The Hox transcription factor Ultrabithorax binds RNA and regulates co-transcriptional splicing through an interplay with RNA polymerase II.

Transcription factors (TFs) play a pivotal role in cell fate decision by coordinating gene expression programs. Although most TFs act at the DNA layer, few TFs bind RNA and modulate splicing. Yet, the mechanistic cues underlying TFs activity in splicing remain elusive. Focusing on the Drosophila Hox TF Ultrabithorax (Ubx), our work shed light on a novel layer of Ubx function at the RNA level. Transcriptome and genome-wide binding profiles in embryonic mesoderm and Drosophila cells indicate that Ubx regulates mRNA expression and splicing to promote distinct outcomes in defined cellular contexts. Our results demonstrate a new RNA-binding ability of Ubx. We find that the N51 amino acid of the DNA-binding Homeodomain is non-essential for RNA interaction in vitro, but is required for RNA interaction in vivo and Ubx splicing activity. Moreover, mutation of the N51 amino acid weakens the interaction between Ubx and active RNA Polymerase II (Pol II). Our results reveal that Ubx regulates elongation-coupled splicing, which could be coordinated by a dynamic interplay with active Pol II on chromatin. Overall, our work uncovered a novel role of the Hox TFs at the mRNA regulatory layer. This could be an essential function for other classes of TFs to control cell diversity.

H1 histones control the epigenetic landscape by local chromatin compaction.

H1 linker histones are the most abundant chromatin-binding proteins1. In vitro studies indicate that their association with chromatin determines nucleosome spacing and enables arrays of nucleosomes to fold into more compact chromatin structures. However, the in vivo roles of H1 are poorly understood2. Here we show that the local density of H1 controls the balance of repressive and active chromatin domains by promoting genomic compaction. We generated a conditional triple-H1-knockout mouse strain and depleted H1 in haematopoietic cells. H1 depletion in T cells leads to de-repression of T cell activation genes, a process that mimics normal T cell activation. Comparison of chromatin structure in normal and H1-depleted CD8+ T cells reveals that H1-mediated chromatin compaction occurs primarily in regions of the genome containing higher than average levels of H1: the chromosome conformation capture (Hi-C) B compartment and regions of the Hi-C A compartment marked by PRC2. Reduction of H1 stoichiometry leads to decreased H3K27 methylation, increased H3K36 methylation, B-to-A-compartment shifting and an increase in interaction frequency between compartments. In vitro, H1 promotes PRC2-mediated H3K27 methylation and inhibits NSD2-mediated H3K36 methylation. Mechanistically, H1 mediates these opposite effects by promoting physical compaction of the chromatin substrate. Our results establish H1 as a critical regulator of gene silencing through localized control of chromatin compaction, 3D genome organization and the epigenetic landscape.

Chemical characterization of the lipids in femoral gland secretions of wild male tegu lizards, Salvator merianae (Squamata, Teiidae) in comparison with captive-bred males.

Although chemical interactions play an essential role in lizard social behavior, the chemical composition of the femoral gland secretions that many lizards use for communication is known for only a few species, mainly European Lacertids. The tegu lizard, Salvator merianae, is the only species of the Teiidae family for which there is available information on lipids in femoral secretions, but only for captive bred males from Argentina. Here, based on mass spectra obtained by GC-MS, we found 69 lipophilic compounds in femoral gland secretions of wild males S. merianae from Brazil, including cholesterol and high amounts of saturated fatty acids (mainly hexadecanoic and octadecanoic). We found contrasting differences between wild and captive-bred males, which lack cholesterol but present high amount of 9,12-octadecadienoic acid. These within-species differences between wild and captive lizards strongly suggest the important influence of different diets on the chemical composition of the femoral gland secretion and suggest caution when interpreting results from captive animals, even in the same species.

H1 linker histones silence repetitive elements by promoting both histone H3K9 methylation and chromatin compaction.

