Development of distylous flowers and investment of biomass in male and female function in Palicourea padifolia (Rubiaceae)

Knowledge of developmental pathways for achieving differences in style and anther heights, in concert with those of ancillary features accompanied with data in regard to biomass investment to male and female function, provide an excellent opportunity for examining the developmental correlations between primary and ancillary floral traits so as to understand the evolution of heterostyly. The ontogenetic relationships between bud length and anther height and between bud length and style height, and between bud length versus bud width, anther length, and number of pollen grains per anther for long-styled (LS) and short-styled (SS) morphs of P. PADIFOLIA are described. We also described the ontogenetic biomass allocation to male and female function and to corolla with elongation of buds harvested at regular intervals. We observed an early termination of stylar growth in SS buds, whereas LS styles steadily increased in size. Morph differences for relative growth rates were significant for anther height, anther length, and pollen number but not for bud width. Bud width and anther length had a negative allometric relationship with bud elongation. The relationship between bud length and number of pollen grains per anther was positive and morph differences in pollen number were detected at later stages of development. An increase in corolla mass involved a disproportionate allocation to the female function in SS flowers and male allocation was similar for the two morphs over the course of development. Our results are consistent with theoretical and empirical data for distylous species with an approach herkogamous ancestor, and with the more general hypothesis of ontogenetic lability of heterostyly, in which morph differences in style and anther heights are achieved in various ways. Variations observed in sexual investment between floral morphs suggest differences in sex expression during flower development.     

Vertebrate aging research 2006

This Hot Topics review, the first in a projected annual series, discusses those articles, published in the last year, which seem likely to have a major impact on our understanding of the aging process in mammals and the links between aging and late-life illnesses. The year's highlights include studies of oxidation damage in the very-long-lived naked mole-rat, and of caloric restriction in monkeys, humans, and growth hormone-unresponsive mice. Two studies of resveratrol, one showing its ability to extend lifespan in a short-lived fish, the other demonstrating beneficial effects in mice subjected to a diet high in fat, may well be harbingers of a parade of intervention studies in the coming decade.     

Positive short-term effects of sheep grazing on the alpine avifauna

Grazing by large herbivores may negatively affect bird populations. This is of great conservation concern in areas with intensive sheep grazing. Sheep management varies substantially between regions, but no study has been performed in less intensively grazed systems. In a fully replicated, landscape scale experiment with three levels of sheep grazing, we tested whether the abundance and diversity of an assemblage of mountain birds were negatively affected by grazing or if grazing facilitated the bird assemblage. Density of birds was higher at high sheep density compared with low sheep density or no sheep by the fourth grazing season, while there was no clear effect on bird diversity. Thus, agricultural traditions and land use politics determining sheep density may change the density of avifauna in either positive or negative directions.     

Hazard function for cancer patients and cancer cell dynamics

The aim of the paper is to develop a procedure for an estimate of an analytical form of a hazard function for cancer patients. Although a deterministic approach based on cancer cell population dynamics yields the analytical expression, it depends on several parameters which should be estimated. On the other hand, a kernel estimate is an effective nonparametric method for estimating hazard functions. This method provides the pointwise estimate of the hazard function. Our procedure consists of two steps: in the first step we find the kernel estimate of the hazard function and in the second step the parameters in the deterministic model are obtained by the least squares method. A simulation study with different types of censorship is carried out and the developed procedure is applied to real data.     

Stacks in canonical RNA pseudoknot structures

In this paper we study the distribution of stacks/loops in k-non-crossing, τ-canonical RNA pseudoknot structures (〈k,τ〉-structures). Here, an RNA structure is called k-non-crossing if it has no more than k-1 mutually crossing arcs and τ-canonical if each arc is contained in a stack of length at least τ. Based on the ordinary generating function of 〈k,τ〉-structures [G. Ma, C.M. Reidys, Canonical RNA pseudoknot structures, J. Comput. Biol. 15 (10) (2008) 1257] we derive the bivariate generating function , where T_k,τ(n,t) is the number of 〈k,τ〉-structures having exactly t stacks and study its singularities. We show that for a specific parametrization of the variable u, T_k,τ(x,u) exhibits a unique, dominant singularity. The particular shift of this singularity parametrized by u implies a central limit theorem for the distribution of stack-numbers. Our results are of importance for understanding the ‘language’ of minimum-free energy RNA pseudoknot structures, generated by computer folding algorithms.     

