bluuebunny/crossref_metadata_2025 huggingface dataset:
Does habitat or depth influence catch rates of pelagic species?
Authors: Bigelow Keith A , Maunder Mark N
Published: November 2007

The efficiency of a pelagic longline fishing operation and the species composition of the resulting catch is influenced primarily by the relationship between the distribution of hooks and species vulnerability, with vulnerability described by either depth or some suite of environmental variables. We therefore fitted longline catch rate models to determine whether catch is estimated better by vertically distributing a species by depth or by environmental conditions (e.g., temperature, thermocline gradient, and oxygen concentration). Catch rates were estimated by two methods: (i) monitoring longlines where the vertical distribution of hooks and catch in relation to depth and environmental conditions is known, and (ii) applying a statistical habitat-based standardization (statHBS) model to fishery and environmental data to develop relative abundance indices for bigeye tuna (Thunnus obesus) and blue shark (Prionace glauca). Results indicated that an understanding of gear dynamics and environmental influences are important for analyzing catch-per-unit-effort (CPUE) data correctly. Analyses based on depth-specific catch rates can lead to serious misinterpretation of abundance trends, despite the use of sophisticated statistical techniques (e.g., generalized linear mixed models). This illustrates that inappropriate inclusion or exclusion of important covariates can bias estimates of relative abundance, which may be a common occurrence in CPUE analysis.
Influence of suspended scallop cages and mussel lines on pelagic and benthic biogeochemical fluxes in Havre-aux-Maisons Lagoon, Îles-de-la-Madeleine (Quebec, Canada)
Authors: Richard Marion , Archambault Philippe , Thouzeau Gérard , McKindsey Chris W , Desrosiers Gaston
Published: November 2007

An in situ experiment was done in July 2004 to test and compare the influence of suspended bivalve cultures (1- and 2-year-old blue mussels (Mytilus edulis) and sea scallops (Placopecten magellanicus)) on biogeochemical fluxes in the water column and at the benthic interface in Havre-aux-Maisons Lagoon (Quebec, Canada). Aquaculture structures increased the pelagic macrofaunal biomass (PMB) and acted as an oxygen sink and nutrient source in the water column under dark conditions. Although PMB was lower in scallop culture, the influence of scallop cages on pelagic fluxes was similar to or greater (nitrate and nitrite) than that of mussel lines. Sediments were organically enriched, and benthic macrofaunal abundances were decreased in mussel culture zones relative to the control zone, but such an effect was not observed in the scallop zone. Nevertheless, benthic oxygen demand did not vary among culture types and control zones. Benthic nutrient fluxes were greatest beneath aquaculture structures. Both pelagic and benthic interfaces may modify oxygen and nutrient pools in culture zones in Havre-aux-Maisons Lagoon. The contribution of aquaculture structures to oxygen, ammonium, and phosphate pools may be a function of PMB and type. While aquaculture structures had an important role on nitrate and nitrite cycling, silicate turnover was mainly driven by benthic mineralization of biodeposits.
Why are salmonids pink?
Authors: Rajasingh Hannah , Våge Dag Inge , Pavey Scott A , Omholt Stig W
Published: November 2007

Pigmented flesh, a trait uniquely present in four of the 10 genera of salmonid fishes, is caused by the ubiquitous capacity of these genera for accumulating dietary carotenoids in muscle tissue. Here we combine life history reasoning with current knowledge of carotenoid metabolism to suggest a possible evolutionary scenario accounting for the emergence and maintenance of this phenotype. We claim that a basal carotenoid metabolism and a hormonally controlled targeted degradation of muscle tissue during maturation were established before the anadromous life style and that these proximal features were concomitantly exploited by natural selection in an ancestral anadromous and nest-making salmonid. Three different selection regimes are suggested to account for available empirical data concerning emergence, as well as maintenance, of the flesh pigmentation trait: a primary one driven by the need for enhanced somatic maintenance accompanying nest making under starving conditions, a secondary one driven by sexual selection, and a tertiary one driven by exposure to a meager carotenoid diet in nonanadromous freshwater populations. Finally, an experimental research program thought to be instrumental for fully resolving this evolutionary puzzle is suggested.
Response of summer chlorophyll concentration to reduced total phosphorus concentration in the Rhine River (Netherlands) and the Sacramento – San Joaquin Delta (California, USA)
Authors: Van Nieuwenhuyse Erwin E
Published: November 2007

Reductions in wastewater loading led to significant declines in mean summer total phosphorus (TP) and chlorophyll concentration (Chl) in two large flowing water systems despite their initially shallow (<2 m) euphotic depth and continually high (>40 mg·m-3) soluble reactive P concentration. In the Rhine River, a gradual 2.7-fold reduction in TP resulted in a 4-fold decline in Chl. In the Sacramento – San Joaquin Delta, an abrupt 1.5-fold reduction in TP led to an equally abrupt 2.6-fold reduction in Chl. Neither response could be attributed to coincidental changes in flow, light, or nitrogen concentration. The slope of the response (Chl:TP) in both systems paralleled the average trajectory calculated using an among-system TP–Chl relationship for a broad cross section of flowing waters. The results suggest that TP was the principal determinant of Chl in both systems and that control of phosphorus loading may be an effective tool for managing eutrophication in other flowing water systems with relatively high (10–100 mg·m-3) soluble reactive P concentrations.
Modelling and prediction of dominant height and site index of Eucalyptus globulus plantations using a nonlinear mixed-effects model approach
Authors: Wang Yue , LeMay Valerie M. , Baker Thomas G.
Published: November 2007

