Biology subjects

Rocha, R.

Publications and source records attributed to Rocha, R..

12 recordsLinked to original sources

bioRxiv2025

Habitat use and diel activity of insectivorous bats across land-use types on an Afrotropical oceanic island

Tropical island biodiversity is declining at alarming rates. Yet, understanding how species are coping with such disturbance is largely limited for afro-tropical islands. Here we examined habitat use and diel activity of insectivorous bats across different land-use types covering the endemic-rich Principe Island, Central West Africa. We acoustically surveyed insectivorous bats across 48 sites throughout old-growth forests, secondary re-growth forests, cocoa shaded plantations, and horticultures. Based on 17,527 bat-passes, we were able to record all four insectivorous bat species known to occur on Principe, including the recently described Pseudoromicia principis, the most frequently recorded species. Taphozous mauritianus, a data deficient open-space forager, was the least recorded species. Species activity was lowest in old-growth forests, as well as the activity of the edge-forager P. principis. The activity of the open-space forager Mops pumilus was lowest in forest habitats, whereas Hipposideros ruber, a forest forager, was restricted to these habitats. Diel activity patterns of M. pumilus varied between forests and non-forest habitats, whereas those of P. principis remained similar. Interspecific activity overlap decreased towards more altered land-use types. Our findings emphasize that conserving the remaining forests, along with the current mosaic of land-uses, is needed to maintain Principes complete insectivorous bat assemblages.

ecology↗

bioRxiv2025

Engineered micropillars to unveil oligodendrocyte responses to physical cues

Destruction of myelin internodes, oligodendrocyte (OL) apoptosis, and axonal degeneration characterize diseased or aged central nervous systems. While OLs can partially regenerate myelin sheaths, the remyelination process ultimately fails. Tissue mechanical and physical properties, such as stiffness and axonal curvature, play a role in this process. However, the complexity of existing models has hindered studies of OL mechanobiology. Here, a tissue-engineered model is presented to investigate the impact of stiffness and axonal diameter on OL myelination. The model consists of poly(dimethylsiloxane) micropillars with biologically relevant diameters (1-5 {micro}m), tunable rigidity, and amenable for surface functionalization. The optimized method enables the production of high-aspect-ratio, transparent micropillar arrays, in a reproducible and scalable system, serving as surrogate axons. Additionally, new protocols for quantifying myelin formation are introduced, which can be adapted to any myelination studies. Softer micropillars accelerate OL differentiation, while rigid ones promote the maintenance of mature OL states. Wrapping of OLs increased with micropillar diameter on rigid substrates, but not on softer ones, suggesting a complex interplay between curvature and rigidity. These processes involve calcium-sensitive channels, histone deacetylases, and microtubules dynamics. The proposed platform constitutes a versatile and user-friendly system, with applications from fundamental myelin research to drug discovery.

bioengineering↗

bioRxiv2024

Amphibian and reptile dataset across different land-use types in Guinea-Bissau, West Africa

West Africa is exceptionally biodiverse, yet its wildlife remains largely understudied despite the rapid and ongoing land-use changes. Large swaths of Guinea-Bissaus landscape were historically characterized by native forest-savanna mosaics. However, key areas of savannah habitats have been converted to rice agroecosystems, and forests are being transformed into cashew monocultures at unprecedented rates. Amphibians and reptiles (Testudines and Squamata) comprise some of the most threatened species by human-induced habitat change, and yet are not as studied as other vertebrate terrestrial taxa. Here, we provide two comprehensive datasets on amphibians and reptiles (classes Testudines and Squamata) from northern Guinea-Bissau: (1) a standardized survey dataset (encompassing sampling events and occurrences) in forest fragments, cashew orchards, and rice paddies, and (2) an opportunistic dataset reporting occurrences across the entire study area. Standardized surveys were carried across 21 sampling sites, seven in each habitat type, while opportunistic surveys include all other records. For standardized surveys, a total of 703 amphibian and 265 reptile (class Squamata) encounters are reported, corresponding to nine and 13 taxa, respectively. Opportunistically, we report 62 amphibian and 93 reptile encounters, corresponding to 10 amphibian taxa, 25 Squamata taxa, and two turtles (class Testudines). New informationBased on 126 sampling hours of both diurnal and nocturnal standardized surveys, in addition to opportunistic surveys, these datasets comprise the first overview for amphibians and reptiles in mainland Guinea-Bissau across two seasons and different habitat types. Each of the 968 standardized and 155 opportunistic occurrences corresponds to a genus or species and is accompanied by geographic coordinates, a timestamp, and, for standardized data, the land-use type. The datasets fill the distribution gaps in Guinea-Bissau of at least three species, including the frog Hildebrandtia ornata, the skink Trachylepis keroanensis and the snake Dendroaspis polylepis - and includes the rediscovery of the lizard Latastia ornata in Guinea-Bissau. Before this work, the L. ornata was only known from the 1938 holotype in Bafata (ca. 60 km away from the study area) and, in 2023, from Guinea-Conakry (ca. 700 km away from type specimen location).

