bluuebunny/crossref_metadata_2025 huggingface dataset:
Recent advances in MeCP2 structure and functionThis paper is one of a selection of papers published in this Special Issue, entitled 29th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.
Authors: Hite Kristopher C. , Adams Valerie H. , Hansen Jeffrey C.
Published: February 2009

Mutations in methyl DNA binding protein 2 (MeCP2) cause the neurodevelopmental disorder Rett syndrome (RTT). The mechanism(s) by which the native MeCP2 protein operates in the cell are not well understood. Historically, MeCP2 has been characterized as a proximal gene silencer with 2 functional domains: a methyl DNA binding domain and a transcription repression domain. However, several lines of new data indicate that MeCP2 structure and function relationships are more complex. In this review, we first discuss recent studies that have advanced understanding of the basic structural biochemistry of MeCP2. This is followed by an analysis of cell-based experiments suggesting MeCP2 is a regulator, rather than a strict silencer, of transcription. The new data establish MeCP2 as a multifunctional nuclear protein, with potentially important roles in chromatin architecture, regulation of RNA splicing, and active transcription. We conclude by discussing clinical correlations between domain-specific mutations and RTT pathology to stress that all structural domains of MeCP2 are required to properly mediate cellular function of the intact protein.
A lot about a little dot — lessons learned fromDrosophila melanogasterchromosome 4This paper is one of a selection of papers published in this Special Issue, entitled 29th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.
Authors: Riddle Nicole C. , Shaffer Christopher D. , Elgin Sarah C.R.
Published: February 2009

The fourth chromosome of Drosophila melanogaster has a number of unique properties that make it a convenient model for the study of chromatin structure. Only 4.2 Mb overall, the 1.2 Mb distal arm of chromosome 4 seen in polytene chromosomes combines characteristics of heterochromatin and euchromatin. This domain has a repeat density of ~35%, comparable to some pericentric chromosome regions, while maintaining a gene density similar to that of the other euchromatic chromosome arms. Studies of position-effect variegation have revealed that heterochromatic and euchromatic domains are interspersed on chromosome 4, and both cytological and biochemical studies have demonstrated that chromosome 4 is associated with heterochromatic marks, such as heterochromatin protein 1 and histone 3 lysine 9 methylation. Chromosome 4 is also marked by POF (painting-of-fourth), a chromosome 4-specific chromosomal protein, and utilizes a dedicated histone methyltransferase, EGG. Studies of chromosome 4 have helped to shape our understanding of heterochromatin domains and their establishment and maintenance. In this review, we provide a synthesis of the work to date and an outlook to the future.
Forces and torques in the nucleus: chromatin under mechanical constraintsThis paper is one of a selection of papers published in this Special Issue, entitled 29th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.
Authors: Lavelle Christophe
Published: February 2009

Genomic DNA in eukaryotic cells is organized in discrete chromosome territories, each consisting of a single huge hierarchically supercoiled nucleosomal fiber. Through dynamic changes in structure, resulting from chemical modifications and mechanical constraints imposed by numerous factors in vivo, chromatin plays a critical role in the regulation of DNA metabolism processes, including replication and transcription. Indeed, DNA-translocating enzymes, such as polymerases, produce physical constraints that chromatin has to overcome. Recent techniques, in particular single-molecule micromanipulation, have allowed precise quantization of forces and torques at work in the nucleus and have greatly improved our understanding of chromatin behavior under physiological mechanical constraints. These new biophysical approaches should enable us to build realistic mechanistic models and progressively specify the ad hoc and hazy “because of chromatin structure” argument often used to interpret experimental studies of biological function in the context of chromatin.
DNA sequence-dependent variation in nucleosome structure, stability, and dynamics detected by a FRET-based analysisThis paper is one of a selection of papers published in this Special Issue, entitled 29th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.
Authors: Kelbauskas L. , Woodbury N. , Lohr D.
Published: February 2009

Förster resonance energy transfer (FRET) techniques provide powerful and sensitive methods for the study of conformational features in biomolecules. Here, we review FRET-based studies of nucleosomes, focusing particularly on our work comparing the widely used nucleosome standard, 5S rDNA, and 2 promoter-derived regulatory element-containing nucleosomes, mouse mammary tumor virus (MMTV)-B and GAL10. Using several FRET approaches, we detected significant DNA sequence-dependent structure, stability, and dynamics differences among the three. In particular, 5S nucleosomes and 5S H2A/H2B-depleted nucleosomal particles have enhanced stability and diminished DNA dynamics, compared with MMTV-B and GAL10 nucleosomes and particles. H2A/H2B-depleted nucleosomes are of interest because they are produced by the activities of many transcription-associated complexes. Significant location-dependent (intranucleosomal) stability and dynamics variations were also observed. These also vary among nucleosome types. Nucleosomes restrict regulatory factor access to DNA, thereby impeding genetic processes. Eukaryotic cells possess mechanisms to alter nucleosome structure, to generate DNA access, but alterations often must be targeted to specific nucleosomes on critical regulatory DNA elements. By endowing specific nucleosomes with intrinsically higher DNA accessibility and (or) enhanced facility for conformational transitions, DNA sequence-dependent nucleosome dynamics and stability variations have the potential to facilitate nucleosome recognition and, thus, aid in the crucial targeting process. This and other nucleosome structure and function conclusions from FRET analyses are discussed.
Molecular dynamics of histone H1This paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process.
Authors: Raghuram Nikhil , Carrero Gustavo , Th’ng John , Hendzel Michael J.
Published: February 2009

