Biology subjects

Ferreira, F. C.

Publications and source records attributed to Ferreira, F. C..

14 recordsLinked to original sources

bioRxiv2025

Transmission potential of Culex and Aedes species for Madariaga virus, a member of the eastern equine encephalitis virus complex

Madariaga virus (MADV), widely distributed in Latin America, can cause severe disease in humans and equids, yet, key aspects of its transmission cycle remain unclear. To identify mosquitoes that could act as MADV vectors, we assessed the vector competence of Aedes aegypti, Ae. albopictus, Ae. taeniorhynchus, Culex tarsalis, Cx. coronator, and Cx. quinquefasciatus, following oral exposure to MADV isolated in Panama (all species) or Brazil (Ae. taeniorhynchus only). MADV RNA and infectious virus were quantified from mosquito bodies, legs, and saliva. At 14 days post-exposure, five species had virus in all biological sample types. Culex quinquefasciatus was susceptible to infection and dissemination but had no positive saliva samples. Aedes taeniorhynchus showed higher infection probabilities with MADV-BR. Time-course analysis revealed distinct dynamics in Ae. aegypti and Ae. albopictus. Our findings indicate MADV may be compatible with mosquito species present in endemic regions and areas at risk of virus introduction.

molecular biology↗

bioRxiv2025

ERGA-BGE Reference Genome of Loboptera subterranea: a cave adapted cockroach endemic to the Canary Islands

Species of the genus Loboptera from the Canary Islands are adapted to life in subterranean environments, except Loboptera canariensis and Loboptera decipiens which inhabit epigean, often influenced by human activities. The genome of Loboptera subterranea provides a valuable resource for understanding the genetic basis of how the Canarian Loboptera species evolved and thrived in subterranean environments. A total of 14 contiguous chromosomal pseudomolecules were assembled from the genome sequence. This chromosome-level assembly encompasses 2.7 Gb, composed of 486 contigs and 90 scaffolds, with contig and scaffold N50 values of 13.1 Mb and 202.7 Mb, respectively.

genomics↗

bioRxiv2025

Active surveillance of cats and dogs from households with human COVID-19 cases reveals over one quarter of pets infected with SARS-CoV-2 in 2020-2021 in Texas, United States

Households where people have COVID-19 are high risk environments for companion animals that are susceptible to SARS-CoV-2. We sampled 579 pets from 281 households with one or more laboratory-confirmed person with COVID-19 in central Texas from June 2020 to May 2021. Nineteen out of 396 (4.8%) dogs and 21 out of 157 (13.4%) cats were positive for SARS-CoV-2 by RT-qPCR. Additionally, 95/382 (25%) dogs and 52/146 (36%) cats harbored SARS-CoV-2 neutralizing antibodies. Twenty-six companion animals of ten other species were negative. Overall, 164 (29%) pets were positive for SARS-CoV-2 by molecular and/or serological tests; a total of 110 (39%) out of 281 households had at least one animal with active or past SARS-CoV-2 infection. Cats were more likely to be infected by SARS-CoV-2 and had higher endpoint antibody titers than dogs. Through viral isolation from a subset of respiratory swabs, we documented 6 different lineages in dogs and cats, including the B.1.1 lineage in a cat one month prior to the first known human case in the country. We observed animal and human-pet interaction factors associated with higher risk of infection for dogs and cats, such as days after COVID-19 diagnosis and sharing food. Frequency of clinical signs of disease reported by owners of pets with active infections did not differ from uninfected ones, suggesting that not all reported signs are attributed to SARS-CoV-2 infection. Characterizing animal infections using active SARS-CoV-2 surveillance in pets at risk of infection may aid in One Health pandemic prevention, response, and management.

microbiology↗

bioRxiv2025

ERGA-BGE genome of Stigmatoteuthis arcturi Robson, 1948: the jewelled squid

The Stigmatoteuthis arcturi reference genome offers a valuable resource for understanding the evolutionary patterns of oceanic squids, who perform important ecological roles as both predators and prey in mesopelagic and deep-sea environments, while their genomes remain understudied. The entirety of the genome sequence was assembled into 46 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 3.25 Gb, composed of 1,268 contigs and 497 scaffolds, with contig and scaffold N50 values of 11.0 Mb and 74.6 Mb, respectively.

genomics↗

bioRxiv2025

ERGA-BGE Reference Genome of Phyllidia flava (Nudibranchia: Phyllidiidae), a Relict Species Endemic to the Mediterranean Sea

Phyllidia flava, the only Mediterranean representative of the otherwise Indo-Pacific family Phyllididae, is a radula-less dorid nudibranch that feeds exclusively on toxic sponges, from which it derives defensive and camouflage compounds. Although not currently listed as endangered, this relict species remains vulnerable due to its restricted distribution and the rising temperatures of the Mediterranean Sea. A total of 13 contiguous chromosomal pseudomolecules were assembled, resulting in a chromosome-level genome spanning 1.9 Gb. This assembly comprises 2,032 contigs and 62 scaffolds, with contig and scaffold N50 values of 2.4 Mb and 169.7 Mb, respectively. This reference genome will serve as a valuable resource for conservation efforts, provide a robust calibration point for studying nudibranch phylogenetics based on the Tethys Ocean closure, and lay the groundwork for research into toxic prey diet specialisation.

genomics↗

bioRxiv2024

Respiratory shedding of infectious SARS-CoV-2 Omicron XBB.1.41.1 lineage with increased evolutionary rate among captive white-tailed deer

White-tailed deer (Odocoileus virginianus) have high value for research, conservation, agriculture and recreation, and may be important SARS-CoV-2 reservoirs with unknown human health implications. In November 2023, we sampled 15 female deer in a captive facility in central Texas, USA. All individuals had neutralizing antibodies against SARS-CoV-2 and 11 had RT-qPCR-positive respiratory swabs; one also had a positive rectal swab. Six of 11 respiratory swabs yielded infectious virus with replication kinetics of most samples displaying lower growth 24-48 h post infection in vitro when compared to Omicron lineages isolated from humans in Texas in the same period. However, virus growth was similar between groups by 72 h, suggesting no strong attenuation of deer-derived virus. All deer viruses clustered in XBB Omicron clade, with more mutations than expected compared to contemporaneous viruses in humans, suggesting that crossing the species barrier to deer was accompanied by a high substitution rate.

microbiology↗

bioRxiv2023

Bloodmeal metabarcoding of the argasid tick (Ornithodoros turicata Duges) reveals extensive vector-host associations

Molecular methods to understand host feeding patterns of arthropod vectors are critical to assess exposure risk to vector-borne disease and unveil complex ecological interactions. We build on our prior work discovering the utility of PCR-Sanger sequencing bloodmeal analysis that work remarkably well for soft ticks (Acari: Argasidae), unlike for hard ticks (Acari: Ixodidae), thanks to their unique physiology that retains vertebrate DNA from prior bloodmeals viable for years. Here, we capitalize on this feature and apply bloodmeal metabarcoding using amplicon deep sequencing to identify multiple host species in individual Ornithodoros turicata soft ticks collected from two natural areas in Texas, United States. Of 788 collected O. turicata, 394 were evaluated for bloodmeal source via metabarcoding, revealing 27 different vertebrate host species (17 mammals, 5 birds, 1 reptile, and 4 amphibians) fed upon by 274 soft ticks. Information on multiple hosts for individual O. turicata was derived from 168 of these (61%). Metabarcoding revealed more mixed vertebrate bloodmeals in O. turicata previously processed using Sanger sequencing. These data reveal wide host range of O. turicata and demonstrate the value of bloodmeal metabarcoding for understanding the ecology for known and potential tick-borne pathogens circulating among humans, domestic animals and wildlife such as relapsing fever caused by Borrelia turicatae. Our results also document, for the first time an off-host soft tick collected to have evidence of prior feeding on wild pig which is a critical observation in the context of the threat of enzootic transmission of African swine fever virus if it were introduced to the US. This research enhances our understanding of vector-host associations and offers a promising perspective for biodiversity monitoring and disease control strategies.

ecology↗

bioRxiv2023

Piroplasm parasites (Apicomplexa: Piroplasmida) in northeastern populations of the invasive Asian longhorned tick, Haemaphysalis longicornis Neumann (Ixodida: Ixodidae), in the United States

