Open-3DSIM: an open-source three-dimensional structured illumination microscopy reconstruction platform.

Open-3DSIM is an open-source reconstruction platform for three-dimensional structured illumination microscopy. We demonstrate its superior performance for artifact suppression and high-fidelity reconstruction relative to other algorithms on various specimens and over a range of signal-to-noise levels. Open-3DSIM also offers the capacity to extract dipole orientation, paving a new avenue for interpreting subcellular structures in six dimensions (xyzθλt). The platform is available as MATLAB code, a Fiji plugin and an Exe application to maximize user-friendliness.

Fluorescence Lifetime Super-Resolution Imaging Unveil the Dynamic Relationship between Mitochondrial Membrane Potential and Cristae Structure Using the Förster Resonance Energy Transfer Strategy.

Mitochondrial cristae, invaginations of the inner mitochondrial membrane (IMM) into the matrix, are the main site for the generation of ATP via oxidative phosphorylation, and mitochondrial membrane potential (MMP). Synchronous study of the dynamic relationship between cristae and MMP is very important for further understanding of mitochondrial function. Due to the lack of suitable IMM probes and imaging techniques, the dynamic relationship between MMP and cristae structure alterations remains poorly understood. We designed a pair of FRET-based molecular probes, with the donor (OR-LA) being rhodamine modified with mitochondrial coenzyme lipoic acid and the acceptor (SiR-BA) being silicon-rhodamine modified with a butyl chain, for simultaneous dynamic monitoring of mitochondrial cristae structure and MMP. The FRET process of the molecular pair in mitochondria is regulated by MMP, enabling more precise visualization of MMP through fluorescence intensity ratio and fluorescence lifetime. By combining FRET with FLIM super-resolution imaging technology, we achieved simultaneous dynamic monitoring of mitochondrial cristae structure and MMP, revealing that during the decline of MMP, there is a progression involving cristae dilation, fragmentation, mitochondrial vacuolization, and eventual rupture. Significantly, we successfully observed that the rapid decrease in MMP at the site of mitochondrial membrane rupture may be a critical factor in mitochondrial fragmentation. These data collectively reveal the dynamic relationship between cristae structural alterations and MMP decline, laying a foundation for further investigation into cellular energy regulation mechanisms and therapeutic strategies for mitochondria-related diseases.

Multicolor Tuning of Perylene Diimides Dyes for Targeted Organelle Imaging In Vivo.

The adjustment of the emission wavelengths and cell permeability of the perylene diimides (PDI) for multicolor cell imaging is a great challenge. Herein, based on a bay-region substituent engineering strategy, multicolor perylene diimides (MCPDI) were rationally designed and synthesized by introducing azetidine substituents on the bay region of PDIs. With the fine-tuned electron-donating ability of the azetidine substituents, these MCPDI showed high brightness, orange, red, and near infrared (NIR) fluorescence along with Stokes shifts increasing from 35 to 110 nm. Interestingly, azetidine substituents distorted to the plane of the MCPDI dyes, and the twist angle of monosubstituted MCPDI was larger than that of disubstituted MCPDI, which might efficiently decrease their π-π stacking. Moreover, all of these MCPDI dyes were cell-permeable and selectively stained various organelles for multicolor imaging of multiple organelles in living cells. Two-color imaging of lipid droplets (LDs) and other organelles stained with MCPDI dyes was performed to reveal the interaction between the LDs and other organelles in living cells. Furthermore, a NIR-emitting MCPDI dye with a mitochondria-targeted characteristic was successfully applied for tumor-specific imaging. The facile synthesis, excellent stability, high brightness, tunable fluorescence emission, and Stokes shifts make these MCPDI promising fluorescent probes for biological applications.

Peripheral lymphocyte count defines the clinical phenotypes and prognosis in patients with anti-MDA5-positive dermatomyositis.

OBJECTIVE: To explore the role of peripheral lymphocyte count in phenotyping and prognosis prediction in dermatomyositis (DM) patients with anti-MDA5 antibodies. METHODS: In total, 1669 patients with idiopathic inflammatory myopathy (IIM) were retrospectively enrolled. Clinical characteristics and prognosis of patients with anti-MDA5+ DM were analyzed in association with peripheral lymphocyte counts and clusters determined by unsupervised machine learning. RESULTS: The peripheral lymphocyte count was significantly lower in the anti-MDA5+ DM group (N = 421) than in the other IIM serotype groups. The anti-MDA5+ DM patients were divided into three groups; the severe lymphopenia group had skin ulcers and rapidly progressive interstitial lung disease (RP-ILD); patients with a normal lymphocyte count had a younger age of onset, more frequent arthritis, and normal serum ferritin levels, whereas mild lymphopenia group showed a moderate increase of serum ferritin and intermediate incidence of RP-ILD. Survival analysis revealed that the 3- and 6-month mortality rates were significantly higher in the severe lymphopenia group (29.0% and 42.1%, respectively) than in the mild lymphopenia group and normal lymphocyte count group (p value <0.001). Consistently, unsupervised machine learning identified three similar groups; the arthritis cluster shows the highest lymphocyte counts and best prognosis; the RP-ILD cluster presents the lowest peripheral lymphocyte, high incidence of RP-ILD, and poor prognosis; the typical DM rash cluster had a moderate peripheral lymphocyte count and an intermediate prognosis. CONCLUSIONS: Lymphopenia is a unique manifestation of anti-MDA5+ DM. Peripheral lymphocyte count can define clinical phenotypes and predict prognosis in anti-MDA5+ DM.

Marking ground glass nodules with pulmonary nodules localization needle prior to video-assisted thoracoscopic surgery.

OBJECTIVES: To evaluate the efficacy and safety of marking ground glass nodules (GGNs) with pulmonary nodules localization needle (PNLN) prior to video-assisted thoracoscopic surgery (VATS). MATERIALS AND METHODS: From June 2020 to February 2021, all patients with GGNs who received CT-guided localization using PNLN before VATS were enrolled. Clinical and imaging data were retrospectively analyzed. RESULTS: A total of 352 consecutive patients with 395 GGNs were included in the study. The mean diameter of GGNs was 0.95 ± 0.48 cm, and the shortest distance from nodules to the pleura was 1.73 ± 0.96 cm. All 395 GGNs were marked using PNLNs. The time required for marking was 7.8 ± 2.2 min. The marking success rate was 99.0% (391/395). The marking failure of four nodules was all due to the unsatisfactory position of PNLNs. No marker dislocation occurred. Marking-related complications included pneumothorax in 63 cases (17.9%), hemorrhage in 34 cases (9.7%), and hemoptysis in 6 cases (1.7%). All the complications were minor and did not need special treatment. Localization and VATS were performed on the same day in 95 cases and on different days in 257 cases. All GGNs were successfully removed by VATS. No patient converted to thoracotomy. Histopathological examination revealed 74 (18.7%) benign nodules and 321 (81.3%) malignant nodules. CONCLUSIONS: It is safe and reliable to perform preoperative localization of GGNs using PNLNs, which can effectively guide VATS to remove GGNs. KEY POINTS: • Preoperative localization of GGNs could effectively guide VATS to remove GGNs. • PNLN was based on the marking principle of hook-wire, through the improvement of its material, specially designed to mark pulmonary nodules. • The application of PNLN to mark GGNs had high success rate, good patient tolerance, and no dislocation. Meanwhile, VATS could be performed 2 to 3 days after marking GGNs with PNLN.

Fluorescent probes based on multifunctional encapsulated perylene diimide dyes for imaging of lipid droplets in live cells.

Due to their strong hydrophobicity and the aggregation-caused quenching effect, the application of perylene diimide (PDI) dyes in biological and medicinal fields lags far behind that of other dyes. Based on a multifunctional encapsulation strategy, we prepared isopropylphenyl sulfone encapsulated PDI dyes (SFPDIs). The four hydrophilic sulfone groups on the bay position of the PDIs not only effectively inhibit the fluorescence quenching caused by π-aggregation but also endow the SFPDIs with good live-cell permeability. The six lipophilic isopropylphenyl groups encapsulate PDI emitters and confer SFPDIs with excellent lipid droplet-targeting ability. Furthermore, the strong electron-withdrawing sulfone groups give the PDIs excellent anti-oxidation ability.