The histone H1 family of nucleoproteins represents an important class of structural and architectural proteins that are responsible for maintaining and stabilizing higher-order chromatin structure. Essential for mammalian cell viability, they are responsible for gene-specific regulation of transcription and other DNA-dependent processes. In this review, we focus on the wealth of information gathered on the molecular kinetics of histone H1 molecules using novel imaging techniques, such as fluorescence recovery after photobleaching. These experiments have shed light on the effects of H1 phosphorylation and core histone acetylation in influencing chromatin structure and dynamics. We also delineate important concepts surrounding the C-terminal domain of H1, such as the intrinsic disorder hypothesis, and how it affects H1 function. Finally, we address the biochemical mechanisms behind low-affinity H1 binding.
Nucleotide excision repair and photolyase repair of UV photoproducts in nucleosomes: assessing the existence of nucleosome and non-nucleosome rDNA chromatin in vivoThis paper is one of a selection of papers published in this Special Issue, entitled 29th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.
Authors: Tremblay Maxime , Toussaint Martin , D’Amours Annie , Conconi Antonio
Published: February 2009

The genome is organized into nuclear domains, which create microenvironments that favor distinct chromatin structures and functions (e.g., highly repetitive sequences, centromeres, telomeres, noncoding sequences, inactive genes, RNA polymerase II and III transcribed genes, and the nucleolus). Correlations have been drawn between gene silencing and proximity to a heterochromatic compartment. At the other end of the scale are ribosomal genes, which are transcribed at a very high rate by RNA polymerase I (~60% of total transcription), have a loose chromatin structure, and are clustered in the nucleolus. The rDNA sequences have 2 distinct structures: active rRNA genes, which have no nucleosomes; and inactive rRNA genes, which have nucleosomes. Like DNA transcription and replication, DNA repair is modulated by the structure of chromatin, and the kinetics of DNA repair vary among the nuclear domains. Although research on DNA repair in all chromosomal contexts is important to understand the mechanisms of genome maintenance, this review focuses on nucleotide excision repair and photolyase repair of UV photoproducts in the first-order packing of DNA in chromatin: the nucleosome. In addition, it summarizes the studies that have demonstrated the existence of the 2 rDNA chromatins, and the way this feature of the rDNA locus allows for direct comparison of DNA repair in 2 very different structures: nucleosome and non-nucleosome DNA.
Structure and function of histone methylation binding proteinsThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process.
Authors: Adams-Cioaba Melanie A. , Min Jinrong
Published: February 2009

Chromatin structure is regulated by chromatin remodeling factors, histone exchange, linker histone association, and histone modification. Covalent modification of histones is an important factor in the regulation of the associated processes. The implementation and removal of various histone modifications have been implicated in DNA replication, repair, recombination, and transcription, and in RNA processing. In recent years, histone methylation has emerged as one of the key modifications regulating chromatin function. However, the mechanisms involved are complex and not well understood. A large volume of structural and biochemical information has been recently amassed for the Tudor, plant homeodomain (PHD), and malignant brain tumor (MBT) protein families. This review summarizes current knowledge of the structures and modes of recognition employed by the PHD, Tudor, and MBT domains in their interactions with target histone peptides.
Src kinase Hck association with the WASp and mDia1 cytoskeletal regulators promotes chemoattractant-induced Hck membrane targeting and activation in neutrophilsThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process.
Authors: Shi Yongquan , Dong Baoxia , Miliotis Helen , Liu Junye , Alberts Arthur S. , Zhang Jinyi , Siminovitch Katherine A.
Published: February 2009

The haemopoietic cell kinase (Hck) plays an important but poorly understood role in coupling chemoattractant stimuli to the actin cytoskeletal rearrangement required for neutrophil polarization and chemotaxis. Here, we show that Hck coimmunoprecipitates with the cytoskeletal regulatory Wiskott–Aldrich syndrome protein (WASp) and mammalian diaphanous-related formin 1 (mDia1) in chemoattractant-stimulated neutrophils, and that the 3 proteins inducibly colocalize with one another at the leading edge of chemotaxing cells. Hck interaction with WASp was found to be mediated by the Hck SH3 domain binding to the WASp proline-rich region, while Hck interaction with mDia1 was indirect but was required for binding to WASp. In contrast to wild-type cells, both WASp- and mDia1-deficient neutrophils showed severe impairment of chemokine-induced Hck membrane translocation and induction of Hck binding to WASp, and Hck activation and WASp tyrosine phosphorylation were impaired in mDia1−/−cells. Thus, chemotactic stimulation appears to induce an mDia1/Hck/WASp complex required for Hck membrane targeting and for induction of the Hck-mediated WASp tyrosine phosphorylation thought to be required for WASp-driven actin polymerization. These findings reveal that Hck functions in neutrophils to be realized, at least in part, via its interaction with mDia1 and WASp, and identifies the mDia1/Hck/WASp axis as a cytoskeletal signaling interface linking tyrosine phosphorylation to chemotactic and, possibly, other actin-based neutrophil responses.
Epigenetic specification of centromeresThis paper is one of a selection of papers published in this Special Issue, entitled 29th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.
Authors: Dalal Yamini
Published: February 2009

