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Fernandes, P.

Publications and source records attributed to Fernandes, P..

15 recordsLinked to original sources

Combined impacts of invasive alien species and fire on ecosystems are complex, mostly negative, and understudied: a global review

Invasion-fire interactions can negatively impact ecosystems by driving biodiversity loss, altering ecological processes, modifying habitat structure, and compromising ecosystem functioning. Understanding how this interaction operates is essential to design effective management strategies that are successful in controlling both invasive alien species (IAS) and fire. Therefore, the present literature review aims to synthesize the current knowledge on invasion-fire interaction and its impacts on ecosystems, as well as identify knowledge gaps in the field. The review included 464 studies, from which information on context, species and fire characteristics, interaction outcomes, and research approaches was extracted. Fire generally promotes IAS, although studies on invasive animals are limited and no research has examined the effects of fire on fungi. Management through prescribed fire showed significantly better outcomes than wildfires in suppressing IAS, yet positive impacts still outnumbered the negative ones. In turn, IAS can change fire regimes causing regime shifts, but this direction of interaction is much less studied. Combined impacts of fire and IAS on ecosystems are predominantly negative, although interactions are complex and not always synergistic. Key knowledge gaps include geographic regions with known Invasion-fire interactions that remain underreported, a lack of broad-scale studies, limited management interventions, understudied taxa, and limited understanding of the combined effects on ecosystems. Remote sensing and laboratory experiments, which have been rarely used, could address some of these gaps.

ecology↗

Subliminal beauty engages the brain's valuation circuits

Neuroeconomic models propose that the anterior ventral striatum (aVS) and ventromedial prefrontal cortex (vmPFC) are key regions for computing subjective value (SV) signals that guide choice. However, the role of conscious awareness in this process remains debated. Here we examined whether SV can be automatically computed in these regions without conscious awareness. In an fMRI experiment, participants viewed faces that varied in attractiveness under three conditions: (i) suppressed from awareness via continuous flash suppression (CFS), (ii) clearly visible without suppression, or (iii) absent (background only) with CFS. Participants reported trial-wise facial identity (objective) and visibility (subjective) measures of facial awareness. In a post-fMRI session, they rated the attractiveness of each face as a measure of SV. When faces were seen, task performance (d) exceeded chance and responses were faster than in absent trials. When faces were unseen, performance was at chance but responses were slower than absent trials. Neurally, seen and unseen faces elicited greater neural signal than absent trials and showed similar neural patterns in the fusiform face area (FFA). Critically, neural signal in vmPFC correlated with SV for both seen and unseen faces, with similar neural patterns. In aVS, SV-related signal was only observed for unseen faces. Furthermore, mean face-related signal in FFA correlated with SV-related signals in aVS and vmPFC for unseen faces. These findings demonstrate that SV can be automatically computed in aVS and vmPFC without conscious awareness, suggesting a neural pathway by which subliminal information can influence value-based choice.

neuroscience↗

dnaudit + Pydnaweb: A lightweight text-based planning and documentation workflow for genetic cloning with automatic verification

Life science research often depends on the construction and analysis of recombinant DNA molecules, where sequence accuracy is critical. However, the field continues to face a reproducibility crisis, partly due to the lack of comprehensive, systematic, and verifiable documentation of genetic constructions. Although most cloning procedures are deterministic and theoretically describable in a complete and unambiguous way, published methods are typically described in a form free narrative, making them laborious to reproduce and assess for completeness. Tools like the Python package Pydna support programmable and reproducible cloning strategies but require coding expertise, which can be a barrier for some users. To address this, we developed Pydnaweb and dnaudit, two open-source and complementary web tools that build on Pydna. Pydnaweb offers simulation of unit operations such as PCR and restriction digestion providing results in text format. These results can be collected and combined to form complex cloning strategies in a bottom-up approach. Dnaudit can verify such collections for internal consistency and that the cloning strategy meet a specific goal such as the expression of a protein sequence. The tools are design for a low barrier of entry, and they can be used separately. This workflow enables fully automated validation, providing a no-code, reproducible solution for documenting and sharing molecular cloning workflows. These tools ease compliance with FAIR principles and align with emerging standards for the transparent and reproducible sharing of scientific methods and data.

