Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 59
Filtrar
Mais filtros

País/Região como assunto
Tipo de documento
Intervalo de ano de publicação
1.
BMC Bioinformatics ; 24(1): 70, 2023 Feb 27.
Artigo em Inglês | MEDLINE | ID: mdl-36849917

RESUMO

B cell receptor (BCR) genes exposed to an antigen undergo somatic hypermutations and Darwinian antigen selection, generating a large BCR-antibody diversity. This process, known as B cell affinity maturation, increases antibody affinity, forming a specific B cell lineage that includes the unmutated ancestor and mutated variants. In a B cell lineage, cells with a higher antigen affinity will undergo clonal expansion, while those with a lower affinity will not proliferate and probably be eliminated. Therefore, cellular (genotype) abundance provides a valuable perspective on the ongoing evolutionary process. Phylogenetic tree inference is often used to reconstruct B cell lineage trees and represents the evolutionary dynamic of BCR affinity maturation. However, such methods should process B-cell population data derived from experimental sampling that might contain different cellular abundances. There are a few phylogenetic methods for tracing the evolutionary events occurring in B cell lineages; best-performing solutions are time-demanding and restricted to analysing a reduced number of sequences, while time-efficient methods do not consider cellular abundances. We propose ClonalTree, a low-complexity and accurate approach to construct B-cell lineage trees that incorporates genotype abundances into minimum spanning tree (MST) algorithms. Using both simulated and experimental data, we demonstrate that ClonalTree outperforms MST-based algorithms and achieves a comparable performance to a method that explores tree-generating space exhaustively. Furthermore, ClonalTree has a lower running time, being more convenient for building B-cell lineage trees from high-throughput BCR sequencing data, mainly in biomedical applications, where a lower computational time is appreciable. It is hundreds to thousands of times faster than exhaustive approaches, enabling the analysis of a large set of sequences within minutes or seconds and without loss of accuracy. The source code is freely available at github.com/julibinho/ClonalTree.


Assuntos
Linfócitos B , Receptores de Antígenos de Linfócitos B , Linhagem da Célula/genética , Filogenia , Genótipo , Receptores de Antígenos de Linfócitos B/genética
2.
PLoS Comput Biol ; 18(8): e1010411, 2022 08.
Artigo em Inglês | MEDLINE | ID: mdl-36037250

RESUMO

The adaptive B cell response is driven by the expansion, somatic hypermutation, and selection of B cell clonal lineages. A high number of clonal lineages in a B cell population indicates a highly diverse repertoire, while clonal size distribution and sequence diversity reflect antigen selective pressure. Identifying clonal lineages is fundamental to many repertoire studies, including repertoire comparisons, clonal tracking, and statistical analysis. Several methods have been developed to group sequences from high-throughput B cell repertoire data. Current methods use clustering algorithms to group clonally-related sequences based on their similarities or distances. Such approaches create groups by optimizing a single objective that typically minimizes intra-clonal distances. However, optimizing several objective functions can be advantageous and boost the algorithm convergence rate. Here we propose MobiLLe, a new method based on multi-objective clustering. Our approach requires V(D)J annotations to obtain the initial groups and iteratively applies two objective functions that optimize cohesion and separation within clonal lineages simultaneously. We show that our method greatly improves clonal lineage grouping on simulated benchmarks with varied mutation rates compared to other tools. When applied to experimental repertoires generated from high-throughput sequencing, its clustering results are comparable to the most performing tools and can reproduce the results of previous publications. The method based on multi-objective clustering can accurately identify clonally-related antibody sequences and presents the lowest running time among state-of-art tools. All these features constitute an attractive option for repertoire analysis, particularly in the clinical context. MobiLLe can potentially help unravel the mechanisms involved in developing and evolving B cell malignancies.


