Alien plant species composition and associations with anthropogenic disturbance in North American forests

A probability-based sampling scheme was used to survey plant species composition in forests of 16 states in seven geopolitical regions of the United States (California, Colorado, Minnesota, and parts of the Pacific Northwest, Southeast, Mid-Atlantic, and Northeast) in 1994. The proportion of alien species relative to the total species number and to canopy cover in the ground stratum (0–0.6 m height) was evaluated in 279 plots. Visually evident anthropogenic disturbances (e.g., artificial regeneration, logging, prescribed burning, and grazing by livestock), if any, were recorded on each plot. In each of the seven regions we quantified (1) the percentage of the number of species and total cover comprised of alien species, (2) the difference in these percentages for disturbed and undisturbed plots, and (3) the origin or native range for the alien species.The percentage of alien species ranged from approximately 4.5% (Colorado) to approximately 13.2% (California). The percentage of alien species cover ranged from approximately 1.5% in Colorado to 25% in California. In five regions, species introduced from temperate Eurasia comprised the largest proportion of alien species and cover. In the Southeast, species introduced from far eastern and subtropical Asia dominated the alien flora. In the Mid-Atlantic, the majority of alien species was Eurasian and the majority of alien species cover consisted of far eastern and subtropical Asian species.The proportion of plots in which at least one alien species was recorded was significantly higher in disturbed than undisturbed plots in the Southeast and marginally significantly higher ($p=0.053$) in the Northeast. These results are consistent with other published studies that indicate that anthropogenic disturbance affects the structure and composition of both the ground stratum and upper canopy of forest habitats. In other regions, however, no significant differences were found.     

Blastomycosis in indoor cats: Suburban Chicago, Illinois, USA

Blastomyces dermatitidis, the etiologic agent of blastomycosis, a potentially life-threatening systemic mycosis of humans and animals, is acquired from a yet incompletely defined environmental niche. There is controversy regarding the potential for contact with the fungus in or near one’s home, particularly in urban areas. We investigated an outbreak of blastomycosis among five urban, indoor cats diagnosed at three veterinary clinics March 3–July 13, 2005, in suburban Chicago, Illinois, by owner interviews, site visits, environmental cultures for B. dermatitidis, GIS analysis, and analysis of local weather data. There were no environmental exposures common to the five cats that lived a median of 300 m from nearest body of water, in homes on a loam soil. Closest and farthest case home sites were 3.4 and 26.1 km, respectively. All cats were confined indoors except one cat that averaged 15 min/week in his backyard and was exposed to excavation. B. dermatitidis was not isolated from any of 60 environmental samples. The annualized incidence rate March through July 2005 among 6,761 cats in these practices was 178/100,000, compared to none in the previous 4 years, and 0.14/100,000 cat visits from a nationwide animal hospital registry. Precipitation January through June 2005 was 9.30 versus period mean of 14.05 ± 1.69 inches the previous 4 years (P = 0.01). Circumstantial evidence suggests acquisition of B. dermatitidis from the home site environment in five cats. Relative drought may have contributed to an apparent outbreak of blastomycosis in this urban locale.     

Spatial and temporal heterogeneity of ventilator-associated lung injury after surfactant depletion.

Volutrauma and atelectrauma have been proposed as mechanisms of ventilator-associated lung injury, but few studies have compared their relative importance in mediating lung injury. The objective of our study was to compare the injury produced by stretch (volutrauma) vs. cyclical recruitment (atelectrauma) after surfactant depletion. In saline-lavaged rabbits, we used high tidal volume, low respiratory rate, and low positive end-expiratory pressure to produce stretch injury in nondependent lung regions and cyclical recruitment in dependent lung regions. Tidal changes in shunt fraction were assessed by measuring arterial Po(2) oscillations. After ventilating for times ranging from 0 to 6 h, lungs were excised, sectioned gravitationally, and assessed for regional injury by evaluation of edema formation, chemokine expression, upregulation of inflammatory enzyme activity, and alveolar neutrophil accumulation. Edema formation, lung tissue interleukin-8 expression, and alveolar neutrophil accumulation progressed more rapidly in dependent lung regions, whereas macrophage chemotactic protein-1 expression progressed more rapidly in nondependent lung regions. Temporal and regional heterogeneity of lung injury were substantial. In this surfactant depletion model of acute lung injury, cyclical recruitment produced more injury than stretch.     

Root biomass allocation in the world's upland forests

Because the world's forests play a major role in regulating nutrient and carbon cycles, there is much interest in estimating their biomass. Estimates of aboveground biomass based on well-established methods are relatively abundant; estimates of root biomass based on standard methods are much less common. The goal of this work was to determine if a reliable method to estimate root biomass density for forests could be developed based on existing data from the literature. The forestry literature containing root biomass measurements was reviewed and summarized and relationships between both root biomass density (Mg ha⁻¹) and root:shoot ratios (R/S) as dependent variables and various edaphic and climatic independent variables, singly and in combination, were statistically tested. None of the tested independent variables of aboveground biomass density, latitude, temperature, precipitation, temperature:precipitation ratios, tree type, soil texture, and age had important explanatory value for R/S. However, linear regression analysis showed that aboveground biomass density, age, and latitudinal category were the most important predictors of root biomass density, and together explained 84% of the variation. A comparison of root biomass density estimates based on our equations with those based on use of generalized R/S ratios for forests in the United States indicated that our method tended to produce estimates that were about 20% higher. Received: 3 July 1996 / Accepted: 23 January 1997     

Sequential V(A)/Q distributions in the normal rabbit by micropore membrane inlet mass spectrometry.