Nearly 50% of mouse and human genomes are composed of repetitive sequences. Transcription of these sequences is tightly controlled during development to prevent genomic instability, inappropriate gene activation and other maladaptive processes. Here, we demonstrate an integral role for H1 linker histones in silencing repetitive elements in mouse embryonic stem cells. Strong H1 depletion causes a profound de-repression of several classes of repetitive sequences, including major satellite, LINE-1, and ERV. Activation of repetitive sequence transcription is accompanied by decreased H3K9 trimethylation of repetitive sequence chromatin. H1 linker histones interact directly with Suv39h1, Suv39h2, and SETDB1, the histone methyltransferases responsible for H3K9 trimethylation of chromatin within these regions, and stimulate their activity toward chromatin in vitro. However, we also implicate chromatin compaction mediated by H1 as an additional, dominant repressive mechanism for silencing of repetitive major satellite sequences. Our findings elucidate two distinct, H1-mediated pathways for silencing heterochromatin.

Chemical characterization of the lipids in femoral gland secretions of wild male tegu lizards, Salvator merianae (Squamata, Teiidae) in comparison with captive-bred males

Although chemical interactions play an essential role in lizard social behavior, the chemical composition of the femoral gland secretions that many lizards use for communication is known for only a few species, mainly European Lacertids. The tegu lizard, Salvator merianae, is the only species of the Teiidae family for which there is available information on lipids in femoral secretions, but only for captive bred males from Argentina. Here, based on mass spectra obtained by GC-MS, we found 69 lipophilic compounds in femoral gland secretions of wild males S. merianae from Brazil, including cholesterol and high amounts of saturated fatty acids (mainly hexadecanoic and octadecanoic). We found contrasting differences between wild and captive-bred males, which lack cholesterol but present high amount of 9,12-octadecadienoic acid. These within-species differences between wild and captive lizards strongly suggest the important influence of different diets on the chemical composition of the femoral gland secretion and suggest caution when interpreting results from captive animals, even in the same species.

Chemical characterization of the lipids in femoral gland secretions of wild male tegu lizards, Salvator merianae (Squamata, Teiidae) in comparison with captive-bred males

Although chemical interactions play an essential role in lizard social behavior, the chemical composition of the femoral gland secretions that many lizards use for communication is known for only a few species, mainly European Lacertids. The tegu lizard, Salvator merianae, is the only species of the Teiidae family for which there is available information on lipids in femoral secretions, but only for captive bred males from Argentina. Here, based on mass spectra obtained by GC-MS, we found 69 lipophilic compounds in femoral gland secretions of wild males S. merianae from Brazil, including cholesterol and high amounts of saturated fatty acids (mainly hexadecanoic and octadecanoic). We found contrasting differences between wild and captive-bred males, which lack cholesterol but present high amount of 9,12-octadecadienoic acid. These within-species differences between wild and captive lizards strongly suggest the important influence of different diets on the chemical composition of the femoral gland secretion and suggest caution when interpreting results from captive animals, even in the same species.

Neutral Axis Depth versus Ductility and Plastic Rotation Capacity on Bending in Lightweight-Aggregate Concrete Beams.

This article presents an experimental study on the evolution of the neutral axis depth at failure in the critical section with the flexural ductility and plastic rotation capacity of reinforced concrete (RC) lightweight-aggregate concrete (LWAC) beams. For this, the results of a previous experimental program involving RC LWAC beams tested in flexure until failure are used. The variable studies were the concrete compressive strength (between 22.0 and 60.4 MPa and dry density between 1651 and 1953 kg/m3) and the longitudinal tensile reinforcement ratio (between 0.13% and 2.69%). The flexural ductility and the plastic rotation capacity of the RC LWAC beams are characterized by a ductility index and a plastic trend parameter, respectively. The influence of the variable studies, as well as the relation of the flexural ductility and plastic rotation capacity with the values for the neutral axis depth at failure are analyzed and discussed. Some conclusions are drawn which can be useful for the design of RC LWAC beams for flexure. In particular, it is shown that the practical rule of limiting the neutral axis depth at failure to ensure ductile behavior, as used in normal-weight aggregate concrete beams, is also valid for RC LWAC beams.

Impact of levosimendan on weaning from peripheral venoarterial extracorporeal membrane oxygenation in intensive care unit.

