cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/3ce9r-b9j49
title: Pfl 072309 359bl

description: Prosthecobacter fluviatilis, 09jul27a_359bl_072309_Pfl_032,
description: <strong>Tilt Series Date:</strong> 2009-07-27</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Prosthecobacter fluviatilis</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> imod</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/mpa2009-07-27-29/rawdata/</p>09jul27a_359bl_072309_Pfl_032.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09jul27a_359bl_072309_Pfl_032.rec,  Reconstruction (Pixel Size 1.9 nm), 314.6 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/sseys-0e229
title: Rhodobacter 1558 cryosections

description: Cryosections by MArk Ladinsky
description: <strong>Tilt Series Date:</strong> 2010-10-07</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Rhodobacter sphaeroides</p>
<strong>Strain:</strong> ATCC 17023</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-61.0°, 64.0°), step: 2°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -10.0 μm,  magnification: 34000x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Collaborators and Roles:</strong> Judy Armitage</p>
<strong>Purification / Growth Conditions / Treatment:</strong> grown in SUX media</p>
<strong>Sample Preparation:</strong> prepared for cryosectioning (gold prep see JWIKI)</p>
description: Files available via S3 at ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2010-10-07-8/rawdata/</p>10oct07a_rhcryosections_1_008.st,  Tilt Series (Pixel Size 0.0 nm), 528.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        10oct07a_rhcryosections_1_008.rec,  Reconstruction (Pixel Size 0.0 nm), 188.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2010-10-07-8/3dimage_14944/10oct07a_rhcryosections_1_008.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.fqk2gv
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ictalurus punctatus",
 "Country is Lithuania",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047519-250811113504898/datasets/export for details.
DOI: 10.22002/zwp06-za874
title: Hyphomonas EB session17 27.5KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-06-07</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: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -10.0 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, EB 0.01mg overnight at 4degree...</p>
<strong>Sample Preparation:</strong> QF grid, 10nm gold, 100% humidity...</p>
  jsa2009-06-07-25_slicer8861.jpg: DNA supercoil  .  Hyphomonas neptunium
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-06-07-25/rawdata/</p>09jun07a_bx675a_026.mrc,  Tilt Series (Pixel Size 0.774 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-06-07-25/rawdata/09jun07a_bx675a_026.mrc"
        > <i class="download icon"></i> Download </a></p>

        09jun07a_bx675a_026_1k.rec,  Reconstruction (Pixel Size 1.548 nm), 209.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-06-07-25/3dimage_7987/09jun07a_bx675a_026_1k.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/17qkc-dvz38
title: Bsubtilis349

description: Bsubtilis JFG349 (MJ007, SpoIIIE78-11-GFP)
description: <strong>Tilt Series Date:</strong> 2011-07-19</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Bacillus subtilis </p>
<strong>Strain:</strong> JFG349, ponA null, SpoIIIE73-11-GFP</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> uploadraptor</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> strain from Kit Pogliano at UCSD</p>
<strong>Purification / Growth Conditions / Treatment:</strong> sporulation media</p>
<strong>Sample Preparation:</strong> quantifoil grid R2/2, 20nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-07-19-5/3dimage_24997/</p>349target0006_full.rec,  Reconstruction (Pixel Size 1.9 nm), 780.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-07-19-5/3dimage_24997/349target0006_full.rec"
        > <i class="download icon"></i> Download </a></p>

        349target0006.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-07-19-5/rawdata/349target0006.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/fk8g0-tpg54
title: MamJ deletion (and might contain

description: Raw data files of MamJ deletion (and might contain
description: <strong>Tilt Series Date:</strong> 2010-02-18</p>
<strong>Data Taken By:</strong> Zhuo Li</p>
<strong>Species / Specimen:</strong> Magnetospirillum magneticum</p>
<strong>Strain:</strong> AMB-1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-63.0°, 63.0°), step: 1.5°, constant angular increment, dosage: 110.0 eV/Å²,  defocus: -15.0 μm,  magnification: 18000x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> RAPTOR and Peach</p>
<strong>Collaborators and Roles:</strong> Cell culture were from Arash Komeili. Upon receiving, cells were frozen in 2 hours. Meanwhile they were kept in 30C. Data collected and processed by ZL.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Stationary phase. </p>
<strong>Sample Preparation:</strong> R2/2, 10nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2010-02-18-68/rawdata/</p>10feb18a_dJnofe5_068.mrc,  Tilt Series (Pixel Size 1.192 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2010-02-18-68/rawdata/10feb18a_dJnofe5_068.mrc"
        > <i class="download icon"></i> Download </a></p>

