Publications by authors named "Daniel Franke"

37 Publications

Anomalous SAXS at P12 beamline EMBL Hamburg: instrumentation and applications.

J Synchrotron Radiat 2021 May 14;28(Pt 3):812-823. Epub 2021 Apr 14.

European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany.

Small-angle X-ray scattering (SAXS) is an established method for studying nanostructured systems and in particular biological macromolecules in solution. To obtain element-specific information about the sample, anomalous SAXS (ASAXS) exploits changes of the scattering properties of selected atoms when the energy of the incident X-rays is close to the binding energy of their electrons. While ASAXS is widely applied to condensed matter and inorganic systems, its use for biological macromolecules is challenging because of the weak anomalous effect. Biological objects are often only available in small quantities and are prone to radiation damage, which makes biological ASAXS measurements very challenging. The BioSAXS beamline P12 operated by the European Molecular Biology Laboratory (EMBL) at the PETRA III storage ring (DESY, Hamburg) is dedicated to studies of weakly scattering objects. Here, recent developments at P12 allowing for ASAXS measurements are presented. The beamline control, data acquisition and data reduction pipeline of the beamline were adapted to conduct ASAXS experiments. Modelling tools were developed to compute ASAXS patterns from atomic models, which can be used to analyze the data and to help designing appropriate data collection strategies. These developments are illustrated with ASAXS experiments on different model systems performed at the P12 beamline.
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http://dx.doi.org/10.1107/S1600577521003404DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8127372PMC
May 2021

: expanded functionality and new tools for small-angle scattering data analysis.

J Appl Crystallogr 2021 Feb 1;54(Pt 1):343-355. Epub 2021 Feb 1.

European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany.

The software suite encompasses a number of programs for the processing, visualization, analysis and modelling of small-angle scattering data, with a focus on the data measured from biological macromolecules. Here, new developments in the package are described. They include , for simulating isotropic 2D scattering patterns; , to perform operations on 2D images and masks; , a method for variance estimation of structural invariants through parametric resampling; , which computes the pair distance distribution function by a direct Fourier transform of the scattering data; , to compute the scattering data from a pair distance distribution function, allowing comparison with the experimental data; a new module in for Bayesian consensus-based concentration-independent molecular weight estimation; , an shape analysis method that optimizes the search model directly against the scattering data; , an application to set up the initial search volume for multiphase modelling of membrane proteins; , to perform quasi-atomistic modelling of liposomes with elliptical shapes; , which models conformational changes in nucleic acid structures through normal mode analysis in torsion angle space; , which reconstructs the shape of an unknown intermediate in an evolving system; and and , for modelling multilamellar and asymmetric lipid vesicles, respectively. In addition, technical updates were deployed to facilitate maintainability of the package, which include porting the graphical interface to Qt5, updating - a plugin to run a subset of tools - to be both Python 2 and 3 compatible, and adding utilities to facilitate mmCIF compatibility in future releases. All these features are implemented in , freely available for academic users at https://www.embl-hamburg.de/biosaxs/software.html.
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http://dx.doi.org/10.1107/S1600576720013412DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7941305PMC
February 2021

Simulation of small-angle X-ray scattering data of biological macromolecules in solution.

J Appl Crystallogr 2020 Apr 18;53(Pt 2):536-539. Epub 2020 Feb 18.

European Molecular Biology Laboratory, Notkestrasse 85 c/o DESY, Hamburg, 22607, Germany.

This article presents , an application to simulate two-dimensional small-angle X-ray scattering patterns and, further, one-dimensional profiles from biological macromolecules in solution. implements a statistical approach yielding two-dimensional images in TIFF, CBF or EDF format, which may be readily processed by existing data-analysis pipelines. Intensities and error estimates of one-dimensional patterns obtained from the radial average of the two-dimensional images exhibit the same statistical properties as observed with actual experimental data. With initial input on an absolute scale, [cm]/c[mg ml], the simulated data frames may also be scaled to absolute scale such that the forward scattering after subtraction of the background is proportional to the molecular weight of the solute. The effects of changes of concentration, exposure time, flux, wavelength, sample-detector distance, detector dimensions, pixel size, and the mask as well as incident beam position can be considered for the simulation. The simulated data may be used in method development, for educational purposes, and also to determine the most suitable beamline setup for a project prior to the application and use of the actual beamtime. is available as part of the software package (3.0.0) and is freely available for academic use (http://www.embl-hamburg.de/biosaxs/download.html).
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http://dx.doi.org/10.1107/S1600576720000527DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133063PMC
April 2020

Scalable Synthesis of InAs Quantum Dots Mediated through Indium Redox Chemistry.

J Am Chem Soc 2020 03 19;142(9):4088-4092. Epub 2020 Feb 19.

Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.

Next-generation optoelectronic applications centered in the near-infrared (NIR) and short-wave infrared (SWIR) wavelength regimes require high-quality materials. Among these materials, colloidal InAs quantum dots (QDs) stand out as an infrared-active candidate material for biological imaging, lighting, and sensing applications. Despite significant development of their optical properties, the synthesis of InAs QDs still routinely relies on hazardous, commercially unavailable precursors. Herein, we describe a straightforward single hot injection procedure revolving around In(I)Cl as the key precursor. Acting as a simultaneous reducing agent and In source, In(I)Cl smoothly reacts with a tris(amino)arsenic precursor to yield colloidal InAs quantitatively and at gram scale. Tuning the reaction temperature produces InAs cores with a first excitonic absorption feature in the range of 700-1400 nm. A dynamic disproportionation equilibrium between In(I), In metal, and In(III) opens up additional flexibility in precursor selection. CdSe shell growth on the produced cores enhances their optical properties, furnishing particles with center emission wavelengths between 1000 and 1500 nm and narrow photoluminescence full-width at half-maximum (FWHM) of about 120 meV throughout. The simplicity, scalability, and tunability of the disclosed precursor platform are anticipated to inspire further research on In-based colloidal QDs.
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http://dx.doi.org/10.1021/jacs.9b12350DOI Listing
March 2020

Increasing the penetration depth of temporal focusing multiphoton microscopy for neurobiological applications.

J Phys D Appl Phys 2019 Jun 25;52(26):264001. Epub 2019 Apr 25.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America.

The first ever demonstration of temporal focusing with short wave infrared (SWIR) excitation and emission is demonstrated, achieving a penetration depth of 500 m in brain tissue. This is substantially deeper than the highest previously-reported values for temporal focusing imaging in brain tissue, and demonstrates the value of these optimized wavelengths for neurobiological applications.
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http://dx.doi.org/10.1088/1361-6463/ab16b4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7655118PMC
June 2019

Single Nanocrystal Spectroscopy of Shortwave Infrared Emitters.

ACS Nano 2019 02 30;13(2):1042-1049. Epub 2018 Nov 30.

Department of Chemistry , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States.

Short-wave infrared (SWIR) emitters are at the center of ground-breaking applications in biomedical imaging, next-generation optoelectronic devices, and optical communications. Colloidal nanocrystals based on indium arsenide are some of the most promising SWIR emitters to date. However, the lack of single-particle spectroscopic methods accessible in the SWIR has prevented advances in both nanocrystal synthesis and fundamental characterization of emitters. Here, we demonstrate an implementation of a solution photon correlation Fourier spectroscopy (s-PCFS) experiment utilizing the SWIR sensitivity and time resolution of superconducting nanowire single-photon detectors to extract single-particle emission linewidths from colloidal indium arsenide/cadmium selenide (InAs/CdSe) core/shell nanocrystals emissive from 1.2 to 1.6 μm. We show that the average single InAs/CdSe nanocrystal fluorescence linewidth is, remarkably, as narrow as 52 meV, similar to what has been observed in some of the most narrowband nanostructured emitters in the visible region. Additionally, the single nanocrystal fluorescence linewidth increases with increasing shell thickness, suggesting exciton-phonon coupling as the dominant emission line-broadening mechanism in this system. The development of the SWIR s-PCFS technique has enabled measurements of spectral linewidths of colloidal SWIR-emissive NCs in solution and provides a platform to study the single NC spectral characteristics of SWIR emitters.
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http://dx.doi.org/10.1021/acsnano.8b07578DOI Listing
February 2019

Absorption by water increases fluorescence image contrast of biological tissue in the shortwave infrared.

Proc Natl Acad Sci U S A 2018 09 27;115(37):9080-9085. Epub 2018 Aug 27.

Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139;

Recent technology developments have expanded the wavelength window for biological fluorescence imaging into the shortwave infrared. We show here a mechanistic understanding of how drastic changes in fluorescence imaging contrast can arise from slight changes of imaging wavelength in the shortwave infrared. We demonstrate, in 3D tissue phantoms and in vivo in mice, that light absorption by water within biological tissue increases image contrast due to attenuation of background and highly scattered light. Wavelengths of strong tissue absorption have conventionally been avoided in fluorescence imaging to maximize photon penetration depth and photon collection, yet we demonstrate that imaging at the peak absorbance of water (near 1,450 nm) results in the highest image contrast in the shortwave infrared. Furthermore, we show, through microscopy of highly labeled ex vivo biological tissue, that the contrast improvement from water absorption enables resolution of deeper structures, resulting in a higher imaging penetration depth. We then illustrate these findings in a theoretical model. Our results suggest that the wavelength-dependent absorptivity of water is the dominant optical property contributing to image contrast, and is therefore crucial for determining the optimal imaging window in the infrared.
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http://dx.doi.org/10.1073/pnas.1803210115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6140498PMC
September 2018

Machine Learning Methods for X-Ray Scattering Data Analysis from Biomacromolecular Solutions.

Biophys J 2018 06;114(11):2485-2492

European Molecular Biology Laboratory, Hamburg, Germany.

Small-angle x-ray scattering (SAXS) of biological macromolecules in solutions is a widely employed method in structural biology. SAXS patterns include information about the overall shape and low-resolution structure of dissolved particles. Here, we describe how to transform experimental SAXS patterns to feature vectors and how a simple k-nearest neighbor approach is able to retrieve information on overall particle shape and maximal diameter (D) as well as molecular mass directly from experimental scattering data. Based on this transformation, we develop a rapid multiclass shape-classification ranging from compact, extended, and flat categories to hollow and random-chain-like objects. This classification may be employed, e.g., as a decision block in automated data analysis pipelines. Further, we map protein structures from the Protein Data Bank into the classification space and, in a second step, use this mapping as a data source to obtain accurate estimates for the structural parameters (D, molecular mass) of the macromolecule under study based on the experimental scattering pattern alone, without inverse Fourier transform for D. All methods presented are implemented in a Fortran binary DATCLASS, part of the ATSAS data analysis suite, available on Linux, Mac, and Windows and free for academic use.
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http://dx.doi.org/10.1016/j.bpj.2018.04.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129182PMC
June 2018

Consensus Bayesian assessment of protein molecular mass from solution X-ray scattering data.

Sci Rep 2018 05 8;8(1):7204. Epub 2018 May 8.

European Molecular Biology Laboratory (EMBL) Hamburg Outstation, DESY, Hamburg, Germany.

Molecular mass (MM) is one of the key structural parameters obtained by small-angle X-ray scattering (SAXS) of proteins in solution and is used to assess the sample quality, oligomeric composition and to guide subsequent structural modelling. Concentration-dependent assessment of MM relies on a number of extra quantities (partial specific volume, calibrated intensity, accurate solute concentration) and often yields limited accuracy. Concentration-independent methods forgo these requirements being based on the relationship between structural parameters, scattering invariants and particle volume obtained directly from the data. Using a comparative analysis on 165,982 unique scattering profiles calculated from high-resolution protein structures, the performance of multiple concentration-independent MM determination methods was assessed. A Bayesian inference approach was developed affording an accuracy above that of the individual methods, and reports MM estimates together with a credibility interval. This Bayesian approach can be used in combination with concentration-dependent MM methods to further validate the MM of proteins in solution, or as a reliable stand-alone tool in instances where an accurate concentration estimate is not available.
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http://dx.doi.org/10.1038/s41598-018-25355-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5940760PMC
May 2018

Integrated beamline control and data acquisition for small-angle X-ray scattering at the P12 BioSAXS beamline at PETRAIII storage ring DESY.

J Synchrotron Radiat 2018 May 25;25(Pt 3):906-914. Epub 2018 Apr 25.

Hamburg Outstation, European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany.

The versatility of small-angle X-ray scattering (SAXS) as a structural biology method is apparent by its compatibility with many experimental set-ups. Most advanced SAXS studies are conducted at dedicated synchrotron beamlines yielding high beam brilliance, throughput and temporal resolution. However, utilizing the full potential of the method while preserving a high degree of automation provides a challenge to any SAXS beamline. This challenge is especially pertinent at the P12 BioSAXS beamline of the EMBL at the PETRAIII Synchrotron DESY (Hamburg, Germany), optimized and dedicated to scattering of macromolecular solutions. Over 200 unique set-ups are possible at this beamline offering various functionalities, including different temporal and spatial resolutions. Presented here is a beamline control and data-acquisition software, BECQUEREL, designed to maximize flexibility and automation in the operation of P12. In the frame of a single intuitive interface the control system allows for convenient operation with all hardware set-ups available at P12 including a robotic sample changer, in-line size-exclusion chromatography, stop-flow devices, microfluidic spinning disk and various in-air settings. Additional functionalities are available to assist the data-collection procedure for novice users, and also routine operation of the support staff.
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http://dx.doi.org/10.1107/S1600577518005398DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5929361PMC
May 2018

Shortwave infrared fluorescence imaging with the clinically approved near-infrared dye indocyanine green.

Proc Natl Acad Sci U S A 2018 04 6;115(17):4465-4470. Epub 2018 Apr 6.

Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139;

Fluorescence imaging is a method of real-time molecular tracking in vivo that has enabled many clinical technologies. Imaging in the shortwave IR (SWIR; 1,000-2,000 nm) promises higher contrast, sensitivity, and penetration depths compared with conventional visible and near-IR (NIR) fluorescence imaging. However, adoption of SWIR imaging in clinical settings has been limited, partially due to the absence of US Food and Drug Administration (FDA)-approved fluorophores with peak emission in the SWIR. Here, we show that commercially available NIR dyes, including the FDA-approved contrast agent indocyanine green (ICG), exhibit optical properties suitable for in vivo SWIR fluorescence imaging. Even though their emission spectra peak in the NIR, these dyes outperform commercial SWIR fluorophores and can be imaged in the SWIR, even beyond 1,500 nm. We show real-time fluorescence imaging using ICG at clinically relevant doses, including intravital microscopy, noninvasive imaging in blood and lymph vessels, and imaging of hepatobiliary clearance, and show increased contrast compared with NIR fluorescence imaging. Furthermore, we show tumor-targeted SWIR imaging with IRDye 800CW-labeled trastuzumab, an NIR dye being tested in multiple clinical trials. Our findings suggest that high-contrast SWIR fluorescence imaging can be implemented alongside existing imaging modalities by switching the detection of conventional NIR fluorescence systems from silicon-based NIR cameras to emerging indium gallium arsenide-based SWIR cameras. Using ICG in particular opens the possibility of translating SWIR fluorescence imaging to human clinical applications. Indeed, our findings suggest that emerging SWIR-fluorescent in vivo contrast agents should be benchmarked against the SWIR emission of ICG in blood.
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http://dx.doi.org/10.1073/pnas.1718917115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5924901PMC
April 2018

A Ligand System for the Flexible Functionalization of Quantum Dots via Click Chemistry.

Angew Chem Int Ed Engl 2018 04 13;57(17):4652-4656. Epub 2018 Mar 13.

Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA, 02139, USA.

We present a novel ligand, 5-norbornene-2-nonanoic acid, which can be directly added during established quantum dot (QD) syntheses in organic solvents to generate "clickable" QDs at a few hundred nmol scale. This ligand has a carboxyl group at one terminus to bind to the surface of QDs and a norbornene group at the opposite end that enables straightforward phase transfer of QDs into aqueous solutions via efficient norbornene/tetrazine click chemistry. Our ligand system removes the traditional ligand-exchange step and can produce water-soluble QDs with a high quantum yield and a small hydrodynamic diameter of approximately 12 nm at an order of magnitude higher scale than previous methods. We demonstrate the effectiveness of our approach by incubating azido-functionalized CdSe/CdS QDs with 4T1 cancer cells that are metabolically labeled with a dibenzocyclooctyne-bearing unnatural sugar. The QDs exhibit high targeting efficiency and minimal nonspecific binding.
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http://dx.doi.org/10.1002/anie.201801113DOI Listing
April 2018

Brown adipose tissue thermogenic adaptation requires Nrf1-mediated proteasomal activity.

Nat Med 2018 03 5;24(3):292-303. Epub 2018 Feb 5.

Department of Genetics and Complex Diseases and Sabri Ülker Center, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.

Adipocytes possess remarkable adaptive capacity to respond to nutrient excess, fasting or cold exposure, and they are thus an important cell type for the maintenance of proper metabolic health. Although the endoplasmic reticulum (ER) is a critical organelle for cellular homeostasis, the mechanisms that mediate adaptation of the ER to metabolic challenges in adipocytes are unclear. Here we show that brown adipose tissue (BAT) thermogenic function requires an adaptive increase in proteasomal activity to secure cellular protein quality control, and we identify the ER-localized transcription factor nuclear factor erythroid 2-like 1 (Nfe2l1, also known as Nrf1) as a critical driver of this process. We show that cold adaptation induces Nrf1 in BAT to increase proteasomal activity and that this is crucial for maintaining ER homeostasis and cellular integrity, specifically when the cells are in a state of high thermogenic activity. In mice, under thermogenic conditions, brown-adipocyte-specific deletion of Nfe2l1 (Nrf1) resulted in ER stress, tissue inflammation, markedly diminished mitochondrial function and whitening of the BAT. In mouse models of both genetic and dietary obesity, stimulation of proteasomal activity by exogenously expressing Nrf1 or by treatment with the proteasome activator PA28α in BAT resulted in improved insulin sensitivity. In conclusion, Nrf1 emerges as a novel guardian of brown adipocyte function, providing increased proteometabolic quality control for adapting to cold or to obesity.
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http://dx.doi.org/10.1038/nm.4481DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5839993PMC
March 2018

Next-generation optical imaging with short-wave infrared quantum dots.

Nat Biomed Eng 2017 10;1. Epub 2017 Apr 10.

Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139 (USA).

For imaging, the short-wavelength infrared region (SWIR; 1000-2000 nm) provides several advantages over the visible and near-infrared regions: general lack of autofluorescence, low light absorption by blood and tissue, and reduced scattering. However, the lack of versatile and functional SWIR emitters has prevented the general adoption of SWIR imaging by the biomedical research community. Here, we introduce a class of high-quality SWIR-emissive indium-arsenide-based quantum dots (QDs) that are readily modifiable for various functional imaging applications, and that exhibit narrow and size-tunable emission and a dramatically higher emission quantum yield than previously described SWIR probes. To demonstrate the unprecedented combination of deep penetration, high spatial resolution, multicolor imaging and fast-acquisition-speed afforded by the SWIR QDs, we quantified, in mice, the metabolic turnover rates of lipoproteins in several organs simultaneously and in real time as well as heartbeat and breathing rates in awake and unrestrained animals, and generated detailed three-dimensional quantitative flow maps of the mouse brain vasculature.
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http://dx.doi.org/10.1038/s41551-017-0056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5673283PMC
April 2017

Flavylium Polymethine Fluorophores for Near- and Shortwave Infrared Imaging.

Angew Chem Int Ed Engl 2017 10 14;56(42):13126-13129. Epub 2017 Sep 14.

Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA.

Bright fluorophores in the near-infrared and shortwave infrared (SWIR) regions of the electromagnetic spectrum are essential for optical imaging in vivo. In this work, we utilized a 7-dimethylamino flavylium heterocycle to construct a panel of novel red-shifted polymethine dyes, with emission wavelengths from 680 to 1045 nm. Photophysical characterization revealed that the 1- and 3-methine dyes display enhanced photostability and the 5- and 7-methine dyes exhibit exceptional brightness for their respective spectral regions. A micelle formulation of the 7-methine facilitated SWIR imaging in mice. This report presents the first polymethine dye designed and synthesized for SWIR in vivo imaging.
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http://dx.doi.org/10.1002/anie.201706974DOI Listing
October 2017

Continuous injection synthesis of indium arsenide quantum dots emissive in the short-wavelength infrared.

Nat Commun 2016 11 11;7:12749. Epub 2016 Nov 11.

Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.

With the emergence of applications based on short-wavelength infrared light, indium arsenide quantum dots are promising candidates to address existing shortcomings of other infrared-emissive nanomaterials. However, III-V quantum dots have historically struggled to match the high-quality optical properties of II-VI quantum dots. Here we present an extensive investigation of the kinetics that govern indium arsenide nanocrystal growth. Based on these insights, we design a synthesis of large indium arsenide quantum dots with narrow emission linewidths. We further synthesize indium arsenide-based core-shell-shell nanocrystals with quantum yields up to 82% and improved photo- and long-term storage stability. We then demonstrate non-invasive through-skull fluorescence imaging of the brain vasculature of murine models, and show that our probes exhibit 2-3 orders of magnitude higher quantum yields than commonly employed infrared emitters across the entire infrared camera sensitivity range. We anticipate that these probes will not only enable new biomedical imaging applications, but also improved infrared nanocrystal-LEDs and photon-upconversion technology.
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http://dx.doi.org/10.1038/ncomms12749DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5114595PMC
November 2016

Characterization of Indium Phosphide Quantum Dot Growth Intermediates Using MALDI-TOF Mass Spectrometry.

J Am Chem Soc 2016 Oct 6;138(41):13469-13472. Epub 2016 Oct 6.

CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto Universitario de Nanociencia de Aragón, Department of Chemical Engineering, University of Zaragoza , Mariano Esquillor edif. I+D, Zaragoza 50018, Spain.

Clusters have been identified as important growth intermediates during group III-V quantum dot (QD) formation. Here we report a one-solvent protocol that integrates synthesis, purification, and mass characterization of indium phosphide (InP) QD growth mixtures. The use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) successfully tracks the evolution of clusters and the formation of QDs throughout the synthesis. Similar clusters are observed during the formation of large particles, suggesting that these clusters serve as a reservoir for QD formation. Combining MALDI and NMR techniques further enables us to extract extinction coefficients and construct sizing curves for cluster-free InP QDs. The use of MALDI MS opens new opportunities for characterization and mechanistic studies of small-sized air-sensitive clusters or QDs.
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http://dx.doi.org/10.1021/jacs.6b06468DOI Listing
October 2016

The Unexpected Influence of Precursor Conversion Rate in the Synthesis of III-V Quantum Dots.

Angew Chem Int Ed Engl 2015 Nov 6;54(48):14299-303. Epub 2015 Oct 6.

Department of Chemistry, Massachusetts Institute Of Technology, 77 Massachusetts Avenue, 02139 Cambridge, MA (USA).

Control of quantum dot (QD) precursor chemistry has been expected to help improve the size control and uniformity of III-V QDs such as indium phosphide and indium arsenide. Indeed, experimental results for other QD systems are consistent with the theoretical prediction that the rate of precursor conversion is an important factor controlling QD size and size distribution. We synthesized and characterized the reactivity of a variety of group-V precursors in order to determine if precursor chemistry could be used to improve the quality of III-V QDs. Despite slowing down precursor conversion rate by multiple orders of magnitude, the less reactive precursors do not yield the expected increase in size and improvement in size distribution. This result disproves the widely accepted explanation for the shortcoming of current III-V QD syntheses and points to the need for a new generalizable theoretical picture for the mechanism of QD formation and growth.
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http://dx.doi.org/10.1002/anie.201505972DOI Listing
November 2015

Automated pipeline for purification, biophysical and x-ray analysis of biomacromolecular solutions.

Sci Rep 2015 Jun 1;5:10734. Epub 2015 Jun 1.

European Molecular Biology Laboratory (EMBL) Hamburg, 22607 Hamburg, Germany.

Small angle X-ray scattering (SAXS), an increasingly popular method for structural analysis of biological macromolecules in solution, is often hampered by inherent sample polydispersity. We developed an all-in-one system combining in-line sample component separation with parallel biophysical and SAXS characterization of the separated components. The system coupled to an automated data analysis pipeline provides a novel tool to study difficult samples at the P12 synchrotron beamline (PETRA-3, EMBL/DESY, Hamburg).
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http://dx.doi.org/10.1038/srep10734DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5377070PMC
June 2015

Correlation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra.

Nat Methods 2015 May 6;12(5):419-22. Epub 2015 Apr 6.

European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany.

Assessing similarity between data sets with the reduced χ(2) test requires the estimation of experimental errors, which, if incorrect, may render statistical comparisons invalid. We report a goodness-of-fit test, Correlation Map (CorMap), for assessing differences between one-dimensional spectra independently of explicit error estimates, using only data point correlations. Using small-angle X-ray scattering data, we demonstrate that CorMap maintains the power of the reduced χ(2) test; moreover, CorMap is also applicable to other physical experiments.
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http://dx.doi.org/10.1038/nmeth.3358DOI Listing
May 2015

Versatile sample environments and automation for biological solution X-ray scattering experiments at the P12 beamline (PETRA III, DESY).

J Appl Crystallogr 2015 Apr 12;48(Pt 2):431-443. Epub 2015 Mar 12.

European Molecular Biology Laboratory, Hamburg Outstation , Notkestrasse 85, Hamburg, 22603, Germany.

A high-brilliance synchrotron P12 beamline of the EMBL located at the PETRA III storage ring (DESY, Hamburg) is dedicated to biological small-angle X-ray scattering (SAXS) and has been designed and optimized for scattering experiments on macromolecular solutions. Scatterless slits reduce the parasitic scattering, a custom-designed miniature active beamstop ensures accurate data normalization and the photon-counting PILATUS 2M detector enables the background-free detection of weak scattering signals. The high flux and small beam size allow for rapid experiments with exposure time down to 30-50 ms covering the resolution range from about 300 to 0.5 nm. P12 possesses a versatile and flexible sample environment system that caters for the diverse experimental needs required to study macromolecular solutions. These include an in-vacuum capillary mode for standard batch sample analyses with robotic sample delivery and for continuous-flow in-line sample purification and characterization, as well as an in-air capillary time-resolved stopped-flow setup. A novel microfluidic centrifugal mixing device (SAXS disc) is developed for a high-throughput screening mode using sub-microlitre sample volumes. Automation is a key feature of P12; it is controlled by a beamline meta server, which coordinates and schedules experiments from either standard or nonstandard operational setups. The integrated SASFLOW pipeline automatically checks for consistency, and processes and analyses the data, providing near real-time assessments of overall parameters and the generation of low-resolution models within minutes of data collection. These advances, combined with a remote access option, allow for rapid high-throughput analysis, as well as time-resolved and screening experiments for novice and expert biological SAXS users.
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http://dx.doi.org/10.1107/S160057671500254XDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4379436PMC
April 2015

ISPyB for BioSAXS, the gateway to user autonomy in solution scattering experiments.

Acta Crystallogr D Biol Crystallogr 2015 Jan 1;71(Pt 1):76-85. Epub 2015 Jan 1.

European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, CS 90181, 38042 Grenoble, France.

Logging experiments with the laboratory-information management system ISPyB (Information System for Protein crystallography Beamlines) enhances the automation of small-angle X-ray scattering of biological macromolecules in solution (BioSAXS) experiments. The ISPyB interface provides immediate user-oriented online feedback and enables data cross-checking and downstream analysis. To optimize data quality and completeness, ISPyBB (ISPyB for BioSAXS) makes it simple for users to compare the results from new measurements with previous acquisitions from the same day or earlier experiments in order to maximize the ability to collect all data required in a single synchrotron visit. The graphical user interface (GUI) of ISPyBB has been designed to guide users in the preparation of an experiment. The input of sample information and the ability to outline the experimental aims in advance provides feedback on the number of measurements required, calculation of expected sample volumes and time needed to collect the data: all of this information aids the users to better prepare for their trip to the synchrotron. A prototype version of the ISPyBB database is now available at the European Synchrotron Radiation Facility (ESRF) beamline BM29 and is already greatly appreciated by academic users and industrial clients. It will soon be available at the PETRA III beamline P12 and the Diamond Light Source beamlines I22 and B21.
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http://dx.doi.org/10.1107/S1399004714019609DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4304688PMC
January 2015

Granulocyte-colony stimulating factor response is superior to neutropenia duration in predicting the risk of infection after high-dose chemotherapy for myeloma and lymphoma.

Leuk Lymphoma 2015 Feb 27;56(2):368-76. Epub 2014 May 27.

Schön Klinik Starnberger See , Berg , Germany.

The patient granulocyte-colony stimulating factor (G-CSF) response is represented by the leukocyte peak in the blood induced by a single dose of G-CSF after chemotherapy, and is correlated with subsequent neutropenic infection risk. General patterns for a meaningful risk group stratification, have not yet been determined. Two independent data sets including a total of 306 cases with myeloma or lymphoma and autologous blood stem cell transplant were available. An infection susceptibility curve plotted according to ranked G-CSF responses from a multicenter study reproduced and validated a curve from the previous single center. Two trend changes were seen within these curves at around 11,000 and 22,000 leukocytes/μL, which separated three groups with a high, medium and low risk of infection. While G-CSF response is related to the consecutive duration of neutropenia, it retains additional independent predictive information for infection risk (p<0.0001) and, more important, is a tool available before the onset of the critical period.
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http://dx.doi.org/10.3109/10428194.2014.919631DOI Listing
February 2015

New developments in the program package for small-angle scattering data analysis.

J Appl Crystallogr 2012 Apr 15;45(Pt 2):342-350. Epub 2012 Mar 15.

European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany.

New developments in the program package (version 2.4) for the processing and analysis of isotropic small-angle X-ray and neutron scattering data are described. They include (i) multiplatform data manipulation and display tools, (ii) programs for automated data processing and calculation of overall parameters, (iii) improved usage of high- and low-resolution models from other structural methods, (iv) new algorithms to build three-dimensional models from weakly interacting oligomeric systems and complexes, and (v) enhanced tools to analyse data from mixtures and flexible systems. The new release includes installers for current major platforms (Windows, Linux and Mac OSX) and provides improved indexed user documentation. The web-related developments, including a user discussion forum and a widened online access to run programs, are also presented.
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http://dx.doi.org/10.1107/S0021889812007662DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4233345PMC
April 2012

Pickering emulsion templated soft capsules by self-assembling cross-linkable ferritin-polymer conjugates.

Chem Commun (Camb) 2011 Aug 20;47(29):8376-8. Epub 2011 Jun 20.

DWI an der RWTH Aachen e.V., Lehrstuhl für Makromolekulare Materialien und Oberflächen, RWTH Aachen University, Pauwelsstrasse 8, D-52056 Aachen, Germany.

Oil-in-water (o/w) and water-in-oil (w/o) Pickering emulsions were prepared using ferritin-polymer conjugates. UV cross-linking stabilised the particle assembly around the fluid droplets. The resulting soft protein-polymer capsules were transferred to a medium of equal polarity as the inside of the capsule, creating water-in-water (w/w) and oil-in-oil (o/o) capsules.
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http://dx.doi.org/10.1039/c1cc12005kDOI Listing
August 2011

The dimer interface of the membrane type 1 matrix metalloproteinase hemopexin domain: crystal structure and biological functions.

J Biol Chem 2011 Mar 30;286(9):7587-600. Epub 2010 Dec 30.

Arbeitsgruppe Proteinaseforschung, Max-Planck-Institut fuer Biochemie, Am Klopferspitz 18, D-82152 Martinsried, Germany.

Homodimerization is an essential step for membrane type 1 matrix metalloproteinase (MT1-MMP) to activate proMMP-2 and to degrade collagen on the cell surface. To uncover the molecular basis of the hemopexin (Hpx) domain-driven dimerization of MT1-MMP, a crystal structure of the Hpx domain was solved at 1.7 Å resolution. Two interactions were identified as potential biological dimer interfaces in the crystal structure, and mutagenesis studies revealed that the biological dimer possesses a symmetrical interaction where blades II and III of molecule A interact with blades III and II of molecule B. The mutations of amino acids involved in the interaction weakened the dimer interaction of Hpx domains in solution, and incorporation of these mutations into the full-length enzyme significantly inhibited dimer-dependent functions on the cell surface, including proMMP-2 activation, collagen degradation, and invasion into the three-dimensional collagen matrix, whereas dimer-independent functions, including gelatin film degradation and two-dimensional cell migration, were not affected. These results shed light on the structural basis of MT1-MMP dimerization that is crucial to promote cellular invasion.
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http://dx.doi.org/10.1074/jbc.M110.178434DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3045013PMC
March 2011

Testing G-CSF responsiveness predicts the individual susceptibility to infection and consecutive treatment in recipients of high-dose chemotherapy.

Blood 2011 Feb 16;117(7):2121-8. Epub 2010 Dec 16.

Schön Klinik Starnberger See, Berg, Germany, and Medizinische Klinik Innenstadt der Universität München, Munich, Germany.

The individual risk of infection and requirements for medical treatment after high-dose chemotherapy have been unpredictable. In this prospective, multicenter, open-label study we investigated the potential of granulocyte colony-stimulating factor (G-CSF) responsiveness as a predictor. A total of 168 patients with multiple myeloma or lymphoma received a single dose of subcutaneous G-CSF (lenograstim, 263 μg) after high-dose chemotherapy. Highly variable leukocyte peaks were measured and grouped as low (quartile 1; leukocytes 100-10 100/μL), medium (quartile 2; leukocytes > 10 100-18 300/μL), and high (quartiles 3/4; leukocytes > 18 300-44 800/μL). G-CSF responsiveness (low vs medium vs high) was inversely correlated with febrile neutropenia (77% vs 60% vs 48%; P = .0037); the rate of infection, including fever of unknown origin (91% vs 67% vs 54%; P < .0001); days with intravenous antibiotics (9 vs 6 vs 5; P < .0001); and antifungal therapy (P = .042). In multivariate analysis, G-CSF responsiveness remained the only factor significantly associated with infection (P = .016). In addition, G-CSF responsiveness was inversely correlated with grade 3/4 oral mucositis (67% vs 33% vs 23%; P < .0001). G-CSF responsiveness appears as a signature of the myeloid marrow reserve predicting defense against neutropenic infection after intensive chemotherapy. This study is registered at http://www.clinicaltrials.gov as NCT01085058.
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http://dx.doi.org/10.1182/blood-2010-06-290080DOI Listing
February 2011

, a program for rapid shape determination in small-angle scattering.

J Appl Crystallogr 2009 Apr 24;42(Pt 2):342-346. Epub 2009 Jan 24.

European Molecular Biology Laboratory, Hamburg Outstation Notkestrasse 85, 22603 Hamburg, Germany; Institute of Crystallography, 117333 Moscow, Russian Federation.

, a revised implementation of the - shape-determination program for small-angle scattering data, is presented. The program was fully rewritten, and its algorithm was optimized for speed of execution and modified to avoid limitations due to the finite search volume. Symmetry and anisometry constraints can be imposed on the particle shape, similar to . In equivalent conditions, is 25-40 times faster than on a single CPU. The possibility to utilize multiple CPUs is added to . The application is available in binary form for major platforms.
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http://dx.doi.org/10.1107/S0021889809000338DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5023043PMC
April 2009

Structural and functional characterization of soluble endoglin receptor.

Biochem Biophys Res Commun 2009 Jun 5;383(4):386-91. Epub 2009 Mar 5.

Department of Molecular Cell Biology, Samsung Biomedical Research institute, Sungkyunkwan University School of Medicine, 300 Chunchun-Dong, Suwon 440-746, Republic of Korea.

Endoglin, an accessory membrane receptor of transforming growth factor-beta (TGF-beta)1, modulates the cellular response to TGF-beta via its interaction with type I and II TGF-beta receptors. It has been considered a promising target for the development of therapeutics and cancer markers. We have established stable CHO cell lines that efficiently secrete soluble endoglin (s-endoglin) fused with human growth hormone. Two oligomeric forms were observed in a homogeneous preparation of s-endoglin, as a dimer and a tetramer. The dimeric s-endoglin enhanced TGF-beta responsiveness in U937 cells, thus proving its potential for therapeutic applications. Small angle X-ray scattering (SAXS) experiments revealed elongated conformations of both dimeric and tetrameric s-endoglins in solution, suggesting that s-endoglin might undergo conformational adaptations upon TGF-beta binding. The current results provide important references and material for high-resolution structural studies and for medical applications of s-endoglin.
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http://dx.doi.org/10.1016/j.bbrc.2009.02.162DOI Listing
June 2009