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1.  Imaging ultra thin layers with helium ion microscopy: Utilizing the channeling contrast mechanism 
Summary
Background: Helium ion microscopy is a new high-performance alternative to classical scanning electron microscopy. It provides superior resolution and high surface sensitivity by using secondary electrons.
Results: We report on a new contrast mechanism that extends the high surface sensitivity that is usually achieved in secondary electron images, to backscattered helium images. We demonstrate how thin organic and inorganic layers as well as self-assembled monolayers can be visualized on heavier element substrates by changes in the backscatter yield. Thin layers of light elements on heavy substrates should have a negligible direct influence on backscatter yields. However, using simple geometric calculations of the opaque crystal fraction, the contrast that is observed in the images can be interpreted in terms of changes in the channeling probability.
Conclusion: The suppression of ion channeling into crystalline matter by adsorbed thin films provides a new contrast mechanism for HIM. This dechanneling contrast is particularly well suited for the visualization of ultrathin layers of light elements on heavier substrates. Our results also highlight the importance of proper vacuum conditions for channeling-based experimental methods.
doi:10.3762/bjnano.3.58
PMCID: PMC3458595  PMID: 23019545
channeling; contrast mechanism; helium ion microscopy; ion scattering; thin layers
2.  High Resolution Helium Ion Scanning Microscopy of the Rat Kidney 
PLoS ONE  2013;8(3):e57051.
Helium ion scanning microscopy is a novel imaging technology with the potential to provide sub-nanometer resolution images of uncoated biological tissues. So far, however, it has been used mainly in materials science applications. Here, we took advantage of helium ion microscopy to explore the epithelium of the rat kidney with unsurpassed image quality and detail. In addition, we evaluated different tissue preparation methods for their ability to preserve tissue architecture. We found that high contrast, high resolution imaging of the renal tubule surface is possible with a relatively simple processing procedure that consists of transcardial perfusion with aldehyde fixatives, vibratome tissue sectioning, tissue dehydration with graded methanol solutions and careful critical point drying. Coupled with the helium ion system, fine details such as membrane texture and membranous nanoprojections on the glomerular podocytes were visualized, and pores within the filtration slit diaphragm could be seen in much greater detail than in previous scanning EM studies. In the collecting duct, the extensive and striking apical microplicae of the intercalated cells were imaged without the shrunken or distorted appearance that is typical with conventional sample processing and scanning electron microscopy. Membrane depressions visible on principal cells suggest possible endo- or exocytotic events, and central cilia on these cells were imaged with remarkable preservation and clarity. We also demonstrate the use of colloidal gold probes for highlighting specific cell-surface proteins and find that 15 nm gold labels are practical and easily distinguishable, indicating that external labels of various sizes can be used to detect multiple targets in the same tissue. We conclude that this technology represents a technical breakthrough in imaging the topographical ultrastructure of animal tissues. Its use in future studies should allow the study of fine cellular details and provide significant advances in our understanding of cell surface structures and membrane organization.
doi:10.1371/journal.pone.0057051
PMCID: PMC3591388  PMID: 23505418
3.  High throughput secondary electron imaging of organic residues on a graphene surface 
Scientific Reports  2014;4:7032.
Surface organic residues inhibit the extraordinary electronic properties of graphene, hindering the development of graphene electronics. However, fundamental understanding of the residue morphology is still absent due to a lack of high-throughput and high-resolution surface characterization methods. Here, we demonstrate that secondary electron (SE) imaging in the scanning electron microscope (SEM) and helium ion microscope (HIM) can provide sub-nanometer information of a graphene surface and reveal the morphology of surface contaminants. Nanoscale polymethyl methacrylate (PMMA) residues are visible in the SE imaging, but their contrast, i.e. the apparent lateral dimension, varies with the imaging conditions. We have demonstrated a quantitative approach to readily obtain the physical size of the surface features regardless of the contrast variation. The fidelity of SE imaging is ultimately determined by the probe size of the primary beam. HIM is thus evaluated to be a superior SE imaging technique in terms of surface sensitivity and image fidelity. A highly efficient method to reveal the residues on a graphene surface has therefore been established.
doi:10.1038/srep07032
PMCID: PMC4229663  PMID: 25391356
4.  Digging gold: keV He+ ion interaction with Au 
Summary
Helium ion microscopy (HIM) was used to investigate the interaction of a focused He+ ion beam with energies of several tens of kiloelectronvolts with metals. HIM is usually applied for the visualization of materials with extreme surface sensitivity and resolution. However, the use of high ion fluences can lead to significant sample modifications. We have characterized the changes caused by a focused He+ ion beam at normal incidence to the Au{111} surface as a function of ion fluence and energy. Under the influence of the beam a periodic surface nanopattern develops. The periodicity of the pattern shows a power-law dependence on the ion fluence. Simultaneously, helium implantation occurs. Depending on the fluence and primary energy, porous nanostructures or large blisters form on the sample surface. The growth of the helium bubbles responsible for this effect is discussed.
doi:10.3762/bjnano.4.53
PMCID: PMC3740815  PMID: 23946914
formation and healing of defects in crystals; helium ion microscopy; ion beam/solid interactions; vacancies in crystals
5.  Helium ion microscopy of enamel crystallites and extracellular tooth enamel matrix 
An unresolved problem in tooth enamel studies has been to analyze simultaneously and with sufficient spatial resolution both mineral and organic phases in their three dimensional (3D) organization in a given specimen. This study aims to address this need using high-resolution imaging to analyze the 3D structural organization of the enamel matrix, especially amelogenin, in relation to forming enamel crystals. Chemically fixed hemi-mandibles from wild type mice were embedded in LR White acrylic resin, polished and briefly etched to expose the organic matrix in developing tooth enamel. Full-length amelogenin was labeled with specific antibodies and 10 nm immuno-gold. This allowed us to use and compare two different high-resolution imaging techniques for the analysis of uncoated samples. Helium ion microscopy (HIM) was applied to study the spatial organization of organic and mineral structures, while field emission scanning electron microscopy (FE-SEM) in various modes, including backscattered electron detection, allowed us to discern the gold-labeled proteins. Wild type enamel in late secretory to early maturation stage reveals adjacent to ameloblasts a lengthwise parallel alignment of the enamel matrix proteins, including full-length amelogenin proteins, which then transitions into a more heterogeneous appearance with increasing distance from the mineralization front. The matrix adjacent to crystal bundles forms a smooth and lacey sheath, whereas between enamel prisms it is organized into spherical components that are interspersed with rod-shaped protein. These findings highlight first, that the heterogeneous organization of the enamel matrix can be visualized in mineralized en bloc samples. Second, our results illustrate that the combination of these techniques is a powerful approach to elucidate the 3D structural organization of organic matrix molecules in mineralizing tissue in nanometer resolution.
doi:10.3389/fphys.2014.00395
PMCID: PMC4193210  PMID: 25346697
tooth enamel; matrix organization; amelogenin; immuno-gold labeling; helium ion microscopy; high-resolution microscopy
6.  Nano-structuring, surface and bulk modification with a focused helium ion beam 
Summary
We investigate the ability of a focused helium ion beam to selectively modify and mill materials. The sub nanometer probe size of the helium ion microscope used provides lateral control not previously available for helium ion irradiation experiments. At high incidence angles the helium ions were found to remove surface material from a silicon lamella leaving the subsurface structure intact for further analysis. Surface roughness and contaminants were both reduced by the irradiation process. Fabrication is also realized with a high level of patterning acuity. Implantation of helium beneath the surface of the sample is visualized in cross section allowing direct observation of the extended effects of high dose irradiation. The effect of the irradiation on the crystal structure of the material is presented. Applications of the sample modification process are presented and further prospects discussed.
doi:10.3762/bjnano.3.67
PMCID: PMC3458604  PMID: 23019554
EELS; EFTEM; helium ion microscopy; nanofabrication; TEM
7.  Atomic model of the F420-reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector 
eLife  2014;3:e01963.
