Journal: Nature

Article Title: Heteromeric clusters of ubiquitinated ER-shaping proteins drive ER-phagy.

doi: 10.1038/s41586-023-06090-9

Figure Lengend Snippet: Fig. 5 | FAM134B-mediated ER-phagy requires ARL6IP1 in mice and humans. a, Rational of the mCherry–GFP–FAM134B reporter. b,c, ARL6IP1 loss-of-function compromises ER-phagy. Arl6ip1 WT and KO MEFs (b) or fibroblasts from the patient and the healthy individual (control) (c) were transfected with mCherry– GFP–FAM134B and stained for LC3B. Quantifications of LC3B+mCherry+GFP+ puncta and LC3B+mCherry+GFP– puncta per cell area suggest that the formation of autophagosomes (3 experiments with 10 cells per genotype each; two-sided Mann–Whitney U-test; MEFs, P = 0.0479; human cells, P = 0.0005) and autolysosomes (3 experiments with 10 cells per genotype each; two-sided Mann–Whitney U-test; MEFs, P = 0.0307; human cells, P = 0.0096) is impaired. d,e, ARL6IP1 loss-of-function enlarges ER sheets. Arl6ip1 WT and KO MEFs (d) or fibroblasts from the patient and healthy individual (e) were stained for the ER sheet protein CLIMP63 and the relative CLIMP63+ area per cell calculated (3 experiments with 15 cells per genotype; two-sided Mann–Whitney U-test; MEFs, P = 0.0001; human cells, P = 0.0001). f,g, TEM images showed increased numbers of small highly curved ER protrusions emanating from ER sheets in

Article Snippet: 4 nature portfolio | reporting sum m ary M arch 2021 Materials & experimental systems n/a Involved in the study Antibodies Eukaryotic cell lines Palaeontology and archaeology Animals and other organisms Human research participants Clinical data Dual use research of concern Methods n/a Involved in the study ChIP-seq Flow cytometry MRI-based neuroimaging Antibodies Antibodies used Primary: Actin Sigma (A-5441, Lot 064M4789V) AMFR Proteintech (16675-AP, Lot: 00046373) ARL6IP1 Sigma (PRS3305, Lot 33050404) ARL6IP1 Atlas Antibodies (HPA045307, Lot B118670) ATL2 Proteintech (16688-1-AP, Lot 00053330 ATL3 Proteintech (16921-1-AP, Lot 00008332) CCPG1 polyclonal rabbit, affinity purified with N-term peptide, gift from Simon Wilkinson CLIMP63 (CKAP4) Proteintech (16686-1-AP, Lot 00045668) CLIMP63 (CKAP4) R&D Systems (AF7355, Lot CGDG0118071) FAM134B Proteintech (21537-I-AP, Lot 00014408) FAM134B Genscript.

Techniques: Control, Transfection, Staining, MANN-WHITNEY

Journal:

Article Title: In Situ Gene Expression in Mixed-Culture Biofilms: Evidence of Metabolic Interactions between Community Members

doi:

Figure Lengend Snippet: Online monitoring of GFP expression from Pu and Pm in communities after 1 day of biofilm formation. (A and B) Pu expression in the biofilm formed by the community containing P. putida R1 (Pu::gfp). Note the spherical Acinetobacter sp. strain C6 colony (indicated by an asterisk) in the reflection image (A). The GFP fluorescence (B), visualized as an SFP, shows that Pu was constitutively expressed in the majority of the cells. (C through E) Expression of Pm in the biofilm formed by the community containing P. putida R1 (Pm::gfp). All cells (including the Acinetobacter sp. strain C6 colony indicated with an asterisk) are shown in the reflection image (C), and GFP fluorescence (D) shows the lack of homogeneous Pm expression on day 1. Panel E shows GFP expression quantified along the line shown in panel D and shows that GFP fluorescence increased as cells got closer to the Acinetobacter sp. strain C6 microcolony. The pixel intensities were measured from the maximum projection image (data not shown). (F and G) Biofilm formation by the wild-type community. The reflection image (F) and the SFP (G) show that no cells expressed GFP in the negative control. The asterisk indicates the spherical microcolonies of Acinetobacter sp. strain C6, and the arrows show the direction of flow.

Article Snippet: Multichannel simulated fluorescence projection (SFP) images were generated by using IMARIS software (Bitplane AG, Zürich, Switzerland) running on a Indigo 2 workstation (Silicon Graphics Inc., Mountain View, Calif.).

Techniques: Expressing, Fluorescence, Negative Control

Journal: Bioengineering

Article Title: Emerging Biomedical and Clinical Applications of 3D-Printed Poly(Lactic Acid)-Based Devices and Delivery Systems

doi: 10.3390/bioengineering11070705

Figure Lengend Snippet: Recent studies on 3D-printed PLA-containing training models and simulators.

Article Snippet: Neuraxial anesthesia simulator , CT , PLA, gelatin, psyllium fiber , MEX , The participants were 22 anesthesiologists. Although the model was found to be less realistic in terms of surface palpation than the Simulab phantom, it had significantly better fidelity for the loss of resistance, dural puncture, and ultrasound imaging. , [ ] .

Techniques: Calcium Carbonate, Imaging, Injection

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: Dynamical differential covariance recovers directional network structure in multiscale neural systems

doi: 10.1073/pnas.2117234119

Figure Lengend Snippet: Summary of structural connectivity matrices

Article Snippet: We used two datasets of structural connectome in the simulation: the Human Connectome Project (HCP) diffusion MRI (dMRI) connectome ( ) and the diffusion tensor imaging (DTI) dataset built in the virtual brain simulator (TVB) ( ).

Techniques: