A Statistical Evaluation of Sediment Quality Triad Benthic Community Measurements in PAH-Impacted Sediments at a Manufactured Gas Plant Site along the Hudson River

The sediment quality triad (SQT) assumes that three measurements (sediment chemistry, laboratory bioassay, and benthic macroinvertebrate counts) comprise an independent assessment of impact, which when integrated using a weight-of-evidence approach provides a comprehensive assessment of risk. An SQT assessment was conducted on 41 sediment samples collected adjacent to a manufactured gas plant site on the freshwater reach of the Hudson River in New York State. The assessment shows that the benthic macroinvertebrate data did not correlate with either sediment or pore water polycyclic aromatic hydrocarbon (PAH) concentrations, nor did these data show consistent relationships to the results of laboratory bioassay testing (Hyalella azteca 28-day survival or biomass). The benthic community across the site and reference areas was comprised of few taxa, all of which were pollution-tolerant organisms with tolerance values greater than or equal to five. Only in significantly impacted sediment samples with PAH concentrations in the thousands of milligrams per kilogram, pore water concentrations above 100 toxic units, and visible non-aqueous phase liquid present in the sample did the benthic macroinvertebrate data show a response. In contrast, sediment and pore water PAH measurements and H. azteca toxicity testing provided consistent interpretation of impact. These results illustrate that benthic macroinvertebrate data may contain less information value and be a more challenging line of evidence to interpret in triad studies conducted in certain ecological settings; in this case, a large-order river with a relatively depauperate benthic community dominated by species tolerant of PAHs.     

Evaluation of the Phytoextraction Potential at an Acid-Mine-Drainage-Impacted Site

Four plant species were found naturally growing at an acid mine drainage (AMD)-impacted site contaminated with 9430 mg kg^?1Al, 76,000 Fe mg kg^?1, ～150 mg kg^?1Mn, and 420 mg kg^?1 Mg: soybeans (Glycine max), cattails (Typha latifolia), goldenrods (Solidago sp.), and reed grass (Phragmites australis). The metal uptake selectivity was Fe?Mg～Mn>Al for cattails, Mg>Mn>Fe>Al for goldenrods, and Fe?Al>Mg>Mn for reeds. When metal translocation factors, shoot concentrations, and toxicity of the contaminants were correlated, cattails and reeds were more effective at the site than the soybeans or goldenrods. Cattails had a translocation factor of 3.71 for Al, 3.3 for Mg, 1.98 for Mn, and only 0.2 for Fe. The translocation factors for reeds were much higher for Fe (8.64) and Al (7.3). Cattails (1.11 mg Al g^?1 shoot) and reeds (3.4 mg g^?1 g shoot) were both able to hyperaccumulate Al. Additional research is warranted to ascertain if the uptake efficiencies can be enhanced by the use of chelators.     

A Decision Making Framework for Sediment Assessment Developed for the Great Lakes

A rule-based, weight-of-evidence approach for assessing contaminated sediment on a site-by-site basis in the Laurentian Great Lakes is described. Information from four lines of evidence—surficial sediment chemistry, laboratory toxicity, invertebrate community structure and invertebrate tissue biomagnification—is integrated within each line to produce a pass (‘?’) or fail (‘+’) conclusion, then combined across lines resulting in one of 16 outcome scenarios. For each scenario, the current status of the site, interpretation, and management recommendations are given. Management recommendation(s) can range from no action to risk management required (9 of the 16 scenarios). Within each line of evidence, the strength of each response can also be ranked (e.g., score of 1 to 4), providing managers with more information to aid decision options. Other issues that influence scientific management recommendations include site stability, subsurface contamination and spatial extent of effects. The decision framework is intended to be transparent, comprehensive (incorporating exposure, effect, weight-of-evidence, and risk), and minimally uncertain.     