The introduction of direct electron detectors with higher detective quantum efficiency and fast read-out marks the beginning of a new era in electron cryo-microscopy. Using the FEI Falcon II direct electron detector in video mode, we have reconstructed a map at 3.36 Å resolution of the 1.2 MDa F420-reducing hydrogenase (Frh) from methanogenic archaea from only 320,000 asymmetric units. Videos frames were aligned by a combination of image and particle alignment procedures to overcome the effects of beam-induced motion. The reconstructed density map shows all secondary structure as well as clear side chain densities for most residues. The full coordination of all cofactors in the electron transfer chain (a [NiFe] center, four [4Fe4S] clusters and an FAD) is clearly visible along with a well-defined substrate access channel. From the rigidity of the complex we conclude that catalysis is diffusion-limited and does not depend on protein flexibility or conformational changes.
DOI: http://dx.doi.org/10.7554/eLife.01963.001
eLife digest
Many microbes rely on enzymes known as hydrogenases to catalyse the metabolic reactions that generate energy. These enzymes cleave hydrogen molecules to release electrons that go on to participate in further reactions. In order to fully understand how hydrogenases and other enzymes work it is necessary to work out their structure at the atomic level.
Last year a technique known as electron cryo-microscopy (cryo-EM) was used to show that Frh—a hydrogenase that is crucial for many different steps in the metabolic process of microbes that produce methane—had a tetrahedral structure. Cryo-EM involves freezing the molecule of interest in a layer of ice to preserve its structure as it is imaged with an electron beam. Unfortunately, the signal-to-noise ratio in each image is low, so researchers must combine many separate images in order to determine the structure of the molecule.
The use of a new type of electron detector can improve the performance of an electron cryo-microscope in several ways. Higher frame rates can be used, which makes it possible to correct for movement of the molecule caused by the electron beam. The new electron detectors are also more efficient, so samples can be exposed to lower doses of electrons, reducing damage to the sample.
Using the new direct electron detectors, Allegretti et al. were able to work out the structure of Frh in greater detail than before. The results confirm that the previously reported structure is correct. Furthermore, several new structural features were seen for the first time, including a previously unseen ion located between two protein subunits. Allegretti et al. also revealed that the structure of Frh is highly rigid, and so the process by which it catalyses reactions involving its substrate, the coenzyme F420, does not involve changes in its shape. Instead, the reaction rate depends on the rate at which F420 diffuses to the correct position in the enzyme, where the reaction occurs very rapidly.
DOI: http://dx.doi.org/10.7554/eLife.01963.002
doi:10.7554/eLife.01963
PMCID: PMC3930138  PMID: 24569482
cryo-electron microscopy; [NiFe] hydrogenase; methanogenesis; Methanothermobacter marburgensis; other
8.  On the Formation of (Anionic) Excited Helium Dimers in Helium Droplets 
The Journal of Physical Chemistry. a  2014;118(33):6642-6647.
Metastable atomic and molecular helium anions exhibiting high-spin quartet configurations can be produced in helium droplets via electron impact. Their lifetimes allow detection in mass spectrometric experiments. Formation of atomic helium anions comprises collision-induced excitation of ground state helium and concomitant electron capture. Yet the formation of molecular helium anions in helium droplets has been an unresolved issue. In this work, we explore the interaction of excited helium atoms exhibiting high-spin triplet configurations with ground state helium using the equation-of-motion coupled-cluster method. Transition barriers in the energetically lowest He*–He and He*––He interaction potentials prevent molecule formation at the extremely low temperatures present in helium droplets. In contrast, some excited states allow a barrier-free formation of molecular helium (anions). Moreover, we show that the necessary excitation energies pinpoint (higher) resonances in recently recorded mass spectra and emend the assignment of those resonances that have previously been assigned to electron-impact ionization of ground state helium necessitating subsequent double-electron capture. Embedding molecules or molecular clusters in helium droplets is a predestined experimental technique for the study of phenomena at very low temperatures. Profound knowledge about active processes in the helium environment is required for a proper assessment of experimental data.
doi:10.1021/jp503643r
PMCID: PMC4141897  PMID: 24866535
9.  Detection of Negative Charge Carriers in Superfluid Helium Droplets: The Metastable Anions He*– and He2*– 
Helium droplets provide the possibility to study phenomena at the very low temperatures at which quantum mechanical effects are more pronounced and fewer quantum states have significant occupation probabilities. Understanding the migration of either positive or negative charges in liquid helium is essential to comprehend charge-induced processes in molecular systems embedded in helium droplets. Here, we report the resonant formation of excited metastable atomic and molecular helium anions in superfluid helium droplets upon electron impact. Although the molecular anion is heliophobic and migrates toward the surface of the helium droplet, the excited metastable atomic helium anion is bound within the helium droplet and exhibits high mobility. The atomic anion is shown to be responsible for the formation of molecular dopant anions upon charge transfer and thus, we clarify the nature of the previously unidentified fast exotic negative charge carrier found in bulk liquid helium.
doi:10.1021/jz500917z
PMCID: PMC4106244  PMID: 25068008
10.  Helium Ion Microscopy (HIM) for the imaging of biological samples at sub-nanometer resolution 
Scientific Reports  2013;3:3514.
