cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15274395
title: How do bacterial extracellular Contractile Injection Systems bind target cells? A remarkable diversity of receptor binding domains

description: How do bacterial extracellular Contractile Injection Systems bind target cells?

A remarkable diversity of receptor binding domains

 

Nimrod Nachmias1,*, Zhiren Wang2,*, Feng Jiang2,#, and Asaf Levy1,#

1 Department of Plant Pathology and Microbiology, Institute of Environmental Science, The Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel

2 NHC Key Laboratory of Systems Biology of Pathogens, Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China

 

Abstract:

Extracellular contractile injection systems (eCIS) represent a diverse family of bacteriophage tail-derived protein toxin delivery complexes in prokaryotes. eCIS are vital for microbial interaction with hosts and they use tail fiber proteins for target cell binding. However, the identity of the tail fiber proteins and their target cells are unknown. Here, we conducted a comprehensive exploration of eCIS tail fiber genes, providing insights into their remarkable diversity, target cells, functional adaptations, and intriguing evolutionary dynamics. We identified 3,445 eCIS tail fiber proteins found in 2,585 eCIS loci from 1,069 microbes. These fibers can be categorized by five new N-terminal domains responsible for tail fiber attachment to eCIS baseplates. Importantly, we leveraged structure prediction to divide the fibers into 276 structural clusters and dissected over a thousand domain fold families which seem to facilitate glycan and protein binding on the surface of potential eukaryotes or bacterial targets. These domains are likely acquired from diverse genomes of eukaryotes, bacteria, and viruses. Finally, we experimentally showed that the tail fibers from Paenibacillus eCIS can bind and direct effector injection into THP1 murine monocytes, and may bind D-mannose. This study reveals the exceptional diversity of eCIS target specificity determinants, suggests new eCIS target cells in Nature, and provides thousands of proteins that adhere to different cell types.
DOI: 10.5281/zenodo.15274396
title: How do bacterial extracellular Contractile Injection Systems bind target cells? A remarkable diversity of receptor binding domains

description: How do bacterial extracellular Contractile Injection Systems bind target cells?

A remarkable diversity of receptor binding domains

 

Nimrod Nachmias1,*, Zhiren Wang2,*, Feng Jiang2,#, and Asaf Levy1,#

1 Department of Plant Pathology and Microbiology, Institute of Environmental Science, The Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel

2 NHC Key Laboratory of Systems Biology of Pathogens, Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China

 

Abstract:

Extracellular contractile injection systems (eCIS) represent a diverse family of bacteriophage tail-derived protein toxin delivery complexes in prokaryotes. eCIS are vital for microbial interaction with hosts and they use tail fiber proteins for target cell binding. However, the identity of the tail fiber proteins and their target cells are unknown. Here, we conducted a comprehensive exploration of eCIS tail fiber genes, providing insights into their remarkable diversity, target cells, functional adaptations, and intriguing evolutionary dynamics. We identified 3,445 eCIS tail fiber proteins found in 2,585 eCIS loci from 1,069 microbes. These fibers can be categorized by five new N-terminal domains responsible for tail fiber attachment to eCIS baseplates. Importantly, we leveraged structure prediction to divide the fibers into 276 structural clusters and dissected over a thousand domain fold families which seem to facilitate glycan and protein binding on the surface of potential eukaryotes or bacterial targets. These domains are likely acquired from diverse genomes of eukaryotes, bacteria, and viruses. Finally, we experimentally showed that the tail fibers from Paenibacillus eCIS can bind and direct effector injection into THP1 murine monocytes, and may bind D-mannose. This study reveals the exceptional diversity of eCIS target specificity determinants, suggests new eCIS target cells in Nature, and provides thousands of proteins that adhere to different cell types.
DOI: 10.5284/1132560
title: Digital Archive from an Archaeological Watching Brief and Evaluation at Unit 1, Third Avenue, Southampton, Hampshire, June to October 2017