Improving Brightness and Stability of Si-Rhodamine for Super-Resolution Imaging of Mitochondria in Living Cells.

Photostable and bright organic dyes emitting in the near-infrared region are highly desirable for long-term dynamic bioimaging. Herein, we report a synthetic approach to build novel methoxy modified Si-rhodamine (SiRMO) dyes by introducing the methoxybenzene on the xanthene moiety. The brightness of SiRMO increased from 2300 M-1 cm-1 (SiRMO-0) to 49000 M-1 cm-1 (SiRMO-2) when the substituent 2,5-dimethoxybenzene was replaced with 2,6-dimethoxybenzene. Moreover, the stability of SiRMO-2 was significantly improved due to the steric hindrance protection of the two methoxy groups on the ninth carbon atom of the xanthene. After fast cellular uptake, the SiRMO dyes selectively stained the mitochondria with a low background in live cultured cells and primary neurons. The high brightness and stability of SiRMO-2 significantly improved the capability of monitoring mitochondria dynamic processes in living cells under super-resolution conditions. Moreover, with the fluorescence nanoscopy techniques, we observed the structure of mitochondrial cristae and mitochondria fission, fusion, and apoptosis with a high temporal resolution. Under two-photon illumination, SiRMO-2 showed also enhanced two-photon brightness and stability, which are important for imaging in thick tissue.

Recent advances in FRET probes for mitochondrial imaging and sensing.

Mitochondria, as essential organelles in cells, play a crucial role in cellular growth and apoptosis. Monitoring mitochondria is of great importance, as mitochondrial dysfunction is often considered a hallmark event of cell apoptosis. Traditional fluorescence probes used for mitochondrial imaging and sensing are mostly intensity-based and are susceptible to factors such as concentration, the probe environment, and fluorescence intensity. Probes based on fluorescence resonance energy transfer (FRET) can effectively overcome external interference and achieve high-contrast imaging of mitochondria as well as quantitative monitoring of mitochondrial microenvironments. This review focuses on recent advances in the application of FRET-based probes for mitochondrial structure imaging and microenvironment sensing.

Visualization of cristae and mtDNA interactions via STED nanoscopy using a low saturation power probe.

Mitochondria are crucial organelles closely associated with cellular metabolism and function. Mitochondrial DNA (mtDNA) encodes a variety of transcripts and proteins essential for cellular function. However, the interaction between the inner membrane (IM) and mtDNA remains elusive due to the limitations in spatiotemporal resolution offered by conventional microscopy and the absence of suitable in vivo probes specifically targeting the IM. Here, we have developed a novel fluorescence probe called HBmito Crimson, characterized by exceptional photostability, fluorogenicity within lipid membranes, and low saturation power. We successfully achieved over 500 frames of low-power stimulated emission depletion microscopy (STED) imaging to visualize the IM dynamics, with a spatial resolution of 40 nm. By utilizing dual-color imaging of the IM and mtDNA, it has been uncovered that mtDNA tends to habitat at mitochondrial tips or branch points, exhibiting an overall spatially uniform distribution. Notably, the dynamics of mitochondria are intricately associated with the positioning of mtDNA, and fusion consistently occurs in close proximity to mtDNA to minimize pressure during cristae remodeling. In healthy cells, >66% of the mitochondria are Class III (i.e., mitochondria >5 µm or with >12 cristae), while it dropped to <18% in ferroptosis. Mitochondrial dynamics, orchestrated by cristae remodeling, foster the even distribution of mtDNA. Conversely, in conditions of apoptosis and ferroptosis where the cristae structure is compromised, mtDNA distribution becomes irregular. These findings, achieved with unprecedented spatiotemporal resolution, reveal the intricate interplay between cristae and mtDNA and provide insights into the driving forces behind mtDNA distribution.

Water-soluble fluorescent probes based on dendronized polyfluorenes for cell imaging.

Novel water-soluble dendronized fluorescent polyfluorenes (DFPFs) are prepared from hydrophilic monomers and hydrophobic comonomers. Incomplete energy transfer is found to result in a two-color emission of the DFPFs at around 410 and 650 nm. The incomplete energy transfer can be attributed to the poor compatibility between the fluorene and benzothiadiazole units. Polyethylene oxide (PEO) encapsulation of the DFPFs shows over 90% cell viability, indicating good biocompatibility. These DFPFs show differential cellular uptake. P1 with fewer PEO chains exhibits limited cellular membrane uptake and low brightness in cells. By contrast, P3 with more PEO chains is efficiently internalized by cells and accumulated in the cytoplasm. A strong fluorescence from whole cells is also observed.

