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Fonseca, A.

Publications and source records attributed to Fonseca, A..

15 recordsLinked to original sources

Infauna selectively enhance DNA virus diversity and activity in marine sediments

Viruses regulate microbial mortality and biogeochemical cycling in marine sediments; however, the ecological drivers of sediment viral communities remain unclear. Infauna, including sediment-dwelling meiofauna and macrofauna, are major ecosystem engineers that reshape sediment structures and microbial processes, but their influence on viruses is unknown. We combined infaunal gradient incubations with metagenomic and metatranscriptomic analyses to assess viral DNA and RNA responses. DNA viruses showed increased abundance (3-fold), diversity, richness, and transcriptional activity under higher infauna abundance conditions, whereas RNA viruses remained unaffected, revealing striking selectivity. This selectivity reflects an infauna-dependent component mediated by bacterial activity that cannot be explained by host abundance alone. Infection profiling revealed increased transcription of viral replication and structural genes, and lytic viruses under high infauna conditions. These findings establish infauna as a previously overlooked regulator of DNA virus dynamics, integrating viral ecology into faunal-microbial frameworks in benthic ecosystems and suggesting potential influences on geochemical cycles. TeaserInfauna selectively shape viral communities in marine sediments, revealing an overlooked effect on DNA viruses.

microbiology↗

Metabarcoding reveals that bacterial and fungal microbiomes are perturbed by micropollutants in a fjord system (Hakefjorden and Askerofjorden) at the Swedish west coast

Fjord systems are susceptible to anthropogenic pressures, including discharges from wastewater treatment plants (WWTPs), which introduce micropollutants into coastal waters. We investigated the impact of micropollutants on bacteria and fungi within a fjord system adjacent to a significant petrochemical industry hub on the Swedish west coast. We characterised microbial assemblages along a land-to-sea transect, encompassing freshwater streams receiving agricultural and urban runoff, as well as the direct effluent from a WWTP. Our findings revealed elevated concentrations and a diverse array of micropollutants in the WWTP effluent and the stream running through the urban/industrial zone, highlighting these areas as major sources of pollution to the fjord. Bacterial and fungal communities inhabiting the WWTP effluent and the receiving marine waters near the marine outflow exhibited distinct structural compositions, indicating a selective pressure exerted in part by the micropollutant load. While freshwater sites generally displayed higher overall microbial diversity compared to marine sites, the WWTP effluent showed reduced diversity in both bacterial and fungal communities, likely due to the impact of micropollutants. Interestingly, marine sites far from the WWTP discharges exhibited a recovery in bacterial diversity, suggesting a potential response or adaptation. In contrast, fungal diversity remained comparable to that observed in other marine locations. Multivariate analyses identified physicochemical parameters and nutrients, alongside with summed fungicides and antibiotic stress as key factors driving the community dissimilarities across the fjord. Significant disruptions in potential bacterial metabolism and fungal ecological functions were evident at the WWTP discharge point, underscoring the ecological consequences of wastewater pollution. HighlightsO_LIWWTP discharge is the primary source of complex micropollutants in the fjord. C_LIO_LIAntibiotics and fungicides significantly shape bacterial and fungal communities. C_LIO_LIWastewater impacts reduce microbial diversity and disrupt functional potential. C_LIO_LIMarine sites show microbial recovery and enrichment away from discharge points. C_LIO_LIeDNA and toxic unit modeling link chemical stress to microbiome restructuring. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/711609v1_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@1751e5forg.highwire.dtl.DTLVardef@1d0d78org.highwire.dtl.DTLVardef@15f446aorg.highwire.dtl.DTLVardef@184bb0a_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

Wastewater-impacted Skagerrak Sea microbiomes anaerobically demethylate micropollutants

