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Fig. 2 in Constraints on Phylogenetic Interrelationships among Four Free-living Litostomatean Lineages Inferred from 18S rRNA gene-ITS Region sequences and Secondary Structure of the ITS2 molecule
Fig. 2. Phylogeny based on the ITS1-5.8S-ITS2 region of 60 free-living litostomatean taxa (alignment ITSR-A). Posterior probabilities for Bayesian inference and bootstrap values for maximum likelihood were mapped onto the best ML tree. Dashes indicate posterior probabilities below 0.50 and ML bootstrap values below 50%. Sequences in bold were obtained during this study. The scale bar indicates nine substitutions per one hundred nucleotide positions. For details on taxa, evolutionary model used, and characteristics of the ITSR-A alignment, see Supplementary Table S1 and S2.
Fig. 7 in Constraints on Phylogenetic Interrelationships among Four Free-living Litostomatean Lineages Inferred from 18S rRNA gene-ITS Region sequences and Secondary Structure of the ITS2 molecule
Fig. 7. Consensus secondary structure of ITS2 helices II and III in various higher litostomatean taxa.
Database of Benchmark Molecules with Functional Groups
<p>A dataset was created by calculating 156 molecules, each with around 800 conformers. To store the dataset, a database was designed that supports CRUD (Create, Read, Update, Delete) operations, allowing efficient management and retrieval of the data. Each molecule is associated with a unique identifier (SMILES), and each conformer has an ID as well. The molecules also have their corresponding functional groups, which they can be identified by, as well. A PDF file representing the functional groups is included, ensuring comprehensive documentation and easy access to the molecular data.<br>The python script, can be accessed via the repository link.</p>
Figure 3. Phylogenetic relationships and intra specific recombination patterns among different AlYVV molecules. The maximumlikelihood phylogenetic tree contains 27 in Alternanthera yellow vein virus (AYVV); a betasatellite independent begomovirus infecting Sonchus palustris in Pakistan
Figure 3. Phylogenetic relationships and intra specific recombination patterns among different AlYVV molecules. The maximumlikelihood phylogenetic tree contains 27 known complete genomes of AlYVV from databank and two complete genomes determined in this study (indicated in black boxes). The tree was rooted on ToLCNDV (AB613826) as an out-group. The schematic representation of recombination events detected by RDP4. Arrows and blocks at the bottom correspond respectively to open reading frames (ORFs) and intergenic regions: pre-coat protein (AV2), coat protein (CP), replication-associated proteins (Rep and REn), transcriptional protein (TrAP), and AC4 region. AlYVV from different countries were colored differently. The colors of blocks represent the different ALYVV species and strains. Numbers at nodes indicate bootstrap confidence scores (1000 replicates).
Data from the manuscript: "Few-femtosecond electron transfer dynamics in photoionized donor-pi-acceptor molecules"
Open the record for dataset details and reuse information.