Scanning Electron Microscopy (SEM) has long been the standard in imaging the sub-micrometer surface ultrastructure of both hard and soft materials. In the case of biological samples, it has provided great insights into their physical architecture. However, three of the fundamental challenges in the SEM imaging of soft materials are that of limited imaging resolution at high magnification, charging caused by the insulating properties of most biological samples and the loss of subtle surface features by heavy metal coating. These challenges have recently been overcome with the development of the Helium Ion Microscope (HIM), which boasts advances in charge reduction, minimized sample damage, high surface contrast without the need for metal coating, increased depth of field, and 5 angstrom imaging resolution. We demonstrate the advantages of HIM for imaging biological surfaces as well as compare and contrast the effects of sample preparation techniques and their consequences on sub-nanometer ultrastructure.
doi:10.1038/srep03514
PMCID: PMC3865489  PMID: 24343236
11.  Fabrication of carbon nanomembranes by helium ion beam lithography 
Summary
The irradiation-induced cross-linking of aromatic self-assembled monolayers (SAMs) is a universal method for the fabrication of ultrathin carbon nanomembranes (CNMs). Here we demonstrate the cross-linking of aromatic SAMs due to exposure to helium ions. The distinction of cross-linked from non-cross-linked regions in the SAM was facilitated by transferring the irradiated SAM to a new substrate, which allowed for an ex situ observation of the cross-linking process by helium ion microscopy (HIM). In this way, three growth regimes of cross-linked areas were identified: formation of nuclei, one-dimensional (1D) and two-dimensional (2D) growth. The evaluation of the corresponding HIM images revealed the dose-dependent coverage, i.e., the relative monolayer area, whose density of cross-links surpassed a certain threshold value, as a function of the exposure dose. A complete cross-linking of aromatic SAMs by He+ ion irradiation requires an exposure dose of about 850 µC/cm2, which is roughly 60 times smaller than the corresponding electron irradiation dose. Most likely, this is due to the energy distribution of secondary electrons shifted to lower energies, which results in a more efficient dissociative electron attachment (DEA) process.
doi:10.3762/bjnano.5.20
PMCID: PMC3943867  PMID: 24605285
carbon nanomembranes; dissociative electron attachment; helium ion microscopy; ion beam-organic molecules interactions; self-assembled monolayers
12.  Coordinated Movement of Cytoplasmic and Transmembrane Domains of RyR1 upon Gating 
PLoS Biology  2009;7(4):e1000085.
Ryanodine receptor type 1 (RyR1) produces spatially and temporally defined Ca2+ signals in several cell types. How signals received in the cytoplasmic domain are transmitted to the ion gate and how the channel gates are unknown. We used EGTA or neuroactive PCB 95 to stabilize the full closed or open states of RyR1. Single-channel measurements in the presence of FKBP12 indicate that PCB 95 inverts the thermodynamic stability of RyR1 and locks it in a long-lived open state whose unitary current is indistinguishable from the native open state. We analyzed two datasets of 15,625 and 18,527 frozen-hydrated RyR1-FKBP12 particles in the closed and open conformations, respectively, by cryo-electron microscopy. Their corresponding three-dimensional structures at 10.2 Å resolution refine the structure surrounding the ion pathway previously identified in the closed conformation: two right-handed bundles emerging from the putative ion gate (the cytoplasmic “inner branches” and the transmembrane “inner helices”). Furthermore, six of the identifiable transmembrane segments of RyR1 have similar organization to those of the mammalian Kv1.2 potassium channel. Upon gating, the distal cytoplasmic domains move towards the transmembrane domain while the central cytoplasmic domains move away from it, and also away from the 4-fold axis. Along the ion pathway, precise relocation of the inner helices and inner branches results in an approximately 4 Å diameter increase of the ion gate. Whereas the inner helices of the K+ channels and of the RyR1 channel cross-correlate best with their corresponding open/closed states, the cytoplasmic inner branches, which are not observed in the K+ channels, appear to have at least as important a role as the inner helices for RyR1 gating. We propose a theoretical model whereby the inner helices, the inner branches, and the h1 densities together create an efficient novel gating mechanism for channel opening by relaxing two right-handed bundle structures along a common 4-fold axis.
Author Summary
Maintaining a precise intracellular calcium concentration is key for cell survival. In skeletal muscle, ryanodine receptor type 1 (RyR1) is an intracellular calcium-release channel that is critical for contraction. Here, we used single-channel techniques to demonstrate the presence of functionally homogenous populations of RyR1 in either the closed or open state and then applied cryo-electron microscopy and image processing to determine the 3D structure of each state. The 3D structures show that RyR1′s ion pathway is formed by two sets of bundles, each containing four rods along a common axis. One set (inner helices) stretches from the lumen to the ion gate, whereas the second (inner branches) stretches from the ion gate to the peripheral cytoplasmic domains. The configuration of the two bundles is clearly different in the two physiological states, allowing a 4 Å increase in diameter of the ion gate upon opening. This diameter increase is sufficient to ensure flow of calcium ions. Upon gating, the cytoplasmic domains undergo a conformational change that converges on the inner branches, revealing a long-range allosteric mechanism that directly connects effectors acting on the cytoplasmic moiety with the ion gate.
Three-dimensional cryo-electron microscopy of the RyR1 calcium release channel in the open and closed states reveals its mechanisms of ion gating and long-range allostery.
doi:10.1371/journal.pbio.1000085
PMCID: PMC2672603  PMID: 19402748
13.  Chemical and Structural Stability of Lithium-Ion Battery Electrode Materials under Electron Beam 
Scientific Reports  2014;4:5694.
The investigation of chemical and structural dynamics in battery materials is essential to elucidation of structure-property relationships for rational design of advanced battery materials. Spatially resolved techniques, such as scanning/transmission electron microscopy (S/TEM), are widely applied to address this challenge. However, battery materials are susceptible to electron beam damage, complicating the data interpretation. In this study, we demonstrate that, under electron beam irradiation, the surface and bulk of battery materials undergo chemical and structural evolution equivalent to that observed during charge-discharge cycling. In a lithiated NiO nanosheet, a Li2CO3-containing surface reaction layer (SRL) was gradually decomposed during electron energy loss spectroscopy (EELS) acquisition. For cycled LiNi0.4Mn0.4Co0.18Ti0.02O2 particles, repeated electron beam irradiation induced a phase transition from an layered structure to an rock-salt structure, which is attributed to the stoichiometric lithium and oxygen removal from 3a and 6c sites, respectively. Nevertheless, it is still feasible to preserve pristine chemical environments by minimizing electron beam damage, for example, using fast electron imaging and spectroscopy. Finally, the present study provides examples of electron beam damage on lithium-ion battery materials and suggests that special attention is necessary to prevent misinterpretation of experimental results.
doi:10.1038/srep05694
PMCID: PMC4100024  PMID: 25027190
14.  The use of quartz crystal microbalance with dissipation (QCM-D) for studying nanoparticle-induced platelet aggregation 
Interactions between blood platelets and nanoparticles have both pharmacological and toxicological significance and may lead to platelet activation and aggregation. Platelet aggregation is usually studied using light aggregometer that neither mimics the conditions found in human microvasculature nor detects microaggregates. A new method for the measurement of platelet microaggregation under flow conditions using a commercially available quartz crystal microbalance with dissipation (QCM-D) has recently been developed. The aim of the current study was to investigate if QCM-D could be used for the measurement of nanoparticle-platelet interactions. Silica, polystyrene, and gold nanoparticles were tested. The interactions were also studied using light aggregometry and flow cytometry, which measured surface abundance of platelet receptors. Platelet activation was imaged using phase contrast and scanning helium ion microscopy. QCM-D was able to measure nanoparticle-induced platelet microaggregation for all nanoparticles tested at concentrations that were undetectable by light aggregometry and flow cytometry. Microaggregates were measured by changes in frequency and dissipation, and the presence of platelets on the sensor surface was confirmed and imaged by phase contrast and scanning helium ion microscopy.
doi:10.2147/IJN.S26679
PMCID: PMC3263416  PMID: 22275839
platelet aggregation; nanoparticles; light aggregometer; quartz crystal microbalance with dissipation; scanning helium ion microscopy
15.  Free-energy Landscapes of Ion-channel Gating Are Malleable: changes in the number of bound ligands are accompanied by changes in the location of the transition state in acetylcholine-receptor channels† 
Biochemistry  2003;42(50):14977-14987.
