The High-Pressure Freezing Laboratory for Macromolecular Crystallography (HPMX), an ancillary tool for the macromolecular crystallography beamlines at the ESRF

This article describes the High-Pressure Freezing Laboratory for Macromolecular Crystallography (HPMX) at the ESRF, and highlights new and complementary research opportunities that can be explored using this facility. The laboratory is dedicated to investigating interactions between macromolecules and gases in crystallo, and finds applications in many fields of research, including fundamental biology, biochemistry, and environmental and medical science. At present, the HPMX laboratory offers the use of different high-pressure cells adapted for helium, argon, krypton, xenon, nitrogen, oxygen, carbon dioxide and methane. Important scientific applications of high pressure to macromolecules at the HPMX include noble-gas derivatization of crystals to detect and map the internal architecture of proteins (pockets, tunnels and channels) that allows the storage and diffusion of ligands or substrates/products, the investigation of the catalytic mechanisms of gas-employing enzymes (using oxygen, carbon dioxide or methane as substrates) to possibly decipher intermediates, and studies of the conformational fluctuations or structure modifications that are necessary for proteins to function. Additionally, cryo-cooling protein crystals under high pressure (helium or argon at 2000 bar) enables the addition of cryo-protectant to be avoided and noble gases can be employed to produce derivatives for structure resolution. The high-pressure systems are designed to process crystals along a well defined pathway in the phase diagram (pressure-temperature) of the gas to cryo-cool the samples according to the three-step `soak-and-freeze method'. Firstly, crystals are soaked in a pressurized pure gas atmosphere (at 294 K) to introduce the gas and facilitate its interactions within the macromolecules. Samples are then flash-cooled (at 100 K) while still under pressure to cryo-trap macromolecule-gas complexation states or pressure-induced protein modifications. Finally, the samples are recovered after depressurization at cryo-temperatures. The final section of this publication presents a selection of different typical high-pressure experiments carried out at the HPMX, showing that this technique has already answered a wide range of scientific questions. It is shown that the use of different gases and pressure conditions can be used to probe various effects, such as mapping the functional internal architectures of enzymes (tunnels in the haloalkane dehalogenase DhaA) and allosteric sites on membrane-protein surfaces, the interaction of non-inert gases with proteins (oxygen in the hydrogenase ReMBH) and pressure-induced structural changes of proteins (tetramer dissociation in urate oxidase). The technique is versatile and the provision of pressure cells and their application at the HPMX is gradually being extended to address new scientific questions.

ID22 - the high-resolution powder-diffraction beamline at ESRF

Following Phase 2 of the upgrade of the ESRF in which the storage ring was replaced by a new low-emittance ring along with many other facility upgrades, the status of ID22, the high-resolution powder-diffraction beamline, is described. The beamline has an in-vacuum undulator as source providing X-rays in the range 6-75 keV. ID22's principle characteristics include very high angular resolution as a result of the highly collimated and monochromatic beam, coupled with a 13-channel Si 111 multi-analyser stage between the sample and a Dectris Eiger2 X 2M-W CdTe pixel detector. The detector's axial resolution allows recorded 2θ values to be automatically corrected for the effects of axial divergence, resulting in narrower and more-symmetric peaks compared with the previous fixed-axial-slit arrangement. The axial acceptance can also be increased with increasing diffraction angle, thus simultaneously improving the statistical quality of high-angle data. A complementary Perkin Elmer XRD1611 medical-imaging detector is available for faster, lower-resolution data, often used at photon energies of 60-70 keV for pair-distribution function analysis, although this is also possible in high-resolution mode by scanning up to 120° 2θ at 35 keV. There are various sample environments, allowing sample temperatures from 4 K to 1600°C, a capillary cell for non-corrosive gas atmospheres in the range 0-100 bar, and a sample-changing robot that can accommodate 75 capillary samples compatible with the temperature range 80 K to 950°C.

The effects of a brief hope intervention on decision-making in chronic kidney disease patients: A study protocol for a randomized controlled trial

AIMS

This study describes the study protocol of a manualized brief hope intervention that is based on the theoretical proposition - hope theory.

BACKGROUND

Patients with stage 5 chronic kidney disease often had decisional regret when facing the tension of treatment alternatives between dialysis initiation and palliative care. Hope has been found to account for therapeutic changes in clients with depressive symptoms, heightens positive expectations, and striving to accomplish chosen goals. Nevertheless, little is known about the effect of hope on decisional conflict and its influences to the quality of life in these chronic kidney disease patients.

DESIGN

This study is a single-blinded, randomized controlled trial.

METHODS

Participants will be recruited from a regional hospital (approved in April 2018). They will be randomly assigned in equal numbers to either the brief hope intervention or the control arm on completion of the baseline assessment on the possible need of dialysis initiation. Participants in the intervention group will receive the pre-dialysis education and a 4-week Brief Hope Intervention [consisting of four sessions at weekly intervals (two face-to-face sessions and two telephone follow-up sessions in between)], while those allocated to the control arm will receive the renal education and social chats. Outcome measures will be carried out prior to the intervention (baseline), immediately, and 1 month after the intervention. These consist of the hope level, decisional conflict, and quality of life. Healthcare resources use data will be reported.

IMPACT

The study results have the potential to add scientific evidence to the research-tested programme when developing renal services integral to multimodal care management to optimize decision-making and attain better health outcomes.

CM01: a facility for cryo-electron microscopy at the European Synchrotron

Recent improvements in direct electron detectors, microscope technology and software provided the stimulus for a `quantum leap' in the application of cryo-electron microscopy in structural biology, and many national and international centres have since been created in order to exploit this. Here, a new facility for cryo-electron microscopy focused on single-particle reconstruction of biological macromolecules that has been commissioned at the European Synchrotron Radiation Facility (ESRF) is presented. The facility is operated by a consortium of institutes co-located on the European Photon and Neutron Campus and is managed in a similar fashion to a synchrotron X-ray beamline. It has been open to the ESRF structural biology user community since November 2017 and will remain open during the 2019 ESRF-EBS shutdown.

A high-energy-resolution resonant inelastic X-ray scattering spectrometer at ID20 of the European Synchrotron Radiation Facility

An end-station for resonant inelastic X-ray scattering and (resonant) X-ray emission spectroscopy at beamline ID20 of ESRF - The European Synchrotron is presented. The spectrometer hosts five crystal analysers in Rowland geometry for large solid angle collection and is mounted on a rotatable arm for scattering in both the horizontal and vertical planes. The spectrometer is optimized for high-energy-resolution applications, including partial fluorescence yield or high-energy-resolution fluorescence detected X-ray absorption spectroscopy and the study of elementary electronic excitations in solids. In addition, it can be used for non-resonant inelastic X-ray scattering measurements of valence electron excitations.

A large-solid-angle X-ray Raman scattering spectrometer at ID20 of the European Synchrotron Radiation Facility

An end-station for X-ray Raman scattering spectroscopy at beamline ID20 of the European Synchrotron Radiation Facility is described. This end-station is dedicated to the study of shallow core electronic excitations using non-resonant inelastic X-ray scattering. The spectrometer has 72 spherically bent analyzer crystals arranged in six modular groups of 12 analyzer crystals each for a combined maximum flexibility and large solid angle of detection. Each of the six analyzer modules houses one pixelated area detector allowing for X-ray Raman scattering based imaging and efficient separation of the desired signal from the sample and spurious scattering from the often used complicated sample environments. This new end-station provides an unprecedented instrument for X-ray Raman scattering, which is a spectroscopic tool of great interest for the study of low-energy X-ray absorption spectra in materials under in situ conditions, such as in operando batteries and fuel cells, in situ catalytic reactions, and extreme pressure and temperature conditions.

RixsToolBox: software for the analysis of soft X-ray RIXS data acquired with 2D detectors

A software with a graphical user interface has been developed with the aim of facilitating the data analysis for users of a new resonant inelastic X-ray scattering (RIXS) spectrometer installed at the ESRF beamline ID32. The software is organized in modules covering all relevant steps in the data reduction from a stack of several hundred two-dimensional CCD images to a single RIXS spectrum. It utilizes both full charge integration and single-photon centroiding to cope with high-flux and high-resolution requirements. Additional modules for further data analysis and the extraction of instrumental parameters are available. The software has been in routine use for about a year now and in that time many additional features have been incorporated. It now meets the users' need for an easy-to-use data analysis tool that allows looking at and understanding data as it is acquired and thus steering users' experiments more efficiently.

Big-Science facilities in Europe need greater coordination of resources

The leading role in science played by crystallography is heavily dependent on Big-Science facilities. The need for Europe-wide coordination of operational resources in Big Science is discussed with particular reference to neutron sources.

The high-field magnet endstation for X-ray magnetic dichroism experiments at ESRF soft X-ray beamline ID32

A new high-field magnet endstation for X-ray magnetic dichroism experiments has been installed and commissioned at the ESRF soft X-ray beamline ID32. The magnet consists of two split-pairs of superconducting coils which can generate up to 9 T along the beam and up to 4 T orthogonal to the beam. It is connected to a cluster of ultra-high-vacuum chambers that offer a comprehensive set of surface preparation and characterization techniques. The endstation and the beam properties have been designed to provide optimum experimental conditions for X-ray magnetic linear and circular dichroism experiments in the soft X-ray range between 400 and 1600 eV photon energy. User operation started in November 2014.

Facilitating best practices in collecting anomalous scattering data for de novo structure solution at the ESRF Structural Biology Beamlines

The constant evolution of synchrotron structural biology beamlines, the viability of screening protein crystals for a wide range of heavy-atom derivatives, the advent of efficient protein labelling and the availability of automatic data-processing and structure-solution pipelines have combined to make de novo structure solution in macromolecular crystallography a less arduous task. Nevertheless, the collection of diffraction data of sufficient quality for experimental phasing is still a difficult and crucial step. Here, some examples of good data-collection practice for projects requiring experimental phasing are presented and recent developments at the ESRF Structural Biology beamlines that have facilitated these are illustrated.

The time-resolved and extreme conditions XAS (TEXAS) facility at the European Synchrotron Radiation Facility: the general-purpose EXAFS bending-magnet beamline BM23

BM23 is the general-purpose EXAFS bending-magnet beamline at the ESRF, replacing the former BM29 beamline in the framework of the ESRF upgrade. Its mission is to serve the whole XAS user community by providing access to a basic service in addition to the many specialized instruments available at the ESRF. BM23 offers high signal-to-noise ratio EXAFS in a large energy range (5-75 keV), continuous energy scanning for quick-EXAFS on the second timescale and a micro-XAS station delivering a spot size of 4 µm × 4 µm FWHM. It is a user-friendly facility featuring a high degree of automation, online EXAFS data reduction and a flexible sample environment.

Combined creatinine velocity and nadir creatinine: A reliable predictor of renal outcome in neonatally diagnosed posterior urethral valves

INTRODUCTION

Nadir creatinine (lowest creatinine during the first year following diagnosis) is a recognised indicator of future chronic renal impairment (CRI) in posterior urethral valve (PUV) patients. We recently described "creatinine velocity" (Cvel), the rate of change of creatinine following initial bladder drainage, as a new early predictor of CRI in neonatally diagnosed PUV. Rising Cvel (>3 μmol/L/day) is associated with increased risk of CRI.

OBJECTIVE

We studied these two prognostic indicators in combination, as a test for future CRI in neonatally diagnosed PUV patients.

STUDY DESIGN

Medical records for patients treated by endoscopic valve ablation at our institution between 1993 and 2004 were reviewed. Simple linear regression was used to calculate Cvel. Creatinine velocity and nadir creatinine were considered predictive of future CRI if they were greater than 3 μmol/L/day or greater than 75 μmol/L (0.85 mg/dL), respectively. Chronic renal insufficiency was defined as CKD2 or higher. Outcomes in test groups were analysed by Fisher exact test. Statistical significance was defined as p < 0.05.

RESULTS

Sixty-two patients were treated within the first 30 days of life and had sufficient data to calculate both Cvel and nadir creatinine. Mean follow-up was 9.4 years. Patients were grouped as having both risk factors (Group A), one risk factor (Group B), or neither risk factor (Group C). All four (100%) patients from Group A developed CRI, compared with 11 of 17 (64.7%) patients from Group B and three of 41 (7.3%) patients from Group C (p ≤ 0.0005). As a diagnostic test for future CRI, "presence of at least one risk factor" had a specificity of 86.4%, sensitivity of 83.3%, positive predictive value of 71.4%, and negative predictive value of 92.7%. Additional prognostic information was obtained by assigning a score from 1 to 3 for each prognostic indicator (Table). The sum of these scores gave a PUV Risk Score. No patient with a PUV Risk Score of 2 developed CRI, while all patients with a Score of 6 developed CRI. Incidence of CRI in patients with PUV Risk Scores of 3, 4, and 5 was 8.3%, 50%, and 63.6%, respectively (p ≤ 0.0005).

CONCLUSION

Considered together, these prognostic indicators provide a powerful test for future CRI. Presence of at least one of these risk factors should be considered "at risk for CRI". Patients with neither risk factor are unlikely to develop CRI. Calculation of the PUV Risk Score provides an even more accurate prognosis.

Glomerular diseases outcome at one year in a tertiary care centre

Objectives:

To determine outcome in primary and secondary glomerular diseases at one year follow up.

Methods:

Study design is observational cohort, done in out-patient department, Dow Iinternational Medical College, DUHS. All information gathered on a proforma. All patients with dipstick positive proteinuria and clinical glomerular disease were included in study. Patients with no proteinuria were excluded so were patients with stage 5 CKD. Patients were followed for proteinuria and renal insufficiency at completion of one year follow up. Statistical analysis was done on SPSS version 16.

Result:

Total number of patients who completed one year follow up was 173. Mean age of patients was 51.67+ 10.16 (range 15 to 75 years). Ninety two (53.2%), were males and 81(46.8%) were females, ratio being 1.1: 1.0. Mean weight of our patients was 67.43+ 14.13 Kg, (35 to 107 kg). Commonest cause of glomerular disease in our patient was diabetic nephropathy which was seen in 94.2% patients. Commonest associated problem with glomerular disease was hypertension seen in 66.5% of patients. Four out of 173 patients had stage 5 CKD at end of follow up at one year while quantitativ proteinuria remained same at one year follow up.

Conclusion:

One year follow up is critical for patients with glomerular disease associated with stage 4 CKD as progression to end stage renal failure may be seen within one year in these patients.

Hemodialysis patients profile at Dow University of Health Sciences, Karachi. Pakistan

Objectives: To determine the frequency of diseases contributing to End Stage Renal Failure (ESRF) and to determine the frequency of seropositivity for hepatitis B and hepatitis C in our patients.

Methods: This is an observational study of two years duration from January 2012 till December 2013, done at Dow university of Health Sciences. Sample size is 189 by convenient method. Data collection is retrospective. Inclusion criteria includes all patients ever hemodialysed at DIMC with age 14 or above. Exclusion criteria is age below 14. Data maintained and analyzed on SPSS version 16. All categorical data in percentages and numeric data is given in frequencies and mean with Standard deviation.

Result: Total number of patients included in study were 189, Males were 94/189 (49.7%), females were 95/189 (50.3%), Male to female ratio was 0.98: 1.0. Mean age was 51.88+15.2, range was14-86 years. Patients started on Hemodialysis were found to have hypertension in 40.2%, both diabetes and hypertension was present in 42.8%, diabetes alone in 3.1% of patients as likely etiology of renal failure. Seropositivity for HBV was found 4/189(2.1%) and HCV in 31/189(16.4%) at initiation of Hemodialysis.

Conclusion: Hypertension alone is an important disease found in patients with renal failure as likely cause followed by diabetes. Hepatitis C positivity at start of hemodialysis is 16%.

Structure of internalin InlK from the human pathogen Listeria monocytogenes

Listeria monocytogenes is a human pathogen that employs a wide variety of virulence factors in order to adhere to, invade, and replicate within target cells. Internalins play key roles in processes ranging from adhesion to receptor recognition and are thus essential for infection. Recently, InlK, a surface-associated internalin, was shown to be involved in Listeria's ability to escape from autophagy by recruitment of the major vault protein (MVP) to the bacterial surface. Here, we report the structure of InlK, which harbors four domains arranged in the shape of a "bent arm". The structure supports a role for the "elbow" of InlK in partner recognition, as well as of two Ig-like pedestals intercalated by hinge regions in the projection of InlK away from the surface of the bacterium. The unusual fold and flexibility of InlK could be essential for MVP binding and concealment from recognition by molecules involved in the autophagic process.

Lanthanum carbonate for hyperphosphatemia in patients with advanced CKD and patients receiving dialysis

Reduced renal excretion of phosphate leads to hyperphosphatemia, which is prevalent in patients with end-stage renal disease, and is associated with increased morbidity and mortality. Dialysis alone is unable to adequately remove the ingested phosphate contained in food. It is therefore usually necessary to supplement food with drugs that reduce the intestinal absorption of dietary phosphate in order to control serum phosphate. Lanthanum carbonate is a recently introduced nonaluminum, noncalcium phosphate binder licensed for the management of serum phosphate in end-stage renal failure. It appears safe and effective, with data demonstrating no toxic effects in man after continuous exposure for up to 6 years. It is well tolerated and has a positive effect on bone histology in the context of renal osteodystrophy. Lanthanum carbonate's high affinity for phosphate rapid binding, palatability, low pill burden and absence of evident toxicity compare favorably with what are considered to be the ideal characteristics of an oral phosphate binder.