Possible interference of fertilization in the natural recovery of a declining sugar maple stand in southern Quebec

A five year study was conducted in a 100–120 year old even-aged sugar maple stand in southern Quebec (46°07N 73° 56W; 305 m altitude) to explore the effect of different fertilization formulations aimed at 1) correcting the most common nutrient deficiencies observed in declining maple stands (K and Mg), 2) decreasing soil acidity, and 3) simulating enrichment with atmospheric N. Seven fertilizer mixtures were applied in the spring of 1987: 400 kg ha^-1 of K₂SO₄, CaCO₃, CaMg(CO₃)₂, (NH₄)₂SO₄, complete fertilizer (Maplegro) and 800 kg ha^-1 of an equal mixture of K₂SO₄+CaCO₃ or K₂SO₄+CaMg(CO₃)₂. The site was divided into twenty-four 25×25 m plots and treatments including control were replicated three times. Leaves and soils (organic and mineral) were sampled in 1987, 1988 and 1991. Trees were cored at 1.2 m to measure their response in diameter growth. The application of K₂SO₄+CaMg(CO₃)₂ was the only treatment that significantly increased (+13%) the average growth rate over the five year period after fertilization. The application of (NH₄)₂SO₄, Maplegro, CaMg(CO₃)₂ and K₂SO₄ reduced growth relative to the control for the five year period by 29, 24, 20 and 12 %, respectively. Positive and negative effects on growth can be explained mainly in terms of changes in leaf K. Both the application of Maplegro and (NH₄)₂SO₄ increased soil P availability. Overall, the rate of growth showed a cubic pattern of change over the 5 year period with peaks in 1988 and 1991. Trees in control plots went from a limiting foliar status of Ca and Mg, and surplus N in 1987 to a surplus of Ca and Mg, and lower N concentration in 1991. Our results suggest that nutrient deficiencies observed at our site were associated with a disturbance of the biogeochemical cycle of nutrients rather than soil nutrient depletion.Abbreviations BS base saturation - CEC cation exchange capacity - DRIS diagnosis and recommendation integrated system     

Clathrin heavy chain is required for pinocytosis, the presence of large vacuoles, and development in Dictyostelium

To investigate the intracellular role of the clathrin heavy chain in living cells, we have used "antisense" RNA to engineer mutant Dictyostelium discoideum cells that are severely deficient in clathrin heavy chain expression. Immunoblots stained with an anti-clathrin heavy chain antiserum revealed that mutant cells contained undetectable amounts of clathrin heavy chain protein. Similarly, Northern blots showed an absence of clathrin heavy chain mRNA. Clathrin heavy chain-deficient Dictyostelium cells were viable, but exhibited growth rates twofold slower than parental cells. Whereas many morphological features of the mutant cells were normal, mutant cells lacked coated pits and coated vesicles. Clathrin-deficient cells were also missing large translucent vacuoles that serve as endosomes and contractile vacuoles. In the absence of clathrin heavy chain, mutant cells displayed three distinct functional defects: (a) impairment in endocytosis of fluid phase markers, but competence in another endocytic pathway, the phagocytosis of solid particles; (b) defects in osmoregulation; and (c) inability to complete the starvation-induced development cycle.     

Habitat associations of Eurasian Skylarks Alauda arvensis breeding on Irish farmland and implications for agri-environment planning

Capsule Skylarks breeding in Ireland prefer extensive grassland habitats and almost completely avoid tillage habitats.

Aims To describe the distribution and habitat use of breeding Skylarks in Ireland, particularly in lowland agricultural habitats, and to use this information to inform conservation measures for this species.

Methods Countryside Bird Survey (CBS) and Farmland Bird Project (FBP) data were examined to determine large-scale (national) distribution and habitat selection, in addition to smaller-scale (farm- and field-level) habitat use. The CBS is a national breeding bird monitoring scheme involving 397 1-km squares. The FBP collected detailed bird and habitat data from 122 farms.

Results CBS and FBP data both showed significant regional differences in breeding Skylark densities, with the highest relative abundances in the northwest and west. Dry grassland/grass moor habitats supported the highest densities of breeding Skylarks in the CBS, which were significantly higher than in improved grassland or tillage. At the farm-level, Skylark numbers were positively related to wetland habitats but negatively associated with trees in field boundaries, dense ground vegetation and overall density of farm boundaries. At the field-scale, larger fields and unimproved grasslands were preferred.

Conclusion Agri-environment measures tailored to region-specific requirements and to the relatively local habitat preferences of target species are required if population declines of species of conservation concern, including Skylarks, are to be reversed.     

Opt-Out Panel Testing for HIV,Hepatitis B and Hepatitis C in an Urban Emergency Department: A Pilot Study

Objectives

Studies suggest 2 per 1000 people in Dublin are living with HIV, the level above which universal screening is advised. We aimed to assess the feasibility and acceptability of a universal opt-out HIV, Hepatitis B and Hepatitis C testing programme for Emergency Department patients and to describe the incidence and prevalence of blood-borne viruses in this population.

Methods

An opt-out ED blood borne virus screening programme was piloted from March 2014 to January 2015. Patients undergoing blood sampling during routine clinical care were offered HIV 1&2 antibody/antigen assay, HBV surface antigen and HCV antibody tests. Linkage to care where necessary was co-ordinated by the study team. New diagnosis and prevalence rates were defined as the new cases per 1000 tested and number of positive tests per 1000 tested respectively.

