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1,243 results for “Agonist”
Dataset (II) related to publication: Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist
<p>MD simulation data related to the publication Rashidian et al.: Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist. <a href="https://doi.org/10.1016/j.csbj.2022.06.020">https://doi.org/10.1016/j.csbj.2022.06.020</a></p> <p>Individual .zip files contain raw-desmond trajectories (-out.cms files and trj-files)</p> <p>dataset I: systems SRL+Co, C-100 and BAY-1797</p> <p>dataset I: each file contains all branched replicas and the main replica.</p> <p>dataset1: C_100_Replica1 contains four branched replicas and the main replica. The two of four branched replicas which stem from the middle of the main replica named: b_c_D1_r1_2285 (corresponding name in the SI data is R1_a) and b_c_D1_2285_r1_2 (corresponding name in the SI data is R1_b).</p> <p>dataset1: C_100_Replica2–5 , each file contains one main replica and the two branches.</p> <p>dataset I: system SRL+Co ;each file contains one main replica</p> <p>dataset I: system BAY-1797; each file contains one main replica</p> <p>dataset II:system SRL ; each file contains one main replica.</p>
Dataset (I) related to publication: Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist
<p>MD simulation data related to the publication Rashidian et al.: Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist. <a href="https://doi.org/10.1016/j.csbj.2022.06.020">https://doi.org/10.1016/j.csbj.2022.06.020</a></p> <p>Individual .zip files contain raw-desmond trajectories (-out.cms files and trj-files)</p> <p>dataset I: systems SRL+Co, C-100 and BAY-1797</p> <p>dataset I: each file contains all branched replicas and the main replica.</p> <p>dataset1: C_100_Replica1 contains four branched replicas and the main replica. The two of four branched replicas which stem from the middle of the main replica named: b_c_D1_r1_2285 (corresponding name in the SI data is R1_a) and b_c_D1_2285_r1_2 (corresponding name in the SI data is R1_b).</p> <p>dataset1: C_100_Replica2–5 , each file contains one main replica and the two branches.</p> <p>dataset I: system SRL+Co ;each file contains one main replica</p> <p>dataset I: system BAY-1797; each file contains one main replica</p> <p>dataset II:system SRL ; each file contains one main replica.</p>
Dataset (III) related to publication: Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist
<p>MD simulation data related to the publication Rashidian et al.: Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist. <a href="https://doi.org/10.1016/j.csbj.2022.06.020">https://doi.org/10.1016/j.csbj.2022.06.020</a></p> <p>Individual .zip files contain raw-desmond trajectories (-out.cms files and trj-files)</p> <p>dataset I: systems SRL+Co, C-100 and BAY-1797</p> <p>dataset I: each file contains all branched replicas and the main replica.</p> <p>dataset1: C_100_Replica1 contains four branched replicas and the main replica. The two of four branched replicas which stem from the middle of the main replica named: b_c_D1_r1_2285 (corresponding name in the SI data is R1_a) and b_c_D1_2285_r1_2 (corresponding name in the SI data is R1_b).</p> <p>dataset1: C_100_Replica2–5 , each file contains one main replica and the two branches.</p> <p>dataset I: system SRL+Co ;each file contains one main replica</p> <p>dataset I: system BAY-1797; each file contains one main replica</p> <p>dataset II:system SRL ; each file contains one main replica.</p> <p>dataset III:system C-100+Co (compound 100 in presence of SRC-1 coactivator) ; each file contains one main replica.</p>
Figure 2 in A comparison between affiliative and agonistic behaviours in wild and captive Sapajus libidinosus (Spix, 1823) (Mammalia, Primates, Cebidae)
Figure 2. Relative frequencies of social activities presented by free-living (Grey) and captive individuals (Black): (A) Affiliative behaviours and (B) Agonistic behaviours. We observed 10 different types of social behaviour, which occurred under both captivity and free-living conditions.
Figure 4 in A comparison between affiliative and agonistic behaviours in wild and captive Sapajus libidinosus (Spix, 1823) (Mammalia, Primates, Cebidae)
Figure 4. Captivity reduces agonistic interactions and does not change affiliative interactions. (A) Median and quartiles of the frequency of affiliative (A) and agonistic (B) behaviours presented by captive and free-living groups of S. libidinosus, separated by sex.
