Rewiring of the epigenome and chromatin architecture by exogenously induced retinoic acid signaling during zebrafish embryonic development.

Retinoic acid (RA) is the ligand of RA receptors (RARs), transcription factors that bind to RA response elements. RA signaling is required for multiple processes during embryonic development, including body axis extension, hindbrain antero-posterior patterning and forelimb bud initiation. Although some RA target genes have been identified, little is known about the genome-wide effects of RA signaling during in vivo embryonic development. Here, we stimulate the RA pathway by treating zebrafish embryos with all-trans-RA (atRA) and use a combination of RNA-seq, ATAC-seq, ChIP-seq and HiChIP to gain insight into the molecular mechanisms by which exogenously induced RA signaling controls gene expression. We find that RA signaling is involved in anterior/posterior patterning, central nervous system development, and the transition from pluripotency to differentiation. AtRA treatment also alters chromatin accessibility during early development and promotes chromatin binding of RARαa and the RA targets Hoxb1b, Meis2b and Sox3, which cooperate in central nervous system development. Finally, we show that exogenous RA induces a rewiring of chromatin architecture, with alterations in chromatin 3D interactions involving target genes. Altogether, our findings identify genome-wide targets of RA signaling and provide a molecular mechanism by which developmental signaling pathways regulate target gene expression by altering chromatin topology.

Optical pH Sensor Based on a Long-Period Fiber Grating Coated with a Polymeric Layer-by-Layer Electrostatic Self-Assembled Nanofilm.

An optical fiber pH sensor based on a long-period fiber grating (LPFG) is reported. Two oppositely charged polymers, polyethylenimine (PEI) and polyacrylic acid (PAA), were alternately deposited on the sensing structure through a layer-by-layer (LbL) electrostatic self-assembly technique. Since the polymers are pH sensitive, their refractive index (RI) varies when the pH of the solution changes due to swelling/deswelling phenomena. The fabricated multilayer coating retained a similar property, enabling its use in pH-sensing applications. The pH of the PAA dipping solution was tuned so that a coated LPFG achieved a pH sensitivity of (6.3 ± 0.2) nm/pH in the 5.92-9.23 pH range. Only two bilayers of PEI/PAA were used as an overlay, which reduces the fabrication time and increases the reproducibility of the sensor, and its reversibility and repeatability were demonstrated by tracking the resonance band position throughout multiple cycles between different pH solutions. With simulation work and experimental results from a low-finesse Fabry-Perot (FP) cavity on a fiber tip, the coating properties were estimated. When saturated at low pH, it has a thickness of 200 nm and 1.53 ± 0.01 RI, expanding up to 310 nm with a 1.35 ± 0.01 RI at higher pH values, mostly due to the structural changes in the PAA.

Wild, tamed, and domesticated: Three fire macroregimes for global pyrogeography in the Anthropocene.

Climate and natural vegetation dynamics are key drivers of global vegetation fire, but anthropogenic burning now prevails over vast areas of the planet. Fire regime classification and mapping may contribute towards improved understanding of relationships between those fire drivers. We used 15 years of daily active fire data from the MODIS fire product (MCD14ML, collection 6) to create global maps of six fire descriptors (incidence, size inequality, season length, interannual variability, intensity, and fire season modality). Using multiple correspondence analysis (MCA) and hierarchical agglomerative clustering, we identified three fire macroregimes: Wild, Tamed, and Domesticated, each of which splitting into prototypical and transitional regimes. Interpretation of the six fire regimes in terms of their main drivers relied on the global maps of anthromes and Köppen climate types. The analysis yielded a two-dimensional space where the principal dimension of variability is primarily defined by interannual variability in fire activity and fire season length, and the secondary axis is based mainly on fire incidence. The Wild fire macroregime occurs mostly in cold wildlands, where burning is sporadic and fire seasons are short. Tamed fires predominate in seasonally dry tropical rangelands and croplands with high fire incidence. Domesticated fires are characteristic of humid, warm temperate and tropical croplands and villages with low fire incidence. The Tamed and Domesticated fire macroregimes, representing managed burning, account for 86% of all active fires in our dataset and for 70% of the global burnable area. Fourteen percent of active fires were found in the cold wildlands, and in the rangelands and forests of steppe and desert climates of the Wild macroregime. These results highlight the extent of human control over global pyrogeography in the Anthropocene.