A nonlinear mixed-effects model approach was used to model dominant height and site index for Eucalyptus globulus Labill. plantations in southeastern Australia. Mixed effects were considered initially for all three parameters of a modified Chapman–Richards model. Inclusion of random effects improved fitting and accounted for the within-plot heteroscedasticity. To correct for within-plot autocorrelation, a power autocorrelation model allowing for irregular intervals for remeasurements was found to be most appropriate. Additional fertilizer application at age 1 year and a number of environmental variables were related to the fixed-effects parameters, but these were not statistically significant, whereas mean annual rainfall and average daily maximum temperature in July (winter) greatly reduced the residual variability among plots. The resulting nonlinear mixed-effects model combines dominant height and site index prediction into a single model and predicts polymorphic height growth rates on different sites. The model can be used to predict population-mean dominant heights and site indices for different growing conditions of E. globulus plantations using existing information of annual rainfall and daily maximum temperature. When prior measures of dominant heights at several ages are available for a plot, specific random effects can be estimated and localized predictions of dominant height or site index can be obtained.
The effects of crown ratio on the transition from juvenile to mature wood production in lodgepole pine in western Canada
Authors: Mansfield Shawn D. , Parish Roberta , Goudie James W. , Kang Kyu-Young , Ott Peter
Published: November 2007

Crown depth, tree spacing, and stand density have major effects on wood quality and fibre characteristics of trees. Lodgepole pine ( Pinus contorta Doug. ex Loud.) trees from a mixture of plantation and fire origin stands were employed to determine how crown ratio, a surrogate for stand density, affected mature wood production. In total, 104 trees were sampled, ranging from 24 to 110 years of age, from stands in western Alberta and interior British Columbia, Canada. Samples taken along the bole were measured for wood density, which was subject to segmented regression analysis to identify the transition point from juvenile to mature wood production. On average, the lodgepole pine trees were 31 (±17 SD) years old before mature wood production began. A mixed-effects model, in which combination of fixed effects (tree age, height of the sample disc relative to crown base, and crown length) and random effects (site, trees nested in sites, and discs nested in both trees and sites) proved to be the best predictor of years of mature wood production along the bole. The transition from juvenile to mature wood was shown to be below the crown base in trees <50 years old with deep crowns, and above the crown base otherwise.
Biodiversity and multiple disturbances: boreal forest ground beetle (Coleoptera: Carabidae) responses to wildfire, harvesting, and herbicide
Authors: Cobb T.P. , Langor D.W. , Spence J.R.
Published: November 2007

Rising societal demands for forest resources along with existing natural disturbance regimes suggest that sustainable forest management will increasingly depend on better understanding the cumulative effects of natural and anthropogenic disturbances. In North America, for example, there is increasing economic pressure to salvage log burned forests, although the ecological consequences of combining fire and harvesting on the same sites are unclear. We examined the short-term (2 year) responses of boreal forest ground beetles (Coleoptera: Carabidae) to the individual and combined effects of wildfire, harvesting, and herbicide. Ground beetle responses to wildfire and forestry-related disturbances differed strongly and suggested that, although some species may appear to benefit from disturbance combinations (e.g., Sericoda quadripunctata (DeGeer)), these effects are detrimental to others (e.g., Sericoda bembidioides Kirby). Species compositional variability was significantly reduced by disturbance combinations suggesting that multiple disturbances may lead to a simplification of this entire assemblage. In addition, ground beetle responses were correlated with changes in several key habitat parameters such as amount of woody debris, exposed ground, and plant species richness suggesting avenues for future study. Overall, however, our results suggest that efforts to avoid compounding disturbances on any site should be considered when developing current and future forest management guidelines.
Overstory tree mortality resulting from reintroducing fire to long-unburned longleaf pine forests: the importance of duff moisture
Authors: Varner J. Morgan , Hiers J. Kevin , Ottmar Roger D. , Gordon Doria R. , Putz Francis E. , Wade Dale D.
Published: November 2007

In forests historically maintained by frequent fire, reintroducing fire after decades of exclusion often causes widespread overstory mortality. To better understand this phenomenon, we subjected 16 fire-excluded (ca. 40 years since fire) 10 ha longleaf pine ( Pinus palustris Mill.) stands to one of four replicated burning treatments based on volumetric duff moisture content (VDMC): wet (115% VDMC); moist (85% VDMC); dry (55% VDMC); and a no-burn control. During the first 2 years postfire, overstory pines in the dry burns suffered the greatest mortality (mean 20.5%); pine mortality in the wet and moist treatments did not differ from the control treatment. Duff reduction was greatest in the dry burns (mean 46.5%), with minimal reduction in the moist and wet burns (14.5% and 5%, respectively). Nested logistic regression using trees from all treatments revealed that the best predictors of individual pine mortality were duff consumption and crown scorch (P < 0.001; R2 = 0.34). Crown scorch was significant only in dry burns, whereas duff consumption was significant across all treatments. Duff consumption was related to moisture content in lower duff (Oa; R2 = 0.78, P < 0.001). Restoring fire to long-unburned forests will require development of burn prescriptions that include the effects of duff consumption, an often overlooked fire effect.
Chlorophyll fluorescence response of red spruce and balsam fir to a watershed calcium fertilization experiment in New Hampshire
Authors: Boyce Richard L.
Published: November 2007

Decreases in soil exchangeable calcium (Ca) due to acid deposition have been linked with declines of forest species in the northeastern United States, particularly red spruce (Picea rubens Sarg.). In 2005, chlorophyll fluorescence measurements were taken on red spruce and balsam fir (Abies balsamea (L.) Mill.) trees growing on two watersheds at the Hubbard Brook Experimental Forest (HBEF) in New Hampshire. One watershed had been fertilized with CaSiO3 in 1999 to replace the soil Ca losses of the past 50 years, and the other was a reference watershed. In March, there were no differences in any chlorophyll fluorescence parameter between sites or species. In August, however, dark-adapted ratios of variable fluorescence to maximum fluorescence (Fv/Fm) were significantly greater (p = 0.05) in the Ca-treated watershed for both spruce and fir, and spruce values were significantly greater than fir. No differences were found in the light-adapted fluorescence parameters. These results suggest that both spruce and fir respond to increases in Ca availability, even though fir does not exhibit the decline symptoms seen in spruce. It is unclear what physiological effect is responsible for the observed differences in Fv/Fm. The Fv/Fm values appear to respond to differences in Ca availability in forest tree species; thus, the ratio has the potential to be used in these two watersheds at HBEF to determine if other forest species are also responding to Ca additions.
Forest sampling combining fixed- and variable-radius sample plots
Authors: Packard Kevin C. , Radtke Philip J.
Published: November 2007

We examine the statistical properties of a forest sampling strategy that combines methods of fixed- and variable-radius plot sampling. Circular fixed-radius plots are established at the same locations as variable-radius plots to take advantage of their known efficiencies for unbiasedly estimating stem density and basal area, respectively. The design eliminates the need for measuring stem diameters, except to check borderline trees on variable-radius plots. Separate controls on allowable error for stem density and basal area estimates are possible. An unbiased estimator of volume (Vol) is derived that uses an existing volume equation having the form Vol = a + bd2h, where d is tree diameter at breast height, h is tree height, and a and b are model parameters. Calculation of volume requires only the measurement of heights for those trees tallied on the variable-radius plots. Properties of the estimator are demonstrated for a mixed-species hardwood forest in the southern Appalachian Mountains of North Carolina, USA.
The law of one price in the United States and Canadian newsprint markets
Authors: Tang Xiaoli , Laaksonen-Craig Susanna
Published: November 2007

The paper presents an econometric analysis of spatial integration of the United States and Canadian newsprint markets as reflected in newsprint prices. It applies the Johansen multivariate cointegration procedure to test the law of one price for five regional markets (British Columbia, Ontario, Quebec, US east, and US west) of newsprint using monthly data for 1988–2004. Preliminary data analysis shows that all price series are nonstationary I(1) processes. The hypothesis that the law of one price holds for all five regional newsprint markets simultaneously was not supported by the Johansen multivariate test. The law of one price was also tested for national markets, and it was found to hold between US west and US east newsprint prices. The results suggested that there is a single newsprint market in the United States, whereas there are several distinct newsprint markets in Canada.
Optimized harvest planning under alternative foliage-protection scenarios to reduce volume losses to spruce budworm
Authors: Hennigar Chris R. , MacLean David A. , Porter Kevin B. , Quiring Dan T.
Published: November 2007

Spruce budworm ( Choristoneura fumiferana Clem.) severely defoliates balsam fir ( Abies balsamea (L.) Mill.) and spruce ( Picea spp.) in large periodic outbreaks and represents one of Canada’s most damaging and widespread forest insects. We present a modeling framework that integrates stand-level spruce budworm volume impacts used in the Spruce Budworm Decision Support System (SBWDSS) into an industrial-scale timber supply model for the 209 000 ha Black Brook District in northwestern New Brunswick, Canada. This approach uses linear optimization of harvest scheduling, salvage, and insecticide application to minimize volume reduction. One hundred and ninety-five scenarios were simulated, including normal and severe spruce budworm outbreaks, beginning in 2002, with combinations of varying insecticide efficacy, timing, and spatial extent of protection. After simulated severe defoliation from 2007 to 2016, maximum harvest reductions of 35% were predicted for a normal outbreak for the 2012–2016 period, and 46% for a severe outbreak for the 2017–2021 period; these impacts were reduced to 25% and 34% using re-optimized harvest scheduling and salvage. Results suggest that combined optimized salvage and harvest rescheduling could reduce future harvest reductions by up to 12%. Spatial optimization of protected areas gave similar results to those obtained using protection priority assignments based on marginal stand-level volume reduction in the SBWDSS.
A validation and evaluation of the Prognosis individual-tree basal area increment model
Authors: Froese Robert E. , Robinson Andrew P.
Published: November 2007