Figure 3 in A comparison between affiliative and agonistic behaviours in wild and captive Sapajus libidinosus (Spix, 1823) (Mammalia, Primates, Cebidae)
Figure 3. Relative frequency of social behaviours for each of the ten studied groups (BG = Baixa Grande; JB = Jurubeba; PF = Pedra Furada; OT = Oitenta; GT = Gato; FJZB = Fundação Jardim Zoológico de Brasília; PEDI = Parque Estadual Dois Irmãos; PZT2 = Parque Zoobotânico deTeresina (ilha 2); PZT3 = Parque Zoobotânico de Teresina (ilha 3); PZT1 = Parque Zoobotânico de Teresina (ilha 1). Under free-living conditions, agonistic behaviours were proportionally more frequent than were affiliative behaviours.
Small Molecule Agonist Binding at human NOP Receptor Data
<p>This entry contains:</p> <ul> <li>MD input files and scripts to run the simulations of N/OFQ(1-13)-NH2 in complex with the human NOP receptor (PDB ID: 8F7X)</li> <li>Initial docking poses and MD input files and scripts to run the simulations of predicted small molecule agonist in complex with the human NOP receptor <br> <table> <tbody> <tr> <td>Ligand</td> <td>Binding Mode</td> <td>Receptor Structure</td> </tr> <tr> <td><strong>(<em>R</em>)-Ro 65-6570</strong></td> <td>RBM01 </td> <td>8F7X</td> </tr> <tr> <td><strong>(<em>R</em>)-Ro 65-6570</strong></td> <td>RBM03 </td> <td>8F7X_mod</td> </tr> <tr> <td><strong>MCOPPB </strong></td> <td>MBM04</td> <td>8F7X_mod</td> </tr> <tr> <td><strong>MCOPPB </strong></td> <td>MBM05</td> <td>8F7X_mod</td> </tr> </tbody> </table> </li> <li>MD topology (.psf) and trajectory (.dcd) files of all five simulated systems (three replicas each)</li> </ul>
Table 3 in Description Of The Agonistic Behavior Of Aegla Longirostri (Decapoda: Aeglidae)
<p>Table 3. Definition of levels of aggression intensity shown by males of <i>Aegla longirostri</i>.</p><table><tbody><tr><th>Level</th><th>Behavior</th><th>Definition</th></tr></tbody><tbody><tr><th>-2</th><td>Fleeing</td><td>Walking rapidly, away from the opponent, tail flipping against opponent, being</td></tr><tr><th></th><td></td><td>caught, pulled, pushed, turned over, and/or climbed by opponent.</td></tr><tr><th>-1</th><td>Avoiding/Walking away</td><td>Walking slowly away from the opponent, without physical touch, and/or being</td></tr><tr><th></th><td></td><td>touched by opponent.</td></tr><tr><th>0</th><td>Separated without displacement (without physical touch)</td><td>Animals remain not physically touching, without moving, and ignoring the</td></tr><tr><th>opponent.</th></tr><tr><th>1</th><td>Separated with moving (without physical touch)</td><td>Animals remain without physical touching, moving around the arena, with</td></tr><tr><th></th><td></td><td>displacement or climbing the arena and ignoring the opponent.</td></tr><tr><th>2</th><td>Approaching (without physical contact)</td><td>Animals approach each other slowly and remain face to face for a short time.</td></tr><tr><th>3</th><td>Physical contact (not using chelae to hold)</td><td>Chasing, slapping, and whipping with antennae, touching and hitting with</td></tr><tr><th>chelipeds.</th></tr><tr><th>4</th><td>Physical contact (chelae used to hold)</td><td>Chelae used to pull, hold, and catch the opponent, displace the opponent with the</td></tr><tr><th></th><td></td><td>body, turn, and go up on the opponent’s body, fight.</td></tr><tr><th>5</th><td>Intense combat</td><td>No restrictions to using chelae.</td></tr></tbody></table>
Table 1 in Description Of The Agonistic Behavior Of Aegla Longirostri (Decapoda: Aeglidae)