Seed Plant Endemism on Hainan Island: A Framework for Conservation Actions

Hainan, the second largest island of China, has the most extensive and best preserved tropical forests of this country. A network of 68 protected areas (54 of them are terrestrial) provides in situ conservation for the unique ecosystems of the island. We: (1) discuss an updated check-list of seed-plant species that are endemic to Hainan, (2) evaluate the extent to which the endemic flora has been the subject of molecular studies, and (3) investigate the conservation status of these species. We recognize 397 endemic species on the island, 271 of which are reported in the protected areas, and 144 of which have been Red-Listed (85 assigned to the Critically Endangered (40) or Endangered (45) IUCN categories). The families with the highest number of endemics are Rubiaceae (33 species), Lauraceae (27 species), and Poaceae (26 species). The island has only seven endemic genera, all of which are unispecific. Compared with other tropical islands, Hainan has a low number of endemics but our preliminary observations suggest that the island has a highly disharmonic flora when compared with that from the mainland. Nevertheless, most of the major clades of the seed-plant tree of life with representatives in China also have endemic species on the island. We argue that the low levels of endemism reflect the continental nature of Hainan and the fact that several areas of the island have not been fully inventoried. We were unable to find a single molecular systematic study focusing exclusively on the Hainan endemics; however, 24 of the endemic species have been included in phylogenetic studies targeting particular genera or families. Future research/conservation actions for the endemic flora of Hainan should focus in developing: (1) a red-list that assesses all 397 endemic species, (2) comprehensive floristic studies for the protected areas, (3) molecular phylogenetic and conservation genetic studies with a primary focus on the endemics, (4) studies to understand what ecological interactions are important in the biology of the endemic species, and (5) eco-geographical studies to identify Important Biodiversity Zones of endemism within Hainan and therefore potential new protected areas.     

Initial Development and Evaluation of a Sediment Quality Index for the Great Lakes Region

A sediment quality index (SQI) based on the Canadian Water Quality Index was developed and applied to the assessment of sediment quality in two Great Lakes Areas Of Concern where metals are the primary contaminants of potential concern, Peninsula Harbour (Lake Superior) and Collingwood Harbour (Lake Huron). The SQI was calculated according to an equation incorporating two elements; scope—the number of variables that do not meet guideline objectives; and, amplitude—the magnitude by which variables exceed guideline objectives. Categorizations of sediment quality were developed based on SQI scores. The robustness of the SQI was evaluated through comparison of the relative rankings of sediment quality in the two test areas with results obtained from principle components analysis (PCA) incorporating reference sites, and calculations of hazard quotients (HQs). Trends and rankings in sediment quality determined by the SQI were similar to those calculated using PCA at both test areas. The HQs also appeared to be good indicators of sediment quality. Both the SQI and HQ methods are based on existing Sediment Quality Guidelines, but the SQI had the added benefit of allowing straightforward integration of multiple contaminants. The SQI and PCA analyses appeared complementary in that the SQI incorporated information on the number of variables exceeding guideline values and the degree to which these guidelines were exceeded. The PCA allowed a simple check of the SQI by relating test conditions to regional background. It is recommended that this analysis be performed concurrently with SQI to ensure that non-anthropogenic sources of contaminants (metals in this case) are not considered as representing an anthropogenic hazard.     

Site selection for the cleavage furrow at cytokinesis

The question of how the site for division of the cytoplasm is determined at the end of mitosis has been studied for over a century, and it remains an active, controversial and fascinating problem in cell biology. This problem draws on the use of several model cell types, with the goal of understanding and identifying how the cell cycle regulates signals between the mitotic apparatus and the cell cortex. Studies in different cell types and using a vast array of techniques reveal different answers: these might reflect differences in experimental approaches, multiple and redundant mechanisms and, importantly, diversity in biology. In this article (which is part of the Cytokinesis series), we present a summary and critique of the major models for the roles of the mitotic apparatus microtubules in stimulating furrow formation at cytokinesis.     

Evaluation of a Collagen-Chitosan Hydrogel for Potential Use as a Pro-Angiogenic Site for Islet Transplantation

Islet transplantation to treat type 1 diabetes (T1D) has shown varied long-term success, due in part to insufficient blood supply to maintain the islets. In the current study, collagen and collagen:chitosan (10:1) hydrogels, +/- circulating angiogenic cells (CACs), were compared for their ability to produce a pro-angiogenic environment in a streptozotocin-induced mouse model of T1D. Initial characterization showed that collagen-chitosan gels were mechanically stronger than the collagen gels (0.7kPa vs. 0.4kPa elastic modulus, respectively), had more cross-links (9.2 vs. 7.4/µm²), and were degraded more slowly by collagenase. After gelation with CACs, live/dead staining showed greater CAC viability in the collagen-chitosan gels after 18h compared to collagen (79% vs. 69%). In vivo, collagen-chitosan gels, subcutaneously implanted for up to 6 weeks in a T1D mouse, showed increased levels of pro-angiogenic cytokines over time. By 6 weeks, anti-islet cytokine levels were decreased in all matrix formulations ± CACs. The 6-week implants demonstrated increased expression of VCAM-1 in collagen-chitosan implants. Despite this, infiltrating vWF⁺ and CXCR4⁺ angiogenic cell numbers were not different between the implant types, which may be due to a delayed and reduced cytokine response in a T1D versus non-diabetic setting. The mechanical, degradation and cytokine data all suggest that the collagen-chitosan gel may be a suitable candidate for use as a pro-angiogenic ectopic islet transplant site.     