We subjected the individual-tree, aspatial basal area increment model developed for the Inland Empire Variant of the Forest Vegetation Simulator to validation and evaluation tests. We used a large set of independent data from the Forest Inventory and Analysis program that covers the geographic extent to which the model is usually applied. Equivalence tests did not validate the model as a predictive tool using nominated criteria, though they usually did validate the model structure as a theory. Design-unbiased estimates of prediction error suggest that the model overpredicts diameter and volume increment by 14% and 2%, respectively. Relationships between species, bias, and predictor variables suggest the model may overpredict most on productive sites. We spatially interpolated the model performance across the study area using thin-plate splines. The observed regional patterns are examined using a selection of cross-sectional transects, and reveal a complex relationship between bias and the way climate effects are incorporated in the model structure that involve differences between the fitting and testing data. The model structure is surprisingly robust, but the representation of climate effects should be a priority in future revisions.
Seasonal variation in throughfall and stemflow chemistry beneath a European beech (Fagus sylvatica) tree in relation to canopy phenology
Authors: Staelens Jeroen , De Schrijver An , Verheyen Kris
Published: November 2007

The effect of canopy phenology on major ion fluxes beneath a mature European beech ( Fagus sylvatica L.) tree is examined. Annual and seasonal ion fluxes to the forest floor were significantly higher than the incoming wet-only deposition for all ions measured other than H+. The annual throughfall to wet deposition ratio generally ranged from 2.1 to 4.8. Stemflow contributed 9%–19% of the ion input to the forest floor, except for H+. Throughfall enrichment of K+, Ca2+, Mg2+, and NO3– was significantly higher in the leafed than in the leafless season, in contrast to Na+, NH4+, and H+. The temporal pattern of ion enrichment indicated canopy release of K+, Ca2+, and Mg2+ throughout the leafed season, of Na+, Cl–, and NH4+ from emerging leaves, and of Cl– and SO42– from senescing leaves. The contribution of canopy leaching to annual net throughfall and stemflow was estimated at 96% (K+), 54% (Ca2+), 40% (Mg2+), 12% (Cl–), and 7% (Na+, SO42–). Dry deposition accounted for 58%–75% of the total deposition onto the canopy. The throughfall enrichment during the leafless season indicated high particulate and gaseous dry deposition onto the woody canopy as well as K+ release from European beech branches.
Differential impacts of the southern pine beetle, Dendroctonus frontalis, on Pinus palustris and Pinus taeda
Authors: Friedenberg Nicholas A. , Whited Brenda M. , Slone Daniel H. , Martinson Sharon J. , Ayres Matthew P.
Published: November 2007

Patterns of host use by herbivore pests can have serious consequences for natural and managed ecosystems but are often poorly understood. Here, we provide the first quantification of large differential impacts of the southern pine beetle, Dendroctonus frontalis Zimmermann, on loblolly pine, Pinus taeda L., and longleaf pine, Pinus palustris P. Mill., and evaluate putative mechanisms for the disparity. Spatially extensive survey data from recent epidemics indicate that, per square kilometre, stands of loblolly versus longleaf pine in four forests (380–1273 km2) sustained 3–18 times more local infestations and 3–116 times more tree mortality. Differences were not attributable to size or age structure of pine stands. Using pheromone-baited traps, we found no differences in the abundance of dispersing D. frontalis or its predator Thanasimus dubius Fabricius between loblolly and longleaf stands. Trapping triggered numerous attacks on trees, but the pine species did not differ in the probability of attack initiation or in the surface area of bark attacked by growing aggregations. We found no evidence for postaggregation mechanisms of discrimination or differential success on the two hosts, suggesting that early colonizers discriminate between host species before a pheromone plume is present.
Consistent estimation of long-run nonindustrial private forest owner timber supply using micro data
Authors: Favada Ibrahim M. , Kuuluvainen Jari , Uusivuori Jussi
Published: November 2007

In this paper, the effects of stumpage prices and forest and landowner characteristics on nonindustrial private forest owners’ long-run timber supply are examined using cross-sectional variation in a data set of 1860 landowners in Finland during 1994–1998. We estimate an inverse hyperbolic sine Tobit model allowing for heteroscedasticity and non-normality of errors. The hypotheses of the rotation model can be examined by decomposing the effects of the exogenous variables into the effects on the conditional mean of nonzero harvests and the effects on the probability of nonzero harvest. The results of the study are consistent with the Faustmann rotation model when the forest owner simultaneously decides both the optimal rotation age of an even-aged stand and the optimal life-cycle consumption of goods and services with in situ valuation of standing timber.
Variation in Scots pine needle longevity and nutrient conservation in different habitats and latitudes
Authors: Pensa Margus , Jalkanen Risto , Liblik Valdo
Published: November 2007