Assuntos
Linfócitos B , Sequenciamento de Nucleotídeos em Larga Escala , Algoritmos , Anticorpos , Análise por Conglomerados , Sequenciamento de Nucleotídeos em Larga Escala/métodos
3.
Nanomedicine ; 24: 102130, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31760163

RESUMO

Many studies have shown that silver nanoparticles (AgNP) induce oxidative stress, and it is commonly assumed that this is the main mechanism of AgNP cytotoxicity. Most of these studies rely on antioxidants to establish this cause-and-effect relationship; nevertheless, details on how these antioxidants interact with the AgNP are often overlooked. This work aimed to investigate the molecular mechanisms underlying the use of antioxidants with AgNP nanoparticles. Thus, we studied the molecular interaction between the thiol-antioxidants (N-acetyl-L-Cysteine, L-Cysteine, and glutathione) or non-thiol-antioxidants (Trolox) with chemically and biologically synthesized AgNP. Both antioxidants could mitigate ROS production in Huh-7 hepatocarcinoma cells, but only thiol-antioxidants could prevent the cytotoxic effect, directly binding to the AgNP leading to aggregation. Our findings show that data interpretation might not be straightforward when using thiol-antioxidants to study the interactions between metallic nanoparticles and cells. This artifact exemplifies potential pitfalls that could hinder the progress of nanotechnology and the understanding of the nanotoxicity mechanism.


Assuntos
Antioxidantes/química , Nanopartículas Metálicas/química , Prata/química , Compostos de Sulfidrila/química , Linhagem Celular Tumoral , Humanos , Modelos Teóricos , Nanotecnologia/métodos , Estresse Oxidativo/fisiologia , Espécies Reativas de Oxigênio/química
4.
An Acad Bras Cienc ; 92 Suppl 1: e20190169, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32638864

RESUMO

Abstract: This study assessed the effect of salinity on embryonic development, larval growth and survival of the yellow clam Mesodesma mactroides in laboratory. Embryos and larvae of M. mactroides were submitted and maintained at four different salinities: 20, 25, 30 and 35 ppt, to determine optimal conditions for the species. Through descriptive analysis, the results showed that the embryos tolerate salinities between 25 - 35 ppt, presenting fast metamorphoses at salinities 30 and 35 ppt, during experimental period of 27 hours. The same tolerance pattern was observed in larval stage (25 - 35 ppt), showing a better development in salinity of 35 ppt. This result is verified in biometric analyzes of height and length of the shells and survival rate, with higher averages in treatments with salinity 35 ppt. The experimental period of this stage lasted 27 days, when the larvae were able to settle. These results indicate that embryos and larvae of M. mactroides tolerate salinities between (25-35 ppt), with the best growth and survival on high salinities being recommended to better yields in laboratory.


Assuntos
Bivalves , Salinidade , Animais , Desenvolvimento Embrionário , Larva
5.
An Acad Bras Cienc ; 92 Suppl 1: e20190053, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32348413

RESUMO

The yellow clam Mesodesma mactroides (Reeve, 1854) is a sand mollusc with historical and socioeconomic importance in Brazil, Uruguay and Argentina. A guaranteed form to access a successful reestablishment of the species in their natural environment is directly linked to their reproduction biology. Then, our report introduces the embryonic and larval development of the yellow clam reared in laboratory for such purposes. M. mactroides broodstock were selected as specimens who possess a mean total shell length and weight of 66 ± 3.82 mm and 27.15 ± 4.07 g for an afterwards spawn induction through stripping technique. Regarding the embryonic development, newly fertilized oocytes exhibited a mean diameter of 51.20 ± 6.64 µm. The first polar corpuscle, trochophores and D-veliger appeared at 20 min, 18 and 24 h after fertilization, respectively. Umbonate and pediveliger larvae were noticed on the 8th and 25th day, respectively, with complete metamorphosis occurring only at the 27th day, when all larvae were retained in a 200 µm nylon mesh. Therefore, with that basic understanding of the embryonic and larval development of M. mactroides in the laboratory, forwards studies will focus in establish a technological package for this species.