Application of a Demographic Model for Evaluating Proposed Oyster-Restoration Actions in Chesapeake Bay

A demographic model was developed for oyster populations in the Chesapeake Bay, USA, to explore population responses to proposed management actions in support of an Environmental Impact Statement and Environmental Risk Assessment for oyster restoration. The model indicated that high natural mortality due to disease strongly controlled the population of native Eastern oysters. Continuing restoration effort at recent levels was predicted not to increase oyster populations. An enhanced restoration program that included habitat improvement and stocking would likely increase populations, particularly in areas with lower salinity where disease prevalence was lower. However, population numbers would likely reach a plateau much less than the restoration goal a few years after enhanced restoration efforts ended. A harvest moratorium was predicted to have a smaller positive effect than enhanced restoration. A moratorium likely would take much longer than the 10-year restoration period to meet restoration goals given the present high natural mortality rates. The proposed introduction of non-native Suminoe oysters was not modeled because insufficient data existed with which to parameterize the model. These results were used semi-quantitatively in the Ecological Risk Assessment to evaluate population trajectories and speculate about population changes more than 10 years after implementation of a management action.     

Development and Application of a Framework for Analyzing the Impacts of Urban Transportation

To adequately analyze the impacts associated with the rising use of automobiles, an assessment framework is needed that includes environment, health, economic, and sociocultural impacts. Such a framework was developed and applied to a proposed freeway-widening project in Edmonton, Canada. The assessment framework was developed using both Multi-Criteria Analysis and the Ecosystem Approach to Human Health (Ecohealth). Community participation was vital in the application of the assessment framework to this case study. Six stakeholder groups, including community members, City Councillors, and health, environment, and transportation experts, provided needed qualitative data for the assessment framework. Quantitative data were gathered from an ecological study design that associated traffic volumes with respiratory conditions in Edmonton. Community members perceptions about the impacts of the freeway widening differed from those of the expert groups in a number of areas. Environmental and health degradation was more of an issue to community members than to expert groups. Though respiratory conditions were not projected to increase by a significant amount because of the freeway widening, further analysis is necessary on other biophysical and socioeconomic impacts listed in the assessment framework. The divergence in opinion between community members and experts suggests that more communication is needed between these groups in relation to transportation planning. The Ecohealth approach ensures that community concerns are addressed in transportation planning.     

Evaluation of the Antioxidant Actions of Ferulic Acid and Catechins

We have evaluated the abilities of ferulic acid, (±) catechin, (+) catechin and (-) epicatechin to scavenge the reactive oxygen species hydroxyl radical (OH±), hypochlorous acid (HOCl) and peroxyl radicals (RO₂).

Ferulic acid tested at concentrations up to 5 mM inhibited the peroxidation of phospholipid liposomes. Both (±) and (+) catechin and (-) epicatechin were much more effective. All the compounds tested reacted with trichloromethyl peroxyl radical (CCl₃O₂) with rate constants > 1 × 10⁶M^?1s^?1.

A mixture of FeCl₃-EDTA, hydrogen peroxide (H₂O₂) and ascorbic acid at pH 7.4, has often been used to generate hydroxyl radicals (OH.) which are detected by their ability to cause damage to the sugar deoxyribose. Ferulic acid, (+) and (±) catechin and (-) epicatechin inhibited deoxyribose damage by reacting with OH. with rate constants of 4.5 × 10⁹M^?1s^?1, 3.65 × 10⁹M^?1s^?1, 2.36 × 10⁹M^?1s^?1 and 2.84 × 10⁹M^?1s^?1 respectively. (-) Epicatechin, ferulic acid and the (+) and (±) catechins exerted pro-oxidant action, accelerating damage to DNA in the presence of a bleomycin-iron complex. On a molar basis, ferulic acid was less effective in causing damage to DNA compared with the catechins.

