JEOL Resourceshttps://www.jeolusa.com/RESOURCES/Electron-Optics/Documents-Downloads(S)TEM Tomographyhttps://www.jeolusa.com/RESOURCES/Electron-Optics/Documents-Downloads/stem-tomographyTransmission Electron Microscope (TEM)Wed, 05 Oct 2022 13:21:34 GMTTomography is a technique that employs a series of images successively recorded from an object at different tilt angles with respect to the electron beam in order to obtain that object’s three-dimensional structure using a back projection technique. The images can be recorded in a Transmission Electron Microscope (TEM) or a Scanning Transmission Electron Microscope (STEM). JEOL have adopted SerialEM (Boulder laboratory for 3D electron microscopy of cells BL3DEMC) to either modality making tomography an accessible, efficient and easy technique for all aspects of scientific, industrial and medical research.<p>The modality of imaging depends primarily on the object being studied. For example, structures that show strong diffraction effects, very common in Materials, tend to be studied most effectively in STEM mode using images acquired on a High Angle Annular Detector (HAADF). Conversely, specimens in Life Sciences, characterized by an abundance of low Z elements and thus fairly devoid of diffraction effects, tend to be studied mostly using TEM bright field. SerialEM tomography can be applied to all TEMs in the JEOL line-­up thus providing a solution for every aspect of microscopy that targets 3D structures.</p> <p>Tomography is applicable to a wide variety of samples, such as ranging from beam-­resistant FIB lift-­out to frozen-­hydrated specimens. A low-­dose option in SerialEM tomography allows specimens to be imaged whilst in their native state, i.e., after vitrification. Entire tomographic series can be obtained without visibly damaging the sample (Fig. 2). JEOL USA’s choice for tomography includes processing using IMOD (also available from the BL3DEMC).</p> <p style="text-align: center;"><img alt="Fig.2: 3D rendering in chimera of frozen-­hydrated vesicles coated with viral proteins after tomography in a JEM-­3200FSC at 300 kV and 20 eV zero-­loss imaging. Processing included NAD filtering (Sample courtesy of B. Russin, Northwestern U.)" class="img-responsive" src="https://jeolusa.s3.amazonaws.com/resources_eo/(S)TEM%20Tomography%20002.jpg?AWSAccessKeyId=AKIAQJOI4KIAZPDULHNL&Expires=2145934800&Signature=5mkSX4VJO8vicdk%2FaYnN12SbjYo%3D" /><br /> <strong>Fig.2:</strong> 3D rendering in chimera of frozen-­hydrated vesicles coated with viral proteins after tomography in a JEM-­3200FSC at 300 kV and 20 eV zero-­loss imaging. Processing included NAD filtering (Sample courtesy of B. Russin, Northwestern U.)</p> <p>The low-­dose option also allows the use of extremely high magnification for imaging, as is the case for instance in STEM mode (Fig.3). The ability to perform critical steps in tomography, such as tracking, focusing and recording the final image, at different magnifications, ensures the operator that the object of interest remains on the camera/detector under all conditions as the sample is being tilted.</p> <p style="text-align: center;"><img alt="Fig. 3: 3D rendering in chimera of catalytic sample acquired in HAADF STEM mode in a JEM-­ARM200CF (Sample courtesy of R. Klie, UIC)." class="img-responsive" src="https://jeolusa.s3.amazonaws.com/resources_eo/(S)TEM%20Tomography%20003.jpg?AWSAccessKeyId=AKIAQJOI4KIAZPDULHNL&Expires=2145934800&Signature=IQSP06Q2Xvl3xLvZS7Y6g%2FoZ5JE%3D" /><br /> <strong>Fig. 3:</strong> 3D rendering in chimera of catalytic sample acquired in HAADF STEM mode in a JEM-­ARM200CF (Sample courtesy of R. Klie, UIC).</p> <p>Tomography is now also being applied in the field of diagnostic imaging, for instance in primary ciliary dyskineasia (see Brink and Carson, MSA Proc. (2010) 16: 970). Shown is a cilia cross section that has been obtained after applying 3D imaging by tomography. The reconstruction is rotated so as to yield views that are identical to perfect axial cross sections through the cilia (Fig. 4). Note the microtubule doublets in this view indicating the proper orientation of the cilia. A reliable workflow can thus be established that gives quick answers as this reconstruction can be obtained in roughly 30 minutes.</p> <p>Finally, SerialEM has the ability to capture large-scale montages as exemplified in the work from the Marc lab at University of Utah (Fig.4).