Ab initio protein folding simulations using atomic burials as informational intermediates between sequence and structure

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Rapid morphological changes in populations of hybrids between Africanized and European honey bees

African honey bees, introduced to Brazil in 1956, rapidly dominated the previously introduced European subspecies. To better understand how hybridization between these different types of bees proceeded, we made geometric morphometric analyses of the wing venation patterns of specimens resulting from crosses made between Africanized honey bees (predominantly Apis mellifera scutellata) and Italian honey bees (A. mellifera ligustica) from 1965 to 1967, at the beginning of the Africanization process, in an apiary about 150 km from the original introduction site. Two virgin queens reared from an Italian parental were instrumentally inseminated with semen from drones from an Africanized parental. Six F-1 queens from one of these colonies were open mated with Africanized drones. Resultant F-1 drones were backcrossed to 50 Italian and 50 Africanized parental queens. Five backcross workers were collected from each of eight randomly selected colonies of each type of backcross (N = 5 bees x 8 colonies x 2 types of backcrosses). The F-1 progeny (40 workers and 30 drones) was found to be morphologically closer to the Africanized than to the European parental (N = 20 drones and 40 workers, each); Mahalanobis square distances = 21.6 versus 25.8, respectively, for the workers, and 39.9 versus 46.4, respectively, for the drones. The worker progenies of the backcrosses (N = 40, each) were placed between the respective parental and the F-1 progeny, although closer to the Africanized than to the Italian parentals (Mahalanobis square distance = 6.2 versus 12.1, respectively). Consequently, the most common crosses at the beginning of the Africanization process would have generated individuals more similar to Africanized than to Italian bees. This adds a genetic explanation for the rapid changes in the populational morphometric profile in recently colonized areas. Africanized alleles of wing venation pattern genes are apparently dominant and epistatic.

Gametic phase disequilibrium between the syntenic multiallelic HTG4 and HMS3 markers widely used for parentage testing in Thoroughbred horses

Validation of parentage and horse breed registries through DNA typing relies on estimates of random match probabilities with DNA profiles generated from multiple polymorphic loci. Of the twenty-seven microsatellite loci recommended by the International Society for Animal Genetics for parentage testing in Thoroughbred horses, eleven are located on five chromosomes. An important aspect in determining combined exclusion probabilities is the ascertainment of the genetic linkage status of syntenic markers, which may affect reliable use of the product rule in estimating random match probabilities. In principle, linked markers can be in gametic phase disequilibrium (GD). We aimed at determining the extent, by frequency and strength, of GD between the HTG4 and HMS3 multiallelic loci, syntenic on chromosome 9. We typed the qualified offspring (n (1) = 27; n (2) = 14) of two Quarter Bred stallions (registered by the Brazilian Association of Quarter Horse Breeders) and 121 unrelated horses from the same breed. In the 41 informative meioses analyzed, the frequency of recombination between the HTG4 and HMS3 loci was 0.27. Consistent with genetic map distances, this recombination rate does not fit to the theoretical distribution for independently segregated markers. We estimated sign-based D' coefficients as a measure of GD, and showed that the HTG4 and HMS3 loci are in significant, yet partial and weak, disequilibrium, with two allele pairs involved (HTG4*M/HMS3*P, D'(+) = 0.6274; and HTG4*K/HMS3*P, D'(-) = -0.6096). These results warn against the inadequate inclusion of genetically linked markers in the calculation of combined power of discrimination for Thoroughbred parentage validation.

Assessing apical transportation in curved canals: comparison between cross-sections and micro-computed tomography