description: This collection consists of images and GIS data from an archaeological watching brief and evaluation by Allen Archaeology. Work occurred at Unit 1, Third Avenue, Southampton, Hampshire, from June to October 2017. This was a condition of planning consent for erection of seven new commercial units.
DOI: 10.22033/esgf/cmip6.1379
title: CNRM-CERFACS CNRM-CM6-1 model output prepared for CMIP6 GMMIP

description: Coupled Model Intercomparison Project Phase 6 (CMIP6) datasets: These data include all datasets published for 'CMIP6.GMMIP.CNRM-CERFACS.CNRM-CM6-1' with the full Data Reference Syntax following the template 'mip_era.activity_id.institution_id.source_id.experiment_id.member_id.table_id.variable_id.grid_label.version'.
 
 The CNRM-CM6-1 climate model, released in 2017, includes the following components:
 aerosol: prescribed monthly fields computed by TACTIC_v2 scheme, atmos: Arpege 6.3 (T127; Gaussian Reduced with 24572 grid points in total distributed over 128 latitude circles (with 256 grid points per latitude circle between 30degN and 30degS reducing to 20 grid points per latitude circle at 88.9degN and 88.9degS); 91 levels; top level 78.4 km), atmosChem: OZL_v2, land: Surfex 8.0c, ocean: Nemo 3.6 (eORCA1, tripolar primarily 1deg; 362 x 294 longitude/latitude; 75 levels; top grid cell 0-1 m), seaIce: Gelato 6.1. 
The model was run by the CNRM (Centre National de Recherches Meteorologiques, Toulouse 31057, France), CERFACS (Centre Europeen de Recherche et de Formation Avancee en Calcul Scientifique, Toulouse 31057, France) (CNRM-CERFACS) in native nominal resolutions: aerosol: 250 km, atmos: 250 km, atmosChem: 250 km, land: 250 km, ocean: 100 km, seaIce: 100 km. 

Project: These data have been generated as part of the internationally-coordinated Coupled Model Intercomparison Project Phase 6 (CMIP6; see also GMD Special Issue: http://www.geosci-model-dev.net/special_issue590.html). The simulation data provides a basis for climate research designed to answer fundamental science questions and serves as resource for authors of the Sixth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC-AR6).

CMIP6 is a project coordinated by the Working Group on Coupled Modelling (WGCM) as part of the World Climate Research Programme (WCRP). Phase 6 builds on previous phases executed under the leadership of the Program for Climate Model Diagnosis and Intercomparison (PCMDI) and relies on the Earth System Grid Federation (ESGF) and the Centre for Environmental Data Analysis (CEDA) along with numerous related activities for implementation. The original data is hosted and partially replicated on a federated collection of data nodes, and most of the data relied on by the IPCC is being archived for long-term preservation at the IPCC Data Distribution Centre (IPCC DDC) hosted by the German Climate Computing Center (DKRZ).

The project includes simulations from about 120 global climate models and around 45 institutions and organizations worldwide. - Project website: https://pcmdi.llnl.gov/CMIP6.
DOI: 10.22033/esgf/cmip6.4188
title: CNRM-CERFACS CNRM-ESM2-1 model output prepared for CMIP6 LUMIP ssp126-ssp370Lu

description: Coupled Model Intercomparison Project Phase 6 (CMIP6) datasets: These data include all datasets published for 'CMIP6.LUMIP.CNRM-CERFACS.CNRM-ESM2-1.ssp126-ssp370Lu' with the full Data Reference Syntax following the template 'mip_era.activity_id.institution_id.source_id.experiment_id.member_id.table_id.variable_id.grid_label.version'.
 
