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153 results for “Orphans”
Data_text section_ 11βHSD1_11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ
<p>Data from kinetic characterization (Km and vmaxapp) described in text section 3.1 of 11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ</p> <p>Dataset (doi:10.1194/jlr.M092908) contains values from kinetic characterization (Km and vmaxapp) described in text section (Kinetic values_11βHSD1.PNG) corresponding to raw data obtained from LC-MS/MS analysis provided as three files in CSV format (31003A-179400_DATE_KB_27Oxysterol_4_6_1-3). All further experiment related information and subsequent data analysis provided as two meta-data-files (31003A-179400_DATE_KB_27Oxysterol_4_6_M_1-2) as TXT format and PDF format.</p>
Supplementary material for "Surface frustration re-patterning underlies the structural landscape and evolvability of fungal orphan candidate effectors"
<p><strong>Tables</strong></p> <p>Table S1. List of fungal genomes analyzed in this work, associated references and properties.</p> <p>Table S2. List of all secreted proteins less than 300 amino-acids from the 20 fungal genomes. The table includes Signalp4.0 output, mature sequence, Espritz % disorder, pfam domains, AlphaFold top prediction pLDDT and the associated pdb file in Dataset S1.</p> <p>Table S3. Top Hits to pdb database for all OCE structures. 'network_node_name' corresponds to the portein identifier in the OCE structure similarity network provided in Dataset S3. 'Hidef_raw_community' corresponds to groups of structural OCE analogs identified by HiDEF community detection performed on the network provided in Dataset S3.</p> <p>Table S4. Table S4. List of the 62 major OCE folds with associated statistics. Columns I to AB provide the number of occurrences per species. Note that the actual number of members per species might be underestimated due to the stringent pipeline used for OCE identification (excluding proteins larger than 300 amino acids or containing PFAMs for instance).</p> <p> </p> <p>Table S5. Relative surface exposure, conformational flexibility and conservation data mapped on residues of members of the Alt-A1 and BoNT families. RMSD, root mean square deviation for all aligned atoms; Conservation, percentage conservation in multiple structure alignment.</p> <p>Table S6. Assignment of NCBI accessions to MMseqs clusters and assignment of MMseqs clusters to HMM matching-based super-clusters.</p> <p>Table S7. Co-mutation occurrences and associated p-values in two OCE clades from the Alt-A1 and KP6 families.</p> <p>Table S8. Amino acid properties inferred from mutation scans and frustration analyses in Alt-A1 cluster yellow1 and KP6 cluster 43. 'Number of aa variants' corresponds to the number of different amino acids found at each position (deletion counts as 1). 'Alanine scan ∆Z' and 'Deletion scan ∆Z' correspond to the difference between Z-score for the native protein agains itself and Z-score for the native protein against mutant at each position (either Alanine replacement or 5-aa deletion). 'Destabilization factor' is the average of column E and F. 'Stabilization factor' corresponds to the difference between expected structural variation due to destabilization factor and the observed structural variation in multiple mutants. 'netEffect' is difference between column G and H. 'Max co-mutation %' is the highest frequency of co-mutation observed with other residues in natural variants, with 'Min co-mutation p-value (Bonferroni corrected)' the associated p-value.Table S9. Sequence and delta Z of natural variants and mutants from AA1_cl25</p> <p>Table S9. List of natural variants and <em>in silico</em> mutants from the Alt-A1 cluster 25 analyzed in this work, including protein sequence and structure comparison scores (comparison with the reconstructed clade ancestor n0).</p> <p>Table S10. List of natural variants and in silico mutants from the KP6 cluster 43 analyzed in this work, including protein sequence and structure comparison scores (comparison with the reconstructed clade ancestor n0).</p> <p>Table S11. Summary statistics for the phylogenetic trees of 15 OCE clades analyzed for structure and frustration evolution.</p> <p>Table S12. Mapping of structural and frustration data onto phylogenetic trees for 15 OCE clades. The corresponding trees and protein structures are provided in Dataset S7.</p> <p><strong>Datasets</strong></p> <p>Dataset S1. AlphaFold rank1 models for 3 927 OCEs (.pdb format).</p> <p>Dataset S2. Pairwise structure comparison for 3 911 OCE. DALI matrix output containing pairwise Z-scores.</p> <p>Dataset S3. Network file including 2 561 OCEs with 3 or more vertices of Z-score weight 5.2 or more, in .sif and .xgmml formats.</p> <p>Dataset S4. Videos illustrating the mapping of relative surface exposure and structural variability in Alt-A1 and BoNT groups, amino-acids conservation, co-selected mutation patches and residue net stabilization effects on Alt-A1 clade 25 ancestor and KP6 cluster 43 ancestor. Color scales are as in Figure 2 and 3 respectively (.mp4 format).