The aim of this study was to compare two methods of assessing apical transportation in curved canals after rotary instrumentation, namely, cross-sections and micro-computed tomography (mu CT). Thirty mandibular molars were divided into two groups and prepared according to the requirements of each method. In G1 (cross-sections), teeth were embedded in resin blocks and sectioned at 2.0, 3.5, and 5.0 mm from the anatomic apex. Pre- and postoperative sections were photographed and analyzed. In G2 (mu CT), teeth were embedded in a rubber-base impression material and scanned before and after instrumentation. Mesiobuccal canals were instrumented with the Twisted File (TF) system (SybronEndo, Orange, USA), and mesiolingual canals, with the Endo Sequence (ES) system (Brasseler, Savannah, USA). Images were reconstructed, and sections corresponding to distances 2.0, 3.5, and 5.0 mm from the anatomic apex were selected for comparison. Data were analyzed using Mann-Whitney's test at a 5% significance level. The TF and ES instruments produced little deviation from the root canal center, with no statistical difference between them (P > 0.05). The canal transportation results were significantly lower (0.056 mm) in G2 than in G1 (0.089 mm) (p = 0.0012). The mu CT method was superior to the cross-section method, especially in view of its ability to preserve specimens and provide results that are more closely related to clinical situations.

Multiple Radial Midpupil Lid Distances: A Simple Method for Lid Contour Analysis

Purpose: To describe a new computerized method for the analysis of lid contour based on the measurement of multiple radial midpupil lid distances. Design: Evaluation of diagnostic technology. Participants and Controls: Monocular palpebral fissure images of 35 patients with Graves' upper eyelid retraction and of 30 normal subjects. Methods: Custom software was used to measure the conventional midpupil upper lid distance (MPLD) and 12 oblique MPLDs on each 15 degrees across the temporal (105 degrees, 120 degrees, 135 degrees, 150 degrees, 165 degrees, and 180 degrees) and nasal (75 degrees, 60 degrees, 45 degrees, 30 degrees, 15 degrees, and 0 degrees) sectors of the lid fissure. Main Outcome Measures: Mean, standard deviation, 5th and 95th percentiles of the oblique MPLDs obtained for patients and controls. Temporal/nasal MPLD ratios of the same angles with respect to the midline. Results: The MPLDs increased from the vertical midline in both nasal and temporal sectors of the fissure. In the control group the differences between the mean central MPLD (90 degrees) and those up to 30 degrees in the nasal (75 degrees and 60 degrees) and temporal sectors (105 degrees and 120 degrees) were not significant. For greater eccentricities, all temporal and nasal mean MPLDs increased significantly. When the MPLDs of the same angles were compared between groups, the mean values of the Graves' patients differed from control at all angles (F = 4192; P<0.0001). The greatest temporal/nasal asymmetry occurred 60 degrees from the vertical midline. Conclusions: The measurement of radial MPLD is a simple and effective way to characterize lid contour abnormalities. In patients with Graves' upper eyelid retraction, the method demonstrated that the maximum amplitude of the lateral lid flare sign occurred at 60 degrees from the vertical midline. Financial Disclosure(s): The authors have no proprietary or commercial interest in any of the materials discussed in this article. Ophthalmology 2012; 119: 625-628 (C) 2012 by the American Academy of Ophthalmology.

Genetic structure and connectivity between populations of two common Mediterranean sessile invertebrates

Population genetic and phylogeography of two common mediterranean species were studied in 10 localities located on the coasts of Toscana, Puglia and Calabria. The aim of the study was to verify the extent of genetic breaks, in areas recognized as boundaries between Mediterranean biogeographic sectors. From about 100 sequences obtained from the mitochondrial Cytochrome Oxidase subunit I (COI) gene of Halocynthia papillosa and Hexaplex trunculus genetic diversity, genetic structure at small and large distances and demographic history of both specieswere analyzed. No evidences of genetic breaks were found for the two species in Toscana and Puglia. The genetic structure of H. trunculus evidences the extent of a barrier to gene flow localized in Calabria, which could be represented by the Siculo-Tunisian Strait and the Strait of Messina. The observed patterns showed similar level of gene flow at small distances in both species, although the two species have different larval ecology. These results suggest that other factors, such as currents, local dynamics and seasonal temperatures, influence the connectivity along the Italian peninsula. The geographic distribution of the haplotypes shows that H. papillosacould represent a single genetic pool in expansion, whereas H. trunculus has two distinct genetic pools in expansion. The demographic pattern of the two species suggests that Pleistocene sea level oscillations, in particular of the LGM, may have played a key role in shaping genetic structure of the two species. This knowledge provides basic information, useful for the definition of management plans, or for the design of a network of marine protected areas along the Italian peninsula.