Evaluating priority locations and potential benefits for building a nation-wide fuel break network in Portugal.

Despite growing interest in developing extensive fuel treatment programs to prevent catastrophic wildfires in the Mediterranean region, there is little information on the projected effectiveness of fuel treatments in terms of avoided exposure and risk. In Portugal, a fuel management plan aiming to prevent loss of lives, reduce large fires (>500 ha), and reduce annual burned area is under implementation, with particular emphasis on the nation-wide fuel break network (FBN). In this study, we evaluated the effectiveness of the planned FBN in terms of meeting fire management objectives, costs, and benefits. We first estimated the overall effectiveness of the FBN at intersecting modeled large fires (>500 ha) and at reducing exposure to protected areas and residential buildings using wildfire simulation modeling. Then, the fuel break burn-over percentage, i.e. the percentage of fires that are not contained at the FBN, was modeled as a function of pre-defined flame length thresholds for individual FBN segments. For the planned FBN, the results suggested a potential reduction of up to 13% in the annual burned area due to large fires (ca. 13,000 ha), of up to 8% in the annual number of residential buildings exposed (ca. 100 residential buildings), and up to 14% in the annual burned area in protected areas (ca. 2400 ha). The expected burn-over percentage was highly variable among the segments in response to estimated fire intensity, and an average decrease of 40% of the total benefits was estimated. The most important fuel breaks typically showed a higher percentage of fire burn-over, and hence reduction in effectiveness. We also showed that the current implementation of FBN follows a random sequence, suboptimal for all objectives. Our results suggest that additional landscape-scale fuel reduction strategies are required to meet short-term national wildfire management targets.

R loops: new modulators of genome dynamics and function.

R loops are nucleic acid structures composed of an RNA-DNA hybrid and a displaced single-stranded DNA. Recently, evidence has emerged that R loops occur more often in the genome and have greater physiological relevance, including roles in transcription and chromatin structure, than was previously predicted. Importantly, however, R loops are also a major threat to genome stability. For this reason, several DNA and RNA metabolism factors prevent R-loop formation in cells. Dysfunction of these factors causes R-loop accumulation, which leads to replication stress, genome instability, chromatin alterations or gene silencing, phenomena that are frequently associated with cancer and a number of genetic diseases. We review the current knowledge of the mechanisms controlling R loops and their putative relationship with disease.

R loops are linked to histone H3 S10 phosphorylation and chromatin condensation.

R loops are transcription byproducts that constitute a threat to genome integrity. Here we show that R loops are tightly linked to histone H3 S10 phosphorylation (H3S10P), a mark of chromatin condensation. Chromatin immunoprecipitation (ChIP)-on-chip (ChIP-chip) analyses reveal H3S10P accumulation at centromeres, pericentromeric chromatin, and a large number of active open reading frames (ORFs) in R-loop-accumulating yeast cells, better observed in G1. Histone H3S10 plays a key role in maintaining genome stability, as scored by ectopic recombination and plasmid loss, Rad52 foci, and Rad53 checkpoint activation. H3S10P coincides with the presence of DNA-RNA hybrids, is suppressed by ribonuclease H overexpression, and causes reduced accessibility of restriction endonucleases, implying a tight connection between R loops, H3S10P, and chromatin compaction. Such histone modifications were also observed in R-loop-accumulating Caenorhabditis elegans and HeLa cells. We therefore provide a role of RNA in chromatin structure essential to understand how R loops modulate genome dynamics.

The Nup84 complex coordinates the DNA damage response to warrant genome integrity.

DNA lesions interfere with cellular processes such as transcription and replication and need to be adequately resolved to warrant genome integrity. Beyond their primary role in molecule transport, nuclear pore complexes (NPCs) function in other processes such as transcription, nuclear organization and DNA double strand break (DSB) repair. Here we found that the removal of UV-induced DNA lesions by nucleotide excision repair (NER) is compromised in the absence of the Nup84 nuclear pore component. Importantly, nup84Δ cells show an exacerbated sensitivity to UV in early S phase and delayed replication fork progression, suggesting that unrepaired spontaneous DNA lesions persist during S phase. In addition, nup84Δ cells are defective in the repair of replication-born DSBs by sister chromatid recombination (SCR) and rely on post-replicative repair functions for normal proliferation, indicating dysfunctions in the cellular pathways that enable replication on damaged DNA templates. Altogether, our data reveal a central role of the NPC in the DNA damage response to facilitate replication progression through damaged DNA templates by promoting efficient NER and SCR and preventing chromosomal rearrangements.

The Npl3 hnRNP prevents R-loop-mediated transcription-replication conflicts and genome instability.

Transcription is a major obstacle for replication fork (RF) progression and a cause of genome instability. Part of this instability is mediated by cotranscriptional R loops, which are believed to increase by suboptimal assembly of the nascent messenger ribonucleoprotein particle (mRNP). However, no clear evidence exists that heterogeneous nuclear RNPs (hnRNPs), the basic mRNP components, prevent R-loop stabilization. Here we show that yeast Npl3, the most abundant RNA-binding hnRNP, prevents R-loop-mediated genome instability. npl3Δ cells show transcription-dependent and R-loop-dependent hyperrecombination and genome-wide replication obstacles as determined by accumulation of the Rrm3 helicase. Such obstacles preferentially occur at long and highly expressed genes, to which Npl3 is preferentially bound in wild-type cells, and are reduced by RNase H1 overexpression. The resulting replication stress confers hypersensitivity to double-strand break-inducing agents. Therefore, our work demonstrates that mRNP factors are critical for genome integrity and opens the option of using them as therapeutic targets in anti-cancer treatment.

Putting fire on the map of Brazilian savanna ecoregions.

The Brazilian savanna (Cerrado) is considered the most floristically diverse savanna in the world, home to more than seven thousand species. The region is a mosaic of savannas, grasslands and forests whose unique biophysical and landscape attributes are on the basis of a recent ecoregional map, paving the way to improved region-based strategies for land management actions. However, as a fire-prone ecosystem, Cerrado owes much of its distribution and ecological properties to the fire regime and contributes to an important parcel of South America burned area. Accordingly, any attempt to use ecoregion geography as a guide for management strategies should take fire into account, as an essential variable. The main aim of this study is to complement the ecoregional map of the Cerrado with information related to the fire component. Using remotely sensed information, we identify patterns and trends of fire frequency, intensity, seasonality, extent and scar size, and combine this information for each ecoregion, relying on a simple classification that summarizes the main fire characteristics over the last two decades. Results show a marked north-south fire activity gradient, with increased contributions from MATOPIBA, the latest agricultural frontier. Five ecoregions alone account for two thirds of yearly burned area. More intense fires are found in the Arc of Deforestation and eastern ecoregions, while ecoregions in MATOPIBA display decreasing fire intensity. An innovative analysis of fire scars stratified by size class shows that infrequent large fires are responsible for the majority of burned area. These large fires display positive trends over many ecoregions, whereas smaller fires, albeit more frequent, have been decreasing in number. The final fire classification scheme shows well defined spatially-aggregated groups, where trends are found to be the key factor to evaluate fire within their regional contexts. Results presented here provide new insights to improve fire management strategies under a changing climate.

Novel Antiretroviral Therapeutic Strategies for HIV.

When the first cases of HIV infection appeared in the 1980s, AIDS was a deadly disease without any therapeutic alternatives. Currently, there is still no cure for most cases mainly due to the multiple tissues that act as a reservoir for this virus besides the high viral mutagenesis that leads to an antiretroviral drug resistance. Throughout the years, multiple drugs with specific mechanisms of action on distinct targets have been approved. In this review, the most recent phase III clinical studies and other research therapies as advanced antiretroviral nanodelivery systems will be here discussed. Although the combined antiretroviral therapy is effective in reducing viral loading to undetectable levels, it also presents some disadvantages, such as usual side effects, high frequency of administration, and the possibility of drug resistance. Therefore, several new drugs, delivery systems, and vaccines have been tested in pre-clinical and clinical trials. Regarding drug delivery, an attempt to change the route of administration of some conventional antiretrovirals has proven to be successful and surpassed some issues related to patient compliance. Nanotechnology has brought a new approach to overcoming certain obstacles of formulation design including drug solubility and biodistribution. Overall, the encapsulation of antiretroviral drugs into nanosystems has shown improved drug release and pharmacokinetic profile.

