Expression and characterization of a histidine-rich protein, Hpn: Potential for Ni2+ storage in Helicobacter pylori

Hpn is a small cytoplasmic protein found in Helicobacter pylori, which binds Ni2+ ions with moderate affinity. Consisting of 60 amino acids, the protein is rich in histidine (28 residues, 46.7%), as well as glutamate, glycine and serine residues (in total 31.7%), and contains short repeating motifs. In the present study, we report the detailed biophysical characterization of the multimeric status and Ni2+-binding properties of purified recombinant Hpn under physiologically relevant conditions. The protein exists as an equilibration of multimeric forms in solution, with 20-mers (approx. 136 kDa) being the predominant species. Using equilibrium dialysis, ICP-MS (inductively coupled plasma MS) and UV/visible spectroscopy, Hpn was found to bind five Ni2+ ions per monomer at pH 7.4, with a dissociation constant (Kd) of 7.1 μM. Importantly, Ni2+ binding to Hpn is reversible: metal is released either in the presence of a chelating ligand such as EDTA, or at a slightly acidic pH (pH for half dissociation, pH1/2 ∼6.3). Ni2+ binding induces conformational changes within the protein, increasing β-sheet and reducing α-helical content, from 22% to 37%, and 20% to 10% respectively. Growth curves of Escherichia coli BL21(DE3) both with and without the hpn gene performed under Ni2+ pressure clearly implied a role for Hpn to protect the cells from higher concentrations of external metal ions. Similarly, the accumulation of Ni2+ in these cells expressing Hpn from a plasmid was approx. 4-fold higher than in uninduced controls or control cultures that lacked the plasmid. Similarly, levels of Ni2+ in wild-type H. pylori 26695 cells were higher than those in H. pylori hpn-deletion mutant strains. Hpn may potentially serve multiple roles inside the bacterium: storage of Ni 2+ ions in a 'reservoir'; donation of Ni2+ to other proteins; and detoxification via sequestration of excess Ni2+. © 2006 Biochemical Society.published_or_final_versio

COBRA - Double beta decay searches using CdTe detectors

A new approach (called COBRA) for investigating double beta decay using CdTe (CdZnTe) semiconductor detectors is proposed. It follows the idea that source and detector are identical. This will allow simultaneous measurements of 5 $\beta^-\beta^-$ - and 4 $\beta^+\beta^+$ - emitters at once. Half-life limits for neutrinoless double beta decay of Cd-116 and Te-130 can be improved by more than one order of magnitude with respect to current limits and sensitivities on the effective Majorana neutrino mass of less than 1 eV can be obtained. Furthermore, for the first time a realistic chance of observing double electron capture processes exists. Additional searches for rare processes like the 4-fold forbidden Cd-113 $\beta$-decay, the electron capture of Te-123 and dark matter detection can be performed. The achievable limits are evaluated for 10 kg of such detectors and can be scaled accordingly towards higher detector masses because of the modular design of the proposed experiment.Comment: 13 pages, 3 eps-figures, submitte

Assessing the Potential of Deep Learning for Emulating Cloud Superparameterization in Climate Models with Real-Geography Boundary Conditions

We explore the potential of feed-forward deep neural networks (DNNs) for emulating cloud superparameterization in realistic geography, using offline fits to data from the Super Parameterized Community Atmospheric Model. To identify the network architecture of greatest skill, we formally optimize hyperparameters using ~250 trials. Our DNN explains over 70 percent of the temporal variance at the 15-minute sampling scale throughout the mid-to-upper troposphere. Autocorrelation timescale analysis compared against DNN skill suggests the less good fit in the tropical, marine boundary layer is driven by neural network difficulty emulating fast, stochastic signals in convection. However, spectral analysis in the temporal domain indicates skillful emulation of signals on diurnal to synoptic scales. A close look at the diurnal cycle reveals correct emulation of land-sea contrasts and vertical structure in the heating and moistening fields, but some distortion of precipitation. Sensitivity tests targeting precipitation skill reveal complementary effects of adding positive constraints vs. hyperparameter tuning, motivating the use of both in the future. A first attempt to force an offline land model with DNN emulated atmospheric fields produces reassuring results further supporting neural network emulation viability in real-geography settings. Overall, the fit skill is competitive with recent attempts by sophisticated Residual and Convolutional Neural Network architectures trained on added information, including memory of past states. Our results confirm the parameterizability of superparameterized convection with continents through machine learning and we highlight advantages of casting this problem locally in space and time for accurate emulation and hopefully quick implementation of hybrid climate models.Comment: 32 Pages, 13 Figures, Revised Version Submitted to Journal of Advances in Modeling Earth Systems April 202

Protocol for the Foot in Juvenile Idiopathic Arthritis trial (FiJIA): a randomised controlled trial of an integrated foot care programme for foot problems in JIA

<b>Background</b>: Foot and ankle problems are a common but relatively neglected manifestation of juvenile idiopathic arthritis. Studies of medical and non-medical interventions have shown that clinical outcome measures can be improved. However existing data has been drawn from small non-randomised clinical studies of single interventions that appear to under-represent the adult population suffering from juvenile idiopathic arthritis. To date, no evidence of combined therapies or integrated care for juvenile idiopathic arthritis patients with foot and ankle problems exists. <b>Methods/design</b>: An exploratory phase II non-pharmacological randomised controlled trial where patients including young children, adolescents and adults with juvenile idiopathic arthritis and associated foot/ankle problems will be randomised to receive integrated podiatric care via a new foot care programme, or to receive standard podiatry care. Sixty patients (30 in each arm) including children, adolescents and adults diagnosed with juvenile idiopathic arthritis who satisfy the inclusion and exclusion criteria will be recruited from 2 outpatient centres of paediatric and adult rheumatology respectively. Participants will be randomised by process of minimisation using the Minim software package. The primary outcome measure is the foot related impairment measured by the Juvenile Arthritis Disability Index questionnaire's impairment domain at 6 and 12 months, with secondary outcomes including disease activity score, foot deformity score, active/limited foot joint counts, spatio-temporal and plantar-pressure gait parameters, health related quality of life and semi-quantitative ultrasonography score for inflammatory foot lesions. The new foot care programme will comprise rapid assessment and investigation, targeted treatment, with detailed outcome assessment and follow-up at minimum intervals of 3 months. Data will be collected at baseline, 6 months and 12 months from baseline. Intention to treat data analysis will be conducted. A full health economic evaluation will be conducted alongside the trial and will evaluate the cost effectiveness of the intervention. This will consider the cost per improvement in Juvenile Arthritis Disability Index, and cost per quality adjusted life year gained. In addition, a discrete choice experiment will elicit willingness to pay values and a cost benefit analysis will also be undertaken

High Performance PbS Quantum Dot/Graphene Hybrid Solar Cell with Efficient Charge Extraction.

Hybrid colloidal quantum dot (CQD) solar cells are fabricated from multilayer stacks of lead sulfide (PbS) CQD and single layer graphene (SG). The inclusion of graphene interlayers is shown to increase power conversion efficiency by 9.18%. It is shown that the inclusion of conductive graphene enhances charge extraction in devices. Photoluminescence shows that graphene quenches emission from the quantum dot suggesting spontaneous charge transfer to graphene. CQD photodetectors exhibit increased photoresponse and improved transport properties. We propose that the CQD/SG hybrid structure is a route to make CQD thin films with improved charge extraction, therefore resulting in improved solar cell efficiency

Intransitivity and coexistence in four species cyclic games

Intransitivity is a property of connected, oriented graphs representing species interactions that may drive their coexistence even in the presence of competition, the standard example being the three species Rock-Paper-Scissors game. We consider here a generalization with four species, the minimum number of species allowing other interactions beyond the single loop (one predator, one prey). We show that, contrary to the mean field prediction, on a square lattice the model presents a transition, as the parameter setting the rate at which one species invades another changes, from a coexistence to a state in which one species gets extinct. Such a dependence on the invasion rates shows that the interaction graph structure alone is not enough to predict the outcome of such models. In addition, different invasion rates permit to tune the level of transitiveness, indicating that for the coexistence of all species to persist, there must be a minimum amount of intransitivity.Comment: Final, published versio

Cytoskeletal protein Flightless I inhibits apoptosis, enhances tumor cell invasion and promotes cutaneous squamous cell carcinoma progression

This work was supported by grant from DEBRA Australia to AJC and ZK. AJC is supported by the NHMRC Senior Research Fellowship (#1002009). ZK is supported by the NHMRC Early Career Fellowship (#1036509)

Variation in the SLC23A1 gene does not influence cardiometabolic outcomes to the extent expected given its association with L-ascorbic acid

Background: Observational studies showed that circulating l-ascorbic acid (vitamin C) is inversely associated with cardiometabolic traits. However, these studies were susceptible to confounding and reverse causation. Objectives:We assessed the relation between l-ascorbic acid and 10 cardiometabolic traits by using a single nucleotide polymorphism in the solute carrier family 23 member 1 (SLC23A1) gene (rs33972313) associated with circulating l-ascorbic acid concentrations. The observed association between rs33972313 and cardiometabolic outcomes was compared with that expected given the rs33972313-l-ascorbic acid and l-ascorbic acid–outcome associations. Design: A meta-analysis was performed in the following 5 independent studies: the British Women's Heart and Health Study (n = 1833), the MIDSPAN study (n = 1138), the Ten Towns study (n = 1324), the British Regional Heart Study (n = 2521), and the European Prospective Investigation into Cancer (n = 3737). Results: With the use of a meta-analysis of observational estimates, inverse associations were shown between l-ascorbic acid and systolic blood pressure, triglycerides, and the waist-hip ratio [the strongest of which was the waist-hip ratio (−0.13-SD change; 95% CI: −0.20-, −0.07-SD change; P = 0.0001) per SD increase in l-ascorbic acid], and a positive association was shown with high-density lipoprotein (HDL) cholesterol. The variation at rs33972313 was associated with a 0.18-SD (95% CI: 0.10-, 0.25-SD; P = 3.34 × 10−6) increase in l-ascorbic acid per effect allele. There was no evidence of a relation between the variation at rs33972313 and any cardiometabolic outcome. Although observed estimates were not statistically different from expected associations between rs33972313 and cardiometabolic outcomes, estimates for low-density lipoprotein cholesterol, HDL cholesterol, triglycerides, glucose, and body mass index were in the opposite direction to those expected. Conclusions: The nature of the genetic association exploited in this study led to limited statistical application, but despite this, when all cardiometabolic traits were assessed, there was no evidence of any trend supporting a protective role of l-ascorbic acid. In the context of existing work, these results add to the suggestion that observational relations between l-ascorbic acid and cardiometabolic health may be attributable to confounding and reverse causation