Piroplasms, which include the agents of cattle fever and human and dog babesiosis, are a diverse group of blood parasites of significant veterinary and medical importance. The invasive Asian longhorned tick, Haemaphysalis longicornis, is a known vector of piroplasms in its native range in east Asia and invasive range in Australasia. In the US state of Virginia, H. longicornis has been associated with Theileria orientalis Ikeda outbreaks that caused cattle mortality. We examined 667 H. longicornis collected in 2021 from three sites in New Brunswick, New Jersey, the US state where established populations of this species were first detected in 2017. We used primers targeting the 18S small subunit rRNA and the cytochrome b oxidase loci and unveiled the presence of DNA from an unidentified Theileria species (in 1 nymph) and Theileria cervi type F (1 adult, 5 nymphs). In addition, we sequenced a 130 bp fragment of the cytochrome oxidase b locus from Odocoileus virginianus, the white-tailed deer, in a partially engorged questing H. longicornis, supporting the association of this tick species with deer. We also detected DNA from an undescribed Babesia sensu stricto ( true Babesia, 2 adults, 2 nymphs) as well as Babesia sp. Coco (1 adult, 1 nymph). Finally, we detected DNA from Babesia microti S837 (1 adult, 4 nymphs). Babesia microti S837 has been sequenced from striped skunks, Mephitis mephitis, and is closely related to the human pathogen B. microti US-type. The five parasites we are associating with H. longicornis represent a diverse assemblage spanning three clades in the piroplasm phylogeny, two undescribed, raising concerns of transmission amplification of veterinary pathogens as well as spillover of pathogens from wildlife to humans.

ecology↗

bioRxiv2023

Ticks (Acari: Ixodida) on synanthropic small and medium-sized mammals in areas of the northeastern United States infested with the Asian longhorned tick, Haemaphysalis longicornis

The northeastern United States is a hot spot for tick-borne diseases. Adding to an already complex vector landscape, in 2017 large populations of the invasive Haemaphysalis longicornis, the Asian longhorned tick, were detected in New Jersey (NJ) and later found to be widespread from Connecticut to Georgia. In its native range in northeastern Asia, H. longicornis is considered an important vector of deadly pathogens to humans, companion animals, and livestock. To identify the primary hosts of H. longicornis we surveyed synanthropic small and medium-sized mammals in three different sites in suburban New Brunswick, NJ. Specifically, we collected approximately 9,000 tick specimens belonging to nine species from 11 different species of mammals sampled between May and September 2021. We found that H. longicornis feeds more frequently on rodents than previously thought, and that this invasive tick is likely exposed to important enzootic and zoonotic pathogens. Overall, we obtained detailed information about the seasonal dynamics and feeding patterns of six tick species common in the northeastern US, Haemaphysalis longicornis, Amblyomma americanum, Dermacentor variabilis, Ixodes scapularis, I. texanus and I. cookei. We found that unlike I. scapularis that feeds on mammals of all sizes, H. longicornis feeds on hosts following the general pattern of A. americanum, favoring larger species such as skunks, groundhogs, and raccoons. However, our survey revealed that unlike A. americanum, H. longicornis reaches high densities on Virginia opossum. Overall, the newly invasive H. longicornis was the most abundant tick species both on multiple host species and in the environment, raising significant questions regarding its role in the epidemiology of tick-borne pathogens, especially those affecting livestock, companion animals and wildlife. In conclusion, our findings provide valuable insights into the tick species composition on mammal hosts in New Jersey and the ongoing national expansion of H. longicornis.

ecology↗

bioRxiv2023

Cell-derived ECM loaded electrospun Polycaprolactone/Chitosan nanofibrous scaffolds for periodontal regeneration

