Cooperative effects on the compaction of DNA fragments by the nucleoid protein H-NS and the crowding agent PEG probed by Magnetic Tweezers.

BACKGROUND: DNA bridging promoted by the H-NS protein, combined with the compaction induced by cellular crowding, plays a major role in the structuring of the E. coli genome. However, only few studies consider the effects of the physical interplay of these two factors in a controlled environment. METHODS: We apply a single molecule technique (Magnetic Tweezers) to study the nanomechanics of compaction and folding kinetics of a 6 kb DNA fragment, induced by H-NS bridging and/or PEG crowding. RESULTS: In the presence of H-NS alone, the DNA shows a step-wise collapse driven by the formation of multiple bridges, and little variations in the H-NS concentration-dependent unfolding force. Conversely, the DNA collapse force observed with PEG was highly dependent on the volume fraction of the crowding agent. The two limit cases were interpreted considering the models of loop formation in a pulled chain and pulling of an equilibrium globule respectively. CONCLUSIONS: We observed an evident cooperative effect between H-NS activity and the depletion of forces induced by PEG. GENERAL SIGNIFICANCE: Our data suggest a double role for H-NS in enhancing compaction while forming specific loops, which could be crucial in vivo for defining specific mesoscale domains in chromosomal regions in response to environmental changes.

[Should physical activity be contraindicated during pregnancy in relation to its potentially related risks?] / L'activité physique devrait-elle être contre-indiquée pendant la grossesse au regard des risques qui lui sont potentiellement associés ?

OBJECTIVE: This paper aimed at providing a critical analysis of data on the risks associated with physical activity of women during their pregnancy. METHODS: Cochrane Library, Google Scholar, PubMed (Medline) and Web of Sciences were searched using a combination of MeSH terms associated to "Physical activity", "Pregnancy" and "Adverse events" or "Risks". Only review papers published from inception of these databases to November 2016 were used in the present analysis. RESULTS: The electronic search yield a total of 104 citations. After a critical analysis of abstracts and/or full-texts, only a systematic review and cohort study on injuries related to physical activity during pregnancy appeared relevant for the current study. Data reveals a very small proportion (<1 %) of adverse events in direct link with the physical activity behavior of pregnant women. Furthermore, there would be less than one serious adverse event per 5000hours of physical activity. The only serious adverse event attributable to physical activity during pregnancy was uterine contractions. The threat of preterm labor and miscarriage risk cannot be primarily attributed to the participation of pregnant women in a physical activity, even vigorous. Moreover, no adverse effects of maternal physical activity on neonatal outcomes were found. CONCLUSION: Physical activity-related risks during pregnancy appear to be infrequent and of minor severity. Though further studies are required to better understand the risk/benefit balance of physical activity during pregnancy, current data do not support the contraindication of this behavior in pregnant women.

Effects of cytosine methylation on DNA morphology: An atomic force microscopy study.

Methylation is one of the most important epigenetic mechanisms in eukaryotes. As a consequence of cytosine methylation, the binding of proteins that are implicated in transcription to gene promoters is severely hindered, which results in gene regulation and, eventually, gene silencing. To date, the mechanisms by which methylation biases the binding affinities of proteins to DNA are not fully understood; however, it has been proposed that changes in double-strand conformations, such as stretching, bending, and over-twisting, as well as local variations in DNA stiffness/flexibility may play a role. The present work investigates, at the single molecule level, the morphological consequences of DNA methylation in vitro. By tracking the atomic force microscopy images of single DNA molecules, we characterize DNA conformations pertaining to two different degrees of methylation. In particular, we observe that methylation induces no relevant variations in DNA contour lengths, but produces measurable incremental changes in persistence lengths. Furthermore, we observe that for the methylated chains, the statistical distribution of angles along the DNA coordinate length is characterized by a double exponential decay, in agreement with what is predicted for polyelectrolytes. The results reported herein support the claim that the biological consequences of the methylation process, specifically difficulties in protein-DNA binding, are at least partially due to DNA conformation modifications.

