Scaffold/matrix attachment regions (S/MARs) are DNA elements that serve to compartmentalize the chromatin into structural and functional domains. These elements are involved in control of gene expression which governs the phenotype and also plays role in disease biology. Therefore, genome-wide understanding of these elements holds great therapeutic promise. Several attempts have been made toward identification of S/MARs in genomes of various organisms including human. However, a comprehensive genome-wide map of human S/MARs is yet not available. Toward this objective, ChIP-Seq data of 14 S/MAR binding proteins were analyzed and the binding site coordinates of these proteins were used to prepare a non-redundant S/MAR dataset of human genome. Along with co-ordinate (location) details of S/MARs, the dataset also revealed details of S/MAR features, namely, length, inter-SMAR length (the chromatin loop size), nucleotide repeats, motif abundance, chromosomal distribution and genomic context. S/MARs identified in present study and their subsequent analysis also suggests that these elements act as hotspots for integration of retroviruses. Therefore, these data will help toward better understanding of genome functioning and designing effective anti-viral therapeutics. In order to facilitate user friendly browsing and retrieval of the data obtained in present study, a web interface, MARome (http://bioinfo.net.in/MARome), has been developed.

Avian infectious bronchitis virus (IBV) is responsible of significant economic losses for poultry industry around the world, through evolution of its pathogenicity, inadequacy of vaccines, and virus evasion. Such evasion is related to the unstable nature of its RNA, in particular the S glycoprotein encoding gene, which raises great challenges with regard to the control of the disease, along with the lack of proof reading mechanisms of the RNA polymerase. The emergence of new variants might be a reason for the endemic outbreaks that are being reported in Tunisia, in addition to poor vaccination techniques and ineffective prophylactic programs. In the present study, partial nucleotide sequences of the S1 glycoprotein gene and the 3'-untranslated region (UTR) of 2 Tunisian isolates, TN1011/16 and TN1012/16, identified in 2016, were determined. Specific mutations were found in S1 gene as well as in 3'UTR region. Phylogenetic analysis of the S1 nucleotide sequences showed that both isolates are closely related to the Algerian strains, and formed a common cluster within the genotype I. In addition, these isolates were non-recombinant ones, confirming that they are unique variants. Based on their S1 gene sequences, TN1011/16 and TN1012/16 strains were distant from the H120 vaccine strain, commercially used in Tunisia along with the variant vaccine 793B type (4/91). A comparison between nucleotide sequences of their 3'UTR region and S1 gene showed a difference in IBV classification. The obtained results have confirmed that the IBVsequence continues to drift and brings valuable information in relation with its evolution, vaccine development and better control of the disease.

Assembly factors provide speed and directionality to the maturation process of the 30S subunit in bacteria. To gain a more precise understanding of how these proteins mediate 30S maturation, it is important to expand on studies of 30S assembly intermediates purified from bacterial strains lacking particular maturation factors. To reveal the role of the essential protein Era in the assembly of the 30S ribosomal subunit, we analyzed assembly intermediates that accumulated in Era-depleted Escherichia coli cells using quantitative mass spectrometry, high resolution cryo-electron microscopy and in-cell footprinting. Our combined approach allowed for visualization of the small subunit as it assembled and revealed that with the exception of key helices in the platform domain, all other 16S rRNA domains fold even in the absence of Era. Notably, the maturing particles did not stall while waiting for the platform domain to mature and instead re-routed their folding pathway to enable concerted maturation of other structural motifs spanning multiple rRNA domains. We also found that binding of Era to the mature 30S subunit destabilized helix 44 and the decoding center preventing binding of YjeQ, another assembly factor. This work establishes Era's role in ribosome assembly and suggests new roles in maintaining ribosome homeostasis.