Acute modulation of myocardial function by angiotensin 1–7

Angiotensin 1–7 is a bioactive heptapeptide of the renin–angiotensin system. Its cardiovascular actions have recently acquired growing relevance, mainly due to its counter-regulatory actions in the angiotensin cascade. The aim of the present study was to evaluate the actions of angiotensin 1–7 on myocardial function. Increasing concentrations of angiotensin 1–7 (10⁻⁹ to 10⁻⁵ M) were added to rabbit right papillary muscles: (1) in baseline conditions with intact endocardial endothelium (EE); (2) after selective removal of the EE with Triton X-100 (1 s, 0.01%); (3) with intact EE in the presence of the Mas receptor antagonist A-779, the AT₁ receptor antagonist ZD-7155, the AT₂ receptor antagonist PD-123,319 or the nitric oxide synthesis inhibitor NG-nitro-l-arginine (l-NA). Concerning the effects on contractility, we observed a significant decrease on active tension, dT/dt_max, peak shortening and dL/dt_max of −10.5 ± 3.6%, −8.0 ± 3.0%, −5.3 ± 2.6% and −5.7 ± 2.3%, respectively. There was no change on relaxation parameters, namely dT/dt_min or dL/dt_min. Time to half relaxation was significantly decreased. The presence of ZD-7155 or PD-123,319 did not change these effects. However, angiotensin 1–7 effects on myocardial properties were abolished after selective EE removal and in the presence of A-779 or l-NA. In conclusion, in this animal species, angiotensin 1–7 through its binding to Mas receptor induces a negative inotropic effect modulated by the EE and nitric oxide and independent of AT₁ or AT₂ receptors activation. As the effects described in the present work were influenced by the endocardial endothelium, they may be disrupted in situations associated to endothelial dysfunction, as in heart failure or myocardial ischemia.     

Lead chloride affects sperm motility and acrosome reaction in mice

Lead is highly toxic and persistent in the environment and, thus, a major concern for public health. In this study, the effects of lead chloride (PbCl₂) on mouse epididymal sperm were evaluated. Male mice were subcutaneously injected with 74 and 100 mg PbCl₂/kg body weight for four consecutive days. Sperm was collected from the epididymis and several parameters of sperm function, such as sperm density, motility, viability, mitochondrial function, acrosome integrity and morphology, were evaluated. Furthermore, DNA fragmentation was assessed by the terminal deoxylnucleotidyl transferase-mediated deoxyuridine triphosphate (dUTP) nick-end labelling (TUNEL) assay and chromatin integrity was evaluated by sperm chromatin structure assay (SCSA). In order to assess direct effects on existing sperm population, we sacrificed one group for each condition at day 5. The effects of lead upon one entire spermatogenic cycle were evaluated on day 35. Both lead concentrations used in this work affected sperm motility, although no significant differences were observed in sperm viability, mitochondrial function and DNA/chromatin integrity. However, a decrease in the percentage of intact acrosomes was also observed, mirroring a lead-induced premature acrosome reaction. Thus, the results obtained indicate that, together with impaired motility, the effect of lead toxicity on acrosome integrity, leading to premature reaction, may compromise the ability of sperm to fertilize the oocyte.     

Using genetic algorithms to select most predictive protein features

Many important characteristics of proteins such as biochemical activity and subcellular localization present a challenge to machine-learning methods: it is often difficult to encode the appropriate input features at the residue level for the purpose of making a prediction for the entire protein. The problem is usually that the biophysics of the connection between a machine-learning method's input (sequence feature) and its output (observed phenomenon to be predicted) remains unknown; in other words, we may only know that a certain protein is an enzyme (output) without knowing which region may contain the active site residues (input). The goal then becomes to dissect a protein into a vast set of sequence-derived features and to correlate those features with the desired output. We introduce a framework that begins with a set of global sequence features and then vastly expands the feature space by generically encoding the coexistence of residue-based features. It is this combination of individual features, that is the step from the fractions of serine and buried (input space 20 + 2) to the fraction of buried serine (input space 20 * 2) that implicitly shifts the search space from global feature inputs to features that can capture very local evidence such as a the individual residues of a catalytic triad. The vast feature space created is explored by a genetic algorithm (GA) paired with neural networks and support vector machines. We find that the GA is critical for selecting combinations of features that are neither too general resulting in poor performance, nor too specific, leading to overtraining. The final framework manages to effectively sample a feature space that is far too large for exhaustive enumeration. We demonstrate the power of the concept by applying it to prediction of protein enzymatic activity.     

