Effect of Warmup Protocol and Sampling Time on Convergence of Molecular Dynamics Simulations of a DNA Dodecamer Using AMBER 4.1 and Particle-Mesh Ewald Method

Abstract

This report describes one 3000 ps and two 1500 ps molecular dynamic simulations on a TATA box containing dodecamer DNA duplex in a periodic box of TIP3P water molecules, using the AMBER 4.1 implementation of the particle-mesh Ewald method. We compare the effect of warmup protocol and simulation time length on the root-mean square deviation (RMSD) parameter. For the longer simulation, the RMSD computed for the 500–1000 ps time interval is representative of longer time intervals, including 500–3000 ps. The various warmup protocols do not appear to have a significant effect on the simulation results. Based on the present results, DNA sequence-dependent differences in RMSD, or related properties, should exceed two standard deviations before being attributed to non-simulation factors, such as warmup protocol and sampling time effects; we recommend a minimum criterion of at least a three standard deviation difference with a sampling period of at least 500–1000 ps. In addition, while end effects appear negligible there is a consistent dependence of RMSD on DNA helix length.     

Incongruence between life-history traits and conservation status in reef corals

Coral Reefs - Comparative lists of species’ extinction risk are increasingly being used to prioritise conservation resources. Extinction risk is most rigorously assessed using quantitative...     

Functional characterization of a synthetic hydrophilic antifungal peptide derived from the marine snail Cenchritis muricatus

Antimicrobial peptides have been found in mollusks and other sea animals. In this report, a crude extract of the marine snail Cenchritis muricatus was evaluated against human pathogens responsible for multiple deleterious effects and diseases. A peptide of 1485.26 Da was purified by reversed-phase HPLC and functionally characterized. This trypsinized peptide was sequenced by MS/MS technology, and a sequence (SRSELIVHQR), named Cm-p1 was recovered, chemically synthesized and functionally characterized. This peptide demonstrated the capacity to prevent the development of yeasts and filamentous fungi. Otherwise, Cm-p1 displayed no toxic effects against mammalian cells. Molecular modeling analyses showed that this peptide possible forms a single hydrophilic α-helix and the probable cationic residue involved in antifungal activity action is proposed. The data reported here demonstrate the importance of sea animals peptide discovery for biotechnological tools development that could be useful in solving human health and agribusiness problems.     

Genetic characterization and construction of an auxotrophic strain of Saccharomyces cerevisiae JP1, a Brazilian industrial yeast strain for bioethanol production

Used for millennia to produce beverages and food, Saccharomyces cerevisiae also became a workhorse in the production of biofuels, most notably bioethanol. Yeast strains have acquired distinct characteristics that are the result of evolutionary adaptation to the stresses of industrial ethanol production. JP1 is a dominant industrial S. cerevisiae strain isolated from a sugarcane mill and is becoming increasingly popular for bioethanol production in Brazil. In this work, we carried out the genetic characterization of this strain and developed a set of tools to permit its genetic manipulation. Using flow cytometry, mating type, and sporulation analysis, we verified that JP1 is diploid and homothallic. Vectors with dominant selective markers for G418, hygromycin B, zeocin, and ρ-fluoro-dl-phenylalanine were used to successfully transform JP1 cells. Also, an auxotrophic ura3 mutant strain of JP1 was created by gene disruption using integration cassettes with dominant markers flanked by loxP sites. Marker excision was accomplished by the Cre/loxP system. The resulting auxotrophic strain was successfully transformed with an episomal vector that allowed green fluorescent protein expression.     

Molecular detection of XO - Turner syndrome

Turner syndrome is caused by haploinsufficiency of the short arm of X-chromosome, and is usually diagnosed by karyotyping. This procedure is time-consuming, expensive and unfeasible for population screening. We propose molecular detection of 45XO Turner patients based on the ability of HpaII, a methylation sensitive endonuclease, to induce the cleavage of non-methylated DNA in the active X-allele. Genomic DNA was obtained from 22 patients with Turner syndrome confirmed by karyotype (45XO, N = 18; 45XO/46XX, N = 4). After digestion, DNA was amplified with primers directed to exon 1 of the androgen receptor (AR) gene and to the GAPDH control gene. Normal control females or mosaic patients, with a second methylated X-chromosome, escaped from HpaII digestion and produced a band corresponding to AR gene amplification. 45XO patients have just one active non-methylated X-chromosome, completely digested by HpaII, thus preventing the amplification of the AR gene. Three of the 45XO cases gave amplified bands, suggesting low-frequency mosaicisms that are not detected by karyotyping. Compared to classical karyotype studies for the detection of 45XO Turner patients, this new molecular method is simpler, faster and less expensive.     