We developed micropore membrane inlet mass spectrometer (MMIMS) probes to rapidly measure inert-gas partial pressures in small blood samples. The mass spectrometer output was linearly related to inert-gas partial pressure (r(2) of 0.996-1.000) and was nearly independent of large variations in inert-gas solubility in liquid samples. We infused six inert gases into five pentobarbital-anesthetized New Zealand rabbits and used the MMIMS system to measure inert-gas partial pressures in systemic and pulmonary arterial blood and in mixed expired gas samples. The retention and excretion data were transformed into distributions of ventilation-to-perfusion ratios (V(A)/Q) with the use of linear regression techniques. Distributions of V(A)/Q were unimodal and broad, consistent with prior reports in the normal rabbit. Total blood sample volume for each VA/Q distribution was 4 ml, and analysis time was 8 min. MMIMS provides a convenient method to perform the multiple inert-gas elimination technique rapidly and with small blood sample volumes.     

Fast parallel tandem mass spectral library searching using GPU hardware acceleration

Mass spectrometry-based proteomics is a maturing discipline of biologic research that is experiencing substantial growth. Instrumentation has steadily improved over time with the advent of faster and more sensitive instruments collecting ever larger data files. Consequently, the computational process of matching a peptide fragmentation pattern to its sequence, traditionally accomplished by sequence database searching and more recently also by spectral library searching, has become a bottleneck in many mass spectrometry experiments. In both of these methods, the main rate-limiting step is the comparison of an acquired spectrum with all potential matches from a spectral library or sequence database. This is a highly parallelizable process because the core computational element can be represented as a simple but arithmetically intense multiplication of two vectors. In this paper, we present a proof of concept project taking advantage of the massively parallel computing available on graphics processing units (GPUs) to distribute and accelerate the process of spectral assignment using spectral library searching. This program, which we have named FastPaSS (for Fast Parallelized Spectral Searching), is implemented in CUDA (Compute Unified Device Architecture) from NVIDIA, which allows direct access to the processors in an NVIDIA GPU. Our efforts demonstrate the feasibility of GPU computing for spectral assignment, through implementation of the validated spectral searching algorithm SpectraST in the CUDA environment.     

Physiological and hypoxic O2 tensions rapidly regulate NO production by stimulated macrophages

Nitric oxide (NO) production by inducible NO synthase (iNOS) is dependent on O₂ availability. The duration and degree of hypoxia that limit NO production are poorly defined in cultured cells. To investigate short-term O₂-mediated regulation of NO production, we used a novel forced convection cell culture system to rapidly (response time of 1.6 s) and accurately (±1 Torr) deliver specific O₂ tensions (from <1 to 157 Torr) directly to a monolayer of LPS- and IFN-stimulated RAW 264.7 cells while simultaneously measuring NO production via an electrochemical probe. Decreased O₂ availability rapidly (30 s) and reversibly decreased NO production with an apparent K_mO₂ of 22 (SD 6) Torr (31 µM) and a V_max of 4.9 (SD 0.4) nmol·min^–1·10^–6 cells. To explore potential mechanisms of decreased NO production during hypoxia, we investigated O₂-dependent changes in iNOS protein concentration, iNOS dimerization, and cellular NO consumption. iNOS protein concentration was not affected (P = 0.895). iNOS dimerization appeared to be biphasic [6 Torr (P = 0.008) and 157 Torr (P = 0.258) >36 Torr], but it did not predict NO production. NO consumption was minimal at high O₂ and NO tensions and negligible at low O₂ and NO tensions. These results are consistent with O₂ substrate limitation as a regulatory mechanism during brief hypoxic exposure. The rapid and reversible effects of physiological and pathophysiological O₂ tensions suggest that O₂ tension has the potential to regulate NO production in vivo. inducible nitric oxide synthase; substrate limitation; nitric oxide consumption     

Phosphodiesterase PdeD,dynacortin, and a Kelch repeat‐containing protein are direct GSK3 substrates in Dictyostelium that contribute to chemotaxis towards cAMP

The migration of cells according to a diffusible chemical signal in their environment is called chemotaxis, and the slime mold Dictyostelium discoideum is widely used for the study of eukaryotic chemotaxis. Dictyostelium must sense chemicals, such as cAMP, secreted during starvation to move towards the sources of the signal. Previous work demonstrated that the gskA gene encodes the Dictyostelium homologue of glycogen synthase kinase 3 (GSK3), a highly conserved serine/threonine kinase, which plays a major role in the regulation of Dictyostelium chemotaxis. Cells lacking the GskA substrates Daydreamer and GflB exhibited chemotaxis defects less severe than those exhibited by gskA^‐ (GskA null) cells, suggesting that additional GskA substrates might be involved in chemotaxis. Using phosphoproteomics we identify the GskA substrates PdeD, dynacortin and SogA and characterize the phenotypes of their respective null cells in response to the chemoattractant cAMP. All three chemotaxis phenotypes are defective, and in addition, we determine that carboxylesterase D2 is a common downstream effector of GskA, its direct substrates PdeD, GflB and the kinases GlkA and YakA, and that it also contributes to cell migration. Our findings identify new GskA substrates in cAMP signalling and break down the essential role of GskA in myosin II regulation.