Honeycomb gold specimen supports enabling orthogonal focussed ion beam-milling of elongated cells for cryo-ET

Cryo-focussed ion beam (FIB)-milling is a powerful technique that opens up thick, cellular specimens to high-resolution structural analysis by electron cryotomography (cryo-ET). FIB-milled lamellae can be produced from cells on grids, or cut from thicker, high-pressure frozen specimens. However, these approaches can put geometrical constraints on the specimen that may be unhelpful, particularly when imaging structures within the cell that have a very defined orientation. For example, plunge frozen rod-shaped bacteria orient parallel to the plane of the grid, yet the Z-ring, a filamentous structure of the tubulin-like protein FtsZ and the key organiser of bacterial division, runs around the circumference of the cell such that it is perpendicular to the imaging plane. It is therefore difficult or impractical to image many complete rings with current technologies. To circumvent this problem, we have fabricated monolithic gold specimen supports with a regular array of cylindrical wells in a honeycomb geometry, which trap bacteria in a vertical orientation. These supports, which we call "honeycomb gold discs", replace standard EM grids and when combined with FIB-milling enable the production of lamellae containing cross-sections through cells. The resulting lamellae are more stable and resistant to breakage and charging than conventional lamellae. The design of the honeycomb discs can be modified according to need and so will also enable cryo-ET and cryo-EM imaging of other specimens in otherwise difficult to obtain orientations.

Accurate magnification determination for cryoEM using gold

Determining the correct magnified pixel size of single-particle cryoEM micrographs is necessary to maximize resolution and enable accurate model building. Here we describe a simple and rapid procedure for determining the absolute magnification in an electron cryomicroscope to a precision of <0.5%. We show how to use the atomic lattice spacings of crystals of thin and readily available test specimens, such as gold, as an absolute reference to determine magnification for both room temperature and cryogenic imaging. We compare this method to other commonly used methods, and show that it provides comparable accuracy in spite of its simplicity. This magnification calibration method provides a definitive reference quantity for data analysis and processing, simplifies the combination of multiple datasets from different microscopes and detectors, and improves the accuracy with which the contrast transfer function of the microscope can be determined. We also provide an open source program, magCalEM, which can be used to accurately estimate the magnified pixel size of a cryoEM dataset ex post facto.

Structure determination by cryoEM at 100 keV

Electron cryomicroscopy can, in principle, determine the structures of most biological molecules but is currently limited by access, specimen preparation difficulties, and cost. We describe a purpose-built instrument operating at 100 keV-including advances in electron optics, detection, and processing-that makes structure determination fast and simple at a fraction of current costs. The instrument attains its theoretical performance limits, allowing atomic resolution imaging of gold test specimens and biological molecular structure determination in hours. We demonstrate its capabilities by determining the structures of eleven different specimens, ranging in size from 140 kDa to 2 MDa, using a fraction of the data normally required. CryoEM with a microscope designed specifically for high-efficiency, on-the-spot imaging of biological molecules will expand structural biology to a wide range of previously intractable problems.

Cryomicroscopy in situ: what is the smallest molecule that can be directly identified without labels in a cell?

Electron cryomicroscopy (cryoEM) has made great strides in the last decade, such that the atomic structure of most biological macromolecules can, at least in principle, be determined. Major technological advances - in electron imaging hardware, data analysis software, and cryogenic specimen preparation technology - continue at pace and contribute to the exponential growth in the number of atomic structures determined by cryoEM. It is now conceivable that within the next decade we will have structures for hundreds of thousands of unique protein and nucleic acid molecular complexes. But the answers to many important questions in biology would become obvious if we could identify these structures precisely inside cells with quantifiable error. In the context of an abundance of known structures, it is appropriate to consider the current state of electron cryomicroscopy for frozen specimens prepared directly from cells, and try to answer to the question of the title, both now and in the foreseeable future.

Imaging biological macromolecules in thick specimens: The role of inelastic scattering in cryoEM

We investigate potential improvements in using electron cryomicroscopy to image thick specimens with high-resolution phase contrast imaging. In particular, using model experiments, electron scattering theory, Monte Carlo and multislice simulations, we determine the potential for improving electron cryomicrographs of proteins within a cell using chromatic aberration (C_c) correction. We show that inelastically scattered electrons lose a quantifiable amount of spatial coherence as they transit the specimen, yet can be used to enhance the signal from thick biological specimens (in the 1000 to 5000 Å range) provided they are imaged close to focus with an achromatic lens. This loss of information quantified here, which we call "specimen induced decoherence", is a fundamental limit on imaging biological molecules in situ. We further show that with foreseeable advances in transmission electron microscope technology, it should be possible to directly locate and uniquely identify sub-100 kDa proteins without the need for labels, in a vitrified specimen taken from a cell.

