Comparative genomics of the social amoebae <Emphasis Type="Italic">Dictyostelium discoideum</Emphasis> and <Emphasis Type="Italic">Dictyostelium purpureum</Emphasis>

Background

The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk cells. There are four groups of dictyostelids, with the most derived being a group that contains the model species Dictyostelium discoideum.

Results

We have produced a draft genome sequence of another group dictyostelid, Dictyostelium purpureum, and compare it to the D. discoideum genome. The assembly (8.41 × coverage) comprises 799 scaffolds totaling 33.0 Mb, comparable to the D. discoideum genome size. Sequence comparisons suggest that these two dictyostelids shared a common ancestor approximately 400 million years ago. In spite of this divergence, most orthologs reside in small clusters of conserved synteny. Comparative analyses revealed a core set of orthologous genes that illuminate dictyostelid physiology, as well as differences in gene family content. Interesting patterns of gene conservation and divergence are also evident, suggesting function differences; some protein families, such as the histidine kinases, have undergone little functional change, whereas others, such as the polyketide synthases, have undergone extensive diversification. The abundant amino acid homopolymers encoded in both genomes are generally not found in homologous positions within proteins, so they are unlikely to derive from ancestral DNA triplet repeats. Genes involved in the social stage evolved more rapidly than others, consistent with either relaxed selection or accelerated evolution due to social conflict.

Conclusions

The findings from this new genome sequence and comparative analysis shed light on the biology and evolution of the Dictyostelia.

     

The polyketide MPBD initiates the SDF-1 signaling cascade that coordinates terminal differentiation in Dictyostelium

Dictyostelium uses a wide array of chemical signals to coordinate differentiation as it switches from a unicellular to a multicellular organism. MPBD, the product of the polyketide synthase encoded by stlA, regulates stalk and spore differentiation by rapidly stimulating the release of the phosphopeptide SDF-1. By analyzing specific mutants affected in MPBD or SDF-1 production, we delineated a signal transduction cascade through the membrane receptor CrlA coupled to Gα1, leading to the inhibition of GskA so that the precursor of SDF-1 is released. It is then processed by the extracellular protease of TagB on prestalk cells. SDF-1 apparently acts through the adenylyl cyclase ACG to activate the cyclic AMP (cAMP)-dependent protein kinase A (PKA) and trigger the production of more SDF-1. This signaling cascade shows similarities to the SDF-2 signaling pathway, which acts later to induce rapid spore encapsulation.     

Redescription of Neotrombicula naultini (Dumbleton, 1947) and descriptions of two new species of chiggers from New Zealand (Acari: Trombiculidae)

Abstract

Neotrombicula naultini (Dumbleton, 1947) was redescribed from the type specimen and additional specimens collected off Hoplodactylus granulatus (= Dactylocnemus granulatus), Hoplodactylus maculatus, and Hoplodactylus pacificus in New Zealand. Neotrombicula sphenodonti and Microtrombicula hoplodactyla were described, as new species, from specimens collected from New Zealand reptiles.     

Static and dynamic error of a biplanar videoradiography system using marker-based and markerless tracking techniques

The use of biplanar videoradiography technology has become increasingly popular for evaluating joint function in vivo. Two fundamentally different methods are currently employed to reconstruct 3D bone motions captured using this technology. Marker-based tracking requires at least three radio-opaque markers to be implanted in the bone of interest. Markerless tracking makes use of algorithms designed to match 3D bone shapes to biplanar videoradiography data. In order to reliably quantify in vivo bone motion, the systematic error of these tracking techniques should be evaluated. Herein, we present new markerless tracking software that makes use of modern GPU technology, describe a versatile method for quantifying the systematic error of a biplanar videoradiography motion capture system using independent gold standard instrumentation, and evaluate the systematic error of the W.M. Keck XROMM Facility's biplanar videoradiography system using both marker-based and markerless tracking algorithms under static and dynamic motion conditions. A polycarbonate flag embedded with 12 radio-opaque markers was used to evaluate the systematic error of the marker-based tracking algorithm. Three human cadaveric bones (distal femur, distal radius, and distal ulna) were used to evaluate the systematic error of the markerless tracking algorithm. The systematic error was evaluated by comparing motions to independent gold standard instrumentation. Static motions were compared to high accuracy linear and rotary stages while dynamic motions were compared to a high accuracy angular displacement transducer. Marker-based tracking was shown to effectively track motion to within 0.1?mm and 0.1 deg under static and dynamic conditions. Furthermore, the presented results indicate that markerless tracking can be used to effectively track rapid bone motions to within 0.15 deg for the distal aspects of the femur, radius, and ulna. Both marker-based and markerless tracking techniques were in excellent agreement with the gold standard instrumentation for both static and dynamic testing protocols. Future research will employ these techniques to quantify in vivo joint motion for high-speed upper and lower extremity impacts such as jumping, landing, and hammering.     

Spore coat formation and timely sporulation depend on cellulose in Dictyostelium

Cellulose is a major component of the extracellular coat that surrounds the terminally-differentiated spore of Dictyostelium. It is sandwiched between two layers of proteins that derive from prespore vesicles by exocytosis. Strains unable to synthesize cellulose due to null mutations in the gene encoding the catalytic subunit of cellulose synthase (dcsA) failed to make detergent-resistant spores but produced small, highly refractile, round spore-like cells up to a day late. Although these cells resembled spores in appearance, they were unstable, only transiently ellipsoid in shape, and sensitive to hypo-osmotic shock, drying, or detergents. Differentiation of these pseudo-spores was induced in the normal time frame by activation of the cAMP-dependent protein kinase or co-development with wild type cells, and coat proteins were secreted by the dcsA-null cells at the same time as wild type cells. A substantial fraction of secreted coat proteins was loosely associated with the surface of the mutant cells, resembling the precoat posited to form early during normal sporulation. Transmission electron microscopy revealed that the precoat had little ultrastructural organization in the absence of cellulose. Thus, cellulose in the coat appears to be required for the organization of the pre-coat precursors as well as the stability, dormancy, and shape of the spore.     

Dictyostelium discoideum chemotaxis: threshold for directed motion

The chemotactic response of Dictyostelium discoideum cells to stationary, linear gradients of cyclic adenosine 3',5'-monophosphate (cAMP) was studied using microfluidic devices. In shallow gradients of less than 10(-3) nM/microm, the cells showed no directional response and exhibited a constant basal motility. In steeper gradients, cells moved up the gradient on average. The chemotactic speed and the motility increased with increasing steepness up to a plateau at around 10(-1) nM/microm. In very steep gradients, above 10 nM/microm, the cells lost directionality and the motility returned to the sub-threshold level. In the regime of optimal response the difference in receptor occupancy at the front and back of the cell is estimated to be only about 100 molecules.     

The Concept of Hormesis in Developmental Toxicology

Animal bioassay experiments are frequently conducted to assess the toxicity of chemicals on the developing fetus. Experiments are normally conducted at dosage levels that are much higher than human exposure levels to elicit the toxic reproductive effect of the chemical in a limited number of litters. Recently there has been much discussion on the fact that some chemicals may have beneficial effects at low doses and become toxic at high doses. This concept, known as chemical hormesis, has been the focus of attention in many investigations. Here, we consider the prevalence of hormesis in developmental toxicology and show that current design of developmental toxicity testing does not accommodate the study of hormesis. If it can be proved that some developmental toxicants may have stimulatory low dose effects, then design and analysis of developmental toxicity experiments need to be revised by the scientific community and the regulatory agencies. Using a thorough analysis of an experimental data set, we further demonstrate that in order to establish the possible hormetic effects of a chemical in reproduction, often a multiple replication of the experiment may be necessary to examine such effects. Using a trend test, we illustrate that while it is possible that one replicate of a developmental toxicity experiment with a known teratogen shows strong evidence of hormesis, other replicates may show no sign of beneficial effects at low doses.     

LH secretion and testosterone concentrations are blunted after resistance exercise in men.

This study examined the hypothesis that exercise-induced changes in circulating testosterone would be centrally mediated via hypothalamic-pituitary release of luteinizing hormone (LH). We tested this hypothesis by examining overnight LH, total and free testosterone (TT and FT), and cortisol (C) concentrations in 10 young healthy men (21 +/- 1 yr) during two experimental sessions: a control and an acute heavy-resistance exercise bout (50 total sets consisting of squats, bench press, leg press, and latissimus dorsi pull-down). Exercise was performed from 1500 to 1700, and blood sampling began at 1700 and continued until 0600 the next morning. Blood was sampled every 10 min for LH and every hour for TT, FT, and C. Hormonal concentrations were determined via RIA, and the secretion characteristics of LH were analyzed with deconvolution analysis. When overnight postexercise concentrations were compared with control concentrations, no statistically significant (P < or = 0.05) differences were observed for LH half-life, LH pulse frequency, interpulse interval, pulse amplitude, or pulse mass. Significant differences were observed for LH production rate (13.6 +/- 4 and 17.9 +/- 5 IU. l distribution volume(-1) x day(-1) for exercise and control, respectively, a 24% reduction). For the ANOVA marginal main effect means due to condition, C was significantly elevated (5.9 +/- 0.7 vs. 4.0 +/- 0.4 microg/dl), while TT (464 +/- 23 vs. 529 +/- 32 ng/dl) and FT (15.6 +/- 0.7 vs. 18.3 +/- 0.9 pg/ml) were significantly decreased for the exercise condition. These data demonstrate that the decline in overnight testosterone concentrations after acute heavy-resistance exercise is accompanied by a blunted LH production rate and elevated C concentrations.