Biomarkers of fungal lung infection.

PURPOSE OF REVIEW: The incidence of lung fungal infections, namely invasive pulmonary aspergillosis (IPA) and mucormycosis, is increasing in neutropenic and nonneutropenic patients. As they are a major cause of death, early diagnosis and antifungal therapy are crucial for outcome. The role of biomarkers in the management of this infections is the scope of this review. RECENT FINDINGS: Galactomannan in bronchoalveolar lavage shows the best discriminatory power for IPA diagnosis. At baseline, serum galactomannan may be useful to predict outcome and its kinetics may be informative to assess response to antifungal therapy. Recent standardization of PCR technology brought some improvements in IPA and mucormycosis diagnosis. Several new biomarkers are currently under investigation, but none showed a better performance than current available biomarkers. To improve diagnostic accuracy, a combination of biomarkers, including galactomannan, has been proposed. SUMMARY: Biomarkers may play an important role in the early diagnosis of fungal lung infections and in prognostic assessment and response monitoring, but more research is needed to determine the best strategy for their clinical use.

Excess of Yra1 RNA-Binding Factor Causes Transcription-Dependent Genome Instability, Replication Impairment and Telomere Shortening.

Yra1 is an essential nuclear factor of the evolutionarily conserved family of hnRNP-like export factors that when overexpressed impairs mRNA export and cell growth. To investigate further the relevance of proper Yra1 stoichiometry in the cell, we overexpressed Yra1 by transforming yeast cells with YRA1 intron-less constructs and analyzed its effect on gene expression and genome integrity. We found that YRA1 overexpression induces DNA damage and leads to a transcription-associated hyperrecombination phenotype that is mediated by RNA:DNA hybrids. In addition, it confers a genome-wide replication retardation as seen by reduced BrdU incorporation and accumulation of the Rrm3 helicase. In addition, YRA1 overexpression causes a cell senescence-like phenotype and telomere shortening. ChIP-chip analysis shows that overexpressed Yra1 is loaded to transcribed chromatin along the genome and to Y' telomeric regions, where Rrm3 is also accumulated, suggesting an impairment of telomere replication. Our work not only demonstrates that a proper stoichiometry of the Yra1 mRNA binding and export factor is required to maintain genome integrity and telomere homeostasis, but suggests that the cellular imbalance between transcribed RNA and specific RNA-binding factors may become a major cause of genome instability mediated by co-transcriptional replication impairment.

Nebulization of Antiinfective Agents in Invasively Mechanically Ventilated Adults: A Systematic Review and Meta-analysis.

BACKGROUND: Nebulization of antiinfective agents is a common but unstandardized practice in critically ill patients. METHODS: A systematic review of 1,435 studies was performed in adults receiving invasive mechanical ventilation. Two different administration strategies (adjunctive and substitute) were considered clinically relevant. Inclusion was restricted to studies using jet, ultrasonic, and vibrating-mesh nebulizers. Studies involving children, colonized-but-not-infected adults, and cystic fibrosis patients were excluded. RESULTS: Five of the 11 studies included had a small sample size (fewer than 50 patients), and only 6 were randomized. Diversity of case-mix, dosage, and devices are sources of bias. Only a few patients had severe hypoxemia. Aminoglycosides and colistin were the most common antibiotics, being safe regarding nephrotoxicity and neurotoxicity, but increased respiratory complications in 9% (95% CI, 0.01 to 0.18; I = 52%), particularly when administered to hypoxemic patients. For tracheobronchitis, a significant decrease in emergence of resistance was evidenced (risk ratio, 0.18; 95% CI, 0.05 to 0.64; I = 0%). Similar findings were observed in pneumonia by susceptible pathogens, without improvement in mortality or ventilation duration. In pneumonia caused by resistant pathogens, higher clinical resolution (odds ratio, 1.96; 95% CI, 1.30 to 2.96; I = 0%) was evidenced. These findings were not consistently evidenced in the assessment of efficacy against pneumonia caused by susceptible pathogens. CONCLUSIONS: Performance of randomized trials evaluating the impact of nebulized antibiotics with more homogeneous populations, standardized drug delivery, predetermined clinical efficacy, and safety outcomes is urgently required. Infections by resistant pathogens might potentially have higher benefit from nebulized antiinfective agents. Nebulization, without concomitant systemic administration of the drug, may reduce nephrotoxicity but may also be associated with higher risk of respiratory complications.