</p> <p style="text-align: center;"><img alt="Fig. 4: 3D rendered cilia from sick patient after SerialEM tomography in a JEM-­1400 showing the disconnected dynein arms (Sample courtesy of Dr. Carson, UNC)." class="img-responsive" src="https://jeolusa.s3.amazonaws.com/resources_eo/(S)TEM%20Tomography%20004.jpg?AWSAccessKeyId=AKIAQJOI4KIAZPDULHNL&Expires=2145934800&Signature=iRamGgqTlykw%2FwjD6PNitkfMqkY%3D" /><br /> <strong>Fig. 4:</strong> 3D rendered cilia from sick patient after SerialEM tomography in a JEM-­1400 showing the disconnected dynein arms (Sample courtesy of Dr. Carson, UNC).</p> <p>Montages such as these are at the fingertips of researchers through a robust and easy to set up GUI in SerialEM. The montaging feature makes use of either stage-based or deflector-based navigation.</p> <p style="text-align: center;"><img alt="Fig. 5: Montage of mouse retina obtained in a JEM-­1400 using SerialEM stage-­based montaging. The area measures approx. 0.5 x 0.5 mm and was imaged at a magnification of 5000x. The montage contains circa 1000 images acquired from the 4k x 4k CCD camera." class="img-responsive" src="https://jeolusa.s3.amazonaws.com/resources_eo/(S)TEM%20Tomography%20005.jpg?AWSAccessKeyId=AKIAQJOI4KIAZPDULHNL&Expires=2145934800&Signature=dwxyQA8bgJCG7wbG%2BJmNMWS%2Fnyg%3D" /><br /> <strong>Fig. 5:</strong> Montage of mouse retina obtained in a JEM-­1400 using SerialEM stage-­based montaging. The area measures approx. 0.5 x 0.5 mm and was imaged at a magnification of 5000x. The montage contains circa 1000 images acquired from the 4k x 4k CCD camera.</p> 1.8 Å resolution structure of β-galactosidase with a 200 kV CRYO ARM electron microscopehttps://www.jeolusa.com/RESOURCES/Electron-Optics/Documents-Downloads/18-resolution-structure-of-galactosidase-with-a-200-kv-cryo-arm-electron-microscopeCRYO ARM™ 200Thu, 10 Dec 2020 11:35:20 GMTAs seen in IUCrJ Volume 7, July 2020, pages 639-643.<p>See <a href="https://journals.iucr.org/m/issues/2020/04/00/eh5008/index.html" target="_blank">IUCrJ Volume 7, July 2020, pages 639-643</a>.</p> A New Take on the Phase Platehttps://www.jeolusa.com/RESOURCES/Electron-Optics/Documents-Downloads/a-new-take-on-the-phase-plate200kVThu, 10 Dec 2020 11:40:13 GMTTEM phase plate development was extensively pursued by Prof Nagayama’s lab in Japan for over ten years. Prof Chiu of Baylor College of Medicine has successfully applied the phase plate system on his Omega filtered TEM (JEM-2200FS) to the molecular structure characterization for proteins.<p>TEM phase plate development was extensively pursued by Prof Nagayama’s lab in Japan for over ten years. Prof Chiu of Baylor College of Medicine has successfully applied the phase plate system on his Omega filtered TEM (JEM-2200FS) to the molecular structure characterization for proteins.</p> <p>A reprint from <i>Lab Product News.</i></p> Ad-hoc Auto Tuninghttps://www.jeolusa.com/RESOURCES/Electron-Optics/Documents-Downloads/ad-hoc-auto-tuningNEOARMThu, 10 Dec 2020 11:09:18 GMTAuto Tuning for HR-STEM for crystalline sample.<p>Auto Tuning for HR-STEM for crystalline sample.</p> Air-Isolated Sampling of Solid-State Battery for TEMhttps://www.jeolusa.com/RESOURCES/Electron-Optics/Documents-Downloads/air-isolated-sampling-of-solid-state-battery-for-temTransmission Electron Microscope (TEM)Thu, 23 Sep 2021 11:53:17 GMTA solid-state battery is made of cathode, anode and electrolyte. This type of battery doesn’t use liquid state electrolyte, so it tends to avoid the issues associated with leakage of electrolyte and ignition/explosion. Recently, silicon has been used as an anode material to improve the battery charge capacity (can store ten times more charge as compared to graphite anodes), but some challenges remain in terms of volume expansion during cycling, low electrical conductivity, and instability of the SEI (solid electrolyte interphase) layer caused by repeated volume changes of the Si material.<p>A solid-state battery is made of cathode, anode and electrolyte (Fig. 1). This type of battery doesn’t use liquid state electrolyte, so it tends to avoid the issues associated with leakage of electrolyte and ignition/explosion. Recently, silicon has been used as an anode material to improve the battery charge capacity (can store ten times more charge as compared to graphite anodes), but some challenges remain in terms of volume expansion during cycling, low electrical conductivity, and instability of the SEI (solid electrolyte interphase) layer caused by repeated volume changes of the Si material.