A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays

<p>Abstract</p> <p>Background</p> <p>Regulation of gene expression is essential for normal development and cellular growth. Transcriptional events are tightly controlled both spatially and temporally by specific DNA-protein interactions. In this study we finely map the genome-wide targets of the CREB protein across all known and predicted human promoters, and characterize the functional consequences of a subset of these binding events using high-throughput reporter assays. To measure CREB binding, we used HaloCHIP, an antibody-free alternative to the ChIP method that utilizes the HaloTag fusion protein, and also high-throughput promoter-luciferase reporter assays, which provide rapid and quantitative screening of promoters for transcriptional activation or repression in living cells.</p> <p>Results</p> <p>In analysis of CREB genome-wide binding events using a comprehensive DNA microarray of human promoters, we observe for the first time that CREB has a strong preference for binding at bidirectional promoters and unlike unidirectional promoters, these binding events often occur downstream of transcription start sites. Comparison between HaloCHIP-chip and ChIP-chip data reveal this to be true for both methodologies, indicating it is not a bias of the technology chosen. Transcriptional data obtained from promoter-luciferase reporter arrays also show an unprecedented, high level of activation of CREB-bound promoters in the presence of the co-activator protein TORC1.</p> <p>Conclusion</p> <p>These data suggest for the first time that TORC1 provides directional information when CREB is bound at bidirectional promoters and possible pausing of the CREB protein after initial transcriptional activation. Also, this combined approach demonstrates the ability to more broadly characterize CREB protein-DNA interactions wherein not only DNA binding sites are discovered, but also the potential of the promoter sequence to respond to CREB is evaluated.</p

Gastric non-Hodgkin Lymphoma

Extranodal lymphomas account for about 30% of all non-Hodgkin lymphomas (NHL), and although they can originate in any tissue, the gastrointestinal tract is the most commonly affected structure with the stomach being the most common subtype. Diffuse Large B cell lymphoma (DLBCL) and MALT (mucosa associated lymphoid tissue) lymphoma account for more than 95% of the cases of gastric lymphoma. The indolent development of MALT lymphoma stands out as it is a type of cancer subject to chronic antigen stimulation by the Helicobacter pylori bacteria. Conversely, diffuse large B cell lymphomas, whose pathogenesis is uncertain, can be a transformation from MALT NHL or perhaps a new type of lymphoma. In this study we carried out a review of the literature, stressing the key aspects of these lymphomas in the clinical practice.Os linfomas extralinfonodais representam aproximadamente 1/3 de todos os linfomas não Hodgkin (LNH) e, embora possam ter início em qualquer tecido, mais frequentemente acometem o trato gastrointestinal, sendo o estômago o órgão responsável pela grande maioria dos casos. Os linfomas primários gástricos são comumente LNH, sendo representados em mais de 95% dos casos pelo linfoma difuso de grandes células B e pelo linfoma MALT (mucosa associated lymphoid tissue). De evolução indolente, o linfoma MALT destaca-se por ser um modelo de câncer secundário à estimulação antigênica crônica exercida por uma bactéria denominada Helicobacter pylori (HP). No outro polo, situa-se o linfoma difuso de células B (LDGCB), que, de patogênese duvidosa, pode tratar-se de uma transformação de LNH MALT ou ainda se caracterizar por um linfoma "de novo". Neste estudo, revisamos a literatura, enfatizando aspectos importantes à prática clínica destes linfomas

Ab initio study of the volume dependence of dynamical and thermodynamical properties of silicon

Motivated by the negative thermal expansion observed for silicon between 20 K and 120 K, we present first an ab initio study of the volume dependence of interatomic force constants, phonon frequencies of TA(X) and TA(L) modes, and of the associated mode Gruneisen parameters. The influence of successive nearest neighbors shells is analysed. Analytical formulas, taking into account interactions up to second nearest neighbors, are developped for phonon frequencies of TA(X) and TA(L) modes and the corresponding mode Gruneisen parameters. We also analyze the volume and pressure dependence of various thermodynamic properties (specific heat, bulk modulus, thermal expansion), and point out the effect of the negative mode Gruneisen parameters of the acoustic branches on these properties. Finally, we present the evolution of the mean square atomic displacement and of the atomic temperature factor with the temperature for different volumes, for which the anomalous effects are even greater.Comment: 24 pages, Revtex 3.0, 11 figures, accepted for publication in Phys. Rev.