A mixture of hypoxanthine and xanthine oxidase generates O₂ which reduces cytochrome c to ferrocytochrome c. (+) Catechin and (-) epicatechin inhibited the reduction of cytochrome c in a concentration dependent manner. Ferulic acid and (±) catechin had only weak effects.

All the compounds tested were able to scavenge hypochlorous acid at a rate sufficient to protect alpha-1-antiproteinase against inactivation. Our results show that catechins and ferulic acid possess antioxidant properties. This may become important given the current search for “natural” replacements for synthetic antioxidant food additives.     

Evaluation of an Integrated Framework for Biodiversity with a New Metric for Functional Dispersion

Growing interest in understanding ecological patterns from phylogenetic and functional perspectives has driven the development of metrics that capture variation in evolutionary histories or ecological functions of species. Recently, an integrated framework based on Hill numbers was developed that measures three dimensions of biodiversity based on abundance, phylogeny and function of species. This framework is highly flexible, allowing comparison of those diversity dimensions, including different aspects of a single dimension and their integration into a single measure. The behavior of those metrics with regard to variation in data structure has not been explored in detail, yet is critical for ensuring an appropriate match between the concept and its measurement. We evaluated how each metric responds to particular data structures and developed a new metric for functional biodiversity. The phylogenetic metric is sensitive to variation in the topology of phylogenetic trees, including variation in the relative lengths of basal, internal and terminal branches. In contrast, the functional metric exhibited multiple shortcomings: (1) species that are functionally redundant contribute nothing to functional diversity and (2) a single highly distinct species causes functional diversity to approach the minimum possible value. We introduced an alternative, improved metric based on functional dispersion that solves both of these problems. In addition, the new metric exhibited more desirable behavior when based on multiple traits.     

GPU-Accelerated Framework for Intracoronary Optical Coherence Tomography Imaging at the Push of a Button

Frequency domain optical coherence tomography (FD-OCT) has become one of the important clinical tools for intracoronary imaging to diagnose and monitor coronary artery disease, which has been one of the leading causes of death. To help more accurate diagnosis and monitoring of the disease, many researchers have recently worked on visualization of various coronary microscopic features including stent struts by constructing three-dimensional (3D) volumetric rendering from series of cross-sectional intracoronary FD-OCT images. In this paper, we present the first, to our knowledge, "push-of-a-button" graphics processing unit (GPU)-accelerated framework for intracoronary OCT imaging. Our framework visualizes 3D microstructures of the vessel wall with stent struts from raw binary OCT data acquired by the system digitizer as one seamless process. The framework reports the state-of-the-art performance; from raw OCT data, it takes 4.7 seconds to provide 3D visualization of a 5-cm-long coronary artery (of size 1600 samples x 1024 A-lines x 260 frames) with stent struts and detection of malapposition automatically at the single push of a button.     

Tn7 Transposition Creates a Hotspot for Homologous Recombination at the Transposon Donor Site

Homologous recombination at the bacterial transposon Tn7 donor site is stimulated 10-fold when Tn7 is activated to transpose at high frequency in RecD(-) Escherichia coli, where recombination is focused near the ends of double-chain breaks. This is observed as an increase in recombination between two lacZ heteroalleles when one copy of lacZ carries within it a Tn7 that is transposing at high frequency. This stimulation of recombination is dependent upon the presence of homology with the donor site, is independent of SOS induction, and is not due to a global stimulation of recombination. When stimulated by Tn7 transposition, the conversion events giving rise to Lac(+) recombinants occur preferentially at the site of Tn7, suggesting that transposition is stimulating gene conversion at the donor site. These results support the model that Tn7 transposition occurs by a ``cut and paste' mechanism, leaving a double-chain break at the donor site that is repaired by the host homologous recombination machinery; normally, repair would use homology in a sister chromosome to regenerate a copy of the transposon. This proposed series of events allows transposition that is nonreplicative, per se, to be effectively replicative.     

