Functional and cellular characterization of human Retinoic Acid Induced 1 (RAI1) mutations associated with Smith-Magenis Syndrome

<p>Abstract</p> <p>Background</p> <p>Smith-Magenis Syndrome is a contiguous gene syndrome in which the dosage sensitive gene has been identified: the Retinoic Acid Induced 1 (<it>RAI1</it>). Little is known about the function of human RAI1.</p> <p>Results</p> <p>We generated the full-length cDNA of the wild type protein and five mutated forms: <it>RAI1-HA </it>2687delC, <it>RAI1-HA </it>3103delC, <it>RAI1 </it>R960X, <it>RAI1-HA </it>Q1562R, and <it>RAI1-HA </it>S1808N. Four of them have been previously associated with SMS clinical phenotype. Molecular weight, subcellular localization and transcription factor activity of the wild type and mutant forms were studied by western blot, immunofluorescence and luciferase assays respectively. The wild type protein and the two missense mutations presented a higher molecular weight than expected, localized to the nucleus and activated transcription of a reporter gene. The frameshift mutations generated a truncated polypeptide with transcription factor activity but abnormal subcellular localization, and the same was true for the 1-960aa N-terminal half of RAI1. Two different C-terminal halves of the RAI1 protein (1038aa-end and 1229aa-end) were able to localize into the nucleus but had no transactivation activity.</p> <p>Conclusion</p> <p>Our results indicate that transcription factor activity and subcellular localization signals reside in two separate domains of the protein and both are essential for the correct functionality of RAI1. The pathogenic outcome of some of the mutated forms can be explained by the dissociation of these two domains.</p

Multiple effects of silymarin on the hepatitis C virus lifecycle

Silymarin, an extract from milk thistle (Silybum marianum), and its purified flavonolignans have been recently shown to inhibit hepatitis C virus (HCV) infection, both in vitro and in vivo. In the current study, we further characterized silymarin's antiviral actions. Silymarin had antiviral effects against hepatitis C virus cell culture (HCVcc) infection that included inhibition of virus entry, RNA and protein expression, and infectious virus production. Silymarin did not block HCVcc binding to cells but inhibited the entry of several viral pseudoparticles (pp), and fusion of HCVpp with liposomes. Silymarin but not silibinin inhibited genotype 2a NS5B RNA-dependent RNA polymerase (RdRp) activity at concentrations 5 to 10 times higher than required for anti-HCVcc effects. Furthermore, silymarin had inefficient activity on the genotype 1b BK and four 1b RDRPs derived from HCV-infected patients. Moreover, silymarin did not inhibit HCV replication in five independent genotype 1a, 1b, and 2a replicon cell lines that did not produce infectious virus. Silymarin inhibited microsomal triglyceride transfer protein activity, apolipoprotein B secretion, and infectious virion production into culture supernatants. Silymarin also blocked cell-to-cell spread of virus. CONCLUSION: Although inhibition of in vitro NS5B polymerase activity is demonstrable, the mechanisms of silymarin's antiviral action appear to include blocking of virus entry and transmission, possibly by targeting the host cell

Requirement for PBAF in transcriptional repression and repair at DNA breaks in actively transcribed regions of chromatin

Actively transcribed regions of the genome are vulnerable to genomic instability. Recently, it was discovered that transcription is repressed in response to neighboring DNA double-strand breaks (DSBs). It is not known whether a failure to silence transcription flanking DSBs has any impact on DNA repair efficiency or whether chromatin remodelers contribute to the process. Here, we show that the PBAF remodeling complex is important for DSB-induced transcriptional silencing and promotes repair of a subset of DNA DSBs at early time points, which can be rescued by inhibiting transcription globally. An ATM phosphorylation site on BAF180, a PBAF subunit, is required for both processes. Furthermore, we find that subunits of the PRC1 and PRC2 polycomb group complexes are similarly required for DSB-induced silencing and promoting repair. Cancer-associated BAF180 mutants are unable to restore these functions, suggesting PBAF's role in repressing transcription near DSBs may contribute to its tumor suppressor activity

