cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/7t9zz-erk19
title: Hyphomonas session9 34KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-03-07</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> Hyphomonas neptunium</p>
<strong>Strain:</strong> ATCC 15444</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-64.0°, 64.0°), step: 2°, constant angular increment, dosage: 140.0 eV/Å²,  defocus: -8.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> Cultured by Jian; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> exponential phase in PYE media...</p>
<strong>Sample Preparation:</strong> C-flat grid, 10nm gold, 100% humidity...</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-03-07-32/rawdata/</p>09mar07a_36c_033.mrc,  Tilt Series (Pixel Size 0.632 nm), 553.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-03-07-32/rawdata/09mar07a_36c_033.mrc"
        > <i class="download icon"></i> Download </a></p>

        09mar07a_36c_033_full.rec,  Reconstruction (Pixel Size 1.264 nm), 419.4 MB  
        
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DOI: 10.22002/7tkfb-j2323
title: Eco 082509 MP15

description: Escherichia coli, 09sep10b_082509MP15_712ly_073,
description: <strong>Tilt Series Date:</strong> 2009-09-10</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> 7.1.2 Martin</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> cultured by Martin Pilhofer; data collected by Martin Pilhofer; processed by Martin Pilhofer</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity, blotting 1/-2/2/0/1/4/200</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2009-09-10-1/rawdata/</p>09sep10b_082509MP15_712ly_073.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09sep10b_082509MP15_712ly_073_part.rec,  Reconstruction (Pixel Size 1.9 nm), 838.9 MB  
        
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DOI: 10.22002/wfn3q-86x56
title: Pdb 082609 MP18

description: Prosthecobacter debontii, 09sep10b_082609_MP18Pde_048,
description: <strong>Tilt Series Date:</strong> 2009-09-10</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Prosthecobacter dejongeii</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> cultured by Martin Pilhofer; data collected by Martin Pilhofer; processed by Martin Pilhofer</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity, blotting 1/-2/2/0/1/4/200</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2009-09-10-31/rawdata/</p>09sep10b_082609_MP18Pde_048.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        09sep10b_082609_MP18Pde_048_full.rec,  Reconstruction (Pixel Size 1.9 nm), 838.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.2wyp8a
title: Occurrence Download

description: A dataset containing 1810 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Elaeagnus angustifolia",
 "Country is Ukraine",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1810 records from 73 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045476-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/x9f12-p8g38
title: Hyphomonas session7 50KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-02-05</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> Hyphomonas neptunium</p>
<strong>Strain:</strong> ATCC 15444</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-61.0°, 61.0°), step: 1°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -6.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
<strong>Collaborators and Roles:</strong> Cultured by Jian; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> exponential phase in PYE media...</p>
<strong>Sample Preparation:</strong> C-flat grid, 10nm gold, 100% humidity...</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-02-05-1/rawdata/</p>09feb05a_Hm7I_003.mrc,  Tilt Series (Pixel Size 0.422 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09feb05a_Hm7I_003_1k.rec,  Reconstruction (Pixel Size 0.844 nm), 130.2 MB  
        
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DOI: 10.22002/pqzwn-mxg81
title: B141,6/9/09,V52,delta-CTX,Kan-R

description: Raw data files of B141,6/9/09,V52,delta-CTX,Kan-R
description: <strong>Tilt Series Date:</strong> 2009-08-14</p>
<strong>Data Taken By:</strong> Zhuo Li</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> V52</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-63.0°, 63.0°), step: 1°, constant angular increment, dosage: 190.0 eV/Å²,  defocus: -12.0 μm,  magnification: 18000x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> RAPTOR, Peach, IMOD</p>
<strong>Collaborators and Roles:</strong> Cells were provided by Marek Basler at Harvard University,data collected by ZL</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Exponential phase</p>
<strong>Sample Preparation:</strong> quantifoil grid R2/2, 10nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-08-14-6/rawdata/</p>09aug14a_VCB141_021.mrc,  Tilt Series (Pixel Size 1.192 nm), 1.0 GB  
        
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        09aug14a_VCB141_021_part.rec,  Reconstruction (Pixel Size 2.384 nm), 471.9 MB  
        
