The first transcriptome of Italian wall lizard, a new tool to infer about the Island Syndrome

Some insular lizards show a high degree of differentiation from their conspecific mainland populations, like Licosa island lizards, which are described as affected by Reversed Island Syndrome (RIS). In previous works, we demonstrated that some traits of RIS, as melanization, depend on a differential expression of gene encoding melanocortin receptors. To better understand the basis of syndrome, and providing raw data for future investigations, we generate the first de novo transcriptome of the Italian wall lizard. Comparing mainland and island transcriptomes, we link differences in life-traits to differential gene expression. Our results, taking together testis and brain sequences, generated 275,310 and 269,885 transcripts, 18,434 and 21,606 proteins in Gene Ontology annotation, for mainland and island respectively. Variant calling analysis identified about the same number of SNPs in island and mainland population. Instead, through a differential gene expression analysis we found some putative genes involved in syndrome more expressed in insular samples like Major Histocompatibility Complex class I, Immunoglobulins, Melanocortin 4 receptor, Neuropeptide Y and Proliferating Cell Nuclear Antigen

A retrospective study on IVF outcome in euthyroid patients with anti-thyroid antibodies: effects of levothyroxine, acetyl-salicylic acid and prednisolone adjuvant treatments

<p>Abstract</p> <p>Background</p> <p>Anti-thyroid antibodies (ATA), even if not associated with thyroid dysfunction, are suspected to cause poorer outcome of in vitro fertilization (IVF).</p> <p>Methods</p> <p>We retrospectively analyzed: (a) the prevalence of ATA in euthyroid infertile women, (b) IVF outcome in euthyroid, ATA+ patients, and (c) the effect of adjuvant treatments (levothyroxine alone or associated with acetylsalicylic acid and prednisolone) on IVF results in ATA+ patients. One hundred twenty-nine euthyroid, ATA+ women undergoing IVF were compared with 200 matched, ATA-controls. During IVF cycle, 38 ATA+ patients did not take any adjuvant treatment, 55 received levothyroxin (LT), and 38 received LT +acetylsalicylic acid (ASA)+prednisolone (P).</p> <p>Results</p> <p>The prevalence of ATA among euthyroid, infertile patients was 10.5%, similar to the one reported in euthyroid women between 18 and 45 years. ATA+ patients who did not receive any adjuvant treatment showed significantly poorer ovarian responsiveness to stimulation and IVF results than controls. ATA+ patients receiving LT responded better to ovarian stimulation, but had IVF results as poor as untreated ATA+ women. Patients receiving LT+ASA+P had significantly higher pregnancy and implantation rates than untreated ATA+ patients (PR/ET 25.6% and IR 17.7% vs. PR/ET 7.5% and IR 4.7%, respectively), and overall IVF results comparable to patients without ATA (PR/ET 32.8% and IR 19%).</p> <p>Conclusion</p> <p>These observations suggest that euthyroid ATA+ patients undergoing IVF could have better outcome if given LT+ASA+P as adjuvant treatment. This hypothesis must be verified in further randomized, prospective studies.</p

Biapenem Inactivation by B2 Metallo β-Lactamases: Energy Landscape of the Post-Hydrolysis Reactions

<div><h3>Background</h3><p>The first line of defense by bacteria against <em>β</em>-lactam antibiotics is the expression of β-lactamases, which cleave the amide bond of the β-lactam ring. In the reaction of biapenem inactivation by B2 metallo β-lactamases (MβLs), after the β-lactam ring is opened, the carboxyl group generated by the hydrolytic process and the hydroxyethyl group (common to all carbapenems) rotate around the C5–C6 bond, assuming a new position that allows a proton transfer from the hydroxyethyl group to C2, and a nucleophilic attack on C3 by the oxygen atom of the same side-chain. This process leads to the formation of a bicyclic compound, as originally observed in the X-ray structure of the metallo β-lactamase CphA in complex with product.</p> <h3>Methodology/Principal Findings</h3><p>QM/MM and metadynamics simulations of the post-hydrolysis steps in solution and in the enzyme reveal that while the rotation of the hydroxyethyl group can occur in solution or in the enzyme active site, formation of the bicyclic compound occurs primarily in solution, after which the final product binds back to the enzyme. The calculations also suggest that the rotation and cyclization steps can occur at a rate comparable to that observed experimentally for the enzymatic inactivation of biapenem only if the hydrolysis reaction leaves the N4 nitrogen of the β-lactam ring unprotonated.</p> <h3>Conclusions/Significance</h3><p>The calculations support the existence of a common mechanism (in which ionized N4 is the leaving group) for carbapenems hydrolysis in all MβLs, and suggest a possible revision of mechanisms for B2 MβLs in which the cleavage of the β-lactam ring is associated with or immediately followed by protonation of N4. The study also indicates that the bicyclic derivative of biapenem has significant affinity for B2 MβLs, and that it may be possible to obtain clinically effective inhibitors of these enzymes by modification of this lead compound.</p> </div

Helicobacter pylori regulates iNOS promoter by histone modifications in human gastric epithelial cells. [R. Pero* corresponding author]

Inducible nitric oxide synthase (iNOS) expression is altered in gastrointestinal diseases. Helicobacter pylori (Hp) infection may have a critical role in iNOS disregulation. We undertook this study to investigate possible chromatin changes occurring early during iNOS gene activation as a direct consequence of Hp???gastric cells interaction. We show that Hp infection is followed by different expression and chromatin modifications in gastric cells including (1) activation of iNOS gene expression, (2) chromatin changes at iNOS promoter including decreased H3K9 methylation and increased H3 acetylation and H3K4 methylation levels, (3) selective release of methyl-CpG-binding protein 2 from the iNOS promoter. Moreover, we show that Hp-induced activation of iNOS is delayed, but not eliminated, by the treatment with LSD1 inhibitors. Our data suggest a role for specific chromatin-based mechanisms in the control of human iNOS gene expression upon Hp exposure

Childhood asthma and indoor allergens in Native Americans in New York

BACKGROUND: The objective of this study was to assess the correlation between childhood asthma and potential risk factors, especially exposure to indoor allergens, in a Native American population. METHODS: A case-control study of St. Regis Mohawk tribe children ages 2–14 years, 25 diagnosed with asthma and 25 controls was conducted. Exposure was assessed based on a personal interview and measurement of mite and cat allergens (Der p 1, Fel d 1) in indoor dust. RESULTS: A non-significant increased risk of childhood asthma was associated with self-reported family history of asthma, childhood environmental tobacco smoke exposure, and air pollution. There was a significant protective effect of breastfeeding against current asthma in children less than 14 years (5.2 fold lower risk). About 80% of dust mite and 15% of cat allergen samples were above the threshold values for sensitization of 2 and 1 μg/g, respectively. The association between current asthma and exposure to dust mite and cat allergens was positive but not statistically significant. CONCLUSION: This research identified several potential indoor and outdoor risk factors for asthma in Mohawks homes, of which avoidance may reduce or delay the development of asthma in susceptible individuals

One ligand, two regulators and three binding sites: How KDPG controls primary carbon metabolism in Pseudomonas

Effective regulation of primary carbon metabolism is critically important for bacteria to successfully adapt to different environments. We have identified an uncharacterised transcriptional regulator; RccR, that controls this process in response to carbon source availability. Disruption of rccR in the plant-associated microbe Pseudomonas fluorescens inhibits growth in defined media, and compromises its ability to colonise the wheat rhizosphere. Structurally, RccR is almost identical to the Entner-Doudoroff (ED) pathway regulator HexR, and both proteins are controlled by the same ED-intermediate; 2-keto-3-deoxy-6-phosphogluconate (KDPG). Despite these similarities, HexR and RccR control entirely different aspects of primary metabolism, with RccR regulating pyruvate metabolism (aceEF), the glyoxylate shunt (aceA, glcB, pntAA) and gluconeogenesis (pckA, gap). RccR displays complex and unusual regulatory behaviour; switching repression between the pyruvate metabolism and glyoxylate shunt/gluconeogenesis loci depending on the available carbon source. This regulatory complexity is enabled by two distinct pseudo-palindromic binding sites, differing only in the length of their linker regions, with KDPG binding increasing affinity for the 28 bp aceA binding site but decreasing affinity for the 15 bp aceE site. Thus, RccR is able to simultaneously suppress and activate gene expression in response to carbon source availability. Together, the RccR and HexR regulators enable the rapid coordination of multiple aspects of primary carbon metabolism, in response to levels of a single key intermediate