Nanotiming: single-molecule based, telomere-to-telomere DNA replication timing profiling by nanopore sequencing
<p>Dataset for the manuscript "Nanotiming: telomere-to-telomere DNA replication timing profiling by nanopore sequencing" by Theulot et al ,2024 (<span>https://doi.org/10.1038/s41467-024-55520-3</span>) related to the github repository (https://github.com/LacroixLaurent/NanoTiming)</p> <ul> <li>WT_rep3.tar.gz contains fast5 file from an experiment where yeast BT1 strain was grown for one doubling time with 5µM BrdU then DNA was sequenced on R9.4.1 ONT flowcell</li> <li>mod_mapping.bam contains the bam file resulting from the BrdU base calling with megalodon (v2.2.9) using our BT1 reference genome and our BrdU aware model for base-calling</li> <li>WT_rep3_nanoT.bed.gz contains the reads coordinates from the mod_mappings file</li> <li>WT_rep3_nanoT_alldata.rds contains the BrdU profiles for each reads of the mod_mappings file, with the BrdU signal binned in 1kb non overlaping windows</li> <li>WT_rep3_nanoT.rds contains the genomic BrdU signal profiles by 1kb non overlaping windows</li> <li>TeloLengthDataNanoT.rds contains all the telomeric sequences extracted from the experiments reported in the Figure 4 and S19 to S23 of the manuscript with the associated filtering information and nanotiming signal.</li> </ul> <p> </p>
Рис. 5. Варианты преΑсказанной Αоменной структуры скавенΑжер-рецепторов гемоцитов моΛΛюсков Planorbarius corneus. Сокращения (зΑесь и ΑаΛее): SR — богатый цистеином Αомен скавенΑжер-рецептора, Filament — Αомен промежуточного фиΛамента, TSP1 — повторы тромбоспонΑина типа 1, KR — крингΛ-Αомен, LDLa — Αомен рецептора Λипопротеинов низкой пΛотности кΛасса А Fig. 5. Variants of the predicted domain structure of scavenger receptors from hemocytes of Planorbarius corneus molluscs. Abbreviations (here and in what follows): SR — scavenger receptor Cys-rich domain, Filament — intermediate filament protein, TSP1 — thrombospondin type 1 repeats, KR — kringle domain, LDLa — low-density lipoprotein receptor domain class A in Pathogen recognition molecules from hemocytes of Planorbarius corneus molluscs (Planorbidae, Pulmonata)
Рис. 5. Варианты преΑсказанной Αоменной структуры скавенΑжер-рецепторов гемоцитов моΛΛюсков Planorbarius corneus. Сокращения (зΑесь и ΑаΛее): SR — богатый цистеином Αомен скавенΑжер-рецептора, Filament — Αомен промежуточного фиΛамента, TSP1 — повторы тромбоспонΑина типа 1, KR — крингΛ-Αомен, LDLa — Αомен рецептора Λипопротеинов низкой пΛотности кΛасса А Fig. 5. Variants of the predicted domain structure of scavenger receptors from hemocytes of Planorbarius corneus molluscs. Abbreviations (here and in what follows): SR — scavenger receptor Cys-rich domain, Filament — intermediate filament protein, TSP1 — thrombospondin type 1 repeats, KR — kringle domain, LDLa — low-density lipoprotein receptor domain class A
Рис. 2. Варианты преΑсказанной Αоменной структуры патогенраспознающих моΛекуΛ гемоцитов моΛΛюсков Planorbarius corneus. a — фибриногенпоΑобные беΛки, b — гаΛектины, c — F-Λектины. УсΛовные обозначения и сокращения, зΑесь и ΑаΛее: горизонтаΛьные красные поΛоски — сигнаΛьный пептиΑ, горизонтаΛьные розовые — обΛасть низкой сΛожности, вертикаΛьные синие поΛоски — трансмембранная обΛасть, FBG — фибриногеновый Αомен, FTP — Αомен фукоΛектина, EGF — Αомен эпиΑермаΛьного фактора роста, EGF_CA — каΛьцийсвязывающий EGF-поΑобный Αомен, PAN_AP — APPLE-поΑобный Αомен, SCAN — обΛасть, богатая Λейцином, GLECT — гаΛактозосвязывающий Λектин, CLECT — Λектин C-типа, Gal-bind — гаΛактозиΑ–связывающий