Binding and release of cholesterol in the Osh4 protein of yeast

Sterols have been shown experimentally to bind to the Osh4 protein (a homolog of the oxysterol binding proteins) of Saccharomyces cerevisiae within a binding tunnel, which consists of antiparallel beta-sheets that resemble a beta-barrel and three alpha-helices of the N-terminus. This and other Osh proteins are essential for intracellular transport of sterols and ultimately cell life. Molecular dynamics (MD) simulations are used to study the binding of cholesterol to Osh4 at the atomic level. The structure of the protein is stable during the course of all MD simulations and has little deviation from the experimental crystal structure. The conformational stability of cholesterol within the binding tunnel is aided in part by direct or water-mediated interactions between the 3-hydroxyl (3-OH) group of cholesterol and Trp(46), Gln(96), Tyr(97), Asn(165), and/or Gln(181) as well as dispersive interactions with Phe(42), Leu(24), Leu(39), Ile(167), and Ile(203). These residues along with other nonpolar residues in the binding tunnel and lid contribute nearly 75% to the total binding energy. The strongest and most populated interaction is between Gln(96) and 3-OH with a cholesterol/Gln(96) interaction energy of -4.5 +/- 1.0 kcal/mol. Phe(42) has a similar level of attraction to cholesterol with -4.1 +/- 0.3 kcal/mol. A MD simulation without the N-terminus lid that covers the binding tunnel resulted in similar binding conformations and binding energies when compared with simulations with the full-length protein. Steered MD was used to determine details of the mechanism used by Osh4 to release cholesterol to the cytoplasm. Phe(42), Gln(96), Asn(165), Gln(181), Pro(211), and Ile(206) are found to direct the cholesterol as it exits the binding tunnel as well as Lys(109). The mechanism of sterol release is conceptualized as a molecular ladder with the rungs being amino acids or water-mediated amino acids that interact with 3-OH.     

On the general dynamic model of oceanic island biogeography

Aim To investigate the biological meaning of equations used to apply the general dynamic model (GDM) of oceanic island biogeography proposed by R. J. Whittaker, K. A. Triantis and R. J. Ladle. Location Analyses are presented for 17 animal groups living on the Aeolian Islands, a volcanic archipelago in the central Mediterranean, near Sicily. Methods In addition to the mathematical implementation of the GDM proposed by Whittaker, Triantis and Ladle, and termed here logATT² (, where S is species number or any other diversity metric, t is island age, A is island area, and a, b, c and d are fitted parameters), a new implementation based on the Arrhenius equation of the species–area relationship (SAR) is investigated. The new model (termed powerATT²) is: . For logATT² and powerATT² models, equations were developed to calculate (1) the expected number of species at equilibrium (i.e. when the island has reached maturity) per unit area (S_eq), and (2) the time required to obtain this value (t_eq). Whereas the intercept in the Gleason model (S = C + z log A) or the coefficient of the Arrhenius power model (S = CA^z) of the SAR can be considered measures of the expected number of species per unit area, this is not the case for the parameter a of the ATT² models. However, values of S_eq can be used for this purpose. The index of ‘colonization ability’ (CAB), calculated as the ratio , may provide a measure of the mean number of species added per unit area per unit time. Results Both ATT² models fitted most of the data well, but the powerATT² model was in most cases superior. Equilibrial values of species richness (S_eq) varied from c. 3 species km^?2 (reptiles) to 100 species km^?2 (mites). The fitted curves for the powerATT² model showed large variations in d, from 0.03 to 3. However, most groups had values of d around 0.2–0.4, as commonly observed for the z‐values of SARs modelled by a power function. Equilibration times ranged from about 170,000 years to 400,000 years. Mites and springtails had very high values of CAB, thus adding many more species per unit area per unit time than others. Reptiles and phytophagous scarabs showed very low values, being the groups that added fewest species per unit area per unit time. Main conclusions Values of equilibrial species richness per unit area are influenced by species biology (e.g. body size and ecological specialization). Theoretical and empirical evidence suggests that higher immigration rates should increase the z‐values of the Arrhenius model. Thus, in the same archipelago, groups with larger z‐values should be characterized by higher dispersal ability. Results obtained here for the parameter d conform to this prediction.