Structural Basis for The Recognition of Deaminated Nucleobases by An Archaeal DNA Polymerase

With increasing temperature, nucleobases in DNA become increasingly damaged by hydrolysis of exocyclic amines. The most prominent damage includes the conversion of cytosine to uracil and adenine to hypoxanthine. These damages are mutagenic and put the integrity of the genome at risk if not repaired appropriately. Several archaea live at elevated temperatures and thus, are exposed to a higher risk of deamination. Earlier studies have shown that DNA polymerases of archaea have the property of sensing deaminated nucleobases in the DNA template and thereby stalling the DNA synthesis during DNA replication providing another layer of DNA damage recognition and repair. However, the structural basis of uracil and hypoxanthine sensing by archaeal B-family DNA polymerases is sparse. Here we report on three new crystal structures of the archaeal B-family DNA polymerase from Thermococcus kodakarensis (KOD) DNA polymerase in complex with primer and template strands that have extended single stranded DNA template 5’-overhangs. These overhangs contain either the canonical nucleobases as well as uracil or hypoxanthine, respectively, and provide unprecedented structural insights into their recognition by archaeal B-family DNA polymerases.     

Mitotic Diversity in Homeostatic Human Interfollicular Epidermis

Despite decades of skin research, regulation of proliferation and homeostasis in human epidermis is still insufficiently understood. To address the role of mitoses in tissue regulation, we utilized human long-term skin equivalents and systematically assessed mitoses during early epidermal development and long-term epidermal regeneration. We now demonstrate four different orientations: (1) horizontal, i.e., parallel to the basement membrane (BM) and suggestive of symmetric divisions; (2) oblique with an angle of 45°–70°; or (3) perpendicular, suggestive of asymmetric division. In addition, we demonstrate a fourth substantial fraction of suprabasal mitoses, many of which are committed to differentiation (Keratin K10-positive). As verified also for normal human skin, this spatial mitotic organization is part of the regulatory program of human epidermal tissue homeostasis. As a potential marker for asymmetric division, we investigated for Numb and found that it was evenly spread in almost all undifferentiated keratinocytes, but indeed asymmetrically distributed in some mitoses and particularly frequent under differentiation-repressing low-calcium conditions. Numb deletion (stable knockdown by CRISPR/Cas9), however, did not affect proliferation, neither in a three-day follow up study by life cell imaging nor during a 14-day culture period, suggesting that Numb is not essential for the general control of keratinocyte division.     

Mechanical analysis of circular liners with particular reference to composite supports. For example, liners consisting of shotcrete and steel sets

This paper describes a methodology for the mechanical analysis of composite supports, such as liners consisting of shotcrete and steel sets. The methodology presented here is based on an established technique of structural analysis commonly referred to as the ‘equivalent section’ approach. This technique consists in treating the composite section of a straight beam as a homogenized section of equivalent mechanical properties. The equations presented in this paper have been derived from application of the theory of elastic shells (or curved beams) and therefore are more appropriate for the analysis of circular tunnel liners. The proposed methodology for the design of liners is based on the construction of capacity diagrams, another established technique of structural analysis and concrete design that can be conveniently extended to the analysis of composite sections for tunnel liners. When applying the theory of elastic shells to derive the equations that conform to the proposed methodology, the problem of determining the mechanical response of semi-circular arches treated with the theory of thin and thick formulations has been re-visited. Observations of practical interest arising from the comparison of results obtained with both approaches are discussed.     

3D random Voronoi grain-based models for simulation of brittle rock damage and fabric-guided micro-fracturing

A grain-based distinct element model featuring three-dimensional （3D） Voronoi tessellations （randompoly-crystals） is proposed for simulation of crack damage development in brittle rocks. The grainboundaries in poly-crystal structure produced by Voronoi tessellations can represent flaws in intact rockand allow for numerical replication of crack damage progression through initiation and propagation ofmicro-fractures along grain boundaries. The Voronoi modelling scheme has been used widely in the pastfor brittle fracture simulation of rock materials. However the difficulty of generating 3D Voronoi modelshas limited its application to two-dimensional （2D） codes. The proposed approach is implemented inNeper, an open-source engine for generation of 3D Voronoi grains, to generate block geometry files thatcan be read directly into 3DEC. A series of Unconfined Compressive Strength （UCS） tests are simulated in3DEC to verify the proposed methodology for 3D simulation of brittle fractures and to investigate therelationship between each micro-parameter and the model＇s macro-response. The possibility of numericalreplication of the classical U-shape strength curve for anisotropic rocks is also investigated innumerical UCS tests by using complex-shaped （elongated） grains that are cemented to one another alongtheir adjoining sides. A micro-parameter calibration procedure is established for 3D Voronoi models foraccurate replication of the mechanical behaviour of isotropic and anisotropic （containing a fabric） rocks.
2014 Institute of Rock and Soil Mechanics, Chinese Academy of Sciences. Production and hosting byElsevier B.V. All rights reserved.     

Crystal structure of the effector-binding domain of the trehalose-repressor of Escherichia coli, a member of the LacI family, in its complexes with inducer trehalose-6-phosphate and noninducer trehalose

The crystal structure of the Escherichia coli trehalose repressor (TreR) in a complex with its inducer trehalose-6-phosphate was determined by the method of multiple isomorphous replacement (MIR) at 2.5 A resolution, followed by the structure determination of TreR in a complex with its noninducer trehalose at 3.1 A resolution. The model consists of residues 61 to 315 comprising the effector binding domain, which forms a dimer as in other members of the LacI family. This domain is composed of two similar subdomains each consisting of a central beta-sheet sandwiched between alpha-helices. The effector binding pocket is at the interface of these subdomains. In spite of different physiological functions, the crystal structures of the two complexes of TreR turned out to be virtually identical to each other with the conformation being similar to those of the effector binding domains of the LacI and PurR in complex with their effector molecules. According to the crystal structure, the noninducer trehalose binds to a similar site as the trehalose portion of trehalose-6-phosphate. The binding affinity for the former is lower than for the latter. The noninducer trehalose thus binds competitively to the repressor. Unlike the phosphorylated inducer molecule, it is incapable of blocking the binding of the repressor headpiece to its operator DNA. The ratio of the concentrations of trehalose-6-phosphate and trehalose thus is used to switch between the two alternative metabolic uses of trehalose as an osmoprotectant and as a carbon source.     

Urodynamically controlled management of spinal cord injury in children

Spinal cord injuries in children are relatively uncommon. However, infants with cervical spine injury have an especially high risk of renal damage. Six patients, 4 of them tetraplegic, aged 15 months to 8 years, were primarily treated by oral anticholinergic medication and intermittent catheterization. With this concept, satisfactory results were achieved in 4 of 6 children for a mean follow-up of 17.7 months. Mean bladder capacity increased by 128% and intravesical pressure was reduced by 35%. While all patients initially presented with a detrusor leak point pressure above 40 cm H2O, in 4 patients detrusor leak point pressure could be sufficiently reduced by initial treatment. One patient required intravesical instillation of oxybutynin; in another patient sphincterotomy was performed. No patient had signs of renal damage. In summary, even in tetraplegic infants, oral anticholinergic medication and intermittent catheterization is a safe and well-tolerated treatment.     

Assessment of strain bursting in deep tunnelling by using the finite-discrete element method

Rockbursting in deep tunnelling is a complex phenomenon posing significant challenges both at the design and construction stages of an underground excavation within hard rock masses and under high in situ stresses. While local experience, field monitoring, and informed data-rich analysis are some of the tools commonly used to manage the hazards and the associated risks, advanced numerical techniques based on discontinuum modelling have also shown potential in assisting in the assessment of rockbursting. In this study, the hybrid finite-discrete element method (FDEM) is employed to investigate the failure and fracturing processes, and the mechanisms of energy storage and rapid release resulting in bursting, as well as to assess its utility as part of the design process of underground excavations. Following the calibration of the numerical model to simulate a deep excavation in a hard, massive rock mass, discrete fracture network (DFN) geometries are integrated into the model in order to examine the impact of rock structure on rockbursting under high in situ stresses. The obtained analysis results not only highlight the importance of explicitly simulating pre-existing joints within the model, as they affect the mobilised failure mechanisms and the intensity of strain bursting phenomena, but also show how the employed joint network geometry, the field stress conditions, and their interaction influence the extent and depth of the excavation induced damage. Furthermore, a rigorous analysis of the mass and velocity of the ejected rock blocks and comparison of the obtained data with well-established semi-empirical approaches demonstrate the potential of the method to provide realistic estimates of the kinetic energy released during bursting for determining the energy support demand.     

Must radiation dose for CT of the maxilla and mandible be higher than that for conventional panoramic radiography?

We evaluated the feasibility of performing preoperative spiral CT of the maxilla and mandible with a radiation dose similar to that used for conventional panoramic radiography. The skin entrance doses of radiation used for spiral CT (collimation, 1 mm; pitch, 2; tube voltage, 80 kV; tube current, 40 mA) and for panoramic radiography (75 kV, 8 mA, 15 seconds) were measured in one patient by using thermoluminescent dosimeter chips. Results were 0.56 +/- 0.06 mGy for CT and 0.59 +/- 0.04 mGy for radiography. Image quality was adequate for preoperative implant planning. Spiral CT of the mandible and maxilla may therefore be feasible with a radiation dose of similar magnitude as that used for conventional panoramic radiography.