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DNA point accumulation for imaging in nanoscale topography (DNA-PAINT) was applied to measure EGFR receptor in resting and EGF-stimulated fixed HeLa cells. Pre-incubated antibody-nanobody construct was used to label EGFR. R3 docking strand was conjugated to the nanobody and complimentary imager strand was coupled to Cy3b fluorophore.

Organisms: Homo sapiens

Immunofluorescent images of male adolescent rat brain. Rats were exposed to 3,3'-dichloro-biphenyl-4-ol (sham, low, medium, and high groups) in a 28-day polymeric implant study. Four brain regions were analyzed.

Imaging Methods: confocal microscopy

Organisms: Rattus norvegicus

During ovariogenesis, more than two-thirds of germ cells are sacrificed to improve the quality of the remaining oocytes. However, the detailed mechanisms behind this selection process are not fully understood in mammals. Here, we developed a high-resolution, four-dimensional ovariogenesis imaging system to track the progression of oocyte fate determination in live mouse ovaries. Through this, we identified a cyst-independent oocyte phagocytosis mechanism that plays a key role in determining oocyte survival. We found that oocytes act as individual cells, rather than connected cyst structures, during ovarian reserve construction. In this process, dominant oocytes capture and absorb cell debris from sacrificed oocytes to enrich their cytoplasm and support their survival. Single-cell sequencing indicated that the sacrificed oocytes are regulated by autophagy. When oocyte sacrifice was inhibited using autophagy inhibitors, the pool of surviving oocytes expanded, but they failed to fully develop and contribute to fertility. Our study suggests that mammals have evolved a cyst-independent selection system to improve oocyte quality, which is essential for sustaining a long reproductive lifespan.

Imaging Methods: spinning disk confocal microscopy

Organisms: Mus musculus

Biomolecular condensates mediate dynamic compartmentalization of cellular processes. The multivalent interactions that underlie biomolecular condensation are often promoted by intrinsically disordered regions (IDRs) within proteins. While the role of IDRs in biomolecular condensates is well appreciated, predicting whether an IDR forms condensates in cells remains challenging. Here, we developed a machine learning model to accurately predict the condensation behavior of IDRs, analyzing 215 IDRs from fusion oncoproteins in HEK293T cells. We identified distinct sequence-derived physicochemical features associated with condensation. Leveraging these data, our model predicts that ~12% of the ~13,000 IDRs in the human proteome are likely to form cellular condensates, establishing a robust framework for proteome-wide analysis of IDR-mediated biomolecular condensation. Notably, proteins with condensate-forming IDRs are significantly enriched in RNA processing and splicing functions and are predominantly localized to membrane-less organelles (MLOs), highlighting a central role of IDR-mediated biomolecular condensation in cellular organization and RNA biology.

Imaging Methods: confocal microscopy

Organisms: Homo sapiens

Phase separation (PS) of biomolecular condensates is often assumed to be driven by interactions involving nucleic acids and intrinsically disordered regions (IDRs) of proteins. PGL-3 is a component of P granules, biomolecular condensates in C. elegans, that contains two structured domains in tandem (D1-D2), an internal IDR, and a C-terminal IDR rich with RGG motifs. Theoretical and in vitro studies have implicated the internal IDR and RGG motifs in driving PGL-3 PS via self-interactions and binding to RNA. Studies in cells, however, have implicated the D1 and D2 domains. Here, we investigate the molecular basis of PGL-3 PS in vitro using microscopy, crosslinking mass spectrometry and biophysical measurements. We find that D1-D2 oligomerizes and is necessary and sufficient for PS. The terminal RGG domain interacts with D1-D2 in a manner that enhances PS even in the absence of RNA.. In contrast, the internal IDR is neither necessary nor sufficient for PS. These findings support a new model for PGL-3 PS that is driven by oligomerization of structured domains and enhanced by RGG repeats.

Imaging Methods: confocal microscopy

Organisms: Caenorhabditis elegans

Oblique plane microscopy (OPM) is a form of light-sheet fluorescence microscopy (LSFM) employing a single microscope objective at the sample for both fluorescence excitation and detection. Dual-view OPM (dOPM) is an optically folded form of OPM. We present an improved dOPM system employing a 60×/1.2NA water immersion primary objective and measure the spatial resolution and fluorescence collection efficiency for illumination angles of 35° and 45° with respect to the coverslip. Illumination at 35° provides slightly better lateral resolution and collection efficiency. Collection efficiency measurements are compared to a full vectorial raytracing simulation of the system. Using a light-sheet angle of 35°, the median bead FWHM for 100 nm diameter fluorescent beads in x, y and z and the optical sectioning strength were measured over a volume of 100×100×100 μm³, to be 0.29, 0.31, 0.83 and 2.45-3.00 μm respectively when the two dOPM views are fused. We demonstrate less photobleaching in time-lapse dOPM of live mEmerald-expressing organoids compared to widefield epi-fluorescence z-stack imaging under the condition of equal detected fluorescence signal from a point object in focus. We demonstrate dOPM for multi-field-of-view 3D imaging of biological samples in 96-well plates and apply it to imaging cells in collagen gel and quantifying the FUCCI cell-cycle reporter to provide drug dose-response curves in spheroids. We also use it to perform time-lapse multi-field-of-view imaging and demonstrate the detection of organoid lumen closure and reopening, organoid migration within a collagen gel and observing dynamic events in arrays of ex vivo tissue slices.

Organisms: Homo sapiens Mus musculus

Human triple negative breast cancer tissue samples including cores and resections from Neoadjuvant Chemotherapy (NACT) responders and non-responders. Samples were acquired as part of the Wellcome Leap DeltaTissue project and were stained with the nuclear dye SiR-DNA followed by imaging using FLIM to detect chromatin compaction

Imaging Methods: fluorescence lifetime imaging microscopy

Organisms: Homo sapiens

See details in Sato Y, et. al. (2023) Development. Jun 1;150(11):dev201275.

Imaging Methods: recorded image time lapse microscopy confocal microscopy

Organisms: Coturnix japonica

Biological systems are inherently noisy; however, they produce highly stereotyped tissue morphology. Drosophila pupal wings show a highly stereotypic folding through uniform expansion and subsequent buckling of wing epithelium within a surrounding cuticle sac. The folding pattern produced by buckling is generally stochastic; it is thus unclear how buckling leads to stereotypic tissue folding of the wings. The authors found that the extracellular matrix (ECM) protein, Dumpy, guides the position and direction of buckling-induced folds. Dumpy anchors the wing epithelium to the overlying cuticle at specific tissue positions. Tissue-wide alterations of Dumpy deposition and degradation yielded different buckling patterns. In summary, they propose that spatiotemporal ECM remodeling shapes stereotyped tissue folding through dynamic interactions between the epithelium and its external structures.

Imaging Methods: recorded image confocal microscopy time lapse microscopy multi-photon microscopy

Organisms: Drosophila

IL-31 receptor blockade suppresses pruritus of atopic dermatitis. However, cell-type-specific contributions of IL-31 receptor to itch, its expression mechanism, and the downstream signaling pathway to induce itch remain unknown. In this report, using conditional knockout mice, the authors demonstrate that IL-31-induced itch requires sensory neuronal IL-31 receptor and STAT3. They find that IL-31 receptor expression is dependent on STAT3 in sensory neurons. In addition, pharmacological experiments suggest that STAT3 activation is important for the itch-inducing signaling downstream of the IL-31 receptor. A cutaneous IL-31 injection induces the nuclear accumulation of activated STAT3 first in sensory neurons that abundantly express IL-31 receptor and then in other itch-transmitting neurons. IL-31 enhances itch induced by various pruritogens including even chloroquine. Finally, pruritus associated with dermatitis is partially dependent on sensory neuronal IL-31 receptor and strongly on sensory neuronal STAT3. Thus, sensory neuronal STAT3 is essential for IL-31-induced itch and further contributes to IL-31-independent inflammatory itch.

Imaging Methods: recorded image confocal microscopy

Organisms: Mus musculus

Plants maintain nutrient homeostasis by controlling the activities and abundance of nutrient transporters. In Arabidopsis thaliana, the borate (B) transporter BOR1 plays a role in the efficient translocation of B under low-B conditions. BOR1 undergoes polyubiquitination in the presence of sufficient B and is then transported to the vacuole via multivesicular bodies (MVBs) to prevent B accumulation in tissues at a toxic level. A previous study indicated that BOR1 physically interacts with mu subunits of adaptor protein complexes AP-3 and AP-4, both involved in vacuolar sorting pathways. In this study, we investigated the roles of AP-3 and AP-4 subunits in BOR1 trafficking in Arabidopsis. The lack of AP-3 subunits did not affect either vacuolar sorting or polar localization of BOR1-GFP, whereas the absence of AP-4 subunits resulted in a delay in high-B-induced vacuolar sorting without affecting polar localization. Super-resolution microscopy revealed a rapid sorting of BOR1-GFP into AP-4-positive spots in the trans-Golgi network (TGN) upon high-B supply. These results indicate that AP-4 is involved in sequestration of ubiquitinated BOR1 into a TGN-specific subdomain 'vacuolar-trafficking zone', and is required for efficient sorting of MVB and vacuole. Their findings have thus helped elucidate the rapid vacuolar sorting process facilitated by AP-4 in plant nutrient transporters.

Imaging Methods: recorded image confocal microscopy time lapse microscopy

Organisms: Arabidopsis thaliana

Background: Mouse nodal immotile cilia mechanically sense the bending direction for left–right (L–R) determination and activate the left-side-specific signaling cascade, leading to increased Nodal activity. Asymmetric distribution of Pkd2, a crucial channel for L–R determination, on immotile cilia has been reported recently. However, the causal relationship between the asymmetric Pkd2 distribution and direction-dependent flow sensing is not well understood. Furthermore, the underlying molecular mechanism directing this asymmetric Pkd2 distribution remains unclear. Results: The effects of several recombinant proteins and inhibitors on the Pkd2 distribution were analyzed using super-resolution microscopy. Notably, bone morphogenetic protein 4 (BMP4) affected the Pkd2 distribution. Addi- tionally, three-dimensional manipulation of nodal immotile cilia using optical tweezers revealed that excess BMP4 caused defects in the mechanosensing abil- ity of the cilia. Conclusions: Experimental data together with model calculations suggest that BMP4 regulates the asymmetric distribution of Pkd2 in nodal immotile cilia, thereby affecting the ability of these cilia to sense the bending direction for L– R determination. This study, for the first time, provides insight into the rela- tionship between the asymmetric protein distribution in cilia and their function.

Imaging Methods: recorded image confocal microscopy stimulated emission depletion (STED) time lapse microscopy

Organisms: NCBITaxon:10090