</p> <p>For the purpose of observing structure and shape of anode silicon grains (charged 90 %), a TEM sample was prepared under air isolated condition.</p> <p style="text-align: center;"><img alt="" class="img-responsive" src="https://jeolusa.s3.amazonaws.com/resources_eo/Air-Isolated%20Sampling%20of%20Solid-State%20Battery%20f1.jpg?AWSAccessKeyId=AKIAQJOI4KIAZPDULHNL&Expires=2145934800&Signature=IgiweGxq3nmzL8xZbprIaEtDD7Q%3D" /><br /> Fig. 1. The schematic of a structure of solid-state battery and charge/discharge</p> <h3>TEM Sampling Process under Air-Isolated Condition</h3> <p>A lithium battery sample was made under air-isolated conditions from start of preparation to observation to avoid reaction with air and potential oxidation (Fig. 2). For the sample transfer between instruments, a transfer vessel and slide cover holder were used. For the TEM sample preparation by FIB, an in-chamber manipulator (OmniProbe350, Oxford Instruments) was used. A cross section was first prepared by Ar-ion beam Cross-section Polisher (CP) to expose a large area showing the inner grain part of the battery, and subsequently decide the FIB processing area. JEOL air-isolated preparation methodology allows movement between all steps - CP process, SEM observation/analysis and TEM sampling - by using just one sample holder.</p> <p style="text-align: center;"><img alt="" class="img-responsive" src="https://jeolusa.s3.amazonaws.com/resources_eo/Air-Isolated%20Sampling%20of%20Solid-State%20Battery%20f2.jpg?AWSAccessKeyId=AKIAQJOI4KIAZPDULHNL&Expires=2145934800&Signature=463RIpHM64TJhkRUaai5MRiXzMQ%3D" /><br /> Fig. 2. Process of FIB TEM sample preparation under air-isolated condition</p> <h3>TEM sample preparation from CP-processed surface</h3> <p>A TEM sample of silicon anode material of charged all solid-state battery was made under air-isolated process which is shown in Fig. 2. Fig. 3 shows backscatter electron compositional (BEC) image and EDS map. This surface was prepared by CP. FIB process used this CP surface for choosing the correct position on the anode grain to subsequently prepare a thin TEM lamella (Fig. 4).</p> <p style="text-align: center;"><img alt="" class="img-responsive" src="https://jeolusa.s3.amazonaws.com/resources_eo/Air-Isolated%20Sampling%20of%20Solid-State%20Battery%20f3.jpg?AWSAccessKeyId=AKIAQJOI4KIAZPDULHNL&Expires=2145934800&Signature=SChYDHAxOpSj3OX1xiFhS%2FOsDbk%3D" /><br /> Fig. 3 SEM BEC image (left) and EDS map (right) of CP processed surface. The silicon grain position was found from SEM BEC image and EDS map. TEM lamella position is identified by the red line.</p> <p style="text-align: center;"><img alt="" class="img-responsive" src="https://jeolusa.s3.amazonaws.com/resources_eo/Air-Isolated%20Sampling%20of%20Solid-State%20Battery%20f4.jpg?AWSAccessKeyId=AKIAQJOI4KIAZPDULHNL&Expires=2145934800&Signature=D%2B%2FRGH4NFe1fBUF5aXwaW0Al%2FHo%3D" /><br /> Fig. 4 Images during FIB process of making TEM sample. Sample block (left) and TEM lamella (right). The sample block was made at the silicon grain position (left), and it was fixed to the FIB grid by using OmniProbe350, Oxford Instruments. After that, it was made into a lamella sample for TEM observation (right).</p> <h3>TEM observation and confirmation of air-isolated condition</h3> <p>Fig. 5 shows BF-STEM image of TEM sample. The red line encompasses the targeted silicon grain. After TEM observation, the sample was exposed to air, causing a change due to oxidation (Fig. 6). This result indicates that the entire sampling processes was indeed performed under air isolated condition.</p> <p style="text-align: center;"><img alt="" class="img-responsive" src="https://jeolusa.s3.amazonaws.com/resources_eo/Air-Isolated%20Sampling%20of%20Solid-State%20Battery%20f5.jpg?AWSAccessKeyId=AKIAQJOI4KIAZPDULHNL&Expires=2145934800&Signature=ZKA9Fu9WsyMwI59pz4Gl0%2BpdvWQ%3D" /><br /> Fig. 5 BF-STEM image. There were three layers in silicon grain inner part from the center to outside.<br /> It is speculated that the center part was a silicon single crystal, and the lithium density increases from the center to the outside.</p> <p style="text-align: center;"><img alt="" class="img-responsive" src="https://jeolusa.s3.amazonaws.com/resources_eo/Air-Isolated%20Sampling%20of%20Solid-State%20Battery%20f6.jpg?AWSAccessKeyId=AKIAQJOI4KIAZPDULHNL&Expires=2145934800&Signature=IjxZvQdv2nAZIaYlln8qk%2BqBZZQ%3D" /><br /> Fig. 6 BE-STEM image after exposed to air.<br /> After observation, the sample was exposed to air. Then retaken TEM image shows that it has reacted with air.