Continuous Subcutaneous Foslevodopa/Foscarbidopa in Parkinson’s Disease: Safety and Efficacy Results From a 12-Month, Single-Arm, Open-Label, Phase 3 Study

\ua9 2023, The Author(s). Introduction: Foslevodopa/foscarbidopa, a soluble formulation of levodopa/carbidopa (LD/CD) prodrugs for the treatment of Parkinson’s disease (PD), is administered as a 24-hour/day continuous subcutaneous infusion (CSCI) with a single infusion site. The efficacy and safety of foslevodopa/foscarbidopa versus oral immediate-release LD/CD was previously demonstrated in patients with PD in a 12-week, randomized, double-blind, phase 3 trial (NCT04380142). We report the results of a separate 52-week, open-label, phase 3 registrational trial (NCT03781167) that evaluated the safety/tolerability and efficacy of 24-hour/day foslevodopa/foscarbidopa CSCI in patients with advanced PD. Methods: Male and female patients with levodopa-responsive PD and ≥ 2.5 hours of “Off” time/day received 24-hour/day foslevodopa/foscarbidopa CSCI at individually optimized therapeutic doses (approximately 700–4250 mg of LD per 24 hours) for 52 weeks. The primary endpoint was safety/tolerability. Secondary endpoints included changes from baseline in normalized “Off” and “On” time, percentage of patients reporting morning akinesia, Movement Disorder Society Unified Parkinson’s Disease Rating Scale (MDS-UPDRS), Parkinson’s Disease Sleep Scale–2 (PDSS-2), 39-item Parkinson’s Disease Questionnaire (PDQ-39), and EuroQol 5-dimension questionnaire (EQ-5D-5L). Results: Of 244 enrolled patients, 107 discontinued, and 137 completed treatment. Infusion site events were the most common adverse events (AEs). AEs were mostly nonserious (25.8% of patients reported serious AEs) and mild/moderate in severity. At week 52, “On” time without troublesome dyskinesia and “Off” time were improved from baseline (mean [standard deviation (SD)] change in normalized “On” time without troublesome dyskinesia, 3.8 [3.3] hours; normalized “Off” time, −3.5 [3.1] hours). The percentage of patients experiencing morning akinesia dropped from 77.7% at baseline to 27.8% at week 52. Sleep quality (PDSS-2) and quality of life (PDQ-39 and EQ-5D-5L) also improved. Conclusion: Foslevodopa/foscarbidopa has the potential to provide a safe and efficacious, individualized, 24-hour/day, nonsurgical alternative for patients with PD. Trial Registration Number: ClinicalTrials.gov identifier NCT03781167

De novo unbalanced translocations have a complex history/aetiology

We investigated 52 cases of de novo unbalanced translocations, consisting in a terminally deleted or inverted-duplicated deleted (inv-dup del) 46th chromosome to which the distal portion of another chromosome or its opposite end was transposed. Array CGH, whole-genome sequencing, qPCR, FISH, and trio genotyping were applied. A biparental origin of the deletion and duplication was detected in 6 cases, whereas in 46, both imbalances have the same parental origin. Moreover, the duplicated region was of maternal origin in more than half of the cases, with 25% of them showing two maternal and one paternal haplotype. In all these cases, maternal age was increased. These findings indicate that the primary driver for the occurrence of the de novo unbalanced translocations is a maternal meiotic non-disjunction, followed by partial trisomy rescue of the supernumerary chromosome present in the trisomic zygote. In contrast, asymmetric breakage of a dicentric chromosome, originated either at the meiosis or postzygotically, in which the two resulting chromosomes, one being deleted and the other one inv-dup del, are repaired by telomere capture, appears at the basis of all inv-dup del translocations. Notably, this mechanism also fits with the origin of some simple translocations in which the duplicated region was of paternal origin. In all cases, the signature at the translocation junctions was that of non-homologous end joining (NHEJ) rather than non-allelic homologous recombination (NAHR). Our data imply that there is no risk of recurrence in the following pregnancies for any of the de novo unbalanced translocations we discuss here