Atp7b deficiency induces zebrafish eye developmental defects.

As a copper (Cu) transport ATPase, ATP7B plays an important role in maintaining Cu homeostasis in the body and its dysfunction is associated with retinal disease. How ATP7B dysfunction and the subsequent Cu overload induce retinal damage, however, are unknown. Here, we show that atp7b-/- homozygous zebrafish larvae are insensitive to light stimulation, with a reduction in retinal cells but normal like morphological phenotypes. Additionally, a series of differentially expressed genes are unveiled in atp7b-/- mutated larvae, which enrich in photo-transduction, structural constituent of eye lens, sensory perception of light stimulus, oxidative phosphorylation, and ATPase activity. Moreover, we show the Cu accumulation in retinal cells in atp7b-/- mutated larvae, which results in endoplasmic reticulum (ER) stress and retinal cell apoptosis and subsequent retinal defects. The integral data in this study demonstrate that atp7b mutation leads to Cu accumulation in zebrafish retinal cells and the consequence ER stress and retinal cell death. These data may give some possible hints to explain retinal disease occurred in the Cu dysregulation syndromes Wilson's disease with ATP7B mutation.

Air embolism after CT-guided localization of pulmonary ground-glass nodules.

OBJECTIVE: To investigate the incidence of air embolism (AE) related to CT-guided localization of pulmonary ground-glass nodules (GGNs) prior to video-assisted thoracoscopic surgery (VATS). METHODS: The data of all patients who received CT-guided localization of GGNs before VATS from May 2020 to October 2021 were retrospectively analyzed. RESULTS: A total of 1395 consecutive patients with 1553 GGNs were enrolled. AEs occurred in seven patients (0.5%). In four of the seven patients with AE, the embolism was detected before the patients left the CT table and emergency treatments were carried out. Among them, one patient had chest tightness and unilateral limb dyskinesia, one patient had convulsions and transient loss of consciousness, and two patients had no definite clinical symptoms. After a short-term high-flow oxygen inhalation, the clinical symptoms of two patients with symptomatic AE disappeared and two patients with asymptomatic AE did not show any symptoms. In the remaining three patients with AE, the embolism were detected retrospectively when evaluating the images in the PACS for this study. Fortunately, these three patients never developed clinical symptoms related to AE. All seven patients with AE underwent VATS on the day of localization and all GGNs were successfully removed under the guidance of markers. CONCLUSION: The incidence of AE related to CT-guided localization of GGNs was 0.5%, which was significantly higher than expected. Post-localization whole thoracic CT should be performed and observed carefully so as to avoid missed AE and delayed treatment. ADVANCES IN KNOWLEDGE: The incidence of AE related to CT-guided localization of GGNs was 0.5%. In order to timely detect AE, whole thoracic CT scan rather than local CT in the lesion area should be performed after localization. A small amount of AE may be missed if the post- localization CT images are not carefully observed.

Copper overload impairs hematopoietic stem and progenitor cell proliferation via prompting HSF1/SP1 aggregation and the subsequently downregulating FOXM1-Cytoskeleton axis.

Unbalanced Cu homeostasis has been suggested to be associated with hematopoietic disease, but the roles of Cu overload in the hematopoietic system and the potential mechanisms are obscure. Here, we report a novel association and the novel potential pathways for Cu overload to induce proliferation defects in zebrafish embryonic hematopoietic stem and progenitor cells (HSPCs) via down-regulating expression of foxm1-cytoskeleton axis, which is conserved from fish to mammals. Mechanistically, we show the direct binding of Cu to transcriptional factors HSF1 and SP1 and that Cu overload induces the cytoplasmic aggregation of proteins HSF1 and SP1. These result in the reduced transcriptional activities of HSF1 and SP1 on their downstream FOXM1 as well as the FOXM1 transcriptional activities on cytoskeletons in HSPCs, which leads to ultimately cell proliferation impairment. These findings unveil the novel linkage of Cu overload with specific signaling transduction as well as the subsequent HSPC proliferation defects.