Centromeres are the discrete sites of spindle microtubule attachment on chromosomes during mitosis and meiosis in all eukaryotes. These highly specialized chromatin structures typically occupy the same site for thousands of generations, yet the mechanism by which centromeres are established, maintained, and function remain a mystery. In metazoans, centromeric DNA sequence has proven not to be the key determinant of centromeric identity; therefore, centromeres are thought to be epigenetically specified by their specialized chromatin structure. In all eukaryotes, the centromere-specific histone H3 variant CenH3 replaces canonical H3 within nucleosomes at centric chromatin. This specialized nucleosome is the building block upon which all other centromere-associated proteins depend. This review highlights exciting new findings that have resulted in a paradigm shift in our understanding of CenH3 assembly into centromeric chromatin, CenH3 nucleosomal structure, CenH3 chromatin folding, the contribution of these factors to centromeric identity, and finally, the intimate role cell-cycle-regulated transcription and pericentric heterochromatin play in the maintenance and integrity of centromeres.
Climate and hydrological changes in the northeastern United States: recent trends and implications for forested and aquatic ecosystemsThis article is one of a selection of papers from NE Forests 2100: A Synthesis of Climate Change Impacts on Forests of the Northeastern US and Eastern Canada.
Authors: Huntington Thomas G. , Richardson Andrew D. , McGuire Kevin J. , Hayhoe Katharine
Published: February 2009

We review twentieth century and projected twenty-first century changes in climatic and hydrologic conditions in the northeastern United States and the implications of these changes for forest ecosystems. Climate warming and increases in precipitation and associated changes in snow and hydrologic regimes have been observed over the last century, with the most pronounced changes occurring since 1970. Trends in specific climatic and hydrologic variables differ in their responses spatially (e.g., coastal vs. inland) and temporally (e.g., spring vs. summer). Trends can differ depending on the period of record analyzed, hinting at the role of decadal-scale climatic variation that is superimposed over the longer-term trend. Model predictions indicate that continued increases in temperature and precipitation across the northeastern United States can be expected over the next century. Ongoing increases in growing season length (earlier spring and later autumn) will most likely increase evapotranspiration and frequency of drought. In turn, an increase in the frequency of drought will likely increase the risk of fire and negatively impact forest productivity, maple syrup production, and the intensity of autumn foliage coloration. Climate and hydrologic changes could have profound effects on forest structure, composition, and ecological functioning in response to the changes discussed here and as described in related articles in this issue of the Journal.
Climate change effects on native fauna of northeastern forestsThis article is one of a selection of papers from NE Forests 2100: A Synthesis of Climate Change Impacts on Forests of the Northeastern US and Eastern Canada.
Authors: Rodenhouse Nicholas L. , Christenson Lynn M. , Parry Dylan , Green Linda E.
Published: February 2009

We review the observed and potential effects of climate change on native fauna of forests in northeastern North America by focusing on mammals, birds, amphibians, and insects. Our assessment is placed in the context of recent regional-scale climate projections. Climate change, particularly in recent decades, has affected the distribution and abundance of numerous wildlife species. Warming temperatures, alterations to precipitation regimes, seasonality, and climatic extremes are projected to affect species directly or indirectly in each of the focal taxa. Greatest climate change will occur during winter, and the survival of winter-active species as well as the survival, distribution, and abundance of hibernating mammals, amphibians, resident birds, and diapausing insects may be altered. Even under low emissions scenarios, effects on native fauna may be profound, affecting iconic species, endangered species, and species that provide economically valuable services, such as pollination and regulation of insect populations. However, much research that is essential to assessing the effects of climate change on the native fauna of northeastern forests remains to be done. Research that reveals causal mechanisms and relates these findings to population and community level processes will be most valuable.
Six years of plant community development after clearcut harvesting in western Washington
Authors: Peter David H. , Harrington Constance
Published: February 2009

