Biology subjects

Silva, F.

Publications and source records attributed to Silva, F..

12 recordsLinked to original sources

bioRxiv2026

Wildlife disease surveillance under uncertainty: an adaptive search-theoretic framework for early detection of transboundary animal diseases

Rapid detection is critical for successful management of transboundary animal disease incursions in wild host populations. However, decisions about how best to allocate wildlife disease surveillance effort must be made under high uncertainty. Risk-based surveillance can improve efficiency but approaches that focus surveillance too narrowly on expected high risk areas could have low power to detect unexpected events. We developed and field-tested an adaptive, search-theoretic surveillance framework for detecting transboundary animal disease incursions in wild ungulates in New South Wales, Australia. Key principles that guided the frameworks development included accommodating uncertainty, regularly updating search priorities based on expected risk and spatial coverage, and a flexible structure that allows the system to respond to changing information or conditions over time. We created a coarse state-wide risk map that served as a weakly informative prior describing expected variability in disease incursion risk, loosely focused on foot and mouth disease virus (FMDv). Risk and search values were updated every three months based on realised surveillance effort and estimated detection probabilities over the preceding 12 months, meaning that areas of persistently high risk could nonetheless have low search value if they had recently been intensively searched. Surveillance activities collected blood and swab samples from 1,964 wild pigs (Sus scrofa) during 110 sampling occasions over a two-year evaluation and refinement period. Activities sought to simulate FMDv surveillance operations, but FMDv serological tests were not available at the time. Effort was consistently concentrated in areas of high search value, with at least 74% of sampled cells in the highest risk class. Estimated surveillance system sensitivity ranged from 0.86 to 0.93 over five successive updating cycles and increased as operational procedures were refined. Although the surveillance program was based on FMDv incursion risk, it also fulfilled its secondary objective of detecting unexpected events, including detecting Japanese encephalitis virus in wild pigs before detections in humans and domestic animals. By combining risk-based surveillance with adaptive updating of search priorities in a modular structure, the framework provided a flexible and generalisable approach for early detection of transboundary and emerging animal disease incursions in wildlife populations under high uncertainty.

zoology↗

bioRxiv2026

Early metabolic reprogramming licenses Streptococcus pneumoniae for Influenza-driven superinfection

Bacterial pneumonia remains a major cause of morbidity and mortality following influenza A virus (IAV) infection. However, the adaptive mechanisms that enable pathogen expansion in the post-viral lung remain poorly defined. Here, using a mouse model of IAV-Streptococcus pneumoniae superinfection, we characterize bacterial transcriptional reprogramming in vivo. We identify alcohol dehydrogenases (AdhA and AdhE), that support NAD regeneration during mixed-acid fermentation, as key determinants of bacterial fitness specifically in the IAV-primed lung. Genetic deletion of these results in a pronounced fitness defect during superinfection but not in primary bacterial pneumonia. Consistent with this requirement, pharmacological inhibition of alcohol dehydrogenases limits bacterial expansion and dissemination following IAV infection. Mechanistically, we show that IAV infection profoundly remodels the lung environment, inducing hypoxia and increasing the availability of alternative carbon sources, which together impose a metabolic dependency on Adh for bacterial expansion. Our findings place metabolic adaptation as a central driver of pneumococcal outgrowth following viral infection and reveal exploitable vulnerabilities for therapeutic intervention.

microbiology↗

bioRxiv2024

Estimating the effective population size across space and time in the Critically Endangered western chimpanzee in Guinea-Bissau: challenges and implications for conservation management