bioinformatics↗

Subliminal risk influences subjective value in the ventromedial prefrontal cortex

The relationship between conscious awareness and decisions has been heavily debated. Here we investigated whether subliminal probabilities are integrated with conscious rewards to form subjective value (SV) representations in the anterior ventral striatum (aVS) and ventromedial prefrontal cortex (vmPFC). Participants played an incentivized competitive game with risky choice to accumulate points across trials in a behavioral and fMRI experiment. The game was a modified attentional-blink paradigm that rendered a probability cue unseen (indicating a 100% or 0% chance to win a risky reward). Following the probability cue, participants chose between a safe (1 point with certainty) or risky option (>1 or 0 points depending on probability cue). The risky reward was either 2 or 5 points, varying across trials. In some trials the probability cue was absent (replaced by a random distractor) and the probability to win the risky reward was 50%. When probability cues were unseen, they did not influence choice, as value-maximizing choice (d) was not greater than chance, but they did influence reaction time in both experiments. Consistent with SV integration, the BOLD signal in aVS and vmPFC was higher for both conscious rewards (high > low) and subliminal probabilities (high > low) and could not be explained by subliminal salience (cue present > absent). Moreover, multivariate pattern similarity between conscious rewards and subliminal probabilities in vmPFC suggest integration into an abstract value representation. Additionally, we found brain-wide subliminal probability and salience effects. Taken together, these results suggest that conscious awareness is not necessary for probability to be integrated with conscious rewards to form an abstract "common currency" SV representation in vmPFC. Additionally, brain-wide subliminal probability and salience effects suggests information can have "global access" without conscious awareness.

neuroscience↗

CCRL2 promotes the interferon-γ signaling response in myeloid neoplasms with erythroid differentiation and mutated TP53

Patients with myeloid neoplasms with loss-of-function TP53 mutations and erythroid differentiation have poor outcomes, and a better understanding of disease biology is required. Upregulation of interferon-{gamma} (IFN-{gamma}) signaling has been associated with acute myeloid leukemia (AML) progression and chemotherapy resistance, but its drivers remain unclear. In this study, we found that the surface receptor C-C motif chemokine receptor-like 2 (CCRL2) is overexpressed in AML with erythroid differentiation and TP53 mutations compared to other AML subtypes and healthy hematopoietic cells. The knockout (KO) of CCRL2 suppressed erythroleukemia growth in vitro and in vivo. Further proteomics and transcriptomics analysis revealed IFN-{gamma} signaling response as the top CCRL2-regulated pathway in erythroleukemia. Our mechanistic studies support direct CCRL2 driven IFN-{gamma} signaling independent of exogenous IFN-{gamma}, through phosphorylation of STAT1, via JAK2-dependent and independent mechanisms. CCRL2/IFN-{gamma} signaling is upregulated in erythroid leukemias, and TP53 mutated AML without concurrent increase of IFN-{gamma} secretion in the bone marrow microenvironment and is directly induced by TP53 KO. Finally, CCRL2/IFN-{gamma} signaling is associated with the transformation of pre-leukemic single-hit TP53 clones to multi-hit TP53 mutated AML, increased resistance to venetoclax and worse survival in AML. Overall, our findings support that CCRL2 is an essential driver of cell-autonomous IFN-{gamma} signaling response in myeloid neoplasms with erythroid differentiation and TP53 mutations and highlight CCRL2 as a relevant novel target for these neoplasms. One Sentence SummaryCCRL2 is overexpressed in AML with loss-of-function TP53 mutations and erythroid differentiation and promotes IFN-{gamma} signaling response via a cell-intrinsic mechanism.

cancer biology↗

Vagus nerve mediated liver-brain axis is a major regulator of the metabolic landscape in the liver