Periodontitis is an inflammatory infection caused by bacterial plaque accumulation that affects the periodontium, a complex structure of different tissues (cementum, periodontal ligament and alveolar bone) that surrounds and supports the teeth. Current treatments lack bioactive signals to induce tissue repair and coordinated regeneration of the periodontium, thus alternative strategies are needed to improve clinical outcomes. Cell-derived extracellular matrix (ECM) has been combined with biomaterials to enhance their biofunctionality for various tissue engineering (TE) applications. In this work, bioactive cell-derived ECM loaded electrospun polycaprolactone/chitosan (PCL/CTS) nanofibrous scaffolds were developed combining polymer solutions with lyophilized decellularized ECM (dECM) derived from human Periodontal Ligament Stem/Stromal Cells (PDLSCs). The works aims were to fabricate and characterize cell-derived ECM electrospun PCL/CTS scaffolds in terms of morphology, physico-chemical, thermal and mechanical properties and assess their ability to enhance the osteogenic differentiation of PDLSCs, envisaging periodontal TE applications. PDLSCs were cultured and used for dECM production. PDLSCs-derived dECM was characterized regarding morphology, protein expression, DNA removal efficiency, and glycosaminoglycans and collagen contents. Osteogenic differentiation of PDLSCs was performed on PCL, PCL/CTS and PCL/CTS/ECM electrospun scaffolds for 21 days. The obtained results demonstrate that PCL/CTS/ECM scaffolds promoted cell proliferation compared to PCL and PCL/CTS scaffolds, while maintaining similar physical and mechanical properties of PCL/CTS scaffolds. PCL/CTS/ECM scaffolds enhanced the osteogenic differentiation of PDLSCs, confirmed by increased alkaline phosphatase activity, calcium deposition, and bone-specific marker genes expression. Moreover, PCL/CTS scaffolds showed higher levels of cell mineralization than PCL scaffolds. Overall, this work describes the first use of lyophilized cell-derived ECM loaded electrospun scaffolds for periodontal TE applications and highlights its potential as a promising therapeutic strategy for periodontitis treatment.

bioengineering↗

bioRxiv2022

Great-tailed Grackles (Quiscalus mexicanus) as a tolerant host of avian malaria parasites

Great-tailed Grackles (Quiscalus mexicanus) are a social, polygamous bird species whose populations have rapidly expanded their geographic range across North America over the past century. Before 1865, Great-tailed Grackles were only documented in Central America, Mexico, and southern Texas in the USA. Given the rapid northern expansion of this species, it is relevant to study its role in the dynamics of avian blood parasites. Here, 87 Great-tailed grackles in Arizona (a population in the new center of the range) were screened for haemosporidian parasites using microscopy and PCR targeting the parasite mitochondrial cytochrome b gene. Individuals were caught in the wild from January 2018 until February 2020. Haemosporidian parasite prevalence was 60.9% (53/87). A high Plasmodium prevalence was found (59.8%, 52/87), and one grackle was infected with Haemoproteus (Parahaemoproteus) sp. (lineage SIAMEX01). Twenty-one grackles were infected with P. cathemerium, sixteen with P. homopolare, four with P. relictum (strain GRW04), and eleven with three different genetic lineages of Plasmodium spp. that have not been characterized to species level (MOLATE01, PHPAT01, and ZEMAC01). Gametocytes were observed in birds infected with three different Plasmodium lineages, revealing that grackles are competent hosts for some parasite species. This study also suggests that grackles are highly susceptible and develop chronic infections consistent with parasite tolerance, making them competent to transmit some generalist haemosporidian lineages. It can be hypothesized that, as the Great-tailed Grackle expands its geographic range, it may affect local bird communities by increasing the transmission of local parasites but not introducing new species into the parasite species pool.

zoology↗

bioRxiv2022

Transcriptional response of individual Hawaiian Culex quinquefasciatus mosquitoes to the avian malaria parasite Plasmodium relictum