Thermal Casimir effect at fluid interfaces: Fluctuation-induced forces between anisotropic colloids

We study the effective interaction between two ellipsoidal particles at the interface of two fluid phases which are mediated by thermal fluctuations of the interface. Within a coarse-grained picture, the properties of fluid interfaces are very well described by an effective capillary wave Hamiltonian which governs both the equilibrium interface configuration and the thermal fluctuations (capillary waves) around this equilibrium (or mean-field) position. As postulated by the Goldstone theorem the capillary waves are long-range correlated. The interface breaks the continuous translational symmetry of the system, and in the limit of vanishing external fields - like gravity - it has to be accompanied by easily excitable long wavelength (Goldstone) modes – precisely the capillary waves. In this system the restriction of the long-ranged interface fluctuations by particles gives rise to fluctuation-induced forces which are equivalent to interactions of Casimir type and which are anisotropic in the interface plane. Since the position and the orientation of the colloids with respect to the interface normal may also fluctuate, this system is an example for the Casimir effect with fluctuating boundary conditions. In the approach taken here, the Casimir interaction is rewritten as the interaction between fluctuating multipole moments of an auxiliary charge density-like field defined on the area enclosed by the contact lines. These fluctuations are coupled to fluctuations of multipole moments of the contact line position (due to the possible position and orientational fluctuations of the colloids). We obtain explicit expressions for the behavior of the Casimir interaction at large distances for arbitrary ellipsoid aspect ratios. If colloid fluctuations are suppressed, the Casimir interaction at large distances is isotropic, attractive and long ranged (double-logarithmic in the distance). If, however, colloid fluctuations are included, the Casimir interaction at large distances changes to a power law in the inverse distance and becomes anisotropic. The leading power is 4 if only vertical fluctuations of the colloid center are allowed, and it becomes 8 if also orientational fluctuations are included.

A comparison between 2D and 3D cephalometry on CBCT scans of human skulls

The purpose of this study was to evaluate whether measurements on conventional cephalometric radiographs are comparable with 3D measurements on 3D models of human skulls, derived from cone beam CT (CBCT) data. A CBCT scan and a conventional cephalometric radiograph were made of 40 dry skulls. Standard cephalometric software was used to identify landmarks on both the 2D images and the 3D models. The same operator identified 17 landmarks on the cephalometric radiographs and on the 3D models. All images and 3D models were traced five times with a time-interval of 1 week and the mean value of repeated measurements was used for further statistical analysis. Distances and angles were calculated. Intra-observer reliability was good for all measurements. The reproducibility of the measurements on the conventional cephalometric radiographs was higher compared with the reproducibility of measurements on the 3D models. For a few measurements a clinically relevant difference between measurements on conventional cephalometric radiographs and 3D models was found. Measurements on conventional cephalometric radiographs can differ significantly from measurements on 3D models of the same skull. The authors recommend that 3D tracings for longitudinal research are not used in cases were there are only 2D records from the past.

Phenotypic novelty in experimental hybrids is predicted by the genetic distance between species of cichlid fish

Background: Transgressive segregation describes the occurrence of novel phenotypes in hybrids with extreme trait values not observed in either parental species. A previously experimentally untested prediction is that the amount of transgression increases with the genetic distance between hybridizing species. This follows from QTL studies suggesting that transgression is most commonly due to complementary gene action or epistasis, which become more frequent at larger genetic distances. This is because the number of QTLs fixed for alleles with opposing signs in different species should increase with time since speciation provided that speciation is not driven by disruptive selection. We measured the amount of transgression occurring in hybrids of cichlid fish bred from species pairs with gradually increasing genetic distances and varying phenotypic similarity. Transgression in multi-trait shape phenotypes was quantified using landmark-based geometric morphometric methods. Results: We found that genetic distance explained 52% and 78% of the variation in transgression frequency in F1 and F2 hybrids, respectively. Confirming theoretical predictions, transgression when measured in F2 hybrids, increased linearly with genetic distance between hybridizing species. Phenotypic similarity of species on the other hand was not related to the amount of transgression. Conclusion: The commonness and ease with which novel phenotypes are produced in cichlid hybrids between unrelated species has important implications for the interaction of hybridization with adaptation and speciation. Hybridization may generate new genotypes with adaptive potential that did not reside as standing genetic variation in either parental population, potentially enhancing a population's responsiveness to selection. Our results make it conceivable that hybridization contributed to the rapid rates of phenotypic evolution in the large and rapid adaptive radiations of haplochromine cichlids.

