Biology subjects

Alves, L. C.

Publications and source records attributed to Alves, L. C..

4 recordsLinked to original sources

bioRxiv2026

Structural modelling and biophysical analyses reveal a dimeric coiled-coil architecture in the FAZ10 central region of Trypanosoma brucei

Trypanosoma brucei relies on the flagellum attachment zone (FAZ) to coordinate flagellum positioning, cell morphology, and cytokinesis. The giant FAZ10 protein, which contains both repetitive and structured regions, is essential for correct cleavage-furrow placement, yet its molecular organization remains unresolved due to its exceptional size. In this study, we define the architecture of the FAZ10 central region through structural modelling and biophysical validation. AlphaFold2 and molecular dynamics simulations defined a parallel coiled-coil dimer flanked by symmetric globular domains, with canonical hydrophobic core packing, complementary interhelical contacts, and local heptad discontinuities, including a stammer-stutter pair that modulates the superhelical geometry. Biophysical analyses show that this region forms a stable dimer in solution, mediated by the coiled-coil domain and consistent with a predominantly -helical structure. Together, these findings identify the FAZ10 central region as a semi-flexible dimeric scaffold that provides a structural framework for understanding FAZ supramolecular organization and the integration of large cytoskeletal assemblies in trypanosomatids.

biophysics↗

bioRxiv2024

CODARFE: Unlocking the prediction of continuous environmental variables based on microbiome

Despite the surge in data acquisition, there is a limited availability of tools capable of effectively analyzing microbiome data that identify correlations between taxonomic compositions and continuous environmental factors. Furthermore, existing tools also do not predict the environmental factors in new samples, underscoring the pressing need for innovative solutions to enhance our understanding of microbiome dynamics and fulfill the prediction gap. Here, we introduce CODARFE, a novel tool for sparse compositional microbiome-predictors selection and prediction of continuous environmental factors. We tested CODARFE against four state-of-the-art tools in two experiments. First, CODARFE outperformed predictor selection in 21 out of 24 databases in terms of correlation. Second, among all the tools, CODARFE achieved the highest number of previously identified bacteria linked to environmental factors for human data--that is, at least 7% more. We also tested CODARFE in a cross-study, using the same biome but under different external effects (e.g., ginseng field and cattle for arable soil, and HIV and crohns disease for human gut), using a model trained on one dataset to predict environmental factors on another dataset, achieving 11% of mean absolute percentage error. Finally, CODARFE is available in five formats, including a Windows version with a graphical interface, to installable source code for Linux servers and an embedded Jupyter notebook available at MGnify - https://github.com/alerpaschoal/CODARFE.

bioinformatics↗

bioRxiv2020

Larvicidal activity of Azadirachta indica, Melaleuca alternifolia, and Carapa guianensis oil compounds and Carica papaya fermented extract on Aedes aegypti

The aim of this study was to evaluate the structural changes of Aedes aegypti larvae submitted to treatment with a product based on Azadirachta indica, Melaleuca alternifolia, Carapa guianensis oils and Carica papaya fermented extract. The larvae were exposed for 24h to the experimental groups: product formulated in concentrations of 50% (G1), 25% (G2), and 12.5% (G3); and negative control groups based on water (CN1) and dimethyl sulfoxide (CN2). By the end of the experimental period, some larvae were fixed in 4% buffered glutaraldehyde solution to be processed for optical microscopy. Larvae exposed to G2 and G3 presented more structural damage of the mesentery, Malpighi tubules and nerve ganglia. We conclude that the product formulated in 12.5% and 25% concentrations can be used in the population control of the 3rd larvae stage of Aedes aegypti by causing lethal injuries and avoiding the larvae development.

systems biology↗

bioRxiv2019

Population mobility and dengue fever transmission in a major city in Southeastern Brazil, 2007-2015

BackgroundAround 14% of world dengue virus (DENV) cases occur in the Americas, the majority of them in Brazil. Although socioeconomic, environmental and behavioral correlates of dengue have been analyzed for different contexts, the role played by population mobility on DENV epidemics, especially at the local level, remains scant. This study assesses whether the daily pattern of population mobility is associated with DENV transmission in Campinas, a Brazilian major city with over 1.2 million inhabitants in Sao Paulo state.\n\nMethodology/Principal FindingsDENV notifications from 2007 to 2015 were geocoded at street level (n=114,884) and combined with sociodemographic and environmental data from the 2010 Population Census. Population mobility was extracted from the Origin-Destination Survey (ODS), carried out in 2011, and daily precipitation was obtained from satellite imagery. Zero-Inflated Negative Binomial (ZINB) regression models controlled by demographic and environmental factors revealed that high population mobility had a substantial positive effect on higher risk for DENV transmission. High income and residence in apartments were found to be protective against the disease, while unpaved streets, number of strategic points (such as scrapyards and tire repair shops), and precipitation were consistently risk factors for DENV infection.\n\nConclusions/SignificanceThe use of fine-scale geographical data can unravel transmission idiosyncrasies not evident from a coarse spatial analysis. Even in a major city like Campinas, the vast majority of population daily mobility occurs at short distances. Based on our results, public policies on DENV transmission control should dedicate special attention to local hubs of population mobility, especially during high transmission weeks and in high dengue incidence areas.\n\nAuthor SummaryCurrently, about half of the world population is at risk of a dengue infection. Numerous studies have addressed the socioeconomic and environmental determinants of the disease. However, little is known about the role played by population mobility on dengue transmission, particularly at the local scale. This study aims at investigating this issue. Our hypothesis was that population movements are a prominent driving force for dengue diffusion locally. We investigated the case of Campinas, a municipality with over 1.2 million inhabitants in Brazil that recorded dengue epidemics in 2007, 2014 and 2015. Our study focused on the years 2007 to 2015, comprising more than 114 thousand cases, geocoded to the household address, and combined with socioeconomic, environmental and daily population mobility data. Our results showed that even controlling for demographic and environmental factors, population mobility was the most important predictor for dengue fever incidence.

ecology↗