You shall not pass! Unveiling the barriers for cohesin-mediated loop extrusion.

Dequeker and colleagues performed elegant in vivo, in silico, and in vitro experiments to demonstrate that the MCM complex, an essential DNA replication factor, is an obstacle for the DNA loop formation by cohesin.

PM10-bound trace elements in pan-European urban atmosphere.

Although many studies have discussed the impact of Europe's air quality, very limited research focused on the detailed phenomenology of ambient trace elements (TEs) in PM10 in urban atmosphere. This study compiled long-term (2013-2022) measurements of speciation of ambient urban PM10 from 55 sites of 7 countries (Switzerland, Spain, France, Greece, Italy, Portugal, UK), aiming to elucidate the phenomenology of 20 TEs in PM10 in urban Europe. The monitoring sites comprised urban background (UB, n = 26), traffic (TR, n = 10), industrial (IN, n = 5), suburban background (SUB, n = 7), and rural background (RB, n = 7) types. The sampling campaigns were conducted using standardized protocols to ensure data comparability. In each country, PM10 samples were collected over a fixed period using high-volume air samplers. The analysis encompassed the spatio-temporal distribution of TEs, and relationships between TEs at each site. Results indicated an annual average for the sum of 20 TEs of 90 ± 65 ng/m3, with TR and IN sites exhibiting the highest concentrations (130 ± 66 and 131 ± 80 ng/m3, respectively). Seasonal variability in TEs concentrations, influenced by emission sources and meteorology, revealed significant differences (p < 0.05) across all monitoring sites. Estimation of TE concentrations highlighted distinct ratios between non-carcinogenic and carcinogenic metals, with Zn (40 ± 49 ng/m3), Ti (21 ± 29 ng/m3), and Cu (23 ± 35 ng/m3) dominating non-carcinogenic TEs, while Cr (5 ± 7 ng/m3), and Ni (2 ± 6 ng/m3) were prominent among carcinogenic ones. Correlations between TEs across diverse locations and seasons varied, in agreement with differences in emission sources and meteorological conditions. This study provides valuable insights into TEs in pan-European urban atmosphere, contributing to a comprehensive dataset for future environmental protection policies.

Fetal membrane cells for treatment of steroid-refractory acute graft-versus-host disease.

The placenta protects the fetus from the mother's immune system. We have previously found that fetal membrane cells (FMCs) isolated from term placenta prevent alloreactivity in vitro. FMCs share many features with bone marrow-derived mesenchymal stromal cells (MSCs), which we previously introduced to treat severe acute graft-versus-host disease (GVHD). Here, we tested FMCs for treatment of steroid-refractory acute GVHD. After two passages in culture, approximately 10(9) FMCs were obtained from one single placenta, although not all cells from passage 0 and passage 1 were used for expansion. The FMCs were positive for CD29, CD44, CD73, CD90, CD105, and CD49d but were negative for hematopoietic, endothelial, and epithelial markers. Microsatellite polymorphism analysis showed that FMCs were of maternal origin. All FMCs used showed normal karyotype. Nine patients who had undergone hematopoietic stem cell transplantation (HSCT) and who had developed steroid-refractory grade III-IV acute GVHD were given 0.9-2.8 × 10(6) FMCs per kg at 15 infusions. Median age was 57 years. There was no toxicity from infusion of FMCs in eight patients. One patient had seizures after infusion. Two of eight evaluable patients had a complete response and four had a partial response, giving an overall response rate of 75%. Two patients showed no response at all. Three patients are alive from 6 to 21 months after HSCT. One patient is well and two have chronic GVHD. Thus, FMCs may be successfully used for immune modulation and tissue repair.

Effects of road dust suppressants on PM levels in a Mediterranean urban area.

