Role of Lamin B1 in Chromatin Instability

Nuclear lamins play important roles in the organization and structure of the nucleus; however, the specific mechanisms linking lamin structure to nuclear functions are poorly defined. We demonstrate that reducing nuclear lamin B1 expression by short hairpin RNA-mediated silencing in cancer cell lines to approximately 50% of normal levels causes a delay in the cell cycle and accumulation of cells in early S phase. The S phase delay appears to be due to the stalling and collapse of replication forks. The double-strand DNA breaks resulting from replication fork collapse were inefficiently repaired, causing persistent DNA damage signaling and the assembly of extensive repair foci on chromatin. The expression of multiple factors involved in DNA replication and repair by both nonhomologous end joining and homologous repair is misregulated when lamin B1 levels are reduced. We further demonstrate that lamin B1 interacts directly with the promoters of some genes associated with DNA damage response and repair, including BRCA1 and RAD51. Taken together, the results suggest that the maintenance of lamin B1 levels is required for DNA replication and repair through regulation of the expression of key factors involved in these essential nuclear functions.     

Decreasing trend of Helicobacter pylori infection in children with gastrointestinal symptoms from Buenos Aires, Argentina

Background: Helicobacter pylori infection is declining in developed and developing countries. The aim of this study was to retrospectively evaluate over an 8‐year period the rate of H. pylori infection in children with gastrointestinal symptoms from Buenos Aires, Argentina. Materials and Methods: We reviewed the records of children referred from 2002 to 2009 to the gastroenterology unit of the Children Hospital “Superiora Sor Maria Ludovica” for evaluation of upper gastrointestinal signs and symptoms in which the ¹³C‐urea breath test was performed to diagnose H. pylori infection and a sociodemographic questionnaire was obtained. Results: Records of a total of 1030 children and adolescents with a mean age of 9.99 years were included in the analysis. We found an H. pylori prevalence of 41.2% (95% CI, 36.9–46.0%) for the triennium 2002–2004, dropping to 26.0% (95% CI, 20.7–31.8%) in the triennium 2007–2009. Conclusion: Our results showed a significant decrease in H. pylori infection rates from children referred for upper gastrointestinal symptoms evaluation from 2002 to 2009, following the H. pylori epidemiologic trend reported in other countries.     

What's in a likelihood? Simple models of protein evolution and the contribution of structurally viable reconstructions to the likelihood

Most phylogenetic models of protein evolution assume that sites are independent and identically distributed. Interactions between sites are ignored, and the likelihood can be conveniently calculated as the product of the individual site likelihoods. The calculation considers all possible transition paths (also called substitution histories or mappings) that are consistent with the observed states at the terminals, and the probability density of any particular reconstruction depends on the substitution model. The likelihood is the integral of the probability density of each substitution history taken over all possible histories that are consistent with the observed data. We investigated the extent to which transition paths that are incompatible with a protein's three-dimensional structure contribute to the likelihood. Several empirical amino acid models were tested for sequence pairs of different degrees of divergence. When simulating substitutional histories starting from a real sequence, the structural integrity of the simulated sequences quickly disintegrated. This result indicates that simple models are clearly unable to capture the constraints on sequence evolution. However, when we sampled transition paths between real sequences from the posterior probability distribution according to these same models, we found that the sampled histories were largely consistent with the tertiary structure. This suggests that simple empirical substitution models may be adequate for interpolating changes between observed sequences during phylogenetic inference despite the fact that the models cannot predict the effects of structural constraints from first principles. This study is significant because it provides a quantitative assessment of the biological realism of substitution models from the perspective of protein structure, and it provides insight on the prospects for improving models of protein sequence evolution.     

Quality monitoring of microbial contamination of cryopreserved parathyroid tissue

Cryopreservation of parathyroid tissue (PT) provides patients undergoing parathyroidectomy with an option for delayed autologous heterotopic parathyroid transplantation. A standard protocol for quality monitoring of PT has not been established. This article describes a method for detecting the presence of bacterial contamination in PT tissue intended for autologous transplantation. PT was received in the tissue bank, processed under aseptic conditions, and placed into cryopreservation medium. Sterility testing was performed at 2 time points prior to cryopreservation. From January 2005 to October 2008, 47 PT samples were cryopreserved. The following bacteria were isolated from 11 PT specimens: Staphylococcus epidermidis, Staphylococcus capitis subspecies ureolyticus, Staphylococcus lugdunensis, Bacillus pumilus, and corynebacteria (diphtheroids). 23% of PTs were contaminated at the time of collection, predominantly with indigenous bacteria. Quality monitoring using this protocol is a useful tool to identify tissues contaminated with bacteria.     

Pharmacogenetic approaches to the treatment of alcohol addiction

Addictive disorders are partly heritable, chronic, relapsing conditions that account for a tremendous disease burden. Currently available addiction pharmacotherapies are only moderately successful, continue to be viewed with considerable scepticism outside the scientific community and have not become widely adopted as treatments. More effective medical treatments are needed to transform addiction treatment and address currently unmet medical needs. Emerging evidence from alcoholism research suggests that no single advance can be expected to fundamentally change treatment outcomes. Rather, studies of opioid, corticotropin-releasing factor, GABA and serotonin systems suggest that incremental advances in treatment outcomes will result from an improved understanding of the genetic heterogeneity among patients with alcohol addiction, and the development of personalized treatments.     

PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment

Background  

The Monte Carlo simulation of sequence evolution is routinely used to assess the performance of phylogenetic inference methods and sequence alignment algorithms. Progress in the field of molecular evolution fuels the need for more realistic and hence more complex simulations, adapted to particular situations, yet current software makes unreasonable assumptions such as homogeneous substitution dynamics or a uniform distribution of indels across the simulated sequences. This calls for an extensible simulation framework written in a high-level functional language, offering new functionality and making it easy to incorporate further complexity.     

Attenuation of host NO production by MAMPs potentiates development of the host in the squid-vibrio symbiosis

Bacterial pathogens typically upregulate the host's production of nitric oxide synthase (NOS) and nitric oxide (NO) as antimicrobial agents, a response that is often mediated by microbe-associated molecular patterns (MAMPs) of the pathogen. In contrast, previous studies of the beneficial Euprymna scolopes/Vibrio fischeri symbiosis demonstrated that symbiont colonization results in attenuation of host NOS/NO, which occurs in high levels in hatchling light organs. Here, we sought to determine whether V. fischeri MAMPs, specifically lipopolysaccharide (LPS) and the peptidoglycan derivative tracheal cytotoxin (TCT), attenuate NOS/NO, and whether this activity mediates the MAMPs-induced light organ morphogenesis. Using confocal microscopy, we characterized levels of NOS with immunocytochemistry and NO with a NO-specific fluorochrome. When added exogenously to seawater containing hatchling animals, V. fischeri LPS and TCT together, but not individually, induced normal NOS/NO attenuation. Further, V. fischeri mutants defective in TCT release did not. Experiments with NOS inhibitors and NO donors provided evidence that NO mediates apoptosis and morphogenesis associated with symbiont colonization. Attenuation of NOS/NO by LPS and TCT in the squid-vibrio symbiosis provides another example of how the host's response to MAMPs depends on the context. These data also provide a mechanism by which symbiont MAMPs regulate host development.     

Analysis of impulse oscillometric measures of lung function and respiratory system model parameters in small airway-impaired and healthy children over a 2-year period

Background

Is Impulse Oscillometry System (IOS) a valuable tool to measure respiratory system function in Children?Asthma (A) is the most prevalent chronic respiratory disease in children. Therefore, early and accurate assessment of respiratory function is of tremendous clinical interest in diagnosis, monitoring and treatment of respiratory conditions in this subpopulation.IOS has been successfully used to measure lung function in children with a high degree of sensitivity and specificity to small airway impairments (SAI) and asthma. IOS measures of airway function and equivalent electrical circuit models of the human respiratory system have been developed to quantify the severity of these conditions. Previously, we have evaluated several known respiratory models based on the Mead's model and more parsimonious versions based on fitting IOS data known as extended RIC (eRIC) and augmented RIC (aRIC) models have emerged, which offer advantages over earlier models.

Methods

IOS data from twenty-six children were collected and compared during pre-bronchodilation (pre-B) and post- bronchodilation (post-B) conditions over a period of 2 years.

Results and Discussion

Are the IOS and model parameters capable of differentiating between healthy children and children with respiratory system distress?Children were classified into two main categories: Healthy (H) and Small Airway-Impaired (SAI). The IOS measures and respiratory model parameters analyzed differed consistently between H and SAI children. SAI children showed smaller trend of "growth" and larger trend of bronchodilator responses than H children.The two model parameters: peripheral compliance (Cp) and peripheral resistance (Rp) tracked IOS indices of small airway function well. Cp was a more sensitive index than Rp. Both eRIC and aRIC Cps and the IOS Reactance Area, AX, (also known as the "Goldman Triangle") showed good correlations.

Conclusions

What are the most useful IOS and model parameters?In this work we demonstrate that IOS parameters such as resistance at 5 Hz (R5), frequency-dependence of resistance (fdR: R5-R20), reactance area (AX), and parameter estimates of respiratory system such as Cp and Rp provide sensitive indicators of lung function and have the capacity to differentiate between obstructed and non-obstructed airway conditions. They are also capable of demonstrating airway growth-related changes over a two-year period.We conclude that the IOS parameters AX and the eRIC model derived parameter Cp are the most reliable parameters to track lung function in children before and after bronchodilator and over a time period (2 years).Which model is more suitable for interpreting IOS data?IOS data are equally well-modelled by eRIC and aRIC models, based on the close correlations of their corresponding parameters - excluding upper airway shunt compliance. The eRIC model is a more parsimonious and equally powerful model in capturing the differences in IOS indices between SAI and H children. Therefore, it may be considered a clinically-preferred model of lung function.

     

SLIT/ROBO1 signaling suppresses mammary branching morphogenesis by limiting basal cell number

In the field of breast biology, there is a growing appreciation for the "gatekeeping function" of basal cells during development and disease processes yet mechanisms regulating the generation of these cells are poorly understood. Here, we report that the proliferation of basal cells is controlled by SLIT/ROBO1 signaling and that production of these cells regulates outgrowth of mammary branches. We identify the negative regulator TGF-β1 upstream of Robo1 and show that it induces Robo1 expression specifically in the basal layer, functioning together with SLIT2 to restrict branch formation. Loss of SLIT/ROBO1 signaling in this layer alone results in precocious branching due to a surplus of basal cells. SLIT2 limits basal cell proliferation by inhibiting canonical WNT signaling, increasing the cytoplasmic and membrane pools of β-catenin at the expense of its nuclear pool. Together, our studies provide mechanistic insight into how specification of basal cell number influences branching morphogenesis.