Assuntos
Bivalves/embriologia , Bivalves/crescimento & desenvolvimento , Animais , Bivalves/classificação , Laboratórios , Larva/crescimento & desenvolvimento , Óvulo/crescimento & desenvolvimento
6.
Plant Cell ; 28(3): 616-28, 2016 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-26941092

RESUMO

The absorption of visible light in aquatic environments has led to the common assumption that aquatic organisms sense and adapt to penetrative blue/green light wavelengths but show little or no response to the more attenuated red/far-red wavelengths. Here, we show that two marine diatom species, Phaeodactylum tricornutum and Thalassiosira pseudonana, possess a bona fide red/far-red light sensing phytochrome (DPH) that uses biliverdin as a chromophore and displays accentuated red-shifted absorbance peaks compared with other characterized plant and algal phytochromes. Exposure to both red and far-red light causes changes in gene expression in P. tricornutum, and the responses to far-red light disappear in DPH knockout cells, demonstrating that P. tricornutum DPH mediates far-red light signaling. The identification of DPH genes in diverse diatom species widely distributed along the water column further emphasizes the ecological significance of far-red light sensing, raising questions about the sources of far-red light. Our analyses indicate that, although far-red wavelengths from sunlight are only detectable at the ocean surface, chlorophyll fluorescence and Raman scattering can generate red/far-red photons in deeper layers. This study opens up novel perspectives on phytochrome-mediated far-red light signaling in the ocean and on the light sensing and adaptive capabilities of marine phototrophs.


Assuntos
Diatomáceas/fisiologia , Transdução de Sinal Luminoso/efeitos da radiação , Fitocromo/efeitos da radiação , Plantas/efeitos da radiação , Adaptação Fisiológica , Clorofila/metabolismo , Diatomáceas/efeitos da radiação , Oceanos e Mares , Análise Espectral Raman , Luz Solar
7.
PLoS Comput Biol ; 14(3): e1005992, 2018 03.
Artigo em Inglês | MEDLINE | ID: mdl-29543809

RESUMO

We present a new educational initiative called Meet-U that aims to train students for collaborative work in computational biology and to bridge the gap between education and research. Meet-U mimics the setup of collaborative research projects and takes advantage of the most popular tools for collaborative work and of cloud computing. Students are grouped in teams of 4-5 people and have to realize a project from A to Z that answers a challenging question in biology. Meet-U promotes "coopetition," as the students collaborate within and across the teams and are also in competition with each other to develop the best final product. Meet-U fosters interactions between different actors of education and research through the organization of a meeting day, open to everyone, where the students present their work to a jury of researchers and jury members give research seminars. This very unique combination of education and research is strongly motivating for the students and provides a formidable opportunity for a scientific community to unite and increase its visibility. We report on our experience with Meet-U in two French universities with master's students in bioinformatics and modeling, with protein-protein docking as the subject of the course. Meet-U is easy to implement and can be straightforwardly transferred to other fields and/or universities. All the information and data are available at www.meet-u.org.


Assuntos
Biologia Computacional/educação , Biologia Computacional/métodos , Pesquisa/educação , Humanos , Projetos de Pesquisa , Estudantes , Universidades
8.
PLoS Comput Biol ; 12(7): e1005038, 2016 07.
Artigo em Inglês | MEDLINE | ID: mdl-27472895