What roles do ruderals and residuals play in early forest succession and how does repeated disturbance affect them? We examined this question by monitoring plant cover and composition on a productive site for 6 years after clearcutting and planting Douglas-fir ( Pseudotsuga menziesii (Mirb.) Franco). The replicated experiment included three treatments: vegetation control with five annual herbicide applications superimposed over two levels of slash removal (bole only or total tree plus most other wood) and an untreated control. Three species groups were analyzed: native forest, native ruderals, and exotic ruderals. Without vegetation control, the understory was rapidly invaded by exotic ruderals but was codominated by native and exotic ruderals by year 6. Douglas-fir cover surpassed covers in the three species group covers at least 3 years sooner with herbicide treatments than without. Species richness and coverage were lower for all species groups with vegetation control than without vegetation control. The effects of organic matter removal were much less than that of vegetation control. As predicted by the Intermediate Disturbance Hypothesis, repeated vegetation control resulted in declining cover and richness; however, native forest species were surprisingly resilient, maintaining as much or more cover and richness as the ruderal groups.
Responses of insect pests, pathogens, and invasive plant species to climate change in the forests of northeastern North America: What can we predict?This article is one of a selection of papers from NE Forests 2100: A Synthesis of Climate Change Impacts on Forests of the Northeastern US and Eastern Canada.
Authors: Dukes Jeffrey S. , Pontius Jennifer , Orwig David , Garnas Jeffrey R. , Rodgers Vikki L. , Brazee Nicholas , Cooke Barry , Theoharides Kathleen A. , Stange Erik E. , Harrington Robin , Ehrenfeld Joan , Gurevitch Jessica , Lerdau Manuel , Stinson Kristina , Wick Robert , Ayres Matthew
Published: February 2009

Climate models project that by 2100, the northeastern US and eastern Canada will warm by approximately 3–5 °C, with increased winter precipitation. These changes will affect trees directly and also indirectly through effects on “nuisance” species, such as insect pests, pathogens, and invasive plants. We review how basic ecological principles can be used to predict nuisance species’ responses to climate change and how this is likely to impact northeastern forests. We then examine in detail the potential responses of two pest species (hemlock woolly adelgid ( Adelges tsugae Annand) and forest tent caterpillar ( Malacosoma disstria Hubner)), two pathogens (armillaria root rot ( Armillaria spp.) and beech bark disease ( Cryptococcus fagisuga Lind. + Neonectria spp.)), and two invasive plant species (glossy buckthorn ( Frangula alnus Mill.) and oriental bittersweet ( Celastrus orbiculatus Thunb.)). Several of these species are likely to have stronger or more widespread effects on forest composition and structure under the projected climate. However, uncertainty pervades our predictions because we lack adequate data on the species and because some species depend on complex, incompletely understood, unstable relationships. While targeted research will increase our confidence in making predictions, some uncertainty will always persist. Therefore, we encourage policies that allow for this uncertainty by considering a wide range of possible scenarios.
Effects of climate change, land-use change, and invasive species on the ecology of the Cumberland forests
Authors: Dale Virginia H. , Lannom Karen O. , Tharp M. Lynn , Hodges Donald G. , Fogel Jonah
Published: February 2009

Model projections suggest that both climate and land-use changes have large effects on forest biomass and composition in the Cumberland forests of Tennessee and Kentucky. These forests have high levels of diversity, ecological importance, land-use changes, and pressures due to invasive herbivorous insects and climate change. Three general circulation models project warming for all months in 2030 and 2080 and complex patterns of precipitation change. Climate changes from 1980 to 2100 were developed from these projections and used in the forest ecosystem model LINKAGES to estimate transient changes in forest biomass and species composition over time. These projections show that climate changes can instigate a decline in forest stand biomass and then recovery as forest species composition shifts. In addition, a landscape model (LSCAP) estimates changes in land-cover types of the Cumberlands based on projected land-use changes and the demise of eastern hemlock ( Tsuga canadensis (L.) Carrière) due to the spread of the hemlock adelgid ( Adelges tsugae Annand). LSCAP suggests that land-cover changes can be quite large and can cause a decline not only in the area of forested lands but also in the size and number of large contiguous forest patches that are necessary habitat for many forest species characteristic of the Cumberlands.
Forest management optimization in Eucalyptus plantations: a goal programming approach
Authors: Bertomeu Mercedes , Diaz-Balteiro Luis , Giménez Juan Carlos
Published: February 2009

In Galicia (Spain), many Eucalyptus plantations are managed using the area-control method. The ultimate goal is to guarantee an even flow of wood in perpetuity by reaching the normal age-class distribution of the fully regulated forest by the end of a given planning horizon. However, given that the productivity of coppice stands differs throughout the successive rotation intervals, the application of this method triggers excessive fragmentation of the forest area. We present a model with the same long-term goal that does not force plantations into any given final age-class distribution. The model permits the plantations to reach a final structure with fewer harvest units of larger average size. To illustrate this approach, we developed two models and applied them to a case study. The first model used the principle of area control to achieve the fully regulated structure in each site and rotation interval of one full plantation cycle. The second model guaranteed a constant yield beyond the planning horizon without imposing any specific final age distribution on the plantation area. Both models considered objectives such as a constant yield during the planning horizon and the net present value of harvests.
Nutrient cycling in two continuous cover scenarios for forest conversion of pine plantations on sandy soil. II. Nutrient cycling via throughfall deposition and seepage flux
Authors: Gielis L. , De Schrijver A. , Wuyts K. , Staelens J. , Vandenbruwane J. , Verheyen K.
Published: February 2009