Methylated micropollutants such as naproxen and caffeine persist in wastewater effluents and accumulate in coastal sediments, including Hakefjorden, Skagerrak Sea, yet their anaerobic fate and role in methane emissions remain unresolved. Here we traced the fate and microbiome responses to {superscript 1}3C-labeled naproxen and caffeine in sediment microcosms. We show that naproxen underwent rapid O-demethylation to desmethylnaproxen, with 90% {+/-} 15.5% removed within 25 days, producing primarily {superscript 1}3CO2 and some {superscript 1}3CH. Naproxen enriched methylotrophic and hydrogenotrophic Methanomicrobia, alongside Lokiarchaeia, Bathyarchaeia, and bacterial taxa like Eubacterium and Syntrophomonadaceae. Metagenomics revealed O-demethylation genes in enriched bacterial MAGs affiliated with uncultured Thermoanaerobaculia, indicating a bacterial demethylation potential. In contrast, caffeine was largely recalcitrant to degradation ([~]85% {+/-} 5% remaining), yet its 13C-labeled N-methyl groups fueled {superscript 1}3CH production, coinciding with enrichment of Bathyarchaeia and Methanosarcina. These results show that methylated micropollutants can activate both bacterial and archaeal demethylation pathways in coastal sediment microbiomes.

microbiology↗

Quantitative RNA spatial profiling using single-molecule RNA FISH on plant tissue cryosections

Single-molecule fluorescence in situ hybridization (smFISH) has emerged as a powerful tool to study gene expression dynamics with unparalleled precision and spatial resolution in a variety of biological systems. Recent advancements have expanded its application to encompass plant studies, yet a demand persists for a simple and robust smFISH method adapted to plant tissue sections. Here, we present an optimized smFISH protocol (cryo-smFISH) for visualizing and quantifying single mRNA molecules in plant tissue cryosections. This method exhibits remarkable sensitivity, capable of detecting low-expression transcripts, including long non-coding RNAs. Integrating a deep learning-based algorithm in our image analysis pipeline, our method enables us to assign RNA abundance precisely in nuclear and cytoplasmic compartments. Compatibility with Immunofluorescence also allows RNA and endogenous proteins to be visualized and quantified simultaneously. Finally, this study presents for the first time the use of smFISH for single-cell RNA sequencing (scRNA-seq) validation in plants. By extending the smFISH method to plant cryosections, an even broader community of plant scientists will be able to exploit the multiple potentials of quantitative transcript analysis at cellular and subcellular resolutions.

cell biology↗

Differences in RAD51 transcriptional response and cell cycle dynamics reveal varying sensitivity to DNA damage among Arabidopsis thaliana root cell types

O_LIThroughout their lifecycle, plants are subjected to DNA damage from various sources, both environmental and endogenous. Investigating the mechanisms of the DNA damage response (DDR) is essential to unravel how plants adjust to the changing environment that can elicit varying amounts of DNA damage. C_LIO_LIUsing a combination of state-of-the-art cell biology methods including whole-mount single-molecule RNA fluorescence in situ hybridization (WM-smFISH), allowing detection of individual mRNA molecules in intact plant tissue and plant cell cycle reporter lines we investigated how the transcriptional activation of a key homologous recombination (HR) gene, RAD51, occurs in response to increasing amounts of DNA damage in Arabidopsis thaliana roots. C_LIO_LIThe results uncover consistent variations in RAD51 transcriptional response and cell cycle arrest among distinct cell types and developmental zones. Furthermore, we demonstrate that DNA damage induced by genotoxic stress results in RAD51 transcription throughout the whole cell cycle, dissociating its traditional link with S/G2 phases. C_LIO_LIThis work advances the current comprehension of DNA damage response in plants showing quantitative differences in DDR activation. In addition, it reveals new associations with the cell cycle and cell types, providing crucial insights for further studies of the broader response mechanisms in plants. C_LI

plant biology↗

Regulatory T cells control type 1-driven immunopathology restraining GM-CSF-producing helper T cells