RESUMO

Traditional protein annotation methods describe known domains with probabilistic models representing consensus among homologous domain sequences. However, when relevant signals become too weak to be identified by a global consensus, attempts for annotation fail. Here we address the fundamental question of domain identification for highly divergent proteins. By using high performance computing, we demonstrate that the limits of state-of-the-art annotation methods can be bypassed. We design a new strategy based on the observation that many structural and functional protein constraints are not globally conserved through all species but might be locally conserved in separate clades. We propose a novel exploitation of the large amount of data available: 1. for each known protein domain, several probabilistic clade-centered models are constructed from a large and differentiated panel of homologous sequences, 2. a decision-making protocol combines outcomes obtained from multiple models, 3. a multi-criteria optimization algorithm finds the most likely protein architecture. The method is evaluated for domain and architecture prediction over several datasets and statistical testing hypotheses. Its performance is compared against HMMScan and HHblits, two widely used search methods based on sequence-profile and profile-profile comparison. Due to their closeness to actual protein sequences, clade-centered models are shown to be more specific and functionally predictive than the broadly used consensus models. Based on them, we improved annotation of Plasmodium falciparum protein sequences on a scale not previously possible. We successfully predict at least one domain for 72% of P. falciparum proteins against 63% achieved previously, corresponding to 30% of improvement over the total number of Pfam domain predictions on the whole genome. The method is applicable to any genome and opens new avenues to tackle evolutionary questions such as the reconstruction of ancient domain duplications, the reconstruction of the history of protein architectures, and the estimation of protein domain age. Website and software: http://www.lcqb.upmc.fr/CLADE.


Assuntos
Domínios Proteicos , Proteínas/química , Alinhamento de Sequência/métodos , Análise de Sequência de Proteína/métodos , Sequência de Aminoácidos , Biologia Computacional , Sequência Consenso , Bases de Dados de Proteínas , Plasmodium falciparum/genética , Plasmodium falciparum/metabolismo , Proteínas/genética , Proteínas/metabolismo , Proteínas de Protozoários/química , Proteínas de Protozoários/metabolismo
9.
Malar J ; 16(1): 241, 2017 06 07.
Artigo em Inglês | MEDLINE | ID: mdl-28592293

RESUMO

BACKGROUND: With the availability of complete genome sequences of both human and non-human Plasmodium parasites, it is now possible to use comparative genomics to look for orthology across Plasmodium species and for species specific genes. This comparative analyses could provide important clues for the development of new strategies to prevent and treat malaria in humans, however, the number of functionally annotated proteins is still low for all Plasmodium species. In the context of genomes that are hard to annotate because of sequence divergence, such as Plasmodium, domain co-occurrence becomes particularly important to trust predictions. In particular, domain architecture prediction can be used to improve the performance of existing annotation methods since homologous proteins might share their architectural context. RESULTS: Plasmobase is a unique database designed for the comparative study of Plasmodium genomes. Domain architecture reconstruction in Plasmobase relies on DAMA, the state-of-the-art method in architecture prediction, while domain annotation is realised with CLADE, a novel annotation tool based on a multi-source strategy. Plasmobase significantly increases the Pfam domain coverage of all Plasmodium genomes, it proposes new domain architectures as well as new domain families that have never been reported before for these genomes. It proposes a visualization of domain architectures and allows for an easy comparison among architectures within Plasmodium species and with other species, described in UniProt. CONCLUSIONS: Plasmobase is a valuable new resource for domain annotation in Plasmodium genomes. Its graphical presentation of protein sequences, based on domain architectures, will hopefully be of interest for comparative genomic studies. It should help to discover species-specific genes, possibly underlying important phenotypic differences between parasites, and orthologous gene families for deciphering the biology of these complex and important Apicomplexan organisms. In conclusion, Plasmobase is a flexible and rich site where any biologist can find something of his/her own interest. AVAILABILITY: Plasmobase is accessible at http://genome.lcqb.upmc.fr/plasmobase/ .


