Study of nickel silicide as a copper diffusion barrier in monocrystalline silicon solar cells

Includes bibliographical references

Can retention forestry help conserve biodiversity?

Industrial forestry typically leads to a simplified forest structure and altered species composition. Retention of trees at harvest was introduced about 25years ago to mitigate negative impacts on biodiversity, mainly from clearcutting, and is now widely practiced in boreal and temperate regions. Despite numerous studies on response of flora and fauna to retention, no comprehensive review has summarized its effects on biodiversity in comparison to clearcuts as well as un-harvested forests. Using a systematic review protocol, we completed a meta-analysis of 78 studies including 944 comparisons of biodiversity between retention cuts and either clearcuts or un-harvested forests, with the main objective of assessing whether retention forestry helps, at least in the short term, to moderate the negative effects of clearcutting on flora and fauna. Retention cuts supported higher richness and a greater abundance of forest species than clearcuts as well as higher richness and abundance of open-habitat species than un-harvested forests. For all species taken together (i.e. forest species, open-habitat species, generalist species and unclassified species), richness was higher in retention cuts than in clearcuts. Retention cuts had negative impacts on some species compared to un-harvested forest, indicating that certain forest-interior species may not survive in retention cuts. Similarly, retention cuts were less suitable for some open-habitat species compared with clearcuts. Positive effects of retention cuts on richness of forest species increased with proportion of retained trees and time since harvest, but there were not enough data to analyse possible threshold effects, that is, levels at which effects on biodiversity diminish. Spatial arrangement of the trees (aggregated vs. dispersed) had no effect on either forest species or open-habitat species, although limited data may have hindered our capacity to identify responses. Results for different comparisons were largely consistent among taxonomic groups for forest and open-habitat species, respectively.Synthesis and applications. Our meta-analysis provides support for wider use of retention forestry since it moderates negative harvesting impacts on biodiversity. Hence, it is a promising approach for integrating biodiversity conservation and production forestry, although identifying optimal solutions between these two goals may need further attention. Nevertheless, retention forestry will not substitute for conservation actions targeting certain highly specialized species associated with forest-interior or open-habitat conditions.Our meta-analysis provides support for wider use of retention forestry since it moderates negative harvesting impacts on biodiversity. Hence, it is a promising approach for integrating biodiversity conservation and production forestry, although identifying optimal solutions between these two goals may need further attention. Nevertheless, retention forestry will not substitute for conservation actions targeting certain highly specialized species associated with forest-interior or open-habitat conditions

Vegetation - environment relationships of forest communities on central eastern Vancouver Island

The Habitat Type classification system, as introduced in coastal British Columbia by MacMillan Bloedel Limited, was used for classification of old-growth plant communities in four vegetation zones on central eastern Vancouver Island. A total of 14 forest habitat types were identified. A combination of ordination and traditional association table synthesis was used in defining types. Polar ordination and an improved reciprocal averaging technique named DEtrended CORrespondence ANAlysis (DECORANA) were found to be useful for both the classification and evaluation of environmental relationships among the types. Findings substantiate claims that DECORANA is the best general purpose, indirect ordination technique currently available. In most cases, DECORANA produced superior results to polar ordination with the same data input. The most successful ordinations of individual vegetation zones were obtained for understory percent coverage data transformed to an 8-point scale. Ordinations of tree species alone, or tree and understory species combined were less useful. The distribution of old-growth vegetation in response to environmental gradients was interpreted. A moisture gradient accounted for most of the variation between habitat types within any single vegetation zone. Interpretation of the moisture gradient was tested using a Water Stress Index (WSI), which predicts potential soil moisture stress from site and climatic data. Climatic data used for input in the WSI model were extrapolated from the nearest available Resource Analysis Branch (RAB) or Atmospheric Environment Service (AES) climatological stations. Soil texture, rooting depth, coarse fragment content and depth of the surface organic horizons were used to calculate Available Water Storage Capacity (AWSC) for use in the model. The WSI proved to be a useful integrator for general site comparison of potential moisture stress. In most cases, the WSI prediction showed a closer relationship to ordination axes interpreted as moisture gradients than any other single factor, except for sites with primary moisture inputs from seepage, high water table, or those with complex orographic rainfall influences. Lack of accurate climatic data, difficulty in quantifying soil moisture relationships and the influence of complex microclimatic effects reduced the utility of the index. The temperature data available were suitable for quantifying some of the broad macroclimatic differences between zones, and for evaluating differences between samples at the elevational extremes within the Tsuga heterophylla and Abies amabi1is - Tsuga heterophylla vegetation zones. They were not adequate for a comparison of many of the plots on a site-specific basis because of problems in extrapolation from a limited data base and because of the exclusion of soil temperature and cold air drainage relationships. Potential solar radiation was used as an integrator of slope, aspect and latitude. Some habitat types were found to occur more frequently in certain radiation environments. The elevational location of vegetation zones varied by as much as 80 metres as a result of solar radiation effects. Detailed transect sampling of continuous old-growth forests in leave-strips in the Cameron and Nanaimo River valleys revealed substantial differences in species composition and distribution between the two valleys that were accounted for by climate and overall soil texture. The wetter climate and finer-textured soils of the Cameron valley supported habitat types dominated by Polyst ichum muniturn (swordfern) and Achlys triphylla (vanilla leaf) with an absence of Gaultheria shallon (salal) dominated habitat types. The drier climate and coarser-textured soils in the Nanaimo valley supported salal-dominated habitat types along the entire south-facing slope and lower north-facing slope. Significant differences in tree species distribution were also observed. Habitat types were related to units in the existing plant community classifications in B.C. and the Pacific Northwestern U.S. Most of the habitat types could be related to types previously described in British Columbia, and many were similar to those found in coastal Oregon and Washington. Some differences in the flora of Vancouver Island and the mainland were noted. There is a need for a compilation of the descriptions of all of the plant communities on Vancouver Island in a single volume.Forestry, Faculty ofGraduat

Effects of Low Levels of Dispersed Retention on the Growth and Survival of Young, Planted Douglas-Fir

Three large-scale, experimental, dispersed residual tree sites established in coastal British Columbia, Canada were measured for planted Douglas-fir tree growth and survival five to six years after planting. The dispersed trees were predominantly large diameter (60 cm+) Douglas-fir left with a range of 0% to 30% of the original forest stand basal area (0 m2 ha−1 to 14 m2 ha−1). Two sites had 0%, 5% and 15% retention, while one site had 0%, 5%, 10% and 30% retention. The trees were measured in sector plots established to randomly sample the range of microsites in each treatment. There was no detectable difference between height and basal diameter growth or mortality rates between the retention treatments over the measurement period, except for a reduction of basal diameter growth at the 30% retention level (p < 0.05). Thus a statistically significant impact on growth was demonstrated for the 30% retention compared to the 0% retention level. We expected intermediate growth rates between the 0% and the other lower retention levels but were unable to demonstrate this due to the low statistical power of the test (10 observations) and high site variability for these very young trees

Two decades of variable retention in British Columbia: a review of its implementation and effectiveness for biodiversity conservation

Stand-level retention is an important component of sustainable forest management which aims to balance ecological, social and economic objectives. Long-term retention of mature forest structures at the time of harvesting (variable retention) is intended to produce future forest stands that more closely resemble conditions that develop after natural disturbances, thereby maintaining greater diversity of habitats for a variety of organisms. Structure includes features such as live and dead trees representing multiple canopy layers, undisturbed understory vegetation and coarse woody debris. Over the past two decades, variable retention has become common on forest lands in the temperate rainforests of coastal British Columbia (BC) and has been applied to a lesser extent in inland forest types. Our review of studies in BC and in similar forest types in our region indicates that both aggregated and dispersed retention can contribute to biodiversity conservation by providing short-term ‘life-boating’ habitat for some species and by enhancing the structural characteristics of future stands. For example, greater abundance of species present in the pre-harvest forest have been documented for vegetation, birds, carabid beetles, gastropods, ectomycorrhizal fungi and soil fauna in retention cutblocks compared to clearcuts. There are, however, some negative consequences for timber production such as wind damage to retained trees and reduced growth rates of tree regeneration compared to clearcuts. The authors suggest an adaptive management approach for balancing competing objectives when faced with uncertainty. This includes monitoring the implementation and effectiveness of various strategies for achieving goals. Over two decades of experience applying variable retention harvesting to industrial-scale management of forest lands in BC suggests that it is possible to balance production of wood with biodiversity conservation.Other UBCNon UBCReviewedFacult

Revealing the role of the product metal in DNA polymerase β catalysis

DNA polymerases catalyze a metal-dependent nucleotidyl transferase reaction during extension of a DNA strand using the complementary strand as a template. The reaction has long been considered to require two magnesium ions. Recently, a third active site magnesium ion was identified in some DNA polymerase product crystallographic structures, but its role is not known. Using quantum mechanical/ molecular mechanical calculations of polymerase β, we find that a third magnesium ion positioned near the newly identified product metal site does not alter the activation barrier for the chemical reaction indicating that it does not have a role in the forward reaction. This is consistent with time-lapse crystallographic structures following insertion of S(p)-dCTPαS. Although sulfur substitution deters product metal binding, this has only a minimal effect on the rate of the forward reaction. Surprisingly, monovalent sodium or ammonium ions, positioned in the product metal site, lowered the activation barrier. These calculations highlight the impact that an active site water network can have on the energetics of the forward reaction and how metals or enzyme side chains may interact with the network to modulate the reaction barrier. These results also are discussed in the context of earlier findings indicating that magnesium at the product metal position blocks the reverse pyrophosphorolysis reaction

Requirement for transient metal ions revealed through computational analysis for DNA polymerase going in reverse

DNA polymerases facilitate faithful insertion of nucleotides, a central reaction occurring during DNA replication and repair. DNA synthesis (forward reaction) is “balanced,” as dictated by the chemical equilibrium by the reverse reaction of pyrophosphorolysis. Two closely spaced divalent metal ions (catalytic and nucleotide-binding metals) provide the scaffold for these reactions. The catalytic metal lowers the pK(a) of O3′ of the growing primer terminus, and the nucleotide-binding metal facilitates substrate binding. Recent time-lapse crystallographic studies of DNA polymerases have identified an additional metal ion (product metal) associated with pyrophosphate formation, leading to the suggestion of its possible involvement in the reverse reaction. Here, we establish a rationale for a role of the product metal using quantum mechanical/molecular mechanical calculations of the reverse reaction in the confines of the DNA polymerase β active site. Additionally, site-directed mutagenesis identifies essential residues and metal-binding sites necessary for pyrophosphorolysis. The results indicate that the catalytic metal site must be occupied by a magnesium ion for pyrophosphorolysis to occur. Critically, the product metal site is occupied by a magnesium ion early in the pyrophosphorolysis reaction path but must be removed later. The proposed dynamic nature of the active site metal ions is consistent with crystallographic structures. The transition barrier for pyrophosphorolysis was estimated to be significantly higher than that for the forward reaction, consistent with kinetic activity measurements of the respective reactions. These observations provide a framework to understand how ions and active site changes could modulate the internal chemical equilibrium of a reaction that is central to genome stability

Retention forestry to maintain multifunctional forests: a World perspective

The majority of the world's forests are used for multiple purposes, which often include the potentially conflicting goals of timber production and biodiversity conservation. A scientifically validated management approach that can reduce such conflicts is retention forestry, an approach modeled on natural processes, which emerged in the last 25 years as an alternative to clearcutting. A portion of the original stand is left unlogged to maintain the continuity of structural and compositional diversity. We detail retention forestry's ecological role, review its current practices, and summarize the large research base on the subject. Retention forestry is applicable to all forest biomes, complements conservation in reserves, and represents bottom-up conservation through forest manager involvement. A research challenge is to identify thresholds for retention amounts to achieve desired outcomes. We define key issues for future development and link retention forestry with land-zoning allocation at various scales, expanding its uses to forest restoration and the management of unevenage forests.Fil: Gustafsson, Lena. Sveriges Lantbruksuniversitet; SueciaFil: Baker, Susan C.. University of Tasmania; AustraliaFil: Bauhus, Jrgen. Universität Freiburg Im Breisgau; AlemaniaFil: Beese, William J.. Vancouver Island University; CanadáFil: Brodie, Angus. No especifica;Fil: Kouki, Jari. Itä-suomen Yliopisto; FinlandiaFil: Lindenmayer, David B.. Australian National University; AustraliaFil: Lhmus, Asko. University Of Tartu; EstoniaFil: Martínez Pastur, Guillermo José. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Austral de Investigaciones Científicas; ArgentinaFil: Messier, Christian. Le Réseau de L'université Du Québec; CanadáFil: Neyland, Mark. Forestry Tasmania; AustraliaFil: Palik, Brian. United States Department of Agriculture; ArgentinaFil: Sverdrup Thygeson, Anne. Universitetet For Miljø- Og Biovitenskap; NoruegaFil: Volney, W. Jan A.. Northern Forestry Centre; CanadáFil: Wayne, Adrian. Western Australia Department Of Environment And Conservation; AustraliaFil: Franklin, Jerry F.. University Of Washington, Seattle

An intramolecular FRET system monitors fingers subdomain opening in Klentaq1

A major goal of polymerase research is to determine the mechanism through which a nucleotide complementary to a templating DNA base is selected and delivered to the polymerase active site. Structural evidence suggests a large open-to-closed conformational change affecting the fingers subdomain as being crucial to the process. We previously designed a FRET system capable of measuring the rate of fingers subdomain closure in the presence of correct nucleotide. However, this FRET system was limited in that it could not directly measure the rate of fingers subdomain opening by FRET after polymerization or in the absence of DNA. Here we report the development of a new system capable of measuring both fingers subdomain closure and reopening by FRET, and show that the rate of fingers subdomain opening is limited only by the rate of polymerization. We anticipate that this system will scale down to the single molecule level, allowing measurement of fingers subdomain movements in the presence of incorrect nucleotide and in the absence of DNA