Effective population size (Ne) is a key concept in evolutionary and conservation biology. The western chimpanzee (Pan troglodytes verus) is a Critically Endangered taxon. In Guinea-Bissau, chimpanzees are mainly threatened by habitat loss, hunting and diseases. Guinea-Bissau is considered a key area for its conservation. Genetic tools have not yet been applied to inform management and no estimates of Ne have been obtained. In this study, we use countrys range-wide microsatellite data and five whole-genome sequences to estimate several Ne and infer the recent and ancient demographic history of populations using different methods. We also aim to integrate the different Ne estimates to improve our understanding of the evolutionary history and current demography of this great ape and to discuss strengths and limitations of each estimator and their complementarity in informing conservation decisions. Results from the PSMC method suggest a large ancestral Ne, likely due to ancient structure over the whole subspecies distribution until approximately 10-15,000 years ago. After that, a change in connectivity, a real decrease in size or a combination of both occurred, which reduced the then still large ancestral population to a smaller size (MSVAR: [~]10,000 decreasing to 1,000-6,000 individuals), possibly indicating a fragmentation into coastal and inner subpopulations. In the most recent past, contemporary Ne is below or close to 500 (GONE: 116-580, NeEstimator: 107-549), suggesting a high risk of extinction. The populations at coastal Parks may have been small or isolated for several generations whereas the Boe Park one exhibit higher long-term Ne estimates and can be considered a stronghold of chimpanzee conservation. Through combining different types of molecular markers and analytical methodologies, we try to overcome the limitations of obtaining high quality DNA sampling from wild threatened populations and estimate Ne at different temporal and spatial scales, which is crucial information to make informed conservation decisions at local and regional scales.

genomics↗

bioRxiv2024

Lactate-carried Mitochondrial Energy Overflow

We addressed the question of mitochondrial lactate metabolism using genetically-encoded sensors. The organelle was found to contain a dynamic lactate pool that leads to dose- and time-dependent protein lactylation. In neurons, mitochondrial lactate reported blood lactate levels with high fidelity. The exchange of lactate across the inner mitochondrial membrane was found to be mediated by a high affinity H+-coupled transport system involving the mitochondrial pyruvate carrier MPC. Assessment of electron transport chain activity and determination of lactate flux showed that mitochondria are tonic lactate producers, a phenomenon driven by energization and stimulated by hypoxia. We conclude that an overflow mechanism caps the redox level of mitochondria, while saving energy in the form of lactate. One Sentence SummaryMitochondrial lactate production

biochemistry↗

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↗

bioRxiv2024

Electrical stimulation of grape berries as new alternative for post-harvest infection management

Viticulture stands out as a primary agricultural sector in the EU. However, an intensive regime of chemical pesticides is used to meet production standards. Consequently, the EU has taken measures to encourage the promotion of sustainable agrochemical practices. It has recently been demonstrated that low voltage and electrical current can also successfully destroy different type of microorganisms such as bacteria and fungi. However, the application of electric current has not been much explored for preventing early stages of fresh fruit rotting. As a result, an innovative setup was developed to study the effect of an alternating current (50 mA) on grapes previously contaminated with E. coli. A visual analysis of the state of degradation of the grapes 12 days after the electrical treatment allowed us to conclude that the contaminated grapes subjected to electrical treatment (at day 1) did not show visual contamination, when compared to the contaminated grapes without electrical treatment, presenting a similar appearance to the grapes used as control. The quantitative assay also confirmed this result since on the NB agar plates it was possible to visualize a significant reduction in colonies, corresponding to 2 log10 CFU/mL, indicating that approximately 99% of the E. coli previously attached to the berry surface was eradicated. This environmentally sustainable solution aims to reduce dependence on pesticides. Still, other studies will focus on validating its effectiveness against target microorganisms and optimizing a conductive network for applying electrical stimuli to a bunch of grapes.

microbiology↗

bioRxiv2023

The landscape of tolerated genetic variation in humans and primates

Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole genome sequencing data for 809 individuals from 233 primate species, and identified 4.3 million common protein-altering variants with orthologs in human. We show that these variants can be inferred to have non-deleterious effects in human based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases. One Sentence SummaryDeep learning classifier trained on 4.3 million common primate missense variants predicts variant pathogenicity in humans.

genomics↗

bioRxiv2022

Estimating sequence diversity of prion protein gene (PRNP) in Portuguese populations of two cervid species: red deer and fallow deer.

Among the transmissible spongiform encephalopathies (TSEs), chronic wasting disease (CWD) in cervids is now a rising concern in wildlife within Europe, after the detection of the first case in Norway in 2016, in a wild reindeer and until June 2022 a total of 34 cases were described in Norway, Sweden and Finland. The definite diagnosis is postmortem, performed in target areas of the brain and lymph nodes. Samples are first screened using a rapid test and, if positive, confirmed by immunohistochemistry and Western immunoblotting. The study of the genetics of the prion protein gene, PRNP, has been proved to be a valuable tool for determining the relative susceptibility to TSEs. In the present study, the exon 3 of PRNP gene of 143 samples from red deer (Cervus elaphus) and fallow deer (Dama dama) of Portugal was analyzed. Three single nucleotide polymorphisms (SNPs) were found in red deer - codon A136A, codon T98A, codon Q226E - and no sequence variation was detected in fallow deer. The low genetic diversity found in our samples is compatible with previous studies in Europe. The comparison with results from North America, suggests that the free-ranging deer from our study may present susceptibility to CWD, although lack of experimental data and the necessity of extensive survey are necessary to evaluate these populations.