RFID Transponders : Link between information and material flows. How reliable are identification procedures?

Along with the growing complexity of logistic chains the demand for transparency of informations has increased. The use of intelligent RFID-Technology offers the possibility to optimize and control all capacities in use, since it enables the identification and tracking of goods alongside the entire supply chain. Every single product can be located at any given time and a multitude of current and historical data can be transferred. The interaction of the flow of material and the flow of information between the various process steps can be optimized by using RFID-Technology since it guarantees that all required data is available at the right time and at the right place. The local accessibility and convertibility of data allows a flexible, decentralised control of logistic systems. As additional advantages of RFID-Components can be considered that they are individually writable and that their identification can be achieved over considerable distances even if there is no intervisibility between tag and reader. The use of RFID-Transponder opens up new potentials regarding process security, reduction of logistic costs or availability of products. These advantages depend on reliability of the identification processes. The undisputed potentials that are made accessible by the use of RFID-Elements can only be beneficial when the informations that are decentralised and attached to goods and loading equipment can be reliably retrieved at the required points. The communication between tag and reader can be influenced by different materials such as metal, that can disturbed or complicate the radio contact. The communications reliability is subject of various tests and experiments that analyse the effects of different filling materials as well as different alignments of tags on the loading equipment.

Recent speciation between sympatric Tanganyikan cichlid colour morphs

Lake Tanganyika, Africa’s oldest lake, harbours an impressive diversity of cichlid fishes. Although diversification in its radiating groups is thought to have been initially rapid, cichlids from Lake Tanganyika show little evidence for ongoing speciation. In contrast, examples of recent divergence among sympatric colour morphs are well known in haplochromine cichlids from Lakes Malawi and Victoria. Here, we report genetic evidence for recent divergence between two sympatric Tanganyikan cichlid colour morphs. These Petrochromis morphs share mitochondrial haplotypes, yet microsatellite loci reveal that their sympatric populations form distinct genetic groups. Nuclear divergence between the two morphs is equivalent to that which arises geographically within one of the morphs over short distances and is substantially smaller than that among other sympatric species in this genus. These patterns suggest that these morphs diverged only recently, yet that barriers to gene flow exist which prevent extensive admixture despite their sympatric distribution. The morphs studied here provide an unusual example of active diversification in Lake Tanganyika’s generally ancient cichlid fauna and enable comparisons of speciation processes between Lake Tanganyika and other African lakes.

Relation between Excitation Power Density and Er3+ Doping Yielding the Highest Absolute Upconversion Quantum Yield

The upconversion quantum yield (UCQY) is one of the most significant parameters for upconverter materials. A high UCQY is essential for a succesful integration of upconversion in many applications, such as harvesting of the solar radiation. However, little is known about which doping level of the rare-earth ions yields the highest UCQY in the different host lattices and what are the underlying causes. Here, we investigate which Er3+ doping yields the highest UCQY in the host lattices β-NaYF4 and Gd2O2S under 4I15/2 → 4I13/2 excitation. We show for both host lattices that the optimum Er3+ doping is not fixed and it actually decreases as the irradiance of the excitation increases. To find the optimum Er3+ doping for a given irradiance, we determined the peak position of the internal UCQY as a function of the average Er−Er distance. For this purpose, we used a fit on experimental data, where the average Er−Er distance was calculated from the Er3+ doping of the upconverter samples and the lattice parameters of the host materials. We observe optimum average Er−Er distances for the host lattices β-NaYF4 and Gd2O2S with differences <14% at the same irradiance levels, whereas the optimum Er3+ doping are around 2× higher for β-NaYF4 than for Gd2O2S. Estimations by extrapolation to higher irradiances indicate that the optimum average Er−Er distance converges to values around 0.88 and 0.83 nm for β-NaYF4 and Gd2O2S, respectively. Our findings point to a fundamental relationship and focusing on the average distance between the active rare-earth ions might be a very efficient way to optimize the doping of rare-earth ions with regard to the highest achievable UCQY.

