EFFECTS OF LIGHT ON PHOTOSYNTHESIS,GRAZING, AND POPULATION DYNAMICS OF THE HETEROTROPHIC DINOFLAGELLATE PFIESTERIA PISCICIDA (DINOPHYCEAE)1

In studying how environmental factors control the population dynamics of Pfiesteria piscicida Steidinger et Burkholder, we examined the influence of light regime on kleptoplastidic photosynthesis, growth, and grazing. Prey (Rhodomonas sp.)‐saturated growth rate of P. piscicida increased (0.67 ± 0.03 d^?1 to 0.91 ± 0.11 d^?1) with light intensity varying from 0 to 200 μmol photons·m^?2·s^?1. No significant effect was observed on grazing, excluding the possibility that light enhanced P. piscicida growth through stimulating grazing. Light‐grown P. piscicida exhibited a higher gross growth efficiency (0.78 ± 0.10) than P. piscicida incubated in the dark (0.32 ± 0.16), and photosynthetic inhibitors significantly decreased growth of recently fed populations. These results demonstrate a role of kleptoplastidic photosynthesis in enhancing growth in P. piscicida. However, when the prey alga R. sp. was depleted, light's stimulating effect on P. piscicida growth diminished quickly, coinciding with rapid disappearance of Rhodomonas‐derived pigments and RUBISCO from P. piscicida cells. Furthermore, the effect of light on growth was reversed after extended starvation, and starved light‐grown P. piscicida declined at a rate significantly greater than dark‐incubated cultures. The observed difference in rates of decline appeared to be attributable to light‐dependent cannibalism. Using a 5‐chloromethylfluorescein diacetate staining technique, cannibalistic grazing was observed after 7 days of starvation, at a rate four times greater under illumination than in the dark. The results from this study suggest that kleptoplastidy enhances growth of P. piscicida only in the presence of algal prey. When prey is absent, P. piscicida populations may become vulnerable to light‐stimulated cannibalism.     

Mitochondrial data support an odd-nosed colobine clade

To obtain a more complete understanding of the evolutionary history of the leaf-eating monkeys we have examined the mitochondrial genome sequence of two African and six Asian colobines. Although taxonomists have proposed grouping the "odd-nosed" colobines (proboscis monkey, douc langur, and the snub-nosed monkey) together, phylogenetic support for such a clade has not been tested using molecular data. Phylogenetic analyses using parsimony, maximum likelihood, and Bayesian methods support a monophyletic clade of odd-nosed colobines consisting of Nasalis, Pygathrix, and Rhinopithecus, with tentative support for Nasalis occupying a basal position within this clade. The African and Asian colobine lineages are inferred to have diverged by 10.8 million years ago (mya or Ma). Within the Asian colobines the odd-nosed clade began to diversify by 6.7 Ma. These results augment our understanding of colobine evolution, particularly the nature and timing of the colobine expansion into Asia. This phylogenetic information will aid those developing conservation strategies for these highly endangered, diverse, and unique primates.     

Comparisons of Allergenic and Metazoan Parasite Proteins: Allergy the Price of Immunity

Allergic reactions can be considered as maladaptive IgE immune responses towards environmental antigens. Intriguingly, these mechanisms are observed to be very similar to those implicated in the acquisition of an important degree of immunity against metazoan parasites (helminths and arthropods) in mammalian hosts. Based on the hypothesis that IgE-mediated immune responses evolved in mammals to provide extra protection against metazoan parasites rather than to cause allergy, we predict that the environmental allergens will share key properties with the metazoan parasite antigens that are specifically targeted by IgE in infected human populations. We seek to test this prediction by examining if significant similarity exists between molecular features of allergens and helminth proteins that induce an IgE response in the human host. By employing various computational approaches, 2712 unique protein molecules that are known IgE antigens were searched against a dataset of proteins from helminths and parasitic arthropods, resulting in a comprehensive list of 2445 parasite proteins that show significant similarity through sequence and structure with allergenic proteins. Nearly half of these parasite proteins from 31 species fall within the 10 most abundant allergenic protein domain families (EF-hand, Tropomyosin, CAP, Profilin, Lipocalin, Trypsin-like serine protease, Cupin, BetV1, Expansin and Prolamin). We identified epitopic-like regions in 206 parasite proteins and present the first example of a plant protein (BetV1) that is the commonest allergen in pollen in a worm, and confirming it as the target of IgE in schistosomiasis infected humans. The identification of significant similarity, inclusive of the epitopic regions, between allergens and helminth proteins against which IgE is an observed marker of protective immunity explains the ‘off-target’ effects of the IgE-mediated immune system in allergy. All these findings can impact the discovery and design of molecules used in immunotherapy of allergic conditions.     