Assuntos
Bases de Dados Genéticas , Genoma de Protozoário , Plasmodium/genética , Genômica
10.
BMC Bioinformatics ; 16: 34, 2015 Feb 05.
Artigo em Inglês | MEDLINE | ID: mdl-25651949

RESUMO

BACKGROUND: An important problem in computational biology is the automatic detection of protein families (groups of homologous sequences). Clustering sequences into families is at the heart of most comparative studies dealing with protein evolution, structure, and function. Many methods have been developed for this task, and they perform reasonably well (over 0.88 of F-measure) when grouping proteins with high sequence identity. However, for highly diverged proteins the performance of these methods can be much lower, mainly because a common evolutionary origin is not deduced directly from sequence similarity. To the best of our knowledge, a systematic evaluation of clustering methods over distant homologous proteins is still lacking. RESULTS: We performed a comparative assessment of four clustering algorithms: Markov Clustering (MCL), Transitive Clustering (TransClust), Spectral Clustering of Protein Sequences (SCPS), and High-Fidelity clustering of protein sequences (HiFix), considering several datasets with different levels of sequence similarity. Two types of similarity measures, required by the clustering sequence methods, were used to evaluate the performance of the algorithms: the standard measure obtained from sequence-sequence comparisons, and a novel measure based on profile-profile comparisons, used here for the first time. CONCLUSIONS: The results reveal low clustering performance for the highly divergent datasets when the standard measure was used. However, the novel measure based on profile-profile comparisons substantially improved the performance of the four methods, especially when very low sequence identity datasets were evaluated. We also performed a parameter optimization step to determine the best configuration for each clustering method. We found that TransClust clearly outperformed the other methods for most datasets. This work also provides guidelines for the practical application of clustering sequence methods aimed at detecting accurately groups of related protein sequences.


Assuntos
Algoritmos , Análise por Conglomerados , Evolução Molecular , Família Multigênica , Proteínas/química , Alinhamento de Sequência/métodos , Humanos , Análise de Sequência de Proteína/métodos
11.
Carbohydr Polym ; 330: 121740, 2024 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-38368119

RESUMO

Cellulose cryogels are promising eco-friendly materials that exhibit low density, high porosity, and renewability. However, the applications of these materials are limited by their lower mechanical and water resistance compared to petrochemical-based lightweight materials. In this work, nanocelluloses were functionalized with cationic and anionic groups, and these nanomaterials were combined to obtain strong and water-resilient cryogels. To prepare the cryogels, anionic and cationic micro- and nanofibrils (CNFs) were produced at three different sizes and combined in various weight ratios, forming electrostatic complexes. The complex phase was concentrated by centrifugation and freeze-dried. Porous and open cellular structures were assembled in all compositions tested (porosity >90 %). Compressive testing revealed that the most resistant cryogels (1.7 MPa) were obtained with equivalent amounts of negatively and positively charged CNFs with lengths between 100 and 1200 nm. The strength at this condition was achieved as CNF electrostatic complexes assembled in thick cells, as observed by synchrotron X-ray tomography. In addition to mechanical strength, electrostatic complexation provided remarkable structural stability in water for the CNF cryogels, without compromising their biodegradability. This route by electrostatic complexation is a practical strategy to combine and concentrate nanocelluloses to tailor biodegradable lightweight materials with high strength and wet stability.

12.
Top Companion Anim Med ; 58: 100826, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-37884174

RESUMO

The aim of this study was to determine the occurrence of zoonotic enteroparasites in the feces of dogs from public shelters, squares, parks, and public roads in the city of Guarapuava, Paraná, Brazil, and to evaluate the perception of dog guardians regarding zoonoses and their risk to public health. Fecal samples were collected, coproparasitological examinations were performed to detect zoonotic enteroparasites, and polymerase chain reaction (PCR) was used to identify Giardia spp. and Cryptosporidium spp. Questionnaires were given to guardians who walked their dogs in parks, squares, and public roads, as to assess their perception of zoonoses. A total of 333 samples were collected, of these 75, 123, and 135 of them were from public shelters, squares and parks, and public roads, respectively. One or more parasites were identified in 166 (50 %) samples, of which 58/75 (77 %) were from public shelters, 50/123 (41 %) from squares and parks, and 58/135 (43 %) from public roads. The parasites detected included Ancylostoma spp., Giardia spp., Trichuris spp., Toxocara spp., and Cystoisospora spp., with Ancylostoma spp. having the highest occurrence. PCR was performed on 161 samples for convenience due to financial limitations, because only a portion of the study was funded by the municipal government, of which 15.6 % were positive for Giardia spp., and all were negative for Cryptosporidium spp. In total, 246 guardians were interviewed, of which 36 % said they did not collect their animals' feces during walks, 20 % did not use anti-helminthics on their dogs, and 23 % did not know which diseases could be transmitted by feces. Therefore, we conclude that there is a high infection rate of parasites with zoonotic potential in public places, showing the need to raise awareness among guardians about the diseases transmitted by dog feces, correct vermifugation and the importance of collecting feces in public places.