A cross-sectional nationwide survey on esophageal atresia and tracheoesophageal fistula.

BACKGROUND: Our study aims at disclosing epidemiology and most relevant clinical features of esophageal atresia (EA) pointing to a model of multicentre collaboration. METHODS: A detailed questionnaire was sent to all Italian Units of pediatric surgery in order to collect data of patients born with EA between January and December 2012. The results were crosschecked by matching date and place of birth of the patients with those of diagnosis-related group provided by the Italian Ministry of Health (MOH). RESULTS: A total of 146 questionnaires were returned plus a further 32 patients reported in the MOH database. Basing on a total of 178 patients with EA born in Italy in 2012, the incidence of EA was calculated in 3.33 per 10,000 live births. Antenatal diagnosis was suspected in 29.5% patients. 55.5% showed associated anomalies. The most common type of EA was Gross type C (89%). Postoperative complications occurred in 37% of type C EA and 100% of type A EA. A 9.5% mortality rate was reported. CONCLUSIONS: This is the first Italian cross-sectional nationwide survey on EA. We can now develop shared guidelines and provide more reliable prognostic expectations for our patients.

Serum and bal beta-D-glucan for the diagnosis of Pneumocystis pneumonia in HIV positive patients.

BACKGROUND/PURPOSE: The diagnosis of patients with pulmonary infiltrates and human immunodeficiency virus (HIV) infection remains a challenge. In current clinical practice the gold standard for Pneumocystis jirovecii pneumonia (PCP) diagnosis remains the identification of the organism in bronco alveolar lavage (BAL) using microscopy (e.g., silver stain). (1->3)-ß -d-glucan (BG) is a polysaccharide that is present within the cell wall of Pneumocystis and other fungi. METHODS: We analyzed serum and BAL lavage fluid from a cohort of 119 patients that did have HIV, a diagnosis of pneumonia and underwent bronchoscopy (FOB) for diagnosis of PCP. RESULTS: The discriminative power of serum BG for the diagnosis of PCP in this group of patients was very high. Using a cutoff of 300 pg/mL, the sensitivity, specificity, positive predictive value(PPV) and negative predictive value (NPV) were 91%, 92%, 89% and 93% respectively. A model for ROC with just serum BG (N = 108) had an AUC of 0.95. Serum procalcitonin (PCT) and BAL BG were not as accurate for the diagnosis of PCP. For BAL BG using a cutoff of 783 pg/mL, the sensitivity,specificity, positive predictive value (PPV) and negative predictive value (NPV) were 72%, 79%,72% and 79% respectively. The differences between the medians for serum PCT between the group with a without PCP did not reach statistical significance (p = 0.6137). CONCLUSION: The measurement of serum BG should be incorporated in the diagnostic work up of HIV positive patients with dyspnea and infiltrates on chest X X-ray. Our study confirms the diagnostic value of serum BG previously reported by others but we add a cutoff value that we believe is more accurate for patients with AIDS and suspicion of PCP.

A case of spontaneous gastric rupture in a 5 years girl.

We describe a case of spontaneous gastric rupture in a child of 5 years old. The patient reached us in a serious condition; the anamnesis was negative for traumatic events or gastrointestinal disorders. An abdominal X-ray and CT scan revealed free air and fluid in the abdominal cavity, leading to the diagnosis of gastro-intestinal perforation. Submitted to urgent surgery, a rupture of the posterior wall of the stomach was found that was treated with gastrectomy "à la demande". The surgery follow-up was regular. Morphological and immunohistochemical study showed some muscular abnormalities of the muscular gastric wall.

Capacitive mixing for the extraction of energy from salinity differences: survey of experimental results and electrochemical models.

The "capacitive mixing" (CAPMIX) technique is an emerging technology aimed at the extraction of energy from salinity differences, e.g. between sea and river waters. CAPMIX benefits from the voltage rise that takes place between two electrodes dipped in a saline solution when its salt concentration is changed. Several kinds of electrodes have been proposed so far: activated carbon materials (Brogioli, 2009), membrane-based ion-selective electrodes (Sales et al., 2010), and battery electrodes (Biesheuvel and van der Wal, 2010). The power production mainly depends on two properties of each single electrode: the amplitude of the potential rise upon salinity change, and the potential in the high-salinity solution. The various electrode materials that have been used returned different values of the two parameters, and hence to different power productions. In this paper, we apply electrokinetic and electrochemical models to qualitatively explain the experimentally observed behaviors of various materials under different experimental conditions. The analysis allows to devise techniques for tailoring new materials, particularly suited for the CAPMIX technique.

Biophysical characterization of a binding site for TLQP-21, a naturally occurring peptide which induces resistance to obesity.

Recently, we demonstrated that TLQP-21 triggers lipolysis and induces resistance to obesity by reducing fat accumulation [1]. TLQP-21 is a 21 amino acid peptide cleavage product of the neuroprotein VGF and was first identified in rat brain. Although TLQP-21 biological activity and its molecular signaling is under active investigation, a receptor for TLQP-21 has not yet been characterized. We now demonstrate that TLQP-21 stimulates intracellular calcium mobilization in CHO cells. Furthermore, using Atomic Force Microscopy (AFM), we also provide evidence of TLQP-21 binding-site characteristics in CHO cells. AFM was used in force mapping mode equipped with a cantilever suitably functionalized with TLQP-21. Attraction of this functionalized probe to the cell surface was specific and consistent with the biological activity of TLQP-21; by contrast, there was no attraction of a probe functionalized with biologically inactive analogues. We detected interaction of the peptide with the binding-site by scanning the cell surface with the cantilever tip. The attractive force between TLQP-21 and its binding site was measured, statistically analyzed and quantified at approximately 40 pN on average, indicating a single class of binding sites. Furthermore we observed that the distribution of these binding sites on the surface was relatively uniform.

Thermodynamic relation between voltage-concentration dependence and salt adsorption in electrochemical cells.

Electrochemical cells containing two electrodes dipped in an ionic solution are widely used as charge accumulators, either with polarizable (supercapacitor) or nonpolarizable (battery) electrodes. Recent applications include desalination ("capacitive deionization") and energy extraction from salinity differences ("capacitive mixing"). In this Letter, we analyze a general relation between the variation of the electric potential as a function of the concentration and the salt adsorption. This relation comes from the evaluation of the electrical and mechanical energy exchange along a reversible cycle, which involves salt adsorption and release by the electrodes. The obtained relation thus describes a connection between capacitive deionization and capacitive mixing. We check this relation with experimental data already reported in the literature, and moreover by some classical physical models for electrodes, including polarizable and nonpolarizable electrodes. The generality of the relation makes it very useful in the study of the properties of the electric double layer.

Single-molecule study of the DNA denaturation phase transition in the force-torsion space.

We use the "magnetic tweezers" technique to show the structural transitions that the DNA undergoes in the force-torsion space. In particular, we focus on the regions corresponding to negative supercoiling. These regions are characterized by the formation of the so-called denaturation bubbles, which play an essential role in the replication and transcription of DNA. We experimentally map the region of the force-torsion space where the denaturation takes place. We observe that large fluctuations in DNA extension occur at one of the boundaries of this region, i.e., when the formation of denaturation bubbles and of plectonemes compete. To describe the experiments, we introduce a suitable extension of the classical model. The model correctly describes the position of the denaturation regions, the transition boundaries, and the measured values of the DNA extension fluctuations.

Photon correlation spectroscopy with incoherent light.

Photon correlation spectroscopy (PCS) is based on measuring the temporal correlation of the light intensity scattered by the investigated sample. A typical setup requires a temporally coherent light source. Here, we show that a short-coherence light source can be used as well, provided that its coherence properties are suitably modified. This results in a "skewed-coherence" light beam allowing that restores the coherence requirements. This approach overcomes the usual need for beam filtering, which would reduce the total brightness of the beam.

[Digital clubbing]. / L'hippocratisme digital.

Digital clubbing is a clinical sign known for centuries. Though, no theory could yet explain this entire phenomenon, neither in its primary nor its secondary form. This article reviews the actual hypotheses bringing a plausible explanation, regarding the most current pathologies associated with digital clubbing. A focus is made on pulmonary and digestive pathologies, and particularly cirrhosis. The knowledge of the mechanisms underlying finger clubbing might lead, in the future, to an effective treatment.

Nanoparticle characterization by using tilted laser microscopy: back scattering measurement in near field.

By using scattering in near field techniques, a microscope can be easily turned into a device measuring static and dynamic light scattering, very useful for the characterization of nanoparticle dispersions. Up to now, microscopy based techniques have been limited to forward scattering, up to a maximum of 30 degrees . In this paper we present a novel optical scheme that overcomes this limitation, extending the detection range to angles larger than 90 degrees (back-scattering). Our optical scheme is based on a microscope, a wide numerical aperture objective, and a laser illumination, with the collimated beam positioned at a large angle with respect to the optical axis of the objective (Tilted Laser Microscopy, TLM). We present here an extension of the theory of near field scattering, which usually applies only to paraxial scattering, to our strongly out-of-axis situation. We tested our instrument and our calculations with calibrated spherical nanoparticles of several different diameters, performing static and dynamic scattering measurements up to 110 degrees . The measured static spectra and decay times are compatible with the Mie theory and the diffusion coefficients provided by the Stokes-Einstein equation. The ability of performing backscattering measurements with this modified microscope opens the way to new applications of scattering in near field techniques to the measurement of systems with strongly angle dependent scattering.

Characterization of anisotropic nano-particles by using depolarized dynamic light scattering in the near field.

Light scattering techniques are widely used in many fields of condensed and soft matter physics. Usually these methods are based on the study of the scattered light in the far field. Recently, a new family of near field detection schemes has been developed, mainly for the study of small angle light scattering. These techniques are based on the detection of the light intensity near to the sample, where light scattered at different directions overlaps but can be distinguished by Fourier transform analysis. Here we report for the first time data obtained with a dynamic near field scattering instrument, measuring both polarized and depolarized scattered light. Advantages of this procedure over the traditional far field detection include the immunity to stray light problems and the possibility to obtain a large number of statistical samples for many different wave vectors in a single instantaneous measurement. By using the proposed technique we have measured the translational and rotational diffusion coefficients of rod-like colloidal particles. The obtained data are in very good agreement with the data acquired with a traditional light scattering apparatus.

Repression of Gadd45alpha by activated FLT3 and GM-CSF receptor mutants contributes to growth, survival and blocked differentiation.

The tumor suppressor Gadd45alpha was earlier shown to be a repressed target of sustained receptor-mediated ERK1/2 signaling. We have identified Gadd45alpha as a downregulated gene in response to constitutive signaling from two FLT3 mutants (FLT3-ITD and FLT3-TKD) commonly found in AML, and a leukemogenic GM-CSF receptor trans-membrane mutant (GMR-V449E). GADD45A mRNA downregulation is also associated with FLT3-ITD(+) AML. Sustained ERK1/2 signaling contributes significantly to receptor-mediated downregulation of Gadd45alpha mRNA in FDB1 cells expressing activated receptor mutants, and in the FLT3-ITD(+) cell line MV4;11. Knockdown of Gadd45alpha with shRNA led to increased growth and survival of FDB1 cells and enforced expression of Gadd45alpha in FDB1 cells expressing FLT3-ITD or GMR-V449E resulted in reduced growth and viability. Gadd45alpha overexpression in FLT3-ITD(+) AML cell lines also resulted in reduced growth associated with increased apoptosis and G(1)/S cell cycle arrest. Overexpression of Gadd45alpha in FDB1 cells expressing GMR-V449E was sufficient to induce changes associated with myeloid differentiation suggesting Gadd45alpha downregulation contributes to the maintenance of receptor-induced myeloid differentiation block. Thus, we show that ERK1/2-mediated downregulation of Gadd45alpha by sustained receptor signaling contributes to growth, survival and arrested differentiation in AML.