Culex quinquefasciatus, the mosquito vector of avian malaria in Hawai{square}i, became established in the islands in the 1820s and the deadly effects of malaria on endemic bird species have been documented for many decades. To evaluate the gene expression response of the mosquito to the parasite, we let the offspring of wild-collected Hawaiian Cx. quinquefasciatus feed on a domestic canary infected with Plasmodium relictum GRW4 freshly isolated from a wild-caught Hawaiian honeycreeper. Control mosquitoes were fed on an uninfected canary. We sequenced the individual transcriptomes of five infected and three uninfected individual mosquitoes at three different stages of the parasite life cycle: 24 h post feeding (hpf) during ookinete invasion; 5 days post feeding (dpf) when oocysts are developing; 10 dpf when sporozoites are released and invade the salivary glands. Differential gene expression analyses showed that during ookinete invasion (24 hpf), genes related to oxidoreductase activity and galactose catabolism had lower expression levels in infected mosquitoes compared to controls. Oocyst development (5 dpf) was associated with reduced expression of a gene with a predicted innate immune function. At 10 dpf, infected mosquitoes had reduced expression levels of a serine protease inhibitor. Overall, the gene expression response of Hawaiian Culex exposed to a Plasmodium infection intensity that occur naturally in Hawaii was low, but more pronounced during ookinete invasion. The low fitness costs often documented in Culex infected with avian Plasmodium likely reflect the relatively small transcriptional changes observed in mosquito genes related to immune response and nutrient metabolism.

microbiology↗

bioRxiv2022

Bio-inspired artificial printed bioelectronic cardio-3D-cellular constructs

Bioelectronics is a growing field where novel smart materials are required to interface biology with electronic components. Conductive hydrogels have recently emerged as a promising material for biosensing/actuating applications as they can provide a wet, nanostructured and electrically conductive environment, minimising the mismatch between biological and electronic systems. In this work, we propose a strategy to develop conductive bioinks compatible with the freeform reversible embedding of suspended hydrogels (FRESH) extrusion bioprinting method. These bioinks are based on decellularized extracellular matrix (dECM), extracted from three different tissues (small intestine submucosa, liver and bone) and were characterised. 3D structures were manufactured containing human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs), exhibiting cell viabilities >80%. Multi-walled carbon nanotubes (MWCNTs) were selected as an additional component of the bioinks. The addition of the MWCNTs enhanced the conductive features of the hydrogels and the morphology of the dECM fibres. Electrical stimulation (ES) through alternating currents was applied to hPSC-CMs encapsulated in 3D structures manufactured with the previous material and our results indicated two main findings: (1) in the absence of external ES, the conductive properties of the materials can improve the contractile behaviour of the hPSC-CMs and (2) this effect is significantly enhanced under the application of external ES. Genetic markers analysed showed a trend towards a more mature state of the cells evaluated by the TNNI3/TNNI1 ratio, with upregulated SERCA2 and RYR2 calcium handling proteins when compared to controls and downregulation of calcium channels involved in the generation of pacemaking currents (CACNA1H). These results demonstrate the potential of our strategy to manufacture conductive hydrogels in complex geometries for bioactuating purposes. However, further development of the 3D bioprinting techniques is required to achieve higher control over the nano- and microarchitectures of the structures to improve their biomimicry.

bioengineering↗

bioRxiv2021

A gene-based capture assay for surveying patterns of genetic diversity and insecticide resistance in a worldwide group of invasive mosquitoes

Understanding patterns of diversification, genetic exchange, and pesticide resistance in insect species of human health concern is necessary for effective population reduction and management. With the broad availability of next-generation sequencing technologies, one of the best approaches for surveying such patterns involves the simultaneous genotyping of many samples for large numbers of genetic markers from across the known genome. To this end, the targeting of gene sequences of known function or inheritance can be a cost-effective strategy. One insect group of substantial health concern are the mosquito taxa that make up the Culex pipiens complex. Members of this complex transmit damaging arboviruses and filariae worms to humans, as well as other pathogens that are detrimental to endangered vertebrate species such as bird malaria. Here we describe our development of a targeted gene-based assay for surveying genetic diversity and population structure in this mosquito complex. To test the utility of this assay, we examined taxonomic divergence among samples from several members of the complex, as well as distinct populations of the relatively under-studied Culex quinquefasciatus, an urban pantropical species. We also examined the presence of known insecticide-resistance conferring alleles. Broadly, our developed gene-based assay proved effective for examining patterns of taxonomic and geographic clustering within the species complex, as well as for surveying genetic variants that have been associated with insecticide resistance. This assay will be useful for future studies that aim to understand the genetic mechanisms underlying the evolution of ubiquitous and increasingly damaging disease vectors.

genomics↗