</p> <p style="text-align: right;"><em>Sample provider: Prof. Atsunori Matsuda Toyohashi Univ. of Technology</em></p> Atomic resolution structure results from the JEOL 200 kV CRYO ARM™ TEMhttps://www.jeolusa.com/RESOURCES/Electron-Optics/Documents-Downloads/atomic-resolution-structure-results-from-the-jeol-200-kv-cryo-arm-temCRYO ARM™ 200Thu, 10 Dec 2020 11:12:35 GMTHigh resolution structure determination by electron cryo-microscopy (cryoEM) and Single Particle Analysis (SPA) has progressed to the point where structures can be determined routinely to better than 3Å on a 300 kV microscope. Pioneering efforts have shown that similar results can also be achieved on 200 kV platforms. Similarly, efforts are underway to allow for a structure determination within a single day or even less. Here, we show results from Merk et al. at NIH from the JEOL CRYO ARM™ 200 obtained on beta-galactosidase at 1.8Å resolution1. The 3D map shows surprising details in the map reflecting the high resolution quality of the data.<p>High resolution structure determination by electron cryo-microscopy (cryoEM) and Single Particle Analysis (SPA) has progressed to the point where structures can be determined routinely to better than 3Å on a 300 kV microscope. Pioneering efforts have shown that similar results can also be achieved on 200 kV platforms. Similarly, efforts are underway to allow for a structure determination within a single day or even less. Here, we show results from Merk et al. at NIH from the JEOL CRYO ARM™ 200 obtained on beta-galactosidase at 1.8Å resolution1. The 3D map shows surprising details in the map reflecting the high resolution quality of the data.</p> Atomic resolution structure results from the JEOL 300 kV CRYO ARM™ TEMhttps://www.jeolusa.com/RESOURCES/Electron-Optics/Documents-Downloads/atomic-resolution-structure-results-from-the-jeol-300-kv-cryo-arm-temCRYO ARM™ 300Thu, 10 Dec 2020 11:15:12 GMTHigh resolution structure determination by electron cryo-microscopy (cryoEM) and Single Particle Analysis (SPA) has progressed to the point where structures can be determined routinely to better than 2Å on a 300 kV microscope. Here, we show results from Kato et al. at1 Osaka University from the JEOL CRYO ARM™ 300 installed at SPring8 (Riken, Japan), that was obtained on mouse heavy chain apo-ferritin at 1.5Å resolution. The 3D map shows surprising details in the map reflecting the high resolution quality of the data.<p>High resolution structure determination by electron cryo-microscopy (cryoEM) and Single Particle Analysis (SPA) has progressed to the point where structures can be determined routinely to better than 2Å on a 300 kV microscope. Here, we show results from Kato et al. at1 Osaka University from the JEOL CRYO ARM™ 300 installed at SPring8 (Riken, Japan), that was obtained on mouse heavy chain apo-ferritin at 1.5Å resolution. The 3D map shows surprising details in the map reflecting the high resolution quality of the data.</p> Atomic resolution structures of biological macromolecules using microED on JEOL TEMshttps://www.jeolusa.com/RESOURCES/Electron-Optics/Documents-Downloads/atomic-resolution-structures-of-biological-macromolecules-using-microed-on-jeol-temsJEM-ARM300F2 GRAND ARM™2Wed, 09 Dec 2020 13:23:39 GMTMicro electron diffraction, or microED, is a technique aimed at solving structures of biological macromolecules by electron diffraction. Barn-storming work by the group from Prof. Gonen showed the impressive impact and promise of this technique1. The technique borrows from X-ray crystallography in that precession techniques are used for data collection and that much of the well-established software for solving structures by X-ray crystallography can be used for microED. However, it differs in a fundamental way in that electrons are used, which, owing to the substantially larger scattering cross-section of electrons with biological matter, means much smaller crystals can be used.<h3><strong>Also see:</strong> <a href="/RESOURCES/Electron-Optics/Documents-Downloads/jeol-cryo-arm-achieves-top-resolution">JEOL CRYO ARM™ Achieves Top Resolution August 2023</a>.