Within-species variation in needle traits is an important characteristic of conifers enabling trees to grow in different environments. We compared mean needle age (NA), shoot growth, and nutrient conservation in Scots pine ( Pinus sylvestris L.) populations in different habitats and latitudes (peatlands and Vaccinium -type stands in Estonia (59°N) and Lapland (66°30′N)). In Vaccinium-type stands, trees with higher NA (mostly in Lapland) had lower shoot length increment and lower concentration of nitrogen and phosphorus in current-year needles than trees with low NA (mostly in Estonia). However, in peatlands, variation in NA (which was as high as in the Vaccinium-type stands) was weakly or insignificantly related to shoot growth and needle nutrient concentration. Within latitudes, pines with different shoot length increments and needle nutrient concentrations tend to have similar NAs. Resorption efficiency and concentration of nitrogen and phosphorus in senescent needles decreased with the initial concentrations of these nutrients in green needles. Our results demonstrate that slow growth and low needle nutrient concentration are not necessarily followed by higher NA and greater nutrient conservation in Scots pine. This is the opposite of the results often obtained in among-species comparisons or within species along latitudinal and altitudinal gradients.
Presettlement forests and fire in southern Alabama
Authors: Predmore S. Andrew , McDaniel Josh , Kush John S.
Published: November 2007

Although the loss of Pinus palustris P. Mill. (longleaf pine) dominated communities and the alteration of the presettlement fire regimes have been documented, there is little information on the ecology of the presettlement lower Coastal Plain forests of the southeastern United States. We used 12 637 witness trees, which were recorded by General Land Office surveyors between 1820 and 1846, to identify presettlement witness tree associations and to explore witness tree – environmental variable relationships. Detrended correspondence analysis (DCA) was used to identify three witness tree associations including a Pinus spp. – Quercus marilandica (L.) Muenchh. association, a Quercus spp. – Carya spp. association, and a Persea spp. – Fagus grandifolia Ehrh. association. Canonical correspondence analysis and contingency tables were used to describe and test witness tree relationships with slope, elevation, and soil drainage. Additionally, bearing distances, used as an indicator of forest density, were compared among the witness tree associations. Species orientation shown by the DCA ordination diagram was interpreted as a gradient of fire frequency. This interpretation of a fire gradient was supported through the analysis of bearing distances, which showed high bearing distances associated with witness trees located on the high fire frequency end of the gradient. The relationships between witness trees and environmental variables as well as relationships between witness trees and bearing distances suggest that fire-dependent longleaf communities dominated the presettlement study area.
Variable retention harvest of white spruce stands and saproxylic beetle assemblages
Authors: Jacobs Joshua M. , Spence John R. , Langor David W.
Published: November 2007

Dead wood dependent (saproxylic) insects have been identified as vulnerable to the effects of modern forestry practices. We examined the effects of variable retention harvesting on saproxylic beetle assemblages. Variable retention of living green trees seeks to leave more forest structure on the landscape with the goal of maintaining ecosystem function and biodiversity. Ninety flight-intercept traps were divided between recently dead natural snags and snags killed by girdling in three replicated forest stands with 10%, 20%, 50%, and 75% residual structure and in uncut control stands. Beetles were collected and identified during the second and third summers post harvest and grouped for analyses as (i) wood- and bark-borers, (ii) fungivores, and (iii) predators. Harvesting intensity explained a relatively small amount of the variability in the beetle assemblages. However, all groups responded strongly to coarse woody debris variables and especially to snag decay class during the third postharvest summer, suggesting that factors associated with coarse woody debris quality and quantity determine the initial responses and successional trajectories of saproxylic beetle assemblages. The main effects of variable retention on saproxylic assemblages are expected to be mediated through differences in amount of coarse woody debris expected to materialize with the death and decay of green trees left as residual elements.
Species-specific response to climate reconstruction in upper-elevation mixed-conifer forests of the western Sierra Nevada, California
Authors: Hurteau Matthew , Zald Harold , North Malcolm
Published: November 2007

Dendrochronology climate reconstruction studies often sample dominant, open-grown trees to reduce competition effects and isolate annual climate influences on radial increment growth. However, there has been no examination of how species respond as stand densities increase or which species in mixed-conifer forests provide a better record of past climate. We sampled 579 trees representing five upper montane mixed-conifer species at the Teakettle Experimental Forest in California’s southern Sierra Nevada to determine species-specific responses to annual climatic fluctuations. Using the Kalman filter, we examined the affect of local stand density on growth response and whether the growth–climate relationship improved with a time lag. The Kalman filter iteratively calculates error for predicted versus actual radial growth and accounts for this variation in the corrector equation. Under current high-density conditions, shade-tolerant white fir ( Abies concolor (Gord. & Glend.) Lindl.) provided the best model for climate reconstruction. Shade-intolerant Jeffrey pine ( Pinus jeffreyi Grev. & Balf.) had a lagged response to annual climatic fluctuations, possibly because its roots may tap water reserves in granitic bedrock fissures. Open-grown trees provided more accurate records of climate. Changes in forest density in this forest may have resulted in changes in species-specific response to annual climatic fluctuations.
Black spruce (Picea mariana) foliage hosts numerous and potentially endemic fungal endophytes
Authors: Sokolski Serge , Bernier-Cardou Michèle , Piché Yves , Bérubé Jean A.
Published: November 2007