Comparative bioacoustics: a roadmap for quantifying and comparing animal sounds across diverse taxa

Animals produce a wide array of sounds with highly variable acoustic structures. It is possible to understand the causes and consequences of this variation across taxa with phylogenetic comparative analyses. Acoustic and evolutionary analyses are rapidly increasing in sophistication such that choosing appropriate acoustic and evolutionary approaches is increasingly difficult. However, the correct choice of analysis can have profound effects on output and evolutionary inferences. Here, we identify and address some of the challenges for this growing field by providing a roadmap for quantifying and comparing sound in a phylogenetic context for researchers with a broad range of scientific backgrounds. Sound, as a continuous, multidimensional trait can be particularly challenging to measure because it can be hard to identify variables that can be compared across taxa and it is also no small feat to process and analyse the resulting high-dimensional acoustic data using approaches that are appropriate for subsequent evolutionary analysis. Additionally, terminological inconsistencies and the role of learning in the development of acoustic traits need to be considered. Phylogenetic comparative analyses also have their own sets of caveats to consider. We provide a set of recommendations for delimiting acoustic signals into discrete, comparable acoustic units. We also present a three-stage workflow for extracting relevant acoustic data, including options for multivariate analyses and dimensionality reduction that is compatible with phylogenetic comparative analysis. We then summarize available phylogenetic comparative approaches and how they have been used in comparative bioacoustics, and address the limitations of comparative analyses with behavioural data. Lastly, we recommend how to apply these methods to acoustic data across a range of study systems. In this way, we provide an integrated framework to aid in quantitative analysis of cross-taxa variation in animal sounds for comparative phylogenetic analysis. In addition, we advocate the standardization of acoustic terminology across disciplines and taxa, adoption of automated methods for acoustic feature extraction, and establishment of strong data archival practices for acoustic recordings and data analyses. Combining such practices with our proposed workflow will greatly advance the reproducibility, biological interpretation, and longevity of comparative bioacoustic studies.     

Chitinase activity in the epidermis of the fiddler crab, Uca pugilator, as an in vivo screen for molt-interfering xenobiotics

We describe an in vivo screening assay that uses epidermal chitinase activity as the endpoint following a 7-day exposure of Uca pugilator to test chemicals. Chitinase, a chitinolytic enzyme, is the end product of endocrine cascades of a multi-hormonal system for control of crustacean molting. Wherever a molt-interfering agent adversely impacts the Y-organ-ecdysteroid receptor axis, the effect should be manifested by the activity of chitinase in the epidermis. Therefore, epidermal chitinase activity is an ideal endpoint for molt-interfering effects of xenobiotics. The validity of epidermal chitinase activity being used for such a purpose is supported by our finding that two injections of 20-hydroxyecdysone at 25 microg/g live weight induced a twofold increase in chitinase activity in the epidermis of U. pugilator. A total of nine chemicals were screened for molting hormone and anti-molting activities. o,p'-DDT was found to significantly inhibit epidermal chitinase activity while kepone and methoxychlor exhibited a tendency of inhibition of enzymatic activity. None of the remaining six chemicals, namely, p,p'-dichlorodiphenyltrichloroethane (p,p'-DDT), atrazine, tributyltin (TBT), methoprene, dieldrin and permethrin, had an effect on epidermal chitinase activity.     

Left ventricular hypertrophy is prevalent in Sprague-Dawley rats

Unrecognized cardiovascular abnormalities may confound the interpretation of research data collected using rats. However, although SPF rat colonies are screened for microbes and kept under standardized environmental conditions, their cardiovascular status is largely unknown. We recently performed surgery on anesthetized 80-d-old Sprague-Dawley rats and observed a high mortality that could not be attributed to the procedures or preceding treatments. Upon necropsy, cardiomyopathy was readily apparent in a substantial proportion of these rats. To further evaluate the nature of this condition, we evaluated the histology and morphology of hearts from both Sprague-Dawley and Lewis rats. Compared with Lewis rats, Sprague-Dawley rats had greater left ventricular wall thickness and larger cardiomyocyte cell size. Severe left ventricle hypertrophy was present in 38% of young adult Sprague-Dawley rats. These findings may have implications for research models that use Sprague-Dawley rats.     

