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Abstract
The new generation of direct electron detectors has been a major contributor to the recent resolution revolution in cryo-electron microscopy. Optimal use of these new cameras using automated data collection software is critical for high-throughput near-atomic resolution cryo-electron microscopy research. We present an overview of the practical aspects of automated data collection in the context of this new generation of direct detectors, highlighting the differences, challenges, and opportunities the new detectors provide compared to the previous generation of data acquisition media.
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Affiliation(s)
- A Cheng
- Simons Electron Microscopy Center, New York Structural Biology Center, The National Resource for Automated Molecular Microscopy, New York, NY, United States
| | - Y Z Tan
- Simons Electron Microscopy Center, New York Structural Biology Center, The National Resource for Automated Molecular Microscopy, New York, NY, United States; Columbia University, New York, NY, United States
| | - V P Dandey
- Simons Electron Microscopy Center, New York Structural Biology Center, The National Resource for Automated Molecular Microscopy, New York, NY, United States
| | - C S Potter
- Simons Electron Microscopy Center, New York Structural Biology Center, The National Resource for Automated Molecular Microscopy, New York, NY, United States; Columbia University, New York, NY, United States
| | - B Carragher
- Simons Electron Microscopy Center, New York Structural Biology Center, The National Resource for Automated Molecular Microscopy, New York, NY, United States; Columbia University, New York, NY, United States.
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2
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Baudoux AC, Hendrix RW, Lander GC, Bailly X, Podell S, Paillard C, Johnson JE, Potter CS, Carragher B, Azam F. Genomic and functional analysis of Vibrio phage SIO-2 reveals novel insights into ecology and evolution of marine siphoviruses. Environ Microbiol 2012; 14:2071-86. [PMID: 22225728 PMCID: PMC3338904 DOI: 10.1111/j.1462-2920.2011.02685.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We report on a genomic and functional analysis of a novel marine siphovirus, the Vibrio phage SIO-2. This phage is lytic for related Vibrio species of great ecological interest including the broadly antagonistic bacterium Vibrio sp. SWAT3 as well as notable members of the Harveyi clade (V.harveyi ATTC BAA-1116 and V.campbellii ATCC 25920). Vibrio phage SIO-2 has a circularly permuted genome of 80598 bp, which displays unusual features. This genome is larger than that of most known siphoviruses and only 38 of the 116 predicted proteins had homologues in databases. Another divergence is manifest by the origin of core genes, most of which share robust similarities with unrelated viruses and bacteria spanning a wide range of phyla. These core genes are arranged in the same order as in most bacteriophages but they are unusually interspaced at two places with insertions of DNA comprising a high density of uncharacterized genes. The acquisition of these DNA inserts is associated with morphological variation of SIO-2 capsid, which assembles as a large (80 nm) shell with a novel T=12 symmetry. These atypical structural features confer on SIO-2 a remarkable stability to a variety of physical, chemical and environmental factors. Given this high level of functional and genomic novelty, SIO-2 emerges as a model of considerable interest in ecological and evolutionary studies.
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Affiliation(s)
- A-C Baudoux
- Scripps Institution of Oceanography, Marine Biology Research Division, University of California San Diego, La Jolla, CA 92093, USA.
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3
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Abstract
BACKGROUND All AKR/J mice have a subtle defect that involves malformation of the central portion of hair fibres that is best visualized under white and polarized light microscopy. AIMS This study sought to characterize the clinical and ultrastructural features of the hair interior defect (HID) phenotype and to determine the chromosomal localization of the hid mutant gene locus. METHODS White and polarized light microscopy combined with scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were used to characterize the HID phenotype. Complementation testing and gene-linkage studies were performed to map the locus. RESULTS Using SEM, the hair-fibre structure on the surface was found to be similar to hairs obtained from normal BALB/cByJ+/+and C57BL/6 J+/+mice. There were also no differences in sulphur content. TEM revealed degenerative changes in the medulla similar to that seen by light microscopy. This autosomal recessive mutation is called HID (locus symbol: hid). We mapped the hid locus to the distal end of mouse chromosome 1. No genes reported to cause skin or hair abnormalities are known to be within this interval except for the lamin B receptor (Lbr), which had been excluded previously as the cause of the hid phenotype in AKR/J mice. CONCLUSION A potentially novel gene or known gene with a novel phenotype resides within this interval, which may shed light on human diseases with defects in the inner structure of the hair fibre.