This study examined ion throughfall deposition and seepage fluxes in silver birch (Betula pendula L.) and Scots pine (Pinus sylvestris L.) regenerations a decade after a forest conversion intervention in two continuous cover scenarios (shelterwood cut versus group cut), as well as a 70-year-old control stand of Scots pine. Ion throughfall deposition was significantly influenced by the conversion scenario, being higher in the shelterwood cut than in the group cut. Compared with the control stand, nitrogen and acidifying throughfall deposition was significantly lower (–60%) in all regeneration types except for the birch regeneration under shelter. After shelter removal, ion throughfall deposition was significantly lower in all regeneration types than in the control stand. Seepage of NO3– and SO42– was significantly affected by the tree species, being higher in the birch than the pine regenerations, and SO42– seepage was significantly higher under shelter than in the group cut. After shelter removal, neither tree species nor scenario influenced the SO42– seepage, whereas the tree species still affected NO3– seepage. We conclude that the chosen forest conversion scenario is of profound influence on the ion throughfall and seepage fluxes during the first phase of a forest conversion process.
Biomass partitioning in a miniature-scale loblolly pine spacing trial
Authors: Russell Matthew B. , Burkhart Harold E. , Amateis Ralph L.
Published: February 2009

Stand conditions influence the partitioning of biomass to stem, needle, branch, and root components. Using data from 4- to 6-year-old loblolly pine ( Pinus taeda L.) trees grown in a miniature-scale spacing trial, this study determined the effect of initial spacing on the biomass partitioning of loblolly pine. Multivariate analysis of variance procedures concluded that row and column spacing did not have a significant effect on the relative amount of biomass among tree components. Root/shoot and height/diameter ratios, however, differed across densities, indicating that allometric-based partitioning tradeoffs occurred. Results from the miniature-scale trees showed trends similar to those observed with mature-sized trees at operational spatial scales. Stem and woody roots were 70% and 14% of total mass, respectively. Since these trees were physiologically young at the time of harvest, the allocation of mass to needle continued to be a priority, accounting for 10% of the total mass. Initial planting spacing did not directly affect partitioning patterns; however, allometric ratios offered some evidence that partitioning may have changed between above- and below-ground tree components. This analysis offers insight into using principles from similarity analysis to analytically relate biomass partitioning from miniature to operational spatial scales.
Influence of moisture regime and tree species composition on nitrogen cycling dynamics in hardwood forests of Mammoth Cave National Park, Kentucky, USA
Authors: Fabio Eric S. , Arthur Mary A. , Rhoades Charles C.
Published: February 2009

Understanding how natural factors interact across the landscape to influence nitrogen (N) cycling is an important focus in temperate forests because of the great inherent variability in these forests. Site-specific attributes, including local topography, soils, and vegetation, can exert important controls on N processes and retention. Seasonal monitoring of N cycling dynamics was carried out for 2 years in deciduous forest stands that differed in soil moisture status and geologic substrate, and thus, in tree species composition to determine the effects of tree species composition, mediated by moisture and soil chemistry, on N cycling. Geologic substrate influenced soil and soil leachate chemistry but did not appear to affect N cycling in the upper 10 cm. Moisture status was strongly correlated with tree species composition, which was significantly related to N cycling parameters. Sugar maple was associated with high net nitrification rates and soil solution NO3 concentrations, whereas in oak stands nitrification was low and soil solution NO3 was at or near detection limits. Tree species composition in the understory suggests that sugar maple may be increasing in mesic sites and that oak regeneration in all sites is very limited, and a shift in species composition could result in changes to N retention and export.
Canopy tree growth responses following selection harvest in seven species varying in shade tolerance
Authors: Jones Trevor A. , Domke Grant M. , Thomas Sean C.
Published: February 2009

We used tree ring measurements to investigate the temporal response of basal area increment (BAI) of canopy trees following selection harvests by sampling across a chronosequence of stands with known harvest dates in tolerant hardwood (Great Lakes – St. Lawrence) stands in central Ontario. Seven tree species of various shade tolerances ranged widely in their responses to reduced competition. The more shade-tolerant species responded more positively: shade-tolerant species showed an average increase in BAI of 35% 4–15 years postharvest compared with 16% for mid-tolerant species and –7.5% for intolerant species. All species showed a time-lag in postharvest growth responses, with maximum growth responses occurring between 3 and 15 years postharvest. Tree size was the most important factor determining the magnitude of BAI response, with smaller trees consistently responding more than larger trees. We suggest that higher growth responses to selection harvests among shade-tolerant species may contribute to declines in mid-tolerant species abundance in selection-managed stands. More broadly, interspecific variability in canopy tree responses to forest disturbance appears to follow patterns distinct from seedling and sapling responses, with important implications to forest community dynamics in both managed and unmanaged forests.
Forest floor fuel consumption and carbon emissions in Canadian boreal forest fires
Authors: de Groot W.J. , Pritchard J.M. , Lynham T.J.
Published: February 2009

