AFLP phylogeny of the snubnose darters and allies (Percidae: Etheostoma) provides resolution across multiple levels of divergence

The snubnose darters (Percidae: subgenus Ulocentra) are a group of small, brightly colored North American freshwater fish belonging to the genus Etheostoma. Phylogenetic relationships among snubnose species have been a challenge to resolve at all levels of divergence, from the monophyly of species to deeper relationships among subgenera. Here, we used amplified fragment length polymorphisms (AFLPs) to estimate phylogenetic relationships among species from three closely related subgenera: Ulocentra, Etheostoma, and Nanostoma. With nearly complete sampling of recognized species, our analysis yielded a robust tree with statistical support at all nodes. Support was strongest for shallower relationships; support for internal nodes was either comparable to or greater than that of previous studies based on mitochondrial sequence data. Most recovered relationships were consistent with earlier hypotheses based on morphology or mtDNA sequences, with the exception of Etheostoma histrio, which was recovered as sister to Ulocentra. Our analysis indicates that careful use of AFLPs can yield statistically robust estimates of evolutionary relationships across multiple levels of divergence.     

Fission yeast Cyk3p is a transglutaminase-like protein that participates in cytokinesis and cell morphogenesis

Cell morphogenesis is a complex process that relies on a diverse array of proteins and pathways. We have identified a transglutaminase-like protein (Cyk3p) that functions in fission yeast morphogenesis. The phenotype of a cyk3 knockout strain indicates a primary role for Cyk3p in cytokinesis. Correspondingly, Cyk3p localizes both to the actomyosin contractile ring and the division septum, promoting ring constriction, septation, and subsequent cell separation following ring disassembly. In addition, Cyk3p localizes to polarized growth sites and plays a role in cell shape determination, and it also appears to contribute to cell integrity during stationary phase, given its accumulation as dynamic puncta at the cortex of such cells. Our results and the conservation of Cyk3p across fungi point to a role in cell wall synthesis and remodeling. Cyk3p possesses a transglutaminase domain that is essential for function, even though it lacks the catalytic active site. In a wider sense, our work illustrates the physiological importance of inactive members of the transglutaminase family, which are found throughout eukaryotes. We suggest that the proposed evolution of animal transglutaminase cross-linking activity from ancestral bacterial thiol proteases was accompanied by the emergence of a subclass whose function does not depend on enzymatic activity.     

Increased fat deposition in injured skeletal muscle is regulated by sex-specific hormones

Sex differences in skeletal muscle regeneration are controversial; comparisons of regenerative events between sexes have not been rigorously defined in severe injury models. We comprehensively quantified inflammation and muscle regeneration between sexes and manipulated sex-specific hormones to determine effects on regeneration. Cardiotoxin injury was induced in intact, castrated and ovariectomized female and male mice; ovariectomized mice were replaced with low- or high-dose 17-β estradiol (E(2)) or progesterone (P4). Extent of injury was comparable between intact mice, but females were more efficient in removal of necrotic debris, despite similar tissue levels of inflammatory cells and chemokines. Myofiber size during regeneration was equivalent between intact mice and after castration or ovariectomy (OVX) but was decreased (P < 0.001) in ovariectomized mice with high-dose E(2) replacement. Intermuscular adipocytes were absent in uninjured muscle, whereas adipocyte area was increased among regenerated myofibers in all groups. Interestingly, intermuscular fat was greater (P = 0.03) in intact females at day 14 compared with intact males. Furthermore, castration increased (P = 0.01) and OVX decreased adipocyte accumulation. After OVX, E(2), but not P4, replacement decreased (P ≤ 0.03) fat accumulation. In conclusion, sex-dependent differences in regeneration consisted of more efficient removal of necrosis and increased fat deposition in females with similar injury, inflammation, and regenerated myofiber size; high-dose E(2) decreased myofiber size and fat deposition. Adipocyte accumulation in regenerating muscle was influenced by sex-specific hormones. Recovery following muscle injury was different between males and females, and sex-specific hormones contributed to these differences, suggesting that sex-specific treatments could be beneficial after injury.     

