The Caulobacter crescentus DNA-(adenine-N6)-methyltransferase CcrM methylates DNA in a distributive manner

The specificity and processivity of DNA methyltransferases have important implications regarding their biological functions. We have investigated the sequence specificity of CcrM and show here that the enzyme has a high specificity for GANTC sites, with only minor preferences at the central position. It slightly prefers hemimethylated DNA, which represents the physiological substrate. In a previous work, CcrM was reported to be highly processive [Berdis et al. (1998) Proc. Natl Acad. Sci. USA 95: 2874–2879]. However upon review of this work, we identified a technical error in the setup of a crucial experiment in this publication, which prohibits making any statement about the processivity of CcrM. In this study, we performed a series of in vitro experiments to study CcrM processivity. We show that it distributively methylates six target sites on the pUC19 plasmid as well as two target sites located on a 129-mer DNA fragment both in unmethylated and hemimethylated state. Reaction quenching experiments confirmed the lack of processivity. We conclude that the original statement that CcrM is processive is no longer valid

The impact of DNA methylation in Alphaproteobacteria.

Alphaproteobacteria include bacteria with very different modes of life, from free-living to host-associated and pathogenic bacteria. Their genomes vary in size and organization from single circular chromosomes to multipartite genomes and are often methylated by one or more adenine or cytosine methyltransferases (MTases). These include MTases that are part of restriction/modification systems and so-called orphan MTases. The development of novel technologies accelerated the analysis of methylomes and revealed the existence of epigenetic patterns in several Alphaproteobacteria. This review describes the known functions of DNA methylation in Alphaproteobacteria and also discusses its potential drawbacks through the accidental deamination of methylated cytosines. Particular emphasis is given to the strong connection between the cell cycle-regulated orphan MTase CcrM and the complex network that controls gene expression and cell cycle progression in Alphaproteobacteria

Model Assessment of Alternatives for Reducing Seepage from Buried Uranium Mill Talings at the Morton Ranch Site in Central Wyoming

The purpose of this study is to examine potential ground water contamination by seepage from buried tailings under four alternatives of clay liners and tailings placement, which have been proposed for possible use at the Morton Ranch Site. To accomplish this comparison of alternatives, laboratory work and numerous measurements were made on materials typical of the Morton Ranch Site. These measurements provide the soil characteristics necessary for input to the hydrologic flow and transport models

Heterozygous frameshift mutation in keratin 5 in a family with Galli-Galli disease

BACKGROUND: Reticulate pigmentary disorders include the rare autosomal dominant Galli–Galli disease (GGD) and Dowling–Degos disease (DDD). Clinical diagnosis between some of the subtypes can be difficult due to a degree of overlap between clinical features, therefore analysis at the molecular level may be necessary to confirm the diagnosis. OBJECTIVES: To identify the underlying genetic defect in a 48-year-old Asian-American woman with a clinical diagnosis of GGD. METHODS: Histological analysis was performed on a skin biopsy using haematoxylin–eosin staining. KRT5 (the gene encoding keratin 5) was amplified from genomic DNA and directly sequenced. RESULTS: The patient had a history of pruritus and hyperpigmented erythematous macules and thin papules along the flexor surfaces of her arms, her upper back and neck, axillae and inframammary areas. Hypopigmented macules were seen among the hyperpigmentation. A heterozygous 1-bp insertion mutation in KRT5 (c.38dupG; p.Ser14GlnfsTer3) was identified in the proband. This mutation occurs within the head domain of the keratin 5 protein leading to a frameshift and premature stop codon. CONCLUSIONS: From the histological findings and mutation analysis the individual was identified as having GGD due to haploinsufficiency of keratin 5

TRUST: A Computer Program for Variably Saturated Flow in Multidimensional, Deformable Media

The computer code, TRUST. provides a versatile tool to solve a wide spectrum of fluid flow problems arising in variably saturated deformable porous media. The governing equations express the conservation of fluid mass in an elemental volume that has a constant volume of solid. Deformation of the skeleton may be nonelastic. Permeability and compressibility coefficients may be nonlinearly related to effective stress. Relationships between permeability and saturation with pore water pressure in the unsaturated zone may include hysteresis. The code developed by T. N. Narasimhan grew out of the original TRUNP code written by A. L. Edwards. The code uses an integrated finite difference algorithm for numerically solving the governing equation. Narching in time is performed by a mixed explicit-implicit numerical procedure in which the time step is internally controlled. The time step control and related feature in the TRUST code provide an effective control of the potential numerical instabilities that can arise in the course of solving this difficult class of nonlinear boundary value problem. This document brings together the equations, theory, and users manual for the code as well as a sample case with input and output