ecology↗

bioRxiv2024

Inclusion of Salicornia ramosissima biomass in diets for juvenile whiteleg shrimp (Penaeus vannamei) induces favourable but transient effects in the immune and oxidative status

The whiteleg shrimp, Penaeus vannamei, is a highly valued and globally produced crustacean species. However, the rising cost of shrimp feed, exacerbated by increasing cereal prices, prompts the exploration of cost-effective and sustainable formulations for shrimp farming. This study investigates the potential of Salicornia ramosissima, a non-edible biomass co-product, as a substitute for wheat meal in juvenile whiteleg shrimp diets, aiming to create economically and ecologically sound formulations. The present study aimed to assess the impact of incorporating S. ramosissima into whiteleg shrimp aquafeeds on various aspects of shrimp development, including growth performance, survival, immune status, and oxidative status. A commercial-like diet was formulated and served as control, whereas four other diets contained S. ramosissima stems or a combination of leaves and seeds, both at inclusion levels of 5% and 10%, in addition to the control diet. Whiteleg shrimps were fed the experimental diets for 31 and 55 days, followed by a bacterial bath challenge to gauge their immune response to pathogens. At the end of the feeding period, whiteleg shrimps growth performance and survival rates remained consistent across all diets. However, whiteleg shrimp fed diets with S. ramosissima inclusion consumed more feed to achieve similar weights to those fed on the control diet, particularly in diets containing leaves and seeds at a 10% inclusion level, likely due to lower digestibility of dry matter, lipids, and energy. While S. ramosissima biomass inclusion did not affect shrimp weight, relative growth rate, or survival, it did lead to higher feed conversion ratios and feed intake, suggesting differences in nutrient digestibility and metabolic utilization. Additionally, S. ramosissima inclusion affected whiteleg shrimps overall body composition, particularly moisture and ash content. Dietary S. ramosissima inclusion modulated antioxidant enzyme activity in the shrimps hepatopancreas, indicating potential health improvements. The study also observed gene expression changes related to antioxidant enzymes, indicating an overall down-regulation with the inclusion of S. ramosissima. Despite challenges in feeding efficiency, the inclusion of S. ramosissima, especially stems, shows promise in reducing feed costs by utilizing a by-product. Furthermore, S. ramosissima inclusion led to subtle changes in certain plasma humoral parameters and hepatopancreas gene expression. Although some immune parameters varied, these effects appeared to diminish over time. In conclusion, this study highlights the potential of S. ramosissima as a functional feed ingredient capable of enhancing shrimps antioxidant response, aligning with global resource optimization and sustainability initiatives.

immunology↗

bioRxiv2024

Unveiling how herpetofauna cope with land-use changes--insights from forest-cashew-rice landscapes in West Africa

Agricultural-induced land-use change comprises a key driver of biodiversity loss across tropical forests. Guinea-Bissau, in West Africa, was formerly occupied by native forest-savanna mosaics. While savannas have long gave place to traditional rice agroecosystems, forests are now being transformed into cashew monocultures at unprecedented rates. The ecological impact of such rapid change is largely unknown. Here, we examined how rarefied species richness, abundance, and composition of amphibians and reptiles varied across forest remnants, cashew orchards and rice paddies in northern Guinea-Bissau. To do so, visual encounter surveys were carried across 21 sampling sites, seven in each habitat type. A total of 703 amphibian and 266 reptile encounters was recorded from nine and 14 taxa, respectively. The results show class-specific responses to habitat type. Amphibian diversity in forest remnants and cashew orchards remained similar, but rice paddies harboured higher abundance and distinct composition compared to forest remnants. Reptile abundance was highest in cashew orchards, which comprised a distinct species composition, when compared to forest remnants. Rice paddies sustained lower reptile richness and abundance. Overall, our results do not support the expected detrimental impacts of cashew expansion, which might be due to the still high heterogeneity of habitat types within the landscape. Rice paddies proved particularly important for amphibians, and for open-habitat reptiles, boosting the landscape-scale species diversity. In face of the eminent habitat conversion, maintaining heterogeneous landscapes, including the persistence of both forest remnants and rice paddies, is critical to minimize biodiversity loss in West Africa.