Regulatory T (Treg) cells are critical for maintaining peripheral tolerance and preventing autoimmunity. Treg cell depletion or dysfunction rapidly results in fatal multiorgan inflammation linked to unrestrained effector T cell expansion, but the cytokine network underlying immunopathology, and its direct cellular mediators, remain elusive. Here, we combined gene targeting, fate-mapping tools, and high-dimensional cytometry to identify the T helper (TH) cell-derived cytokines and responding cells that execute inflammatory tissue damage upon global loss of peripheral tolerance in mice. We found that TH cell-derived GM-CSF, but not IL-17A, directed the ensuing immunopathology and thereby mortality through recruitment of tissue-invading phagocytes and granulocytes, and enhancement of their reactive oxygen species production and phagocytic proficiency. Our study highlights the critical role of Treg cells in controlling GM-CSF- producing TH cells and type 1-responses to restrain phagocyte-mediated tissue destruction and provides a framework for the use of anti-GM-CSF therapies in patients with chronic inflammatory disorders.

immunology↗

Cell2Sentence: Teaching Large Language Models the Language of Biology

We introduce Cell2Sentence (C2S), a novel method to directly adapt large language models to a biological context, specifically single-cell transcriptomics. By transforming gene expression data into "cell sentences," C2S bridges the gap between natural language processing and biology. We demonstrate cell sentences enable the fine-tuning of language models for diverse tasks in biology, including cell generation, complex cell-type annotation, and direct data-driven text generation. Our experiments reveal that GPT-2, when fine-tuned with C2S, can generate biologically valid cells based on cell type inputs, and accurately predict cell types from cell sentences. This illustrates that language models, through C2S fine-tuning, can acquire a significant understanding of single-cell biology while maintaining robust text generation capabilities. C2S offers a flexible, accessible framework to integrate natural language processing with transcriptomics, utilizing existing models and libraries for a wide range of biological applications.

bioinformatics↗

A Living Organoid Biobank of Crohn's Disease Patients Reveals Molecular Subtypes for Personalized Therapeutics

ABSTRACT (Structured)Crohns disease (CD) is a complex, clinically heterogeneous disease of multifactorial origin; there is no perfect pre-clinical model, little insight into the basis for such heterogeneity, and still no cure. To address these unmet needs, we sought to explore the translational potential of adult stem cell-derived organoids that not only retain their tissue identity, but also their genetic and epigenetic disease-driving traits. We prospectively created a biobank of CD patient-derived organoid cultures (PDOs) using biopsied tissues from colons of 34 consecutive subjects representing all clinical subtypes (Montreal Classification B1-B3 and perianal disease). PDOs were generated also from healthy subjects. Comparative gene expression analyses enabled benchmarking of PDOs as tools for modeling the colonic epithelium in active disease and revealed that despite the clinical heterogeneity there are two major molecular subtypes: immune-deficient infectious-CD [IDICD] and stress and senescence-induced fibrostenotic-CD [S2FCD]. The transcriptome, genome and phenome show a surprising degree of internal consistency within each molecular subtype. The spectrum of morphometric, phenotypic, and functional changes within the "living biobank" reveals distinct differences between the molecular subtypes. These insights enabled drug screens that reversed subtype-specific phenotypes, e.g., impaired microbial clearance in IDICD was reversed using agonists for nuclear receptors, and senescence in S2FCD was rectified using senotherapeutics, but not vice versa. Phenotyped-genotyped CD-PDOs may fill the gap between basic biology and patient trials by enabling pre-clinical Phase 0 human trials for personalized therapeutics. GRAPHIC ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/532245v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@1edcea0org.highwire.dtl.DTLVardef@198a3c8org.highwire.dtl.DTLVardef@28d394org.highwire.dtl.DTLVardef@5a9dbb_HPS_FORMAT_FIGEXP M_FIG C_FIG In BriefThis work creates a prospectively biobanked phenotyped-genotyped Crohns disease patient-derived organoids (CD-PDOs) as platforms for molecular subtyping of disease and for ushering personalized therapeutics. HIGHLIGHTSO_LIProspectively biobanked CD-organoids recapitulate the disease epithelium in patients C_LIO_LIThe phenome-transcriptome-genome of CD-organoids converge on two molecular subtypes C_LIO_LIOne subtype shows impaired microbial clearance, another increased cellular senescence C_LIO_LIPhenotyped-genotyped PDOs are then used for integrative and personalized therapeutics C_LI

