Structural Analysis of the Essential Resuscitation Promoting Factor YeaZ Suggests a Mechanism of Nucleotide Regulation through Dimer Reorganization

Extent: 8p.Background: The yeaZ gene product forms part of the conserved network YjeE/YeaZ/YgjD essential for the survival of many Gram-negative eubacteria. Among other as yet unidentified roles, YeaZ functions as a resuscitation promoting factor required for survival and resuscitation of cells in a viable but non-culturable (VBNC) state. Methodology/Principal Findings: In order to investigate in detail the structure/function relationship of this family of proteins we have performed X-ray crystallographic studies of Vibrio parahaemolyticus YeaZ. The YeaZ structure showed that it has a classic actin-like nucleotide-binding fold. Comparisons of this crystal structure to that of available homologues from E. coli, T. maritima and S. typhimurium revealed two distinctly different modes of dimer formation. In one form, prevalent in the absence of nucleotide, the putative nucleotide-binding site is incomplete, lacking a binding pocket for a nucleotide base. In the second form, residues from the second subunit complete the nucleotide-binding site. This suggests that the two dimer architectures observed in the crystal structures correspond to a free and a nucleotide-bound form of YeaZ. A multiple sequence alignment of YeaZ proteins from different bacteria allowed us to identify a large conserved hydrophobic patch on the protein surface that becomes exposed upon nucleotide-driven dimer re-arrangement. We hypothesize that the transition between two dimer architectures represents the transition between the ‘on’ and ‘off’ states of YeaZ. The effect of this transition is to alternately expose and bury a docking site for the partner protein YgjD. Conclusions/Significance: This paper provides the first structural insight into the putative mechanism of nucleotide regulation of YeaZ through dimer reorganization. Our analysis suggests that nucleotide binding to YeaZ may act as a regulator or switch that changes YeaZ shape, allowing it to switch partners between YjeE and YgjD.Inci Aydin, Yumiko Saijo-Hamano, Keiichi Namba, Connor Thomas and Anna Roujeinikov

Effect of tapered roller bearing supports on the dynamic behaviour of hypoid gear pair differentials

Noise and vibration refinement and energy efficiency are the key drivers in powertrain development. The final drive (the differential) is a source of vibration concern and also contributes to the powertrain inefficiency. To optimise differential characteristics for the key objectives of refinement and efficiency, detailed models of the gear interactions as well as the support bearing dynamics are required. This study reports the integrated lubricated bearing and gear contacts with an eight-degree-of-freedom dynamic analysis (a tribo-dynamic model). Non-Newtonian shear behaviour of thin lubricant-film conjunctions is taken into account in the integrated tribo-dynamic analysis, which has not hitherto been reported in the literature. The results show that the transmitted vibration spectra from the system onto the differential casing are dominated by the bearing frequencies rather than by those due to the meshing of gears. It is also shown that a sufficiently high bearing preload improves the vibration refinement but can lead to a marginally reduced transmission efficiency

Structural insight into SUMO chain recognition and manipulation by the ubiquitin ligase RNF4

The small ubiquitin-like modifier (SUMO) can form polymeric chains that are important signals in cellular processes such as meiosis, genome maintenance and stress response. The SUMO-targeted ubiquitin ligase RNF4 engages with SUMO chains on linked substrates and catalyses their ubiquitination, which targets substrates for proteasomal degradation. Here we use a segmental labelling approach combined with solution nuclear magnetic resonance (NMR) spectroscopy and biochemical characterization to reveal how RNF4 manipulates the conformation of the SUMO chain, thereby facilitating optimal delivery of the distal SUMO domain for ubiquitin transfer

Structural Integrity of Single Shell Tanks at Hanford -9491

ABSTRACT The 149 Single Shell Tanks at the Hanford Site were constructed between the 1940's and the 1960's. Many of the tanks are either known or suspected to have leaked in the past. While the free liquids have been removed from the tanks, they still contain significant waste volumes. Recently, the tank farm operations contractor established a Single Shell Tank Integrity Program. Structural integrity is one aspect of the program. The structural analysis of the Single Shell Tanks has several challenging factors. There are several tank sizes and configurations that need to be analyzed. Tank capacities range from fifty-five thousand gallons to one million gallons. The smallest tank type is approximately twenty feet in diameter, and the three other tank types are all seventy-five feet in diameter. Within each tank type there are varying concrete strengths, types of steel, tank floor arrangements, in-tank hardware, riser sizes and locations, and other appurtenances that need to be addressed. Furthermore, soil properties vary throughout the tank farms. The Pacific Northwest National Laboratory has been conducting preliminary structural analyses of the various single shell tank types to address these parameters. The preliminary analyses will assess which aspects of the tanks will require further detailed analysis. Evaluation criteria to which the tanks will be analyzed are also being developed for the Single Shell Tank Integrity Program. This information will be reviewed by the Single Shell Tank Integrity Expert Panel that has been formed to issue recommendations to the DOE and to the tank farm operations contractor regarding Single Shell Tank Integrity. This paper provides a summary of the preliminary analysis of the single shell tanks, a summary of the recommendations for the detailed analyses, and the proposed evaluation criteria by which the tanks will be judged

Bardet-Biedl syndrome with end-stage kidney disease in a four-year-old Romanian boy: a case report

<p>Abstract</p> <p>Background</p> <p>Bardet-Biedl syndrome is a significant genetic cause of chronic kidney disease in children. Kidney abnormalities are a major cause of morbidity and mortality in Bardet-Biedl syndrome, but the onset of end-stage renal disease at an early age and continuous ambulatory peritoneal dialysis, however, are not commonly mentioned in the literature.</p> <p>Case presentation</p> <p>We present the case of a four-year-old Romanian boy who presented to our department with 'febrile seizures'. After an initial evaluation, we diagnosed our patient as having hypertension, severe anemia and end-stage renal disease. He met the major and minor criteria for the diagnosis of Bardet-Biedl syndrome and underwent continuous ambulatory peritoneal dialysis.</p> <p>Conclusions</p> <p>Close follow-up for renal involvement in patients with Bardet-Biedl syndrome and Alström syndrome from an early age is highly recommended to prevent end-stage renal disease and so renal replacement therapy can be started immediately.</p

Pre-synaptic modulation of quadriceps arthrogenic muscle inhibition

Arthrogenic muscle inhibition (AMI) impedes rehabilitation following knee joint injury by preventing activation of the quadriceps. AMI has been attributed to neuronal reflex activity in which altered afferent input originating from the injured joint results in a diminished efferent motor drive to the quadriceps muscles. Beginning to understand the mechanisms responsible for muscle inhibition following joint injury is vital to control or eliminate this phenomenon. Therefore, the purpose of this investigation is to determine if quadriceps AMI is mediated by a presynaptic regulatory mechanism. Eight adults participated in two sessions: in one session their knee was injected with saline and in the other session it was not. The maximum Hoffmann reflex (H-reflex), M-wave, reflex activation history, plasma epinephrine, and norepinephrine were recorded at: baseline, post needle stick, post lidocaine, and 25 and 45 min post effusion. Measures for the control condition were matched to the effusion condition. The percent of the unconditioned reflex amplitude for reflex activation history and the maximum H-reflex were decreased at 25 and 45 min post effusion as compared to measures taken at baseline, post needle stick, and post lidocaine ( P 0.05). No differences were detected at any time interval for any measure during the control admission ( P >0.05). Quadriceps AMI elicited via an experimental knee joint effusion is, at least in part, mediated by a presynaptic mechanism.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46099/1/167_2004_Article_547.pd

A mathematical and computational review of Hartree-Fock SCF methods in Quantum Chemistry

We present here a review of the fundamental topics of Hartree-Fock theory in Quantum Chemistry. From the molecular Hamiltonian, using and discussing the Born-Oppenheimer approximation, we arrive to the Hartree and Hartree-Fock equations for the electronic problem. Special emphasis is placed in the most relevant mathematical aspects of the theoretical derivation of the final equations, as well as in the results regarding the existence and uniqueness of their solutions. All Hartree-Fock versions with different spin restrictions are systematically extracted from the general case, thus providing a unifying framework. Then, the discretization of the one-electron orbitals space is reviewed and the Roothaan-Hall formalism introduced. This leads to a exposition of the basic underlying concepts related to the construction and selection of Gaussian basis sets, focusing in algorithmic efficiency issues. Finally, we close the review with a section in which the most relevant modern developments (specially those related to the design of linear-scaling methods) are commented and linked to the issues discussed. The whole work is intentionally introductory and rather self-contained, so that it may be useful for non experts that aim to use quantum chemical methods in interdisciplinary applications. Moreover, much material that is found scattered in the literature has been put together here to facilitate comprehension and to serve as a handy reference.Comment: 64 pages, 3 figures, tMPH2e.cls style file, doublesp, mathbbol and subeqn package

Using Intervention Mapping to develop an occupational advice intervention to aid return to work following hip and knee replacement in the United Kingdom

Background There are increasing numbers of total hip replacements (THR) and total knee replacements (TKR) being performed in patients of working age. Providing patients undergoing TKR and THR with return to work advice might facilitate return to work. The aim of this paper is to report on the process used to systematically develop an occupational advice intervention to be delivered in hospital for those undergoing arthroplasty. Methods The six-step Intervention Mapping (IM) approach to development, implementation and evaluation of a theory and evidence-based interventions was followed. This paper reports on the development of the intervention covered by steps 1 to 4 of the IM process. Steps 1-3 gathered data on current practice and barriers to change using a mixed methods approach (cohort study of patients undergoing THR or TKR, stakeholder interviews, survey of practice, evidence synthesis) and provided a theoretical framework for intervention development. Step 4 used information from steps 1-3 in combination with a Delphi consensus process to develop the intervention and the associated tools and materials to facilitate its delivery. Results The final intervention identified included a number of core principles including: early patient identification; delivery of key information to patients and their employers; assessment and support by a member of the orthopaedic team; procedures for escalation based on patient need; mechanisms to support communication; and training and support for the clinical teams delivering care. A total of 13 patient and 20 staff performance objectives as delivery requirements, supported by a range of tools, roles and training resources. The intervention addressed outcomes based at the individual and interpersonal levels of the ecological model. Conclusions Following the IM approach resulted in a structured and justified occupational intervention for delivery in secondary care for patients undergoing total hip and knee replacement. The feasibility of the intervention will subsequently be tested alongside further investigation to establish its effectiveness and cost-effectiveness. Key Words Intervention Mapping Return to Work Occupational advice Arthroplasty Hip Kne

Membrane Docking Geometry of GRP1 PH Domain Bound to a Target Lipid Bilayer: An EPR Site-Directed Spin-Labeling and Relaxation Study

The second messenger lipid PIP3 (phosphatidylinositol-3,4,5-trisphosphate) is generated by the lipid kinase PI3K (phosphoinositide-3-kinase) in the inner leaflet of the plasma membrane, where it regulates a broad array of cell processes by recruiting multiple signaling proteins containing PIP3-specific pleckstrin homology (PH) domains to the membrane surface. Despite the broad importance of PIP3-specific PH domains, the membrane docking geometry of a PH domain bound to its target PIP3 lipid on a bilayer surface has not yet been experimentally determined. The present study employs EPR site-directed spin labeling and relaxation methods to elucidate the membrane docking geometry of GRP1 PH domain bound to bilayer-embedded PIP3. The model target bilayer contains the neutral background lipid PC and both essential targeting lipids: (i) PIP3 target lipid that provides specificity and affinity, and (ii) PS facilitator lipid that enhances the PIP3 on-rate via an electrostatic search mechanism. The EPR approach measures membrane depth parameters for 18 function-retaining spin labels coupled to the PH domain, and for calibration spin labels coupled to phospholipids. The resulting depth parameters, together with the known high resolution structure of the co-complex between GRP1 PH domain and the PIP3 headgroup, provide sufficient constraints to define an optimized, self-consistent membrane docking geometry. In this optimized geometry the PH domain engulfs the PIP3 headgroup with minimal bilayer penetration, yielding the shallowest membrane position yet described for a lipid binding domain. This binding interaction displaces the PIP3 headgroup from its lowest energy position and orientation in the bilayer, but the headgroup remains within its energetically accessible depth and angular ranges. Finally, the optimized docking geometry explains previous biophysical findings including mutations observed to disrupt membrane binding, and the rapid lateral diffusion observed for PIP3-bound GRP1 PH domain on supported lipid bilayers