ecology↗

bioRxiv2023

c-di-AMP determines the hierarchical organization of bacterial RCK proteins

RCK domains or proteins are important regulatory components of cation and K+ channels and transporters both in eukaryotic and prokaryotic organisms. A lasting unanswered question about bacterial RCK proteins relates to the physiological role of the multiple, sometimes closely related, RCK genes encoded in the genome. We explored this question with the Ktr channels of Bacillus subtilis that include two genes encoding RCK proteins (KtrA and KtrC) and two genes encoding their membrane protein partners (KtrB and KtrD). Using a combination of in vivo characterization and in vitro functional analysis, we determined that the two RCK proteins are neither physiologically redundant or functionally equivalent. Instead, KtrC is the physiologically dominant RCK protein due to its ability to mediate K+ transport inactivation by c-di-AMP, a bacterial second messenger that is the master regulator of the K+ machinery in many species, while KtrA assembled channels are very insensitive to the dinucleotide. Moreover, KtrC and KtrA can form heteromeric assemblies that can control the Ktr channel activity and are sensitive to c-di-AMP inhibition. In parallel, we showed that conditions with a large number of Ktr channels assembled with KtrA, or with RCK proteins that do not mediate c-di-AMP inhibition, are toxic to the cell. Altogether, we have demonstrated that c-di-AMP regulation of Ktr channels goes beyond affecting transcription and functional activity, it also determines the hierarchical organization of bacterial RCK proteins.

microbiology↗

bioRxiv2022

First Record of Aedes (Stegomyia) albopictus (Diptera: Culicidae) in the state of Acre, Brazil

IntroductionAedes (Stegomyia) albopictus (Skuse, 1854) was reported in Brazil for the first time in 1986, and has displayed successful expansion throughout the Brazilian territory. MethodsDuring a routine activity to control dengue conducted by the Division of Entomology of the Municipal Health Department in Rio Branco, adults and immatures of Culicidae were collected in a peri-urban area. ResultsThe Culicidae forms identified indicated that they belonged to the species Ae. albopictus. ConclusionsThis is the first official record of the presence of Ae. albopictus in the state of Acre, confirming its current presence in all Brazilian states.

zoology↗

bioRxiv2021

Gut microbiota diversity and C-Reactive Protein are predictors of disease severity in COVID-19 patients

Risk factors for COVID-19 disease severity are still poorly understood. Considering the pivotal role of gut microbiota on host immune and inflammatory functions, we investigated the association between changes in gut microbiota composition and the clinical severity of COVID-19. We conducted a multicentre cross-sectional study prospectively enrolling 115 COVID-19 patients categorized according to: 1) WHO Clinical Progression Scale - mild 19 (16.5%), moderate 37 (32.2%) or severe 59 (51.3%); and 2) location of recovery from COVID-19 - ambulatory 14 (household isolation; 12.2%), hospitalized in ward 40 (34.8%) or intensive care unit 61 (53.0%). Gut microbiota analysis was performed through 16S rRNA gene sequencing and data obtained was further related with clinical parameters of COVID-19 patients. Risk factors for COVID-19 severity were identified by univariate and multivariable logistic regression models. In comparison with mild COVID-19 patients, the gut microbiota of moderate and severe patients has: a) lower Firmicutes/Bacteroidetes ratio, b) higher abundance of Proteobacteria; and c) lower abundance of beneficial butyrate-producing bacteria such as Roseburia and Lachnospira genera. Multivariable regression analysis showed that Shannon index diversity (odds ratio [OR] 2.85 [95% CI 1.09-7.41]; p=0.032) and C-Reactive Protein (OR 3.45 [95% CI 1.33-8.91]; p=0.011) were risk factors for COVID-19 severe disease (a score of 6 or higher in WHO clinical progression scale). In conclusion, our results demonstrated that hospitalised moderate and severe COVID-19 patients have microbial signatures of gut dysbiosis and for the first time, the gut microbiota diversity is pointed out as a prognostic biomarker for COVID-19 disease severity.

microbiology↗

bioRxiv2021

Reducing publication delay to improve the efficiency and impact of conservation science

