Breeding Bird Community Continues to Colonize Riparian Buffers Ten Years after Harvest.

Riparian ecosystems integrate aquatic and terrestrial communities and often contain unique assemblages of flora and fauna. Retention of forested buffers along riparian habitats is a commonly employed practice to reduce potential negative effects of land use on aquatic systems. However, very few studies have examined long-term population and community responses to buffers, leading to considerable uncertainty about effectiveness of this practice for achieving conservation and management outcomes. We examined short- (1-2 years) and long-term (~10 years) avian community responses (occupancy and abundance) to riparian buffer prescriptions to clearcut logging silvicultural practices in the Pacific Northwest USA. We used a Before-After-Control-Impact experimental approach and temporally replicated point counts analyzed within a Bayesian framework. Our experimental design consisted of forested control sites with no harvest, sites with relatively narrow (~13 m) forested buffers on each side of the stream, and sites with wider (~30 m) and more variable width unharvested buffer. Buffer treatments exhibited a 31-44% increase in mean species richness in the post-harvest years, a pattern most evident 10 years post-harvest. Post-harvest, species turnover was much higher on both treatments (63-74%) relative to the controls (29%). We did not find evidence of local extinction for any species but found strong evidence (no overlap in 95% credible intervals) for an increase in site occupancy on both Narrow (short-term: 7%; long-term 29%) and Wide buffers (short-term: 21%; long-term 93%) relative to controls after harvest. We did not find a treatment effect on total avian abundance. When assessing relationships between buffer width and site level abundance of four riparian specialists, we did not find strong evidence of reduced abundance in Narrow or Wide buffers. Silviculture regulations in this region dictate average buffer widths on small and large permanent streams that range from ~22-25 m. Guidelines for this region are within the range of buffers included in our study, in which we observed no evidence for avian species loss or for a decline in species abundance (including riparian associated species).

Effects of management intervention on post-disturbance community composition: an experimental analysis using bayesian hierarchical models.

As human demand for ecosystem products increases, management intervention may become more frequent after environmental disturbances. Evaluations of ecological responses to cumulative effects of management interventions and natural disturbances provide critical decision-support tools for managers who strive to balance environmental conservation and economic development. We conducted an experiment to evaluate the effects of salvage logging on avian community composition in lodgepole pine (Pinus contorta) forests affected by beetle outbreaks in Oregon, USA, 1996-1998. Treatments consisted of the removal of lodgepole pine snags only, and live trees were not harvested. We used a bayesian hierarchical model to quantify occupancy dynamics for 27 breeding species, while accounting for variation in the detection process. We examined how magnitude and precision of treatment effects varied when incorporating prior information from a separate intervention study that occurred in a similar ecological system. Regardless of which prior we evaluated, we found no evidence that the harvest treatment had a negative impact on species richness, with an estimated average of 0.2-2.2 more species in harvested stands than unharvested stands. Estimated average similarity between control and treatment stands ranged from 0.82-0.87 (1 indicating complete similarity between a pair of stands) and suggested that treatment stands did not contain novel assemblies of species responding to the harvesting prescription. Estimated treatment effects were positive for twenty-four (90%) of the species, although the credible intervals contained 0 in all cases. These results suggest that, unlike most post-fire salvage logging prescriptions, selective harvesting after beetle outbreaks may meet multiple management objectives, including the maintenance of avian community richness comparable to what is found in unharvested stands. Our results provide managers with prescription alternatives to respond to severe beetle outbreaks that continue to occur across extensive portions of the dry forests of western North America.

Avian species richness in relation to intensive forest management practices in early seral tree plantations.

BACKGROUND: Managers of landscapes dedicated to forest commodity production require information about how practices influence biological diversity. Individual species and communities may be threatened if management practices truncate or simplify forest age classes that are essential for reproduction and survival. For instance, the degradation and loss of complex diverse forest in young age classes have been associated with declines in forest-associated Neotropical migrant bird populations in the Pacific Northwest, USA. These declines may be exacerbated by intensive forest management practices that reduce hardwood and broadleaf shrub cover in order to promote growth of economically valuable tree species in plantations. METHODOLOGY AND PRINCIPAL FINDINGS: We used a Bayesian hierarchical model to evaluate relationships between avian species richness and vegetation variables that reflect stand management intensity (primarily via herbicide application) on 212 tree plantations in the Coast Range, Oregon, USA. Specifically, we estimated the influence of broadleaf hardwood vegetation cover, which is reduced through herbicide applications, on bird species richness and individual species occupancy. Our model accounted for imperfect detection. We used average predictive comparisons to quantify the degree of association between vegetation variables and species richness. Both conifer and hardwood cover were positively associated with total species richness, suggesting that these components of forest stand composition may be important predictors of alpha diversity. Estimates of species richness were 35-80% lower when imperfect detection was ignored (depending on covariate values), a result that has critical implications for previous efforts that have examined relationships between forest composition and species richness. CONCLUSION AND SIGNIFICANCE: Our results revealed that individual and community responses were positively associated with both conifer and hardwood cover. In our system, patterns of bird community assembly appear to be associated with stand management strategies that retain or increase hardwood vegetation while simultaneously regenerating the conifer cover in commercial tree plantations.