A genome-wide function of THSC/TREX-2 at active genes prevents transcription-replication collisions.

The THSC/TREX-2 complex of Saccharomyces cerevisiae mediates the anchoring of transcribed genes to the nuclear pore, linking transcription elongation with mRNA export and genome stability, as shown for specific reporters. However, it is still unknown whether the function of TREX-2 is global and the reason for its relevant role in genome integrity. Here, by studying two TREX-2 representative subunits, Thp1 and Sac3, we show that TREX-2 has a genome-wide role in gene expression. Both proteins show similar distributions along the genome, with a gradient disposition at active genes that increases towards the 3' end. Thp1 and Sac3 have a relevant impact on the expression of long, G+C-rich and highly transcribed genes. Interestingly, replication impairment detected by the genome-wide accumulation of the replicative Rrm3 helicase is increased preferentially at highly expressed genes in the thp1Δ and sac3Δ mutants analyzed. Therefore, our work provides evidence of a function of TREX-2 at the genome-wide level and suggests a role for TREX-2 in preventing transcription-replication conflicts, as a source of genome instability derived from a defective messenger ribonucleoprotein particle (mRNP) biogenesis.

Enhanced Superconductivity in 2H-TaS2 Devices through in Situ Molecular Intercalation.

The intercalation of guest species into the gap of van der Waals materials often leads to the emergence of intriguing phenomena such as superconductivity. While intercalation-induced superconductivity has been reported in several bulk crystals, reaching a zero-resistance state in flakes remains challenging. Here, we show a simple method for enhancing the superconducting transition in tens-of-nanometers thick 2H-TaS2 crystals contacted by gold electrodes through in situ intercalation. Our approach enables measuring the electrical characteristics of the same flake before and after intercalation, permitting us to precisely identify the effect of the guest species on the TaS2 transport properties. We find that the intercalation of amylamine molecules into TaS2 flakes causes a suppression of the charge density wave and an increase in the superconducting transition with an onset temperature above 3 K. Additionally, we show that a fully developed zero-resistance state can be achieved in flakes by engineering the conditions of the chemical intercalation. Our findings pave the way for the integration of chemically tailored intercalation compounds in scalable quantum technologies.

Essential role of PLD2 in hypoxia-induced stemness and therapy resistance in ovarian tumors.

BACKGROUND: Hypoxia in solid tumors is an important source of chemoresistance that can determine poor patient prognosis. Such chemoresistance relies on the presence of cancer stem cells (CSCs), and hypoxia promotes their generation through transcriptional activation by HIF transcription factors. METHODS: We used ovarian cancer (OC) cell lines, xenograft models, OC patient samples, transcriptional databases, induced pluripotent stem cells (iPSCs) and Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq). RESULTS: Here, we show that hypoxia induces CSC formation and chemoresistance in ovarian cancer through transcriptional activation of the PLD2 gene. Mechanistically, HIF-1α activates PLD2 transcription through hypoxia response elements, and both hypoxia and PLD2 overexpression lead to increased accessibility around stemness genes, detected by ATAC-seq, at sites bound by AP-1 transcription factors. This in turn provokes a rewiring of stemness genes, including the overexpression of SOX2, SOX9 or NOTCH1. PLD2 overexpression also leads to decreased patient survival, enhanced tumor growth and CSC formation, and increased iPSCs reprograming, confirming its role in dedifferentiation to a stem-like phenotype. Importantly, hypoxia-induced stemness is dependent on PLD2 expression, demonstrating that PLD2 is a major determinant of de-differentiation of ovarian cancer cells to stem-like cells in hypoxic conditions. Finally, we demonstrate that high PLD2 expression increases chemoresistance to cisplatin and carboplatin treatments, both in vitro and in vivo, while its pharmacological inhibition restores sensitivity. CONCLUSIONS: Altogether, our work highlights the importance of the HIF-1α-PLD2 axis for CSC generation and chemoresistance in OC and proposes an alternative treatment for patients with high PLD2 expression.