BackgroundThe liver serves as a major energetic reservoir for other tissues and its metabolic function is controlled by humoral and neural factors. The vagus nerve innervating the gastrointestinal tract plays an important role in regulating peripheral metabolism and energy expenditure. Although the liver receives vagus nerve fibers, the impact of this circuitry in the regulation of hepatic metabolism is still poorly understood. MethodsHerein, we used a combination of quantitative proteomics and in vivo imaging techniques to investigate the impact of the vagus nerve on liver metabolism. ResultsVagus nerve shapes the metabolic framework of the liver, as surgical ablation (vagotomy; VNX) of this circuitry led to a significant alteration of the hepatic proteome landscape. Differential protein expression and pathway enrichment analyses showed that glycolytic and fatty acid biosynthesis were increased following VNX, whereas {beta}-oxidation was decreased. This metabolic shift facilitated lipid accumulation in hepatocytes. Furthermore, VNX worsened liver steatosis following high-carbohydrate or high-fat dietary challenges. ConclusionsThis study describes the liver-brain axis mediated by the vagus nerve as an important regulator of the hepatic metabolic landscape. HighlightsO_LIVagus nerve is a novel regulator of the hepatic metabolic landscape. C_LIO_LIAblation of vagus nerve neural circuit by vagotomy resulted in a metabolic shift towards glycolysis and fatty acid biosynthesis. C_LIO_LILipid accumulation was increased in vagotomized mice fed with a standard diet. C_LIO_LILiver steatosis was increased following dietary challenges with high-carbohydrate or high-fat diets. C_LIO_LIVagus nerve can be a promising new target for NAFLD treatment. C_LI

physiology↗

Validation of the in-house designed one-trial inhibitory avoidance test for two strains of adult zebrafish

Open-source validated tools are important for affordable high-quality science. Zebrafish model is often used in behavioral sciences, thus validated tools must be developed for this species. We aimed to implement the memory task one-trial inhibitory avoidance test in our laboratory by creating a custom-built 3D printed apparatus and custom-made hardware and software using microcontrollers; this decreases the costs and increases methodological flexibility. In this task, a mild electric shock (3.3 {+/-} 0.3V and 2A for 5sec) is used as an aversive stimulus for the one-trial inhibitory avoidance task based on classical conditioning. For this study we used 72-adult zebrafish from the AB and TU strain. The aversive stimulus caused a robust and long-lasting memory that was learned in one session. The apparatus consisted in one aquarium with two compartments (white and black) where, during the conditioning session, the shock was delivered in the preferred side (black), followed by 30min of immersion in 20M MK-801, a compound known for inducing amnesia (amnesic group, n= 20 for AB and 17 for TU), or in clean water (control, n= 20 for AB and 15 for TU). Both the AB and TU strain animals from the control group took more time to enter in the black compartment after conditioning (p[≤]0.039), indicating avoidance for the black side, while the latency was not altered in the MK-801 group, demonstrating impaired memory. In summary, this open-source apparatus is an affordable and validated option for memory assessment for the two most used strains of zebrafish in research.

animal behavior and cognition↗

Experimentally induced drought and growing season stage modulate community-level functional traits in a temperate grassland

O_LIExtreme precipitation events are expected to become more intense and frequent with climate change. This climatic shift may impact the structure and dynamics of natural communities and the key ecosystem services they provide. Changes in species abundance under these extreme conditions are thought to be driven by functional traits, morpho-physiological characteristics of an organism that impact its fitness. Future environmental conditions may, therefore, favour different functional traits to those in present-day communities. C_LIO_LIHere, we measure functional traits on 586 vascular plants in a temperate grassland where precipitation has been experimentally manipulated for six years. We calculated community-weighted means of five functional traits (plant height, leaf dry matter content, leaf thickness, specific leaf area, and leaf phosphorus concentration) and compared community-weighted means between three levels of precipitation: drought (-50%), irrigated (+50%), and control. Additionally, we contrasted treatments at two different timings along the growing season: mid-season and late-season. C_LIO_LIWe expected altered community-weighted means for traits associated with a conservative use of water that will result from increased summer stress-induced intraspecific variability in the mid-season and from community composition changes in the late-season, after the field is cut, a common management action across most European grasslands. C_LIO_LIIn the drought treatment, we found significantly lower community-weighted mean plant height and leaf dry matter content. However, we only observed these differences after the mid-season cut. We also observed an increase in leaf phosphorus concentration in the drought treatment before the mid-season cut. A combination of changes in community composition and intraspecific variation contributed to these differences, with community composition being more important after the cut. Species with higher height, leaf dry matter content, and lower leaf thickness showed a more pronounced abundance decline at the drought plots. We observed no changes in functional traits community-weighted means in the irrigated treatment compared to those in control and drought treatments. C_LIO_LISynthesis. Our results suggest how the functional trait composition of grassland communities may shift under climate change-induced drought, stressing the interacting effects with growing season stages. C_LI