        10feb18a_dJnofe5_068_full.rec,  Reconstruction (Pixel Size 2.384 nm), 524.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/8bbhw-nb258
title: Bacillus subtilis JFG351

description: Raw data files of Bacillus subtilis JFG351
description: <strong>Tilt Series Date:</strong> 2009-07-28</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Bacillus subtilis</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (60.0°, -60.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 12.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Collaborators and Roles:</strong> Jennifer (Pogliano lab)</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Induced sporulation t=2.5</p>
<strong>Sample Preparation:</strong> quantifoil grid, 20nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2009-07-28-21/rawdata/</p>09jul28a_pos3_022.mrc,  Tilt Series (Pixel Size 0.961 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2009-07-28-21/rawdata/09jul28a_pos3_022.mrc"
        > <i class="download icon"></i> Download </a></p>

        cell22_full.rec,  Reconstruction (Pixel Size 1.922 nm), 692.1 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2009-07-28-21/3dimage_6253/cell22_full.rec"
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DOI: 10.22002/ayqg1-e0b08
title: Pfl 121509 MP36

description: Prosthecobacter fluviatilis, 10jan14a_MP36_Pfl-stat_028,
description: <strong>Tilt Series Date:</strong> 2010-01-14</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Prosthecobacter fluviatilis</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>
  mpa2010-01-14-23_slicer7158.jpg: Filament
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2010-01-14-23/rawdata/</p>10jan14a_MP36_Pfl-stat_028.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2010-01-14-23/rawdata/10jan14a_MP36_Pfl-stat_028.mrc"
        > <i class="download icon"></i> Download </a></p>

        10jan14a_MP36_Pfl-stat_028_full.rec,  Reconstruction (Pixel Size 1.9 nm), 838.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2010-01-14-23/3dimage_14463/10jan14a_MP36_Pfl-stat_028_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.6084/m9.figshare.29545836
title: Unveiling the cryptic Neotropical species of <i>Phaeoclavulina</i> from the Southern Cone: phylogenetic and morphological analysis

description: Global fungal diversity is estimated at about 6.2 million species, but only 150 000 are currently described. Molecular studies reveal that this diversity is often underestimated, especially in less-studied regions. <i>Phaeoclavulina</i>, a genus of ramarioid fungi, has a wide distribution in areas with temperate and tropical climates. However, in southern South America, research on <i>Phaeoclavulina</i> species has been scarce, with only a few studies conducted in Argentina covering the morphology of a few species. This research aims to analyze <i>Phaeoclavulina</i> species in Argentina, exploring their morphology, ecological roles, and distribution. Four different ecological regions across Argentina were sampled. Molecular data (Sanger and next-generation sequencing [NGS] technology) were obtained to construct their phylogenetic relationships. Our results show a greater diversity of <i>Phaeoclavulina</i> than previously known. Eight taxa are described here, four of which are new species to science (<i>Phaeoclavulina aena, P. angularis, P. prasina</i>, and <i>P. stelligera</i>). Additionally, a neotypification is proposed for <i>Phaeoclavulina camellia</i>. For the other three species (<i>P. articulotela, P. campoi</i>, and <i>P. minutispora</i>), we provide new molecular data and elucidate their phylogenetic relationships with other previously described species. In addition, a key to species of <i>Phaeoclavulina</i> from Argentina and Chile is included to facilitate identification of known taxa. Finally, most <i>Phaeoclavulina</i> species richness is associated with tropical and subtropical forests.
DOI: 10.6084/m9.figshare.29545836.v1
title: Unveiling the cryptic Neotropical species of <i>Phaeoclavulina</i> from the Southern Cone: phylogenetic and morphological analysis

description: Global fungal diversity is estimated at about 6.2 million species, but only 150 000 are currently described. Molecular studies reveal that this diversity is often underestimated, especially in less-studied regions. <i>Phaeoclavulina</i>, a genus of ramarioid fungi, has a wide distribution in areas with temperate and tropical climates. However, in southern South America, research on <i>Phaeoclavulina</i> species has been scarce, with only a few studies conducted in Argentina covering the morphology of a few species. This research aims to analyze <i>Phaeoclavulina</i> species in Argentina, exploring their morphology, ecological roles, and distribution. Four different ecological regions across Argentina were sampled. Molecular data (Sanger and next-generation sequencing [NGS] technology) were obtained to construct their phylogenetic relationships. Our results show a greater diversity of <i>Phaeoclavulina</i> than previously known. Eight taxa are described here, four of which are new species to science (<i>Phaeoclavulina aena, P. angularis, P. prasina</i>, and <i>P. stelligera</i>). Additionally, a neotypification is proposed for <i>Phaeoclavulina camellia</i>. For the other three species (<i>P. articulotela, P. campoi</i>, and <i>P. minutispora</i>), we provide new molecular data and elucidate their phylogenetic relationships with other previously described species. In addition, a key to species of <i>Phaeoclavulina</i> from Argentina and Chile is included to facilitate identification of known taxa. Finally, most <i>Phaeoclavulina</i> species richness is associated with tropical and subtropical forests.
DOI: 10.6084/m9.figshare.29429055
title: Targeting lignocellulolytic gene clusters in novel <i>Trichoderma atroviride</i> and <i>Trichoderma harzianum</i> strains through bacterial artificial chromosome–guided analysis