immunology↗

Computational prediction of human deep intronic variation

The adoption of whole genome sequencing in genetic screens has facilitated the detection of genetic variation in the intronic regions of genes, far from annotated splice sites. However, selecting an appropriate computational tool to differentiate functionally relevant genetic variants from those with no effect is challenging, particularly for deep intronic regions where independent benchmarks are scarce. In this study, we have provided an overview of the computational methods available and the extent to which they can be used to analyze deep intronic variation. We leveraged diverse datasets to extensively evaluate tool performance across different intronic regions, distinguishing between variants that are expected to disrupt splicing through different molecular mechanisms. Notably, we compared the performance of SpliceAI, a widely used sequence-based deep learning model, with that of more recent methods that extend its original implementation. We observed considerable differences in tool performance depending on the region considered, with variants generating cryptic splice sites being better predicted than those that affect splicing regulatory elements or the branchpoint region. Finally, we devised a novel quantitative assessment of tool interpretability and found that tools providing mechanistic explanations of their predictions are often correct with respect to the ground truth information, but the use of these tools results in decreased predictive power when compared to black box methods. Our findings translate into practical recommendations for tool usage and provide a reference framework for applying prediction tools in deep intronic regions, enabling more informed decision-making by practitioners.

bioinformatics↗

Whole-mount smFISH allows combining RNA and protein quantification at cellular and subcellular resolution

Multicellular organisms result from complex developmental processes largely orchestrated through the quantitative spatiotemporal regulation of gene expression. Yet, obtaining absolute counts of mRNAs at a 3-dimensional resolution remains challenging, especially in plants, due to high levels of tissue autofluorescence that prevent the detection of diffraction-limited fluorescent spots. In situ hybridization methods based on amplification cycles have recently emerged, but they are laborious and often lead to quantification biases. In this article, we present a simple method based on single molecule RNA fluorescence in situ hybridization (smFISH) to visualize and count the number of mRNA molecules in several intact plant tissues. In addition, with the use of fluorescent protein reporters, our method also enables simultaneous detection of mRNA and protein quantity, as well as subcellular distribution, in single cells. With this method, research in plants can now fully explore the benefits of the quantitative analysis of transcription and protein levels at cellular and subcellular resolution in plant tissues.

cell biology↗

Dynamic changes in mRNA nucleocytoplasmic localization in the nitrate response of Arabidopsis roots

Nitrate (NO3-) is a signaling molecule that regulates gene expression in plants. The nitrate response has been extensively characterized at the transcriptome level. However, we know little about RNA nucleocytoplasmic dynamics during nitrate response. To understand the role of mRNA localization during the nitrate response, we isolated mRNA from the nucleus, cytoplasm, and whole-cells from nitrate-treated Arabidopsis roots and performed RNA-seq. We identified 402 differentially localized transcripts (DLTs) in response to nitrate. DLTs were enriched in GO-terms related to metabolism, response to stimulus, and transport. DLTs showed five localization patterns: nuclear reduction, cytoplasmic reduction, nuclear accumulation, cytoplasmic accumulation, or delayed-cytoplasmic accumulation in response to nitrate. DLTs exhibited large changes in RNA polymerase II occupancy of cognate genes and high mRNA turnover rates, indicating these are rapidly replaced mRNAs. The NITRATE REDUCTASE 1 (NIA1) transcript exhibited the largest changes in synthesis and decay. Using single-molecule RNA FISH, we showed that NIA1 nuclear accumulation occurs mainly at transcription sites. The decay profiles for NIA1 showed a higher half-life when the transcript accumulated in the nucleus than in the cytoplasm. We propose that regulating nucleocytoplasmic mRNA distribution allows tuning transcript availability of fastly replaced mRNAs, controlling plants adaptive response to nitrogen nutrient signals.

molecular biology↗

Adult Stem Cell-derived Complete Lung Organoid Models Emulate Lung Disease in COVID-19