On the reduction in the effects of radiation damage to two-dimensional crystals of organic and biological molecules at liquid-helium temperature

We have studied the fading of electron diffraction spots from two-dimensional (2D) crystals of paraffin (C₄₄H₉₀), purple membrane (bacteriorhodopsin) and aquaporin 4 (AQP4) at stage temperatures between 4K and 100K. We observed that the diffraction spots at resolutions between 3 Å and 20 Å fade more slowly at liquid-helium temperatures compared to liquid-nitrogen temperatures, by a factor of between 1.2 and 1.8, depending on the specimens. If the reduction in the effective rate of radiation damage for 2D crystals at liquid-helium temperature (as measured by spot fading) can be shown to extend to macromolecular assemblies embedded in amorphous ice, this would suggest that valuable improvements to electron cryomicroscopy (cryoEM) of biological specimens could be made by reducing the temperature of the specimens under irradiation below what is obtainable using standard liquid-nitrogen cryostats.

Phase contrast imaging with inelastically scattered electrons from any layer of a thick specimen

A controversy exists as to whether the signal in a high resolution phase contrast electron micrograph of a particle in a thick specimen is the same irrespective of the particle's position along the beam axis. Different conceptions of inelastic scattering and its effects on wave interference have led to radically different expectations about the degree of phase contrast vs. depth. Here we examine the information available from bright field phase contrast images of small crystalline particles on the top or bottom of a thick support. The support is an aluminium foil which has strong plasmon resonances that cause a large proportion of the electron beam to lose energy in transit. Phase contrast micrographs of the atomic lattice of two ensembles of platinum particles were measured in an energy loss window corresponding to the first plasmon resonance. The signal measured for particles on top was equal to that for particles on the bottom of the foil to within a 99% confidence interval, and the measurements exclude other models of depth dependent phase contrast in the literature to >5σ. These observations are consistent with quantum theory which considers dynamical effects as independent of event sequence and is distinct from the "top-bottom effect" observed in amplitude contrast. We thus confirm that phase contrast using inelastically scattered electrons can be obtained equally well from particles within any layer of a thick specimen.

2.4-Å structure of the double-ring Gemmatimonas phototrophica photosystem

Phototrophic Gemmatimonadetes evolved the ability to use solar energy following horizontal transfer of photosynthesis-related genes from an ancient phototrophic proteobacterium. The electron cryo-microscopy structure of the Gemmatimonas phototrophica photosystem at 2.4 Å reveals a unique, double-ring complex. Two unique membrane-extrinsic polypeptides, RC-S and RC-U, hold the central type 2 reaction center (RC) within an inner 16-subunit light-harvesting 1 (LH1) ring, which is encircled by an outer 24-subunit antenna ring (LHh) that adds light-gathering capacity. Femtosecond kinetics reveal the flow of energy within the RC-dLH complex, from the outer LHh ring to LH1 and then to the RC. This structural and functional study shows that G. phototrophica has independently evolved its own compact, robust, and highly effective architecture for harvesting and trapping solar energy.

Structure of the SARS-CoV-2 RNA-dependent RNA polymerase in the presence of favipiravir-RTP

The RNA polymerase inhibitor favipiravir is currently in clinical trials as a treatment for infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), despite limited information about the molecular basis for its activity. Here we report the structure of favipiravir ribonucleoside triphosphate (favipiravir-RTP) in complex with the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) bound to a template:primer RNA duplex, determined by electron cryomicroscopy (cryoEM) to a resolution of 2.5 Å. The structure shows clear evidence for the inhibitor at the catalytic site of the enzyme, and resolves the conformation of key side chains and ions surrounding the binding pocket. Polymerase activity assays indicate that the inhibitor is weakly incorporated into the RNA primer strand, and suppresses RNA replication in the presence of natural nucleotides. The structure reveals an unusual, nonproductive binding mode of favipiravir-RTP at the catalytic site of SARS-CoV-2 RdRp, which explains its low rate of incorporation into the RNA primer strand. Together, these findings inform current and future efforts to develop polymerase inhibitors for SARS coronaviruses.

The 2.4 Å cryo-EM structure of a heptameric light-harvesting 2 complex reveals two carotenoid energy transfer pathways

We report the 2.4 Ångström resolution structure of the light-harvesting 2 (LH2) complex from Marichromatium (Mch.) purpuratum determined by cryogenic electron microscopy. The structure contains a heptameric ring that is unique among all known LH2 structures, explaining the unusual spectroscopic properties of this bacterial antenna complex. We identify two sets of distinct carotenoids in the structure and describe a network of energy transfer pathways from the carotenoids to bacteriochlorophyll a molecules. The geometry imposed by the heptameric ring controls the resonant coupling of the long-wavelength energy absorption band. Together, these details reveal key aspects of the assembly and oligomeric form of purple bacterial LH2 complexes that were previously inaccessible by any technique.

Defocus-dependent Thon-ring fading

The brightness of modern Schottky field-emission guns can produce electron beams that have very high spatial coherence, especially for the weak-illumination conditions that are used for single-particle electron cryo-microscopy in structural biology. Even so, many users have observed defocus-dependent Thon-ring fading that has led them to restrict their data collection strategy to imaging with relatively small defocus values. In this paper, we reproduce the observation of defocus-dependent Thon-ring fading and produce a quantitative analysis and clear explanation of its causes. We demonstrate that a major cause is the delocalization of high-resolution Fourier components outside the field of view of the camera. We also show that, to correctly characterize the phenomenon, it is important to make a correction for linear magnification anisotropy. Even when the anisotropy is quite small, it is present at all defocus values before circular averaging of the Thon rings, as is also true before merging data from particles in many orientations. Under the conditions used in this paper, which are typical of those used in single-particle electron cryomicroscopy, fading of the Thon rings due to source coherence is negligible. The principal conclusion is that much higher values of defocus can be used to record images than is currently thought to be possible, keeping in mind that the above-mentioned delocalization of Fourier components will ultimately become a limitation. This increased understanding should give electron microscopists the confidence to use higher amounts of defocus to allow, for example, better visibility of their particles and Ewald sphere correction.

Cryo-EM with sub-1 Å specimen movement

Most information loss in cryogenic electron microscopy (cryo-EM) stems from particle movement during imaging, which remains poorly understood. We show that this movement is caused by buckling and subsequent deformation of the suspended ice, with a threshold that depends directly on the shape of the frozen water layer set by the support foil. We describe a specimen support design that eliminates buckling and reduces electron beam-induced particle movement to less than 1 angstrom. The design allows precise foil tracking during imaging with high-speed detectors, thereby lessening demands on cryostage precision and stability. It includes a maximal density of holes, which increases throughput in automated cryo-EM without degrading data quality. Movement-free imaging allows extrapolation to a three-dimensional map of the specimen at zero electron exposure, before the onset of radiation damage.

Structure of the Fanconi anaemia monoubiquitin ligase complex

The Fanconi anaemia (FA) pathway repairs DNA damage caused by endogenous and chemotherapy-induced DNA crosslinks, and responds to replication stress1,2. Genetic inactivation of this pathway by mutation of genes encoding FA complementation group (FANC) proteins impairs development, prevents blood production and promotes cancer1,3. The key molecular step in the FA pathway is the monoubiquitination of a pseudosymmetric heterodimer of FANCD2-FANCI4,5 by the FA core complex-a megadalton multiprotein E3 ubiquitin ligase6,7. Monoubiquitinated FANCD2 then recruits additional protein factors to remove the DNA crosslink or to stabilize the stalled replication fork. A molecular structure of the FA core complex would explain how it acts to maintain genome stability. Here we reconstituted an active, recombinant FA core complex, and used cryo-electron microscopy and mass spectrometry to determine its structure. The FA core complex comprises two central dimers of the FANCB and FA-associated protein of 100 kDa (FAAP100) subunits, flanked by two copies of the RING finger subunit, FANCL. These two heterotrimers act as a scaffold to assemble the remaining five subunits, resulting in an extended asymmetric structure. Destabilization of the scaffold would disrupt the entire complex, resulting in a non-functional FA pathway. Thus, the structure provides a mechanistic basis for the low numbers of patients with mutations in FANCB, FANCL and FAAP100. Despite a lack of sequence homology, FANCB and FAAP100 adopt similar structures. The two FANCL subunits are in different conformations at opposite ends of the complex, suggesting that each FANCL has a distinct role. This structural and functional asymmetry of dimeric RING finger domains may be a general feature of E3 ligases. The cryo-electron microscopy structure of the FA core complex provides a foundation for a detailed understanding of its E3 ubiquitin ligase activity and DNA interstrand crosslink repair.

Updates in Pediatric Hospital Medicine: Six Practical Ways to Improve the Care of Hospitalized Children

BACKGROUND

As pediatric hospital medicine continues to grow, it is important to keep abreast of the current literature. This article provides a summary of six of the most impactful articles published in 2018.

METHODS

The authors reviewed articles published between January 2018 and December 2018 for the 2019 Society of Hospital Medicine national conference presentation of Top Articles in Pediatric Hospital Medicine, where the top 10 articles of 2018 were presented. Six of the 10 articles are highlighted in this review based on article quality and their applicability to change practices in the hospital setting or prompt further research.

RESULTS

Key findings from the articles include: multiple interventions aimed at providers can improve compliance with bronchiolitis guidelines; a developed calculator can improve testing for urinary tract infections in children aged 2-24 months; nonmedical costs of hospitalizations are underappreciated and disproportionately affect those with a lower socioeconomic status; a progress note template in an electronic health record can lead to higher quality and shorter notes; for febrile infants aged 60 days and younger, most blood and cerebrospinal fluid culture pathogens can be identified within 24 hours and nearly all by 36 hours; and the development of a high-value care tool can help to bring concepts of high-value care into family-centered rounds.

CONCLUSION

The six selected articles highlight findings pertinent to pediatric hospital medicine.

The energy dependence of contrast and damage in electron cryomicroscopy of biological molecules

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Carbon elastic and inelastic electron scattering cross sections are measured vs. energy.

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Elastic scattering is compared to energy deposition and radiation damage.

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An optimal energy for cryoEM of a given biological specimen thickness is determined.

We have measured the dependence on electron energy of elastic and inelastic scattering cross-sections from carbon, over the energy range that includes 100 keV to 300 keV. We also compared quantitatively the radiation damage to bacteriorhodopsin and paraffin (C₄₄H₉₀) at 100 keV and 300 keV by observing the fading of the diffraction spots from two-dimensional crystals as a function of electron fluence. The elastic cross-section is 2.01 - fold greater at 100 keV than at 300 keV, whereas the radiation damage increased by only 1.57. This implies that the amount of useful information from diffraction patterns or images of most biological structures should be 25% greater using 100 keV rather than 300 keV electrons. Using these measurements, we calculate the energy dependence of the available information per unit damage for a specimen of a particular thickness, which we call the “information coefficient.” This allows us to determine the optimal energy for imaging a biological specimen of a given thickness. We find that for most single particle cryoEM specimens, 100 keV provides not only the highest potential for information per unit damage, but would also simplify the instrument while retaining the potential to reach high resolution with a minimum of data. These measurements will help guide the development and use of electron cryomicroscopes for biology.

Charge accumulation in electron cryomicroscopy

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A physical account of charge accumulation in low-dose cryoEM is presented.

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We describe electrostatic micro-lenses that are extremely sensitive charge detectors.

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These micro-lenses allow the direct measurement of charge accumulation.

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Charge build-up saturates within the first millisecond of a typical micrograph.

When irradiated in a transmission electron microscope, plunge-frozen, amorphous water ice specimens accumulate a pattern of static charge that changes dynamically as the specimen is irradiated, and which can deflect the transmitted electrons and blur the resultant micrographs. Here we provide a physical description of this charge accumulation and characterise its dynamic behaviour in the context of low-dose electron cryomicroscopy (cryoEM). We observe the accumulation of positive charge in the primary irradiation area as expected from earlier work. To our surprise, we also observed a build-up of negative charge in nearby unirradiated regions of the specimen. Using a standard carbon support foil containing a pure water ice specimen, we collect a portion of this negative charge in the micrometer sized specimen holes which act as electrostatic lenses. These unusual, diverging micro-lenses are extremely sensitive charge detectors that allow us to directly measure the magnitude and dynamics of charge accumulation and neutralisation that occur during cryoEM imaging. Using these measurements, we find that the build-up of charge on the specimen saturates to a dynamic equilibrium at an electron fluence which is orders of magnitude lower than required for a typical low-dose micrograph. The measurements here will guide the development of optimal imaging conditions for biological specimens and contribute to a complete theory of information loss in electron cryomicroscopy.

Microscopic charge fluctuations cause minimal contrast loss in cryoEM

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A physical account of charge fluctuations in low-dose cryoEM is presented.

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We quantify the bee swarm charging phenomenon on cryoEM specimen.

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We measure the envelope function caused by charge fluctuations.

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The effects of these fluctuations are negligible in cryoEM.

The fluctuating granularity or “bee swarm” effect seen in highly defocussed transmission electron micrographs is caused by microscopic charge fluctuations in the specimen created by the illuminating beam. In the field of high-resolution single particle electron cryomicroscopy (cryoEM), there has been a concern that this fluctuating charge might cause defocus-dependent Thon ring fading which would degrade the final image. In this paper, we have analysed the 2.35 Å fringes from the (111) reflection in images of gold nanoparticles embedded in amorphous ice. We show that there is a small, yet detectable amount of defocus-dependent blurring of the lattice fringes when compared with those from a pure gold foil. The transverse electric field associated with the fluctuating charges on the insulating frozen water specimen deflects the electron beam locally and causes image blurring. The perturbation is small, decreasing the amplitude of the 2.35 Å reflection at 10 µm defocus by about 7% (intensity by 14%). For smaller defocus values in the range 2–4 µm and for resolutions that are typical in cryoEM, the effects of source incoherence and the bee swarm effect are negligible for all reasonable cryoEM imaging conditions, assuming that a field emission gun (FEG) is used for illumination. This leaves physical movement of the specimen due to radiation damage as the outstanding problem and the major source of contrast loss in cryoEM micrographs.

A precision cryostat design for manual and semi-automated cryo-plunge instruments

Here we describe a bench-top cryostat system to control the temperature of liquid ethane in a cryo-plunge apparatus designed for biological specimen preparation for electron cryomicroscopy. It comprises a foam insulated Dewar containing a copper cryostat cup, whose temperature is controlled via an active feedback system to within 0.1 K. The device can easily be incorporated into existing manual and semi-automatic cryo-plunge instruments that are not equipped with cryogenic temperature control. Over the course of normal use, we find that using a cryostat is convenient, fast, and does not require special mixtures of cryogens like ethane/propane. This simple cryostat improves the reliability and reproducibility of biological specimen preparation for electron cryomicroscopy.

Specimen Preparation for High-Resolution Cryo-EM

Imaging a material with electrons at near-atomic resolution requires a thin specimen that is stable in the vacuum of the transmission electron microscope. For biological samples, this comprises a thin layer of frozen aqueous solution containing the biomolecular complex of interest. The process of preparing a high-quality specimen is often the limiting step in the determination of structures by single-particle electron cryomicroscopy (cryo-EM). Here, we describe a systematic approach for going from a purified biomolecular complex in aqueous solution to high-resolution electron micrographs that are suitable for 3D structure determination. This includes a series of protocols for the preparation of vitrified specimens on various supports, including all-gold and graphene. We also describe techniques for troubleshooting when a preparation fails to yield suitable specimens, and common mistakes to avoid during each part of the process. Finally, we include recommendations for obtaining the highest quality micrographs from prepared specimens with current microscope, detector, and support technology.

Progress towards an optimal specimen support for electron cryomicroscopy

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Physical principles of electron scattering govern the design of specimen supports.

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Radiation-induced motion causes loss of resolution in electron micrographs.

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Specimen supports can now be designed to reduce specimen motion.

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Tailored surfaces in the support allow control of particle distribution and orientation.

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Future developments in support technology will further improve image quality.

The physical principles of electron–specimen interaction govern the design of specimen supports for electron cryomicroscopy (cryo-EM). Supports are constructed to suspend biological samples within the vacuum of the electron microscope in a way that maximises image contrast. Although the problem of specimen motion during imaging has been known since cryo-EM was first developed, the role of the support in this movement has only been recently identified. Here we review the key technological advances in specimen supports for cryo-EM. This includes the use of graphene as a surface for the adsorption of proteins and the design of an ultrastable, all-gold substrate that reduces the motion of molecules during electron irradiation. We discuss the implications of these and other recent improvements in specimen supports on resolution, and place them in the context of important developments in structure determination by cryo-EM.

Advances in Single-Particle Electron Cryomicroscopy Structure Determination applied to Sub-tomogram Averaging

Recent innovations in specimen preparation, data collection, and image processing have led to improved structure determination using single-particle electron cryomicroscopy (cryo-EM). Here we explore some of these advances to improve structures determined using electron cryotomography (cryo-ET) and sub-tomogram averaging. We implement a new three-dimensional model for the contrast transfer function, and use this in a regularized likelihood optimization algorithm as implemented in the RELION program. Using direct electron detector data, we apply both single-particle analysis and sub-tomogram averaging to analyze radiation-induced movements of the specimen. As in single-particle cryo-EM, we find that significant sample movements occur during tomographic data acquisition, and that these movements are substantially reduced through the use of ultrastable gold substrates. We obtain a sub-nanometer resolution structure of the hepatitis B capsid, and show that reducing radiation-induced specimen movement may be central to attempts at further improving tomogram quality and resolution.

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The Bayesian approach in RELION is extended to sub-tomogram averaging

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A new 3D CTF and missing-wedge model for sub-tomogram averaging is proposed

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Ultrastable gold supports reduce radiation-induced motion in tomography tilt series

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Using the above, an 8 Å structure of hepatitis B capsid from cryo-ET is presented

Electron microscopy: Ultrastable gold substrates for electron cryomicroscopy

Despite recent advances, the structures of many proteins cannot be determined by electron cryomicroscopy because the individual proteins move during irradiation. This blurs the images so that they cannot be aligned with each other to calculate a three-dimensional density. Much of this movement stems from instabilities in the carbon substrates used to support frozen samples in the microscope. Here we demonstrate a gold specimen support that nearly eliminates substrate motion during irradiation. This increases the subnanometer image contrast such that α helices of individual proteins are resolved. With this improvement, we determine the structure of apoferritin, a smooth octahedral shell of α-helical subunits that is particularly difficult to solve by electron microscopy. This advance in substrate design will enable the solution of currently intractable protein structures.

Robust evaluation of 3D electron cryomicroscopy data using tilt-pairs

Determining the structure of a protein complex using electron microscopy requires the calculation of a 3D density map from 2D images of single particles. Since the individual images are taken at low electron dose to avoid radiation damage, they are noisy and difficult to align with each other. This can result in incorrect maps, making validation essential. Pairs of electron micrographs taken at known angles to each other (tilt-pairs) can be used to measure the accuracy of assigned projection orientations and verify the soundness of calculated maps. Here we establish a statistical framework for evaluating images and density maps using tilt-pairs. The directional distribution of such angular data is modelled using a Fisher distribution on the unit sphere. This provides a simple, quantitative and easily comparable metric, the concentration parameter κ, for evaluating the quality of datasets and density maps that is independent of the data collection and analysis methods. A large κ is indicative of good agreement between the particle images and the 3D density map. For structure validation, we recommend κ>10 and a p-value <0.01. The statistical framework herein allows one to objectively answer the question: Is a reconstructed density map correct within a particular confidence interval?

Controlling protein adsorption on graphene for cryo-EM using low-energy hydrogen plasmas

Despite its many favorable properties as a sample support for biological electron microscopy, graphene is not widely used because its hydrophobicity precludes reliable protein deposition. We describe a method to modify graphene with a low-energy hydrogen plasma, which reduces hydrophobicity without degrading the graphene lattice. Use of plasma-treated graphene enables better control of protein distribution in ice for electron cryo-microscopy and improves image quality by reducing radiation-induced sample motion.

Impact of brain tissue filtering on neurostimulation fields: a modeling study

Electrical neurostimulation techniques, such as deep brain stimulation (DBS) and transcranial magnetic stimulation (TMS), are increasingly used in the neurosciences, e.g., for studying brain function, and for neurotherapeutics, e.g., for treating depression, epilepsy, and Parkinson's disease. The characterization of electrical properties of brain tissue has guided our fundamental understanding and application of these methods, from electrophysiologic theory to clinical dosing-metrics. Nonetheless, prior computational models have primarily relied on ex-vivo impedance measurements. We recorded the in-vivo impedances of brain tissues during neurosurgical procedures and used these results to construct MRI guided computational models of TMS and DBS neurostimulatory fields and conductance-based models of neurons exposed to stimulation. We demonstrated that tissues carry neurostimulation currents through frequency dependent resistive and capacitive properties not typically accounted for by past neurostimulation modeling work. We show that these fundamental brain tissue properties can have significant effects on the neurostimulatory-fields (capacitive and resistive current composition and spatial/temporal dynamics) and neural responses (stimulation threshold, ionic currents, and membrane dynamics). These findings highlight the importance of tissue impedance properties on neurostimulation and impact our understanding of the biological mechanisms and technological potential of neurostimulatory methods.

Management of pediatric skin abscesses in pediatric, general academic and community emergency departments

OBJECTIVES

To compare the evaluation and management of pediatric cutaneous abscess patients at three different emergency department (ED) settings.

METHOD

We conducted a retrospective cohort study at two academic pediatric hospital EDs, a general academic ED and a community ED in 2007, with random sampling of 100 patients at the three academic EDs and inclusion of 92 patients from the community ED. Eligible patients were ≤18 years who had a cutaneous abscess. We recorded demographics, predisposing conditions, physical exam findings, incision and drainage procedures, therapeutics and final disposition. Laboratory data were reviewed for culture results and antimicrobial sensitivities. For subjects managed as outpatients from the ED, we determined where patients were instructed to follow up and, using electronic medical records, ascertained the proportion of patients who returned to the ED for further management.

RESULT

Of 392 subjects, 59% were female and the median age was 7.7 years. Children at academic sites had larger abscesses compared to community patients, (3.5 versus 2.5 cm, p=0.02). Abscess incision and drainage occurred in 225 (57%) children, with the lowest rate at the academic pediatric hospital EDs (51%) despite the relatively larger abscess size. Procedural sedation and the collection of wound cultures were more frequent at the academic pediatric hospital and the general academic EDs. Methicillin-resistant Staphylococcus aureus (MRSA) prevalence did not differ among sites; however, practitioners at the academic pediatric hospital EDs (92%) and the general academic ED (86%) were more likely to initiate empiric MRSA antibiotic therapy than the community site (71%), (p<0.0001). At discharge, children who received care at the community ED were more likely to be given a prescription for a narcotic (23%) and told to return to the ED for ongoing wound care (65%). Of all sites, the community ED also had the highest percentage of follow-up visits (37%).

CONCLUSION

Abscess management varied among the three settings, with more conservative antibiotic selection and greater implementation of procedural sedation at academic centers and higher prescription rates for narcotics, self-referrals for ongoing care and patient follow-up visits at the community ED.

Sub-angstrom low-voltage performance of a monochromated, aberration-corrected transmission electron microscope

Lowering the electron energy in the transmission electron microscope allows for a significant improvement in contrast of light elements and reduces knock-on damage for most materials. If low-voltage electron microscopes are defined as those with accelerating voltages below 100 kV, the introduction of aberration correctors and monochromators to the electron microscope column enables Angstrom-level resolution, which was previously reserved for higher voltage instruments. Decreasing electron energy has three important advantages: (1) knock-on damage is lower, which is critically important for sensitive materials such as graphene and carbon nanotubes; (2) cross sections for electron-energy-loss spectroscopy increase, improving signal-to-noise for chemical analysis; (3) elastic scattering cross sections increase, improving contrast in high-resolution, zero-loss images. The results presented indicate that decreasing the acceleration voltage from 200 kV to 80 kV in a monochromated, aberration-corrected microscope enhances the contrast while retaining sub-Angstrom resolution. These improvements in low-voltage performance are expected to produce many new results and enable a wealth of new experiments in materials science.

Eddies in a bottleneck: an arbitrary Debye length theory for capillary electroosmosis

Using an applied electrical field to drive fluid flows becomes desirable as channels become smaller. Although most discussions of electroosmosis treat the case of thin Debye layers, here electroosmotic flow (EOF) through a constricted cylinder is presented for arbitrary Debye lengths (kappa(-1)) using a long wavelength perturbation of the cylinder radius. The analysis uses the approximation of small potentials. The varying diameter of the cylinder produces radially and axially varying effective electric fields, as well as an induced pressure gradient. We predict the existence of eddies for certain constricted geometries and propose the possibility of electrokinetic trapping in these regions. We also present a leading-order criterion which predicts central eddies in very narrow constrictions at the scale of the Debye length. Eddies can be found both in the center of the channel and along the perimeter, and the presence of the eddies is a consequence of the induced pressure gradient that accompanies electrically driven flow into a narrow constriction.

Cryptic striations in the upper mantle revealed by hafnium isotopes in southeast Indian ridge basalts

The Earth's mantle is isotopically heterogeneous on length scales ranging from centimetres to more than 10(4) kilometres. This heterogeneity originates from partial melt extraction and plate tectonic recycling, whereas stirring during mantle convection tends to reduce it. Here we show that mid-ocean ridge basalts from 2,000 km along the southeast Indian ridge (SEIR) display a bimodal hafnium isotopic distribution. This bimodality reveals the presence of ancient compositional striations (streaks) in the Indian Ocean upper mantle. The number density of the streaks is described by a Poisson distribution, with an average thickness of approximately 40 km. Such a distribution is anticipated for a well-stirred upper mantle, in which heterogeneity is continually introduced by plate tectonic recycling, and redistributed by viscous stretching and convective refolding.

Association of NEDD4L Ubiquitin Ligase With Essential Hypertension

NEDD4L is a ubiquitin ligase that controls cell surface expression of kidney epithelial Na+ channels by ubiquitin-mediated endocytosis and lysosome targeting. Thus, it is a significant determinant of Na+ reabsorption in the distal nephron. The NEDD4L gene is located on human chromosome 18q21 within several blood pressure quantitative trait loci, including those for familial orthostatic hypotension, essential hypertension, pulse pressure, and systolic blood pressure response to postural challenge. Because of the importance of NEDD4L to Na+ balance, many of these studies have proposed that mutations in NEDD4L may be responsible for these blood pressure phenotypes. To test this hypothesis, we fine-mapped the NEDD4L region in 2 families with orthostatic hypotension, which we previously reported to be linked to human chromosome 18q21 but failed to implicate NEDD4L in these families. We also typed multiple NEDD4L single-nucleotide polymorphisms (SNPs) in a collection of US whites, Greek whites, and African-Americans individuals with essential hypertension. A significant association between several SNPs and hypertension was observed in all 3 populations. One of the SNPs associated in African Americans is known to result in premature truncation of the NEDD4L protein. Thus, genetic variation in NEDD4L may play a role in the development or progression of some forms of abnormal blood pressure.

Birthdate and cell marker analysis of scrambler: a novel mutation affecting cortical development with a reeler-like phenotype

The reeler mutation in mice produces an especially well characterized disorder, with systematically abnormal migration of cerebral cortical neurons. The reeler gene encodes a large protein, termed Reelin, that in the cortex is synthesized and secreted exclusively in the Cajal-Retzius neurons of the cortical marginal zone (D'Arcangelo et al., 1995). In reeler mutant mice, loss of Reelin protein is associated with a systematic loss of the normal, "inside-out" sequence of neurogenesis in the cortex: neurons are formed in the normal sequence but become localized in the cortex in a somewhat inverted, although relatively disorganized "outside-in" pattern. Here we show that the scrambler mutant mouse exhibits a loss of lamination in the cortex and hippocampus that is indistinguishable from that seen in the reeler mouse. We use BrdU birthdating studies to show that scrambler cortex shows a somewhat inverted "outside-in" sequence of birthdates for cortical neurons that is similar to that previously described in reeler cortex. Finally, we perform staining with the CR-50 monoclonal antibody (Ogawa et al., 1995), which recognizes the Reelin protein (D'Arcangelo et al., 1997). We show that Reelin immunoreactivity is present in the scrambler cortex in a normal pattern, suggesting that Reelin is synthesized and released normally. Our data suggest that scrambler is a mutation in the same gene pathway as the reeler gene (Relnrl) and is most likely downstream of Relnrl.

Aberrant splicing of a mouse disabled homolog, mdab1, in the scrambler mouse

Although accurate long-distance neuronal migration is a cardinal feature of cerebral cortical development, little is known about control of this migration. The scrambler (scm) mouse shows abnormal cortical lamination that is indistinguishable from reeler. Genetic and physical mapping of scm identified yeast artificial chromosomes containing an exon of mdab1, a homolog of Drosophila disabled, which encodes a phosphoprotein that binds nonreceptor tyrosine kinases. mdab1 transcripts showed abnormal splicing in scm homozygotes, with 1.5 kb of intracisternal A particle retrotransposon sequence inserted into the mdab1 coding region in antisense orientation, producing a mutated and truncated predicted protein. Therefore, mdab1 is most likely the scm gene, thus implicating nonreceptor tyrosine kinases in neuronal migration and lamination in developing cerebral cortex.

Patient preferences for stroke outcomes

BACKGROUND AND PURPOSE

In clinical trials stroke is reported as a major morbid outcome, but the impact of stroke on patients is not directly assessed. This study examines patient preferences for different outcomes of stroke, including death.

METHODS

We presented patients with written case scenarios of stroke outcomes. The scenarios represented four categories of stroke severity (mild, moderate, severe, and fatal), and for nonfatal strokes the scenarios described motor, language, and cognitive deficits. Patients reported values for each of the 10 stroke scenarios using a rank-and-scale method over a 100-point range, with 100 representing perfect health and 0 corresponding to the worst possible health state.

RESULTS

One hundred seventeen of 209 consecutive patients at risk for stroke participated in this study. Severe strokes were uniformly rated as having low preference weights (mean +/- SD [median]: 3 +/- 4 [1] for disabling hemiplegia, 8 +/- 9 [5] for confusion, and 15 +/- 14 [10] for global aphasia), and severe motor impairment (a disabling hemiplegia) was rated as significantly worse than death. Even mild deficits resulted in substantial loss to patients (54 +/- 21 [55] for dysarthria and 53 +/- 21 [50] for mild anomia).

CONCLUSIONS

Strokes may result in a wide variety of post-stroke consequences for patients. Severe strokes may be viewed by patients as tantamount to or worse than death. Even mild strokes may cause significant declines in patient preferences for health states. These data are useful in interpreting studies that report stroke and death, in designing new studies that measure stroke in at-risk populations, and in helping patients reach treatment decisions about therapies designed to prevent strokes.