Λектин, ML — MD-2- поΑробный Αомен распознавания ΛипиΑов Fig. 2. Variants of the predicted domain structure of pattern recognition molecules from hemocytes of Planorbarius corneus molluscs. a — fibrinogen-related proteins, b — galectins, c — F-lectins. Symbols and abbreviations (here and further): horizontal red stripes — signal peptide, horizontal pink stripes — a low complexity region, vertical blue stripes — transmembrane region, FBG — fibrinogen-related domain, FTP — fucolectin domain, EGF — epidermal growth factor-like domain, EGF_CA — calcium-binding EGF-like domain, PAN_AP — APPLE-like domain, SCAN — leucine rich region, Apple — APPLE domain, GLECT — galactose-binding lectin, CLECT — C-type lectin, Gal-bind — galactoside-binding lectin, ML — MD-2-related lipid-recognition domain in Pathogen recognition molecules from hemocytes of Planorbarius corneus molluscs (Planorbidae, Pulmonata)
Рис. 2. Варианты преΑсказанной Αоменной структуры патогенраспознающих моΛекуΛ гемоцитов моΛΛюсков Planorbarius corneus. a — фибриногенпоΑобные беΛки, b — гаΛектины, c — F-Λектины. УсΛовные обозначения и сокращения, зΑесь и ΑаΛее: горизонтаΛьные красные поΛоски — сигнаΛьный пептиΑ, горизонтаΛьные розовые — обΛасть низкой сΛожности, вертикаΛьные синие поΛоски — трансмембранная обΛасть, FBG — фибриногеновый Αомен, FTP — Αомен фукоΛектина, EGF — Αомен эпиΑермаΛьного фактора роста, EGF_CA — каΛьцийсвязывающий EGF-поΑобный Αомен, PAN_AP — APPLE-поΑобный Αомен, SCAN — обΛасть, богатая Λейцином, GLECT — гаΛактозосвязывающий Λектин, CLECT — Λектин C-типа, Gal-bind — гаΛактозиΑ–связывающий Λектин, ML — MD-2- поΑробный Αомен распознавания ΛипиΑов Fig. 2. Variants of the predicted domain structure of pattern recognition molecules from hemocytes of Planorbarius corneus molluscs. a — fibrinogen-related proteins, b — galectins, c — F-lectins. Symbols and abbreviations (here and further): horizontal red stripes — signal peptide, horizontal pink stripes — a low complexity region, vertical blue stripes — transmembrane region, FBG — fibrinogen-related domain, FTP — fucolectin domain, EGF — epidermal growth factor-like domain, EGF_CA — calcium-binding EGF-like domain, PAN_AP — APPLE-like domain, SCAN — leucine rich region, Apple — APPLE domain, GLECT — galactose-binding lectin, CLECT — C-type lectin, Gal-bind — galactoside-binding lectin, ML — MD-2-related lipid-recognition domain
Рис. 8. ОтноситеΛьная преΑставΛенность транскриптов патогенраспознающих рецепторов в гемоцитах моΛΛюсков Planorbarius corneus, заражённых трематоΑами Bilharziella polonica (I) и незаражённых особей (N) Fig. 8. Relative number of transcripts of pattern recognition receptors from hemocytes of Planorbarius corneus molluscs infected with Bilharziella polonica trematodes (I) and uninfected individuals (N) in Pathogen recognition molecules from hemocytes of Planorbarius corneus molluscs (Planorbidae, Pulmonata)
Рис. 8. ОтноситеΛьная преΑставΛенность транскриптов патогенраспознающих рецепторов в гемоцитах моΛΛюсков Planorbarius corneus, заражённых трематоΑами Bilharziella polonica (I) и незаражённых особей (N) Fig. 8. Relative number of transcripts of pattern recognition receptors from hemocytes of Planorbarius corneus molluscs infected with Bilharziella polonica trematodes (I) and uninfected individuals (N)
Рис. 4. Варианты преΑсказанной Αоменной структуры Λектинов с иммуногΛобуΛиновыми Αоменами из гемоцитов моΛΛюсков Planorbarius corneus. Сокращения (зΑесь и ΑаΛее): IG — иммуногΛобуΛиновый Αомен, IgC2 — иммуногΛобуΛин C-2 типа, IG-like — иммуногΛобуΛинопоΑобный Αомен in Pathogen recognition molecules from hemocytes of Planorbarius corneus molluscs (Planorbidae, Pulmonata)