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Basaltic Dyke with Specific Volcanogenic Structures and its geomorphic evolution: Unique Geoheritage of the Faroe Islands (North Atlantic Ocean)

Volcanic landforms resulting from Cenozoic volcanism represent the most peculiar features of global geodiversity and provide eminent narratives for geoeducation. Among them, however, relict volcanic forms and site-specific landforms in remote areas have received less attention. In this paper, we provide the first description of unique volcanogenic features (hereinafter referred to as pseudo-hieroglyphs) developed on a summit rock wall at the Sandfelli ridge near the village of Gjógv in the N Eysturoy Island (Faroe Islands). The geomorphic evolution of the ridge and rock wall during the Quaternary is described and detailed petrographic analyses of the volcanogenic features are provided. Based on observed petrographical features, we interpret the pseudo-hieroglyphs to probably represent unique examples of chaotic horizontal columnar jointing. Following the geomorphological and petrographic examination of the study site, we analyse current Faroese legislation aiming at nature conservation and use this case to discuss broader implications of geoheritage conservation and geotourism in distant regions.Vulkanická krajina vzniklá kenozoickým vulkanismem představuje nejpodivnější rysy globální geodiversity a poskytuje vynikající příběhy pro geovzdělávání. Méně pozornosti se však dostává reliktním vulkanickým formám a lokálním tvarům reliéfu v odlehlých oblastech. V tomto článku přinášíme první popis unikátních vulkanogenních tvarů (dále jen "pseudo-hieroglyfy"), které se vyvíjely na skalní stěně vrcholu na hřbetě Sandfelli u vesnice Gjógv v severní části ostrova Eysturoy (Faerské ostrovy). Je popsán geomorfologický vývoj hřbetu a skalní stěny během kvartéru a jsou uvedeny podrobné petrografické analýzy vulkanogenních vlastností. Na základě pozorovaných petrografických rysů interpretujeme pseudo-hieroglyfy, které pravděpodobně představují jedinečné příklady chaotické horizontální sloupcovité odlučnosti. Po geomorfologickém a petrografickém studiu zájmové lokality analyzujeme současnou faerskou legislativu zaměřenou na ochranu přírody a užíváme tohoto příkladu k diskusi širších důsledků zachování a geoturistiky geografického dědictví ve vzdálených regionech

FKBP5 splicing concurs to Treg differentiation of Tconv cells

FKBP51 (FKBP5 gene) is an immunophilin physiologically expressed by immune cells. Thanks to its scaffold and isomerase activity supporting IKK complex assembly and function, FKBP51 plays a relevant role in NF-κB activation. Recently, we identified a splicing isoform, shorter than the canonical one, termed FKBP51s. FKBP51s acts as a PD-L1 foldase, assisting to protein maturation and expression on plasma membrane. Particularly, FKBP51s was firstly identified in TILs and PBMCs of melanoma patients. In these patients, FKBP51s marked a subset of Tregs with an increased phospho-mTOR and Ki67 expression. Logistic regression analysis suggested that FKBP51sTreg is a valuable element which predicts the probability of response to ipilimumab. Given the foregoing, we attempted to investigate FKBP5 splicing during T lymphocyte activation and assess its role in Treg formation and suppression capability. We found that FKBP5 splicing occurred early in the course of a suboptimal but not maximal PBMCs stimulation. The increase in FKBP51s was transient and associated with a delay in Akt and STAT5 activation. When splicing was prevented, Treg count was decreased and Tconv cell proliferation increased. Moreover, measure of FKBP51s level in Foxp3CD25high Treg subset showed highest levels in PBMCs cultures under suboptimal CD3 co-stimulation. Coculture suppression assays showed that Treg silenced for FKBP51s had a significantly reduced suppressive capability, compared with non-silenced Tregs. In conclusion, our findings suggest that FKBP5 splicing occurs under conditions of suboptimal CD3 co-stimulation of Tconv cells and concurs to their differentiation into Tregs. Manipulating FKBP5 splicing can be a means to control tumor tolerance