Fungal foliar endophytes (hereinafter endophytes) were isolated on malt agar from black spruce ( Picea mariana (Mill.) BSP) needles from the Quebec boreal forest during 2 successive years to study their distribution along a latitudinal transect. Twenty sites were sampled in 2002, 8 of which were sampled again in 2003, in an area located between 47°N and 54°N in the province of Quebec. The endophytes were named whenever possible, using homologies of ITS rDNA sequences from GenBank. In 2002, 232 morphotypes were classified in 40 operational taxonomic units (OTUs), and in 2003, 93 morphotypes were classified in 16 OTUs, for a total of 44 OTUs. Isolation frequencies of the most common endophyte species were 28% for Lophodermium piceae (Fuchel) Höhn., 17% for Darkera parca Whitney, Reid & Piroz, and 9% for Dwayaangam colodena Sokolski & Bérubé. Of the 44 OTUs identified, 18 were unique to P. mariana and found on one site only, possibly constituting rare endemic species. There was some evidence that needles colonized with rare endophyte species were more abundant in the western and southern regions than in the northern region. This supports our hypothesis that as the diversity of tree species surrounding the P. mariana decrease from the southern region to the northern region, the diversity of endophytes also decreases.
Partial cutting as an analogue to stem exclusion and dieback in trembling aspen (Populus tremuloides) dominated boreal mixedwoods: implications for deadwood dynamicsThis article is one of a selection of papers published in the Special Forum IUFRO 1.05 Uneven-Aged Silvicultural Research Group Conference on Natural Disturbance-Based Silviculture: Managing for Complexity.
Authors: Harvey B. D. , Brais S.
Published: November 2007

In the winter of 1998–1999, two partial harvesting treatments that removed 33% (1/3) and 61% (2/3) of stand basal area were applied to even-aged trembling aspen ( Populus tremuloides Michx.) stands and compared with unharvested control stands. Stands in the 1/3 treatment were low thinned, while stands in the 2/3 removal were crown thinned. Coarse woody debris dynamics were assessed during the following 6 years by means of permanent sampling plots and downed wood inventories. Between 1999 and 2004, tree mortality was, respectively, 18%, 17%, and 32% in control stands and 1/3 and 2/3 harvesting treatments. Although total snag density was similar between controls and partial cutting treatments, total snag basal area was significantly higher in controls in 2004. Between 1999 and 2004, net change in aspen snag density was positive for controls and negative for both partial cutting treatments. Partial cutting also exacerbated mortality of small-diameter white birch ( Betula papyrifera Marsh.). Downed wood volume increased by 35 m3·ha–1 in controls and by 25 m3·ha–1 in the 2/3 harvesting treatment, while it decreased by 7 m3·ha–1 in the 1/3 harvesting treatment. Coarse woody debris goals can be established in silviculture prescriptions; type, timing, and intensity of partial cutting are crucial to the outcome.
Natural canopy gap disturbances and their role in maintaining mixed-species forests of central Quebec, CanadaThis article is one of a selection of papers published in the Special Forum IUFRO 1.05 Uneven-Aged Silvicultural Research Group Conference on Natural Disturbance-Based Silviculture: Managing for Complexity.
Authors: Kneeshaw Daniel D. , Prévost Marcel
Published: November 2007

Until recently, natural dynamics of mixedwood stands have been largely ignored, resulting in the transformation of many North American mixedwoods into conifer- or hardwood-dominated stand types. The goal of this study was to examine canopy gap dynamics in balsam fir ( Abies balsamea (L.) Mill.) – yellow birch ( Betula alleghaniensis Britt.) mixedwoods to better understand possible mechanisms for species coexistence. Gap proportion in 12 study stands varied between 9% and 30% of the total stand area, while gap size varied from 20 to 2100 m2. Balsam fir mortality was the primary cause of gap formation. Balsam fir and mountain maple ( Acer spicatum Lamb.) dominated the tree and shrub regeneration layers, respectively. Shrub competition slows the natural filling of gaps by tree species. Our results indicate that yellow birch is most abundant in gaps over 800 m2 and balsam fir in those under 200 m2. Transition models showed that the greater longevity of yellow birch than balsam fir ensured its maintenance as a dominant. Dominant species coexistence thus results from divergent use of available resources through time and space. Forest management should maintain variability in harvest timing and size because the use of one gap size or a single rotation age will lead to an imbalance in species proportion relative to natural stands.
Residual-tree growth responses to partial stand harvest in the black spruce (Picea mariana) boreal forestThis article is one of a selection of papers published in the Special Forum IUFRO 1.05 Uneven-Aged Silvicultural Research Group Conference on Natural Disturbance-Based Silviculture: Managing for Complexity.
Authors: Thorpe H. C. , Thomas S. C. , Caspersen J. P.
Published: November 2007