The abatement of road dust emissions is currently a major challenge for sustainable transportation, causing exceedances of limits on particulate matter (PM) and high population exposures to mineral dust and metals. Mitigation measures have been proposed such as improved street cleaning and the use of dust suppressants. This study evaluated, for the first time, the effectiveness of calcium-magnesium acetate (CMA) and MgCl2 in reducing road dust emissions in a Mediterranean city. During a two-month campaign, a typical urban road in the city of Barcelona was sprayed, and changes in PMx levels and components were monitored at four traffic sites and one background monitoring sites. The integrated results indicate no statistically significant effectiveness of dust suppressants on PM10 and PM2.5-10 levels. Episodic reductions of Al, K, Mg, Cr, Li, Cu, and Zn were observed during CMA applications, but they were not systematically statistically significant over different stations and spreading days. MgCl2 days showed lower PM10 mean concentrations, but these reductions were not statistically significant and were not supported by significant drops in mineral and brake-wear metals. Based on our literature review, it can be postulated that the higher the road dust loading, the higher the dust suppressant effectiveness.

Repli-seq Sample Preparation using Cell Sorting with Cell-Permeant Dyes.

Replication timing is significantly correlated with gene expression and chromatin organization, changes dynamically during cell differentiation, and is altered in diseased states. Genome-wide analysis of replication timing is performed in actively replicating cells by Repli-seq. Current methods for Repli-seq require cells to be fixed in large numbers. This is a barrier for sample types that are sensitive to fixation or are in very limited numbers. In this article, we outline optimized methods to process live cells and intact nuclei for Repli-seq. Our protocol enables the processing of a smaller number of cells per sample and reduces processing time and sample loss while obtaining high-quality data. Further, for samples that tend to form clumps and are difficult to dissociate into a single-cell suspension, we also outline methods for isolation, staining, and processing of nuclei for Repli-seq. The Repli-seq data obtained from live cells and intact nuclei are comparable to those obtained from the standard protocols. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Live cell isolation and staining Alternate Protocol: Nuclei isolation and staining.

N-acetyl-L-cysteine increases acute graft-versus-host disease and promotes T-cell-mediated immunity in vitro.

N-acetyl-L-cysteine (NAC) is a thiol antioxidant that stimulates glutathione synthesis in cells. Several studies indicate that NAC possesses immunomodulatory properties in vitro, but both inhibitory and activating effects on immunity have been reported. We observed that allogeneic stem cell transplantation (ASCT) patients who were randomized to receive NAC 100 mg/kg/day (n=73) had an increased prevalence of grade II-V acute graft-versus-host disease (GvHD) compared to patients who did not receive NAC (n=87), indicating that NAC has an immunostimulatory effect in vivo. When studying the effect of NAC on T-cell-mediated immunity in vitro, we found that moderate levels of NAC (0.4-3.2 mM) increased alloantigen-induced proliferation, expression of activation markers CD25 and CD71 on T cells, and production of IFN-γ and IL-10. In contrast, high concentrations of NAC (12.5-50 mM) were suppressive, which may explain previously conflicting data. NAC did not cause an increase in expression of CD86, CD80, and CD83 on mature DCs at any concentration, whereas high concentrations suppressed DC maturation. Furthermore, T cells exposed to suppressive concentrations of NAC in a primary stimulation were highly responsive when re-stimulated in the absence of NAC. To conclude, NAC appears to increase acute GvHD and has an immunostimulatory effect on alloantigen-specific T cells.

[Clinical guideline for the prevention, diagnosis and treatment of ischemic cerebral disease]. / Guía de práctica clínica. Enfermedad vascular cerebral isquémica.

Stroke is considered a big public health problem in adults and older adults. Increased life expectancy is one of the greatest achievements of development; however it is also a great challenge because of the implications with regard to increasing chronic disease that it will lead complications such as stroke. Stroke is the leading cause of disability worldwide in adulthood and the second leading cause of dementia. In developing countries, it is estimated that the costs of care for stroke are from 6000 to 8000 euros, as well as the social costs of informal care and changes in family dynamics around patients. So the purpose of this clinical practice guideline is to define recommendations based on the best available evidence for the standardization of health care of patients with stroke.