Controls for orbital assembly of large space structures

The topics covered are presented in viewgraph form and include the following: flexible structure control; decentralized control for flexible multi-body systems; control of structures during assembly; decentralized control using structural partitioning; reduced-orded model-based controller design; ROM/residual mode filters (RMF) control of large flexible structures;RMF in a distributed parameter system (DPS); LSS active control simulation; 3-D truss beam; mobile transporter with RMS; and flexible robot manipulator

Stochastic Dynamics of Lexicon Learning in an Uncertain and Nonuniform World

We study the time taken by a language learner to correctly identify the meaning of all words in a lexicon under conditions where many plausible meanings can be inferred whenever a word is uttered. We show that the most basic form of cross-situational learning - whereby information from multiple episodes is combined to eliminate incorrect meanings - can perform badly when words are learned independently and meanings are drawn from a nonuniform distribution. If learners further assume that no two words share a common meaning, we find a phase transition between a maximally-efficient learning regime, where the learning time is reduced to the shortest it can possibly be, and a partially-efficient regime where incorrect candidate meanings for words persist at late times. We obtain exact results for the word-learning process through an equivalence to a statistical mechanical problem of enumerating loops in the space of word-meaning mappings.Comment: 7 pages, 3 figures. Version 2 contains additional discussion and will appear in Phys. Rev. Let

Shape-sensing robotic-assisted bronchoscopy for pulmonary nodules: initial multicenter experience using the Ion™ Endoluminal System

BACKGROUND: Traditional bronchoscopy provides limited approach to peripheral nodules. Shape-sensing robotic-assisted bronchoscopy (SSRAB, Ion™ Endoluminal System) is a new tool for minimally invasive peripheral nodule biopsy. We sought to answer the research question: Does SSRAB facilitate sampling of pulmonary nodules during bronchoscopists\u27 initial experience? METHODS: The lead-in stage of a multicenter, single-arm, prospective evaluation of the Ion Endoluminal System (PRECIsE) is described. Enrolled subjects ≥ 18 years old had recent computed tomography evidence of one or more solid or semi-solid pulmonary nodules ≥ 1.0 to ≤ 3.5 cm in greatest dimension and in any part of the lung. Subjects were followed at 10- and 30-days post-procedure. This stage provided investigators and staff their first human experience with the SSRAB system; safety and procedure outcomes were analyzed descriptively. Neither diagnostic yield nor sensitivity for malignancy were assessed in this stage. Categorical variables are summarized by percentage; continuous variables are summarized by median/interquartile range (IQR). RESULTS: Sixty subjects were enrolled across 6 hospitals; 67 nodules were targeted for biopsy. Median axial, coronal and sagittal diameters were \u3c 18 mm with a largest cardinal diameter of 20.0 mm. Most nodules were extraluminal and distance from the outer edge of the nodule to the pleura or nearest fissure was 4.0 mm (IQR: 0.0, 15.0). Median bronchial generation count to the target location was 7.0 (IQR: 6.0, 8.0). Procedure duration (catheter-in to catheter-out) was 66.5 min (IQR: 50.0, 85.5). Distance from the catheter tip to the closest edge of the virtual nodule was 7.0 mm (IQR: 2.0, 12.0). Biopsy completion was 97.0%. No pneumothorax or airway bleeding of any grade was reported. CONCLUSIONS: Bronchoscopists leveraged the Ion SSRAB\u27s functionality to drive the catheter safely in close proximity of the virtual target and to obtain biopsies. This initial, multicenter experience is encouraging, suggesting that SSRAB may play a role in the management of pulmonary nodules. Clinical Trial Registration identifier and date NCT03893539; 28/03/2019

Effect of gadolinium adatoms on the transport properties of graphene

The electrical transport properties of graphene doped with gadolinium (Gd) adatoms have been measured. The gate voltage dependence of the conductivity shows that Gd produces n doping of graphene. The charged Gd ions act as scattering centers, lowering the sample mobility for both electrons and holes. The doping efficiency of Gd at 77 K reproduces theoretical predictions (0.7 electron per Gd adatom). On raising the sample temperature to even 150 K, clustering effects are observed and substantially modify the transport