Steps and bumps:precision extraction of discrete states of molecular machines

We report statistical time-series analysis tools providing improvements in the rapid, precision extraction of discrete state dynamics from time traces of experimental observations of molecular machines. By building physical knowledge and statistical innovations into analysis tools, we provide techniques for estimating discrete state transitions buried in highly correlated molecular noise. We demonstrate the effectiveness of our approach on simulated and real examples of steplike rotation of the bacterial flagellar motor and the F1-ATPase enzyme. We show that our method can clearly identify molecular steps, periodicities and cascaded processes that are too weak for existing algorithms to detect, and can do so much faster than existing algorithms. Our techniques represent a step in the direction toward automated analysis of high-sample-rate, molecular-machine dynamics. Modular, open-source software that implements these techniques is provided.

A framework for automatic feature extraction from airborne light detection and ranging data

Recent advances in airborne Light Detection and Ranging (LIDAR) technology allow rapid and inexpensive measurements of topography over large areas. Airborne LIDAR systems usually return a 3-dimensional cloud of point measurements from reflective objects scanned by the laser beneath the flight path. This technology is becoming a primary method for extracting information of different kinds of geometrical objects, such as high-resolution digital terrain models (DTMs), buildings and trees, etc. In the past decade, LIDAR gets more and more interest from researchers in the field of remote sensing and GIS. Compared to the traditional data sources, such as aerial photography and satellite images, LIDAR measurements are not influenced by sun shadow and relief displacement. However, voluminous data pose a new challenge for automated extraction the geometrical information from LIDAR measurements because many raster image processing techniques cannot be directly applied to irregularly spaced LIDAR points. ^ In this dissertation, a framework is proposed to filter out information about different kinds of geometrical objects, such as terrain and buildings from LIDAR automatically. They are essential to numerous applications such as flood modeling, landslide prediction and hurricane animation. The framework consists of several intuitive algorithms. Firstly, a progressive morphological filter was developed to detect non-ground LIDAR measurements. By gradually increasing the window size and elevation difference threshold of the filter, the measurements of vehicles, vegetation, and buildings are removed, while ground data are preserved. Then, building measurements are identified from no-ground measurements using a region growing algorithm based on the plane-fitting technique. Raw footprints for segmented building measurements are derived by connecting boundary points and are further simplified and adjusted by several proposed operations to remove noise, which is caused by irregularly spaced LIDAR measurements. To reconstruct 3D building models, the raw 2D topology of each building is first extracted and then further adjusted. Since the adjusting operations for simple building models do not work well on 2D topology, 2D snake algorithm is proposed to adjust 2D topology. The 2D snake algorithm consists of newly defined energy functions for topology adjusting and a linear algorithm to find the minimal energy value of 2D snake problems. Data sets from urbanized areas including large institutional, commercial, and small residential buildings were employed to test the proposed framework. The results demonstrated that the proposed framework achieves a very good performance. ^

Dual layer solid phase extraction based on molecular imprinting technology: Seeking a route to enhance selectivity for trace analysis of pesticide residues in olive oil.

Aiming to introduce a multiresidue analysis for the trace detection of pesticide residues belonging to organophosphorus and triazine classes from olive oil samples, a new sample preparation methodology comprising the use of a dual layer of “tailor-made” molecularly imprinted polymers (MIPs) SPE for the simultaneous extraction of both pesticides in a single procedure has been attempted. This work has focused on the implementation of a dual MIP-layer SPE procedure (DL-MISPE) encompassing the use of two MIP layers as specific sorbents. In order to achieve higher recovery rates, the amount of MIP layers has been optimized as well as the influence of MIP packaging order. The optimized DL-MISPE approach has been used in the preconcentration of spiked organic olive oil samples with concentrations of dimethoate and terbuthylazine similar to the maximum residue limits and further quantification by HPLC. High recovery rates for dimethoate (95%) and terbuthylazine (94%) have been achieved with good accuracy and precision. Overall, this work constitutes the first attempt on the development of a dual pesticide residue methodology for the trace analysis of pesticide residues based on molecular imprinting technology. Thus, DL-MISPE constitutes a reliable, robust, and sensitive sample preparation methodology that enables preconcentration of the target pesticides in complex olive oil samples, even at levels similar to the maximum residue limits enforced by the legislation.