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DOI: 10.22002/rfjw4-fds31
title: Hyphomicrobium facile session13 34KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-04-14</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> Hyphomicrobium facile</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-64.0°, 64.0°), step: 1.5°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -7.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> Cultured by Jian; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> exponential phase in ATCC-656 media...</p>
<strong>Sample Preparation:</strong> C-flat grid, 10nm gold, 100% humidity...</p>
description: Files available via S3 at ttps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-04-14-29/rawdata/</p>09apr14a_Bhf2b_030.mrc,  Tilt Series (Pixel Size 0.632 nm), 738.2 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-04-14-29/rawdata/09apr14a_Bhf2b_030.mrc"
        > <i class="download icon"></i> Download </a></p>

        09apr14a_Bhf2b_030_part.rec,  Reconstruction (Pixel Size 1.264 nm), 314.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-04-14-29/3dimage_7567/09apr14a_Bhf2b_030_part.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/dx07d-80z44
title: Hyphomonas EB session21 34KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-07-14</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> Hyphomonas neptunium</p>
<strong>Strain:</strong> ATCC 15444</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -7.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> Cultured by Jian; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> exponential phase in PYE media, EB 0.02mg/ml overnight 4degree...</p>
<strong>Sample Preparation:</strong> QF grid, 10nm gold, 100% humidity...</p>
  jsa2009-07-14-71_slicer8915.jpg: Hyphomonas Neptunium .  Unknown filament
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-07-14-71/rawdata/</p>09jul14a_b200c_071.mrc,  Tilt Series (Pixel Size 0.632 nm), 553.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-07-14-71/rawdata/09jul14a_b200c_071.mrc"
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        09jul14a_b200c_071_full.rec,  Reconstruction (Pixel Size 1.264 nm), 367.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/gwcg5-4hj36
title: Hyphomonas session8 34KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-03-06</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> Hyphomonas neptunium</p>
<strong>Strain:</strong> ATCC 15444</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-64.0°, 64.0°), step: 2°, constant angular increment, dosage: 140.0 eV/Å²,  defocus: -8.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> Cultured by Jian; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> exponential phase in PYE media...</p>
<strong>Sample Preparation:</strong> C-flat grid, 5nm gold, 100% humidity...</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-03-06-33/rawdata/</p>09mar06a_20d_033.mrc,  Tilt Series (Pixel Size 0.632 nm), 553.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-03-06-33/rawdata/09mar06a_20d_033.mrc"
        > <i class="download icon"></i> Download </a></p>

        09mar06a_20d_033_full.rec,  Reconstruction (Pixel Size 1.264 nm), 377.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-03-06-33/3dimage_7432/09mar06a_20d_033_full.rec"
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DOI: 10.5522/04/26268520
title: Complement-mediated killing of <i>Escherichia coli</i> by mechanical destabilization of the cell envelope

description: Data for research published as preprint in https://doi.org/10.1101/2023.12.10.570986 and as peer-reviewed paper in Benn, Bortolini et al., EMBO Journal (2024) 43: 6152 - 6160, http://dx.doi.org/10.1038/s44318-024-00266-3, with data here grouped by main figures as in the submitted manuscript.Complement proteins eliminate Gram-negative bacteria in the blood via the formation of membrane attack complex (MAC) pores in the outer membrane. However, it remains unclear how outer membrane poration leads to inner membrane permeation and cell lysis. Using atomic force microscopy (AFM) on living <i>Escherichia coli</i> (<i>E. coli</i>), we probed MAC-induced changes in the cell envelope and correlated these with subsequent cell death. Initially, bacteria survived despite the formation of hundreds of MACs randomly distributed over the cell surface. This was followed by larger-scale disruption of the outer membrane, including propagating defects and fractures, and by an overall swelling and stiffening of the bacterial surface, which precede inner membrane permeation. We conclude that bacterial cell lysis is only an indirect effect of MAC formation; outer membrane poration leads to mechanical destabilization of the cell envelope, reducing its ability to contain the turgor pressure, leading to inner membrane permeation and cell death.The data stored here include AFM data of living <i>E. coli</i> cells exposed to complement proteins and particularly the membrane attack complex; results of data processing in the form of background subtracted images and mechanical data; and brightfield and fluorescence microscopy images that were taken complementary to AFM data on the same cells.Data files can be open with open-source AFM image processing software (e.g., Gwyddion), general image viewers (e.g., for jpeg, tiff, pdf) or any spreadsheet text readers (for e.g. txt and csv files).
DOI: 10.5522/04/26268520.v1
title: Complement-mediated killing of <i>Escherichia coli</i> by mechanical destabilization of the cell envelope