Evidence-based decision making is most effective with comprehensive access to scientific studies. If studies face delays or barriers to being published, the useful information they contain may not reach decision-makers in a timely manner. This represents a potential problem for mission-oriented disciplines where access to the latest data is paramount to ensure effective actions are deployed. We sought to analyse the severity of publication delay in conservation science -- a field that requires urgent action to prevent the loss of biodiversity. We used the Conservation Evidence database to assess the length of publication delay (time from finishing data collection to publication) in the literature that tests the effectiveness of conservation interventions. From 7,415 peer-reviewed and non-peer-reviewed studies of conservation interventions published over eleven decades, we find that the mean publication delay (time from completing data collection to publication) was 3.6 years and varied by conservation subject -- a smaller delay was observed for studies focussed on the management of captive animals. Publication delay was significantly smaller for studies in the non-journal literature (typically non-peer-reviewed) compared to studies published in scientific journals. Although we found publication delay has marginally increased over time (1912-2020), this change was weak post-1980s. Publication delay also varied inconsistently between studies on species with different IUCN Red List statuses and there was little evidence that studies on more threatened species were subject to a smaller delay. We discuss the possible drivers of publication delay and present suggestions for scientists, funders, publishers, and practitioners to reduce the time taken to publish studies. Although our recommendations are aimed at conservation science, they are highly relevant to other mission-driven disciplines where the rapid dissemination of scientific findings is important.

scientific communication and education↗

bioRxiv2021

Uncovered genetic diversity in Hemidactylus mabouia (Reptilia: Gekkonidae) from Madeira Island reveals uncertain sources of introduction

Hemidactylus mabouia is one of the most widely distributed species within its genus. It was first reported to Madeira in 2002 and the first individuals were considered to have originated from Cape Verde. Almost 20 years later, we found that H. mabouia has substantially expanded its distribution and can now be found >10 km away from Funchal, where it was first reported. Based on a 12S phylogenetic analysis and using 29 individuals from Funchal and Camara de Lobos we found that Madeira actually harbours two distinct lineages of H. mabouia: one exclusively South American and another widespread in America and Africa. However, the lack of genetic diversity typical of this species outside its native range and the obtained phylogenetic pattern prevent us to infer possible introduction routes or sources. Our study emphasizes that authorities should remain vigilant regarding the arrival of other non-natives and act to prevent their establishment as soon as they are detected.

evolutionary biology↗

bioRxiv2019

Insights from two decades of the Student Conference on Conservation Science

Conservation science is a crisis-oriented discipline focused on delivering robust answers to reducing human impacts on nature. To explore how the field might have changed during the past two decades, we analyzed 3,245 applications for oral presentations submitted to the Student Conference on Conservation Science (SCCS) in Cambridge, UK. SCCS has been running every year since 2000, aims for global representation by providing bursaries to early-career conservationists from lower-income countries, and has never had a thematic focus, beyond conservation in the broadest sense. We found that the majority of submissions to SCCS were based on primary biological data collection from local scale field studies in the tropics, contrary to established literature which highlights gaps in tropical research. Our results showed a small increase over time in submissions framed around how nature benefits people as well as a small increase in submissions integrating social science. Our findings also suggest that students and early-career conservationists could provide pathways to increased availability of data from the tropics and for addressing well-known biases in the published literature towards wealthier countries. We hope this research will motivate efforts to support student projects, ensuring data and results are published and made publicly available.

ecology↗

bioRxiv2019

Erosion of phylogenetic diversity in Neotropical bat assemblages: findings from a whole-ecosystem fragmentation experiment

The traditional focus on taxonomic diversity metrics for investigating species responses to habitat loss and fragmentation has limited our understanding on how biodiversity is impacted by habitat modification. This is particularly true for taxonomic groups such as bats which exhibit species-specific responses. Here, we investigate phylogenetic alpha and beta diversity of Neotropical bat assemblages across two environmental gradients, one in habitat quality and one in habitat amount. We surveyed bats in 39 sites located across a whole-ecosystem fragmentation experiment in the Brazilian Amazon, representing a gradient of habitat quality (interior-edge-matrix, hereafter IEM) in both continuous forest and forest fragments of different sizes (1, 10, and 100 ha; forest size gradient). For each habitat category, we quantified alpha and beta phylogenetic diversity, then used linear models and cluster analysis to explore how forest area and IEM gradient affect phylogenetic diversity. We found that the secondary forest matrix harboured significantly lower total evolutionary history compared to the fragment interiors, especially the 1 ha fragments, containing bat assemblages with more closely related species. Forest fragments [≥] 10 ha had levels of phylogenetic richness similar to continuous forest, suggesting that large fragments retain considerable levels of evolutionary history. The edge and matrix adjacent to large fragments tend to have closely related lineages nonetheless, suggesting phylogenetic homogenization in these IEM gradient categories. Thus, despite the high mobility of bats, fragmentation still induces considerable levels of erosion of phylogenetic diversity, suggesting that the various evolutionary history might not be able to persist in present-day human-modified landscapes.

ecology↗