</h3> <p>Micro electron diffraction, or microED, is a technique aimed at solving structures of biological macromolecules by electron diffraction. Barn-storming work by the group from Prof. Gonen showed the impressive impact and promise of this technique<sup>1</sup>. The technique borrows from X-ray crystallography in that precession techniques are used for data collection and that much of the well-established software for solving structures by X-ray crystallography can be used for microED. However, it differs in a fundamental way in that electrons are used, which, owing to the substantially larger scattering cross-section of electrons with biological matter, means much smaller crystals can be used. Thus, crystals the size of a few microns are perfectly adequate for microED. The current crop of cameras and levels of microscope automation allow for the rapid collection of a full data set in a matter of minutes. By combining microED with the principle steps of SPA as employed in SerialEM<sup>2</sup>, a single overnight run can yield hundreds of microED data sets<sup>3</sup>. Note that because diffraction data is collected, the acquisition process is immune to mechanical vibrations and drift; only a shift caused by poor eucentricity that would move the crystal out of the selected aperture field of view would impact the data collection.</p> <p>MicroED can be applied on every new electron microscope in the JEOL TEM line-up. Precise control of the goniometer’s tilting speed compatible with microED is standard and can be set through either SerialEM or Recorder, the latter being part of JEOL’s TEMography package (SIF). SerialEM was first introduced on a JEOL JEM-2200FS in 2006 and is now fully compatible with all of JEOL’s electron microscopes. A record-breaking 1.34Å structure of apo-ferritin was recently obtained from JEOL’s latest generation of cryo-TEMs, the CRYO ARM™, a microscope available at 200 and 300 kV with a cold field emission gun and in-column energy filter<sup>4</sup>.</p> <p>This application note reports on microED results obtained on a JEOL JEM-F200 outfitted with a cold FEG and a Gatan Elsa holder to keep the sample at -177ºC for the sake of reducing radiation damage<sup>5</sup>. Figure 1 shows a gallery of principle checks whether crystals of L-histidine will deliver high-resolution diffraction patterns for microED. The micro-crystals are deposited on ultrathin carbon films overlaid on lacey carbon. </p> <p><strong><img alt="" class="img-responsive" src="https://jeolusa.s3.amazonaws.com/resources_eo/647/microED%2001.png?AWSAccessKeyId=AKIAQJOI4KIAZPDULHNL&Expires=2145934800&Signature=ckExexcwf58QyC63uGcNf%2F9BCLM%3D" /><br /> Fig. 1:</strong> Diffraction images of L-histidine in defocused diffraction mode without (left) and with (middle) a selected area aperture inserted showing the L-histidine crystals. The focused diffraction pattern is shown on the right showing strong Bragg reflections.</p> <p>Figure 2 shows several frames from one of the microED data sets acquired under continuous rotation at 0.25º/sec from -30º to +30º. The beam stopper is used to prevent the central, undiffracted beam from hitting the camera’s sensor.</p> <p><strong><img alt="" class="img-responsive" src="https://jeolusa.s3.amazonaws.com/resources_eo/647/microED%20fig2.jpg?AWSAccessKeyId=AKIAQJOI4KIAZPDULHNL&Expires=2145934800&Signature=xbJWg6zXYR8v2iN7aMQk16E4MIM%3D" /><br /> Fig. 2:</strong> Selected focused diffraction patterns from -30º to +30º microED series acquired at 0.25º/sec. Total dose was 2.4 el/Å2. </p> <p>After unpacking the movies, the individual frames are processed using standard X-ray crystallographic packages – SIR2019 and SHELXL. Table 1 shows the experimental results whereas Figure 3 shows the structures calculated from the data using direct methods. The refined map after running SHELXL shows clearly the expected atoms in the structure.</p> <table class="table"> <tbody> <tr> <th colspan="2">Table 1: experimental results</th> </tr> <tr> <td>Molecular weight (Da)</td> <td>155.16</td> </tr> <tr> <td>Measurement temperature (K)</td> <td>96</td> </tr> <tr> <td>Space group</td> <td>P212121</td> </tr> <tr> <td><em>a, b, c</em> (Å)</td> <td>5.27, 7.44, 18.99</td> </tr> <tr> <td># of reflections</td> <td>417</td> </tr> <tr> <td>R factor (%)</td> <td>19.81</td> </tr> </tbody> </table> <p><strong><img alt="" class="img-responsive" src="https://jeolusa.s3.amazonaws.com/resources_eo/647/microED%20fig3.jpg?AWSAccessKeyId=AKIAQJOI4KIAZPDULHNL&Expires=2145934800&Signature=jDuC0Wm8aGey%2FIMADEMFbw3PoyE%3D" /><br /> Fig 3:</strong> Structure of L-histidine after initial direct method calculation using SIR2019 (left) and after refinement using SHELXL (middle) with the structure formula shown right.