Epigenomic signatures associated with spontaneous and replication stress-induced DNA double strand breaks.

Common fragile sites (CFSs) are specific regions of all individuals' genome that are predisposed to DNA double strand breaks (DSBs) and undergo subsequent rearrangements. CFS formation can be induced in vitro by mild level of DNA replication stress, such as DNA polymerase inhibition or nucleotide pool disturbance. The mechanisms of CFS formation have been linked to DNA replication timing control, transcription activities, as well as chromatin organization. However, it is unclear what specific cis- or trans-factors regulate the interplay between replication and transcription that determine CFS formation. We recently reported genome-wide mapping of DNA DSBs under replication stress induced by aphidicolin in human lymphoblastoids for the first time. Here, we systematically compared these DSBs with regards to nearby epigenomic features mapped in the same cell line from published studies. We demonstrate that aphidicolin-induced DSBs are strongly correlated with histone 3 lysine 36 trimethylation, a marker for active transcription. We further demonstrate that this DSB signature is a composite effect by the dual treatment of aphidicolin and its solvent, dimethylsulfoxide, the latter of which potently induces transcription on its own. We also present complementing evidence for the association between DSBs and 3D chromosome architectural domains with high density gene cluster and active transcription. Additionally, we show that while DSBs were detected at all but one of the fourteen finely mapped CFSs, they were not enriched in the CFS core sequences and rather demarcated the CFS core region. Related to this point, DSB density was not higher in large genes of greater than 300 kb, contrary to reported enrichment of CFS sites at these large genes. Finally, replication timing analyses demonstrate that the CFS core region contain initiation events, suggesting that altered replication dynamics are responsible for CFS formation in relatively higher level of replication stress.

Saharan dust contribution to PM10, PM2.5 and PM1 in urban and suburban areas of Rome: a comparison between single-particle SEM-EDS analysis and whole-sample PIXE analysis.

From February 15th to April 15th 2009, a period characterised by two episodes of Saharan dust outbreaks in Italy, particulate matter (PM) samples were collected at two stations (urban and suburban) in Rome. Some samples were selected and analysed using the SEM-EDS technique to characterise PM, focussing especially on the mineral contribution. Samples were representative both of days affected by Saharan dust episodes and days without this contribution. Cluster analysis allowed the attribution of each of about 67,000 analysed particles to one of the seven main statistical groups based on their composition. Characteristics of the particulate components identified using SEM-EDS analysis were verified by PIXE analysis carried out on filters collected in a suburban area. Ultimately, the contribution of crustal particles was revealed to be consistently high, highlighting the importance of local and regional mineral contributions, as well as those of Saharan origin. Therefore, quantifying all mineral contributions to resuspended particulate could lead to significant reductions of the PM level also on days not influenced by Saharan dust, thus limiting conditions when PM10 daily limit value (DLV) established by European legislation is exceeded.

Immunofluorescent Staining for Visualization of Heterochromatin Associated Proteins in Drosophila Salivary Glands.

Visualization of heterochromatin aggregates by immunostaining can be challenging. Many mammalian components of chromatin are conserved in Drosophila melanogaster. Therefore, it is an excellent model to study heterochromatin formation and maintenance. Polytenized cells, such as the ones found in salivary glands of third instar D. melanogaster larvae, provide an excellent tool to observe the chromatin amplified nearly a thousand times and have allowed researchers to study changes in the distribution of heterochromatin in the nucleus. Although the observation of heterochromatin components can be carried out directly in polytene chromosome preparations, the localization of some proteins can be altered by the severity of the treatment. Therefore, the direct visualization of heterochromatin in cells complements this type of study. In this protocol, we describe the immunostaining techniques used for this tissue, the use of secondary fluorescent antibodies, and confocal microscopy to observe these heterochromatin aggregates with greater precision and detail.

Towards a model for aerosol removal by rain scavenging: The role of physical-chemical characteristics of raindrops.