BACKGROUND: Few data are available on the impact of levosimendan in refractory cardiogenic shock patients undergoing peripheral venoarterial extracorporeal membrane oxygenation (VA-ECMO). The aim of this study was to evaluate the impact of levosimendan on VA-ECMO weaning in patients hospitalized in intensive care unit (ICU). METHODS: This retrospective cohort study was conducted in a French university hospital from 2010 to 2017. All patients hospitalized in ICU undergoing VA-ECMO were consecutively evaluated. RESULTS: A total of 150 patients undergoing VA-ECMO were eligible for the study. Thirty-eight propensity-matched patients were evaluated in the levosimendan group and 65 in the non-levosimendan group. In patients treated with levosimendan, left ventricular ejection fraction had increased from 21.5 ± 9.1% to 30.7 ± 13.5% (P < 0.0001) and aortic velocity-time integral from 8.9 ± 4 cm to 12.5 ± 3.8 cm (P = 0.002) 24 h after drug infusion. After propensity score matching, levosimendan was the only factor associated with a significant reduction in VA-ECMO weaning failure rates (hazard ratio = 0.16; 95% confidence interval 0.04-0.7; P = 0.01). Kaplan-Meier survival curves showed that survival rates at 30 days were 78.4% for the levosimendan group and 49.5% for the non-levosimendan group (P = 0.02). After propensity score matching analysis, the difference in 30-day mortality between the two groups was not significant (hazard ratio = 0.55; 95% confidence interval 0.27-1.10; P = 0.09). CONCLUSIONS: Our results suggest that levosimendan was associated with a beneficial effect on VA-ECMO weaning in ICU patients.

Cannula-Related Infection in Patients Supported by Peripheral ECMO: Clinical and Microbiological Characteristics.

Little is known about cannula-related infection (CRI) in patients supported by extracorporeal membrane oxygenation (ECMO). The aim of this study was to assess the incidence, the risk factors, prognosis, and microbiological characteristics of CRI in patients supported by ECMO. This retrospective cohort study was conducted in one intensive care unit (ICU). Among 220 consecutive patients with peripheral ECMO, 39 (17.7%) developed CRI. The incidence of CRI was 17.2 per 1,000 ECMO days. The main isolated microorganisms were Enterobacteriaceae (38%), Staphylococcus spp. (28.2%; 8.5% were methicillin-sensitive Staphylococcus aureus and 19.7% were coagulase-negative staphylococci), and Pseudomonas aeruginosa (18.3%). Bacteremia was present in 23 cases (59.7%). In multivariate analysis, the risk factors for CRI were longer ECMO duration (p = 0.006) and higher Simplified Acute Physiology Score 2 (p = 0.004). Forty-one percentage of patients with CRI needed surgical management of the infected site. Cannula-related infection was not associated with higher in-hospital mortality (p = 0.73), but it was associated with a longer stay in ICU (p < 0.0001) and a longer stay in hospital (p = 0.002). In conclusion, CRI is frequent in patients with ECMO and associated with a longer stay in hospital. Risk factors for CRI were longer ECMO duration and higher Simplified Acute Physiology Score 2. Concomitant bacteremia was frequent (59.7%) and CRI should be strongly investigated in cases of positive blood culture.

Complication patterns in patients undergoing venoarterial extracorporeal membrane oxygenation in intensive care unit: Multiple correspondence analysis and hierarchical ascendant classification.

BACKGROUND: Treatment by venoarterial extracorporeal membrane oxygenation (VA-ECMO) is widely used today, even though it is associated with high risks of complications and death. While studies have focused on the relationship between some of these complications and the risk of death, the relationship between different complications has never been specifically examined, despite the fact that the occurrence of one complication is known to favor the occurrence of others. Our objective was to describe the relationship between complications in patients undergoing VA-ECMO in intensive care unit (ICU) and to identify, if possible, patterns of patients according to complications. METHODS AND FINDINGS: As part of a retrospective cohort study, we conducted a multiple correspondence analysis followed by a hierarchical ascendant classification in order to identify patterns of patients according to main complications (sepsis, thromboembolic event, major transfusion, major bleeding, renal replacement therapy) and in-ICU death. Our cohort of 145 patients presented an in-ICU mortality rate of 50.3%. Morbidity was high, with 36.5% of patients presenting three or more of the five complications studied. Multiple correspondence analysis revealed a cumulative inertia of 76.9% for the first three dimensions. Complications were clustered together and clustered close to death, prompting the identification of four patterns of patients according to complications, including one with no complications. CONCLUSIONS: Our study, based on a large cohort of patients undergoing VA-ECMO in ICU and presenting a mortality rate comparable to that reported in the literature, identified numerous and often interrelated complications. Multiple correspondence analysis and hierarchical ascendant classification yielded clusters of patients and highlighted specific links between some of the complications studied. Further research should be conducted in this area.