Essentials Endothelial colony forming cells (ECFCs) are a powerful tool to study vascular diseases ex vivo. Separate ECFC lines show variations in morphology and von Willebrand factor-related parameters. Maximum cell density is correlated with von Willebrand factor expression in ECFCs. Variations in ECFC lines are dependent on the age and mesenchymal state of the cells. ABSTRACT: Background Endothelial colony forming cells (ECFCs) are cultured endothelial cells derived from peripheral blood. ECFCs are a powerful tool to study pathophysiological mechanisms underlying vascular diseases, including von Willebrand disease. In prior research, however, large variations between ECFC lines were observed in, among others, von Willebrand factor (VWF) expression. Objective Understand the relation between phenotypic characteristics and VWF-related parameters of healthy control ECFCs. Methods ECFC lines (n = 16) derived from six donors were studied at maximum cell density. Secreted and intracellular VWF antigen were measured by ELISA. The angiogenic capacity of ECFCs was investigated by the Matrigel tube formation assay. Differences in expression of genes involved in angiogenesis, aging, and endothelial to mesenchymal transition (EndoMT) were measured by quantitative PCR. Results Different ECFC lines show variable morphologies and cell density at maximum confluency and cell lines with a low maximum cell density show a mixed and more mesenchymal phenotype. We identified a significant positive correlation between maximum cell density and VWF production, both at protein and mRNA level. Also, significant correlations were observed between maximum cell density and several angiogenic, aging and EndoMT parameters. Conclusions We observed variations in morphology, maximum cell density, VWF production, and angiogenic potential between healthy control ECFCs. These variations seem to be attributable to differences in aging and EndoMT. Because variations correlate with cell density, we believe that ECFCs maintain a powerful tool to study vascular diseases. It is however important to compare cell lines with the same characteristics and perform experiments at maximum cell density.

We study the ultrafast relaxation dynamics of hydrated proton clusters in acetonitrile using femtosecond mid-infrared pump-probe spectroscopy. We observe a strong dependence of transient absorption dynamics on the frequency of excitation. When we excite the OH vibrations with frequencies ≤3100 cm-1, we observe an ultrafast energy relaxation that leads to the heating of the local environment of the proton. This response is assigned to the OH vibrations of the water molecules in the core of the hydrated proton cluster. When we excite with frequencies ≥3200 cm-1, we observe a relatively slow vibrational relaxation with a T1 time constant ranging from 0.22 ± 0.04 ps at νex = 3200 cm-1 to 0.37 ± 0.02 ps at νex = 3520 cm-1. We assign this response to water molecules in the outer part of the hydrated proton cluster.

The contemporary capacity of genome sequence analysis significantly lags behind the rapidly evolving sequencing technologies. Retrieving biological meaningful information from an ever-increasing amount of genome data would be significantly beneficial for functional genomic studies. For example, the duplication, organization, evolution, and function of superfamily genes are arguably important in many aspects of life. However, the incompleteness of annotations in many sequenced genomes often results in biased conclusions in comparative genomic studies of superfamilies. Here, we present a Perl software, called Closing Target Trimming (CTT), for automatically identifying most, if not all, members of a gene family in any sequenced genomes on CentOS 7 platform. To benefit a broader application on other operating systems, we also created a Docker application package, CTTdocker. Our test data on the F-box gene superfamily showed 78.2 and 79% gene finding accuracies in two well annotated plant genomes, Arabidopsis thaliana and rice, respectively. To further demonstrate the effectiveness of this program, we ran it through 18 plant genomes and five non-plant genomes to compare the expansion of the F-box and the BTB superfamilies. The program discovered that on average 12.7 and 9.3% of the total F-box and BTB members, respectively, are new loci in plant genomes, while it only found a small number of new members in vertebrate genomes. Therefore, different evolutionary and regulatory mechanisms of Cullin-RING ubiquitin ligases may be present in plants and animals. We also annotated and compared the Pkinase family members across a wide range of organisms, including 10 fungi, 10 metazoa, 10 vertebrates, and 10 additional plants, which were randomly selected from the Ensembl database. Our CTT annotation recovered on average 14% more loci, including pseudogenes, of the Pkinase superfamily in these 40 genomes, demonstrating its robust replicability and scalability in annotating superfamiy members in any genomes.

Despite advances in healthcare, stillbirth rates remain relatively unchanged. We conducted a systematic review to quantify the risks of stillbirth and neonatal death at term (from 37 weeks gestation) according to gestational age.