A one-year study was carried out in León, Spain, in order to characterize physically and chemically the precipitation. With the aim of studying the scavenging process of atmospheric pollutants, scavenging ratio and removal coefficients were calculated through physical parameters of raindrops (obtained by disdrometer data) and through chemical properties of aerosols. Finally, linear models for the prediction of the chemical composition of rainwater and the efficiency of the removal effect were established. In general, the rainwater was dominated by NH4+ > SO42- > NO3- in all seasons. Higher ion concentrations and conductivity and lowest pH were observed in summer, due to the low volume of rain. In winter, the high values of Na+ and Cl- in the rainwater showed the contribution from marine sources, while in summer the high concentrations of Ca2+, Mg2+, SO42-, NH4+ and NO3- reflected the contribution from both crustal and anthropogenic sources. The linear models revealed that the amount of dissolved organic carbon and of the water-soluble ions in rain samples, Ca2+, SO42-, NO3-, increases with the volume swept by the falling drops. Insoluble carbon fraction has a negative dependence with the volume swept and positive with the diameter of the raindrop. Removal coefficients are affected by the concentration in the air of each species before precipitation, the duration of the event and the time elapsed between two precipitation events.

Characterization of aerosol sources in León (Spain) using Positive Matrix Factorization and weather types.

A one-year aerosol sampling campaign, between 2016 and 2017, was conducted in a suburban area of León city, Spain. An association between the Positive Matrix Factorization (PMF) results and air masses through circulation weather types was carried out, through the construction of linear models from the PM10 concentrations and its chemical composition. The aerosol sources, identified by PMF six-factor solution, were: traffic (29%), aged sea salt (26%), secondary aerosols (16%), dust (13%), marine aerosol (7%) and biomass burning (3%). Traffic and secondary factors showed the highest PM10 contribution in the hybrid cyclonic types with wind component from the first and second quadrant. Anticyclonic types with wind component from the first quadrant exhibited high values of secondary, aged sea salt and dust factors. The highest contributions of the dust factor were also associated with northerly types. The linear models built for estimating the source apportionment of PM10, from aerosol chemical composition and geostrophic flow, showed positive coefficients for: westerly flows (WF) in marine factor, southerly flows (SF) in secondary and traffic factors, and shear southerly vorticities (ZS) in dust factor. Negative dependences were observed for ZS in aged sea salt factor and for SF in dust factor. The PM10 mass concentration calculated by the linear models and by the PMF model were strongly correlated. This can be very useful to determine the contribution of a specific source to PM10 in León, only by knowing some meteorological and chemical variables.

Molecular effects of dADD1 misexpression in chromatin organization and transcription.

BACKGROUND: dADD1 and dXNP proteins are the orthologs in Drosophila melanogaster of the ADD and SNF2 domains, respectively, of the ATRX vertebrate's chromatin remodeler, they suppress position effect variegation phenotypes and participate in heterochromatin maintenance. RESULTS: We performed a search in human cancer databases and found that ATRX protein levels were elevated in more than 4.4% of the samples analyzed. Using the Drosophila model, we addressed the effects of over and under-expression of dADD1 proteins in polytene cells. Elevated levels of dADD1 in fly tissues caused different phenotypes, such as chromocenter disruption and loss of banding pattern at the chromosome arms. Analyses of the heterochromatin maintenance protein HP1a, the dXNP ATPase and the histone post-translational modification H3K9me3 revealed changes in their chromatin localization accompanied by mild transcriptional defects of genes embedded in heterochromatic regions. Furthermore, the expression of heterochromatin embedded genes in null dadd1 organisms is lower than in the wild-type conditions. CONCLUSION: These data indicate that dADD1 overexpression induces chromatin changes, probably affecting the stoichiometry of HP1a containing complexes that lead to transcriptional and architectural changes. Our results place dADD1 proteins as important players in the maintenance of chromatin architecture and heterochromatic gene expression.