SARS-CoV-2, the virus responsible for COVID-19, causes widespread damage in the lungs in the setting of an overzealous immune response whose origin remains unclear. We present a scalable, propagable, personalized, cost-effective adult stem cell-derived human lung organoid model that is complete with both proximal and distal airway epithelia. Monolayers derived from adult lung organoids (ALOs), primary airway cells, or hiPSC-derived alveolar type-II (AT2) pneumocytes were infected with SARS-CoV-2 to create in vitro lung models of COVID-19. Infected ALO-monolayers best recapitulated the transcriptomic signatures in diverse cohorts of COVID-19 patient-derived respiratory samples. The airway (proximal) cells were critical for sustained viral infection, whereas distal alveolar differentiation (AT2[->]AT1) was critical for mounting the overzealous host immune response in fatal disease; ALO monolayers with well-mixed proximodistal airway components recapitulated both. Findings validate a human lung model of COVID-19, which can be immediately utilized to investigate COVID-19 pathogenesis and vet new therapies and vaccines. GRAPHIC ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=176 SRC="FIGDIR/small/344002v4_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@1d1507aorg.highwire.dtl.DTLVardef@faa17forg.highwire.dtl.DTLVardef@80ceb1org.highwire.dtl.DTLVardef@81d61c_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIHuman lung organoids with mixed proximodistal epithelia are created C_LIO_LIProximal airway cells are critical for viral infectivity C_LIO_LIDistal alveolar cells are important for emulating host response C_LIO_LIBoth are required for the overzealous response in severe COVID-19 C_LI IN BRIEFAn integrated stem cell-based disease modeling and computational approach demonstrate how both proximal airway epithelium is critical for SARS-CoV-2 infectivity, but distal differentiation of alveolar pneumocytes is critical for simulating the overzealous host response in fatal COVID-19.

cell biology↗

E-cigarettes compromise the gut barrier and trigger gut inflammation

E-cigarette and vaping device use continue to rise, particularly in adolescents and young adults, but the safety of inhaling the multitude of chemicals within e-cigarette aerosols has been questioned. While several studies have evaluated vaping effects on the lungs and heart; effects on the gastrointestinal tract remain unknown. Using established murine models of acute (1 week) and chronic (3 month) daily e-cigarette aerosol inhalation, both with nicotine-containing and vehicle control e-liquids, murine colon transcriptomics and organoid co-culture models, we assessed the effects of e-cigarette use on the gut barrier and mucosal health. Histologic analyses revealed that chronic exposure to nicotine-free e-cigarette aerosols induced mucosal inflammation. Transcriptome analyses revealed that chronic, but not acute, nicotine-free e-cigarette use significantly reduced expression of tight junction markers, including occluding, and drove expression of pro-inflammatory cytokines. Exposure of murine and human enteroid-derived monolayers (EDMs) to nicotine-free e-cigarette aerosols alone, or in co-culture with invasive E. coli, confirmed that repetitive exposure was sufficient to recapitulate the key findings observed in vivo, i.e., barrier-disruption, downregulation of occludin, inflammation, and an accentuated risk of and response to bacterial infection. These data highlight an unexpected harmful effect of e-cigarette use on the gut barrier and pinpoint non-nicotine chemical components common across >90% of e-cigarette e-liquids as the source of harm. Given the ever-expanding importance of the integrity of the gut barrier for host fitness, and impact of gut mucosal inflammation on a multitude of chronic diseases, these findings are broadly relevant to medicine and public health. SIGNIFICANCEThe safety of electronic cigarettes has been questioned amidst emerging evidence that they may derail our immune system and increase our susceptibility to infections. Despite these insights, their impact on the most critical entity that separates trillions of microbes from the largest immune system in our body, i.e., the gut barrier, remains unexplored. Using a combination of mouse models, gut transcriptomics, and murine and human gut-derived organoids, here we show that chronic exposure to aerosols of electronic-cigarette disrupts the gut barrier, increases its susceptibility to bacterial infections and triggers inflammation. Given the importance of the gut barrier in the maintenance of immune homeostasis, these findings provide valuable insights into the potential long-term harmful effects of electronic cigarettes on health.

immunology↗

Transcription factor TGA2 is essential for UV-B stress tolerance controlling oxidative stress in Arabidopsis

