The northern limit of Pinus banksiana Lamb. in Canada: explaining the difference between the eastern and western distributions

Aim Present northern distribution limit of jack pine (Pinus banksiana Lamb.) follows the northern limit of continuous open boreal forest in western Canada, but not in eastern Canada where it is located further south. We tested the hypothesis that fire plays a more important role than climate in explaining the present position of the northern distribution limit of jack pine. Location An experimental jack pine plantation was set up in 1992, c. 300 km north of the present distribution limit of the species, in the Boniface river area of northern Québec (57°43′ N, 76°05′ W). Methods Climate and fire data were used to compare sites at and north of the present distribution limit of jack pine. In 2001, surviving individuals from the plantation were measured (total height, annual shoot elongation, basal diameter, and presence/absence of cones). Results Climate data from the ten weather stations used in this study did not show major differences. The northern limit of jack pine distribution is closely associated with the occurrence of fires larger than 200 ha. Survival of the planted jack pines was 31%. About 25% of the surviving pines qualified as normal, single‐stem individuals; the others were slightly uprooted and/or showed marks of erosion or foraging. Cones were produced, although no viable seeds were found. Main conclusions The low number of degree‐days above 5 °C at the plantation site could explain why the seeds were not viable. However, such climate conditions are not sufficient to prevent growth, as was shown by annual shoot elongation measurements. Most of the surviving jack pines from the Boniface river plantation are relatively healthy and follow a normal developmental programme. Low fire frequency and small fire size are amongst the main factors that prevented P. banksiana from migrating further north or east following deglaciation in northern Québec and Labrador.     

Aberrant allele frequencies of the SNPs located in microRNA target sites are potentially associated with human cancers

MicroRNAs (miRNAs) are a class of noncoding small RNAs that regulate gene expression by base pairing with target mRNAs at the 3'-terminal untranslated regions (3'-UTRs), leading to mRNA cleavage or translational repression. Single-nucleotide polymorphisms (SNPs) located at miRNA-binding sites (miRNA-binding SNPs) are likely to affect the expression of the miRNA target and may contribute to the susceptibility of humans to common diseases. We herein performed a genome-wide analysis of SNPs located in the miRNA-binding sites of the 3'-UTR of various human genes. We found that miRNA-binding SNPs are negatively selected in respect to SNP distribution between the miRNA-binding 'seed' sequence and the entire 3'-UTR sequence. Furthermore, we comprehensively defined the expression of each miRNA-binding SNP in cancers versus normal tissues through mining EST databases. Interestingly, we found that some miRNA-binding SNPs exhibit significant different allele frequencies between the human cancer EST libraries and the dbSNP database. More importantly, using human cancer specimens against the dbSNP database for case-control association studies, we found that twelve miRNA-binding SNPs indeed display an aberrant allele frequency in human cancers. Hence, SNPs located in miRNA-binding sites affect miRNA target expression and function, and are potentially associated with cancers.     

Characterization of a C-C bond hydrolase from Sphingomonas wittichii RW1 with novel specificities towards polychlorinated biphenyl metabolites

Sphingomonas wittichii RW1 degrades chlorinated dibenzofurans and dibenzo-p-dioxins via meta cleavage. We used inverse PCR to amplify dxnB2, a gene encoding one of three meta-cleavage product (MCP) hydrolases identified in the organism that are homologues of BphD involved in biphenyl catabolism. Purified DxnB2 catalyzed the hydrolysis of 8-OH 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate (HOPDA) approximately six times faster than for HOPDA at saturating substrate concentrations. Moreover, the specificity of DxnB2 for HOPDA (k(cat)/K(m) = 1.2 x 10(7) M(-1) s(-1)) was about half that of the BphDs of Burkholderia xenovorans LB400 and Rhodococcus globerulus P6, two potent polychlorinated biphenyl (PCB)-degrading strains. Interestingly, DxnB2 transformed 3-Cl and 4-OH HOPDAs, compounds that inhibit the BphDs and limit PCB degradation. DxnB2 had a higher specificity for 9-Cl HOPDA than for HOPDA but a lower specificity for 8-Cl HOPDA (k(cat)/K(m) = 1.7 x 10(6) M(-1) s(-1)), the chlorinated analog of 8-OH HOPDA produced during dibenzofuran catabolism. Phylogenetic analyses based on structure-guided sequence alignment revealed that DxnB2 belongs to a previously unrecognized class of MCP hydrolases, evolutionarily divergent from the BphDs although the physiological substrates of both enzyme types are HOPDAs. However, both classes of enzymes have mainly small hydrophobic residues lining the subsite that binds the C-6 phenyl of HOPDA, in contrast to the bulky hydrophobic residues (Phe106, Phe135, Trp150, and Phe197) found in the class II enzymes that prefer substrates possessing a C-6 alkyl. Thr196 and/or Asn203 appears to be an important determinant of specificity for DxnB2, potentially forming hydrogen bonds with the 8-OH substituent. This study demonstrates that the substrate specificities of evolutionarily divergent hydrolases may be useful for degrading mixtures of pollutants, such as PCBs.     

A wavelet‐based approach to evaluate the roles of structural and functional landscape heterogeneity in animal space use at multiple scales

The functional relationship between habitat utilization and landscape spatial heterogeneity is fundamental to understanding the spatial nature of animal distribution across scales. Although structural and functional properties of landscape spatial heterogeneity can have different consequences for animal species, few studies have explicitly considered both forms of heterogeneity, partly due to the lack of general methods for direct assessment of scale‐specific associations between variables. We present a wavelet‐based approach to evaluate the roles of structural and functional landscape spatial heterogeneity in animal space use at multiple spatial scales. As a case study, we examined scale‐specific space use patterns of American black bears Ursus americanus in response to structural and functional spatial heterogeneity as well as spatial patterns of vegetation age‐classes in a Canadian boreal forest. We found strong differences in the effects of structural and functional spatial heterogeneity and the scales at which they are associated with the patterns of habitat use by black bears. Functional heterogeneity alone affected space use at 800 and 1600‐m scales, but had significant effects when interacting with structural heterogeneity at 400, 800, and 1600‐m scales. Compared with male bears, female black bears were most sensitive to patterns of forage abundance at intermediate scales, or more specifically, in young and regenerating forests that provide abundant soft mast in boreal forests. Our study highlights the importance of accounting for scale‐dependent properties of (structural and functional) spatial heterogeneity in assessing the ecological effects of landscape components and the effectiveness of the wavelet transform technique in identifying such scale‐specific relationships.     

Early medication use in new-onset rheumatoid arthritis may delay joint replacement: results of a large population-based study

IntroductionUse of disease-modifying anti-rheumatic drugs (DMARDs) in rheumatoid arthritis (RA) may prevent joint damage and potentially reduce joint replacement surgeries. We assessed the association between RA drug use and joint replacement in Quebec, Canada.MethodsA cohort of new-onset RA patients was identified from Quebec’s physician billing and hospitalization databases from 2002–2011. The outcome was defined using procedure codes submitted by orthopedic surgeons. Medication use was obtained from pharmacy databases. We used alternative Cox regression models with time-dependent variables measuring the cumulative effects of past use during different time windows (one model focussing on the first year after cohort entry) for methotrexate (MTX), and other DMARDs. Models were adjusted for baseline sociodemographics, co-morbidity and prior health service use, time-dependent cumulative use of other drugs (anti-tumor necrosis factor [anti-TNF] agents, other biologics, cyclooxygenase-2 inhibitors [COXIBs], nonselective nonsteroidal antiinflammatory drugs [NSAIDs], and systemic steroids), and markers of disease severity.ResultsDuring follow-up, 608 joint replacements occurred among 11,333 patients (median follow-up: 4.6 years). The best-fitting model relied on the cumulative early use (within the first year after cohort entry) of MTX and of other DMARDs, with an interaction between MTX and other DMARDs. In this model, greater exposure within the first year, to either MTX (adjusted hazard ratio, HR = 0.95 per 1 month, 95 % confidence interval, 95 % CI 0.93-0.97) or other DMARDs (HR = 0.97, 95 % CI 0.95-0.99) was associated with longer time to joint replacement.ConclusionsOur results suggest that longer exposure to either methotrexate (MTX) or other DMARDs within the first year after RA diagnosis is associated with longer time to joint replacement surgery.

Electronic supplementary material

The online version of this article (doi:10.1186/s13075-015-0713-3) contains supplementary material, which is available to authorized users.     

Biodiversity conservation in old-growth boreal forest: black spruce and balsam fir snags harbour distinct assemblages of saproxylic beetles

Biodiversity conservation of forest ecosystems strongly relies on effective dead wood management. However, the responses of saproxylic communities to variations in dead wood characteristics remains poorly documented, a lack of knowledge that may impede the development of efficient management strategies. We established the relationship between saproxylic beetles—at the species and community levels—and attributes of black spruce and balsam fir in old-growth boreal forests. The relationship was first evaluated for individual snag bole segments, and then for forest stands. A total of 168 bole sections were collected in summer 2006 along a compositional gradient ranging from black spruce-dominated stands to balsam fir-dominated ones, in a boreal forest dominated by >90-year-old stands. A total of 16,804 beetles belonging to 47 species emerged from bole segments, with 21% of the species being found exclusively in black spruce snags and 36% exclusively in balsam fir snags. Black spruce and balsam fir snags thus contributed differently to forest biodiversity by being inhabited by different saproxylic communities. Wood density was an important attribute in the host-use patterns for several species of saproxylic beetles, but no relationship was found between snag availability within stands and abundance of beetles strongly linked to either black spruce or balsam fir. Our study outlines the relative contribution of tree compositional diversity to saproxylic species, while highlighting the contribution of black spruce and balsam fir to animal diversity in old-growth boreal forests.     