<p>Table 1. Behavioral acts by males of <i>Aegla longirostri</i>, codes and descriptions.</p><table><tbody><tr><th>Code</th><th>Behavior</th><th>Description</th></tr><tr><th>NON-AGGRESSIVE ACTS</th></tr><tr><th>Without displacement</th></tr></tbody><tbody><tr><th>WD1</th><td>Without activity</td><td>The animal stands still, without moving its appendages, with the body near the</td></tr><tr><th></th><td></td><td>substrate, chelipeds directed forwards (near the back) and fingers open, or</td></tr><tr><th></th><td></td><td>chelipeds folded toward the cephalothorax, antennae directed forward, held</td></tr><tr><th></th><td></td><td>horizontally parallel to the body axis (on chelipeds).</td></tr><tr><th>WD2</th><td>With activity</td><td>The animal moves the pereiopods constantly (leg waving) and/or chelipeds or</td></tr><tr><th></th><td></td><td>antennae, always still; and keeps the chelipeds folded near the body and the</td></tr><tr><th></th><td></td><td>maxillipeds in motion.</td></tr><tr><th>With displacement (without real aggression)</th></tr><tr><th>WK</th><td>Walking</td><td>The animal walks slowly in the arena, with the body near the substrate, antennae</td></tr><tr><th></th><td></td><td>directed forward, parallel to the body axis, chelipeds directed down, folded, not</td></tr><tr><th></th><td></td><td>directed forward, or else chelipeds towards the front and open. Sometimes the</td></tr><tr><th></th><td></td><td>animal brings the cheliped to the maxillipeds, and moves the appendices</td></tr><tr><th></th><td></td><td>(antennae). This action is a way of exploring the arena.</td></tr><tr><th>CA</th><td>Climbing arena</td><td>The animal makes an attempt with chelipeds, pereiopods, and abdomen to climb the</td></tr><tr><th></th><td></td><td>arena walls. Antennae and chelipeds directed forward, chelipeds open, tailflips,</td></tr><tr><th></th><td></td><td>and movement of pereiopods.</td></tr><tr><th>AGGRESSIVE ACTS</th></tr><tr><th>AP</th><td>Approaching</td><td>An animal walks slowly toward the opponent; sometimes the antennae are directed</td></tr><tr><th></th><td></td><td>forwards and are in motion.</td></tr><tr><th>WA</th><td>Walking away</td><td>The animal slowly moves aside from the opponent, with abdomen directed toward the</td></tr><tr><th></th><td></td><td>opponent, generally it goes to one of the corners of the arena. The animal walks</td></tr><tr><th></th><td></td><td>away while the other animal approaches, but this does not characterize escaping,</td></tr><tr><th></th><td></td><td>because there is no signal of contact, only the approach of one animal leads the</td></tr><tr><th></th><td></td><td>other to walk away.</td></tr><tr><th>FF</th><td>Face to face</td><td>The animals remain still, face to face, one body length apart, antennae directed to the</td></tr><tr><th></th><td></td><td>front, chelipeds also directed to the front and very stretched, but sometimes the</td></tr><tr><th></th><td></td><td>chelipeds move toward the maxilliped.</td></tr><tr><th>To attack/the attack: when an animal chases its opponent and there is physical contact. The animals show the following behavioral postures during the</th></tr><tr><th>performance of the acts: chelipeds directed to the front, open and slightly raised; or chelipeds open and held high, antennae held perpendicular to the</th></tr><tr><th>animal’s body.</th><td></td></tr><tr><th>HQ</th><td>Hitting with chelipeds</td><td>An animal hits or ‘‘passes’’ with chelipeds on the opponent’s carapace or chelipeds.</td></tr><tr><th>TO</th><td>Being touched with chelipeds</td><td>When an animal is touched with the opponent’s chelipeds.</td></tr><tr><th>PQ</th><td>Pulling/pinching with chelipeds</td><td>Consists of pressing and pulling quickly the cheliped (or the pereiopods) of the</td></tr><tr><th></th><td></td><td>opponent. The animal tries to catch the opponent, but it cannot, during this act the</td></tr><tr><th></th><td></td><td>antennae (generally) remain horizontal to the body.</td></tr><tr><th>PO</th><td>Being pulled with chelipeds</td><td>When the animal is pulled by the opponent’s chelipeds, which may pull on both the</td></tr><tr><th></th><td></td><td>chelipeds and pereiopods.</td></tr><tr><th>CQ</th><td>Holding (catching) with chelipeds</td><td>Consists of holding (catching) the opponent with chelipeds. Generally the part which</td></tr><tr><th></th><td></td><td>is held is the chelipeds of the other animal or even the pereiopods and antennae,</td></tr><tr><th></th><td></td><td>and sometimes the animals try to catch the opponent’s cephalothorax.