Predictors of red blood cell transfusion and its association with prognosis in patients undergoing extracorporeal membrane oxygenation.

PURPOSE: Few data are available on the potential benefits and risks of red blood cell transfusion in patients undergoing extracorporeal membrane oxygenation. The aim of this study was to identify the determinants and prognosis of red blood cell transfusion in patients undergoing extracorporeal membrane oxygenation, with a special focus on biological parameters during extracorporeal membrane oxygenation treatment. METHODS: We conducted a single-center retrospective cohort study including all consecutive patients who underwent extracorporeal membrane oxygenation between January 2010 and December 2015. RESULTS: The 201 evaluated patients received a median of 0.9 [0.5-1.7] units of red blood cell per day. Significant and clinically relevant variables that best correlated with units of red blood cell transfused per day of extracorporeal membrane oxygenation were lower median daily prothrombin time in percentage (Quick) ( t = -0.016, p < 0.0001), higher median daily free bilirubin level ( t = 0.016, p < 0.0001), and lower pH ( t = -2.434, p < 0.0001). In multivariate analysis, red blood cell transfusion was associated with a significantly higher rate of in-intensive care unit mortality (per red blood cell unit increment; adjusted odds ratio: 1.07, 95% confidence interval: 1.02-1.12, p = 0.005). It was also associated with higher rates of acute renal failure ( p = 0.025), thromboembolic complications ( p = 0.0045), and sepsis ( p = 0.015). CONCLUSION: This study suggests that red blood cell transfusion may be associated with a higher mortality rate and with severe complications. However, we cannot conclude a direct causal relationship, as red blood cell transfusion may be only a marker of poor outcome. We recommend that physicians correct acidosis and hemolysis in patients undergoing extracorporeal membrane oxygenation whenever possible.

Long noncoding RNA Sox2ot and transcription factor YY1 co-regulate the differentiation of cortical neural progenitors by repressing Sox2.

Long noncoding RNAs (lncRNAs) are emerging as key regulators of crucial cellular processes. However, the molecular mechanisms of many lncRNA functions remain uncharacterized. Sox2ot is an evolutionarily conserved lncRNA that transcriptionally overlaps the pluripotency gene Sox2, which maintains the stemness of embryonic stem cells and tissue-specific stem cells. Here, we show that Sox2ot is expressed in the developing mouse cerebral cortex, where it represses neural progenitor (NP) proliferation and promotes neuronal differentiation. Sox2ot negatively regulates self-renewal of neural stem cells, and is predominately expressed in the nucleus and inhibits Sox2 levels. Sox2ot forms a physical interaction with a multifunctional transcriptional regulator YY1, which binds several CpG islands in the Sox2 locus in a Sox2ot-dependent manner. Similar to Sox2ot, YY1 represses NP expansion in vivo. These results demonstrate a regulatory role of Sox2ot in promoting cortical neurogenesis, possibly by repressing Sox2 expression in NPs, through interacting with YY1.

Hepatitis B and hepatitis D virus infections in the Central African Republic, twenty-five years after a fulminant hepatitis outbreak, indicate continuing spread in asymptomatic young adults.