Comparative shotgun proteomic analysis of Clostridium acetobutylicum from butanol fermentation using glucose and xylose

Background

Cytokinin is a plant hormone that plays a crucial role in several processes of plant growth and development. In recent years, major breakthroughs have been achieved in the elucidation of the metabolism, the signal perception and transduction, as well as the biological functions of cytokinin. An important activity of cytokinin is the involvement in chloroplast development and function. Although this biological function has already been known for 50 years, the exact mechanisms remain elusive.

Results

To elucidate the effects of altered endogenous cytokinin content on the structure and function of the chloroplasts, chloroplast subfractions (stroma and thylakoids) from transgenic Pssu-ipt and 35S:CKX1 tobacco (Nicotiana tabacum) plants with, respectively, elevated and reduced endogenous cytokinin content were analysed using two different 2-DE approaches. Firstly, thykaloids were analysed by blue-native polyacrylamide gel electrophoresis followed by SDS-PAGE (BN/SDS-PAGE). Image analysis of the gel spot pattern thus obtained from thylakoids showed no substantial differences between wild-type and transgenic tobacco plants. Secondly, a quantitative DIGE analysis of CHAPS soluble proteins derived from chloroplast subfractions indicated significant gel spot abundance differences in the stroma fraction. Upon identification by MALDI-TOF/TOF mass spectrometry, these proteins could be assigned to the Calvin-Benson cycle and photoprotective mechanisms.

Conclusion

Taken together, presented proteomic data reveal that the constitutively altered cytokinin status of transgenic plants does not result in any qualitative changes in either stroma proteins or protein complexes of thylakoid membranes of fully developed chloroplasts, while few but significant quantitative differences are observed in stroma proteins.     

Trafficking of surface-linked and encapsulated liposomal antigens in macrophages: an immunocytochemical study.

Liposomal antigens are potent adjuvants of humoral and cell-mediated immunity. Although this property requires as an essential condition a physical association between the antigen and the phospholipid vehicle, the nature of the association, i.e., encapsulation or surface linkage, markedly influences the outcome of the elicited response. Available evidence suggests that macrophages are involved in this fine tuning of the immune response in a manner that is not yet clearly established. It is postulated that this might be related to their capacity to interact differently with surface-linked and encapsulated formulations. Using conalbumin as a model antigen, we address the question by analyzing the movements of encapsulated and surface-linked antigen as well as those of MHC-II molecules in macrophages in a pulse-chase immunoelectron microscopic study carried out over a 24-hr period. The antigen was followed using a polyclonal serum specifically raised against fragmented conalbumin (fCA) that allows the detection of processed antigen and of some MHC-peptide complexes. The results indicate that, in macrophages, the two liposomal formulations affect macrophage morphology in distinct ways and circulate through the various subcellular compartments with different kinetics. On the basis of the overall results, we conclude that surface-linked antigen gains access less readily to the endogenous presentation pathway than encapsulated antigen but can favor a more sustained activation of the immune system through its production of exosome-like structures and its more thorough utilization of the MHC-II pathway.     

Plant virus RNAs. Coordinated recruitment of conserved host functions by (+) ssRNA viruses during early infection events

Positive-sense single-stranded RNA viruses have developed strategies to exploit cellular resources at the expense of host mRNAs. The genomes of these viruses display a variety of structures at their 5' and 3' ends that differentiate them from cellular mRNAs. Despite this structural diversity, viral RNAs are still circularized by juxtaposition of their 5' and 3' ends, similar to the process used by cellular mRNAs. Also reminiscent of the mechanisms used by host mRNAs, translation of viral RNAs involves the recruitment of translation initiation factors. However, the roles played by these factors likely differ from those played by cellular mRNAs. In keeping with the general parsimony typical of RNA viruses, these host factors also participate in viral RNA replication. However, the dual use of host factors requires that viral RNA template utilization be regulated to avoid conflict between replication and translation. The molecular composition of the large ribonucleoprotein complexes that form the viral RNA replication and translation machineries likely evolves over the course of infection to allow for switching template use from translation to replication.