Crystal structure of a three-tetrad, parallel, K+-stabilized human telomeric G-quadruplex at 1.35†Šresolution.

The crystal structure of the G-rich human telomeric DNA Tel22 has been determined at 1.35 Šresolution in space group P6. Tel22 forms a non-canonical DNA structure called the G-quadruplex. The space group and unit-cell parameters are comparable to those in the crystal structures with PDB codes 6ip3 (1.40 Šresolution) and 1kf1 (2.15 Šresolution). The G-quadruplexes are highly similar in all of the structures. However, this structure of Tel22 displays clear density for polyethylene glycol and two potassium ions, which are located outside the ion channel in the G-quadruplex and play an important role in stabilizing the crystal contacts. In addition, 111 water molecules were identified (compared with 79 and 68 in PDB entries 6ip3 and 1kf1, respectively) that participate in intricate and extensive networks providing high stability to the G-quadruplex.

External validation of the Oldham composite Covid-19 associated mortality model (OCCAM), a prognostic model for death in patients hospitalised with Covid-19.

OBJECTIVE: External validation of the Oldham Composite Covid-19 associated Mortality Model (OCCAM), a prognostic model for Covid-19 mortality in hospitalised patients comprised of age, history of hypertension, current or previous malignancy, admission platelet count < 150 × 103/µL, admission CRP ≥ 100 µg/mL, acute kidney injury (AKI), and radiographic evidence of > 50% total lung field infiltrates. PATIENTS AND METHODS: Retrospective study assessing discrimination (c-statistic) and calibration of OCCAM for death in hospital or within 30 days of discharge. 300 adults admitted to six district general and teaching hospitals in North West England for treatment of Covid-19 between September 2020 and February 2021 were included. RESULTS: Two hundred and ninety-seven patients were included in the validation cohort analysis, with a mortality rate of 32.8%. The c-statistic was 0.794 (95% confidence interval 0.742-0.847) vs. 0.805 (95% confidence interval 0.766 - 0.844) in the development cohort. Visual inspection of calibration plots demonstrate excellent calibration across risk groups, with a calibration slope for the external validation cohort of 0.963. CONCLUSION: The OCCAM model is an effective prognostic tool that can be utilised at the time of initial patient assessment to aid decisions around admission and discharge, use of therapeutics, and shared decision-making with patients. Clinicians should remain aware of the need for ongoing validation of all Covid-19 prognostic models in light of changes in host immunity and emerging variants.

Patient characteristics and predictors of mortality in 470 adults admitted to a district general hospital in England with Covid-19.

Understanding risk factors for death from Covid-19 is key to providing good quality clinical care. We assessed the presenting characteristics of the 'first wave' of patients with Covid-19 at Royal Oldham Hospital, UK and undertook logistic regression modelling to investigate factors associated with death. Of 470 patients admitted, 169 (36%) died. The median age was 71 years (interquartile range 57-82), and 255 (54.3%) were men. The most common comorbidities were hypertension (n = 218, 46.4%), diabetes (n = 143, 30.4%) and chronic neurological disease (n = 123, 26.1%). The most frequent complications were acute kidney injury (AKI) (n = 157, 33.4%) and myocardial injury (n = 21, 4.5%). Forty-three (9.1%) patients required intubation and ventilation, and 39 (8.3%) received non-invasive ventilation. Independent risk factors for death were increasing age (odds ratio (OR) per 10 year increase above 40 years 1.87, 95% confidence interval (CI) 1.57-2.27), hypertension (OR 1.72, 95% CI 1.10-2.70), cancer (OR 2.20, 95% CI 1.27-3.81), platelets <150 × 103/µl (OR 1.93, 95% CI 1.13-3.30), C-reactive protein ≥100 µg/ml (OR 1.68, 95% CI 1.05-2.68), >50% chest radiograph infiltrates (OR 2.09, 95% CI 1.16-3.77) and AKI (OR 2.60, 95% CI 1.64-4.13). There was no independent association between death and gender, ethnicity, deprivation level, fever, SpO2/FiO2, lymphopoenia or other comorbidities. These findings will inform clinical and shared decision making, including use of respiratory support and therapeutic agents.

A New Method for Analyzing Powder Diffraction Patterns: Confirmation of a Predicted Phase of SF6.

A recent computer simulation reproduced all of the solid-state transitions known for sulfur hexafluoride and predicted the unknown structure of its coldest phase. Subsequent neutron diffraction experiments that were performed to establish the structure of this phase could not be interpreted by conventional procedures. A method for analyzing Debye-Scherrer diffraction patterns was designed to avoid the many false minima that are encountered in standard analyses of low-symmetry phases. The structure found with this method confirmed the previous theoretical prediction.

Small-angle neutron scattering from native and irradiated superoxide dismutase in aqueous solution.

The approximate size and shape of holo and apo forms of bovine cupro-zinc erythrocyte superoxide dismutase (EC 1.15.1.1) were determined by small-angle neutron scattering from aqueous solutions at neutral pH. A model assuming a cylindrical shape gave the best fit to the data for both forms of the enzyme. The radius of gyration, Rg, of the apoenzyme was found to be marginally larger than that of the holoenzyme. Scattering from the protein vanished for H2O/2H2O mixtures containing 42(+/- 2)% 2H2O, and the negligible dependence of Rg on the 2H2O fraction indicated uniform scattering density. Irradiation with 60Co gamma-rays resulted in aggregation of superoxide dismutase molecules; scattering at small doses was interpreted in terms of pairwise side-by-side aggregation. For large doses (approx. 3.8 X 10(3) Gy) and at relatively high enzyme concentrations (320 microM), the interpretation of the neutron scattering data is ambiguous. The value of Rg suggests that end-to-end stacking of the cylindrical molecules is one possibility. The equilibrium concentration of separated subunits was found to be unobservable and calculations showed that denaturation did not contribute significantly to our neutron scattering measurements for the radiation doses employed (maximum 3.8 X 10(5) Gy). High-performance liquid chromatography (HPLC) data showed that in mixtures the apo and holo forms of superoxide dismutase interact with one another, and that the side-by-side aggregates, induced by irradiation of the enzyme, are readily dissociated, resulting in a single elution peak that is resolved from the later peak common to both the apo and holo forms.

Intermolecular potentials for alpha-glycine from Raman and infrared scattering measurements.

The frequencies of intermolecular modes in alpha-glycine-d0 and -d5 have been measured at 300 and 85 K by Raman and infrared scattering techniques. These frequencies were analyzed in terms of simple analytic interatomic potentials. Buckingham potentials were assumed for the nonbonded and hydrogen-bond interactions, and Coulomb and screened Coulomb potentials were assumed for the electrostatic interactions. The observed frequencies are well described by the simple model and the parameters of the hydrogen-bond potentials and the molecular charge distribution were determined from the analysis.

Dehydration of cytosine monohydrate at physiological temperatures.

Neutron diffraction, thermogravimetric, and mass spectrographic measurements have been used to show that cytosine monohydrate loses its water of hydration at physiological temperatures (approximately equal to 37 degrees C) and converts to cytosine. The "activation energy" for the dehydration process has been determined from isothermal weight curves and is 27.1 +/- 0.6 kcal . mol-1. It is suggested that pyrimidine dehydration may be involved in structural changes in DNA.

Hydrogen bonding in DNA base complexes.

Experimental intermolecular frequencies in the DNA base complexes 1-methylthymine (1-MT) and cytosine monohydrate (CMH) are analyzed in terms of simple analytic interatomic potentials. Calculations with two different values for the constants of the nonbonded interactions are considered, and the hydrogen bond potentials are determined for each of these models. The observed frequencies in 1-MT are reasonably well described, although corresponding potentials are very different in the two models. The observed frequencies in CMH are less well described, although corresponding hydrogen bond potentials are similar in the two models. Hydration interactions are found to be important in CMH and the role of the water molecule is discussed. Possible reasons for the shortcomings of this simple analysis are considered.

Physical characteristics of human transferrin from small angle neutron scattering.

The technique of small angle neutron scattering has been used to determine the molecular shape, the volume, and the molecular weight of pooled human transferrin in an aqueous solution isotonic with blood. Analysis of the measurements assuming a spheroidal molecular shape indicates that an oblate spheroid with semi-axes of length 46.6 +/- 1.4, 46.6 +/- 1.4 and 15.8 +/- 3.8 A, and a molecular volume of (144 +/- 45) X 10(3) A3 is the best simple approximation to the shape of the transferrin molecule. The radius of gyration, Rg, determined from a Guinier plot is 30.25 +/- 0.49 A, in agreement with Rg calculated for the oblate spheroidal shape. The molecular weight is determined to be (75 +/- 5) X 10(3). The shape-independent molecular volume is found to be (98 +/- 10) X 10(3) A3. The difference in the two volumes suggests that transferrin is not a uniform spheroid but may have a more complex shape.