Acetylcholine-receptor channels (AChRs) are allosteric membrane proteins that mediate synaptic transmission by alternatively opening and closing (‘gating’) a cation-selective transmembrane pore. Although ligand binding is not required for the channel to open, the binding of agonists (for example, acetylcholine) increases the closed ⇌ open equilibrium constant because the ion-impermeable → ion-permeable transition of the ion pathway is accompanied by a low → high affinity change at the agonist-binding sites. The fact that the gating conformational change of muscle AChRs can be kinetically modeled as a two-state reaction has paved the way to the experimental characterization of the corresponding transition state, which represents a snapshot of the continuous sequence of molecular events separating the closed and open states. Previous studies of fully (di-) liganded AChRs, combining single-channel kinetic measurements, site-directed mutagenesis, and data analysis in the framework of the linear free-energy relationships of physical organic chemistry, have suggested a transition-state structure that is consistent with channel opening being an asynchronous conformational change that starts at the extracellular agonist-binding sites and propagates towards the intracellular end of the pore. In this paper, I characterize the gating transition state of unliganded AChRs, and report a remarkable difference: unlike that of diliganded gating, the unliganded transition state is not a hybrid of the closed- and open-state structures but, rather, is almost indistinguishable from the open state itself. This displacement of the transition state along the reaction coordinate obscures the mechanism underlying the unliganded closed ⇌ open reaction but brings to light the malleable nature of free-energy landscapes of ion-channel gating.
The muscle acetylcholine receptor channel (AChR)1 is the neurotransmitter-gated ion channel that mediates neuromuscular synaptic transmission in vertebrates (1). Although the structure of this large pentameric transmembrane protein (∼470 residues per subunit) is not known with atomic resolution, a wealth of structural information exists, mainly from mutational studies, affinity labeling, chemical modification of specific residues, electron microscopy, and crystallography (reviewed in ref. 2). As is the case of any other allosteric protein, the dynamic behavior of this receptor-channel can be understood in the framework of thermodynamic cycles, with conformational changes and ligand-binding events as the elementary steps (3-5). Thus, the AChR can adopt a variety of different conformations that can interconvert (closed, open, and desensitized ‘states’), and each conformation has a distinct ligand-binding affinity (low affinity in the closed state and high affinity in the open and desensitized states) and a particular ‘catalytic efficiency’ (ion-impermeable in the closed and desensitized states, and ion-permeable in the open state). To meet the physiological requirement of a small closed ⇌ open (‘gating’) equilibrium constant for the unliganded receptor, and a large gating equilibrium constant for the ACh-diliganded receptor, the affinity of the AChR for ACh must be higher in the open than in the closed conformation (4-6). This follows from the notion that the equilibrium constants governing the different reaction steps (ligand binding and gating) of these cyclic reaction schemes are constrained by the principle of detailed balance.
Hence, irrespective of whether the receptor is diliganded, monoliganded or unliganded, two changes must take place in going from the closed state (low ligand affinity and ion-impermeable) to the open state (high ligand affinity and ion-permeable): a) the pore becomes permeable to ions, and b) the transmitter-binding sites, some 50 Å away from the pore domain (7), increase their affinity for the ligand (with the reverse changes taking place during closing). The apparent lack of stable intermediates between the closed and open conformations, inferred from kinetic modeling of the diliganded-gating reaction (8), suggests that these two changes occur as a result of a one-step, global conformational change. The question, then, arises as to whether this concerted conformational change proceeds synchronously (i.e., every residue of the protein moves ‘in unison’) or asynchronously (i.e., following a sequence of events; ref. 9) and, if the latter were the case, whether multiple, few, or just one sequence of events is actually traversed by the channel to ‘connect’ the end states.
Analysis of the correlation between rate and equilibrium constants of gating in diliganded AChRs has allowed us to address some of these issues by probing the structure of the transition state (8, 10-12), that is, the intermediate species between the end states of a one-step reaction that can be most easily studied. Interpretation of these results in the framework of the classical rate-equilibrium free-energy relationships of physical organic chemistry (13, 14), revealed that AChR diliganded gating is a highly asynchronous reaction, and suggested that the transition-state ensemble is quite homogeneous, as if the crossing of the energy barrier were confined to a narrow pass at the top of the energy landscape. In the opening direction, the conformational rearrangement that leads to the low-to-high affinity change at the extracellular binding sites precedes the conformational rearrangement of the pore that renders the channel ion-permeable. This propagated global conformational change, which we have referred to as a ‘conformational wave’ (11), must reverse during channel closing so that closing starts at the pore and propagates all the way to the binding sites.
It is not at all obvious why the diliganded-gating conformational change starts at the binding sites when the channel opens, nor even why the conformational change propagates at all through the receptor, instead of taking place synchronously throughout the protein. Is there any correlation between the location of the domain that binds agonist and the location of the initiation site for the opening conformational change? Could the latter have started from the intracellular end of the pore, for example, and have propagated to the (extracellular) transmitter-binding sites? What difference does it make to be liganded or unliganded as far as the mechanism of the gating conformational change is concerned? To address these issues, I set out to explore the mechanism of gating in unliganded AChRs by probing the structure of the corresponding transition state using kinetic measurements, site-directed mutagenesis, and the concepts of rate-equilibrium free-energy relationships and Φ-value analysis.
Briefly, a Φ-value can be assigned to any position in the protein by estimating the slope of a ‘Brönsted plot’2 [log (gating rate constant) versus log (gating equilibrium constant)] where each point corresponds to a different amino-acid substitution at that given position. More coarsegrained Φ-values can also be obtained by using different agonists or different transmembrane potentials, for example, as a means of altering the rate and equilibrium constants of gating. Very often, rate-equilibrium plots are linear, and 0 < Φ < 1. A value of Φ = 0 suggests that the position in question (in the case of a mutation series) experiences a closed-state-like environment at the transition state whereas a value of Φ = 1 suggests an open-state-like environment. A fractional Φ-value suggests an environment that is intermediate between those experienced in the closed and open states (16).