genetics↗

bioRxiv2020

AraC mutations that suppress inactivating mutations in the C-terminal domain of the RpoA subunit of Escherichia coli RNA polymerase

In E. coli, transcriptional activation is often mediated by the C-terminal domain of RpoA, the subunit of RNA polymerase. Mutations that prevent activation of the arabinose PBAD promoter are clustered in a small region of the -CTD domain around K271. To determine the target(s) of RpoA in the PBAD promoter, we have isolated suppressors of rpoA -CTD mutations. The suppressors map to the N-terminal domain of AraC, the main transcriptional regulator of ara gene expression. No mutation was found in the large DNA regulatory region between araC and PBAD, suggesting that, in this system, RpoA does not activate transcription through its direct DNA binding. One class of araC mutations result in substitutions in the core of the N-terminal domain suggesting that they may affect its conformation. Another class of suppressors define genetically a domain that potentially interacts with the C-terminal domain of RpoA. Surprisingly, in rpoA+ strains lacking CRP, the araC mutations largely restore arabinose gene expression, suggesting that they somehow strengthen the AraC:-CTD interaction. Thus, the N-terminal domain of AraC exhibits at least three activities: dimerization, arabinose binding and transcriptional activation via RpoA. ImportanceGene expression is most often controlled at the level of transcription by regulators that interact with RNA polymerase. The C-terminal domain of Escherichia coli RpoA is attached to the core enzyme by a flexible linker and serves as a hub that interacts with many regulators and even with DNA sites to activate transcription. Mutations in a RpoA subdomain interfere with activation of the main arabinose promoter by AraC, the regulator that either activates or represses expression of the arabinose operons. We define here genetically the target of RpoA in the main arabinose promoter. Suppressors of most RpoA mutations map to the N-terminal domain of AraC that promotes its dimerization and binds to arabinose, the inducer. Thus, our results identify a third function for this AraC domain. Some suppressors define a potential binding site for RpoA, while others, at internal residues, probably affect the conformation of the AraC domain.

molecular biology↗

bioRxiv2020

MORPHO-MOLECULAR MECHANISMS STUDY OF PHOTODYNAMIC THERAPY AND CURCUMIN LARVICIDE ACTION ON WILD MOSQUITOES LARVAE OF GENUS Aedes

IntroductionUntil the first two weeks of October 2019, 1.489,457 probable dengue cases have been reported in Brazil, with an incidence rate of 708.8 cases per 100 thousand inhabitants. Still in 2019, in the same period, 123.407 probable cases of chikungunya were reported, with 15 deaths confirmed by clinical and epidemiological criteria. Regarding Zika, in that period, 10.441 probable cases were recorded, been the northeast region with the highest number of notifications, followed by the midwest one. It is well known that current policies to control the vectors of those arboviruses are not effective. Studies for use of light-activated photosensitizers as an alternative to conventional insecticides for sustainable control of mosquitoes vector such as Aedes (dengue, yellow fever, chikungunya, zika), Anopheles (malaria), Culex (yellow fever) can already be found showing advantages over conventional insecticides (efficacy, safety, non-mutagenicity and fast degradation). ObjectiveTo evaluate the effectiveness of Photodynamic Therapy (PDT), mediated by curcumin and blue LED (460nm) in mortality of wild mosquitoes larvae of genus Aedes and also to verify, through confocal microscopy, how the photosensitizer internalizes in larvae organism. In addition to evaluating the action of PDT on the larvae with Raman spectroscopy and histological technique. Materials and methodsOvitraps were placed in the city of Vitoria da Conquista, Bahia, and the larvae collected in stages L2 and L3 were fed for 24 hours with curcumin in concentrations of 10, 20 and 50% mixed with fish feed and then subjected to irradiation with blue LED for 2h (22mW / cm2 and 158.4 J / cm2). The larvae were placed in a container with dechlorinated water and mortality was monitored for 24 and 48 hours. Control groups in which only the larvae were exposed to blue LED for 2 hours and in which the larvae were only fed with fish feed mixed with curcumin (10, 20 and 50%) were included in the study, in addition to the group without treatment. All experiments were repeated after a 2-month interval to confirm the results, totaling 240 tests (tests 1 and 2, n = 15) between groups PDT 10%, PDT 20%, PDT 50%, curcumin 10%, curcumin 20%, curcumin 50%, blue LED and untreated group. The larvae belonging to the PDT 20% group, 20% curcumin, blue LED and control were submitted to histological slides, confocal microscopy and Raman spectroscopy. Larvae mortality rates were compared between groups using univariate descriptive analysis. ResultsAll PDT groups showed larvicidal activity, with the PDT group 20% showing the highest larval mortality in the shortest time. The images from confocal microscopy by laser scanning showed that curcumin was distributed throughout the digestive system of larvae and the analysis by Raman microspectroscopy have shown patterns of alteration and cell death, corroborated by histological sections. ConclusionIt was concluded that PDT in all concentrations was effective in larval mortality, with PDT 20% having the best activity with mortality of 100% in 24 hours.