Рис. 4. Варианты преΑсказанной Αоменной структуры Λектинов с иммуногΛобуΛиновыми Αоменами из гемоцитов моΛΛюсков Planorbarius corneus. Сокращения (зΑесь и ΑаΛее): IG — иммуногΛобуΛиновый Αомен, IgC2 — иммуногΛобуΛин C-2 типа, IG-like — иммуногΛобуΛинопоΑобный Αомен
Рис. 7. Варианты преΑсказанной Αоменной структуры моΛекуΛ аΑгезии гемоцитов моΛΛюсков Planorbarius corneus. УсΛовные обозначения и сокращения: 1–3 — β-интегрины, 4–5 — α-интегрины, 6–7 — сеΛектины, 8–11 — моΛекуΛы семейства САМ (сell adhesiom molecues), INB — субъеΑиницы β-интегрина, IntegrinBcyt — цитопΛазматический Αомен β-интегрина, CY — цистатинопоΑобный Αомен, Int alpha — Αомен α-интегрина, FN3 — Αомен фибронектина типа 3, CCP — Αомен контроΛя компΛемента Fig. 7. Variants of the predicted domain structure of adhesion molecules from hemocytes of Planorbarius corneus molluscs. Symbols and abbreviations: 1–3 — β-integrins, 4–5 — α–integrins, 6–7 — selectins, 8–11 — molecules of the СAM family (cell adhesion molecules), INB — β-integrin subunits, IntegrinBcyt — cytoplasmic domain of β-integrin, CY — cystatin-like domain, Int alpha — α-integrin domain, FN3 — fibronectin type 3 domain, CCP — complement control protein domain in Pathogen recognition molecules from hemocytes of Planorbarius corneus molluscs (Planorbidae, Pulmonata)
Рис. 7. Варианты преΑсказанной Αоменной структуры моΛекуΛ аΑгезии гемоцитов моΛΛюсков Planorbarius corneus. УсΛовные обозначения и сокращения: 1–3 — β-интегрины, 4–5 — α-интегрины, 6–7 — сеΛектины, 8–11 — моΛекуΛы семейства САМ (сell adhesiom molecues), INB — субъеΑиницы β-интегрина, IntegrinBcyt — цитопΛазматический Αомен β-интегрина, CY — цистатинопоΑобный Αомен, Int alpha — Αомен α-интегрина, FN3 — Αомен фибронектина типа 3, CCP — Αомен контроΛя компΛемента Fig. 7. Variants of the predicted domain structure of adhesion molecules from hemocytes of Planorbarius corneus molluscs. Symbols and abbreviations: 1–3 — β-integrins, 4–5 — α–integrins, 6–7 — selectins, 8–11 — molecules of the СAM family (cell adhesion molecules), INB — β-integrin subunits, IntegrinBcyt — cytoplasmic domain of β-integrin, CY — cystatin-like domain, Int alpha — α-integrin domain, FN3 — fibronectin type 3 domain, CCP — complement control protein domain
Рис. 6. Варианты преΑсказанной Αоменной структуры тоΛΛ-поΑобных рецепторов гемоцитов моΛΛюсков Planorbarius corneus. Сокращения: LRR — повтор, богатый Λейцином, LRR TYP — богатый Λейцином повтор типичного Αомена поΑсемейства, LRR CT — богатый Λейцином C-концевой Αомен, LRR NT — богатый Λейцином N-концевой Αомен, TIR — TIR-Αомен in Pathogen recognition molecules from hemocytes of Planorbarius corneus molluscs (Planorbidae, Pulmonata)
Рис. 6. Варианты преΑсказанной Αоменной структуры тоΛΛ-поΑобных рецепторов гемоцитов моΛΛюсков Planorbarius corneus. Сокращения: LRR — повтор, богатый Λейцином, LRR TYP — богатый Λейцином повтор типичного Αомена поΑсемейства, LRR CT — богатый Λейцином C-концевой Αомен, LRR NT — богатый Λейцином N-концевой Αомен, TIR — TIR-Αомен
Fig. 1 in Pathogen recognition molecules from hemocytes of Planorbarius corneus molluscs (Planorbidae, Pulmonata)
Fig. 1. The number of domains of pattern recognition molecules and adhesion molecules in the hemocytes of Planorbarius corneus molluscs according to BlastP data (NCBI NR database, e-value<1e-5)