Evaluation of five commercial methods for the extraction and purification of DNA from human faecal samples for downstream molecular detection of the enteric protozoan parasites Cryptosporidium spp., Giardia duodenalis, and Entamoeba spp

High quality, pure DNA is required for ensuring reliable and reproducible results in molecular diagnosis applications. A number of in-house and commercial methods are available for the extraction and purification of genomic DNA from faecal material, each one offering a specific combination of performance, cost-effectiveness, and easiness of use that should be conveniently evaluated in function of the pathogen of interest. In this comparative study the marketed kits QIAamp DNA stool mini (Qiagen), SpeedTools DNA extraction (Biotools), DNAExtract-VK (Vacunek), PowerFecal DNA isolation (MoBio), and Wizard magnetic DNA purification system (Promega Corporation) were assessed for their efficacy in obtaining DNA of the most relevant enteric protozoan parasites associated to gastrointestinal disease globally. A panel of 113 stool specimens of clinically confirmed patients with cryptosporidiosis (n = 29), giardiasis (n = 47) and amoebiasis by Entamoeba histolytica (n = 3) or E. dispar (n = 10) and apparently healthy subjects (n = 24) were used for this purpose. Stool samples were aliquoted in five sub-samples and individually processed by each extraction method evaluated. Purified DNA samples were subsequently tested in PCR-based assays routinely used in our laboratory. The five compared methods yielded amplifiable amounts of DNA of the pathogens tested, although performance differences were observed among them depending on the parasite and the infection burden. Methods combining chemical, enzymatic and/or mechanical lysis procedures at temperatures of at least 56 °C were proven more efficient for the release of DNA from Cryptosporidium oocysts.

Fixing, storage time and DNA extraction applied to dT-RFLP for ecological and molecular studies of marine nematodes assemblages

The application of molecular methods offers an alternative faster than traditional methods based on morphology It is nearly impossible to process all the samples in short period using traditional methods, and the deterioration of marine sediments rapidly occurs The dT-RFLP (directed Terminal-Restriction Fragment Length Polymorphism) allows a rapid assessment of biodiversity changes of nematodes assemblages The use of a not suitable fixing, storage time and DNA extraction could be a limitation in molecular analysis like dT-RFLP and real time PCR.Objetives: the best fixative •the level of DNA degradation over the time •the best DNA extraction method for marine nematodes and suitable for dT-RFLP analysis

A Modified Acidic Approach For Dna Extraction From Plant Species Containing High Levels Of Secondary Metabolites.

Purified genomic DNA can be difficult to obtain from some plant species because of the presence of impurities such as polysaccharides, which are often co-extracted with DNA. In this study, we developed a fast, simple, and low-cost protocol for extracting DNA from plants containing high levels of secondary metabolites. This protocol does not require the use of volatile toxic reagents such as mercaptoethanol, chloroform, or phenol and allows the extraction of high-quality DNA from wild and cultivated tropical species.

Protocol for DNA extraction of Cryptosporidium spp. oocysts in fecal samples

Molecular characterization of Cryptosporidium spp.oocysts in clinical samples is useful for public health since it allows the study of sources of contamination as well as the transmission in different geographical regions. Although widely used in developed countries, in Brazil it is restricted to academic studies, mostly using commercial kits for the extraction of genomic DNA, or in collaboration with external reference centers, rendering the method expensive and limited. The study proposes the application of the modifications recently introduced in the method improving feasibility with lower cost. This method was efficient for clinical samples preserved at -20 °C for up to six years and the low number of oocysts may be overcomed by repetitions of extraction.

Power Secant Method applied to natural frequency extraction of Timoshenko beam structures

This work deals with an improved plane frame formulation whose exact dynamic stiffness matrix (DSM) presents, uniquely, null determinant for the natural frequencies. In comparison with the classical DSM, the formulation herein presented has some major advantages: local mode shapes are preserved in the formulation so that, for any positive frequency, the DSM will never be ill-conditioned; in the absence of poles, it is possible to employ the secant method in order to have a more computationally efficient eigenvalue extraction procedure. Applying the procedure to the more general case of Timoshenko beams, we introduce a new technique, named ""power deflation"", that makes the secant method suitable for the transcendental nonlinear eigenvalue problems based on the improved DSM. In order to avoid overflow occurrences that can hinder the secant method iterations, limiting frequencies are formulated, with scaling also applied to the eigenvalue problem. Comparisons with results available in the literature demonstrate the strength of the proposed method. Computational efficiency is compared with solutions obtained both by FEM and by the Wittrick-Williams algorithm.

DNA extraction from hair shafts of wild Brazilian felids and canids

Wild felids and canids are usually the main predators in the food chains where they dwell and are almost invisible to behavior and ecology researchers. Due to their grooming behavior, they tend to swallow shed hair, which shows up in the feces. DNA found in hair shafts can be used in molecular studies that can unravel, for instance, genetic variability, reproductive mode and family structure, and in some species, it is even possible to estimate migration and dispersion rates in given populations. First, however, DNA must be extracted from hair. We extracted successfully and dependably hair shaft DNA from eight wild Brazilian felids, ocelot, margay, oncilla, Geoffroy's cat, pampas cat, jaguarundi, puma, and jaguar, as well as the domestic cat and from three wild Brazilian canids, maned wolf, crab-eating fox, and hoary fox, as well as the domestic dog. Hair samples came mostly from feces collected at the Sao Paulo Zoo and were also gathered from non-sedated pet or from recently dead wild animals and were also collected from museum specimens. Fractions of hair samples were stained before DNA extraction, while most samples were not. Our extraction protocol is based on a feather DNA extraction technique, based in the phenol: chloroform: isoamyl alcohol general method, with proteinase K as digestive enzyme.

Continental passive microwave-based rainfall estimation algorithm: Application to the Amazon Basin

This paper presents a new statistical algorithm to estimate rainfall over the Amazon Basin region using the Tropical Rainfall Measuring Mission (TRMM) Microwave Imager (TMI). The algorithm relies on empirical relationships derived for different raining-type systems between coincident measurements of surface rainfall rate and 85-GHz polarization-corrected brightness temperature as observed by the precipitation radar (PR) and TMI on board the TRMM satellite. The scheme includes rain/no-rain area delineation (screening) and system-type classification routines for rain retrieval. The algorithm is validated against independent measurements of the TRMM-PR and S-band dual-polarization Doppler radar (S-Pol) surface rainfall data for two different periods. Moreover, the performance of this rainfall estimation technique is evaluated against well-known methods, namely, the TRMM-2A12 [ the Goddard profiling algorithm (GPROF)], the Goddard scattering algorithm (GSCAT), and the National Environmental Satellite, Data, and Information Service (NESDIS) algorithms. The proposed algorithm shows a normalized bias of approximately 23% for both PR and S-Pol ground truth datasets and a mean error of 0.244 mm h(-1) ( PR) and -0.157 mm h(-1)(S-Pol). For rain volume estimates using PR as reference, a correlation coefficient of 0.939 and a normalized bias of 0.039 were found. With respect to rainfall distributions and rain area comparisons, the results showed that the formulation proposed is efficient and compatible with the physics and dynamics of the observed systems over the area of interest. The performance of the other algorithms showed that GSCAT presented low normalized bias for rain areas and rain volume [0.346 ( PR) and 0.361 (S-Pol)], and GPROF showed rainfall distribution similar to that of the PR and S-Pol but with a bimodal distribution. Last, the five algorithms were evaluated during the TRMM-Large-Scale Biosphere-Atmosphere Experiment in Amazonia (LBA) 1999 field campaign to verify the precipitation characteristics observed during the easterly and westerly Amazon wind flow regimes. The proposed algorithm presented a cumulative rainfall distribution similar to the observations during the easterly regime, but it underestimated for the westerly period for rainfall rates above 5 mm h(-1). NESDIS(1) overestimated for both wind regimes but presented the best westerly representation. NESDIS(2), GSCAT, and GPROF underestimated in both regimes, but GPROF was closer to the observations during the easterly flow.

A possible role of ground-based microorganisms on cloud formation in the atmosphere

The formation of clouds is an important process for the atmosphere, the hydrological cycle, and climate, but some aspects of it are not completely understood. In this work, we show that microorganisms might affect cloud formation without leaving the Earth's surface by releasing biological surfactants (or biosurfactants) in the environment, that make their way into atmospheric aerosols and could significantly enhance their activation into cloud droplets. In the first part of this work, the cloud-nucleating efficiency of standard biosurfactants was characterized and found to be better than that of any aerosol material studied so far, including inorganic salts. These results identify molecular structures that give organic compounds exceptional cloud-nucleating properties. In the second part, atmospheric aerosols were sampled at different locations: a temperate coastal site, a marine site, a temperate forest, and a tropical forest. Their surface tension was measured and found to be below 30 mN/m, the lowest reported for aerosols, to our knowledge. This very low surface tension was attributed to the presence of biosurfactants, the only natural substances able to reach to such low values. The presence of strong microbial surfactants in aerosols would be consistent with the organic fractions of exceptional cloud-nucleating efficiency recently found in aerosols, and with the correlations between algae bloom and cloud cover reported in the Southern Ocean. The results of this work also suggest that biosurfactants might be common in aerosols and thus of global relevance. If this is confirmed, a new role for microorganisms on the atmosphere and climate could be identified.

On molecular chirality within naturally occurring secondary organic aerosol particles from the central Amazon Basin

In this perspectives article, we reflect upon the existence of chirality in atmospheric aerosol particles. We then show that organic particles collected at a field site in the central Amazon Basin under pristine background conditions during the wet and dry seasons consist of chiral secondary organic material. We show how the chiral response from the aerosol particles can be imaged directly without the need for sample dissolution, solvent extraction, or sample preconcentration. By comparing the chiral-response images with optical images, we show that chiral responses always originate from particles on the filter, but not all aerosol particles produce chiral signals. The intensity of the chiral signal produced by the size resolved particles strongly indicates the presence of chiral secondary organic material in the particle. Finally, we discuss the implications of our findings on chiral atmospheric aerosol particles in terms of climate-related properties and source apportionment.

Observation of cooperative Mie scattering from an ultracold atomic cloud

Scattering of light at a distribution of scatterers is an intrinsically cooperative process, which means that the scattering rate and the angular distribution of the scattered light are essentially governed by bulk properties of the distribution, such as its size, shape, and density, although local disorder and density fluctuations may have an important impact on the cooperativity. Via measurements of the radiation pressure force exerted by a far-detuned laser beam on a very small and dense cloud of ultracold atoms, we are able to identify the respective roles of superradiant acceleration of the scattering rate and of Mie scattering in the cooperative process. They lead, respectively, to a suppression or an enhancement of the radiation pressure force. We observe a maximum in the radiation pressure force as a function of the phase shift induced in the incident laser beam by the cloud's refractive index. The maximum marks the borderline of the validity of the Rayleigh-Debye-Gans approximation from a regime, where Mie scattering is more complex. Our observations thus help to clarify the intricate relationship between Rayleigh scattering of light at a coarse-grained ensemble of individual scatterers and Mie scattering at the bulk density distribution.

Extraction of manganese peroxidase produced by Lentinula edodes

Lentinula edodes, commonly called shiitake, is considered a choice edible mushroom with exotic taste and medicinal quality. L. edodes grows very well and produces a range of enzymes when cultivated on eucalyptus residues. Development of appropriate experimental procedures for recovery and determination of enzymes became a widely important cash crop. In this work, enzymes produced by L. edodes were extracted using different pH buffer and determined regarding peroxidases and proteases. Lignin peroxidase (LiP) was not detected in the extracts based on veratryl alcohol or azure B oxidation. Proteases were very low while Mn-peroxidases (MnP) predominated. The optimal pH for MnP recovery was 5.0, under agitation at 25 degrees C. The oxidation of phenol red decreased after dark-colored small compounds or ions were eliminated by dialysis. The extract of L. edodes contained components of high molecular weight, such as proteases or high polyphenol, that could be involved in the LiP inactivation. L. edodes sample previously submitted to dialysis was also joined to UP of Phanerochaete chrysosporium and a total inhibition of UP was observed. (C) 2007 Elsevier Ltd. All rights reserved.

Total Soluble Solids from Banana: Evaluation and Optimization of Extraction Parameters

Banana, an important component in the diet of the global population, is one of the most consumed fruits in the world. This fruit is also very favorable to industry processes (e. g., fermented beverages) due to its rich content on soluble solids and minerals, with low acidity. The main objective of this work was to evaluate the influence of factors such as banana weight and extraction time during a hot aqueous extraction process on the total soluble solids content of banana. The extract is to be used by the food and beverage industries. The experiments were performed with 105 mL of water, considering the moisture of the ripe banana (65%). Total sugar concentrations were obtained in a beer analyzer and the result expressed in degrees Plato (degrees P, which is the weight of the extract or the sugar equivalent in 100 g solution at 20 degrees C), aiming at facilitating the use of these results by the beverage industries. After previous studies of characterization of the fruit and of ripening performance, a 2(2) full-factorial star design was carried out, and a model was developed to describe the behavior of the dependent variable (total soluble solids) as a function of the factors (banana weight and extraction time), indicating as optimum conditions for extraction 38.5 g of banana at 39.7 min.