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Affiliation(s)
- K A Giehl
- Department of Dermatology, Ludwig Maximilian University, Munich, Germany
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4
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Decker KLM, Potter CS, Bebout BM, Marais DJD, Carpenter S, Discipulo M, Hoehler TM, Miller SR, Thamdrup B, Turk KA, Visscher PT. Mathematical simulation of the diel O, S, and C biogeochemistry of a hypersaline microbial mat. FEMS Microbiol Ecol 2005; 52:377-95. [PMID: 16329922 DOI: 10.1016/j.femsec.2004.12.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2004] [Revised: 09/16/2004] [Accepted: 12/08/2004] [Indexed: 11/18/2022] Open
Abstract
The creation of a mathematical simulation model of photosynthetic microbial mats is important to our understanding of key biogeochemical cycles that may have altered the atmospheres and lithospheres of early Earth. A model is presented here as a tool to integrate empirical results from research on hypersaline mats from Baja California Sur (BCS), Mexico into a computational system that can be used to simulate biospheric inputs of trace gases to the atmosphere. The first version of our model, presented here, calculates fluxes and cycling of O(2), sulfide, and dissolved inorganic carbon (DIC) via abiotic components and via four major microbial guilds: cyanobacteria (CYA), sulfate reducing bacteria (SRB), purple sulfur bacteria (PSB) and colorless sulfur bacteria (CSB). We used generalized Monod-type equations that incorporate substrate and energy limits upon maximum rates of metabolic processes such as photosynthesis and sulfate reduction. We ran a simulation using temperature and irradiance inputs from data collected from a microbial mat in Guerrero Negro in BCS (Mexico). Model O(2), sulfide, and DIC concentration profiles and fluxes compared well with data collected in the field mats. There were some model-predicted features of biogeochemical cycling not observed in our actual measurements. For instance, large influxes and effluxes of DIC across the MBGC mat boundary may reveal previously unrecognized, but real, in situ limits on rates of biogeochemical processes. Some of the short-term variation in field-collected mat O(2) was not predicted by MBGC. This suggests a need both for more model sensitivity to small environmental fluctuations for the incorporation of a photorespiration function into the model.
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Affiliation(s)
- K L M Decker
- Division of Science and Environmental Policy, California State University, Monterey Bay, Mail Stop 242-4, Moffett Field, CA 94035, USA.
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Amthor JS, Chen JM, Clein JS, Frolking SE, Goulden ML, Grant RF, Kimball JS, King AW, McGuire AD, Nikolov NT, Potter CS, Wang S, Wofsy SC. Boreal forest CO2exchange and evapotranspiration predicted by nine ecosystem process models: Intermodel comparisons and relationships to field measurements. ACTA ACUST UNITED AC 2001. [DOI: 10.1029/2000jd900850] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
Since the foundation for the three-dimensional image reconstruction of helical objects from electron micrographs was laid more than 30 years ago, there have been sustained developments in specimen preparation, data acquisition, image analysis, and interpretation of results. However, the boxing of filaments in large numbers of images--one of the critical steps toward the reconstruction at high resolution--is still constrained by manual processing even though interactive interfaces have been built to aid the tedious and sometimes inaccurate boxing process. This article describes an accurate approach for automated detection of filamentous structures in low-contrast images acquired in defocus pairs using cryoelectron microscopy. The performance of the approach has been evaluated across various magnifications and at a series of defocus values using tobacco mosaic virus (TMV) preserved in vitreous ice as a test specimen. By integrating the proposed approach into our automated data acquisition and reconstruction system, we are now able to generate a three-dimensional map of TMV to approximately 10-A resolution within 24 h of inserting the specimen grid into the microscope.