With support of the national tuberculosis (TB) program, KHANA (a local non-governmental organization in Cambodia) has implemented an innovative approach using a seed-and-recruit model to actively find TB cases in the community. The model engaged community members including TB survivors as seed and newly diagnosed people with TB as recruiters to recruit presumptive TB cases in their social network in a snowball approach for screening and linkage to treatment. This study aimed to explore the acceptability of the active case finding with the seed-and-recruit model in detecting new TB cases and determine the characteristics of successful seeds.

The Gram-negative pathogen, Acinetobacter baumannii has emerged as a global nosocomial health threat affecting the majority of hospitals in the U.S. and abroad. The redox protein thioredoxin has been shown to play several roles in modulation of cellular functions affecting various virulence factors in Gram-negative pathogens. This study aims to explore the role of thioredoxin-A protein (TrxA) in A. baumannii virulence. We determined that deletion of the TrxA gene did not significantly affect resistance to environmental stressors such as temperature, salt, and pH. However, TrxA was critical for survival in the presence of elevated levels of hydrogen peroxide. Lack of TrxA was associated with decreased expression of type IV pili related genes and an inability to undergo normal twitching motility. Interestingly, the TrxA-null mutant was able to form biofilms better than the wildtype (WT) and was observed to be significantly less virulent than the WT in a pulmonary infection model. These results are supportive of thioredoxin playing a key role in A. baumannii virulence.

Truenat is a novel molecular assay that rapidly detects tuberculosis (TB) and rifampicin-resistance. Due to the portability of its battery-powered testing platform, it may be valuable in peripheral healthcare settings in India.

Mammary glands are unique organs in which major adaptive changes occur in morphogenesis and development after birth. Breast cancer is the most common cancer and a major cause of mortality in females worldwide. We have previously identified the loss of expression of the transcription regulator DC-SCRIPT (Zfp366) as a prominent prognostic event in estrogen receptor positive breast cancer patients. DC-SCRIPT affects multiple transcriptional events in breast cancer cells, including estrogen and progesterone receptor-mediated transcription, and promotes CDKN2B-related cell cycle arrest. As loss of DC-SCRIPT expression appears an early event in breast cancer development, we here investigated the role of DC-SCRIPT in mammary gland development using wild-type and DC-SCRIPT knockout mice. Mice lacking DC-SCRIPT exhibited severe breeding problems and showed significant growth delay relative to littermate wild-type mice. Subsequent analysis revealed that DC-SCRIPT was expressed in mouse mammary epithelium and that DC-SCRIPT deficiency delayed mammary gland morphogenesis in vivo. Finally, analysis of 3D mammary gland organoid cultures confirmed that loss of DC-SCRIPT dramatically delayed mammary organoid branching in vitro. The study shows for the first time that DC-SCRIPT deficiency delays mammary gland morphogenesis in vivo and in vitro. These data define DC-SCRIPT as a novel modulator of mammary gland development.

Tissue factor (TF) is the primary cause of atherothrombosis, the rupture of atherosclerotic plaques with subsequent thrombosis, leading to acute cardiovascular events, such as myocardial infarction and stroke. Wogonin (Wog) is an active component of Scutellaria baicalensis, used for inflammatory diseases, atherosclerosis, and hyperlipidemia. The anticoagulant effect of Wog on TF expression remains unexplored. In this study, we have investigated the effects of Wog on TF gene expression and its underlying molecular mechanism in human vascular endothelial cells (ECs). We found that Wog dose-dependently inhibited PMA-enhanced TF mRNA, protein, and activity in ECs. This inhibition was attributed to its decreasing nuclear accumulations of transcription factors, phospho-c-Jun and early growth response-1(Egr-1), not nuclear factor-κB (NF-κB), through blocking extracellular signal-regulated kinase (ERK) and c-Jun N-terminal kinase (JNK) signaling pathways. Reduction by Wog of Egr-1 nuclear level and Egr-1/DNA binding activity was associated with its inhibition of Egr-1 de novo synthesis. Wog as well as inhibitors to ERK and JNK suppressed TF promoter activity and protein expression in reporter gene and Western blot analyses. Furthermore, it also exhibited anticoagulant function by inhibiting TF expression and activity in tumor necrosis factor-alpha (TNF-α)- and lipopolysaccharide (LPS)-treated ECs and THP-1 cells. These results suggest that Wog inhibits ERK/Egr-1- and JNK/AP-1-mediated transactivation of TF promoter activity, leading to downregulation of TF expression and activity induced by inflammatory mediators. Wog targeting pathological TF expression without affecting its basal level may be a safer templet in the development of anticoagulant agent for cardiovascular thrombotic diseases related to atherothrombosis.