ecology↗

Flexible estimation of biodiversity with short-range multispectral imaging in a temperate grassland

O_LIImage sensing technologies are rapidly increasing the cost-effectiveness of biodiversity monitoring efforts. Species differences in the reflectance of electromagnetic radiation have recently been highlighted as a promising target to estimate plant biodiversity using multispectral image data. C_LIO_LIHowever, these efforts are currently hampered by logistical difficulties in broad-scale implementation and their use in characterizing biodiversity at different spatial scales. C_LIO_LIHere, we investigate the utility of multispectral imaging technology from commercially available unmanned aerial vehicles (UAVs, or drones) in estimating biodiversity metrics at short-range (<10 m image recording height) in a temperate calcareous grassland ecosystem in Oxfordshire, UK. We calculate a suite of moments (coefficient of variation, standard deviation, skew, kurtosis) for the distribution of radiance from multispectral images at five wavelength bands (Blue 450{+/-}16 nm; Green 560{+/-}16 nm; Red 650{+/-}16 nm; Red Edge 730{+/-}16 nm; Near Infrared 840{+/-}16 nm) and test their effectiveness at estimating ground-truthed biodiversity metrics from in-situ botanical surveys for 37 - 1 m x 1 m quadrats. C_LIO_LIWe find positive associations between the average coefficient of variation in spectral radiance and both the Shannon-Weiner and Simpsons biodiversity indices. Furthermore, we find that the average coefficient of variation in spectral radiance is consistent and highly repeatable, across sampling days and recording heights. Positive associations with biodiversity indices hold irrespective of the image recording height (2-8 m), but we report reductions in estimates of spectral diversity with increases to UAV recording height. UAV imaging reduced sampling time by 16-fold relative to in-situ botanical surveys. C_LIO_LISynthesis - We demonstrate the utility of multispectral radiance moments as an indicator of grassland biodiversity metrics at high spatial resolution using a widely available UAV monitoring system at a coarse spectral resolution. The use of UAV technology with multispectral sensors has far-reaching potential to provide cost-effective and high-resolution monitoring of biodiversity in complex environments. C_LI

ecology↗

The AMA1-RON complex drives Plasmodium sporozoite invasion in the mosquito and mammalian hosts

Plasmodium sporozoites that are transmitted by blood-feeding female Anopheles mosquitoes invade hepatocytes for an initial round of intracellular replication, leading to the release of merozoites that invade and multiply within red blood cells. Sporozoites and merozoites share a number of proteins that are expressed by both stages, including the Apical Membrane Antigen 1 (AMA1) and the Rhoptry Neck Proteins (RONs). Although AMA1 and RONs are essential for merozoite invasion of erythrocytes during asexual blood stage replication of the parasite, their function in sporozoites is still unclear. Here we show that AMA1 interacts with RONs in mature sporozoites. By using DiCre-mediated conditional gene deletion in P. berghei, we demonstrate that loss of AMA1, RON2 or RON4 in sporozoites impairs colonization of the mosquito salivary glands and invasion of mammalian hepatocytes, without affecting transcellular parasite migration. Our data establish that AMA1 and RONs facilitate host cell invasion across Plasmodium invasive stages, and suggest that sporozoites use the AMA1-RON complex to safely enter the mosquito salivary glands without causing cell damage, to ensure successful parasite transmission. These results open up the possibility of targeting the AMA1-RON complex for transmission-blocking antimalarial strategies.

microbiology↗

Plasmodium sporozoites require the protein B9 to invade hepatocytes

Plasmodium sporozoites are transmitted to a mammalian host during blood feeding by an infected mosquito and invade hepatocytes for initial replication of the parasite in the liver. This leads to the release of thousands of merozoites into the blood circulation and initiation of the pathogenic blood stages of malaria. Merozoite invasion of erythrocytes has been well characterized at the molecular and structural levels. In sharp contrast, the molecular mechanisms of sporozoite invasion of hepatocytes are poorly characterized. Here we report a new role during sporozoite entry for the B9 protein, a member of the 6-cysteine domain protein family. Using genetic tagging and gene deletion approaches in rodent malaria parasites, we show that B9 is secreted from sporozoite micronemes and is required for productive invasion of hepatocytes. Structural modelling indicates that the N-terminus of B9 forms a beta-propeller domain structurally related to CyRPA, a cysteine-rich protein forming an invasion complex with Rh5 and RIPR in P. falciparum merozoites. We provide evidence that the beta-propeller domain of B9 is essential for protein function during sporozoite entry and interacts with P36 and P52, both also essential for productive invasion of hepatocytes. Our results suggest that, despite using distinct sets of parasite and host entry factors, Plasmodium sporozoites and merozoites may share common structural modules to assemble protein complexes for invasion of host cells.

microbiology↗

Developmental changes and metabolic reprogramming during establishment of infection and progression of Trypanosoma brucei brucei through its insect host

Trypanosoma brucei ssp., unicellular parasites causing human and animal trypanosomiasis, are transmitted between mammals by tsetse flies. Periodic changes in variant surface glycoproteins (VSG), which form the parasite coat in the mammal, allow them to evade the host immune response. Different isolates of T. brucei show heterogeneity in their repertoires of VSG genes and have single nucleotide polymorphisms and indels that can impact on genome editing. T. brucei brucei EATRO1125 (AnTaR1 serodeme) is an isolate that is used increasingly often because it is pleomorphic in mammals and fly transmissible, two characteristics that have been lost by the most commonly used laboratory stocks. We present a genome assembly of EATRO1125, including contigs for the intermediate and mini-chromosomes that serve as repositories of VSG genes. In addition, de novo transcriptome assemblies were performed using Illumina sequences from tsetse-derived trypanosomes. Reads of 150 bases enabled closely related members of multigene families to be discriminated. This revealed that the transcriptome of midgut-derived parasites is dynamic, starting with the expression of high affinity hexose transporters and glycolytic enzymes and then switching to proline uptake and catabolism. These changes resemble the transition from early to late procyclic forms in culture. Further metabolic reprogramming, including upregulation of tricarboxylic acid cycle enzymes, occurs in the proventriculus. Many transcripts upregulated in the salivary glands encode surface proteins, among them 7 metacyclic VSGs, multiple BARPs and GCS1/HAP2, a marker for gametes. A novel family of transmembrane proteins, containing polythreonine stretches that are predicted to be O-glycosylation sites, was also identified. Finally, RNA-Seq data were used to create an optimised annotation file with 5 and 3 untranslated regions accurately mapped for 9302 genes. We anticipate that this will be of use in identifying transcripts obtained by single cell sequencing technologies. AUTHOR SUMMARYTrypanosoma brucei ssp. are single-celled parasites that cause two tropical diseases: sleeping sickness in humans and nagana in domestic animals. Parasites survive in the host bloodstream because they periodically change their surface coats and also because they can switch from slender dividing forms to stumpy non-dividing forms. The latter can be transmitted to their second host, the tsetse fly. Although closely related, different geographical isolates differ in their repertoire of surface coats and have small, but important differences in their DNA sequences. In addition, laboratory strains that are transferred between mammals by needle passage lose the ability to produce stumpy forms and to infect flies. The isolate T. b. brucei EATRO1125 is often used for research as it produces stumpy forms and is fly transmissible. We provide an assembly of the genome of this isolate, including part of the repertoire of coat proteins, and a detailed analysis of the genes that the parasites express as they establish infection and progress through the fly. This has provided new insights into trypanosome biology. The combined genomic (DNA) and transcriptomic (RNA) data will be useful resources for the trypanosome research community.