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Affiliation(s)
- Y Zhu
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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7
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Rouiller I, Pulokas J, Butel VM, Milligan RA, Wilson-Kubalek EM, Potter CS, Carragher BO. Automated image acquisition for single-particle reconstruction using p97 as the biological sample. J Struct Biol 2001; 133:102-7. [PMID: 11472082 DOI: 10.1006/jsbi.2001.4367] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have used Leginon, a fully automatic system capable of acquiring cryo-electron micrographs, to collect data of single particles, specifically of the AAA ATPase p97. The images were acquired under low-dose conditions and required no operator intervention other than the initial setup and periodic refilling of the cold-stage dewar. Each image was acquired at two different defocus values. Two-dimensional projection maps of p97 were calculated from these data and compared to results previously obtained using the conventional manual data collection methods to film. The results demonstrate that Leginon performs as well as an experienced microscopist for the acquisition of single-particle data. The general advantages of automation are discussed.
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Affiliation(s)
- I Rouiller
- Department of Cell Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, USA
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Carragher B, Kisseberth N, Kriegman D, Milligan RA, Potter CS, Pulokas J, Reilein A. Leginon: an automated system for acquisition of images from vitreous ice specimens. J Struct Biol 2000; 132:33-45. [PMID: 11121305 DOI: 10.1006/jsbi.2000.4314] [Citation(s) in RCA: 226] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have developed a system to automatically acquire cryo-electron micrographs. The system is designed to emulate all of the decisions and actions of a highly trained microscopist in collecting data from a vitreous ice specimen. These include identifying suitable areas of vitreous ice at low magnification, determining the presence and location of specimen on the grid, automatically adjusting imaging parameters (focus, astigmatism) under low-dose conditions, and acquiring images at high magnification to either film or a digital camera. This system is responsible for every aspect of image acquisition and can run unattended, other than requiring periodic refilling of the cryogens, for over 24 h. The system has been tested out on a variety of specimens that represent typical challenges in the field of cryo-electron microscopy. The results show that the overall performance of the system is equivalent to that of an experienced microscopist.
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Affiliation(s)
- B Carragher
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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9
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Abstract
We have developed a method to improve the accuracy for absolute relocation of a target specimen using the goniometer on a Philips transmission electron microscope. We have achieved this by characterizing the performance of the Philips compustage, modeling its behavior, and using this model to calculate the goniometer movements required for accurate target relocation. This resulted in a 10-fold improvement in the positioning accuracy of the goniometer.
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Affiliation(s)
- J Pulokas
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois, 61801, USA
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Potter CS, Chu H, Frey B, Green C, Kisseberth N, Madden TJ, Miller KL, Nahrstedt K, Pulokas J, Reilein A, Tcheng D, Weber D, Carragher B. Leginon: a system for fully automated acquisition of 1000 electron micrographs a day. Ultramicroscopy 1999; 77:153-61. [PMID: 10406132 DOI: 10.1016/s0304-3991(99)00043-1] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We have developed a system to automatically acquire large numbers of acceptable quality images from specimens of negatively stained catalase, a biological protein which forms crystals. In this paper we will describe the details of the system architecture and analyze the performance of the system as compared to a human operator. The ultimate goal of the system if to automate the process of acquiring cryo-electron micrographs.
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Affiliation(s)
- C S Potter
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign 61801, USA.
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11
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Abstract
JavaScope is a Web-based java applet that implements an "exploration/browser" tool for operating a Philips CM200 transmission electron microscope and viewing digital images remotely. The primary use of the application is as a collaborative tool for remote consultations.