Solvation-guided design of fluorescent probes for discrimination of amyloids

The deposition of insoluble protein aggregates in the brain is a hallmark of many neurodegenerative diseases. While their exact role in neurodegeneration remains unclear, the presence of these amyloid deposits often precedes clinical symptoms. As a result, recent progress in imaging methods that utilize amyloid-specific small molecule probes have become a promising avenue for antemortem disease diagnosis. Here, we present a series of amino-aryl cyanoacrylate (AACA) fluorophores that show a turn-on fluorescence signal upon binding to amyloids in solution and in tissue. Using a theoretical model for environmental sensitivity of fluorescence together with ab initio computational modeling of the effects of polar environment on electron density distribution and conformational dynamics, we designed, synthesized, and evaluated a set of fluorophores that (1) bind to aggregated forms of Alzheimer's-related beta-amyloid peptides with low micromolar to high nanomolar affinities and (2) have the capability to fluorescently discriminate different amyloids based on differences in amino acid composition within the binding pocket through exploitation of their solvatochromic properties. These studies showcase the rational design of a family of amyloid-binding imaging agents that could be integrated with new optical approaches for the clinical diagnosis of amyloidoses, where accurate identification of the specific neurodegenerative disease could aid in the selection of a proper course for treatment

TRIM16 Acts as an E3 Ubiquitin Ligase and Can Heterodimerize with Other TRIM Family Members

The TRIM family of proteins is distinguished by its tripartite motif (TRIM). Typically, TRIM proteins contain a RING finger domain, one or two B-box domains, a coiled-coil domain and the more variable C-terminal domains. TRIM16 does not have a RING domain but does harbour two B-box domains. Here we showed that TRIM16 homodimerized through its coiled-coil domain and heterodimerized with other TRIM family members; TRIM24, Promyelocytic leukaemia (PML) protein and Midline-1 (MID1). Although, TRIM16 has no classic RING domain, three-dimensional modelling of TRIM16 suggested that its B-box domains adopts RING-like folds leading to the hypothesis that TRIM16 acts as an ubiquitin ligase. Consistent with this hypothesis, we demonstrated that TRIM16, devoid of a classical RING domain had auto-polyubiquitination activity and acted as an E3 ubiquitin ligase in vivo and in vitro assays. Thus via its unique structure, TRIM16 possesses both heterodimerization function with other TRIM proteins and also has E3 ubiquitin ligase activity

Anthropology on Economic Development in Hanoi, Capital of Vietnam Analysis of Commercial Activities of Hanghom Paint Shops Street

The killer immunoglobulin-like receptors (KIRs), found predominantly on the surface of natural killer (NK) cells and some T-cells, are a collection of highly polymorphic activating and inhibitory receptors with variable specificity for class I human leukocyte antigen (HLA) ligands. Fifteen KIR genes are inherited in haplotypes of diverse gene content across the human population, and the repertoire of independently inherited KIR and HLA alleles is known to alter risk for immune-mediated and infectious disease by shifting the threshold of lymphocyte activation. We have conducted the largest disease-association study of KIR-HLA epistasis to date, enabled by the imputation of KIR gene and HLA allele dosages from genotype data for 12,214 healthy controls and 8,107 individuals with the HLA-B*27-associated immune-mediated arthritis, ankylosing spondylitis (AS). We identified epistatic interactions between KIR genes and their ligands (at both HLA subtype and allele resolution) that increase risk of disease, replicating analyses in a semi-independent cohort of 3,497 cases and 14,844 controls. We further confirmed that the strong AS-association with a pathogenic variant in the endoplasmic reticulum aminopeptidase gene ERAP1, known to alter the HLA-B*27 presented peptidome, is not modified by carriage of the canonical HLA-B receptor KIR3DL1/S1. Overall, our data suggests that AS risk is modified by the complement of KIRs and HLA ligands inherited, beyond the influence of HLA-B*27 alone, which collectively alter the proinflammatory capacity of KIR-expressing lymphocytes to contribute to disease immunopathogenesis