Results

Over 45 weeks of testing, of 10,000 patient visits, 8,839 individual patient samples were available for analysis following removal of duplicates. A sustained target uptake of >50% was obtained after week 3. 97(1.09%), 44(0.49%) and 447(5.05%) HIV, Hepatitis B and Hepatitis C tests were positive respectively. Of these, 7(0.08%), 20(0.22%) and 58(0.66%) were new diagnoses of HIV, Hepatitis B and Hepatitis C respectively. The new diagnosis rate for HIV, Hepatitis B and Hepatitis C was 0.8, 2.26 and 6.5 per 1000 and study prevalence for HIV, Hepatitis B and Hepatitis C was 11.0, 5.0 and 50.5 per 1000 respectively.

Conclusions

Opt-out blood borne viral screening was feasible and acceptable in an inner-city ED. Blood borne viral infections were prevalent in this population and newly diagnosed cases were diagnosed and linked to care. These results suggest widespread blood borne viral testing in differing clinical locations with differing population demographic risks may be warranted.     

Has gene duplication impacted the evolution of Eutherian longevity?

One of the greatest unresolved questions in aging biology is determining the genetic basis of interspecies longevity variation. Gene duplication is often the key to understanding the origin and evolution of important Eutherian phenotypes. We systematically identified longevity‐associated genes in model organisms that duplicated throughout Eutherian evolution. Longevity‐associated gene families have a marginally significantly higher rate of duplication compared to non‐longevity‐associated gene families. Anti‐longevity‐associated gene families have significantly increased rate of duplication compared to pro‐longevity gene families and are enriched in neurodegenerative disease categories. Conversely, duplicated pro‐longevity‐associated gene families are enriched in cell cycle genes. There is a cluster of longevity‐associated gene families that expanded solely in long‐lived species that is significantly enriched in pathways relating to 3‐UTR‐mediated translational regulation, metabolism of proteins and gene expression, pathways that have the potential to affect longevity. The identification of a gene cluster that duplicated solely in long‐lived species involved in such fundamental processes provides a promising avenue for further exploration of Eutherian longevity evolution.     

A multi‐resolution model to capture both global fluctuations of an enzyme and molecular recognition in the ligand‐binding site

In multi‐resolution simulations, different system components are simultaneously modeled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is needed in the active site to capture the chemistry of ligand binding. Global properties of the rest of the protein also play an essential role, determining the structure and fluctuations of the binding site; however, these can be modeled on a coarser level. Similarly, in the most computationally efficient scheme only the solvent hydrating the active site requires atomistic detail. We present a methodology to couple atomistic and coarse‐grained protein models, while solvating the atomistic part of the protein in atomistic water. This allows a free choice of which protein and solvent degrees of freedom to include atomistically. This multi‐resolution methodology can successfully model stable ligand binding, and we further confirm its validity by exploring the reproduction of system properties relevant to enzymatic function. In addition to a computational speedup, such an approach can allow the identification of the essential degrees of freedom playing a role in a given process, potentially yielding new insights into biomolecular function. Proteins 2016; 84:1902–1913. © 2016 Wiley Periodicals, Inc.     

Molecular characterization of rabE, a developmentally regulated Dictyostelium homolog of mammalian rab GTPases

The superfamily of small GTPases includes a subgroup, rab proteins, thought to function in the regulation of discrete steps of membrane traffic. Using a screen based on the polymerase chain reaction, we identified six partial gene sequences of novel rab genes from the soil slime mold amoeba, Dictyostelium. Stretches of conserved sequence for these genes identified them clearly as rab GTPases; unique sequences showed these were novel rab genes. A full-length clone for one gene, which we named rabE, was characterized in detail. The coding sequence of rabE was 1.1 kb in length and contained three introns. RNAse protection analysis revealed rabE expression to be under developmental regulation, with an onset of message expression after 8 h of development. Comparison of the rabE amino acid sequence with the database showed that its unique domains were most similar to the products of four mammalian rab genes. Interestingly, only the rabE protein and its four mammalian homologs contained the sequence WDIAGQE, a variation of a conserved GTPase domain. The WDIAGQE motif thus defines a subgroup of rab proteins. Identification of a Dictyostelium homolog of this group of proteins opens an experimental system to explore the structure and function of this group of WDIAGQE-containing rab proteins.     

Genomic features in the breakpoint regions between syntenic blocks

MOTIVATION: We study the largely unaligned regions between the syntenic blocks conserved in humans and mice, based on data extracted from the UCSC genome browser. These regions contain evolutionary breakpoints caused by inversion, translocation and other processes. RESULTS: We suggest explanations for the limited amount of genomic alignment in the neighbourhoods of breakpoints. We discount inferences of extensive breakpoint reuse as artefacts introduced during the reconstruction of syntenic blocks. We find that the number, size and distribution of small aligned fragments in the breakpoint regions depend on the origin of the neighbouring blocks and the other blocks on the same chromosome. We account for this and for the generalized loss of alignment in the regions partially by artefacts due to alignment protocols and partially by mutational processes operative only after the rearrangement event. These results are consistent with breakpoints occurring randomly over virtually the entire genome.