description: Lignocellulosic biomass is a complex carbon source with recalcitrant properties whose degradation via industrial enzymatic hydrolysis is challenging, directly affecting the cost of reliable energy production. In nature, filamentous fungi, including <i>Trichoderma</i> species, degrade lignocellulose via an arsenal of hydrolytic and oxidative enzymes that act synergistically to process it into soluble sugar monomers. This work explored the genomic content of <i>Trichoderma atroviride</i> and <i>Trichoderma harzianum</i> strains with hydrolytic abilities by identifying regions possessing degradative enzyme–encoding genes, namely, hydrolytic clusters. We employed bacterial artificial chromosome (BAC) methodology to target specific genomic regions and explore their genetic organization, proximal gene context, and gene expression under degradative conditions. With this tool, it was possible to inspect the linear structure and expression profile of target hydrolytic-rich genomic regions. The present work offers a perspective on the organization of genome regions related to carbohydrate metabolism. This study revealed novel genes and genome regions that are positively regulated during cellulose degradation, contributing to elucidating differences in gene organization that potentially impact hydrolysis among <i>Trichoderma</i> species.
DOI: 10.6084/m9.figshare.29429055.v1
title: Targeting lignocellulolytic gene clusters in novel <i>Trichoderma atroviride</i> and <i>Trichoderma harzianum</i> strains through bacterial artificial chromosome–guided analysis

description: Lignocellulosic biomass is a complex carbon source with recalcitrant properties whose degradation via industrial enzymatic hydrolysis is challenging, directly affecting the cost of reliable energy production. In nature, filamentous fungi, including <i>Trichoderma</i> species, degrade lignocellulose via an arsenal of hydrolytic and oxidative enzymes that act synergistically to process it into soluble sugar monomers. This work explored the genomic content of <i>Trichoderma atroviride</i> and <i>Trichoderma harzianum</i> strains with hydrolytic abilities by identifying regions possessing degradative enzyme–encoding genes, namely, hydrolytic clusters. We employed bacterial artificial chromosome (BAC) methodology to target specific genomic regions and explore their genetic organization, proximal gene context, and gene expression under degradative conditions. With this tool, it was possible to inspect the linear structure and expression profile of target hydrolytic-rich genomic regions. The present work offers a perspective on the organization of genome regions related to carbohydrate metabolism. This study revealed novel genes and genome regions that are positively regulated during cellulose degradation, contributing to elucidating differences in gene organization that potentially impact hydrolysis among <i>Trichoderma</i> species.
DOI: 10.22002/dfqxs-hv094
title: Pdb 121509 MP35

description: Prosthecobacter debontii, 10feb07a_MP35_Pdb_exp_029, putative btub structure (2 tubes),
description: <strong>Tilt Series Date:</strong> 2010-02-07</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Prosthecobacter debontii</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>
  mpa2010-02-07-5_slicer4979.jpg: Filaments mpa2010-02-07-5_slicer4981.jpg: Filaments mpa2010-02-07-5_slicer4983.jpg: Granules and vesicle mpa2010-02-07-5_slicer4984.jpg: Pilli
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2010-02-07-5/rawdata/</p>10feb07a_MP35_Pdb_exp_029.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        10feb07a_MP35_Pdb_exp_029_full.rec,  Reconstruction (Pixel Size 1.9 nm), 838.9 MB  
        
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DOI: 10.6084/m9.figshare.29371855
title: <i>Agaricus</i> section <i>Minores</i>: a new species to science, and six species recorded for the first time in Greece

description: <i>Agaricus</i> sect. <i>Minores</i> is characterized by the production of small to medium-sized basidiomata, high species diversity (including several cryptic taxa), and occurrence in a large variety of habitats. A new species to science, i.e. <i>Agaricus draconis</i>, is formally described by adopting an integrative approach based on morphological features, molecular criteria, and habitat characteristics. The multilocus phylogenetic analysis performed through the use of the internal transcribed spacer (ITS), the partial nuc 28S rDNA (28S), and the translation elongation factor 1-alpha (<i>TEF1-α</i>) gene clearly demonstrates that <i>A. draconis</i> is a sister species to <i>A. brunneolus</i> and <i>A. dulcidulus</i>. In addition, <i>A. draconis</i> exhibits distinct morphological features, including a predominantly white, smooth pileus with occasional tinges of gray, orange, violet, or yellowish colors lacking appressed scales and a single, solid rhizomorph at the stipe base. Furthermore, the presence of another 12 species of the <i>A</i>. sect. <i>Minores</i> was assessed in Greece, six of which constitute first national records, i.e. <i>A. edmondoi, A. gemlii, A. heinemannianus, A. jacobi, A. kerriganii</i>, and <i>A. marisae</i>. The most notable morphological features of these six species are presented, and their distribution in Mediterranean Europe is discussed.