</p> <p>Conclusion: Micro electron diffraction data can be readily acquired using a JEOL cryo-electron microscope using relatively shallow tilt series. The resulting data can immediately be processed using available pipe lines for X-ray diffraction data enabling rapid structure determination of small molecules by electron diffraction.</p> <p>Contact your local JEOL representative to learn more about JEOL TEMs and microED using SIF Recorder or SerialEM.</p> <h3>References:</h3> <ol> <li>B.L. Nannenga et al., Nature Methods 11 (2014) 927.</li> <li>D.N. Mastronarde, J. Struct. Biol. 152 (2005) 36.</li> <li>M.J. de la Cruz et al., Ultramicroscopy 201 (2019) 77.</li> <li>M. Tegunov et al. (2020) <a href="https://doi.org/10.1101/2020.06.05.136341" target="_blank">https://doi.org/10.1101/2020.06.05.136341</a>.</li> <li>Guzmán-Afonso et al., Nature Comm 10 (2019) 3537.</li> </ol> CRYO ARM Bibliographyhttps://www.jeolusa.com/RESOURCES/Electron-Optics/Documents-Downloads/cryo-arm-bibliographyCRYO ARM™ 300Wed, 18 Jan 2023 10:32:55 GMTCRYO ARM Bibliography<p style="margin-bottom:11px"><span style="font-size:11pt"><span style="line-height:107%"><span style="font-family:Calibri,sans-serif"><b><span style="font-size:12.0pt"><span style="background:white"><span style="line-height:107%"><span style="font-family:"Times New Roman",serif"><span style="color:#212121">JEOL CRYO ARM 200 - BIBLIOGRAPHY</span></span></span></span></span></b></span></span></span></p> <ol> <li><span style="font-size:11pt"><span style="line-height:107%"><span style="font-family:Calibri,sans-serif"><span style="font-size:12.0pt"><span style="line-height:107%"><span style="font-family:"Times New Roman",serif"></span></span></span><span style="font-size:12.0pt"><span style="background:white"><span style="line-height:107%"><span style="font-family:"Times New Roman",serif"><span style="color:#212121">Young, Lucy C et al. “Destabilizing NF1 variants act in a dominant negative manner through neurofibromin dimerization.” Proceedings of the National Academy of Sciences of the United States of America vol. 120,5 (2023): e2208960120. doi:10.1073/pnas.2208960120</span></span></span></span></span></span></span></span></li> <li><span style="font-size:11pt"><span style="line-height:107%"><span style="font-family:Calibri,sans-serif"><span style="font-size:12.0pt"><span style="line-height:107%"><span style="font-family:"Times New Roman",serif"></span></span></span><span style="font-size:12.0pt"><span style="background:white"><span style="line-height:107%"><span style="font-family:"Times New Roman",serif"><span style="color:#212121">Pöll, Gisela et al. “Impact of the yeast S0/uS2-cluster ribosomal protein rpS21/eS21 on rRNA folding and the architecture of small ribosomal subunit precursors.” PloS one vol. 18,3 e0283698. 30 Mar. 2023, doi:10.1371/journal.pone.0283698</span></span></span></span></span></span></span></span></li> <li><span style="font-size:11pt"><span style="line-height:107%"><span style="font-family:Calibri,sans-serif"><span style="font-size:12.0pt"><span style="line-height:107%"><span style="font-family:"Times New Roman",serif"></span></span></span><span style="font-size:12.0pt"><span style="background:white"><span style="line-height:107%"><span style="font-family:"Times New Roman",serif"><span style="color:#212121">Katsyv, Alexander et al. “Molecular Basis of the Electron Bifurcation Mechanism in the [FeFe]-Hydrogenase Complex HydABC.” Journal of the American Chemical Society vol. 145,10 (2023): 5696-5709. doi:10.1021/jacs.2c11683</span></span></span></span></span></span></span></span></li> <li><span style="font-size:11pt"><span 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JEOL released two electron cryo-microscopes in 2017 specifically designed for automated and unattended, continuous operation at 200 and 300 kV, the CRYO ARM™ series. A recent update on both type of CRYO ARMs has the potential of increasing the throughput well beyond the current limit of 20,000 images/day, namely north of 50,000 images/day as well as extending the resolution to nearly true atomic resolution, i.e. 1.2Å.<h3>Introduction</h3> <p>Cryo-EM has seen an enormous increase in capabilities and potential in recent years owing to a number of technological advances, e.g. direct detector devices and improved scope automation. JEOL released two electron cryo-microscopes in 2017 specifically designed for automated and unattended, continuous operation at 200 and 300 kV, the CRYO ARM™ series. A recent update on both type of CRYO ARMs has the potential of increasing the throughput well beyond the current limit of 20,000 images/day, namely north of 50,000 images/day as well as extending the resolution to nearly true atomic resolution, i.e. 1.2Å.