Localization and density of phoretic deutonymphs of the mite Uropoda orbicularis (Parasitiformes : Mesostigmata) on Aphodius beetles (Aphodiidae) affect pedicel length

The phoretic stage of Uropodina mites is a deutonymph with developed morphological adaptations for dispersal by insects. Phoretic deutonymphs are able to produce a pedicel, a stalk-like temporary attachment structure that connects the mite with the carrier. The aim of our study was to determine whether localization and density of phoretic deutonymphs on the carrier affect pedicel length. The study was conducted on a common phoretic mite-Uropoda orbicularis (Uropodina) and two aphodiid beetles-Aphodius prodromus and Aphodius distinctus. Our results show that pedicel length is influenced by the localization of deutonymphs on the body of the carrier. The longest pedicels are produced by deutonymphs attached to the upper part of elytra, whereas deutonymphs attached to femora and trochanters of the third pair of legs and the apex of elytra construct the shortest pedicels. In general, deutonymphs attached to more exposed parts of the carrier produce longer pedicels, whereas shorter pedicels are produced when deutonymphs are fixed to non-exposed parts of the carrier. A second factor influencing pedicel length is the density of attached deutonymphs. Mean pedicel length and deutonymph densities were highly correlated: higher deutonymph density leads to the formation of longer pedicels. The cause for this correlation is discussed, and we conclude that pedicel length variability can increase successful dispersal

Metamorphosis in the Cirripede Crustacean Balanus amphitrite

Stalked and acorn barnacles (Cirripedia Thoracica) have a complex life cycle that includes a free-swimming nauplius larva, a cypris larva and a permanently attached sessile juvenile and adult barnacle. The barnacle cyprid is among the most highly specialized of marine invertebrate larvae and its settlement biology has been intensively studied. By contrast, surprisingly few papers have dealt with the critical series of metamorphic events from cementation of the cyprid to the substratum until the appearance of a suspension feeding juvenile. This metamorphosis is both ontogenetically complex and critical to the survival of the barnacle. Here we use video microscopy to present a timeline and description of morphological events from settled cyprid to juvenile barnacle in the model species Balanus amphitrite, representing an important step towards both a broader understanding of the settlement ecology of this species and a platform for studying the factors that control its metamorphosis. Metamorphosis in B. amphitrite involves a complex sequence of events: cementation, epidermis separation from the cypris cuticle, degeneration of cypris musculature, rotation of the thorax inside the mantle cavity, building of the juvenile musculature, contraction of antennular muscles, raising of the body, shedding of the cypris cuticle, shell plate and basis formation and, possibly, a further moult to become a suspension feeding barnacle. We compare these events with developmental information from other barnacle species and discuss them in the framework of barnacle settlement ecology

Beta-defensin genomic copy number is not a modifier locus for cystic fibrosis

Human beta-defensin 2 (DEFB4, also known as DEFB2 or hBD-2) is a salt-sensitive antimicrobial protein that is expressed in lung epithelia. Previous work has shown that it is encoded in a cluster of beta-defensin genes at 8p23.1, which varies in copy number between 2 and 12 in different individuals. We determined the copy number of this locus in 355 patients with cystic fibrosis (CF), and tested for correlation between beta-defensin cluster genomic copy number and lung disease associated with CF. No significant association was found