Molecular interactions and signal transfer between sensory rhodopsin-I and its cognate transducer

SRI is unique among known photoreceptors in that it produces opposite signals depending on the color of light stimuli. Absorption of orange light (587 nm) triggers an attractant response by the cell, whereas absorption of orange light followed by near-UV light (373 run) triggers a repellent response. Using behavioral mutants that exhibit aberrant color-sensing ability, we tested a two-conformation equilibrium model, using FRET and EPR spectroscopy. The essence of the model applied to SRI-HtrI is that the complex exists in a metastable two-conformer equilibrium which is shifted in one direction by orange light absorption (producing an attractant signal) and in the opposite direction by a second UV-violet photon (producing a repellent signal). First, by FRET we found that the E-F cytoplasmic loop of SRI moves toward the RAMP domain of the HtrI transducer during the formation of the orange-light activated signaling state of the complex. This is the first localization of a change in the physical relationship between the receptor and transducer subunits of the complex and provides a structural property of the two proposed conformers that we can monitor. Second, EPR spectra of a spin label probe at this cytoplasmic position showed shifts in the dark in the mutants toward shorter or longer EF loop-RAMP distances, explaining their behavior in terms of their mutations causing pre-stimulus shifts into one or the other conformer. ^ Next, we applied a novel electrophysiological method for monitoring the directionality of proton movement during photoactivation of SRI, to investigate the process of proton transfer in the photoactive site from the chromophore to proton acceptors on both the wildtype and aberrant color-response mutants. We observed an unexpected and critical difference in the two signaling conformations of the SRI-HtrI complex. The finding is that the vectoriality (i.e. movement away or toward the cytoplasm) of the light-induced proton transfer from the chromophore to the protein is opposite in formation of the two conformations. Retinylidene proton transfer is a common critical process in rhodopsins and these results are the first to show differences in vectoriality in a rhodopsin receptor, and to demonstrate functional importance of the direction of proton transfer. ^

Maintaining distances with the engineer: patterns of coexistence in plant communities beyond the patch-bare dichotomy

Two-phase plant communities with an engineer conforming conspicuous patches and affecting the performance and patterns of coexisting species are the norm under stressful conditions. To unveil the mechanisms governing coexistence in these communities at multiple spatial scales, we have developed a new point-raster approach of spatial pattern analysis, which was applied to a Mediterranean high mountain grassland to show how Festuca curvifolia patches affect the local distribution of coexisting species. We recorded 22 111 individuals of 17 plant perennial species. Most coexisting species were negatively associated with F. curvifolia clumps. Nevertheless, bivariate nearest-neighbor analyses revealed that the majority of coexisting species were confined at relatively short distances from F. curvifolia borders (between 0-2 cm and up to 8 cm in some cases). Our study suggests the existence of a fine-scale effect of F. curvifolia for most species promoting coexistence through a mechanism we call 'facilitation in the halo'. Most coexisting species are displaced to an interphase area between patches, where two opposite forces reach equilibrium: attenuated severe conditions by proximity to the F. curvifolia canopy (nutrient-rich islands) and competitive exclusion mitigated by avoiding direct contact with F. curvifolia.

Dynamic topic-based adaptation of language models: a comparison between different approaches

This paper presents a dynamic LM adaptation based on the topic that has been identified on a speech segment. We use LSA and the given topic labels in the training dataset to obtain and use the topic models. We propose a dynamic language model adaptation to improve the recognition performance in "a two stages" AST system. The final stage makes use of the topic identification with two variants: the first on uses just the most probable topic and the other one depends on the relative distances of the topics that have been identified. We perform the adaptation of the LM as a linear interpolation between a background model and topic-based LM. The interpolation weight id dynamically adapted according to different parameters. The proposed method is evaluated on the Spanish partition of the EPPS speech database. We achieved a relative reduction in WER of 11.13% over the baseline system which uses a single blackground LM.