</p> <h3>Minimum Fringe Illumination and Aberration Free Image Shift</h3> <p>In order to increase the throughput to current levels two techniques have been critically important. One is the reduction of Fresnel fringes from the CL apertures when matching the beam diameter to the field of view of the camera. JEOL has introduced Köhler illumination on the CRYO ARM series microscopes to achieve this (Fig. 1). For the CRYO ARM™ 200 this results in Minimum Fringe Illumination, whereas on the CRYO ARM™ 300 this is implemented as Zero-Fringe Illumination. The second technique is the implementation of the Aberration Free Image Shift, where a narrow parallel beam gets steered inside the hole of a Quantifoil specimen using beam shift and image shift. This approach can be extended to cover multiple adjacent holes with an optional coma correction. (Fig. 1).</p> <p style="text-align: center;"><img alt="" class="img-responsive" src="https://jeolusa.s3.amazonaws.com/resources_eo/CRYO%20ARM%E2%84%A2%20series%20microscopes%20for%20cryo-EM%20fig%201.jpg?AWSAccessKeyId=AKIAQJOI4KIAZPDULHNL&Expires=2145934800&Signature=5aZGhmREA2XTNv%2BXRh5E8NehXPs%3D" /><br /> <strong>Fig. 1:</strong> Minimum (or Zero) Fringe Illumination implemented on the JEOL CRYO ARM™ series electron cryo-microscopes. Using Köhler illumination the Fresnel fringes  arising from the CL apertures (left) can minimized allowing the beam diameter to be matched to the field of view of the detector without sacrificing usable area (middle left). Using beam shift and image shift  with an optional correction for coma, the narrow, parallel beam can be steered inside a Quantifoil hole to create an intra-hole multi-record (middle right). Extending this to adjacent creates the inter-hole multi-record, here depicted as a 7x7x8 pattern (right).</p> <h3>Long-term stability</h3> <p>To enable long running imaging sessions two other areas were improved, i.e. stability of the Cold Field Emission gun (CFEG) and the Omega-style in-column energy filter. The CFEG requires periodic flashing to reset the emission to 100%. The second-generation CFEG can now operate for an entire day without requiring this (Fig. 2). If flashing is needed, remote control software will interrupt the imaging run, flash the tip and continue, a process which takes < 1 min. No adjustment of coma is required. The stability of the energy filter has also been dramatically improved. Both these improvements not only dramatically increase run times for imaging, but also minimize the amount of time users need to spend with the microscope resulting in better throughput. Finally, tuning of the Omega filter is now done automatically.</p> <p style="text-align: center;"><img alt="" class="img-responsive" src="https://jeolusa.s3.amazonaws.com/resources_eo/CRYO%20ARM%E2%84%A2%20series%20microscopes%20for%20cryo-EM%20fig%202.jpg?AWSAccessKeyId=AKIAQJOI4KIAZPDULHNL&Expires=2145934800&Signature=kY3H55bLd8LdD2oXX8GmRgVz35Q%3D" /><br /> <strong>Fig. 2:</strong> Improvement of the CFEG reveals minimal requirements for flashing the tip (left). The Omega-style energy filter now shows minimal drift of the Zero Loss peak (right).</p> <h3>Interoperability</h3> <p>In order to optimize inter-operability between JEOL and other brands of cryo microscopes it is imperative to be able to transfer frozen-hydrated grids between microscopes. From fig. 3 we can glean that reverse transfers work. Minimal ice contamination is present on the sample after the reverse and subsequent second cryo-transfer.</p> <p style="text-align: center;"><img alt="" class="img-responsive" src="https://jeolusa.s3.amazonaws.com/resources_eo/CRYO%20ARM%E2%84%A2%20series%20microscopes%20for%20cryo-EM%20fig%203.jpg?AWSAccessKeyId=AKIAQJOI4KIAZPDULHNL&Expires=2145934800&Signature=R9bfBluKhgsOkEjeIdVWvGuuXmc%3D" /><br /> <strong>Fig. 3:</strong> Results after first cryo-transfer (left) and after a reverse and subsequent cryo-transfer into a CRYO ARM 300 II (right). Minimal ice contamination accumulates during the second transfer.</p> <p>Figure 4 shows the main cartridges used in the CRYO ARM™ series electron cryo-microscopes for imaging in SPA workflows and single-axis tomography. For complete inter-operability with non-JEOL brand cryo-microscopes JEOL have developed a cartridge that is compatible with AG-clipped grids (Fig. 4). Whereas the standard cartridge uses a c-clip to secure the grid, the AG-cartridge employs a sliding cover.</p> <p style="text-align: center;"><img alt="" class="img-responsive" src="https://jeolusa.s3.amazonaws.com/resources_eo/CRYO%20ARM%E2%84%A2%20series%20microscopes%20for%20cryo-EM%20fig%204.jpg?AWSAccessKeyId=AKIAQJOI4KIAZPDULHNL&Expires=2145934800&Signature=l47z76cVyHjy%2F9YfjmxczogxLjc%3D" /><br /> <strong>Fig. 4:</strong> Standard cartridges for the CRYO ARM™ series microscopes (left) and the AG-compatible cartridges (right).</p> <p>Figure 5 shows results obtained from apo-ferritin using an AG-compatible cartridge after only 30 minutes of data collection. The grid square image does not show significantly larger amounts of ice-contamination. The 3D map was obtained using only 150 micrographs and from the FSC curve can be seen to have a resolution of 2Å.</p> <p style="text-align: center;"><img alt="" class="img-responsive" src="https://jeolusa.s3.amazonaws.com/resources_eo/CRYO%20ARM%E2%84%A2%20series%20microscopes%20for%20cryo-EM%20fig%205.jpg?AWSAccessKeyId=AKIAQJOI4KIAZPDULHNL&Expires=2145934800&Signature=c9zXw6qCozjS6zagqec6D%2BEOh8Y%3D" /><br /> <strong>Fig. 5:</strong> Results from apo-ferritin sample in an AG-compatible cartridge.</p> <h3>Throughput challenge I</h3> <p>Figure 6 shows results from an experiment attempted to determine how much data is needed to break 1.5Å resolution using apo-ferritin mounted in a standard cartridge. On the CRYO ARM™ 300 II this took only a half hour of data collection. In fact, the core of the particle shows a resolution of better than 1.5Å strongly suggesting that a well-behaved sample can yield usable data in about an hour. Whereas elsewhere it has been suggested that screening ought to be done using a dedicated tool, these results suggest that not only can screening be done effectively on a CRYO ARM™ 300 II -note that sample transfer and retrieval does NOT affect already loaded samples - but these results also give a clear indication how well behaved the sample is and thus a good indication how far the data can be pushed.</p> <p style="text-align: center;"><img alt="" class="img-responsive" src="https://jeolusa.s3.amazonaws.com/resources_eo/CRYO%20ARM%E2%84%A2%20series%20microscopes%20for%20cryo-EM%20fig%206.jpg?AWSAccessKeyId=AKIAQJOI4KIAZPDULHNL&Expires=2145934800&Signature=j2DZ8UGVE9R8mevZFI%2F2%2FtVX6sU%3D" /><br /> <strong>Fig. 6:</strong> Results from apo-ferritin obtained to determine the amount of data/time needed to break 1.5Å. The results were obtained after only 30 minutes.</p> <h3>Throughput challenge II</h3> <p>Figure 7 shows results from pushing the data collection and processing as far as it would go within reasonable time frames. A total of 7500 micrographs were collected from which 500,000 particles were selected. Processing yielded a 1.29Å close to the limits discussed by Yip et al. (Nature 587 (2020) 157. The CFEG clearly gives data that is extremely close to be officially called atomic resolution, but in a standard package in for a price considerably less than the other-brand cryo-microscopes.<br /> Final note: all the data collection is done using serialEM employing a multi-record scheme with a 5x5x4 pattern imaged on a K3 camera.</p> <p style="text-align: center;"><img alt="" class="img-responsive" src="https://jeolusa.s3.amazonaws.com/resources_eo/CRYO%20ARM%E2%84%A2%20series%20microscopes%20for%20cryo-EM%20fig%207.jpg?AWSAccessKeyId=AKIAQJOI4KIAZPDULHNL&Expires=2145934800&Signature=CPy9Tw23Updbd3Vj9vqU5I%2F27PM%3D" /><br /> <strong>Fig. 7:</strong> Results from apo-ferritin sample. Final map is at 1.29Å resolution.</p> <h3>Teaser</h3> <p>Ask us about our CRYO ARM™ 200 II electron cryo-microscope. Also, ask us about our uptime guarantee.</p> <div class="alert alert-info"> <ol> <li> <h4>The JEOL CRYO ARM™ series electron cryo-microscopes enable researchers to get <strong>fast results.</strong></h4> </li> <li> <h4>The JEOL CRYO ARM™ series electron cryo-microscopes allow researchers to get <strong>nearly atomic resolution data.</strong></h4> </li> <li> <h4>The JEOL CRYO ARM™ series enjoys impressively <strong>robust usage times</strong> of more than a year with single interruption.</h4> </li> </ol> </div> <hr /> <p style="text-align: center;"><u>Jaap Brink</u><sup>1</sup>, Taku Fukumura<sup>1</sup>, Tom Isabell<sup>1</sup>, Sohei Motoki<sup>2</sup>, Isamu Ishikawa<sup>2</sup>, Yoshi Okhura<sup>2</sup><br /> <small><sup>1</sup>JEOL USA, Inc., Peabody, 01960 MA. USA, <sup>2</sup>JEOL Ltd, 3-1-2 Musashino, Akishima, Tokyo 196-8558, JAPAN</small></p>