microbiology↗

A measles-vectored COVID-19 vaccine induces long-term immunity and protection from SARS-CoV-2 challenge in mice

In light of the expanding SARS-CoV-2 pandemic, developing efficient vaccines that can provide sufficient coverage for the world population is a global health priority. The measles virus (MV)-vectored vaccine is an attractive candidate given the measles vaccines extensive safety history, well-established manufacturing process, and induction of strong, long-lasting immunity. We developed an MV-based SARS-CoV-2 vaccine using either the full-length spike (S) or S2 subunit as the antigen. While the S2 antigen failed to induce neutralizing antibodies, the prefusion-stabilized, full-length S (MV-ATU2-SF-2P-dER) construct proved to be an attractive vaccine candidate, eliciting strong Th1-dominant T-cell and neutralizing antibody responses against the S antigen while minimizing reactivity to the vector itself. Neutralizing antibody titers remained high three months after homologous prime-boost immunization, and infectious virus was undetectable in all animals after challenge with a mouse-adapted SARS-CoV-2 virus.

immunology↗

The dimerisable Cre recombinase allows conditional genome editing in the mosquito stages of Plasmodium berghei

Asexual blood stages of the malaria parasite are readily amenable to genetic modification via homologous recombination, allowing functional studies of parasite genes that are not essential in this part of the life cycle. However, conventional reverse genetics cannot be applied for the functional analysis of genes that are essential during asexual blood-stage replication. Various strategies have been developed for conditional mutagenesis of Plasmodium, including recombinase-based gene deletion, regulatable promoters, and mRNA or protein destabilization systems. Among these, the dimerisable Cre (DiCre) recombinase system has emerged as a powerful approach for conditional gene targeting in P. falciparum. In this system, the bacteriophage Cre is expressed in the form of two separate, enzymatically inactive polypeptides, each fused to a different rapamycin-binding protein. Rapamycin-induced heterodimerization of the two components restores recombinase activity. We have implemented the DiCre system in the rodent malaria parasite P. berghei, and show that rapamycin-induced excision of floxed DNA sequences can be achieved with very high efficiency in both mammalian and mosquito parasite stages. This tool can be used to investigate the function of essential genes not only in asexual blood stages, but also in other parts of the malaria parasite life cycle.

microbiology↗

FANCD2 tunes the UPR preventing mitochondrial stress-induced common fragile site instability.

Common fragile sites (CFSs) are genomic regions frequently involved in cancer-associated rearrangements. Most CFSs lie within large genes, and their instability relies on transcription- and replication-dependent mechanisms. Here, we uncover a role for the UBL5-dependent branch of the unfolded protein response pathway (UPR) in the maintenance of CFS stability. We show that genetic or pharmacological UPR activation induces CFS gene expression and concomitant relocalization of FANCD2, a master regulator of CFS stability, to CFSs. Furthermore, a genomic analysis of FANCD2 binding sites identified an enrichment for mitochondrial UPR transcriptional response elements in FANCD2 bound regions. We demonstrated that depletion of FANCD2 increases CFS gene transcription and their instability while also inducing mitochondrial dysfunction and triggering the activation of the UPR pathway. Depletion of UBL5, a mediator of the UPR, but not ATF4, reduces CFS gene expression and breakage in FANCD2-depleted cells. We thus demonstrate that FANCD2 recruitment and function at CFSs depends on transcription and UPR signaling, and in absence of transcription or UBL5, FANCD2 is dispensable for CFS stability. We propose that FANCD2 coordinates nuclear and mitochondrial activities by tuning the UPR to prevent genome instability.

cell biology↗