 The CNRM-ESM2-1 climate model, released in 2017, includes the following components:
 aerosol: TACTIC_v2, atmos: Arpege 6.3 (T127; Gaussian Reduced with 24572 grid points in total distributed over 128 latitude circles (with 256 grid points per latitude circle between 30degN and 30degS reducing to 20 grid points per latitude circle at 88.9degN and 88.9degS); 91 levels; top level 78.4 km), atmosChem: REPROBUS-C_v2, land: Surfex 8.0c, ocean: Nemo 3.6 (eORCA1, tripolar primarily 1deg; 362 x 294 longitude/latitude; 75 levels; top grid cell 0-1 m), ocnBgchem: Pisces 2.s, seaIce: Gelato 6.1. 
The model was run by the CNRM (Centre National de Recherches Meteorologiques, Toulouse 31057, France), CERFACS (Centre Europeen de Recherche et de Formation Avancee en Calcul Scientifique, Toulouse 31057, France) (CNRM-CERFACS) in native nominal resolutions: aerosol: 250 km, atmos: 250 km, atmosChem: 250 km, land: 250 km, ocean: 100 km, ocnBgchem: 100 km, seaIce: 100 km. 

Project: These data have been generated as part of the internationally-coordinated Coupled Model Intercomparison Project Phase 6 (CMIP6; see also GMD Special Issue: http://www.geosci-model-dev.net/special_issue590.html). The simulation data provides a basis for climate research designed to answer fundamental science questions and serves as resource for authors of the Sixth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC-AR6).

CMIP6 is a project coordinated by the Working Group on Coupled Modelling (WGCM) as part of the World Climate Research Programme (WCRP). Phase 6 builds on previous phases executed under the leadership of the Program for Climate Model Diagnosis and Intercomparison (PCMDI) and relies on the Earth System Grid Federation (ESGF) and the Centre for Environmental Data Analysis (CEDA) along with numerous related activities for implementation. The original data is hosted and partially replicated on a federated collection of data nodes, and most of the data relied on by the IPCC is being archived for long-term preservation at the IPCC Data Distribution Centre (IPCC DDC) hosted by the German Climate Computing Center (DKRZ).

The project includes simulations from about 120 global climate models and around 45 institutions and organizations worldwide. - Project website: https://pcmdi.llnl.gov/CMIP6.
DOI: 10.22033/esgf/cmip6.4203
title: CNRM-CERFACS CNRM-ESM2-1 model output prepared for CMIP6 LUMIP ssp370-ssp126Lu

description: Coupled Model Intercomparison Project Phase 6 (CMIP6) datasets: These data include all datasets published for 'CMIP6.LUMIP.CNRM-CERFACS.CNRM-ESM2-1.ssp370-ssp126Lu' with the full Data Reference Syntax following the template 'mip_era.activity_id.institution_id.source_id.experiment_id.member_id.table_id.variable_id.grid_label.version'.
 
 The CNRM-ESM2-1 climate model, released in 2017, includes the following components:
 aerosol: TACTIC_v2, atmos: Arpege 6.3 (T127; Gaussian Reduced with 24572 grid points in total distributed over 128 latitude circles (with 256 grid points per latitude circle between 30degN and 30degS reducing to 20 grid points per latitude circle at 88.9degN and 88.9degS); 91 levels; top level 78.4 km), atmosChem: REPROBUS-C_v2, land: Surfex 8.0c, ocean: Nemo 3.6 (eORCA1, tripolar primarily 1deg; 362 x 294 longitude/latitude; 75 levels; top grid cell 0-1 m), ocnBgchem: Pisces 2.s, seaIce: Gelato 6.1. 
The model was run by the CNRM (Centre National de Recherches Meteorologiques, Toulouse 31057, France), CERFACS (Centre Europeen de Recherche et de Formation Avancee en Calcul Scientifique, Toulouse 31057, France) (CNRM-CERFACS) in native nominal resolutions: aerosol: 250 km, atmos: 250 km, atmosChem: 250 km, land: 250 km, ocean: 100 km, ocnBgchem: 100 km, seaIce: 100 km. 

Project: These data have been generated as part of the internationally-coordinated Coupled Model Intercomparison Project Phase 6 (CMIP6; see also GMD Special Issue: http://www.geosci-model-dev.net/special_issue590.html). The simulation data provides a basis for climate research designed to answer fundamental science questions and serves as resource for authors of the Sixth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC-AR6).

CMIP6 is a project coordinated by the Working Group on Coupled Modelling (WGCM) as part of the World Climate Research Programme (WCRP). Phase 6 builds on previous phases executed under the leadership of the Program for Climate Model Diagnosis and Intercomparison (PCMDI) and relies on the Earth System Grid Federation (ESGF) and the Centre for Environmental Data Analysis (CEDA) along with numerous related activities for implementation. The original data is hosted and partially replicated on a federated collection of data nodes, and most of the data relied on by the IPCC is being archived for long-term preservation at the IPCC Data Distribution Centre (IPCC DDC) hosted by the German Climate Computing Center (DKRZ).

The project includes simulations from about 120 global climate models and around 45 institutions and organizations worldwide. - Project website: https://pcmdi.llnl.gov/CMIP6.
DOI: 10.22033/esgf/cmip6.1625
title: MRI MRI-AGCM3-2-S model output prepared for CMIP6 HighResMIP

description: Coupled Model Intercomparison Project Phase 6 (CMIP6) datasets: These data include all datasets published for 'CMIP6.HighResMIP.MRI.MRI-AGCM3-2-S' with the full Data Reference Syntax following the template 'mip_era.activity_id.institution_id.source_id.experiment_id.member_id.table_id.variable_id.grid_label.version'.
 
 The MRI-AGCM3-2-S climate model, released in 2017, includes the following components:
 aerosol: Prescribed from MRI-ESM2.0, atmos: MRI-AGCM3.2S (TL959; 1920 x 960 longitude/latitude; 64 levels; top level 0.01 hPa), land: SIB0109. 
The model was run by the Meteorological Research Institute, Tsukuba, Ibaraki 305-0052, Japan (MRI) in native nominal resolutions: aerosol: 250 km, atmos: 25 km, land: 25 km. 

Project: These data have been generated as part of the internationally-coordinated Coupled Model Intercomparison Project Phase 6 (CMIP6; see also GMD Special Issue: http://www.geosci-model-dev.net/special_issue590.html). The simulation data provides a basis for climate research designed to answer fundamental science questions and serves as resource for authors of the Sixth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC-AR6).

CMIP6 is a project coordinated by the Working Group on Coupled Modelling (WGCM) as part of the World Climate Research Programme (WCRP). Phase 6 builds on previous phases executed under the leadership of the Program for Climate Model Diagnosis and Intercomparison (PCMDI) and relies on the Earth System Grid Federation (ESGF) and the Centre for Environmental Data Analysis (CEDA) along with numerous related activities for implementation. The original data is hosted and partially replicated on a federated collection of data nodes, and most of the data relied on by the IPCC is being archived for long-term preservation at the IPCC Data Distribution Centre (IPCC DDC) hosted by the German Climate Computing Center (DKRZ).

The project includes simulations from about 120 global climate models and around 45 institutions and organizations worldwide. - Project website: https://pcmdi.llnl.gov/CMIP6.
DOI: 10.22033/esgf/cmip6.2295
title: INM INM-CM4-8 model output prepared for CMIP6 PMIP

description: Coupled Model Intercomparison Project Phase 6 (CMIP6) datasets: These data include all datasets published for 'CMIP6.PMIP.INM.INM-CM4-8' with the full Data Reference Syntax following the template 'mip_era.activity_id.institution_id.source_id.experiment_id.member_id.table_id.variable_id.grid_label.version'.
 