</td></tr><tr><th>CO</th><td>Being held (caught) with chelipeds</td><td>When the animal is held by the opponent’s chelipeds, which may hold chelipeds,</td></tr><tr><th></th><td></td><td>pereiopods, antennae, and even the cephalothorax of the other animal.</td></tr><tr><th>WhA</th><td>Whipping with antennae</td><td>This is a quick below with the antennae toward the back of the body, and the</td></tr><tr><th></th><td></td><td>opponent is behind the performer of the act.</td></tr><tr><th>TA</th><td>Touch with antennae</td><td>Consists in touching the opponent quickly with the antennae; the opponent being near</td></tr><tr><th></th><td></td><td>the front of the animal, the touch occurs both on the body and the antennae of the</td></tr><tr><th></th><td></td><td>opponent (commonly observed during combat).</td></tr><tr><th>DB</th><td>Pushing the opponent/displacing the body</td><td>One animal tries to displace the other pushing it with its own body (abdomen or</td></tr><tr><th></th><td></td><td>cheliped).</td></tr><tr><th>DO</th><td>Being pushed/ displaced by the opponent’s body</td><td>When the animal is moved by being pushed by the opponent; the pushing is</td></tr><tr><th></th><td></td><td>performed with the chelipeds or even the abdomen.</td></tr><tr><th>TOD</th><td>Turning the opponent upside down</td><td>During the combat an animal turns the opponent over, leaving it with the ventral part</td></tr><tr><th></th><td></td><td>of the body up.</td></tr><tr><th>BTO</th><td>Being turned by the opponent</td><td>When an animal is turned over by its opponent and remains with the ventral part of</td></tr><tr><th></th><td></td><td>the body up.</td></tr><tr><th>GO</th><td>Going up the opponent</td><td>An animal goes totally up over the opponent’s body, even when one of them is</td></tr><tr><th></th><td></td><td>climbing the arena.</td></tr><tr><th>BCO</th><td>Being ‘‘climbed’’ by the opponent</td><td>When an animal is ‘‘climbed’’ by the opponent.</td></tr><tr><th>Ch</th><td>Chasing</td><td>An animal chases (quickly approaching) the opponent, while the latter attempts to</td></tr><tr><th></th><td></td><td>escape.</td></tr><tr><th>Fl</th><td>Fleeing</td><td>The animal attempts to flee, walking or climbing the arena. The opponent approaches</td></tr><tr><th></th><td></td><td>and the animal escaping moves rapidly in another direction. In this act, the animal</td></tr><tr><th></th><td></td><td>keeps the antennae towards the front. One animal chases the other, which escapes,</td></tr><tr><th></th><td></td><td>sometimes with subtle contacts (with chelipeds and/or antennae).</td></tr></tbody></table>
A selective role for receptor activity-modifying protein in sub-chronic action of the amylin selective receptor agonist NN1213 compared to salmon calcitonin on body weight and food intake in male mice
<p>Raw data prism files for the manuscript "A selective role for receptor activity-modifying protein in sub-chronic action of the amylin selective receptor agonist NN1213 compared to salmon calcitonin on body weight and food intake in male mice"</p>
"Structural and Functional Diversity among Agonist-Bound States of the GLP-1 Receptor" - MD trajectories
<p>Topology (.psf) and coordinates (.xtc) files of:</p> <p>- Ex4 WT, D-Ala Ex4, and L-Ala Ex4 (all simulated in water - without receptor)</p> <p>- Partial unbinding and binding simulations of Ex4 WT, D-Ala Ex4 and L-Ala Ex4 from GLP-1R </p> <p>Water molecules, lipids, and ions have been removed.</p> <p> </p>
Effects of the oral angiotensin II type 2 receptor agonist C21 in Sugen-hypoxia induced pulmonary hypertension in rats
<p><span><span>Substantial evidence supports involvement of the renin-angiotensin system in pulmonary hypertension (PH), and the angiotensin II type 2 receptor (AT<sub>2</sub>R) is known to exert tissue-protective actions. The effect of the selective AT<sub>2</sub>R agonist C21 (also known as Compound 21 or buloxibutid) was evaluated in the rat Sugen-hypoxia PH model. After a single injection of Sugen 5416 and hypoxia for 21 days, </span><span>C21</span><span> (2 or 20 mg/kg) or vehicle was administered perorally twice daily from Day 21 to Day 55. On Day 56, hemodynamic assessments were performed, and lung and heart tissue were prepared for quantification of cardiac and vascular remodeling and fibrosis. Treatment with C21 20 mg/kg improved cardiac output and stroke volume and decreased right ventricular hypertrophy (all p<0.05). Treatment with C21 2 mg/kg significantly decreased vessel wall and muscular layer thickness and increased the luminal opening in vessels >100 </span><span>μ</span><span>m (all p<0.05). There were no significant differences between the two C21 doses on any parameter, and <em>post hoc</em> analyses </span><span>comparing the merged C21 groups with the vehicle group showed that C21 treatment reduced vascular remodeling (reduced endothelial proliferation and thickening of the vascular wall) in vessels of all sizes; moreover, the diastolic pulmonary artery pressure and right ventricular pressure were reduced along with reduction of right ventricular hypertrophy. Sugen 5416 and hypoxia increased pulmonary collagen deposition, which was counteracted by C21 20 mg/kg. In conclusion, the effects of C21 on vascular remodeling, hemodynamic alterations, and fibrosis suggest that AT<sub>2</sub>R agonists may have a role in Group 1 and 3 PH treatment.</span><br></span></p>
Human STING is a proton channel (Live-cell GALT pH Measurement upon STING agonist treatment with or without C53)
<p>hTERT-immortalized BJ1 cells (ATCC CRL-2522) were transduced with lentiviral ratiometric reporters targeted to GALT constructed based on designs reported in Linders et al. <em>ACS Chem. Biol. </em>2022, with superecliptic pHluorin and mRuby3. Transduced cells were sorted based on mRuby3 expression using a Sony MA900 sorter. BJ1 SEP-mRuby3 cells were plated in 24-well glass-bottom plates (Greiner Bio-One) at 40,000 cells/well. After 48 hours, cells were stained for 45 minutes at 37°C with 0.5 µg/ml Hoechst 34580 (Thermo Fisher Scientific, cat. #H21486). Cells were then washed and incubated in Fluorobrite DMEM (Thermo Fisher Scientific, cat. #A1896701) medium supplemented with 10% FBS, 1% Pen-strep, and 1x GlutaMAX (Thermo Fisher Scientific, cat. #35050061). For time-course experiments, cells were stimulated with 1 µM Bafilomycin A1 (Santa Cruz Biotechnology cat. #sc-201550),<strong> </strong>1 µM diABZI (Invivogen, #tlrl-diabzi), 20 µg/mL cGAMP (Invivogen, #tlrl-nacga23-1) with 5 ng/µL digitonin (Promega, #G9441) for 1 hr with or without the addition of 10 µM C53 (Cayman, #37354). All images were acquired using a Ti2-E inverted epifluorescence microscope (Nikon) with automated XYZ stage control, hardware autofocus, and a Yokogawa CSU-W1 confocal spinning disk unit with Zyla 4.2 PLUS sCMOS camera. An Okolab cage incubator was set to 37°C with 5% CO2. 405, 488, 561, and 640 nm laser lines were used for fluorescence illumination and all hardware was controlled using NIS elements software. Images were acquired using a 40X 0.95 NA CFI Plan Apo λ objective (Nikon MRD70470) with the following lasers and filters: Hoechst (405 nm laser, Chroma Multi LED set #89401), superecliptic pHluorin (488 nm laser, Chroma Multi LED set #89401), and mRuby3 (561 nm laser, Chroma Multi LED set #89401), assaying three z planes per field of view with 1.25 µm spacing. Fields of view were selected using NIS Elements software coordinates without manual preselection.</p> <p>Images are maximum projections of multiple z-stacks with each frame representing one timepoint: 0, 10, 20, 30, 40, 50, 60 minutes post treatment. Channels are: Hoechst 34580, SEP (super-ecliptic pHluorin), mRuby3, and SEP/mRuby3 (ratio). Crops indicate cropped fields of view presented in the manuscript.</p>
Human STING is a proton channel (Live-cell MGAT pH Measurement upon STING agonist treatment with or without C53)
<p>hTERT-immortalized BJ1 cells (ATCC CRL-2522) were transduced with lentiviral ratiometric reporters targeted to MGAT constructed based on designs reported in Linders et al. <em>ACS Chem. Biol. </em>2022, with superecliptic pHluorin and mRuby3. Transduced cells were sorted based on mRuby3 expression using a Sony MA900 sorter. BJ1 SEP-mRuby3 cells were plated in 24-well glass-bottom plates (Greiner Bio-One) at 40,000 cells/well. After 48 hours, cells were stained for 45 minutes at 37°C with 0.5 µg/ml Hoechst 34580 (Thermo Fisher Scientific, cat. #H21486). Cells were then washed and incubated in Fluorobrite DMEM (Thermo Fisher Scientific, cat. #A1896701) medium supplemented with 10% FBS, 1% Pen-strep, and 1x GlutaMAX (Thermo Fisher Scientific, cat. #35050061). For time-course experiments, cells were stimulated with 1 µM Bafilomycin A1 (Santa Cruz Biotechnology cat. #sc-201550),<strong> </strong>1 µM diABZI (Invivogen, #tlrl-diabzi), 20 µg/mL cGAMP (Invivogen, #tlrl-nacga23-1) with 5 ng/µL digitonin (Promega, #G9441) for 1 hr with or without the addition of 10 µM C53 (Cayman, #37354). All images were acquired using a Ti2-E inverted epifluorescence microscope (Nikon) with automated XYZ stage control, hardware autofocus, and a Yokogawa CSU-W1 confocal spinning disk unit with Zyla 4.2 PLUS sCMOS camera. An Okolab cage incubator was set to 37°C with 5% CO2. 405, 488, 561, and 640 nm laser lines were used for fluorescence illumination and all hardware was controlled using NIS elements software. Images were acquired using a 40X 0.95 NA CFI Plan Apo λ objective (Nikon MRD70470) with the following lasers and filters: Hoechst (405 nm laser, Chroma Multi LED set #89401), superecliptic pHluorin (488 nm laser, Chroma Multi LED set #89401), and mRuby3 (561 nm laser, Chroma Multi LED set #89401), assaying three z planes per field of view with 1.25 µm spacing. Fields of view were selected using NIS Elements software coordinates without manual preselection.</p> <p>Images are maximum projections of multiple z-stacks with each frame representing one timepoint: 0, 10, 20, 30, 40, 50, 60 minutes post treatment. Channels are: Hoechst 34580, SEP (super-ecliptic pHluorin), mRuby3, and SEP/mRuby3 (ratio). Crops indicate cropped fields of view presented in the manuscript.</p>
Human STING is a proton channel (Live-cell MGAT STING WT or S53L pH Measurement upon STING agonist treatment with or without C53)
<p>hTERT-immortalized BJ1 cells (ATCC CRL-2522) were transduced with lentiviral ratiometric reporters targeted to MGAT constructed based on designs reported in Linders et al. <em>ACS Chem. Biol. </em>2022, with superecliptic pHluorin and mRuby3. Transduced cells were sorted based on mRuby3 expression using a Sony MA900 sorter. Cells then were transduced with pXPR023 (lentiCRISPRv2) expressing an sgRNA targeting STING and selected with 0.1 µg/mL puromycin for 5 days. Finally, cells were transduced with blasticidin-STING-HA (WT or S53L) and selected using 10 µg/mL blasticidin HCl for 5 days.<strong> </strong> BJ1 SEP-mRuby3 STING-HA (WT or S53L) cells were plated in 24-well glass-bottom plates (Greiner Bio-One) at 40,000 cells/well. After 48 hours, cells were stained for 45 minutes at 37°C with 0.5 µg/ml Hoechst 34580 (Thermo Fisher Scientific, cat. #H21486). Cells were then washed and incubated in Fluorobrite DMEM (Thermo Fisher Scientific, cat. #A1896701) medium supplemented with 10% FBS, 1% Pen-strep, and 1x GlutaMAX (Thermo Fisher Scientific, cat. #35050061). For time-course experiments, cells were stimulated with 1 µM diABZI (Invivogen, #tlrl-diabzi) for 1 hr with or without the addition of 10 µM C53 (Cayman, #37354). All images were acquired using a Ti2-E inverted epifluorescence microscope (Nikon) with automated XYZ stage control, hardware autofocus, and a Yokogawa CSU-W1 confocal spinning disk unit with Zyla 4.2 PLUS sCMOS camera. An Okolab cage incubator was set to 37°C with 5% CO2. 