Determinants of reef fish assemblages in tropical Oceanic islands

Diversity patterns are determined by biogeographic, energetic, and anthropogenic factors, yet few studies have combined them into a large‐scale framework in order to decouple and compare their relative effects on fish faunas. Using an empirical dataset derived from 1527 underwater visual censuses (UVC) at 18 oceanic islands (five different marine provinces), we determined the relative influence of such factors on reef fish species richness, functional dispersion, density and biomass estimated from each UVC unit. Species richness presented low variation but was high at large island sites. High functional dispersion, density, and biomass were found at islands with large local species pool and distance from nearest reef. Primary productivity positively affected fish richness, density and biomass confirming that more productive areas support larger populations, and higher biomass and richness on oceanic islands. Islands densely populated by humans had lower fish species richness and biomass reflecting anthropogenic effects. Species richness, functional dispersion, and biomass were positively related to distance from the mainland. Overall, species richness and fish density were mainly influenced by biogeographical and energetic factors, whereas functional dispersion and biomass were strongly influenced by anthropogenic factors. Our results extend previous hypotheses for different assemblage metrics estimated from empirical data and confirm the negative impact of humans on fish assemblages, highlighting the need for conservation of oceanic islands.     

Biogeographic responses and niche occupancy of microbial communities following long-term land-use change

Understanding the effects of forest-to-agriculture conversion on microbial diversity has been a major goal in soil ecological studies. However, linking community assembly to the ruling ecological processes at local and regional scales remains challenging. Here, we evaluated bacterial community assembly patterns and the ecological processes governing niche specialization in a gradient of geography, seasonality, and land-use change, totaling 324 soil samples, 43 habitat characteristics (abiotic factors), and 16 metabolic and co-occurrence patterns (biotic factors), in the Brazilian Atlantic Rainforest, a subtropical biome recognized as one the world’s largest and most threatened hotspots of biodiversity. Pairwise beta diversities were lower in pastures than in forest and no-till soils. Pasture communities showed a predominantly neutral model, regarding stochastic processes, with moderate dispersion, leading to biotic homogenization. Most no-till and forest microbial communities followed a niche-based model, with low rates of dispersal and weak homogenizing selection, indicating niche specialization or variable selection. Historical and evolutionary contingencies, as represented by soil type, season, and dispersal limitation were the main drivers of microbial assembly and processes at the local scale, markedly correlated with the occurrence of endemic microbes. Our results indicate that the patterns of assembly and their governing processes are dependent on the niche occupancy of the taxa evaluated (generalists or specialists). They are also more correlated with historical and evolutionary contingencies and the interactions among taxa (i.e., co-occurrence patterns) than the land-use change itself.

     

The role of effective mass and hand speed in the performance of kung fu athletes compared with nonpractitioners

The main goal of this article is to quantify the contribution of effective mass (me) and handspeed (shi) on the palm strike performance of kung fu athletes (kung fu group) compared with nonpractitioners (control group). All subjects were asked to strike a basketball. Hand and ball speed (sbf) were determined by high-speed video analysis. The value for me was determined by an equation that does not depend upon postimpact measurement of the hand speed. The results show that kung fu athletes had greater shi (6.67 [SD 1.42] m/s), p = 0.042), higher me (2.62 [SD 0.33] kg, p = 0.004), and greater sbf (9.00 [SD 1.89] m/s), p = 0.004) than the nonpractitioners (5.04 [SD 0.57] m/s, 1.33 [SD 0.19] kg, and 5.72 [SD 0.44] m/s, respectively). Comparing the average values obtained for me and hand and forearm mass (m), it was found that for the control group me is statistically equal to m (p = 0.917), whereas for the kung fu group me is significant greater than m (p = 0.003). It is suggested that for impacts against heavier objects, the effective mass would be the main factor to distinguish a martial arts-trained from an untrained subject.     

Biology and functional morphology of the pallial organs of the Antarctic bivalve Mysella charcoti (Lamy, 1906) (Galeommatoidea: Lasaeidae)

Mysella charcoti is an Antarctic lasaeid bivalve and the most frequently encountered mollusc in Admiralty Bay, King George Island, South Shetlands. The behaviour of the species in aquaria, combined with analyses of the gross and microscopic morphologies and functioning of the organs in the mantle cavity of living and preserved specimens have allowed an understanding of important aspects of its biology. The role of the foot and its ciliature during the processes of dislodgement and burrowing within the sediment are described. The species is a free-living, shallow-burrower, with a predominantly deposit-feeding habit and derives part of its food from the labile settled organic deposits carried into the mantle cavity by the anterior–posterior current of water. Pedal sweep-feeding was not detected. M. charcoti is the first known lasaeid with ctenidia formed of the descending lamellae of the inner demibranchs only, a feature probably related to its highly specialised brooding habit.