Habitat use and activity influence thermoregulation in a tropical lizard, Ameiva exsul

We examined the contributions of alterations in daily activity and behavioral selection of microhabitat to thermoregulation in a population of the lizard, Ameiva exsul (Teiidae), by combining data on lizard activity with data on the availability of sun-shade patches and operative temperatures (T_e). By comparing T_e distributions predicted by “no thermoregulation” and “only thermoregulation” hypotheses to those predicted by random use of thermal habitat, we assessed the relative contributions of microhabitat selection and daily activity to regulation of body temperature (T_b). Over the course of a day lizards maintained T_b very close to optimal temperature (T_sel) despite T_es that deviated substantially from T_sel. Data demonstrating a unimodal daily activity pattern reject the hypothesis of uniform activity throughout the day. Also, lizard activity was not positively correlated with the proportion of T_es within T_sel nor negatively correlated with the absolute deviation of available T_e from T_sel (d_e) (“only thermoregulation”). Microsite use by A. exsul deviated significantly from predictions of the “no thermoregulation” hypothesis, but our data could not reject predictions of the “only thermoregulation” hypothesis that lizards would use sun-shade patches relative to the proportion of microsites where T_e is within T_sel. Also, lizards appeared to actively select sunlit and partially shaded microsites at different times of day. Thus, despite thermal constraints imposed by the habitat, A. exsul maintained high and relatively constant T_bs throughout its daily activity period and thermoregulated effectively. This appears to be generally representative of West Indian species of Ameiva.     

Mathematical Models for Cell Migration with Real-Time Cell Cycle Dynamics

The fluorescent ubiquitination-based cell cycle indicator, also known as FUCCI, allows the visualization of the G1 and S/G2/M cell cycle phases of individual cells. FUCCI consists of two fluorescent probes, so that cells in the G1 phase fluoresce red and cells in the S/G2/M phase fluoresce green. FUCCI reveals real-time information about cell cycle dynamics of individual cells, and can be used to explore how the cell cycle relates to the location of individual cells, local cell density, and different cellular microenvironments. In particular, FUCCI is used in experimental studies examining cell migration, such as malignant invasion and wound healing. Here we present, to our knowledge, new mathematical models that can describe cell migration and cell cycle dynamics as indicated by FUCCI. The fundamental model describes the two cell cycle phases, G1 and S/G2/M, which FUCCI directly labels. The extended model includes a third phase, early S, which FUCCI indirectly labels. We present experimental data from scratch assays using FUCCI-transduced melanoma cells, and show that the predictions of spatial and temporal patterns of cell density in the experiments can be described by the fundamental model. We obtain numerical solutions of both the fundamental and extended models, which can take the form of traveling waves. These solutions are mathematically interesting because they are a combination of moving wavefronts and moving pulses. We derive and confirm a simple analytical expression for the minimum wave speed, as well as exploring how the wave speed depends on the spatial decay rate of the initial condition.     

Microsphere-based protease assays and screening application for lethal factor and factor Xa.

BACKGROUND: Proteases regulate many biological pathways in humans and are components of several bacterial toxins. Protease studies and development of protease inhibitors do not follow a single established methodology and are mostly protease specific. METHODS: We have created recombinant fusion proteins consisting of a biotinylated attachment sequence linked to a GFP via a protease cleavage site to develop a multiplexable microsphere-based protease assay system. Using the proteases lethal factor and factor Xa, we performed kinetic experiments to determine optimal conditions for inhibitor screens and detect known inhibitors using the HyperCyt flow cytometry system. RESULTS: We have demonstrated specific cleavage of lethal factor and factor Xa substrates, optimized screening conditions for these substrates, shown specific inhibition of the proteases, and demonstrated high throughput detection of these inhibitors. CONCLUSIONS: The assay developed here is adaptable to any site-specific protease, compatible with high throughput flow cytometry systems, and multiplexable. Coupled with flow cytometry, which provides continuous time resolution and intrinsic resolution of free vs. bound fluorophores, this assay will be useful for high throughput screening of protease inhibitors in general and could simplify assays designed to determine protease mechanism.     

The antitumor agent 3-bromopyruvate has a short half-life at physiological conditions

Clinical research is currently exploring the validity of the anti-tumor candidate 3-bromopyruvate (3-BP) as a novel treatment for several types of cancer. However, recent publications have overlooked rarely-cited earlier work about the instability of 3-BP and its decay to 3-hydroxypyruvate (3-HP) which have obvious implications for its mechanism of action against tumors, how it is administered, and for precautions when preparing solutions of 3-BP. This study found the first-order decay rate of 3-BP at physiological temperature and pH has a half-life of only 77 min. Lower buffer pH decreases the decay rate, while choice of buffer and concentration do not affect it. A method for preparing more stable solutions is also reported.