Variants of partial harvesting are gaining favour as means to balance ecosystem management and timber production objectives on managed boreal forest landscapes. Understanding how residual trees respond to these alternative silvicultural treatments is a critical step towards evaluating their potential from either a conservation or a wood supply perspective. We used dendroecological techniques combined with a chronosequence approach to quantify the temporal radial growth response pattern of residual black spruce ( Picea mariana (Mill.) BSP) trees to partial harvest in northeastern Ontario. At its peak, 8–9 years after harvest, radial growth of residual trees had doubled. The growth pattern was characterized by a 2-year phase of no response, a subsequent period of increase 3–9 years after harvest, and a stage of declining rates 10–12 years after harvest. The magnitude of tree growth response depended strongly on tree age: peak postharvest growth was substantially higher for young trees, while old trees displayed only modest growth increases. Both the large magnitude and the time delay in postharvest growth responses have important implications for the development of more accurate quantitative tools to project future yields and, more generally, for determining whether partial harvesting is a viable management option for the boreal forest.
MODELING MATERIALS WITH A STRETCHING THRESHOLD
Authors: FARINA A. , FASANO A. , FUSI L. , RAJAGOPAL K. R.
Published: November 2007

We examine the dynamics of materials characterized by the presence of a deformation threshold beyond which no deformation is possible. The class of bodies that we are interested in studying are described by an implicit constitutive relationship between the Cauchy stress and the deformation gradient.

A specific one-dimensional dynamical problem is studied, showing that the mathematical model takes the form of a hyperbolic free boundary problem in which the free boundary conditions can be of two different types, selected according to whether the stress is continuous at the interface (separating the deformable region from the fully strained region), or whether it is discontinuous. Both situations have been analyzed. Sample numerical computations are carried out using data that are relevant to biological materials.

A comparison with the problem obtained from a limiting procedure for a constitutive model with a piecewise linear elastic response is performed, showing a very interesting feature, namely that the limit does not lead to the solution of the model with a threshold. This is however not surprising as the latter exhibits dissipative behavior.
ROBUST SUBSPACE CORRECTION METHODS FOR NEARLY SINGULAR SYSTEMS
Authors: LEE YOUNG-JU , WU JINBIAO , XU JINCHAO , ZIKATANOV LUDMIL
Published: November 2007

In this paper, we discuss convergence results for general (successive) subspace correction methods for solving nearly singular systems of equations. We provide parameter independent estimates under appropriate assumptions on the subspace solvers and space decompositions. The main assumption is that any component in the kernel of the singular part of the system can be decomposed into a sum of local (in each subspace) kernel components. This assumption also covers the case of "hidden" nearly singular behavior due to decreasing mesh size in the systems resulting from finite element discretizations of second order elliptic problems. To illustrate our abstract convergence framework, we analyze a multilevel method for the Neumann problem (H(grad) system), and also two-level methods for H(div) and H(curl) systems.
Histone deacetylase inhibitor suberoylanilide hydroxamic acid induces apoptosis through both mitochondrial and Fas (Cd95) signaling in head and neck squamous carcinoma cells
Authors: Gillenwater Ann M. , Zhong Meiling , Lotan Reuben
Published: November 2007

Alterations in histone acetylation status have been implicated in carcinogenesis. Histone deacetylase inhibitors, such as suberoylanilide hydroxamic acid (SAHA), can potentially reactivate aberrantly silenced genes by restoring histone acetylation and allowing gene transcription. However, the mechanisms underlying the effects of SAHA on cell growth, differentiation, and death remain unclear. In this study, we assessed the activity of SAHA in modulating cell growth and apoptosis in head and neck squamous cell carcinoma (HNSCC) cells compared with premalignant leukoplakia and normal oral cells. SAHA induced growth inhibition, cell cycle changes, and apoptosis in HNSCC cell lines but had limited effects on premalignant and normal cells. Although SAHA triggered the mitochondrial pathway of apoptosis, including cytochrome c release, caspase-3 and caspase-9 activation, and poly(ADP-ribose) polymerase cleavage in HNSCC cells, specific inhibition of caspase-9 only partially blocked the induction of apoptosis induction. SAHA also activated the extrinsic apoptosis pathway, including increased Fas and Fas ligand (FasL) expression, activation of caspase-8, and cleavage of Bid. Interfering with Fas signaling blocked apoptosis induction and blunted growth inhibition by SAHA. Our results show for the first time that SAHA induces apoptosis in HNSCC cells through activation of the Fas/FasL death pathway in addition to the intrinsic mitochondrial pathway although having comparatively little activity against precancerous and normal oral cells with intrinsic Fas and FasL expression. [Mol Cancer Ther 2007;6(11):2967–75]
MFTZ-1, an actinomycetes subspecies–derived antitumor macrolide, functions as a novel topoisomerase II poison
Authors: Xie Cheng-Ying , Zhu Hong , Lin Li-Ping , Miao Ze-Hong , Geng Mei-Yu , Cai Yu-Jun , Chen Yi , Zhao Hua-Jun , Luo Hai-Bin , Zhang Xiong-Wen , Fan Li-Ming , Shen Yue-Mao , Ding Jian
Published: November 2007