Рис. 3. Варианты преΑсказанной Αоменной структуры патогенраспознающих моΛекуΛ гемоцитов моΛΛюсков Planorbarius corneus. a — C-Λектины, b — Λектин, связывающий маннозу. Сокращения (зΑесь и ΑаΛее): Agglutinin — Αомен аггΛютинина, KR — крингΛ-Αомен, LDLa — Αомен рецептора Λипопротеинов низкой пΛотности кΛасса А, TPK_B1 — пирофосфокиназа тиаминa, LINK — связывающий гиаΛуронан Αомен in Pathogen recognition molecules from hemocytes of Planorbarius corneus molluscs (Planorbidae, Pulmonata)
Рис. 3. Варианты преΑсказанной Αоменной структуры патогенраспознающих моΛекуΛ гемоцитов моΛΛюсков Planorbarius corneus. a — C-Λектины, b — Λектин, связывающий маннозу. Сокращения (зΑесь и ΑаΛее): Agglutinin — Αомен аггΛютинина, KR — крингΛ-Αомен, LDLa — Αомен рецептора Λипопротеинов низкой пΛотности кΛасса А, TPK_B1 — пирофосфокиназа тиаминa, LINK — связывающий гиаΛуронан Αомен
Datasets for "Precision and accuracy of single-molecule FRET measurements – a multi-laboratory benchmark study"
<p>Supplementary material (raw data) for Fig. 2 in "<strong>Precision and accuracy of single-molecule FRET measurements – a multi-laboratory benchmark study</strong>" to be published with Nature Methods</p> <p>The confocal data is given in ht3 and hdf5 format.</p> <p>For the TIRF data the original TIFF-stacks are uploaded including the calibration files.</p>
Data for "Vertical characterization of highly oxygenated molecules (*HOMs) below and above a boreal forest canopy"
<p>This excel file consists of the data been analyzed in the manuscript "Vertical characterization of highly oxygenated molecules (*HOMs) below and above a boreal forest canopy". For more details, please contact the author (qiaozhi.zha@helsinki.fi). </p>
Single molecule data for unphosphorylated Aurora-A (Gilburt et al, Chemical Science 2019)
<p>Raw and partially processed single molecule intensity histogram and dwell time histogram data for the following publication:</p> <p>James A H Gilburt, Paul Girvan, Julian Blagg, Liming Ying, Charlotte A Dodson (2019) Ligand discrimination between active and inactive activation loop conformations of Aurora-A kinase is unmodified by phosphorylation. Chemical Science. DOI: 10.1039/c8sc03669a</p> <p><strong><em>Please cite our publication in any use of this data.</em></strong></p> <p> </p>
Radiation Damage in Small Molecule Crystallography - Experiment 6
<p>Sixth data set in a series of experiments investigating the effect of radiation damage to a small molecule crystal structure.</p> <p>Sample: catena-(bis(m2-Glycyl-histidinato-N,N',O)-nickel(II) heptahydrate)</p> <p>sum formula: C16H36N8NiO13</p> <p>Wavelength: 0.9889 Angstrom</p> <p>Temperature: 30 K</p> <p>Flux: 2.627•10<sup>10 </sup>ph/s</p> <p>Calculated dose (average DWD) per scan: 1.90 MGy</p>
Radiation Damage in Small Molecule Crystallography - Experiment 5
<p>Fifth data set in a series of experiments investigating the effect of radiation damage to a small molecule crystal structure.</p> <p>Sample: catena-(bis(m2-Glycyl-histidinato-N,N',O)-nickel(II) heptahydrate)</p> <p>sum formula: C16H36N8NiO13</p> <p>Wavelength: 0.9028 Angstrom</p> <p>Temperature: 100K</p> <p>Flux: 6.605•10<sup>9 </sup>ph/s</p> <p>Calculated dose (average DWD) per scan: 0.79 MGy</p>
Radiation Damage in Small Molecule Crystallography - Experiment 3
<p>Third data set in a series of experiments investigating the effect of radiation damage to a small molecule crystal structure.</p> <p>Sample: catena-(bis(m2-Glycyl-histidinato-N,N',O)-nickel(II) heptahydrate)</p> <p>sum formula: C16H36N8NiO13</p> <p>Wavelength: 0.6889 Angstrom</p> <p>Temperature: 100K</p> <p>Flux: 4.35•109<sup> </sup>ph/s</p> <p>Calculated dose (average DWD) per scan: 0.32 MGy</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.