 The INM-CM4-8 climate model, released in 2016, includes the following components:
 aerosol: INM-AER1, atmos: INM-AM4-8 (2x1.5; 180 x 120 longitude/latitude; 21 levels; top level sigma = 0.01), land: INM-LND1, ocean: INM-OM5 (North Pole shifted to 60N, 90E; 360 x 318 longitude/latitude; 40 levels; sigma vertical coordinate), seaIce: INM-ICE1. 
The model was run by the Institute for Numerical Mathematics, Russian Academy of Science, Moscow 119991, Russia (INM) in native nominal resolutions: aerosol: 100 km, atmos: 100 km, land: 100 km, ocean: 100 km, seaIce: 100 km. 

Project: These data have been generated as part of the internationally-coordinated Coupled Model Intercomparison Project Phase 6 (CMIP6; see also GMD Special Issue: http://www.geosci-model-dev.net/special_issue590.html). The simulation data provides a basis for climate research designed to answer fundamental science questions and serves as resource for authors of the Sixth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC-AR6).

CMIP6 is a project coordinated by the Working Group on Coupled Modelling (WGCM) as part of the World Climate Research Programme (WCRP). Phase 6 builds on previous phases executed under the leadership of the Program for Climate Model Diagnosis and Intercomparison (PCMDI) and relies on the Earth System Grid Federation (ESGF) and the Centre for Environmental Data Analysis (CEDA) along with numerous related activities for implementation. The original data is hosted and partially replicated on a federated collection of data nodes, and most of the data relied on by the IPCC is being archived for long-term preservation at the IPCC Data Distribution Centre (IPCC DDC) hosted by the German Climate Computing Center (DKRZ).

The project includes simulations from about 120 global climate models and around 45 institutions and organizations worldwide. - Project website: https://pcmdi.llnl.gov/CMIP6.
DOI: 10.3535/hyg-h2e-enk
title: †Strophomenata Williams et al., 1996

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9kv-em8-mxg
title: †Atrypa Dalman, 1828

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/w34-agz-jkf
title: †Placocoenia macrophthalma (Goldfuss, 1826)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/sdt-afg-s3n
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/16b-7gk-y7t
title: Crinoidea Miller, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/07r-3w5-97y
title: Crinoidea Miller, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/fqq-ylb-j8g
title: Crinoidea Miller, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/960-t3j-gst
title: Cnidaria

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/44w-nsm-31t
title: Cnidaria

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/56j-zwz-j9m
title: Graptolithina Bronn, 1849

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/12g-mkl-pm8
title: Oliva Bruguière, 1789

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/2cf-d1g-sza
title: Cnidaria

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/j0v-pbh-dn4
title: Crinoidea Miller, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/avl-rjn-kyq
title: Crinoidea Miller, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rx0-k1n-4r7
title: Corbula scaphoides Hinds, 1843

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/hza-4sg-v14
title: Artinskia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/q5q-98e-9z4
title: †Heterastridium conglobatum Reuss, 1865

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/nva-w1a-fmc
title: †Siderastrea crenulata (Golffuss, 1826)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/s8e-t5g-efr
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tsn-71a-esw
title: Cnidaria

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/e5p-v5h-933
title: †Nephrolepidina tournoueri (Lemoine & Douvillé, 1904)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/d67-3r1-zws
title: Cnidaria

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4ah-bd3-aml
title: †Thamnasteria geometrica (Goldfuss, 1826)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tf6-0m1-34l
title: Cycloseris fragilis (Alcock, 1893)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jba-wvk-9sq
title: Anthozoa

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/d7m-brv-0ej
title: Crassatella Lamarck, 1799

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/fv2-0t4-y90
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qpf-a6s-gy6
title: Crinoidea Miller, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wkc-s2v-nv1
title: Chondrichthyes

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/fmj-dkc-9tk
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vyh-9a1-08m
title: †Heterastridium conglobatum Reuss, 1865

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/azd-52r-lba
title: Cephalopoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/l1w-4d1-v2r
title: Crinoidea Miller, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.mw96gm
title: Occurrence Download

description: A dataset containing 6385 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Oxydendrum DC."
 ]
}

 The dataset includes 6385 records from 107 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008940-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.