description: Data for research published as preprint in https://doi.org/10.1101/2023.12.10.570986 and as peer-reviewed paper in Benn, Bortolini et al., EMBO Journal (2024) 43: 6152 - 6160, http://dx.doi.org/10.1038/s44318-024-00266-3, with data here grouped by main figures as in the submitted manuscript.Complement proteins eliminate Gram-negative bacteria in the blood via the formation of membrane attack complex (MAC) pores in the outer membrane. However, it remains unclear how outer membrane poration leads to inner membrane permeation and cell lysis. Using atomic force microscopy (AFM) on living <i>Escherichia coli</i> (<i>E. coli</i>), we probed MAC-induced changes in the cell envelope and correlated these with subsequent cell death. Initially, bacteria survived despite the formation of hundreds of MACs randomly distributed over the cell surface. This was followed by larger-scale disruption of the outer membrane, including propagating defects and fractures, and by an overall swelling and stiffening of the bacterial surface, which precede inner membrane permeation. We conclude that bacterial cell lysis is only an indirect effect of MAC formation; outer membrane poration leads to mechanical destabilization of the cell envelope, reducing its ability to contain the turgor pressure, leading to inner membrane permeation and cell death.The data stored here include AFM data of living <i>E. coli</i> cells exposed to complement proteins and particularly the membrane attack complex; results of data processing in the form of background subtracted images and mechanical data; and brightfield and fluorescence microscopy images that were taken complementary to AFM data on the same cells.Data files can be open with open-source AFM image processing software (e.g., Gwyddion), general image viewers (e.g., for jpeg, tiff, pdf) or any spreadsheet text readers (for e.g. txt and csv files).
DOI: 10.22002/7dse6-sn958
title: Eco 020509 27b

description: Escherichia coli, 09feb08c_12_2_1_020509_27_046, btub filaments,
description: <strong>Tilt Series Date:</strong> 2009-02-08</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> 12.2.1 Martin</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> cultured by Martin Pilhofer; data collected by Martin Pilhofer; processed by Martin Pilhofer</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity, blotting 1/-2/2/0/1/4/200</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2009-02-08-6/rawdata/</p>09feb08c_12_2_1_020509_27_046.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        09feb08c_12_2_1_020509_27_046_full.rec,  Reconstruction (Pixel Size 1.9 nm), 838.9 MB  
        
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DOI: 10.22002/a0x9k-1js83
title: CB15N w/ MP265

description: Raw data files of CB15N w/ MP265
description: <strong>Tilt Series Date:</strong> 2009-10-10</p>
<strong>Data Taken By:</strong> Zhuo Li</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-63.0°, 63.0°), step: 1°, constant angular increment, dosage: 190.0 eV/Å²,  defocus: -12.0 μm,  magnification: 18000x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> RAPTOR, Peach, IMOD</p>
<strong>Collaborators and Roles:</strong> Experiments done by ZL.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Exponential phase in PYE</p>
<strong>Sample Preparation:</strong> Quantifoil R2/1 or R2/2, 10nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-10-10-94/rawdata/</p>09oct10b_WCm2651_094.mrc,  Tilt Series (Pixel Size 1.192 nm), 1.1 GB  
        
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        09oct10b_WCm2651_094_full.rec,  Reconstruction (Pixel Size 2.384 nm), 471.9 MB  
        
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DOI: 10.22002/e240p-51377
title: CB15N w/ methanol control

description: Raw data files of CB15N w/ methanol control
description: <strong>Tilt Series Date:</strong> 2009-10-10</p>
<strong>Data Taken By:</strong> Zhuo Li</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-63.0°, 63.0°), step: 1°, constant angular increment, dosage: 190.0 eV/Å²,  defocus: -12.0 μm,  magnification: 18000x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> RAPTOR, Peach, IMOD</p>
<strong>Collaborators and Roles:</strong> Experiments done by ZL.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Exponential phase in PYE</p>
<strong>Sample Preparation:</strong> Quantifoil R2/1 or R2/2, 10nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-10-10-7/rawdata/</p>09oct10b_WTCCmet_007.mrc,  Tilt Series (Pixel Size 1.192 nm), 1.1 GB  
        
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        09oct10b_WTCCmet_007_full.rec,  Reconstruction (Pixel Size 2.384 nm), 471.9 MB  
        
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