Hepatitis delta virus (HDV) increases morbidity in Hepatitis B virus (HBV)-infected patients. In the mid-eighties, an outbreak of HDV fulminant hepatitis (FH) in the Central African Republic (CAR) killed 88% of patients hospitalized in Bangui. We evaluated infections with HBV and HDV among students and pregnant women, 25 years after the fulminant hepatitis (FH) outbreak to determine (i) the prevalence of HBV and HDV infection in this population, (ii) the clinical risk factors for HBV and/or HDV infections, and (iii) to characterize and compare the strains from the FH outbreak in the 1980s to the 2010 HBV-HDV strains. We performed a cross sectional study with historical comparison on FH-stored samples (n = 179) from 159 patients and dried blood-spots from volunteer students and pregnant women groups (n = 2172). We analyzed risk factors potentially associated with HBV and HDV. Previous HBV infection (presence of anti-HBc) occurred in 345/1290 students (26.7%) and 186/870 pregnant women (21.4%)(p = 0.005), including 110 students (8.8%) and 71 pregnant women (8.2%), who were also HBsAg-positive (p = 0.824). HDV infection occurred more frequently in pregnant women (n = 13; 18.8%) than students (n = 6; 5.4%) (p = 0.010). Infection in childhood was probably the main HBV risk factor. The risk factors for HDV infection were age (p = 0.040), transfusion (p = 0.039), and a tendency for tattooing (p = 0.055) and absence of condom use (p = 0.049). HBV-E and HDV-1 were highly prevalent during both the FH outbreak and the 2010 screening project. For historical samples, due to storage conditions and despite several attempts, we could only obtain partial HDV amplification representing 25% of the full-length genome. The HDV-1 mid-eighties FH-strains did not form a specific clade and were affiliated to two different HDV-1 African subgenotypes, one of which also includes the 2010 HDV-1 strains. In the Central African Republic, these findings indicate a high prevalence of previous and current HBV-E and HDV-1 infections both in the mid-eighties fulminant hepatitis outbreak and among asymptomatic young adults in 2010, and reinforce the need for universal HBV vaccination and the prevention of HDV transmission among HBsAg-positive patients through blood or sexual routes.

Local compartment changes and regulatory landscape alterations in histone H1-depleted cells.

BACKGROUND: Linker histone H1 is a core chromatin component that binds to nucleosome core particles and the linker DNA between nucleosomes. It has been implicated in chromatin compaction and gene regulation and is anticipated to play a role in higher-order genome structure. Here we have used a combination of genome-wide approaches including DNA methylation, histone modification and DNase I hypersensitivity profiling as well as Hi-C to investigate the impact of reduced cellular levels of histone H1 in embryonic stem cells on chromatin folding and function. RESULTS: We find that depletion of histone H1 changes the epigenetic signature of thousands of potential regulatory sites across the genome. Many of them show cooperative loss or gain of multiple chromatin marks. Epigenetic alterations cluster to gene-dense topologically associating domains (TADs) that already showed a high density of corresponding chromatin features. Genome organization at the three-dimensional level is largely intact, but we find changes in the structural segmentation of chromosomes specifically for the epigenetically most modified TADs. CONCLUSIONS: Our data show that cells require normal histone H1 levels to expose their proper regulatory landscape. Reducing the levels of histone H1 results in massive epigenetic changes and altered topological organization particularly at the most active chromosomal domains. Changes in TAD configuration coincide with epigenetic landscape changes but not with transcriptional output changes, supporting the emerging concept that transcriptional control and nuclear positioning of TADs are not causally related but independently controlled by the locally associated trans-acting factors.

Bisphosphonate and Implant Dentistry - Is it Safe?

Bisphosphonates are a group of drugs that are commonly used to alter bone metabolism in order to prevent bone loss in diseases such as osteoporosis and bone cancers. Unfortunately, the use of bisphosphonates has been associated with bisphosphonate-related osteonecrosis of the jaws. The debate as to whether it is wise to consider implant therapy in patients being treated with bisphosphonate therapy remains a grey area. This review will present the latest evidence and guidelines available on bisphosphonates and their possible effects on implant dentistry. The risk factors, co-morbidities, clinical presentation and findings from various imaging modalities for bisphosphonate-related osteonecrosis of the jaws are highlighted. The management of patients being treated with bisphosphonates, in whom dental implants might be considered or have already been placed, will also be discussed. Finally, the areas requiring future research are considered.

Repression of arterial genes in hemogenic endothelium is sufficient for haematopoietic fate acquisition.