Estimating thresholds in occupancy when species detection is imperfect.

Identification of thresholds (state changes over a narrow range of values) is of basic and applied ecological interest. However, current methods of estimating thresholds in occupancy ignore variation in the observation process and may lead to erroneous conclusions about ecological relationships or to the development of inappropriate conservation targets. We present a model to estimate a threshold in occupancy while accounting for imperfect species detection. The threshold relationship is described by a break-point (threshold) and the change in slope (threshold effect). Imperfect species detection is incorporated by jointly modeling species occurrence and species detection. We used WinBUGS to evaluate the model through simulation and to fit the model to avian occurrence data for three species from 212 sites with two replicate surveys in 2007-2008. To determine if accounting for imperfect detection changed the inference about thresholds in avian occupancy in relation to habitat structure, we compared our model to results from a commonly used threshold model (segmented logistic regression). We fit this model in both frequentist and Bayesian modes of inference. Results of the simulation study showed that 95% posterior intervals contained the true value of the parameter in approximately 95% of the simulations. As expected, the simulations indicated more precise threshold and parameter estimates as sample size increased. In the empirical study, we found evidence for threshold relationships for four species by covariate combinations when ignoring species detection. However, when we included variation from the observation process, threshold relationships were not supported in three of those four cases (95% posterior intervals included 0). In general, confidence intervals for the threshold effect were larger when we accounted for species nondetection than when we ignored nondetection. This model can be extended to investigate abundance thresholds as a function of ecological and anthropogenic factors, as well as multispecies hierarchical models.

Chemoprevention of dibenzo[a,l]pyrene transplacental carcinogenesis in mice born to mothers administered green tea: primary role of caffeine.

Our laboratory recently developed a mouse model of transplacental induction of lymphoma, lung and liver cancer by the polycyclic aromatic hydrocarbon, dibenzo[a,l]pyrene (DBP). Pregnant B6129SF1 females, bred to 129S1/SvIm males, were treated on day 17 of gestation with an oral dose of 15 mg/kg DBP. Beginning on day 0 of gestation, dams were given (ad lib) buffered water, 0.5% green tea, 0.5% decaffeinated green tea, caffeine or epigallocatechin-3-gallate (EGCG) (both at equivalent concentrations found in tea). The concentration of the teas (and corresponding caffeine and EGCG) was increased to 1.0% upon entering the second trimester, 1.5% at onset of the third trimester and continued at 1.5% until pups were weaned at 21 days of age. Offspring were raised with normal drinking water and AIN93G diet. Beginning at 2 months of age, offspring experienced significant mortalities due to an aggressive T-cell lymphoma as seen in our previous studies. Ingestion of caffeinated, but not decaffeinated, green tea provided modest but significant protection (P = 0.03) against mortality. Caffeine provided a more robust (P = 0.006) protection, but EGCG was without effect. Offspring also developed DBP-dependent lung adenomas. All treatments significantly reduced lung tumor multiplicity relative to controls (P < 0.02). EGCG was most effective at decreasing tumor burden (P = 0.005) by on average over 40% compared with controls. Induction of Cytochrome P450 (Cyp)1b1 in maternal liver may reduce bioavailability of DBP to the fetus as a mechanism of chemoprevention. This is the first demonstration that maternal ingestion of green tea, during pregnancy and nursing, provides protection against transplacental carcinogenesis.

Fetal mouse Cyp1b1 and transplacental carcinogenesis from maternal exposure to dibenzo(a,l)pyrene.

Dibenzo(a,l)pyrene (DBP) is among the most potent carcinogenic polycyclic aromatic hydrocarbons. Previously, we showed that DBP administration to pregnant mice resulted in high mortality of offspring from an aggressive T-cell lymphoma. All mice that survive to 10 months of age exhibit lung tumors with high multiplicity. Recombinant cytochrome P450 (cyp) 1b1 from mice and the homologue 1B1 in humans exhibit high activity toward the metabolic activation of DBP. Targeted disruption of the cyp1b1 gene protects against most DBP-dependent cancers. Mice heterozygous for the disrupted cyp1b1 allele were used to examine the effect of cyp1b1 gene dosage on DBP transplacental carcinogenesis. Dams were treated with 1 or 15 mg/kg of DBP or 50 mg/kg of benzo(a)pyrene. Cyp1b1-null offspring did not develop lymphoma, whereas wild-type and heterozygous siblings, born to dams given the high dose of DBP, exhibited significant mortalities between 10 and 30 weeks of age. At 10 months, all groups had lung adenomas or carcinomas [9.5%, 40.3%, 25.6%, and 100% incidences for controls, benzo(a)pyrene, 1 and 15 mg/kg DBP, respectively]. Cyp1b1 status did not alter benzo(a)pyrene-dependent carcinogenesis. At 1 mg/kg DBP, cyp1b1 status altered the incidence of lung tumors (19.0, 27.8, and 28.6% for nulls, heterozygous, and wild-type, respectively). At 15 mg/kg, tumor multiplicities in cyp1b1 wild-type (9.3) and heterozygous (9.5) offspring were nearly twice that of cyp1b1-null siblings (5.0). These data confirm that cyp1b1 bioactivation of DBP occurs in fetal target tissues, following transplacental exposure, with the thymus and lung as primary and secondary targets, respectively.