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Affiliation(s)
- N Kisseberth
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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12
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Kisseberth N, Whittaker M, Weber D, Potter CS, Carragher B. emScope: A Tool Kit for Control and Automation of a Remote Electron Microscope. J Struct Biol 1997; 120:309-19. [PMID: 9441934 DOI: 10.1006/jsbi.1997.3918] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We have developed a portable and extensible set of tools and applications for control of a remote transmission electron microscope (TEM). These tools will be used to develop a system for automatically acquiring large numbers of high quality images from a TEM in a routine, robust, and efficient manner. In particular we plan to develop applications that allow for data collection from specimens preserved in vitreous ice. Copyright 1997 Academic Press. Copyright 1997 Academic Press
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Affiliation(s)
- N Kisseberth
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801
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13
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Showler AT, Potter CS. Synopsis of the 1986–1989 Desert Locust (Orthoptera: Acrididae) Plague and the Concept of Strategic Control. ACTA ACUST UNITED AC 1991. [DOI: 10.1093/ae/37.2.106] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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14
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Crawford JM, Ransil BJ, Potter CS, Westmoreland SV, Gollan JL. Hepatic disposition and biliary excretion of bilirubin and bilirubin glucuronides in intact rats. Differential processing of pigments derived from intra- and extrahepatic sources. J Clin Invest 1987; 79:1172-80. [PMID: 3558820 PMCID: PMC424303 DOI: 10.1172/jci112934] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Mechanisms for transport of bilirubin and its conjugates in hepatocytes have not been defined. We investigated the hepatic processing of bilirubin glucuronides and their precursors, and characterized the disposition of bile pigments arising from intraversus extrahepatic sources. Tracer doses of purified radiolabeled biliverdin, bilirubin, bilirubin monoglucuronide (BMG) or diglucuronide (BDG) were administered intravenously to intact normal or jaundiced homozygous Gunn rats. Rapid sequential analysis of radiolabeled BMG and BDG in bile revealed comparable excretion patterns following biliverdin and bilirubin injection, with BDG as the major pigment. Biliary excretion of radiolabeled conjugates from injected BMG was more rapid, with BMG predominating. Excretion of injected BDG in normal rats and BMG or BDG in Gunn rats was virtually identical to that of unaltered BMG in normal rats. Model independent analysis by deconvolution provided objective comparison of the disposition of radiolabeled pigments from the different sources. These findings indicate that bilirubin glucuronides formed in the liver from endogenous (hepatic) and exogenous (extrahepatic) sources of bilirubin follow a similar excretory pathway. BMG formed endogenously is converted preferentially to BDG, whereas circulating BMG is excreted predominantly unchanged. Exogenous conjugated bilirubins are excreted more rapidly than those generated intrahepatically, by a transcellular pathway that is largely independent of the conjugation system.
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Potter CS, Ragsdale HL, Berish CW. Resorption of foliar nutrients in a regenerating southern Appalachian forest. Oecologia 1987; 73:268-271. [DOI: 10.1007/bf00377517] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/1986] [Indexed: 11/29/2022]
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Gibson T, Hannan SF, Hatfield PJ, Simmonds HA, Cameron JS, Potter CS, Crute CM. The effect of acid loading on renal excretion of uric acid and ammonium in gout. Adv Exp Med Biol 1977; 76B:46-56. [PMID: 16460 DOI: 10.1007/978-1-4684-3285-5_6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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17
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Abstract
An L-form of Serratia marcescens has previously been shown incapable of producing the red pigment, prodigiosin, characteristic of the parent bacteria. Mutants of S. marcesens, unable to form one or the other of the two prodigiosin precursors, 4-methoxy-2,2'-bipyrrole-5-carboxaldehyde or 2-methyl-3-n-amylpyrrole, were used to test the nature of the L-form defect. The L-forms failed to form sufficient amounts of either precursor to be detected by the appropriate mutant, and, when furnished the precursors, failed to couple them to form prodigiosin.