Locating a Lipid at the Portal to the Lipoxygenase Active Site

Lipoxygenase enzymes initiate diverse signaling pathways by specifically directing oxygen to different carbons of arachidonate and other polyunsaturated acyl chains, but structural origins of this specificity have remained unclear. We therefore determined the nature of the lipoxygenase interaction with the polar-end of a paramagnetic lipid by electron paramagnetic resonance spectroscopy. Distances between selected grid points on soybean seed lipoxygenase-1 (SBL1) and a lysolecithin spin-labeled on choline were measured by pulsed (electron) dipolar spectroscopy. The protein grid was designed by structure-based modeling so that five natural side chains were replaced with spin labels. Pairwise distances in 10 doubly spin-labeled mutants were examined by pulsed dipolar spectroscopy, and a fit to the model was optimized. Finally, experimental distances between the lysolecithin spin and each single spin site on SBL1 were also obtained. With these 15 distances, distance geometry localized the polar-end and the spin of the lysolecithin to the region between the two domains in the SBL1 structure, nearest to E236, K260, Q264, and Q544. Mutation of a nearby residue, E256A, relieved the high pH requirement for enzyme activity of SBL1 and allowed lipid binding at pH 7.2. This general approach could be used to locate other flexible molecules in macromolecular complexes.     

Isocitrate Dehydrogenase from Streptococcus mutans: Biochemical Properties and Evaluation of a Putative Phosphorylation Site at Ser102

Isocitrate deyhdrogenase (IDH) is a reversible enzyme in the tricarboxylic acid cycle that catalyzes the NAD(P)⁺-dependent oxidative decarboxylation of isocitrate to α-ketoglutarate (αKG) and the NAD(P)H/CO₂-dependent reductive carboxylation of αKG to isocitrate. The IDH gene from Streptococcus mutans was fused with the icd gene promoter from Escherichia coli to initiate its expression in the glutamate auxotrophic strain E. coli Δicd::kan^r of which the icd gene has been replaced by kanamycin resistance gene. The expression of S. mutans IDH (SmIDH) may restore the wild-type phenotype of the icd-defective strain on minimal medium without glutamate. The molecular weight of SmIDH was estimated to be 70 kDa by gel filtration chromatography, suggesting a homodimeric structure. SmIDH was divalent cation-dependent and Mn²⁺ was found to be the most effective cation. The optimal pH of SmIDH was 7.8 and the maximum activity was around 45°C. SmIDH was completely NAD⁺ dependent and its apparent K _m for NAD⁺ was 137 μM. In order to evaluate the role of the putative phosphorylation site at Ser102 in catalysis, two “stably phosphorylated” mutants were constructed by converting Ser102 into Glu102 or Asp102 in SmIDH to mimick a constitutively phosphorylated state. Meanwhile, the functional roles of another four amino acids (threonine, glycine, alanine and tyrosine) containing variant size of side chains were investigated. The replacement of Asp102 or Glu102 totally inactivated the enzyme, while the S102T, S102G, S102A and S102Y mutants decreased the affinity to isocitrate and only retained 16.0%, 2.8%, 3.3% and 1.1% of the original activity, respectively. These results reveal that Ser102 plays important role in substrate binding and is required for the enzyme function. Also, Ser102 in SmIDH is a potential phosphorylation site, indicating that the ancient NAD-dependent IDHs might be the underlying origin of “phosphorylation mechanism” used by their bacterial NADP-dependent homologs.     

Advancing a Framework to Enable Characterization and Evaluation of Data Streams Useful for Biosurveillance

In recent years, biosurveillance has become the buzzword under which a diverse set of ideas and activities regarding detecting and mitigating biological threats are incorporated depending on context and perspective. Increasingly, biosurveillance practice has become global and interdisciplinary, requiring information and resources across public health, One Health, and biothreat domains. Even within the scope of infectious disease surveillance, multiple systems, data sources, and tools are used with varying and often unknown effectiveness. Evaluating the impact and utility of state-of-the-art biosurveillance is, in part, confounded by the complexity of the systems and the information derived from them. We present a novel approach conceptualizing biosurveillance from the perspective of the fundamental data streams that have been or could be used for biosurveillance and to systematically structure a framework that can be universally applicable for use in evaluating and understanding a wide range of biosurveillance activities. Moreover, the Biosurveillance Data Stream Framework and associated definitions are proposed as a starting point to facilitate the development of a standardized lexicon for biosurveillance and characterization of currently used and newly emerging data streams. Criteria for building the data stream framework were developed from an examination of the literature, analysis of information on operational infectious disease biosurveillance systems, and consultation with experts in the area of biosurveillance. To demonstrate utility, the framework and definitions were used as the basis for a schema of a relational database for biosurveillance resources and in the development and use of a decision support tool for data stream evaluation.