Frequency of appropriate and inappropriate presentation and analysis methods of ordered categorical data in the veterinary dermatology literature from January 2003 to June 2006.

Clinical outcomes that are difficult to measure directly are often graded with ordinal scales in the veterinary dermatology literature to approximate objective evaluation. Ordered categorical scales require statistical presentation and analysis methods consistent with the structure of the data. The objective of this study was to determine the frequency of inappropriate presentation and analysis methods of ordered categorical data in the recent veterinary dermatology literature. A total of 62 articles published between 1 January 2003 and 30 June 2006 in 16 journals reported categorical scales and were included in the study. The presentation and analysis methods of ordered categorical data were classified as appropriate or inappropriate based on published recommendations. Forty articles (64.5%) utilized a median of four ordinal scales (range 1-13). Inappropriate presentation methods of ordered categorical data were identified in 23 of 40 articles (57.5%). These included reporting inappropriate summary statistics (n = 17) and summation of ad hoc numerical rating scales (n = 15). Inappropriate analytical methods were used in nine of 40 articles (22.5%). These included inappropriate use of t-tests (n = 3) and analysis of variance (anova, n = 6). The frequency of inappropriate presentation and analysis methods of ordered categorical data in the veterinary dermatology literature is similar to that reported for several fields in the human medical literature. In order to reduce the likelihood of making unwarranted implications or conclusions regarding ordinal data, authors should follow established guidelines for methods of presentation and analysis of ordered categorical scales.

Urban dust particulate matter alters PAH-induced carcinogenesis by inhibition of CYP1A1 and CYP1B1.

The polycyclic aromatic hydrocarbons (PAHs) benzo[a]pyrene (B[a]P) and dibenzo[a,l]pyrene (DB[a,l]P) are well-studied environmental carcinogens, however, their potency within a complex mixture is uncertain. We investigated the influence of urban dust particulate matter (UDPM) on the bioactivation and tumor initiation of B[a]P and DB[a,l]P in an initiation-promotion tumorigenesis model. SENCAR mice were treated topically with UDPM or in combination with B[a]P or DB[a,l]P, followed by weekly application of the promoter 12-O-tetradecanoylphorbol-13 acetate. UDPM exhibited weak tumor-initiating activity but significantly delayed the onset of B[a]P-induced tumor initiation by two-fold. When cotreated with UDPM, DB[a,l]P-treated animals displayed no significant difference in tumor-initiating activity, compared with DB[a,l]P alone. Tumor initiation correlated with PAH-DNA adducts, as detected by (33)P-postlabeling and reversed-phase high-performance liquid chromatography. Induction of cytochrome P450 (CYP)1A1 and 1B1 proteins was also detected following UDPM treatment or cotreatment with B[a]P or DB[a,l]P, indicating PAH bioactivation. Further genotoxicity analyses by the comet assay revealed that cotreatment of UDPM plus B[a]P or DB[a,l]P resulted in increased DNA strand breaks, compared with PAH treatment alone. The metabolizing activities of CYP1A1 and CYP1B1, as measured by the 7-ethoxyresorufin O-deethylation (EROD) assay, revealed that UDPM noncompetitively inhibited CYP1A1 and CYP1B1 EROD activity in a dose-dependent manner. Overall, these data suggest that components within complex mixtures can alter PAH-induced carcinogenesis by inhibiting CYP bioactivation and influence other genotoxic effects, such as oxidative DNA damage. These data further suggest that in addition to the levels of potent PAH, the effects of other mixture components must be considered when predicting human cancer risk.

Ethanol-dependent toxicity in zebrafish is partially attenuated by antioxidants.

Ethanol is a well-established developmental toxicant; however, the molecular and cellular mechanism(s) of toxicity remains unclear. It has been suggested that ethanol metabolism leads to oxidative stress resulting in an increase in cell death. Alcohol developmental toxicity has not been well studied in zebrafish; however, zebrafish represent an excellent vertebrate model for investigating and understanding normal and aberrant development. To evaluate ethanol metabolism dependent toxicity, chemical inhibitors of the ethanol metabolizing enzymes were utilized. Embryos co-exposed to ethanol and a combination of ethanol metabolism inhibitors led to a significant increase in the occurrence of pericardial edema. Further, in the presence of the inhibitor mixture there was an increase in developmental malformations at lower ethanol concentrations. Cell death has been implicated as a potential explanation for ethanol-dependent toxicity. Using cell death assays, ethanol significantly increased embryonic cell death. To determine if oxidative stress underlies cardiovascular dysfunction, embryos were co-exposed to ethanol and several antioxidants. The antioxidants, glutathione and lipoic acid, partially attenuated the incidence of pericardial edema. The effectiveness of the antioxidants to protect the embryos from ethanol-induced cell death was also evaluated. The antioxidants provided no protection against cell death. Thus, ethanol-mediated pericardial edema and cell death appear to be mechanistically distinct.