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Guze LB, Montgomerie JZ, Potter CS, Kalmanson GM. Pyelonephritis XVI. correlates of parasite virulence in acute ascending Escherichia coli pyelonephritis in mice undergoing diuresis. Yale J Biol Med 1973; 46:203-11. [PMID: 4611057 PMCID: PMC2591987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Potter CS. "Tuned-in" blind people. Rehabil Rec 1973; 14:1-5. [PMID: 4122471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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20
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Harwick HJ, Montgomerie JZ, Kalamanson GM, Hubert EG, Potter CS, Guze LB. Differential action of a streptococcal bacteriocin on mycoplasmas and microbial L-forms. Infect Immun 1971; 4:194-8. [PMID: 5005294 PMCID: PMC416287 DOI: 10.1128/iai.4.3.194-198.1971] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Bacteriocin activity of Streptococcus faecalis var. zymogenes was tested against a variety of bacteria, L-forms, and mycoplasmas. Both a partially purified liquid preparation and a colony overlay technique were used. Other S. faecalis strains were the only bacteria whose growth was inhibited. The liquid preparation inhibited growth of all but three of the tested L-forms (whether derived from gram-positive or gram-negative bacteria), and two of these exceptional organisms were inhibited when the colony overlay technique was employed. On the other hand, the L-form of Streptobacillus moniliformis and all 33 tested mycoplasmas grew readily in the presence of the bacteriocin when either method was employed. It is suggested that the presence of cholesterol in the Streptobacillus and mycoplasmal membranes, unique in this regard among procaryotic cells, may be responsible for the differential pattern of growth inhibition.
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Abstract
L-forms of a strain of Pseudomonas aeruginosa were produced by serial subculture of the bacterial form on agar medium containing sucrose as an osmotic stabilizer and carbenicillin. L-forms eventually became stable, i.e., would not revert in the absence of antibiotic, and were adapted to grow well in broth with the osmotic stabilizer. Gross morphology and light microscopic colony morphology were typical of an L-form. L-form cells were approximately spherical and bounded in part by a plasma membrane; they lacked the triple-layer cell wall structure and coarse, electron-dense nucleoidal granules of the parent bacterial form. The L-form, but not the bacterial form, contained cores, organelles previously reported only in group D streptococci. Antibiotic disc-sensitivity studies showed the stable L-form to be as sensitive as, or more sensitive than, the bacterial form to most antibiotics. Exceptions were polymyxin B, colimycin sulfate, and gentamicin, which were more active against the bacterial form. The remainder of the aminoglycosides and cell wall-active antibiotics showed no inhibition of either form. The L-form was more susceptible to cidal activity of normal human serum than the parent form. The L-form exhibited fewer biochemical activities than the parent bacteria or bacterial forms derived by reversion at a time when the L-form was still unstable. L-form colonies appeared colorless, and chemical analysis demonstrated that, if the L-form produces pigment at all, which was not demonstrated, it could not have been more than 3.6% of that produced by the bacterial form.
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Montgomerie JZ, Potter CS, Kalmanson GM, Guze LB. Penicillin: effect on sodium and potassium transport in bacterial and protoplast forms of Sterptococcus faecalis. Science 1968; 159:1252-4. [PMID: 4975004 DOI: 10.1126/science.159.3820.1252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Streptococcus faecalis, incubated in osmotically stabiliz medium in the presence of 1000 units of penicillin per milliliter, accumulated rather than extruded sodium; they accumulated much less potassium than control cells did. These changes were not due to binding of sodium by cell-wall fragments of cells treated with penicillin. Because penicillin had no effect on cation concentrations in stable protoplasts and nongrowing bacterial cells, this effect appeared to be related to the production of the penicillin-induced lesions of the cell wall.
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Engel AG, Potter CS, Rosevear JW. Studies on carbohydrate metabolism and mitochondrial respiratory activities in primary hypokalemic periodic paralysis. Neurology 1967; 17:329-36 passim. [PMID: 6067069 DOI: 10.1212/wnl.17.4.329] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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