In many forest types, over half of the total stand biomass is located in the forest floor. Carbon emissions during wildland fire are directly related to biomass (fuel) consumption. Consumption of forest floor fuel varies widely and is the greatest source of uncertainty in estimating total carbon emissions during fire. We used experimental burn data (59 burns, four fuel types) and wildfire data (69 plots, four fuel types) to develop a model of forest floor fuel consumption and carbon emissions in nonpeatland standing-timber fuel types. The experimental burn and wildfire data sets were analyzed separately and combined by regression to provide fuel consumption models. Model variables differed among fuel types, but preburn fuel load, duff depth, bulk density, and Canadian Forest Fire Weather Index System components at the time of burning were common significant variables. The regression R2 values ranged from 0.206 to 0.980 (P < 0.001). The log–log model for all data combined explained 79.5% of the regression variation and is now being used to estimate annual carbon emissions from wildland fire. Forest floor carbon content at the wildfires ranged from 40.9% to 53.9%, and the carbon emission rate ranged from 0.29 to 2.43 kg·m–2.
Plot Edge Bias in Forest Stand Growth Simulation Models
Authors: Monserud Robert A. , Ek Alan R.
Published: February 2009

The problem of edge bias arising in the computation of individual tree competition in stand growth simulation models is discussed. The problem arises from difficulty in characterizing tree size and spatial patterns beyond the edge of the simulation plot. Various methods for reducing this bias are reviewed along with related assumptions and major sources of error. Methods which involve shifting the simulation plot image to form a set of border plots are judged best on the basis of likely bias reduction and the relative simplicity of introduced spatial pattern periodicity.
Intraspecific Diameter Differentiation as a Measure of Species Replacement Potential
Authors: Auclair Allan N. , Goff F. Glenn
Published: February 2009

A method is developed to measure species replacement potentials in forest vegetation from tree diameter records taken at a single point in time. Replacement potentials are based on mean diameter differentiation within a species when occurring with other species. The technique incorporates a correction for differences in growth rate and maximum size between species.Successional trends established for Menominee County, Wisconsin and site-successional relations examined by cluster and principal components analyses agreed closely with results of earlier studies in the Lake States. The applicability and limitations of the method are discussed.
Gradients of Cation Concentration in Discolored and Decayed Wood of Red Maple
Authors: Safford L. O. , Shigo Alex L. , Ashley Marilyn
Published: February 2009

Eighteen columns of discolored and decayed wood associated with 2-year-old artificial wounds, and adjacent clear wood in three red maple trees, Acerrubrum L., plus six columns of clear wood in two nonwounded trees were mapped systematically for concentrations of K, Mn, Ca, Mg, and Na. Concentrations of the elements in discolored and decayed wood were higher than in adjacent clear wood in the same tree and in clear wood in the nonwounded trees. Concentration of K was highest in discolored and decayed wood near the wound and the concentration decreased toward the ends of the columns. Concentration of Mg was similar to K but the decrease in concentration toward the ends of the columns was more gradual. Concentrations of Mn and Ca were greatest at points between the wound and the ends of the columns. The different patterns of distribution between K and Mg, and Ca and Mn suggest that these elements may have different roles in the discoloration and decay process.
Relationship Between Specific Gravity and Height in the Stem of Open- and Forest-grown Balsam Fir
Authors: Heger L.
Published: February 2009

The relationship between specific gravity (fresh volume basis, the dependent variable) and height in the stem (equal to 10, 20, …, 90% of the total height) was fitted for 3 sets of 6 open-grown balsam fir (Abiesbalsamea (L.) Mill.) each; and for 3 sets of 6 forest-grown balsam fir each. The resulting polynomials were U-shaped parabolas that differed with respect to level. The difference was not related to age or height. The parabolas constructed from the pooled data, separately for the two kinds of trees, did not differ significantly. The minimum specific gravity was between 30–10% of the total height and was not related to the location of the base of live crown.
Use of Browse by White-Tailed Deer in an Enclosure in New Brunswick
Authors: Drolet C. A.
Published: February 2009

Natural browse use by white-tailed deer (Odocoileusvirginianusborealis Miller) was measured in the fall of two consecutive years using captive animals in enclosures located in regenerative stands. Oven dry twig weight prediction equations were first established for each species in the area, and browse use measured weekly by counting the number of twigs removed. Average daily browse use amounted to 0.75 kg for fawns and to 0.80 kg for adults. Shadbush (Amelanchier spp.) and willow (Salix spp.) were highly preferred by the fawns; lambkill (Kalmiaangustifolia L.), red maple (Acerrubrum L.), and withe-rod (Viburnumcassinoides L.) were preferred by the adults. A shift towards use of conifers by fawns was observed in relation with the appearance of snow. No discernible lasting damage to regeneration of commercial species was noticed even at a browsing pressure evaluated at 2–3 times the normal level.
Microstrobilate Morphology, Microsporogenesis, and Pollen Formation in Western Hemlock
Authors: Ho Rong H. , Owens John N.
Published: February 2009