Insights into HP1a-Chromatin Interactions.

Understanding the packaging of DNA into chromatin has become a crucial aspect in the study of gene regulatory mechanisms. Heterochromatin establishment and maintenance dynamics have emerged as some of the main features involved in genome stability, cellular development, and diseases. The most extensively studied heterochromatin protein is HP1a. This protein has two main domains, namely the chromoshadow and the chromodomain, separated by a hinge region. Over the years, several works have taken on the task of identifying HP1a partners using different strategies. In this review, we focus on describing these interactions and the possible complexes and subcomplexes associated with this critical protein. Characterization of these complexes will help us to clearly understand the implications of the interactions of HP1a in heterochromatin maintenance, heterochromatin dynamics, and heterochromatin's direct relationship to gene regulation and chromatin organization.

4-hours resolution data to study PM10 in a "hot spot" area in Europe.

Nowadays, high-time resolved aerosol studies are mandatory to better understand atmospheric processes, such as formation, removal, transport, deposition or chemical reactions. This work focuses on PM10 physical and chemical characterisation with high-time resolution: elements (from Na to Pb), ions and OC/EC fractions concentration were determined during two weeks in summer and two in winter 2006 with 4-hours resolution. Further measurements aimed at hourly elemental characterisation of fine and coarse fractions and at the determination of particles number concentration in the 0.25-32 microm size range in 31 bins. The chemical mass closure was carried out in both seasons, enhancing intra-day differences in PM10 composition. In Milan, the highest contribution came from organic matter (34% and 33% in summer and winter, respectively); other important contributors were secondary inorganic compounds (16% and 24% in summer and winter, respectively) and, in summer, crustal matter (14%). Temporal trends showed strong variations in PM10 composition during contiguous time-slots and diurnal variations in different components contribution were identified. Moreover, peculiar phenomena, which would have hardly been detected with 24-hours samplings, were evidenced. Particles removal due to precipitations, aerosol local production and long range transport were studied in detail.

Immune profiling and identification of prognostic immune-related risk factors in human ovarian cancer.

Suppression of immune reactivity by increased expression of co-inhibitory receptors has been discussed as a major reason as to why the immune system fails to control tumor development. Elucidating the co-inhibitory expression pattern of tumor-infiltrating lymphocytes in different cancer types will help to develop future treatment strategies. We characterized markers reflecting and affecting T-cell functionality by flow cytometry on lymphocytes isolated from blood, ascites and tumor from advanced ovarian cancer patients (n = 35). Significantly higher proportions of CD4+ and CD8+ T-cells expressed co-inhibitory receptors LAG-3, PD-1 and TIM-3 in tumor and ascites compared to blood. Co-expression was predominantly observed among intratumoral CD8+ T-cells and the most common combination was PD-1 and TIM-3. Analysis of 26 soluble factors revealed highest concentrations of IP-10 and MCP-1 in both ascites and tumor. Correlating these results with clinical outcome revealed the proportion of CD8+ T-cells without expression of LAG-3, PD-1 and TIM-3 to be beneficial for overall survival. In total we identified eight immune-related risk factors associated with reduced survival. Ex vivo activation showed tumor-derived CD4+ and CD8+ T-cells to be functionally active, assessed by the production of IFN-γ, IL-2, TNF-α, IL-17 and CD107a. Blocking the PD-1 receptor resulted in significantly increased release of IFN-γ suggesting potential reinvigoration. The ovarian tumor environment exhibits an inflammatory milieu with abundant presence of infiltrating immune cells expressing inhibitory checkpoints. Importantly, we found subsets of CD8+ T-cells with double and triple expression of co-inhibitory receptors, supporting the need for multiple checkpoint-targeting agents to overcome T-cell dysfunction in ovarian cancer.

No alloantibodies against mesenchymal stromal cells, but presence of anti-fetal calf serum antibodies, after transplantation in allogeneic hematopoietic stem cell recipients.