Aerobic Biotransformation of N-Nitrosodimethylamine and N-Nitrodimethylamine by Benzene-, Butane-, Methane-, Propane-, and Toluene-Fed Cultures

N-Nitrosodimethylamine (NDMA) is an emerging contaminant of concern. N-nitrodimethylamine (DMNA) is a structural analog to NDMA. NDMA and DMNA have been found in drinking water, groundwater, and other media and are of concern due their toxicity. The authors evaluated biotransformation of NDMA and DMNA by cultures enriched from contaminated groundwater growing on benzene, butane, methane, propane, or toluene. Maximum specific growth rates of enriched cultures on butane (μ_max = 1.1 h^?1) and propane (μ_max = 0.65 h^?1) were 1 to 2 orders of magnitude higher than those presented in the literature. Growth rates of mixed cultures grown on benzene (μ_max = 1.3 h^?1), methane (μ_max = 0.09 h^?1), and toluene (μ_max = 0.99 h^?1) in these studies were similar to those presented in the literature. NDMA biotransformation rates for methane oxidizers (υ_max = 1.4 ng min^?1 mg^?1) and toluene oxidizers (υ_max = 2.3 ng min^?1 mg^?1) were comparable to those presented in the literature, whereas the biotransformation rate for propane oxidizers (υ_max = 0.37 ng min^?1 mg^?1) was lower. NDMA biotransformation rates for benzene oxidizers (υ_max = 1.02 ng min^?1 mg^?1) and butane oxidizers (υ_max = 1.2 ng min^?1 mg^?1) were comparable to those reported for other primary substrates. These studies showed that DMNA biotransformation rates for benzene (υ_max = 0.79 ng min^?1 mg^?1), butane (υ_max = 1.0 ng min^?1 mg^?1), methane (υ_max = 2.1 ng min^?1 mg^?1), propane (υ_max = 1.46 ng min^?1 mg^?1), and toluene (υ_max = 0.52 ng min^?1 mg^?1) oxidizers were all comparable. These studies highlight potential bioremediation methods for NDMA and DMNA in contaminated groundwater.     

Hx, a novel fluorescent, minor groove and sequence specific recognition element: design, synthesis, and DNA binding properties of p-anisylbenzimidazole-imidazole/pyrrole-containing polyamides

With the aim of incorporating a recognition element that acts as a fluorescent probe upon binding to DNA, three novel pyrrole (P) and imidazole (I)-containing polyamides were synthesized. The compounds contain a p-anisylbenzimidazolecarboxamido (Hx) moiety attached to a PP, IP, or PI unit, giving compounds HxPP (2), HxIP (3), and HxPI (4), respectively. These fluorescent hybrids were tested against their complementary nonfluorescent, non-formamido tetraamide counterparts, namely, PPPP (5), PPIP (6), and PPPI (7) (cognate sequences 5'-AAATTT-3', 5'-ATCGAT-3', and 5'-ACATGT-3', respectively). The binding affinities for both series of polyamides for their cognate and noncognate sequences were ascertained by surface plasmon resonance (SPR) studies, which revealed that the Hx-containing polyamides gave binding constants in the 10(6) M(-1) range while little binding was observed for the noncognates. The binding data were further compared to the corresponding and previously reported formamido-triamides f-PPP (8), f-PIP (9), and f-PPI (10). DNase I footprinting studies provided additional evidence that the Hx moiety behaved similarly to two consecutive pyrroles (PP found in 5-7), which also behaved like a formamido-pyrrole (f-P) unit found in distamycin and many formamido-triamides, including 8-10. The biophysical characterization of polyamides 2-7 on their binding to the abovementioned DNA sequences was determined using thermal melts (ΔT(M)), circular dichroism (CD), and isothermal titration calorimetry (ITC) studies. Density functional calculations (B3LYP) provided a theoretical framework that explains the similarity between PP and Hx on the basis of molecular electrostatic surfaces and dipole moments. Furthermore, emission studies on polyamides 2 and 3 showed that upon excitation at 322 nm binding to their respective cognate sequences resulted in an increase in fluorescence at 370 nm. These low molecular weight polyamides show promise for use as probes for monitoring DNA recognition processes in cells.     

Flexible Quantitative Risk Assessment for Developmental Toxicity Based on Fractional Polynomial Predictors

Risk assessment for developmental toxicity studies in rodents is faced with the fairly involved data structure of clustered multivariate binary outcomes. While likelihood methods for this setting do not abound, we show that a conditional model, combined with pseudo‐likelihood inference and fractional polynomial predictor functions, as proposed by Royston and Altman (1994), are a promising way forward. The methods are illustrated using teratology data collected under the National Toxicology Program.