Changes in cell fate and identity are essential for endothelial-to-haematopoietic transition (EHT), an embryonic process that generates the first adult populations of haematopoietic stem cells (HSCs) from hemogenic endothelial cells. Dissecting EHT regulation is a critical step towards the production of in vitro derived HSCs. Yet, we do not know how distinct endothelial and haematopoietic fates are parsed during the transition. Here we show that genes required for arterial identity function later to repress haematopoietic fate. Tissue-specific, temporally controlled, genetic loss of arterial genes (Sox17 and Notch1) during EHT results in increased production of haematopoietic cells due to loss of Sox17-mediated repression of haematopoietic transcription factors (Runx1 and Gata2). However, the increase in EHT can be abrogated by increased Notch signalling. These findings demonstrate that the endothelial haematopoietic fate switch is actively repressed in a population of endothelial cells, and that derepression of these programs augments haematopoietic output.

The BET family member BRD4 interacts with OCT4 and regulates pluripotency gene expression.

Embryonic stem cell (ESC) pluripotency is controlled by defined transcription factors. During cellular differentiation, ESCs undergo a global epigenetic reprogramming. Female ESCs exemplify this process as one of the two X-chromosomes is globally silenced during X chromosome inactivation (XCI) to balance the X-linked gene disparity with XY males. The pluripotent factor OCT4 regulates XCI by triggering X chromosome pairing and counting. OCT4 directly binds Xite and Tsix, which encode two long noncoding RNAs (lncRNAs) that suppress the silencer lncRNA, Xist. To control its activity as a master regulator in pluripotency and XCI, OCT4 must have chromatin protein partners. Here we show that BRD4, a member of the BET protein subfamily, interacts with OCT4. BRD4 occupies the regulatory regions of pluripotent genes and the lncRNAs of XCI. BET inhibition or depletion of BRD4 reduces the expression of many pluripotent genes and shifts cellular fate showing that BRD4 is pivotal for transcription in ESCs.

Electronic and electrochemical doping of graphene by surface adsorbates.

Many potential applications of graphene require its precise and controllable doping with charge carriers. Being a two-dimensional material graphene is extremely sensitive to surface adsorbates, so its electronic properties can be effectively modified by deposition of different atoms and molecules. In this paper, we review two mechanisms of graphene doping by surface adsorbates, namely electronic and electrochemical doping. Although, electronic doping has been extensively studied and discussed in the literature, much less attention has been paid to electrochemical doping. This mechanism can, however, explain the doping of graphene by adsorbates for which no charge transfer is expected within the electronic doping model. In addition, electrochemical doping is in the origin of the hysteresis effects often observed in graphene-based field effect transistors when operating in the atmospheric environment.

Sociodemographic determinants of prevalence and incidence of Helicobacter pylori infection in Portuguese adults.

BACKGROUND: Understanding the determinants of Helicobacter pylori infection in adults is essential to predict the burden of H. pylori-related diseases. We aimed to estimate the prevalence and incidence of H. pylori infection and to identify its major sociodemographic correlates in an urban population from the North of Portugal. MATERIAL AND METHODS: A representative sample of noninstitutionalized adult inhabitants of Porto (n = 2067) was evaluated by ELISA (IgG) and a subsample (n = 412) was tested by Western Blot to assess infection with CagA-positive strains. Modified Poisson and Poisson regression models were used to estimate crude and sex-, age-, and education-adjusted prevalence ratios (PR) and incidence rate ratios (RR), respectively. RESULTS: The prevalence of H. pylori infection was 84.2% [95% confidence interval (95%CI): 82.4-86.1]. It increased across age-groups in the more educated subjects, (18-30 years: 72.6%; ≥71 years: 88.1%; p for trend <0.001) and decreased with education in the younger (≤4 schooling years: 100.0%; ≥10 schooling years: 72.6%; p for trend <0.001). Living in a more deprived neighborhood was associated with a higher prevalence of infection, only in the younger (PR = 1.20, 95%CI: 1.03-1.38) and more educated participants (PR = 1.15, 95%CI: 1.03-1.29). Among the infected, the proportion with CagA-positive strains was 61.7% (95%CI: 56.6-66.9). The incidence rate was 3.6/100 person-years (median follow-up: 3 years; 95%CI: 2.1-6.2), lower among the more educated (≥10 vs ≤9: RR = 0.25, 95%CI: 0.06-0.96). The seroreversion rate was 1.0/100 person-years (95%CI: 0.6-1.7). CONCLUSIONS: The prevalence of infection among adults is still very high in Portugal, suggesting that stomach cancer rates will remain high over the next few decades.