14-Ethyl-2,5,11-trimethyl-4,13,19,20-tetraoxa-tricyclo[14.2.1.17,10]eicosane-3,12-dione (MFTZ-1), a new macrolide compound isolated from Streptomyces sp. Is9131, displayed wide cytotoxicity in human tumor cell lines with an average IC50 of 0.905 μmol/L. Notably, MFTZ-1 showed significant cytotoxicity in the three multidrug resistance cell lines with an average resistance factor of 2.08. The in vivo experiments showed that MFTZ-1 had inhibitory effects on the human ovarian carcinoma HO-8910 cell line xenotransplanted in nude mice. Further studies showed that MFTZ-1 induced DNA double-strand breaks and triggered mitochondria-dependent apoptosis in human leukemia HL-60 cells. Using a yeast genetic system, we found that topoisomerase (Topo) II rather than Topo I was the primary cellular target of MFTZ-1. Most importantly, MFTZ-1 functions as a novel nonintercalative Topo II poison via binding to ATPase of Topo II, characterized by its strong inhibition on the decatenation and relaxation of Topo II. The capacity of MFTZ-1 to stabilize Topo II–DNA covalent complexes was comparable with that of the classic Topo II poison, etoposide. Moreover, using a Topo II catalytic inhibitor aclarubicin and Topo II–deficient HL-60/MX2 cells, we further showed that MFTZ-1–triggered DNA double-strand breaks and apoptosis occurred in a Topo II–dependent manner. Together, the well-defined Topo II–poisoning function and the potent antitumor activity, with the appreciable anti–multidrug resistance action in particular, promises MFTZ-1 as a novel potential Topo II–targeted agent, which merits further research and development. [Mol Cancer Ther 2007;6(11):3059–70]
Extended treatment with physiologic concentrations of dietary phytochemicals results in altered gene expression, reduced growth, and apoptosis of cancer cells
Authors: Moiseeva Elena P. , Almeida Gabriela M. , Jones George D.D. , Manson Margaret M.
Published: November 2007

Dietary phytochemicals exhibit chemopreventive potential in vivo through persistent low-dose exposures, whereas mechanistic in vitro studies with these agents generally use a high-dose single treatment. Because the latter approach is not representative of an in vivo steady state, we investigated antitumor activity of curcumin, 3,3′-diindolylmethane (DIM), epigallocatechin gallate (EGCG), genistein, or indole-3-carbinol (I3C) in breast cancer MDA-MB-231 cells, exposed in long-term culture to low concentrations, achievable in vivo. Curcumin and EGCG increased cell doubling time. Curcumin, EGCG, and I3C inhibited clonogenic growth by 55% to 60% and induced 1.5- to 2-fold higher levels of the basal caspase-3/7 activity. No changes in expression of cell cycle–related proteins or survivin were found; however, I3C reduced epidermal growth factor receptor expression, contributing to apoptosis. Because some phytochemicals are shown to inhibit DNA and histone modification, modulation of expression by the agents in a set of genes (cadherin-11, p21Cip1, urokinase-type plasminogen activator, and interleukin-6) was compared with changes induced by inhibitors of DNA methylation or histone deacetylation. The phytochemicals modified protein and/or RNA expression of these genes, with EGCG eliciting the least and DIM the most changes in gene expression. DIM and curcumin decreased cadherin-11 and increased urokinase-type plasminogen activator levels correlated with increased cell motility. Curcumin, DIM, EGCG, and genistein reduced cell sensitivity to radiation-induced DNA damage without affecting DNA repair. This model has revealed that apoptosis and not arrest is likely to be responsible for growth inhibition. It also implicated new molecular targets and activities of the agents under conditions relevant to human exposure. [Mol Cancer Ther 2007;6(11):3071–9]
Synergistic activity of the histone deacetylase inhibitor suberoylanilide hydroxamic acid and the bisphosphonate zoledronic acid against prostate cancer cells in vitro
Authors: Sonnemann Jürgen , Bumbul Beata , Beck James F.
Published: November 2007

Bisphosphonates are widely used agents for the treatment of malignant bone disease. They inhibit osteoclast-mediated bone resorption and can have direct effects on cancer cells. In this study, we investigated whether the anticancer activity of the third-generation bisphosphonate zoledronic acid (ZOL) could be enhanced by combination with the histone deacetylase inhibitor suberoylanilide hydroxamic acid (SAHA). We found that ZOL and SAHA cooperated to induce cell death in the prostate cancer cell lines LNCaP and PC-3. The effect was synergistic, as evidenced by combination index isobologram analysis. ZOL and SAHA synergized to induce dissipation of the mitochondrial transmembrane potential, to activate caspase-3, and to trigger DNA fragmentation, showing that the combination of ZOL and SAHA resulted in the initiation of apoptosis. Because ZOL acts by inhibiting the mevalonate pathway, thereby preventing protein prenylation, we explored whether the mevalonate pathway was also the target of the cooperative action of ZOL and SAHA. We found that geranylgeraniol, but not farnesol, significantly reduced ZOL/SAHA-induced cell death, indicating that the synergistic action of the agents was due to the inhibition of geranylgeranylation. Consistently, a direct inhibitor of geranylgeranylation, GGTI-298, synergized with SAHA to induce cell death, whereas an inhibitor of farnesylation, FTI-277, had no effect. In addition, SAHA synergized with mevastatin, an inhibitor of the proximal enzyme in the mevalonate pathway. These in vitro findings provide a rationale for an in vivo exploration into the potential of combining SAHA and ZOL, or other inhibitors of the mevalonate pathway, as an effective strategy for anticancer therapy. [Mol Cancer Ther 2007;6(11):2976–84]