BACKGROUND AND OBJECTIVES: Mesenchymal stromal cells (MSC) may be used in cellular therapy to treat graft-versus-host-disease and autoimmune disorders, and in regenerative medicine. Preliminary data suggest limited cellular allogeneic rejection, but less is known about humoral responses. The objective of this study was to investigate whether antibodies against MSC were present after hematopoietic stem cell transplantation (HSCT) including treatment with matched or mismatched allogeneic MSC. DESIGN AND METHODS: Twelve patients were evaluated using flow cytometric cross matches (FCXM) and enzyme-linked immunosorbent assays. Expression of blood group antigens, regarded as alloantigens giving rise to humoral alloimmunity, on MSC were explored using flow cytometry and immunofluorescence. RESULTS: Three of 12 patients exhibited late positivity in the FCXM. In absorption studies, antibodies directed against fetal calf serum (FCS), a component of the MSC culture medium, were identified. Healthy individuals expressed varying levels of anti-FCS antibodies and the same pattern was seen in immunosuppressed HSCT patients. MSC did not express blood group antigens. The patients with positive FCXM are alive and well. INTERPRETATION AND CONCLUSIONS: We have shown that immunosuppressed patients can exhibit anti-FCS antibodies, but no alloantibodies, that may bind to MSC. These antibodies seem clinically insignificant.

Frontline Science: Placenta-derived decidual stromal cells alter IL-2R expression and signaling in alloantigen-activated T cells.

This study investigated how stromal cells affect the IL-2 pathway in alloantigen-activated T cells. We found that decidual stromal cells (DSCs) from term placentas promoted a high production of IL-2 in cultures with alloantigen-activated T cells. The intensity of expression of cluster of differentiation 25 (CD25; IL-2Rα) on T cells was increased by DSCs, whereas the frequency and intensity of expression of the signaling subunits CD122 (IL-2Rß) and CD132 (IL-2Rγc) were reduced. Consequently, uptake of IL-2 and STAT5 phosphorylation (pSTAT5) was abrogated. DSCs also decreased the proportion of pSTAT5+ T cells in response to IL-15, which also use CD122 for signaling. Addition of DSCs to the allogeneic cultures did not increase the expression of programmed death 1 (PD-1) or CD95, indicating that they did not promote T cell exhaustion. However, exogenous recombinant (r)IL-2 in similar concentrations in the same setting increased the expression of CD95 and down-regulated CD122 in T cells. The antiproliferative effect of sirolimus (SRL) and cyclosporine A (CsA), which target the IL-2 signaling pathway, was diminished by DSCs in vitro. To conclude, DSCs affect IL-2 production and IL-2R expression and signaling, which may contribute to the stromal cell-mediated immune modulation and phenotype shift seen in activated T cells. Altered proliferation in cultures when combining DSCs and SRL or CsA may be of clinical importance, as stromal cells are used in trials for acute inflammation and are often used in combination with conventional immunosuppressive therapies.

IFN type I and II induce BAFF secretion from human decidual stromal cells.

B cell activating factor (BAFF) is a critical cytokine for maturation of immature B cells. In murine lymph nodes, BAFF is mainly produced by podoplanin-expressing stromal cells. We have previously shown that circulating BAFF levels are maximal at birth, and that farmers' children exhibit higher BAFF levels in cord blood than non-farmers' children. Here, we sought to investigate whether maternal-derived decidual stromal cells from placenta secrete BAFF and examine what factors could stimulate this production. We found that podoplanin is expressed in decidua basalis and in the underlying villous tissue as well as on isolated maternal-derived decidual stromal cells. Decidual stromal cells produced BAFF when stimulated with IFN-γ and IFN-α, and NK cells and NK-T-like cells competent of IFN-γ production were isolated from the decidua. Finally, B cells at different maturational stages are present in decidua and all expressed BAFF-R, while stromal cells did not. These findings suggest that decidual stromal cells are a cellular source of BAFF for B cells present in decidua during pregnancy.