CRISPR-RfxCas13d screening uncovers Bckdk as a post-translational regulator of the maternal-to-zygotic transition in teleosts.

The Maternal-to-Zygotic transition (MZT) is a reprograming process encompassing zygotic genome activation (ZGA) and the clearance of maternally-provided mRNAs. While some factors regulating MZT have been identified, there are thousands of maternal RNAs whose function has not been ascribed yet. Here, we have performed a proof-of-principle CRISPR-RfxCas13d maternal screening targeting mRNAs encoding protein kinases and phosphatases in zebrafish and identified Bckdk as a novel post-translational regulator of MZT. Bckdk mRNA knockdown caused epiboly defects, ZGA deregulation, H3K27ac reduction and a partial impairment of miR-430 processing. Phospho-proteomic analysis revealed that Phf10/Baf45a, a chromatin remodeling factor, is less phosphorylated upon Bckdk depletion. Further, phf10 mRNA knockdown also altered ZGA and Phf10 constitutively phosphorylated rescued the developmental defects observed after bckdk mRNA depletion. Altogether, our results demonstrate the competence of CRISPR-RfxCas13d screenings to uncover new regulators of early vertebrate development and shed light on the post-translational control of MZT mediated by protein phosphorylation.

New antifungal antibiotics.

PURPOSE OF REVIEW: The incidence of both invasive fungal infections and respiratory mould infections is increasing and they cause significant costs, morbidity and mortality. Non-Aspergillus moulds are increasing as cause of lung infections in specific populations and new problems of susceptibility and resistance are appearing. RECENT FINDINGS: The antifungal armamentarium has markedly improved in the past 10 years and some new drugs are in the pipeline. The use of these new agents is one of the drivers of the changes in fungal epidemiology. These new antifungal drugs are discussed in this article. SUMMARY: A good selection of the antifungal, taking into consideration the pathogen, the host and the pharmacokinetic/pharmacodynamics of the drug, is paramount for clinical success.

Tuning the magnetic properties of NiPS3 through organic-ion intercalation.

Atomically thin van der Waals magnetic crystals are characterized by tunable magnetic properties related to their low dimensionality. While electrostatic gating has been used to tailor their magnetic response, chemical approaches like intercalation remain largely unexplored. Here, we demonstrate the manipulation of the magnetism in the van der Waals antiferromagnet NiPS3 through the intercalation of different organic cations, inserted using an engineered two-step process. First, the electrochemical intercalation of tetrabutylammonium cations (TBA+) results in a ferrimagnetic hybrid compound displaying a transition temperature of 78 K, and characterized by a hysteretic behavior with finite remanence and coercivity. Then, TBA+ cations are replaced by cobaltocenium via an ion-exchange process, yielding a ferrimagnetic phase with higher transition temperature (98 K) and higher remanent magnetization. Importantly, we demonstrate that the intercalation and cation exchange processes can be carried out in bulk crystals and few-layer flakes, opening the way to the integration of intercalated magnetic materials in devices.

MacroH2As regulate enhancer-promoter contacts affecting enhancer activity and sensitivity to inflammatory cytokines.

MacroH2A histone variants have a function in gene regulation that is poorly understood at the molecular level. We report that macroH2A1.2 and macroH2A2 modulate the transcriptional ground state of cancer cells and how they respond to inflammatory cytokines. Removal of macroH2A1.2 and macroH2A2 in hepatoblastoma cells affects the contact frequency of promoters and distal enhancers coinciding with changes in enhancer activity or preceding them in response to the cytokine tumor necrosis factor alpha. Although macroH2As regulate genes in both directions, they globally facilitate the nuclear factor κB (NF-κB)-mediated response. In contrast, macroH2As suppress the response to the pro-inflammatory cytokine interferon gamma. MacroH2A2 has a stronger contribution to gene repression than macroH2A1.2. Taken together, our results suggest that macroH2As have a role in regulating the response of cancer cells to inflammatory signals on the level of chromatin structure. This is likely relevant for the interaction of cancer cells with immune cells of their microenvironment.