Assuntos
Criptosporidiose , Cryptosporidium , Doenças do Cão , Parasitos , Animais , Cães , Saúde Pública , Brasil/epidemiologia , Zoonoses/epidemiologia , Fezes/parasitologia , Percepção , Doenças do Cão/epidemiologia , Doenças do Cão/parasitologia , Prevalência
13.
Langmuir ; 29(3): 892-901, 2013 Jan 22.
Artigo em Inglês | MEDLINE | ID: mdl-23256838

RESUMO

Top and bottom surfaces of polyethylene (PE) films exposed to corona discharge display large and opposite electrostatic potentials, forming an electric bilayer in agreement with recent and unexpected findings from Zhiqiang et al. Water wetting, chemical composition and roughness of the two surfaces are different. Surprisingly, the bottom surface, opposite to the corona electrode is charged but it is not oxidized, neither is it wetted with water. Moreover, its morphology is unaltered by charging, while the hydrophilic top surface is much rougher with protruding islands that are the result of oxidation followed by phase separation and polymer-polymer dewetting. Common liquids extract the oxidized, hydrophilic material formed at the upper surface, a result that explains the well-known sensitivity of adhesive joints made using corona-treated thermoplastics to liquids, especially water. These results show that poling the surface closer to the corona electrode triggers another but different charge build-up process at the opposite surface. The outcome is another poled PE surface showing high potential but with unchanged chemical composition, morphology and wetting behavior as the pristine surface, thus opening new possibilities for surface engineering.


Assuntos
Bicamadas Lipídicas/química , Polietileno/química , Proteínas/química , Microscopia de Força Atômica , Microscopia Eletrônica de Transmissão , Tamanho da Partícula , Espectrofotometria , Eletricidade Estática , Propriedades de Superfície , Raios X
14.
Carbohydr Polym ; 302: 120354, 2023 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-36604044

RESUMO

Nanocellulose is a well-known stabilizer for several colloidal dispersions, including emulsions and solid nanoparticles, replacing surfactants, polymers, and other additives, and therefore providing more minimalistic and eco-friendly formulations. However, could this ability be extended to stabilize oil droplets and inorganic nanoparticles simultaneously in the same colloidal system? This work aimed to answer this question. We evaluated both cationic and anionic nanofibrillated celluloses to stabilize both titanium dioxide nanoparticles and oil droplets. The resulting suspensions held their macroscopic stability for up to 2 months, regardless of pH or surface charge. Cryo-TEM images revealed a complex network formation involving nanofibers and TiO2 nanoparticles, which agrees with the high viscosity values and gel-like behavior found in rheology measurements. We propose that the formation of this network is responsible for the simultaneous stabilization of oil droplets and TiO2 nanoparticles, and that this may be used as a formulation tool for other complex systems.