bioengineering↗

bioRxiv2019

Genomic characterization of the non-O1/non-O139 Vibrio cholerae strain that caused a gastroenteritis outbreak in Santiago, Chile, 2018

Vibrio cholerae is a human pathogen, which is transmitted by the consumption of contaminated food or water. V. cholerae strains belonging to the serogroups O1 and O139 can cause cholera outbreaks and epidemics, a severe life-threatening diarrheal disease. In contrast, serogroups other than O1 and O139, denominated as non-O1/non-O139, have been mainly associated with sporadic cases of moderate or mild diarrhea, bacteremia and wound infections. Here we investigated the virulence determinants and phylogenetic origin of a non-O1/non-O139 V. cholerae strain that caused a gastroenteritis outbreak in Santiago, Chile, 2018. We found that this outbreak strain lacks the classical virulence genes harboured by O1 and O139 strains, including the cholera toxin (CT) and the toxin-coregulated pilus (TCP). However, this strain carries genomic islands (GIs) encoding Type III and Type VI secretion systems (T3SS/T6SS) and antibiotic resistance genes. Moreover, we found these GIs are wide distributed among several lineages of non-O1/non-O139 strains. Our results suggest that the acquisition of these GIs may enhance the virulence of non-O1/non-O139 strains that lack the CT and TCP-encoding genes. Our results highlight the pathogenic potential of these V. cholerae strains. DATA SUMMARYSequence data were submitted to GenBank under the accession number SRLP00000000. The authors confirm that all supporting data and protocols have been provided within the article or through supplementary data files. Data statementAll supporting data, code and protocols have been provided within the article or through supplementary data files. Four supplementary tables are available with the online version of this article.

microbiology↗

bioRxiv2017

Innovative assembly strategy contributes to the understanding of evolution and conservation genetics of the critically endangered Solenodon paradoxus from the island of Hispaniola

Solenodons are insectivores living on the Caribbean islands, with few surviving related taxa. The genus occupies one of the most ancient branches among the placental mammals. The history, unique biology and adaptations of these enigmatic venomous species, can be greatly advanced given the availability of genome data, but the whole genome assembly for solenodons has never been previously performed, partially due to the difficulty in obtaining samples from the field. Island isolation has likely resulted in extreme homozygosity within the Hispaniolan solenodon (Solenodon paradoxus), thus we tested the performance of several assembly strategies for performance with genetically impoverished species genomes. The string-graph based assembly strategy seems a better choice compared to the conventional de Brujn graph approach, due to the high levels of homozygosity, which is often a hallmark of endemic or endangered species. A consensus reference genome was assembled from sequences of five individuals from the southern subspecies (S. p. woodi). In addition, we obtained one additional sequence of the northern subspecies (S. p. paradoxus). The resulting genome assemblies were compared to each other, and annotated for genes, with a specific emphasis on the venomous genes, repeats, variable microsatellite loci and other genomic variants. Phylogenetic positioning and selection signatures were inferred based on 4,416 single copy orthologs from 10 other mammals. Patterns of SNP variation allowed us to infer population demography, which indicated a subspecies split within the Hispaniolan solenodon at least 300 Kya.

evolutionary biology↗