Biology subjects

Castro, M. C.

Publications and source records attributed to Castro, M. C..

4 recordsLinked to original sources

bioRxiv2025

Population genomics of Anopheles darlingi, the principal South American malaria vector mosquito

Malaria in South America remains a serious public health problem. Anopheles (Nyssorhynchus) darlingi is the most important malaria vector across tropical Latin America. Vector-targeted disease control efforts require a thorough understanding of mosquito demographic and evolutionary patterns. We present and analyze whole genomes of 1094 A. darlingi (median depth 18x) from six South American countries. We observe deep geographic population structure, high genetic diversity including thirteen putative segregating inversions, and no evidence for cryptic sympatric taxa despite high interpopulation divergence. Strong signals of selection are plausibly driven by insecticides, especially on cytochrome P450 genes, one of which we validated experimentally. Our results will facilitate effective mosquito surveillance and control, while highlighting ongoing challenges that a diverse vector poses for malaria elimination in the western hemisphere.

evolutionary biology↗

bioRxiv2024

Human mobility and malaria risk in peri-urban and rural communities in the Peruvian Amazon

BackgroundWhile the global burden of malaria cases has decreased over the last two decades, the disease remains a major international threat, even on the rise in many regions. More than 85% of Peruvian malaria cases are in the Amazonian region of Loreto. Internal mobility primarily related to occupation is thought to be primarily responsible for maintaining endemicity and introducing and reintroducing malaria parasites into areas of anophelism, a challenge for malaria eradication. MethodsThe assessment of connectivity produced by human mobility was evaluated in three districts of Loreto, through 10 cross-sectional population screening from 2018 to 2020. We use social network analysis (SNA) to obtain weighted and unweighted degrees of connectivity and explore its variability by socio-demographic characteristics. In addition, we integrated travel history and malaria incidence data to estimate parasite connectivity due to internal human mobility between locations. Finally, we used logistic multivariate regressions to explore the factors associated with Plasmodium spp. infection in mobile individuals. ResultsWe found that internal human mobility results in high connectivity between communities from the Mazan, Iquitos, and San Juan Bautista districts. We identified nearby destinations that may act as sinks or sources for malaria transmission, including densely populated towns and rural campsites. In addition, we found that being a male, traveling to rural campsites, and working outdoors are associated with Plasmodium spp. infection in travelers from the Mazan district. ConclusionsWe provide compelling evidence about how human mobility connects rural communities in the Peruvian Amazon. Using SNA, we uncovered district-specific patterns and destinations, providing further evidence of human mobility heterogeneity in the region. To address the challenge of human mobility and malaria in this setting, geographic heterogeneity of malaria transmission must be considered. Author summaryMalaria transmission is complex, involving interactions of parasite, vector biology and ecology, human immune response, and human host behavior. We used social network analysis to understand how the daily lives including occupation-related mobility leads to the maintenance of malaria endemicity and transmission. Rural communities (within the districts of Mazan) and peri-urban communities around the city of Iquitos have different socio-demographic characteristics that determine malaria transmission rates. Networks of fixed rural communities and occupation-related distant camp sites play a key role as reservoirs and sources of parasite movement. Factors including male sex, outdoor occupational activity outdoors, and having rural camp sites as travel destination increase the risk of Plasmodium infection. Factors associated with occupation-related mobility are correlated with incidence and prevalence of malarial disease and parasite infection rates, respectively. This work provides a detailed understanding of the importance of work-related travel to target in malaria elimination programs, key to maintaining malaria transmission both in the Amazon region and more generally.

microbiology↗

bioRxiv2023

CellHeap: A scRNA-seq workflow for large-scalebioinformatics data analysis

AbstractO_ST_ABSBackgroundC_ST_ABSSeveral hundred terabytes of single-cell RNA-seq (scRNA-seq) data are available in public repositories. These data refer to various research projects, from microbial population cells to multiple tissues, involving patients with a myriad of diseases and comorbidities. An increase to several Petabytes of scRNA-seq data available in public repositories is a realistic prediction for coming years. Therefore, thoughtful analysis of these data requires large-scale computing infrastructures and software systems optimized for such platforms to generate correct and reliable biological knowledge. ResultsThis paper presents CellHeap, a flexible, portable, and robust platform for analyzing large scRNA-seq datasets, with quality control throughout the execution steps, and deployable on platforms that support large-scale data, such as supercomputers or clouds. As a case study, we designed a workflow to study particular modulations of Fc receptors, considering mild and severe cases of COVID-19. This workflow, deployed in the Brazilian Santos Dumont supercomputer, processed dozens of Terabytes of COVID-19 scRNA-seq raw data. Our results show that most of the workflow total execution time is spent in its initial phases and that there is great potential for a parallel solution to speed up scRNA-seq data analysis significantly. Thus, this workflow includes an efficient solution to use parallel computational resources, improving total execution time. Our case study showed increased Fc receptors transcription in macrophages of patients with severe COVID-19 symptoms, especially FCGR1A, FCGR2A, and FCGR3A. Furthermore, diverse molecules associated with their signaling pathways were upregulated in severe cases, possibly associated with the prominent inflammatory response observed. ConclusionFrom the CellHeap platform, different workflows capable of analyzing large scRNA-seq datasets can be generated. Our case study, a workflow designed to study particular modulations of Fc receptors, considering mild and severe cases of COVID-19, deployed on the Brazilian supercomputer Santos Dumont, had a substantial reduction in total execution time when jobs are triggered simultaneously using the parallelization strategy described in this manuscript. Regarding biological results, our case study identified specific modulations comparing healthy individuals with COVID-19 patients with mild or severe symptoms, revealing an upregulation of several inflammatory pathways and an increase in the transcription of Fc receptors in severe cases.

bioinformatics↗

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↗