Earlier results indicated that the Φ-values obtained by varying the transmembrane potential are different in diliganded and unliganded AChRs. These Φ-values, which are a measure of the closed-state-like versus open-state-like character of the channel’s voltage-sensing elements at the transition state, are 0.070 ± 0.060 in diliganded receptors (17), and 1.025 ± 0.053 in unliganded AChRs (11, 18). The present study reveals that residues at the transmitter-binding sites (Figure 1), the extracellular loop that links the second (M2) and third (M3) transmembrane segments (M2-M3 linker), and the upper and lower half of M2, which during diliganded gating have Φ-values of ∼1 (ref. 11), ∼0.7 (ref. 10), ∼0.35 (refs 8, 11, 12), and ∼0 (ref. 12), respectively, have also Φ-values very close to 1 during unliganded gating. This generalized shift in Φ-values suggests that the diliganded → unliganded perturbation deforms the energy landscape of gating in such a way that the ‘new’ transition state occurs very close to the open state, to such an extent that all tested positions experience an open-state-like environment at the transition state of unliganded gating. Thus, the transition state occurs so ‘late’ (i.e., so close to the open state) that its inferred structure does not provide any clues as to the intermediate stages of this reaction.
Hence, the mechanism of unliganded gating remains obscure. The change in the position of the transition state along a reaction coordinate, as a result of perturbations to the energy landscape, is a very well known phenomenon in organic chemistry (e.g., refs 20-26), and protein folding (e.g., refs 27-34). In this paper, I show that this phenomenon can also take place in the case of allosteric transitions and, therefore, that the structure of the transition state of a global conformational change need not be fixed; rather, it can change depending on the experimental conditions.
doi:10.1021/bi0354334
PMCID: PMC1463891  PMID: 14674774
16.  Site-Directed Spin Labeling Reveals Pentameric Ligand-Gated Ion Channel Gating Motions 
PLoS Biology  2013;11(11):e1001714.
Pentameric ligand-gated ion channels (pLGICs) are neurotransmitter-activated receptors that mediate fast synaptic transmission. In pLGICs, binding of agonist to the extracellular domain triggers a structural rearrangement that leads to the opening of an ion-conducting pore in the transmembrane domain and, in the continued presence of neurotransmitter, the channels desensitize (close). The flexible loops in each subunit that connect the extracellular binding domain (loops 2, 7, and 9) to the transmembrane channel domain (M2–M3 loop) are essential for coupling ligand binding to channel gating. Comparing the crystal structures of two bacterial pLGIC homologues, ELIC and the proton-activated GLIC, suggests channel gating is associated with rearrangements in these loops, but whether these motions accurately predict the motions in functional lipid-embedded pLGICs is unknown. Here, using site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy and functional GLIC channels reconstituted into liposomes, we examined if, and how far, the loops at the ECD/TMD gating interface move during proton-dependent gating transitions from the resting to desensitized state. Loop 9 moves ∼9 Å inward toward the channel lumen in response to proton-induced desensitization. Loop 9 motions were not observed when GLIC was in detergent micelles, suggesting detergent solubilization traps the protein in a nonactivatable state and lipids are required for functional gating transitions. Proton-induced desensitization immobilizes loop 2 with little change in position. Proton-induced motion of the M2–M3 loop was not observed, suggesting its conformation is nearly identical in closed and desensitized states. Our experimentally derived distance measurements of spin-labeled GLIC suggest ELIC is not a good model for the functional resting state of GLIC, and that the crystal structure of GLIC does not correspond to a desensitized state. These findings advance our understanding of the molecular mechanisms underlying pLGIC gating.
Author Summary
Ligand-gated ion channels reside in the membranes of nerve and muscle cells. These proteins form channels that span the membrane, where they transduce chemical signals into changes in electrical excitability. Neurotransmitters bind to the extracellular surface of these proteins to trigger global structural rearrangements that open the channel, allowing ions to flow across the cell membrane. In the continued presence of neurotransmitters, the channels desensitize and close. Channel opening and closing regulate muscle contraction and signaling in the brain, and defects in these channels lead to a variety of diseases. While crystal structures have provided frozen snapshots of these proteins in presumed closed and open channel states, little is known about how the channels desensitize and move during actual signaling events. Here, we applied a technique to investigate the structure and local dynamics of proteins known as site-directed spin labeling to a prototypical ligand-gated channel, GLIC. We directly quantified ligand-induced motions in regions at the boundary between the binding domain (loops 2 and 9) and the channel domain (M2–M3 loop). We show that a large movement of loop 9 and an immobilization of loop 2, which rearranges the interface between the binding and channel domains, accompanies GLIC channel gating transitions into a desensitized state. These data provide new insights into the protein movements that underlie electrochemical transmission of signals between cells.
doi:10.1371/journal.pbio.1001714
PMCID: PMC3833874  PMID: 24260024
17.  Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles 
eLife  2013;2:e00461.
Although electron cryo-microscopy (cryo-EM) single-particle analysis has become an important tool for structural biology of large and flexible macro-molecular assemblies, the technique has not yet reached its full potential. Besides fundamental limits imposed by radiation damage, poor detectors and beam-induced sample movement have been shown to degrade attainable resolutions. A new generation of direct electron detectors may ameliorate both effects. Apart from exhibiting improved signal-to-noise performance, these cameras are also fast enough to follow particle movements during electron irradiation. Here, we assess the potentials of this technology for cryo-EM structure determination. Using a newly developed statistical movie processing approach to compensate for beam-induced movement, we show that ribosome reconstructions with unprecedented resolutions may be calculated from almost two orders of magnitude fewer particles than used previously. Therefore, this methodology may expand the scope of high-resolution cryo-EM to a broad range of biological specimens.
DOI: http://dx.doi.org/10.7554/eLife.00461.001
eLife digest
Determining the structure of proteins and other biomolecules at the atomic level is central to understanding many aspects of biology. X-ray crystallography is the best-known technique for structural biology but, as the name suggests, it works only with samples that can be crystallized. Electron cryo-microscopy (cryo-EM) could, potentially, be used to determine the atomic structures of biomolecules that cannot be crystallized, but at present the resolution that can be achieved with this approach is sufficient only for imaging certain types of viruses.
In cryo-EM, a solution of the biomolecule of interest is frozen in a thin layer of ice, and this layer is imaged in an electron microscope. By combining images of many identical biomolecules in many different orientations, it is possible to work backwards and determine their 3D structure. However, in order to determine this structure at high resolution, it is necessary to make repeated measurements to reduce high levels of noise in the images.
Cryo-EM images are usually recorded on a photographic film or a CCD (charge-coupled device) camera. However, photographic film is unsuitable for high-throughput methods because it has to be handled manually, while the efficiency of CCD cameras is limited because the electrons have to be converted into visible light to be detected. Digital cameras that can detect electrons directly have become available recently, and these are more efficient than both film and CCD cameras. They are also much faster, which means that it is possible to record videos of the sample during the time (typically ∼1 s) it is being exposed to the electron beam. Processing these videos could then—in theory—compensate for any movements of the biomolecules that are induced by the electron beam. Along with radiation damage caused by the electrons, these beam-induced movements have been a major limitation on the resolution that can be achieved with cryo-EM.
Bai et al. demonstrate the potential of direct-electron detectors in cryo-EM by determining the structures of two ribosomes. Using a novel statistical algorithm to accurately follow the movements of the ribosomes during the time they are exposed to the electron beam, they are able to compensate for these movements, and this makes it possible to determine the structures of the ribosomes with near-atomic precision. Moreover, the resolution they achieve with just ∼30,000 ribosomes is better than that previously achieved with more than a million ribosomes, allowing small details inside the ribosome – such as ß-strands and bulky amino-acid side chains – to be resolved with cryo-EM for the first time. The work of Bai et al. could, therefore, allow researchers to use cryo-EM to determine the structure of many more biomolecules with atomic precision.
DOI: http://dx.doi.org/10.7554/eLife.00461.002
doi:10.7554/eLife.00461
PMCID: PMC3576727  PMID: 23427024
Electron Microscopy; Direct electron detectors; Image processing; T. thermophilus; ribosome; Bayesian; S. cerevisiae
18.  Three-dimensional electron crystallography of protein microcrystals 
eLife  2013;2:e01345.
We demonstrate that it is feasible to determine high-resolution protein structures by electron crystallography of three-dimensional crystals in an electron cryo-microscope (CryoEM). Lysozyme microcrystals were frozen on an electron microscopy grid, and electron diffraction data collected to 1.7 Å resolution. We developed a data collection protocol to collect a full-tilt series in electron diffraction to atomic resolution. A single tilt series contains up to 90 individual diffraction patterns collected from a single crystal with tilt angle increment of 0.1–1° and a total accumulated electron dose less than 10 electrons per angstrom squared. We indexed the data from three crystals and used them for structure determination of lysozyme by molecular replacement followed by crystallographic refinement to 2.9 Å resolution. This proof of principle paves the way for the implementation of a new technique, which we name ‘MicroED’, that may have wide applicability in structural biology.
DOI: http://dx.doi.org/10.7554/eLife.01345.001
eLife digest
X-ray crystallography has been used to work out the atomic structure of a large number of proteins. In a typical X-ray crystallography experiment, a beam of X-rays is directed at a protein crystal, which scatters some of the X-ray photons to produce a diffraction pattern. The crystal is then rotated through a small angle and another diffraction pattern is recorded. Finally, after this process has been repeated enough times, it is possible to work backwards from the diffraction patterns to figure out the structure of the protein.
The crystals used for X-ray crystallography must be large to withstand the damage caused by repeated exposure to the X-ray beam. However, some proteins do not form crystals at all, and others only form small crystals. It is possible to overcome this problem by using extremely short pulses of X-rays, but this requires a very large number of small crystals and ultrashort X-ray pulses are only available at a handful of research centers around the world. There is, therefore, a need for other approaches that can determine the structure of proteins that only form small crystals.
Electron crystallography is similar to X-ray crystallography in that a protein crystal scatters a beam to produce a diffraction pattern. However, the interactions between the electrons in the beam and the crystal are much stronger than those between the X-ray photons and the crystal. This means that meaningful amounts of data can be collected from much smaller crystals. However, it is normally only possible to collect one diffraction pattern from each crystal because of beam induced damage. Researchers have developed methods to merge the diffraction patterns produced by hundreds of small crystals, but to date these techniques have only worked with very thin two-dimensional crystals that contain only one layer of the protein of interest.
Now Shi et al. report a new approach to electron crystallography that works with very small three-dimensional crystals. Called MicroED, this technique involves placing the crystal in a transmission electron cryo-microscope, which is a fairly standard piece of equipment in many laboratories. The normal ‘low-dose’ electron beam in one of these microscopes would normally damage the crystal after a single diffraction pattern had been collected. However, Shi et al. realized that it was possible to obtain diffraction patterns without severely damaging the crystal if they dramatically reduced the normal low-dose electron beam. By reducing the electron dose by a factor of 200, it was possible to collect up to 90 diffraction patterns from the same, very small, three-dimensional crystal, and then—similar to what happens in X-ray crystallography—work backwards to figure out the structure of the protein. Shi et al. demonstrated the feasibility of the MicroED approach by using it to determine the structure of lysozyme, which is widely used as a test protein in crystallography, with a resolution of 2.9 Å. This proof-of principle study paves the way for crystallographers to study protein that cannot be studied with existing techniques.
DOI: http://dx.doi.org/10.7554/eLife.01345.002
doi:10.7554/eLife.01345
PMCID: PMC3831942  PMID: 24252878
electron crystallography; electron diffraction; electron cryomicroscopy (cryo-EM); microED; protein structure; microcrystals; None
19.  Ion-Abrasion Scanning Electron Microscopy Reveals Surface-Connected Tubular Conduits in HIV-Infected Macrophages 
PLoS Pathogens  2009;5(9):e1000591.
HIV-1-containing internal compartments are readily detected in images of thin sections from infected cells using conventional transmission electron microscopy, but the origin, connectivity, and 3D distribution of these compartments has remained controversial. Here, we report the 3D distribution of viruses in HIV-1-infected primary human macrophages using cryo-electron tomography and ion-abrasion scanning electron microscopy (IA-SEM), a recently developed approach for nanoscale 3D imaging of whole cells. Using IA-SEM, we show the presence of an extensive network of HIV-1-containing tubular compartments in infected macrophages, with diameters of ∼150–200 nm, and lengths of up to ∼5 µm that extend to the cell surface from vesicular compartments that contain assembling HIV-1 virions. These types of surface-connected tubular compartments are not observed in T cells infected with the 29/31 KE Gag-matrix mutant where the virus is targeted to multi-vesicular bodies and released into the extracellular medium. IA-SEM imaging also allows visualization of large sheet-like structures that extend outward from the surfaces of macrophages, which may bend and fold back to allow continual creation of viral compartments and virion-lined channels. This potential mechanism for efficient virus trafficking between the cell surface and interior may represent a subversion of pre-existing vesicular machinery for antigen capture, processing, sequestration, and presentation.
Author Summary
Current treatment regimens for HIV-infected individuals are not capable of eradicating HIV infection, even though combinations of highly potent antiviral drugs are used. Indeed, drug regimens must be periodically altered as the virus resurges from a persistent reservoir. Macrophages, which serve as “search-and-destroy” immune surveillance cells of the body, are now thought to be a key component of this reservoir. Evidence suggests that macrophages can harbor infectious HIV virions for long periods, and transmit them to bystander T cells. We have used a new technique called ion abrasion scanning electron microscopy (IA-SEM) to image entire HIV-infected human macrophages at a resolution high enough to see individual HIV virions and their location within the cell. This approach revealed that HIV is present in a system of nanoscale tubes, barely larger than a virus at some places, which connect internal viral reservoirs to the cell surface. These tubes could allow the macrophage to deliver HIV virions to bystander cells from its continually replenished stores of ammunition, held deep within the cell. Our work provides a glimpse of how the structure of these reservoirs allows macrophages to accomplish viral delivery. Discovery of these virion-channeling tubes provides a potential drug target to address the problem of persistent HIV infection.
doi:10.1371/journal.ppat.1000591
PMCID: PMC2743285  PMID: 19779568
20.  BIN1 Localizes the L-Type Calcium Channel to Cardiac T-Tubules 
PLoS Biology  2010;8(2):e1000312.
Cardiac tubular-like membrane invaginations contain the membrane scaffolding protein BIN1, which tethers dynamic microtubules that deliver calcium channels directly to T-tubule membrane.
The BAR domain protein superfamily is involved in membrane invagination and endocytosis, but its role in organizing membrane proteins has not been explored. In particular, the membrane scaffolding protein BIN1 functions to initiate T-tubule genesis in skeletal muscle cells. Constitutive knockdown of BIN1 in mice is perinatal lethal, which is associated with an induced dilated hypertrophic cardiomyopathy. However, the functional role of BIN1 in cardiomyocytes is not known. An important function of cardiac T-tubules is to allow L-type calcium channels (Cav1.2) to be in close proximity to sarcoplasmic reticulum-based ryanodine receptors to initiate the intracellular calcium transient. Efficient excitation-contraction (EC) coupling and normal cardiac contractility depend upon Cav1.2 localization to T-tubules. We hypothesized that BIN1 not only exists at cardiac T-tubules, but it also localizes Cav1.2 to these membrane structures. We report that BIN1 localizes to cardiac T-tubules and clusters there with Cav1.2. Studies involve freshly acquired human and mouse adult cardiomyocytes using complementary immunocytochemistry, electron microscopy with dual immunogold labeling, and co-immunoprecipitation. Furthermore, we use surface biotinylation and live cell confocal and total internal fluorescence microscopy imaging in cardiomyocytes and cell lines to explore delivery of Cav1.2 to BIN1 structures. We find visually and quantitatively that dynamic microtubules are tethered to membrane scaffolded by BIN1, allowing targeted delivery of Cav1.2 from the microtubules to the associated membrane. Since Cav1.2 delivery to BIN1 occurs in reductionist non-myocyte cell lines, we find that other myocyte-specific structures are not essential and there is an intrinsic relationship between microtubule-based Cav1.2 delivery and its BIN1 scaffold. In differentiated mouse cardiomyocytes, knockdown of BIN1 reduces surface Cav1.2 and delays development of the calcium transient, indicating that Cav1.2 targeting to BIN1 is functionally important to cardiac calcium signaling. We have identified that membrane-associated BIN1 not only induces membrane curvature but can direct specific antegrade delivery of microtubule-transported membrane proteins. Furthermore, this paradigm provides a microtubule and BIN1-dependent mechanism of Cav1.2 delivery to T-tubules. This novel Cav1.2 trafficking pathway should serve as an important regulatory aspect of EC coupling, affecting cardiac contractility in mammalian hearts.
Author Summary
Calcium plays a primary role in regulating heart function. During each heartbeat, calcium ions cross the membrane of individual cardiac muscle cells and trigger a rapid increase of calcium within the cell (called the calcium transient). Calcium causes the muscle cells to contract and determines the strength of the overall heartbeat. Each cardiac muscle cell has many small tubular-like membrane invaginations known as T-tubules where calcium channels localize, allowing calcium ions to enter and immediately encounter intracellular calcium release organelles. While this organization is well described, it is not known how calcium channels localize to T-tubule membrane. Here we show that in human and mouse heart cells, a membrane scaffolding protein known as BIN1 is localized together with calcium channels at T-tubules. Using high-resolution live cell microscopy, we found that microtubules, which are necessary for calcium channel delivery to the membrane, are also tethered by BIN1. Loss of BIN1 in cardiac cells impairs delivery of calcium channels to the membrane and diminishes the intracellular calcium transient. According to this model, microtubules function as highways that carry newly synthesized calcium channels to BIN1-containing membrane. Once tethered to T-tubules by BIN1, the microtubules can deliver their calcium channel cargo. We postulate that this calcium channel delivery pathway is important to the regulation of cardiac calcium signaling and beat-to-beat cardiac function.
doi:10.1371/journal.pbio.1000312
PMCID: PMC2821894  PMID: 20169111
21.  Ionic selectivity and thermal adaptations within the voltage-gated sodium channel family of alkaliphilic Bacillus 
eLife  2014;3:e04387.
Entry and extrusion of cations are essential processes in living cells. In alkaliphilic prokaryotes, high external pH activates voltage-gated sodium channels (Nav), which allows Na+ to enter and be used as substrate for cation/proton antiporters responsible for cytoplasmic pH homeostasis. Here, we describe a new member of the prokaryotic voltage-gated Na+ channel family (NsvBa; Non-selective voltage-gated, Bacillus alcalophilus) that is nonselective among Na+, Ca2+ and K+ ions. Mutations in NsvBa can convert the nonselective filter into one that discriminates for Na+ or divalent cations. Gain-of-function experiments demonstrate the portability of ion selectivity with filter mutations to other Bacillus Nav channels. Increasing pH and temperature shifts their activation threshold towards their native resting membrane potential. Furthermore, we find drugs that target Bacillus Nav channels also block the growth of the bacteria. This work identifies some of the adaptations to achieve ion discrimination and gating in Bacillus Nav channels.
DOI: http://dx.doi.org/10.7554/eLife.04387.001
eLife digest
Life essentially runs on electricity: electrical signals cause nerve cells to fire, heart muscles to contract and allow organisms to sense the world around them. These signals are triggered by the movement of positively-charged ions—such as sodium, potassium and calcium—moving into a cell through special ion channels in the cell membrane, which can open and close in response to changes in the voltage across the cell membrane.
With few exceptions, voltage sensitive ion channels usually only let one type of ion pass into the cell. But how do ion channels discriminate amongst ions and how did they acquire this ability during evolution? To address these questions, researchers have studied a family of sodium channels from bacteria for the past decade. Here DeCaen et al. describe a new member from this ion channel family from a bacterium called Bacillus alcalophilus. This ion channel does not discriminate between positively-charged ions and B. alcalophilus needs this ion channel for it to dwell in environments that have high levels of potassium or sodium. DeCaen et al. demonstrate that these ion channels can be made selective for sodium or calcium with as little as two small changes in the gene that encodes the ion channel. Furthermore, making similar genetic mutations in related ion channel genes from other Bacillus species has the same effect. DeCaen et al. suggest that Bacillus ion channel genes are easily adapted to function in a variety of environmental conditions with different levels of positively-charged ions. Thus it is easier for Bacillus channels to evolve to be selective for different ions.
Bacillus bacteria divide rapidly in warm to hot temperatures and under alkaline pH. DeCaen et al. demonstrate that both of these conditions make Bacillus ion channels easier to open in response to voltage. In addition, DeCaen et al. demonstrate that Bacillus ion channels can be targeted by drugs that impair the ability of the bacteria to grow. These findings—together with other work that revealed where drug molecules bind to ion channels—could potentially guide efforts to develop treatments for illnesses caused by other Bacillus strains, which include anthrax and some forms of food poisoning.