Assuntos
Celulose , Nanopartículas , Titânio , Emulsões
15.
Carbohydr Polym ; 304: 120505, 2023 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-36641171

RESUMO

It is advantageous to understand the relationship between cellulose fiber morphology and the rheological behavior of its dispersions so that their application can be optimized. The goal of this study was to produce sugarcane bagasse-sourced cellulose dispersions with different numbers of high-pressure homogenization cycles. Microfluidization produced cellulose nanofibers (between 5 and 80 nm in diameter) with similar surface charge densities and crystallinities (measured on the resulting films). Oscillatory rheology showed that TEMPO-oxidized cellulose dispersions exhibited gel-like behavior. However, not only did the samples with more microfluidization cycles present a lower storage modulus, but the sample with 100 cycles completely lost the gel-like characteristic, presenting a viscous fluid rheological behavior. Thixotropy loop tests revealed the influence of nanofiber length on the dispersion's structure, as evidenced by the decrease in the hysteresis value along with fiber breakage. Therefore, our findings demonstrate that the rheological properties of the dispersion can be tuned according to the length of the nanofibers, allowing for targeted applications.


Assuntos
Celulose Oxidada , Nanofibras , Saccharum , Celulose/química , Nanofibras/química , Reologia/métodos
16.
NAR Genom Bioinform ; 5(2): lqad064, 2023 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-37388820

RESUMO

High throughput sequencing of adaptive immune receptor repertoire (AIRR-seq) has provided numerous human immunoglobulin (IG) sequences allowing specific B cell receptor (BCR) studies such as the antigen-driven evolution of antibodies (soluble forms of the membrane-bound IG part of the BCR). AIRR-seq data allows researchers to examine intraclonal differences caused primarily by somatic hypermutations in IG genes and affinity maturation. Exploring this essential adaptive immunity process could help elucidate the generation of antibodies with high affinity or broadly neutralizing activities. Retracing their evolutionary history could also clarify how vaccines or pathogen exposition drive the humoral immune response, and unravel the clonal architecture of B cell tumors. Computational methods are necessary for large-scale analysis of AIRR-seq properties. However, there is no efficient and interactive tool for analyzing intraclonal diversity, permitting users to explore adaptive immune receptor repertoires in biological and clinical applications. Here we present ViCloD, a web server for large-scale visual analysis of repertoire clonality and intraclonal diversity. ViCloD uses preprocessed data in the format defined by the Adaptive Immune Receptor Repertoire (AIRR) Community. Then, it performs clonal grouping and evolutionary analyses, producing a collection of useful plots for clonal lineage inspection. The web server presents diverse functionalities, including repertoire navigation, clonal abundance analysis, and intraclonal evolutionary tree reconstruction. Users can download the analyzed data in different table formats and save the generated plots as images. ViCloD is a simple, versatile, and user-friendly tool that can help researchers and clinicians to analyze B cell intraclonal diversity. Moreover, its pipeline is optimized to process hundreds of thousands of sequences within a few minutes, allowing an efficient investigation of large and complex repertoires.

17.
Anal Chem ; 84(23): 10191-8, 2012 Dec 04.
Artigo em Inglês | MEDLINE | ID: mdl-23126418

RESUMO

Electrostatic potential at the surface of acidic or basic solids changes under higher relative humidity (RH), as determined by using Kelvin force microscopy (KFM). The potential on acid surfaces becomes more negative as the water vapor pressure increases, while it becomes more positive on basic solids. These results verify the following hypothesis: OH(-) or H(+) ions associated with atmospheric water ion clusters are selectively adsorbed on solid surfaces, depending on the respective Brønsted acid or base character. Therefore, Kelvin microscopy, under variable humidity, is a rigorous but convenient alternative to determine the acid-base character of solid surfaces, with a great advantage: it uses only one amphoteric and simple reagent to determine both the acid and base sites. Moreover, this technique provides information on the spatial distribution of acid-base sites, which is currently inaccessible to any other method.