405, 488, 561, and 640 nm laser lines were used for fluorescence illumination and all hardware was controlled using NIS elements software. Images were acquired using a 40X 0.95 NA CFI Plan Apo λ objective (Nikon MRD70470) with the following lasers and filters: Hoechst (405 nm laser, Chroma Multi LED set #89401), superecliptic pHluorin (488 nm laser, Chroma Multi LED set #89401), and mRuby3 (561 nm laser, Chroma Multi LED set #89401), assaying three z planes per field of view with 1.25 µm spacing. Fields of view were selected using NIS Elements software coordinates without manual preselection.</p> <p>Images are maximum projections of multiple z-stacks with each frame representing one timepoint: 0, 10, 20, 30, 40, 50, 60 minutes post treatment. Channels are: Hoechst 34580, SEP (super-ecliptic pHluorin), mRuby3, and SEP/mRuby3 (ratio). Crops indicate cropped fields of view presented in the manuscript.</p>
Molecular reshaping of phage-displayed Interleukin-2 at beta chain receptor interface to obtain potent super-agonists with improved developability profiles-primary dataset
<div class="c-message_kit__blocks c-message_kit__blocks--rich_text"> <div class="c-message__message_blocks c-message__message_blocks--rich_text"> <div class="p-block_kit_renderer"> <div class="p-block_kit_renderer__block_wrapper p-block_kit_renderer__block_wrapper--first"> </div> </div> </div> </div> <p>Interleukin-2 (IL-2) had been been engineered up to now by yeast display and in silico rational design. In this article we reshaped IL-2 interface with the IL-2 receptor beta subunit to increase binding affinity between both interacting partners, using phage display. Multiple IL-2 mutated variants were selected from large phage-displayed libraries, showing shared molecular patterns. An accumulation of negative charges in the segment 81-87 of IL-2 primary sequence was observed, as well as the strong preponderance of the replacement I92L. The first feature contributed to an optimized electrostatic complementarity between IL-2 and IL-2 receptor beta chain, resulting in higher affinity and faster association kinetics than the ones of previously reported H9 superkine retrieved from yeast display libraries. The presence of a Leu residue at position 92 was the key molecular determinant for a favourable biophysical profile characterized by high stability and production in mammalian-cell based recombinant systems, and decreased aggregation propensity. The new beta super-binders behaved as potent super agonists, both in vitro and in vivo. The latter scenario showed their better preformance when compared to both non-mutated IL-2 and H9. The current dataset contains source data for graphics showing frequency mutations and charge distribution among unselected variants contained in phage-displayed libraries and selected clones enriched after selection on immobilized beta chain. Data showing the direct comparison between different IL-2 mutated variants produced as Fc-fusion proteins are also presented. The comparison includes the results of beta chain binding assays (ELISA), proliferation and phosphorylation assays in vitro, in vivo expansion of lymphocyte populations and anti-tumor activity in animal models. Taken together, the above described data support the unique features of the new beta super-binders and their potential as immunostimulatory and anti-cancer agents.</p>
Assessing Induction of Double Strand Breaks With Androgen Receptor Partial Agonist in Patients on Androgen Suppression
ClinicalTrials.gov study NCT03507608. IPD Sharing: NO. Countries: 1. Publications: 1.
Study to Assess the Efficacy and Safety of the Beta-3 Agonist Mirabegron (YM178) in Patients With Symptoms of Overactive Bladder
ClinicalTrials.gov study NCT00689104. IPD Sharing: YES. Countries: 30. Publications: 3.
Phase 2 Trial of a Nicotinic Agonist in Schizophrenia
ClinicalTrials.gov study NCT00100165. IPD Sharing: UNDECIDED. Countries: 1. Publications: 2.
Inhaled Beta-adrenergic Agonists to Treat Pulmonary Vascular Disease in Heart Failure With Preserved EF (BEAT HFpEF): A Randomized Controlled Trial
ClinicalTrials.gov study NCT02885636. IPD Sharing: NO. Countries: 1. Publications: 2.
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.