approach combines isomer-resolving capabilities with high sensitivity and a large dynamic range^5,6. The first part of the video describes experiments involving burner-stabilized, reduced-pressure (20-80 mbar) laminar premixed flames. A small hydrocarbon fuel was used for the selected flame to demonstrate the general experimental approach. It is shown how species’ profiles are acquired as a function of distance from the burner surface and how the tunability of the VUV photon energy is used advantageously to identify many combustion intermediates based on their ionization energies. For example, this technique has been used to study gas-phase aspects of the soot-formation processes, and the video shows how the resonance-stabilized radicals, such as C₃H₃, C₃H₅, and i-C₄H₅, are identified as important intermediates⁷. The work has been focused on soot formation processes, and, from the chemical point of view, this process is very intriguing because chemical structures containing millions of carbon atoms are assembled from a fuel molecule possessing only a few carbon atoms in just milliseconds. The second part of the video highlights a new experiment, in which an opposed-flow diffusion flame and synchrotron-based aerosol mass spectrometry are used to study the chemical composition of the combustion-generated soot particles⁴. The experimental results indicate that the widely accepted H-abstraction-C₂H₂-addition (HACA) mechanism is not the sole molecular growth process responsible for the formation of the observed large polycyclic aromatic hydrocarbons (PAHs).     

Distinct cytokine-driven responses of activated blood gammadelta T cells: insights into unconventional T cell pleiotropy

Human Vgamma9/Vdelta2 T cells comprise a small population of peripheral blood T cells that in many infectious diseases respond to the microbial metabolite, (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMB-PP), expanding to up to 50% of CD3(+) cells. This "transitional response," occurring temporally between the rapid innate and slower adaptive response, is widely viewed as proinflammatory and/or cytolytic. However, increasing evidence that different cytokines drive widely different effector functions in alphabeta T cells provoked us to apply cDNA microarrays to explore the potential pleiotropy of HMB-PP-activated Vgamma9/Vdelta2 T cells. The data and accompanying validations show that the related cytokines, IL-2, IL-4, or IL-21, each drive proliferation and comparable CD69 up-regulation but induce distinct effector responses that differ from prototypic alphabeta T cell responses. For example, the Th1-like response to IL-2 also includes expression of IL-5 and IL-13 that conversely are not induced by IL-4. The data identify specific molecules that may mediate gammadelta T cell effects. Thus, IL-21 induces a lymphoid-homing phenotype and high, unexpected expression of the follicular B cell-attracting chemokine CXCL13/BCA-1, suggesting a novel follicular B-helper-like T cell that may play a hitherto underappreciated role in humoral immunity early in infection. Such broad plasticity emphasizes the capacity of gammadelta T cells to influence the nature of the immune response to different challenges and has implications for the ongoing clinical application of cytokines together with Vgamma9/Vdelta2 TCR agonists.