18.
Transbound Emerg Dis ; 69(4): 2021-2028, 2022 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-34214245

RESUMO

In Brazil, notification of toxoplasmosis outbreaks and epidemiological investigation is a mandatory activity of health surveillance. We investigated the risk factors for toxoplasmosis during outbreaks, notifications of outbreaks by the health secretary and reports in the literature. Other factors related to the municipalities were determined through the Institute of Geography and Statistics portal. We found that fruits and vegetables were the most described transmission routes in outbreaks, and oocysts were the most common parasitic form; in recent years; there has been an increase in outbreak notifications. We also found that municipalities with high municipal human development index have a higher number of toxoplasmosis infections during outbreaks. There is a need to raise awareness among the population and producers regarding good water management and quality practices and to facilitate the acquisition of complex data to improve preventive strategies.


Assuntos
Toxoplasmose , Animais , Brasil/epidemiologia , Surtos de Doenças/veterinária , Estudos Epidemiológicos , Humanos , Oocistos , Toxoplasmose/epidemiologia , Toxoplasmose/parasitologia
19.
Nanoscale ; 14(47): 17561-17570, 2022 Dec 08.
Artigo em Inglês | MEDLINE | ID: mdl-36346287

RESUMO

Elucidating cellulose-lignin interactions at the molecular and nanometric scales is an important research topic with impacts on several pathways of biomass valorization. Here, the interaction forces between a cellulosic substrate and lignin are investigated. Atomic force microscopy with lignin-coated tips is employed to probe the site-specific adhesion to a cellulose film in liquid water. Over seven thousand force-curves are analyzed by a machine-learning approach to cluster the experimental data into types of cellulose-tip interactions. The molecular mechanisms for distinct types of cellulose-lignin interactions are revealed by molecular dynamics simulations of lignin globules interacting with different cellulose Iß crystal facets. This unique combination of experimental force-curves, data-driven analysis, and molecular simulations opens a new approach of investigation and updates the understanding of cellulose-lignin interactions at the nanoscale.


Assuntos
Celulose , Lignina , Microscopia de Força Atômica , Simulação de Dinâmica Molecular , Aprendizado de Máquina
20.
Transbound Emerg Dis ; 69(3): 1449-1457, 2022 May.
Artigo em Inglês | MEDLINE | ID: mdl-33872467

RESUMO

Toxoplasmosis acquired during pregnancy is one that can lead to death or malformations of the foetus, and it is a complex disease to diagnose. The objective of the study was to evaluate the Surveillance Program of Gestational and Congenital Toxoplasmosis. To assess primary prevention, 424 pregnant women were interviewed regarding their knowledge of prevention measures in 2019. Secondary prevention measures were assessed, and the results of anti-Toxoplasma gondii serological tests were collected from pregnant women, from 2015 to 2018. In tertiary prevention measures, babies of mothers with a recent suspicion of T. gondii infection were screened to verify forwarding to the reference service. As a result, 45.5% (192/424) reported that they had received guidance from health professionals; 35.4% (68/192) changed their risk habits. The variables of schooling and age, having received prior guidance from health professionals and feline possession, proved to be significant when associated with the notions of preventive measures. 90.2% (17,423/19,319) of pregnant women had undergone serological tests to detect anti-T. gondii antibodies, but there was an excess in requests for tests and medication and only 40.6% (26/64) of the children were referred to the reference hospital. The Program presents positive results about the performance of serological screening in prenatal care; however, the dissemination of knowledge as for the prevention of toxoplasmosis and the request for tests need to be improved.


Assuntos
Doenças do Gato , Toxoplasma , Toxoplasmose Congênita , Toxoplasmose , Animais , Anticorpos Antiprotozoários , Gatos , Feminino , Humanos , Imunoglobulina M , Gravidez , Cuidado Pré-Natal , Estudos Soroepidemiológicos , Prevenção Terciária , Toxoplasmose/epidemiologia , Toxoplasmose Congênita/diagnóstico , Toxoplasmose Congênita/epidemiologia , Toxoplasmose Congênita/prevenção & controle
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA