Detection of "punctuated equilibrium" by bayesian estimation of speciation and extinction rates, ancestral character states, and rates of anagenetic and cladogenetic evolution on a molecular phylogeny

Algorithms are presented to simultaneously estimate probabilities of speciation and extinction, rates of anagenetic and cladogenetic phenotypic evolution, as well as ancestral character states, from a complete ultrametric species-level phylogeny with dates assigned to all bifurcations and one or more phenotypes in three or more extant species, using Metropolis-Hastings Markov Chain Monte Carlo sampling. The algorithms also estimate missing phenotypes of extant species and numbers of speciation events that occurred on all branches of the phylogeny. The algorithms are discussed and their performance is evaluated using simulated data. That evaluation shows that precise estimation of rates of evolution of one or a few phenotypes requires large phylogenies. Estimation accuracy improves with the number of species on the phylogeny.     

Expression and characterization of active site mutants of hevamine, a chitinase from the rubber tree Hevea brasiliensis.

Hevamine is a chitinase from the rubber tree Hevea brasiliensis. Its active site contains Asp125, Glu127, and Tyr183, which interact with the -1 sugar residue of the substrate. To investigate their role in catalysis, we have successfully expressed wild-type enzyme and mutants of these residues as inclusion bodies in Escherichia coli. After refolding and purification they were characterized by both structural and enzyme kinetic studies. Mutation of Tyr183 to phenylalanine produced an enzyme with a lower k(cat) and a slightly higher K(m) than the wild-type enzyme. Mutating Asp125 and Glu127 to alanine gave mutants with approximately 2% residual activity. In contrast, the Asp125Asn mutant retained substantial activity, with an approximately twofold lower k(cat) and an approximately twofold higher K(m) than the wild-type enzyme. More interestingly, it showed activity to higher pH values than the other variants. The X-ray structure of the Asp125Ala/Glu127Ala double mutant soaked with chitotetraose shows that, compared with wild-type hevamine, the carbonyl oxygen atom of the N-acetyl group of the -1 sugar residue has rotated away from the C1 atom of that residue. The combined structural and kinetic data show that Asp125 and Tyr183 contribute to catalysis by positioning the carbonyl oxygen of the N-acetyl group near to the C1 atom. This allows the stabilization of a positively charged transient intermediate, in agreement with a previous proposal that the enzyme makes use of substrate-assisted catalysis.     

Functional gamma-secretase inhibitors reduce beta-amyloid peptide levels in brain

To elucidate a role for the cytoskeletal protein actin in post-traumatic apoptotic cell death, the ability of actin-containing tissue extracts to inhibit exogenous DNase I was evaluated. In addition, cortical, hippocampal and thalamic extracts were examined for caspase-mediated actin cleavage and changes in actin polymerization state. Rats were anesthetized, subjected to lateral fluid percussion brain injury of moderate severity, and euthanized at 1 h, 6 h, 24 h, 1 week or 3 weeks post-injury (n = 3 per time-point). Tissue extracts from all brain regions of sham (uninjured) animals inhibited exogenous DNase I activity to a significant extent. However, inhibition of DNase I was significantly reduced at 1 h and 6 h in the injured hippocampus, and at 1 h, 6 h and 3 weeks in the thalamus. DNase I in cortical extracts of all injured animals was inhibited to a similar extent as that in uninjured animals. Actin fragments consistent with caspase-mediated proteolysis were observed in immunoblots of the injured hippocampus and thalamus at 1 h and 24 h, respectively, and were present up to 3 weeks post-injury. Transient actin hyperpolymerization was observed at 1 and 6 h post-injury in the thalamus and hippocampus, while actin depolymerization was observed at 1 and 3 weeks in the cortex and thalamus. Collectively our data suggest that DNase I disinhibition following brain trauma is associated predominantly with actin hyperpolymerization but also with actin depolymerization and concomitant caspase-mediated actin proteolysis.     

Isolation of sertoli cells from adult rat testes: an approach to ex vivo studies of Sertoli cell function

Much of what is known about the molecular regulation and function of adult Sertoli cells has been inferred from in vitro studies of immature Sertoli cells. However, adult and immature cells differ in significant ways and, moreover, many Sertoli cell functions are regulated by conditions that are difficult to replicate in vitro. Our objective was to develop a procedure to isolate Sertoli cells rapidly and in sufficient number and purity to make it possible to assess Sertoli cell function immediately after the isolation of the cells. The isolation procedure described herein takes less than 4 h and does not require culturing the cells. From a single 4-mo-old adult rat, we routinely obtain 7.0 +/- 0.4 x 10(6) Sertoli cells per testis, and from a 21-mo-old rat, 7.2 +/- 0.4 x 10(6) Sertoli cells per testis. The purity, determined by morphologic analyses of plastic-embedded cells or after staining for tyrosine-tubulin or vimentin, averaged 80%. The contaminants typically included germ cells (10%) and myoid cells (10%). The germ cell-expressed genes protamine-2 and hemiferrin were not detected in the Sertoli cell preparations by Northern blot analyses, but the Sertoli cell-expressed genes clusterin, cathepsin L, and transferrin were highly expressed. Transferrin mRNA levels were greater in Sertoli cells isolated from aged than from young adult rats, consistent with previous analyses of whole testes; and cathepsin L mRNA levels were far more highly expressed in Sertoli cells isolated from stages VI-VII than from other stages of the cycle of the seminiferous epithelium, also consistent with previous analyses of whole testes and isolated tubules. These studies indicate that the freshly isolated cells retain differentiated function, and thus it should be possible to assess the in vivo function of adult Sertoli cells by isolating the Sertoli cells and immediately assessing their function.     