Definition of the σW regulon of Bacillus subtilis in the absence of stress

Bacteria employ extracytoplasmic function (ECF) sigma factors for their responses to environmental stresses. Despite intensive research, the molecular dissection of ECF sigma factor regulons has remained a major challenge due to overlaps in the ECF sigma factor-regulated genes and the stimuli that activate the different ECF sigma factors. Here we have employed tiling arrays to single out the ECF σW regulon of the Gram-positive bacterium Bacillus subtilis from the overlapping ECF σX, σY, and σM regulons. For this purpose, we profiled the transcriptome of a B. subtilis sigW mutant under non-stress conditions to select candidate genes that are strictly σW-regulated. Under these conditions, σW exhibits a basal level of activity. Subsequently, we verified the σW-dependency of candidate genes by comparing their transcript profiles to transcriptome data obtained with the parental B. subtilis strain 168 grown under 104 different conditions, including relevant stress conditions, such as salt shock. In addition, we investigated the transcriptomes of rasP or prsW mutant strains that lack the proteases involved in the degradation of the σW anti-sigma factor RsiW and subsequent activation of the σW-regulon. Taken together, our studies identify 89 genes as being strictly σW-regulated, including several genes for non-coding RNAs. The effects of rasP or prsW mutations on the expression of σW-dependent genes were relatively mild, which implies that σW-dependent transcription under non-stress conditions is not strictly related to RasP and PrsW. Lastly, we show that the pleiotropic phenotype of rasP mutant cells, which have defects in competence development, protein secretion and membrane protein production, is not mirrored in the transcript profile of these cells. This implies that RasP is not only important for transcriptional regulation via σW, but that this membrane protease also exerts other important post-transcriptional regulatory functions

The Impact of Self-Agitating Anaerobic Batch Digester Design on Biogas Production of Cattle Manure Co-Digested with Lemna minor

The continuation of utilizing fossil fuels as cooking energy sources in rural communities in the Philippines causes more citizens to be at risk of developing numerous health illnesses. This study aimed to propose a potential solution to this problem by innovating a self-agitating anaerobic batch digester, promoting biogas production of cattle manure co-digested with Lemna minor. Two anaerobic batch digester designs, one with baffles and one without, were observed within 22 days to determine the impact of the anaerobic digester design on mixing and biogas production yield. The study contained two pairs of anaerobic batch digesters, the initial and improved digester. The water displacement method was used to measure the biogas yield from the initial and improved digesters. The results of this study on the quantity of biogas produced between the initial experimental designs measured every six days and revised experimental designs measured every four days concluded that anaerobic batch digester designs with baffles produced a superior amount of biogas with 5468.88 cm³ more yield than the digester without baffles. Utilizing an Independent Sample T-test, the difference in biogas production is considered significant, (p = .174). Similar studies in the future are encouraged to explore variations in the anaerobic digester design outside of the placement of baffles, including factors such as the materials used and the period of observation due to the limitations of this study

PHANGS-JWST: Data-processing Pipeline and First Full Public Data Release

The exquisite angular resolution and sensitivity of JWST are opening a new window for our understanding of the Universe. In nearby galaxies, JWST observations are revolutionizing our understanding of the first phases of star formation and the dusty interstellar medium. Nineteen local galaxies spanning a range of properties and morphologies across the star-forming main sequence have been observed as part of the PHANGS-JWST Cycle 1 Treasury program at spatial scales of ∼5–50 pc. Here, we describe pjpipe, an image-processing pipeline developed for the PHANGS-JWST program that wraps around and extends the official JWST pipeline. We release this pipeline to the community as it contains a number of tools generally useful for JWST NIRCam and MIRI observations. Particularly for extended sources, pjpipe products provide significant improvements over mosaics from the MAST archive in terms of removing instrumental noise in NIRCam data, background flux matching, and calibration of relative and absolute astrometry. We show that slightly smoothing F2100W MIRI data to 0.″9 (degrading the resolution by about 30%) reduces the noise by a factor of ≈3. We also present the first public release (DR1.1.0) of the pjpipe processed eight-band 2–21 μm imaging for all 19 galaxies in the PHANGS-JWST Cycle 1 Treasury program. An additional 55 galaxies will soon follow from a new PHANGS-JWST Cycle 2 Treasury program

Global perspectives on electric vehicle education: part II

In this two-paper set, academics from universities in the Americas, China and Europe discuss educational and pedagogical developments at university level on electric vehicles (EV). EVs, whether battery (BEV), hybrid (HEV) or fuel cell (FCEV), are seen as being a crucial and essential component of sustainable living, and entire industries around the world are evolving to foster the development of electromobility. Thus, university curricula must also adapt. The authors, university by university, investigate the motivations, challenges and adaptations for EV education and the related pedagogy. Aspects of the related curricula are discussed with helpful insights on content and adoption. Challenges and future adaptations are often discussed. Academics from the following universities contribute to the papers, which are presented in two parts in order to cover the topic. Part I: University College Cork (UCC) and US Hybrid (USH), Indiana Institute of Technology (IT), Beijing Jiaotong University (BJTU), and Southern Illinois University Carbondale (SIUC); Part II: Jilin University (JLU), Oregon State University (OSU), Leibniz University Hannover (LUH), and Universidade Federal de Sao Carlos (UFCar). See Part I for the introduction to this two-paper set