We report the effects of protein from different duck products on the intestinal flora and physiology of rats. After 30 days of feeding, rats fed water-boiled salted duck protein had the lowest gut microbial diversity and richness. Allobaculum, Lactobacillus, Coprococcus and Eubacterium increased in rats fed wine-cured duck protein, while rats fed water-boiled salted and wine-cured duck protein showed increased serum urea (UREA) concentrations and serum cholesterol (CHOL) to HDL-cholesterol (HDLC) ratios, but decreased retroperitoneal white adipose tissue (rWAT) and perirenal white adipose tissue (pWAT) to body weight ratios. The changes in gut bacteria were mainly associated with the fat-mass index (weight of rWAT or pWAT to body weight ratio), accompanied by the opposite correlation with UREA content. SIGNIFICANCE: It showed that protein from different duck products impacted the intestinal flora and caused physiological changes in rats. Different sources of processed protein vary in their digestibility and digestive kinetics, all of which can affect the intestinal microbiota and physiology. We report the effects is an effort to map the complex interactions of "host physiology-nutrition-microbiota" in order to provide some insights into that food processing can be improved to promote beneficial gut microbes and enhance human health.

PEP Study: Ethics committee N° 393/2004, EudraCT 2004-004209-98. PEP-X Study: Ethics committee amendment application N° 154/01/2008. ClinicalTrials.gov NCT03751332.

We previously found a dominant mutation, Rwhs, causing white spots on the retina accompanied by retinal folds. Here we identify the mutant gene to be Tmem98. In humans, mutations in the orthologous gene cause nanophthalmos. We modeled these mutations in mice and characterized the mutant eye phenotypes of these and Rwhs.

New technologies are changing the therapeutical options to do indirect restorations and new adhesive systems are continuously introduced to be used by clinicians. Different interactions between restorations, adhesive systems components, enamel and dentin require having criteria based on the selection of the adhesive system, ensuring the longevity of the restorations and the preservation of the biological remnant. The adhesion force to the dental tissue is one of the indicatives of the behavior of the adhesive systems and influences the behavior of the treatments with direct and indirect restorations. The objective of this search was to find the adhesive systems with the best results in terms of the adhesion strength of indirect restorations on the dental tissues. The search was conducted in two MEDLINE digital databases (PubMed), and the Cochrane Library with a search strategy based on the combination of MeSH (Medical Subject Headings) keywords. This systematic review used the PRISMA guide (Preferred Reporting Items for Systematic Reviews and Meta-Analysis). According to this review, the 3-step adhesive systems were the best performing and still are the gold standard for the cementing of indirect restorations. In addition, it can be concluded that self-etched adhesive systems reduce the time spent in clinical practice, however at the interface level they behave as permeable membranes more susceptible to degradation.

It is incompletely understood how self-antigens become targets of humoral immunity in antibody-mediated autoimmune diseases. In this context, alarmins are discussed as an important level of regulation. Alarmins are recognized by various receptors, such as receptor for advanced glycation end products (RAGE). As RAGE is upregulated under inflammatory conditions, strongly binds nucleic acids and mediates pro-inflammatory responses upon alarmin recognition, our aim was to examine its contribution to immune complex-mediated autoimmune diseases. This question was addressed employing RAGE-/- animals in murine models of pristane-induced lupus, collagen-induced, and serum-transfer arthritis. Autoantibodies were assessed by enzyme-linked immunosorbent assay, renal disease by quantification of proteinuria and histology, arthritis by scoring joint inflammation. The associated immune status was determined by flow cytometry. In both disease entities, we detected tendentiously decreased autoantibody levels in RAGE-/- mice, however no differences in clinical outcome. In accordance with autoantibody levels, a subgroup of the RAGE-/- animals showed a decrease in plasma cells, and germinal center B cells and an increase in follicular B cells. Based on our results, we suggest that RAGE deficiency alone does not significantly affect antibody-mediated autoimmunity. RAGE may rather exert its effects along with other receptors linking environmental factors to auto-reactive immune responses.

Auxin plays a key role in different plant growth and development processes, including flower opening and development. The perception and signaling of auxin depend on the cooperative action of various components, among which auxin/indole-3-acetic acid (Aux/IAA) proteins play an imperative role. In a recent study, the entire Aux/IAA gene family was identified and comprehensively analyzed in Hedychium coronarium, a scented species used as an ornamental plant for cut flowers. Phylogenetic analysis showed that the Aux/IAA gene family in H. coronarium is slightly contracted compared to Arabidopsis, with low levels of non-canonical proteins. Sequence analysis of promoters showed numerous cis-regulatory elements related to various phytohormones. HcIAA genes showed distinct expression patterns in different tissues and flower developmental stages, and some HcIAA genes showed significant responses to auxin and ethylene, indicating that Aux/IAAs may play an important role in linking hormone signaling pathways. Based on the expression profiles, HcIAA2, HcIAA4, HcIAA6 and HcIAA12, were selected as candidate genes and HcIAA2 and HcIAA4 were screened for further characterization. Downregulation of HcIAA2 and HcIAA4 by virus-induced gene silencing in H. coronarium flowers modified the total volatile compound content, suggesting that HcIAA2 and HcIAA4 play important roles in H. coronarium floral scent formation. The results presented here will provide insights into the putative roles of HcIAA genes and will assist the elucidation of their precise roles during floral scent formation.

This study aimed to identify and determine the confidence level of community pharmacists in providing different interventions during asthma-targeted medicine use reviews (MURs). A self-administered questionnaire was posted to 487 pharmacies accredited to provide the service, across Greater London, Southampton, Cornwall, Sheffield and Norwich. A total of 122 responses were obtained, giving a response rate of 25% (122/487). Around half of the community pharmacists (51.6%) were providing more than 60 asthma-targeted MURs annually with inhaler technique being the most offered intervention and stepping up/down therapy being the least. The majority of community pharmacists (94.3%) were confident in providing inhaler technique advice, followed by smoking cessation (91%). However, confidence was less with relevant vaccination (61.5%) and stepping up/down patients' therapy (56.6%). Confidence level can vary between community pharmacists regarding different interventions provided during respiratory MURs. The results stress the need to promote community pharmacists' confidence in providing interventions such as stepping up/down therapy during asthma-targeted MURs. Additional research in this field is highly recommended in order to evaluate community pharmacists' confidence level on a national scale and to determine the factors influencing it. The study also suggests that provision of different interventions during respiratory MURs can be related to how community pharmacists perceive their role.

Several studies have demonstrated Si absorption in monocotyledon and dicotyledon species. Regarding Si accumulation, studies in monocotyledons have identified Si deposition around the cell wall, cuticle layer bulliform cells, silica cells and endodermal cells. In previous studies with different citrus species there were evidence of Si accumulation, however no information on Si deposition can be found. Therefore, in this study, Si was applied (0 and 1000 mg L-1) to the roots of two citrus species, 'Delta' Valencia (Citrus sinensis) and 'Nules' Clementine (Citrus reticulata). Si accumulation were investigated in new, and old leaves and roots. Si deposition was investigated through scanning electron microscopy using energy dispersive analysis X-ray, environmental scanning electron microscopy and light microscopy. Si accumulation was significantly higher in Si treated leaves comparatively to the control in both young and mature leaves. Meanwhile, Si accumulation increased with leaf age. Additionally, Si accumulation was significantly higher in roots than in leaves. With respect to Si deposition, granules were identified in the epidermal cells through SEM and ESEM studies. The light microscopy identified the presence of Si granules in the surface and around the outer cell surface forming the cuticle-silica double layer of the lower epidermis in Si treated plants. Silica deposit were not found on the abaxial leaf surface. The findings suggest a passive uptake in citrus species.