In western hemlock (Tsugaheterophylla (Raf.) Sarg.), the number of microstrobili per shoot averages 4.2. Each microstrobilus averages 13.9 bud scales and 17.2 microsporophylls. Microsporangia have a transverse dehiscence layer on the abaxial surface. There are an average of 1476 pollen grains per microsporangium and 17.4 million pollen grains per gram.Meiosis begins in the fall but stops at pachytene in November; it resumes in the middle of February and is completed in 1 week. Three weeks after the completion of meiosis the first prothallial cell forms and two weeks later the pollen grains reach maturity. Pollen shedding occurs 1.5 months after the resumption of meiosis and lasts for 2 weeks. Chromosome behavior and pollen formation are normal in 98.4% of the cells and in 99.7% of the pollen grains. The common abnormalities encountered are chiasma bridges, precocious disjunction, lagging chromosomes, and undersized pollen grains. The abnormalities may be attributed to the low temperatures occurring during meiosis and pollen development.
The Prediction of Heartwood Diameter in Radiata Pine Trees
Authors: Hillis W. E. , Ditchburne Nell
Published: February 2009

Cross-sectional characteristics of Pinusradiata trees grown in different parts of Australia were examined. A regression equation which related heartwood diameter at a given age of the tree to the diameter at breast height outside bark and the product of the tree age and its diameter at 5 years gave a high degree of correspondence between observed and predicted heartwood diameter.
Factor Analytic Models of Bioclimate for Canadian Forest Regions
Authors: Miller Wayne S. , Auclair Allan N.
Published: February 2009

Relational models of bioclimate were formulated for 90 Canadian forest sections defined by J. S. Rowe in 1972. Models were based on component solutions for correlations among climatic attributes believed to be important in tree growth and reproduction. In addition, computer experiments were attempted to find remedial solutions to problems of model resolution and R/Q-mode equivalence.An attribute model based on physiographic and climatic variables was characterized by mean annual temperature, mean annual precipitation, and July average daily maximum temperature. These factors accounted for 57, 18, and 12% of the total variation on components I, II, and III, respectively.A station model based on weighted factor scores of climatic attributes alone gave a consistent and realistic separation of major forest regions. The first component distinguished Boreal forest from Pacific Coastal, Acadian, and to a lesser degree Great Lake – St. Lawrence forest regions. The second component differentiated Columbian, Grassland, and Montane regions from the Boreal maritime and Pacific Coastal forests. In addition to this generalized model, analysis of a qualitative dataset derived to help overcome problems of nonlinearity in the original data was able to identify the mean summer position of the arctic polar front and a regional low pressure locus over central Alberta.Cluster analysis of forest stations was employed to illustrate the utility of factor models. Limitations and forest applications of our results are discussed.
Biomass and Nutrient Content of 4-year-old Fertilized and Unfertilized Northern Hardwood Stands
Authors: Safford L. O. , Filip S. M.
Published: February 2009

Biomass and nutrient content of natural stands of northern hardwood regeneration were measured 4 years after clearcutting. Pin cherry and shrubs made up a significant proportion of the biomass in both unfertilized and fertilized stands. Yet these stands are well stocked with large numbers of desirable commercial species, especially paper and yellow birch. However, fertilizer greatly stimulated pin cherry to the detriment of the commercial species. Paper birch was the only commercial species to increase in average dry weight on the fertilized area.
Transport of Nutrients to Tree Root Systems
Authors: Ballard T. M. , Cole D. W.
Published: February 2009

Calculations suggest that nutrient transport through the soil to roots by mass flow accounts for less than 22, 37, and 80%, respectively, of the N, K, and Ca uptake by a Douglas-fir stand growing on a nitrogen-deficient soil derived from glacial outwash. Diffusion and dispersion, though limited by soil water content, are evidently especially important in nitrogen transport to root systems in this soil.
Vegetative Propagation of Aspen: Clonal Variation in Suckering from Root Cuttings and in Rooting of Sucker Cuttings
Authors: Schier George A.
Published: February 2009

Large clonal differences in sucker production from root cuttings and in rooting of greenwood stem cuttings taken from root suckers were found among nine Wyoming trembling aspen (Populustremuloides Michx.) clones. There appeared to be no correlation between the suckering and rooting capacity of a clone. Formation of callus at the cut ends of sucker cuttings hindered rooting.
Four-year Basal Area Growth Response of a 25-year-old Douglas-fir Stand to Thinning and Urea Fertilization
Authors: Lee Y. Jim
Published: February 2009