A series of C-terminal amino alcohol dipeptide A beta inhibitors

Potent, small molecule A beta inhibitors have been prepared that incorporate an alanine core bracketed by an N-terminal arylacetyl group and various C-terminal amino alcohols. The compounds exhibit stereospecific inhibition as demonstrated in an in vitro assay.     

Control of macroautophagy by calcium, calmodulin-dependent kinase kinase-beta, and Bcl-2

Macroautophagy is an evolutionary conserved lysosomal pathway involved in the turnover of cellular macromolecules and organelles. In spite of its essential role in tissue homeostasis, the molecular mechanisms regulating mammalian macroautophagy are poorly understood. Here, we demonstrate that a rise in the free cytosolic calcium ([Ca(2+)](c)) is a potent inducer of macroautophagy. Various Ca(2+) mobilizing agents (vitamin D(3) compounds, ionomycin, ATP, and thapsigargin) inhibit the activity of mammalian target of rapamycin, a negative regulator of macroautophagy, and induce massive accumulation of autophagosomes in a Beclin 1- and Atg7-dependent manner. This process is mediated by Ca(2+)/calmodulin-dependent kinase kinase-beta and AMP-activated protein kinase and inhibited by ectopic Bcl-2 located in the endoplasmatic reticulum (ER), where it lowers the [Ca(2+)](ER) and attenuates agonist-induced Ca(2+) fluxes. Thus, an increase in the [Ca(2+)](c) serves as a potent inducer of macroautophagy and as a target for the antiautophagy action of ER-located Bcl-2.     

Infection in a rat model reactivates attenuated virulence after long-term axenic culture of Acanthamoeba spp

Prolonged culturing of many microorganisms leads to the loss of virulence and a reduction of their infective capacity. However, little is known about the changes in the pathogenic strains of Acanthamoeba after long culture periods. Our study evaluated the effect of prolonged culturing on the invasiveness of different isolates of Acanthamoeba in an in vivo rat model. ATCC strains of Acanthamoeba, isolates from the environment and clinical cases were evaluated. The in vivo model was effective in establishing the infection and differentiating the pathogenicity of the isolates and re-isolates. The amoebae cultured in the laboratory for long periods were less virulent than those that were recently isolated, confirming the importance of passing Acanthamoeba strains in animal models.     

Photobiomodulation therapy in knee osteoarthritis reduces oxidative stress and inflammatory cytokines in rats

Knee osteoarthritis (OA) is a chronic disease that causes pain and gradual degeneration of the articular cartilage. In this study, MIA‐induced OA knee model was used in rats to test the effects of the photobiomodulation therapy (PBM). We analyzed the inflammatory process (pain and cytokine levels), and its influence on the oxidative stress and antioxidant capacity. Knee OA was induced by monosodium iodoacetate (MIA) intra‐articular injection (1.5 mg/50 μL) and the rats were treated with eight sessions of PBM 3 days/week (904 nm, 6 or 18 J/cm²). For each animal, mechanical and cold hyperalgesia and spontaneous pain were evaluated; biological analyses were performed in blood serum, intra‐articular lavage, knee structures, spinal cord and brainstem. Cytokine assays were performed in knee, spinal cord and brainstem samples. The effects of the 18 J/cm² dose of PBM were promising in reducing pain and neutrophil activity in knee samples, together with reducing oxidative stress damage in blood serum and spinal cord samples. PBM improved the antioxidant capacity in blood serum and brainstem, and decreased the knee pro‐inflammatory cytokine levels. Our study demonstrated that PBM decreased oxidative damage, inflammation and pain. Therefore, this therapy could be an important tool in the treatment of knee OA.     

Kinetic modeling of thermal inactivation of the Bacillus sp. protease P7

Data from thermal stability of a keratinolytic protease produced by the Amazon isolate Bacillus sp. P7 was fitted to various mathematical models. Kinetic modeling showed that Weibull distribution was the best equation to describe the residual activity of protease P7 after heat treatment. The effects of temperature on equation parameters and on characteristics of the inactivation curves were evaluated. As expected, faster inactivation was observed at higher temperatures. The critical temperature to accelerate protease decomposition was about 70 °C. The reliable life (t _R) of the enzyme, analogous to the D value, ranged from 1,824 to 8 min at 45–65 °C. Within these temperatures, an increase of 8.81 °C was needed to lower enzyme t _R in one-log unit. Protease P7 is a potentially useful biocatalyst for various industrial bioprocesses, and therefore, kinetic modeling of thermal inactivation addresses an important topic aiming enzyme characterization and applications.     

Mass extinctions do not explain skew in interspecific body size distributions

In several higher animal taxa, such as mammals and birds, the distribution of species body sizes is heavily skewed towards small size. Previous studies have suggested that small‐bodied organisms are less prone to extinction than large‐bodied species. If small body size is favourable during mass extinction events, a post mass extinction excess of small‐bodied species may proliferate and maintain skewed body size distributions sometime after. Here, we modelled mass extinctions and found that even unrealistically strong body mass selection has little effect on the skew of interspecific body size distributions. Moreover, selection against large body size may, counter intuitively, skew size distributions towards large body size. In any case, subsequent evolutionary diversification rapidly erases these rather small effects mass extinctions may have on size distributions. Next, we used body masses of extant species and phylogenetic methods to investigate possible changes in body size distributions across the Cretaceous–Paleogene (K‐Pg) mass extinction. Body size distributions of extant clades that originated during the Cretaceous are on average more skewed than their subclades that originated during the Paleogene, but the difference is only minor in mammals, and in birds, it can be explained by a positive relationship between species richness and skewness that is also present in clades that originated after the transition. Hence, we cannot infer from extant species whether the K‐Pg mass extinctions were size‐selective, but they are not the reason why most extant bird and mammal species are small‐bodied.