</p> <p>Dataset S5. Phylogenetic trees (.nwk), ancestral (.fasta) and modern variant (.faa) sequences, and AlphaFold best protein models (.pdb) for members of KP6 cluster 43 and Alt-A1 cluster 25. The archive includes 140 Alt-A1 protein structure and 128 KP6 protein structures.</p> <p>Dataset S6. Best predicted structures for 917 natural variants and mutants of AA1_cl25 and 801 natural variants and mutants of KP6_cl43 (.pdb format).</p> <p>Dataset S7. Phylogenetic trees (.nwk) and AlphaFold best protein models (.pdb) for 15 OCE clades. The file includes 2 598 protein structures distributed from clades AA1_s (139), AA1_t (135), AA1_y1 (140), AA1_y2 (90), AA1_y3 (128), BoNT_s (291), CIP_s (167), CIP_t (231), crystallin (233), GNK2 (189), KP6_cl3 (203), KP6_cl26 (111), KP6_cl43 (123), KP6_cl96 (231), KP6_cl242 (187).</p> <p><strong>Text and Figures</strong></p> <p>Text S1. Contains supplementary methods, results and figures S1 to S13.</p>
Data_supplemental Figure 3_11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ
<p>Data of supplemental figure 3 from 11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ</p> <p>Dataset (doi:10.1194/jlr.M092908) contains the original figure as PNG-format (10.1194_jlr.M092908_Fig. S3). Corresponding raw data obtained from liquid scintillation analysis provided as three files in CSV format (31003A-179400_DATE_SK_KB_27Oxysterol_11_6_1-3). All further experiment related information and subsequent data analysis provided as meta-data-file (31003A-179400_DATE_SK_KB_27Oxysterol_11_6_M) as TXT format</p>
Data_Figure 8_11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ
<p>Data of figure 8 from 11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ</p> <p>Dataset (doi:10.1194/jlr.M092908) contains the original figure as TIF-format (10.1194_jlr.M092908_Fig. 8). Corresponding raw data obtained from luminescence measurement analysis (Spectra Max L, Molecular devices, Serial Nr. LU01049) provided as eight files in CSV format (31003A-179400_DATE_SI_KB_27Oxysterol_18_1-2_1-4). All further experiment related information and subsequent data analysis provided as two meta-data-files (31003A-179400_DATE_SI_KB_27Oxysterol_18_1-2_M) as TXT format.</p>
Data_Figure 6_11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ
<p>Data of figure 6 from 11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ</p> <p>Dataset (doi:10.1194/jlr.M092908) contains the original figure as TIF-format (10.1194_jlr.M092908_Fig. 6). Corresponding raw data obtained from docking calculation analysis and calculations provided as four files in TXT format (31003A 179400_DATE_KB_27Oxysterol_19_1-4_1). All further experiment related information and subsequent data analysis provided as four meta-data-files (31003A-179400_DATE_KB_27Oxysterol_19_1-4_M) as TXT format.</p>
Data_Figure 5_11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ
<p>Data of figure 5 from 11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ</p> <p>Dataset (doi:10.1194/jlr.M092908) contains the original figure as TIF-format (10.1194_jlr.M092908_Fig. 5). Corresponding raw data obtained from liquid scintillation analysis provided as seven files in CSV format (31003A-179400_DATE_SK_KB_27Oxysterol_11_4-5_1-4). All further experiment related information and subsequent data analysis provided as two meta-data-file: (31003A-179400_DATE_SK_KB_27Oxysterol_11_4-5_M_1,) as TXT format.</p>
Data_Figure 1_11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ
<p>Data of figure 1 from 11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ</p> <p>Dataset (doi:10.1194/jlr.M092908) contains the original figure as TIF-format (10.1194_jlr.M092908_Fig. 1). Corresponding raw data obtained from LC-MS/MS analysis provided three files in CSV format (31003A-179400_DATE_KB_27Oxysterol_4_1_1-3). All further experiment related information and subsequent data analysis provided as two meta-data-files as TXT format and PDF format.</p>
Fig 4 in A mountain of millipedes III: A new genus for three new species from the Udzungwa Mountains and surroundings, Tanzania, as well as several 'orphaned' species previously assigned to Odontopyge Brandt, 1841 (Diplopoda, Spirostreptida, Odontopygidae)
Fig 4. Geotypodon millemanus gen. et sp. nov., paratype from Kiranzi-Kitungulu FR. A–E: Right gonopod. A. Posterior view. B. Anterior view, telomere in red oval. C. (Posterior-)mesal view, solenomere (yellow) and proximal telomeral spine (green) coloured. D. (Anterior-)mesal view. E. Telomere (part of coxa at lower left), basal (dorsal) view. F. Limbus. Abbreviations: atl = anterior distal lobe of telomere; bl = basal lamella of telomere; itl = intermediate distal lamella of telomere; ll = longitudinal lamella; mf = anteriad metaplical flange; mla = metaplical lamella; mp = metaplica; msp = metaplical spine-like process; pn = posttorsal narrowing; pp = proplica; ptl = posterior distal lobe of telomere; pts = proximal telomeral spine; slm = solenomere; tt = torsotope. Scales: A–E = 0.1 mm, F = 0.01 mm.
Fig. 1 in A mountain of millipedes III: A new genus for three new species from the Udzungwa Mountains and surroundings, Tanzania, as well as several 'orphaned' species previously assigned to Odontopyge Brandt, 1841 (Diplopoda, Spirostreptida, Odontopygidae)
Fig. 1. Map of the Udzungwa Mountains, showing the collecting sites for the three new Geotypodon species, as well as names of the Forest Reserves in question and names of individual mountains in West Kilombero FR. Red diamonds = G. millemanus gen. et sp. nov., yellow dot: G. submontanus gen. et sp. nov., blue triangle: G. iringensis gen. et sp. nov. Based on fig. 1 in Marshall et al. (2010) and information in Doody et al. (2001).
Fig. 2 in A mountain of millipedes III: A new genus for three new species from the Udzungwa Mountains and surroundings, Tanzania, as well as several 'orphaned' species previously assigned to Odontopyge Brandt, 1841 (Diplopoda, Spirostreptida, Odontopygidae)
Fig. 2. Geotypodon millemanus gen. et sp. nov., paratype from West Kilombero Scarp FR after nine years in alcohol. Photograph by N. Ioannou.
Fig. 3 in A mountain of millipedes III: A new genus for three new species from the Udzungwa Mountains and surroundings, Tanzania, as well as several 'orphaned' species previously assigned to Odontopyge Brandt, 1841 (Diplopoda, Spirostreptida, Odontopygidae)
Fig. 3. Body size of males of Geotypodon spp. Bold symbols indicate numbers of podous rings and midbody vertical diameter of the new species described here. Small circles and shaded areas indicate published measurements for other Geotypodon species.
Fig. 5 in A mountain of millipedes III: A new genus for three new species from the Udzungwa Mountains and surroundings, Tanzania, as well as several 'orphaned' species previously assigned to Odontopyge Brandt, 1841 (Diplopoda, Spirostreptida, Odontopygidae)
Fig. 5. Geotypodon submontanus gen. et sp. nov., holotype. A–E. Left gonopod. A. Anterior view. B. Posterior view. C. Apical part of coxa and proximal part of telopodite, anterior view. D. (Anterior-) mesal view. E. Posterior distal lobe of telomere; insertion highlights spine-like process. F. Limbus. Abbreviations: atl = anterior distal lobe of telomere; itl = intermediate distal lamella of telomere; ll = longitudinal lamella; mla = metaplical lamella; msp = metaplical spine-like process; ptl = posterior distal
Fig. 6 in A mountain of millipedes III: A new genus for three new species from the Udzungwa Mountains and surroundings, Tanzania, as well as several 'orphaned' species previously assigned to Odontopyge Brandt, 1841 (Diplopoda, Spirostreptida, Odontopygidae)
Fig. 6. Geotypodon iringensis gen. et sp. nov. A–D. Holotype, left gonopod. A. Anterior view. B. Posterior view. C. Mesal-ventral view. D. Telomere and solenomere, basal (dorsal) view. — E. Paratype, limbus. Abbreviations: atl = anterior distal lobe of telomere, bl = basal lamella of telomere, cx = coxa (seen from the basis, with remains of muscles); itl = intermediate distal lamella of telomere; lc = lateral concavity of coxa; lfl = longitudinally folded lamella; mf = anteriad metaplical flange; mp = metaplica; msp = metaplical spine-like process; pn = posttorsal narrowing; pp = proplica; ptl = posterior distal lobe of telomere; pts = proximal telomeral spine; slm = solenomere; tl = terminal lobe of telomere; tt = torsotope. Scales: A–D = 0.2 mm, E = 0.01 mm.
Locating undocumented orphaned oil and gas wells with smartphones
<p>Majority of the estimated 3 million abandoned oil and gas wells in the U.S. have missing documents and lack surface equipment making them difficult to locate. However, most of them have casings made of iron alloys which are magnetic and can be sensed by magnetometers. Here we utilize an iPhone 12 mini smartphone as a magnetometer to locate two abandoned wells. We designed a simple unmanned aerial vehicle (UAV) survey setup where the iPhone 12 mini was hung from an inexpensive small drone. We surveyed the two sites by flying the drone at altitudes, 10 m, 15 m, and 20 m above ground level. Our results show that at altitude of 10 magl the smartphone magnetometer could pick the magnetic anomaly of either of the wells at intensities ≥ 52 μT; sufficient to accurately locate the wells. At altitude of 15 magl the smartphone could locate the wells within ~5 m radius of the actual wells’ location, and it was unable to detect any magnetic anomalies at 20 magl. Simplicity of the setup, minimal required scientific knowledge and low cost of the setup makes this setup an ideal tool for locating orphaned wells by citizen scientists.</p>
In-situ feeding as a new management tool to conserve orphaned Eurasian lynx (Lynx lynx)
High human-caused mortality due to wildlife-vehicle-collisions and illegal killing leads to frequent cases of orphaned Eurasian lynx juveniles. Under natural conditions, this would result in starvation of the young. To avoid this, wildlife managers conventionally rear animals in captivity and release them later. However, this measure is an undesirable outcome for species conservation, managers and animals alike. Increased awareness of Eurasian lynx orphaned by human-caused mortality means managers must often intervene in endangered populations. In this study we report for the first time a successful case of in-situ feeding designed to avoid captivity of two orphaned Eurasian lynx. We exposed 13 roe deer and 7 red deer carcasses in the field to successfully support two orphans to the age of independence and confirm dispersal from the natal range. We present this management approach as a feasible and complimentary tool that can be considered in small or isolated large carnivore populations where every individual counts towards population viability.
Best fit Orphan stream model in the presence of the LMC
<p>We give the best fit stream model and orbit for Orphan in the presence of the LMC from the work of Erkal et al. 2019 (<a href="https://ui.adsabs.harvard.edu/abs/2019MNRAS.487.2685E">https://ui.adsabs.harvard.edu/abs/2019MNRAS.487.2685E</a>). As described in section 4 of that work, this best fit was achieved in a prolate Milky Way halo which responds to the LMC. See the table in the appendix of that work (A1) for the parameters used in the fit.</p> <p>The file containing the orbit (orphan_orbit.txt) gives the position of the Orphan progenitor, LMC, and Milky Way for the past 5 Gyr. The coordinates are Galactocentric in a right-handed system (i..e the Sun is at (-8.1,0,0) kpc and predominantly moving in the positive y direction). </p> <p>The file containing the stream (orphan_stream.txt) gives the position of the Orphan stream particles in Galactocentric coordinates as well as observables (ra,dec,distance,vr,pmra,pmdec) assuming the Sun is at (-8.1,0,0) kpc and moving with a velocity of (11.1,245,7.3) km/s. The stream is generated using the Lagrange point stripping technique as described in the paper. </p> <p>Please cite Erkal et al. 2019 if you make use of this simulation.</p>
In-situ feeding as a new management tool to conserve orphaned Eurasian lynx (Lynx lynx)
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Data_text section 11βHSD2_11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ
<p>Data from kinetic characterization (Km and vmaxapp) described in text section 3.2 of 11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ</p> <p>Dataset (doi:10.1194/jlr.M092908) contains values from kinetic characterization (Km and vmaxapp) described in text section (kinetic values 11βHSD2.PNG) corresponding to raw data obtained from LC-MS/MS analysis provided as three files in CSV format (31003A-179400_DATE_KB_27Oxysterol_4_7_1-3). All further experiment related information and subsequent data analysis provided as two meta-data-files: (31003A-179400_DATE_KB_27Oxysterol_4_7_M_1-2) as TXT format and PDF format.</p>
Data_supplemental Figure 4_11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ
<p>Data of supplemental figure 4 from 11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ</p> <p>Dataset (doi:10.1194/jlr.M092908) contains the original figure as PNG-format (10.1194_jlr.M092908_Fig. S4). Corresponding raw data obtained from luminescence analysis provided as six files in CSV format (31003A-179400_DATE_SK_KB_27Oxysterol_18_3-4_1-3). All further experiment related information and subsequent data analysis provided as meta-data-file (31003A-179400_DATE_SK_KB_27Oxysterol_18_3-4_M) as TXT format.</p>
Data_supplemental Figure 2_11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ
<p>Data of supplemental figure 2 from 11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ</p> <p>Dataset (doi:10.1194/jlr.M092908) contains the original figure as PNG format (10.1194_jlr.M092908_Fig. S2). All further experiment related information and subsequent data analysis provided as two meta-data-files: (31003A-179400_DATE_SK_KB_27Oxysterol_4_5_M_1-2) as TXT format and PDF-Format.</p>
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