DOI: http://dx.doi.org/10.7554/eLife.04387.002
doi:10.7554/eLife.04387
PMCID: PMC4225499  PMID: 25385530
ion selectivity; bacteria physiology; pharmacology; biochemical adaptations; evolution; antibiotics; None
22.  Cell surface and cell outline imaging in plant tissues using the backscattered electron detector in a variable pressure scanning electron microscope 
Plant Methods  2013;9:40.
Background
Scanning electron microscopy (SEM) has been used for high-resolution imaging of plant cell surfaces for many decades. Most SEM imaging employs the secondary electron detector under high vacuum to provide pseudo-3D images of plant organs and especially of surface structures such as trichomes and stomatal guard cells; these samples generally have to be metal-coated to avoid charging artefacts. Variable pressure-SEM allows examination of uncoated tissues, and provides a flexible range of options for imaging, either with a secondary electron detector or backscattered electron detector. In one application, we used the backscattered electron detector under low vacuum conditions to collect images of uncoated barley leaf tissue followed by simple quantification of cell areas.
Results
Here, we outline methods for backscattered electron imaging of a variety of plant tissues with particular focus on collecting images for quantification of cell size and shape. We demonstrate the advantages of this technique over other methods to obtain high contrast cell outlines, and define a set of parameters for imaging Arabidopsis thaliana leaf epidermal cells together with a simple image analysis protocol. We also show how to vary parameters such as accelerating voltage and chamber pressure to optimise imaging in a range of other plant tissues.
Conclusions
Backscattered electron imaging of uncoated plant tissue allows acquisition of images showing details of plant morphology together with images of high contrast cell outlines suitable for semi-automated image analysis. The method is easily adaptable to many types of tissue and suitable for any laboratory with standard SEM preparation equipment and a variable-pressure-SEM or tabletop SEM.
doi:10.1186/1746-4811-9-40
PMCID: PMC3853341  PMID: 24135233
Backscattered-electron imaging; Plant cell outlines; Image analysis; Arabidopsis thaliana
23.  DNA cell cycle studies in uveal melanoma. 
We analyzed the cell cycling status of a group of irradiated and nonirradiated uveal melanomas using BrdUrd techniques. These data demonstrate that melanomas are relatively slow-growing tumors with a few cells actively cycling at a given time. Radiation has a profound effect on the number of cycling cells (P less than .0001). After treatment with either 20 Gy of pre-enucleation photon or 60 Gy or more of helium ion irradiation, virtually no cells are detected in the synthesis phase of the DNA cell cycle. It is unclear whether the absence of cycling cells after 20 Gy of photon irradiation is permanent or represents a transient cell cycle block, since these tumors were studied within 48 hours after irradiation. In contrast, all melanomas treated with helium ion had been irradiated several months prior to enucleation (mean, 2 years). In the latter group of tumors, the length of time between treatment and cell cycle analysis suggests that these cells had lost their reproductive integrity. These data were substantiated by tissue culture studies. Growth of tumor explants was significantly less (P less than .007) in irradiated than in nonirradiated melanomas. The optimum technology used for measurement of cell cycle status remains to be determined. Measurement of BrdUrd uptake using immunofluorescent microscopy on either standard sections or fine-needle biopsies can be performed. In general, flow cytometric analysis yields similar results. It is difficult with the latter technique to be certain that nontumor cells are not artifactitiously counted in the cell cycle studies. The incorporation of BrdUrd cell cycle analysis with fine-needle biopsy may be useful in the clinical management of irradiated melanomas that have questionable growth after treatment. In a few cases studied, results appeared to correlate with tumor growth activity.
Images
PMCID: PMC1298823  PMID: 2979030
24.  The role of helium gas in medicine 
Medical Gas Research  2013;3:18.
The noble gas helium has many applications owing to its distinct physical and chemical characteristics, namely: its low density, low solubility, and high thermal conductivity. Chiefly, the abundance of studies in medicine relating to helium are concentrated in its possibility of being used as an adjunct therapy in a number of respiratory ailments such as asthma exacerbation, COPD, ARDS, croup, and bronchiolitis. Helium gas, once believed to be biologically inert, has been recently shown to be beneficial in protecting the myocardium from ischemia by various mechanisms. Though neuroprotection of brain tissue has been documented, the mechanism by which it does so has yet to be made clear. Surgeons are exploring using helium instead of carbon dioxide to insufflate the abdomen of patients undergoing laparoscopic abdominal procedures due to its superiority in preventing respiratory acidosis in patients with comorbid conditions that cause carbon dioxide retention. Newly discovered applications in Pulmonary MRI radiology and imaging of organs in very fine detail using Helium Ion Microscopy has opened exciting new possibilities for the use of helium gas in technologically advanced fields of medicine.
doi:10.1186/2045-9912-3-18
PMCID: PMC3751721  PMID: 23916029
Helium; Heliox; Inhalation therapy; Cardioprotection; Neuroprotection; Insufflation
25.  On the Size and Structure of Helium Snowballs Formed around Charged Atoms and Clusters of Noble Gases 
The Journal of Physical Chemistry. a  2013;118(37):8050-8059.
Helium nanodroplets doped with argon, krypton, or xenon are ionized by electrons and analyzed in a mass spectrometer. HenNgx+ ions containing up to seven noble gas (Ng) atoms and dozens of helium atoms are identified; the high resolution of the mass spectrometer combined with advanced data analysis make it possible to unscramble contributions from isotopologues that have the same nominal mass but different numbers of helium or Ng atoms, such as the magic He2084Kr2+ and the isobaric, nonmagic He4184Kr+. Anomalies in these ion abundances reveal particularly stable ions; several intriguing patterns emerge. Perhaps most astounding are the results for HenAr+, which show evidence for three distinct, solid-like solvation shells containing 12, 20, and 12 helium atoms. This observation runs counter to the common notion that only the first solvation shell is solid-like but agrees with calculations by Galli et al. for HenNa+ [J. Phys. Chem. A2011, 115, 730021568337] that reveal three shells of icosahedral symmetry. HenArx+ (2 ≤ x ≤ 7) ions appear to be especially stable if they contain a total of n + x = 19 atoms. A sequence of anomalies in the abundance distribution of HenKrx+ suggests that rings of six helium atoms are inserted into the solvation shell each time a krypton atom is added to the ionic core, from Kr+ to Kr3+. Previously reported strong anomalies at He12Kr2+ and He12Kr3+ [KimJ. H.; et al. J. Chem. Phys.2006, 124, 21430116774401] are attributed to a contamination. Only minor local anomalies appear in the distributions of HenXex+ (x ≤ 3). The distributions of HenKr+ and HenXe+ show strikingly similar, broad features that are absent from the distribution of HenAr+; differences are tentatively ascribed to the very different fragmentation dynamics of these ions.
doi:10.1021/jp406540p
PMCID: PMC4166691  PMID: 24128371

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