Plants possess a diversity of Reactive Oxygen Species (ROS)-processing enzymes involved in sensing and controlling ROS levels under basal and stressful conditions. There is little information on the transcriptional regulators that control the expression of these ROS-processing enzymes, particularly at the onset of the defense response to abiotic stress. Filling this gap, this paper reports a critical role for Arabidopsis TGA class II factors (TGA2, TGA5, and TGA6) in the tolerance response to UV-B light and photooxidative stress, by activating the expression of genes with antioxidative roles. We identified two clusters of genes responsive to UV-B and activated by TGA2/5/6 were identified using RNAseq and clustering analysis. The GSTU gene family, which encodes glutathione transferase enzymes from the Tau subclass, was overrepresented in these clusters. We corroborated the TGA2-mediated activation in response to UV-B for three model genes (GSTU7, GSTU8, and GSTU25) using RT-qPCR and ChIP analyses. Interestingly, using tga256 mutant and TGA2- and GSTU7-complemented mutant plants, we demonstrated that TGA2-mediated induction of GSTU genes is essential to control ROS levels and oxidative damage after UV-B and MeV treatments. This evidence positions TGA class II factors, particularly TGA2, as a key players in the redox signaling network of Arabidopsis plants. HighlightArabidopsis TGA2 transcription factor is part of the redox-signaling network controlling ROS levels and oxidative damage in tolerance response to UV-B and photooxidative stress, via activation of antioxidant GSTU genes.

plant biology↗

Postdoc X-ray in Europe 2017: work conditions, productivity, institutional support and career outlooks

1.Executive SummaryThis survey and data analysis were conducted by the European Network of Postdoctoral Associations (ENPA) with the aim of assessing the current research and work conditions, aspirations and support received by postdoctoral researchers working in Europe. The Results section is structured into three main parts. The first one describes the study sample of European postdoctoral researchers, including participants demographics, funding sources and income, research outputs, and teaching opportunities. The second section focuses on their professional aspirations and institutional support provided. The third part describes the level of engagement of postdoctoral researchers and their institutions in working towards better research conditions and career development, and what initiatives are emerging within this community. Our Conclusions section pulls together this comprehensive analysis, highlighting some of the most concerning issues currently affecting postdoctoral researchers in Europe. We also make a number of recommendations that would significantly improve the career expectations and aspirations of postdoctoral researchers. These are listed below. Conclusions and recommendationsO_LILonger postdoctoral periods in Southern Europe despite higher publication metrics Recommendation Institutions in Southern Europe should develop clear criteria to support postdoctoral researchers career progression. C_LIO_LISouthern and Eastern Europe pay the lowest salaries and have the lowest number of foreign postdoctoral researchers Recommendation The salary differences across European countries should be addressed as this could be a barrier to mobility and knowledge exchange from higher to lower pay regions. C_LIO_LILack of access to funding is a significant concern of postdoctoral researchers Recommendation Discrepancies in access to funding should be minimized across the different European areas. C_LIO_LIPostdoctoral researchers in Europe work longer hours than required by contract Recommendation The culture of overwork in the research environment should be addressed in order to protect researchers against the risks associated with long hours at work. C_LIO_LIThe majority of full-time postdoctoral work contracts includes an exclusivity clause Recommendation Inclusion of exclusivity clauses in contracts for postdoctoral researchers should be optional in order to allow them to enhance their employability outside academia. C_LIO_LIPostdoctoral researchers career development is poorly supported by their institutions Recommendation Postdoctoral researchers career prospects and career management should be much more supported by institutions in coordination with postdoctoral associations. C_LIO_LILack of postdoctoral representation in governance is linked to unclear institutional duties and rights Recommendation Institutional governance bodies should include postdoctoral researcher representatives. This would ensure that the views of this vital staff group are heard, as well as making postdoctoral researchers feel more engaged with their own institutions. A flexible and proactive communication strategy at the institution and research group level should be developed, taking into account the sometimes transient nature of postdoctoral researchers posts. C_LIO_LIResearchers show higher engagement with their local postdoctoral associations than with workers unions Recommendation Postdoctoral associations are an essential way to advocate for postdoctoral researchers at the governance level. Institutions should engage with, promote and support the work of postdoctoral associations. C_LI

scientific communication and education↗