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Macromolecular crystallography (MX) is the dominant means of determining the three-dimensional structures of biological macromolecules. Over the last few decades, most MX data have been collected at synchrotron beamlines using a large number of different detectors produced by various manufacturers and taking advantage of various protocols and goniometries. These data came in their own formats: sometimes proprietary, sometimes open. The associated metadata rarely reached the degree of completeness required for data management according to Findability, Accessibility, Interoperability and Reusability (FAIR) principles. Efforts to reuse old data by other investigators or even by the original investigators some time later were often frustrated. In the culmination of an effort dating back more than two decades, a large portion of the research community concerned with high data-rate macromolecular crystallography (HDRMX) has now agreed to an updated specification of data and metadata for diffraction images produced at synchrotron light sources and X-ray free-electron lasers (XFELs). This 'Gold Standard' will facilitate the processing of data sets independent of the facility at which they were collected and enable data archiving according to FAIR principles, with a particular focus on interoperability and reusability. This agreed standard builds on the NeXus/HDF5 NXmx application definition and the International Union of Crystallo-graphy (IUCr) imgCIF/CBF dictionary, and it is compatible with major data-processing programs and pipelines. Just as with the IUCr CBF/imgCIF standard from which it arose and to which it is tied, the NeXus/HDF5 NXmx Gold Standard application definition is intended to be applicable to all detectors used for crystallography, and all hardware and software developers in the field are encouraged to adopt and contribute to the standard.

In macromolecular crystallography, higher flux, smaller beams, and faster detectors open the door to experiments with very large numbers of very small samples that can reveal polymorphs and dynamics but require re-engineering of approaches to the clustering of images both at synchrotrons and XFELs (X-ray free electron lasers). The need for the management of orders of magnitude more images and limitations of file systems favor a transition from simple one-file-per-image systems such as CBF to image container systems such as HDF5. This further increases the load on computers and networks and requires a re-examination of the presentation of metadata. In this paper, we discuss three important components of this problem-improved approaches to the clustering of images to better support experiments on polymorphs and dynamics, recent and upcoming changes in metadata for Eiger images, and software to rapidly validate images in the revised Eiger format.

The transformations from the primitive cells of the centered Bravais lattices to the corresponding centered cells have conventionally been listed as three-by-three matrices that transform three-space lattice vectors. Using those three-by-three matrices when working in the six-dimensional space of lattices represented as Selling scalars as used in Delone (Delaunay) reduction, one could transform to the three-space representation, apply the three-by-three matrices and then back-transform to the six-space representation, but it is much simpler to have the equivalent six-by-six matrices and apply them directly. The general form of the transformation from the three-space matrix to the corresponding matrix operating on Selling scalars (expressed in space S6) is derived, and the particular S6matrices for the centered Delone types are listed. (Note: in his later publications, Boris Delaunay used the Russian version of his surname, Delone.).

This manuscript is the result of the North American Neuroendocrine Tumor Society consensus conference on the surgical management of pancreatic neuroendocrine tumors from July 19 to 20, 2018. The group reviewed a series of questions of specific interest to surgeons taking care of patients with pancreatic neuroendocrine tumors, and for each, the available literature was reviewed. What follows are these reviews for each question followed by recommendations of the panel.

PurposeLimited options exist for patients with advanced pancreatic cancer progressing after 1 or more lines of therapy. A phase II study in patients with previously treated metastatic pancreatic cancer showed that combining GVAX pancreas (granulocyte-macrophage colony-stimulating factor-secreting allogeneic pancreatic tumor cells) with cyclophosphamide (Cy) and CRS-207 (live, attenuated Listeria monocytogenes expressing mesothelin) resulted in median overall survival (OS) of 6.1 months, which compares favorably with historical OS achieved with chemotherapy. In the current study, we compared Cy/GVAX + CRS-207, CRS-207 alone, and standard chemotherapy in a three-arm, randomized, controlled phase IIb trial.Patients and methodsPatients with previously treated metastatic pancreatic adenocarcinoma were randomized 1:1:1 to receive Cy/GVAX + CRS-207 (arm A), CRS-207 (arm B), or physician's choice of single-agent chemotherapy (arm C). The primary cohort included patients who had failed ≥2 prior lines of therapy, including gemcitabine. The primary objective compared OS between arms A and C in the primary cohort. The second-line cohort included patients who had received 1 prior line of therapy. Additional objectives included OS between all treatment arms, safety, and tumor responses.ResultsThe study did not meet its primary efficacy endpoint. At the final study analysis, median OS [95% confidence interval (CI)] in the primary cohort (N = 213) was 3.7 (2.9-5.3), 5.4 (4.2-6.4), and 4.6 (4.2-5.7) months in arms A, B, and C, respectively, showing no significant difference between arm A and arm C [P = not significant (NS), HR = 1.17; 95% CI, 0.84-1.64]. The most frequently reported adverse events in all treatment groups were chills, pyrexia, fatigue, and nausea. No treatment-related deaths occurred.ConclusionsThe combination of Cy/GVAX + CRS-207 did not improve survival over chemotherapy. (ClinicalTrials.gov ID: NCT02004262)See related commentary by Salas-Benito et al., p. 5435.

Algorithms for quantifying the differences between two lattices are used for Bravais lattice determination, database lookup for unit cells to select candidates for molecular replacement, and recently for clustering to group together images from serial crystallography. It is particularly desirable for the differences between lattices to be computed as a perturbation-stable metric, i.e. as distances that satisfy the triangle inequality, so that standard tree-based nearest-neighbor algorithms can be used, and for which small changes in the lattices involved produce small changes in the distances computed. A perturbation-stable metric space related to the reduction algorithm of Selling and to the Bravais lattice determination methods of Delone is described. Two ways of representing the space, as six-dimensional real vectors or equivalently as three-dimensional complex vectors, are presented and applications of these metrics are discussed. (Note: in his later publications, Boris Delaunay used the Russian version of his surname, Delone.).

The highly automated macromolecular crystallography beamline AMX/17-ID-1 is an undulator-based high-intensity (>5 × 1012 photons s−1), micro-focus (7 µm × 5 µm), low-divergence (1 mrad × 0.35 mrad) energy-tunable (5–18 keV) beamline at the NSLS-II, Brookhaven National Laboratory, Upton, NY, USA. It is one of the three life science beamlines constructed by the NIH under the ABBIX project and it shares sector 17-ID with the FMX beamline, the frontier micro-focus macromolecular crystallography beamline. AMX saw first light in March 2016 and started general user operation in February 2017. At AMX, emphasis has been placed on high throughput, high capacity, and automation to enable data collection from the most challenging projects using an intense micro-focus beam. Here, the current state and capabilities of the beamline are reported, and the different macromolecular crystallography experiments that are routinely performed at AMX/17-ID-1 as well as some plans for the near future are presented.

Pancreatic ductal adenocarcinoma (PDAC) driven by the KRAS-G12D mutation presents a formidable health challenge because of limited treatment options. MRTX1133 is a highly selective and first-in-class KRAS-G12D inhibitor under clinical development. Here, we report that the advanced glycosylation end product–specific receptor (AGER) plays a key role in mediating MRTX1133 resistance in PDAC cells. The up-regulation of AGER within cancer cells instigates macropinocytosis, facilitating the internalization of serum albumin and subsequent amino acid generation. These amino acids are then used to synthesize the antioxidant glutathione, leading to resistance to MRTX1133 treatment due to the inhibition of apoptosis. The underlying molecular mechanism involves AGER's interaction with diaphanous-related formin 1 (DIAPH1), a formin protein responsible for driving Rac family small GTPase 1 (RAC1)–dependent macropinosome formation. The effectiveness and safety of combining MRTX1133 with pharmacological inhibitors of the AGER-DIAPH1 complex (using RAGE299) or macropinocytosis (using EIPA) were confirmed in patient-derived xenografts, orthotopic models, and genetically engineered mouse PDAC models. This combination therapy also induces high-mobility group box 1 (HMGB1) release, resulting in a subsequent antitumor CD8+ T cell response in immunocompetent mice. Collectively, the study findings underscore the potential to enhance the efficacy of KRAS-G12D blockade therapy by targeting AGER-dependent macropinocytosis. Editor's summary: Selective KRAS-G12D inhibitors have become an important treatment option for patients with KRAS-G12D–driven cancers, but the development of drug resistance can limit their efficacy. In this study by Li et al., the authors found that advanced glycosylation end product–specific receptor (AGER) contributed to MRTX1133 resistance in pancreatic ductal adenocarcinoma (PDAC) through modulation of macropinocytosis and glutathione synthesis using patient-derived xenografts and orthotopic and genetically engineered mouse models. The combination of MRTX1133 with inhibition of AGER or macropinocytosis improved survival and reduced tumor burden in a CD8+ T cell–dependent manner. These results suggest that this combination treatment may be an effective strategy to improve MRTX1133 efficacy in KRAS-G12D–driven PDAC and related cancers. —Allison Williams [ABSTRACT FROM AUTHOR]

Background and Aims: Ammonium (NH4+) is an important nitrogen (N) source in many ecosystems and agricultural systems but excessive NH4+ is toxic to root growth and development, especially when NH4+ is the sole N source. Previous studies have shown that polar auxin (indole-3-acetic acid, IAA) transport mediated by PIN2 and AUX1 is critical for maintaining lateral root development under high-NH4+ stress. However, the regulation of subcellular IAA homeostasis under high-NH4+ stress has remained unclear. Methods: Knockout mutants for the intracellular IAA transporter PIN5 and the plasma-membrane H+-ATPases AHA1 and AHA2 were used, and primary root length, transmembrane H+ fluxes, and NH4+ fluxes in the roots were determined. Results: We show that high NH4+ disturbs the subcellular IAA homeostasis by upregulating the expression of PIN5. Knockout of PIN5 resulted in elevated cytoplastic IAA accumulation and reduced NH4+ efflux under high-NH4+ stress. Furthermore, we show that NH4+ treatment promotes H+ efflux at the root elongation zone, in turn promoting NH4+ efflux, with the involvement of PIN5-mediated intracellular IAA transport. Moreover, stabilization of rhizosphere pH reduced NH4+ efflux and promoted primary root growth in the pin5 mutant under high NH4+. Conclusion: Our findings provide a mechanistic explanation for the role of subcellular IAA homeostasis in response to high-NH4+ stress through the coordinated regulation of NH4+ efflux and H+ efflux. [ABSTRACT FROM AUTHOR]