Four-year growth response to nitrogen fertilization and thinning is reported for an experiment established in a 25-year-old Douglas-fir stand of medium site quality. Four levels of nitrogen (0, 112, 224, and 336 kg N/ha), in the form of urea, were tested at two thinning levels in a randomized 4 × 2 × 2 factorial design replicated in 2 Blocks. Fertilizer was applied in spring or fall. Basal area growth per hectare in the thinned stand significantly surpassed that of the unthinned stand in the fourth growing period. Increased rate of nitrogen fertilization resulted in increased growth 1 year after fertilization. Urea applied in the fall resulted in greater growth response than that applied in the spring for the first growing period and over a 4-year period. Increased rate of fertilization increased mortality significantly in the fourth growing period, but had no prior effect. Thinning decreased mortality in all four growing periods.
Crown stratification by species in even-aged mixed stands of Douglas-fir – western hemlock
Authors: Wierman Charles A. , Oliver Chadwick Dearing
Published: February 2009

The pattern of vertical stratification in mixed Douglas-fir (Pseudotsugamenziesii (Mirb.) Franco) and western hemlock (Tsugaheterophylla (Raf.) Sarg.) stands was documented by observing tree interaction patterns on temporary plots in stands between 35 and 80 years old. It was found that Douglas-fir predictably dominated the hemlock. Several possible causes of the stratification were studied. They were differences in ages between species, differences in mortality patterns, and differences in growth rates. Increment borings of trees on sample plots in the 35- to 80-year stands with the observed stratification revealed the overtopping Douglas-firs and suppressed hemlocks to be essentially of the same age. Searches for dead or dying Douglas-fir in groups of mixed stands of 35 to 80 years, 22 to 35 years, and less than 12 years revealed very little Douglas-fir mortality by suppression. Therefore, the possibility of death of intermediate and suppressed Douglas-firs was not an important factor leading to Douglas-firs being found primarily in the upper crown positions. Height and diameter growth patterns of closely growing codominant Douglas-firs, co-dominant hemlocks, and suppressed hemlocks were documented by stem analyses. Douglas-fir became significantly taller than the hemlocks after about 20 years and suppressed competing hemlocks. The possibility of stratification in mixed planted stands is less certain, since only young planted stands were available for study. Management of such mixed stands appears to improve the yield and quantity of wood and reduce or eliminate costly precommercial thinnings.
Predicting the effects of different harvesting regimes on productivity and yield in northern hardwoods
Authors: Aber John D. , Botkin Danield B. , Melillo Jerry M.
Published: February 2009

Projected levels of nitrogen availability resulting from seven different harvesting regimes in northern hardwoods were used as inputs to a forest growth model. Results were analysed in terms of differences in net production and total yield by treatment. Production was highest under long (90-year) rotations and was reduced under short (45- and 30-year) rotations. Intensive harvesting (whole tree and complete forest cutting) removed a greater percentage of net production than clear-cutting. Complete forest utilization on a 90-year rotation produced the greatest total yield assuming that all harvesting treatments had the same effect on rates of regeneration and successional changes in litter input to the forest floor.
A new variety of Phellinuspini associated with cankers and decay in white firs in southwestern Oregon and northern California
Authors: Larsen Michael J. , Lombard Frances F. , Aho Paul E.
Published: February 2009

Phellinuspini var. cancriformans, newly described, is a causal agent of cankers and limited stem decay in white firs in southern Oregon and northern California. Merchantable losses attributed to the effect of this fungus are estimated to be 13% of the standing volume. Sixteen percent of the trees surveyed had large visible cankers.
Effect of SO2 on stomatal aperture and sulfur uptake of woody angiosperm seedlings
Authors: Noland T. L. , Kozlowski T. T.
Published: February 2009

Effects of SO2 pollution on stomatal aperture and sulfur uptake varied with SO2 dosage and plant species. Fumigation of Ulmusamericana L. seedlings with 1 ppm SO2 for 8 h inhibited stomatal closure and fumigation with 2 ppm SO2 for 12 h induced stomatal closure. Sulfur uptake of fumigated Ulmusamericana seedlings depended on stomatal aperture and was much higher in the light than in the dark. Fumigation of water-stressed Ginkgobiloba L. seedlings with 2 ppm SO2 for 6.5 h tended to prevent stomatal closure. However, the effects of SO2 on stomatal aperture were modulated and often overridden by environmental stresses such as low light intensity and drought.
New methods for measuring root growth capacity: their value in assessing lodgepole pine stock quality
Authors: Burdett A. N.
Published: February 2009

The survival of lodgepole pine (Pinusconforta Dougl.) planted in the spring under a variety of conditions was found to be closely related to its root growth capacity as measured by two newly developed methods. One method employed a displacement technique to measure the root volume of test seedlings, nondestructively, both at the beginning and end of a period of growth under standard conditions. The change in root volume that occurred during the test was taken as a measure of root growth capacity. The other method for measuring root growth capacity was to record, by means of a semiquantitative scale, the number of newly elongated roots possessed by test seedlings after a 1-week period of growth under standard conditions. For comparative purposes, it was found that very similar results were obtained in root growth capacity tests of this type run at two widely differing temperatures (30 °C day – 25 °C night temperature, and a constant temperature of 15 °C).