Super-resolution imaging of mitochondrial cristae using a more hydrophobic far-red Si-rhodamine probe.

Mitochondrial probe SiRPFA was synthesized by attaching a long perfluoroalkyl chain on Si-rhodamine cationic dye. High lipophilicity endowed SiRPFA with mitochondrial membrane potential independent properties. Under stimulated emission depletion microscopy, SiRPFA clearly revealed changes in mitochondrial cristae morphology during autophagy induced by starvation or apoptosis.

Photostable fluorescent probes based on multifunctional group substituted naphthalimide dyes for imaging of lipid droplets in live cells.

We designed and synthesized multifunctional group substituted naphthalimide (MFGNI) dyes by introducing glycine ethyl ester and azetidine on 1,8-naphthalimide. With different azetidine substituents, the emission of the MFGNI dyes was shifted from blue to green. These MFGNI dyes exhibited high photoluminescence quantum yields (61% to 85%) and large Stokes shifts (67 nm). The amides and hydroxyl groups improved the photostability of the MFGNI dyes. Due to the small molecular weight and lipophilic properties, these MFGNI dyes specifically stained lipid droplets in living cells.

CT-guided microcoil localization of pulmonary nodules: the effect of the position of microcoil proximal end on the incidence of microcoil dislocation.

OBJECTIVES: To evaluate the effect of the position of microcoil proximal end on the incidence of microcoil dislocation during CT-guided microcoil localization of pulmonary nodules (PNs). METHODS: This retrospective study included all patients with PNs who received CT-guided microcoil localization before video-assisted thoracoscopic urgery (VATS) resection from June 2016 to December 2019 in our institution. The microcoil distal end was less than 1 cm away from the nodule, and the microcoil proximal end was in the pleural cavity (the pleural cavity group) or chest wall (the chest wall group). The length of microcoil outside the pleura was measured and divided into less than 0.5 cm (group A), 0.5 to 2 cm (group B) and more than 2 cm (group C). Microcoil dislocation was defined as complete retraction into the lung (type I) or complete withdrawal from the lung (type II). The rate of microcoil dislocation between different groups was compared. RESULTS: A total of 519 consecutive patients with 571 PNs were included in this study. According to the position of microcoils proximal end on post-marking CT, there were 95 microcoils in the pleural cavity group and 476 in the chest wall group. The number of microcoils in group A, B, and C were 67, 448 and 56, respectively. VATS showed dislocation of 42 microcoils, of which 30 were type II and 12 were type I. There was no statistical difference in the rate of microcoil dislocation between the pleural cavity group and the chest wall group (6.3% vs 7.6%, x2 = 0.18, p = 0.433). The difference in the rate of microcoil dislocation among group A, B, and C was statistically significant (11.9%, 5.8%, and 14.3% for group A, B, and C, respectively, x2 = 7.60, p = 0.008). In group A, 75% (6/8) of dislocations were type I, while all eight dislocations were type II in group C. CONCLUSIONS: During CT-guided microcoil localization of PNs, placing the microcoil proximal end in the pleura cavity or chest wall had no significant effect on the incidence of microcoil dislocation. The length of microcoil outside the pleura should be 0.5 to 2 cm to reduce the rate of microcoil dislocation. ADVANCES IN KNOWLEDGE:: CT-guided microcoil localization can effectively guide VATS to resect invisible and impalpable PNs. Microcoil dislocation is the main cause of localization failure. The length of microcoil outside the pleura is significantly correlated with the rate and type of microcoil dislocation. Placing the microcoil proximal end in the pleura cavity or chest wall has no significant effect on the rate of microcoil dislocation.

Amorphous poly-N-vinylcarbazole polymer as a novel matrix for the determination of low molecular weight compounds by MALDI-TOF MS.

Traditional matrices for matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS) are usually crystalline small molecules. The heterogeneous co-crystallization of the analyte and the matrix creates a sweet spot effect and reduces point-to-point reproducibility. In this study, an amorphous poly-N-vinylcarbazole polymer (PVK) was studied as a novel matrix for MALDI-TOF MS to detect various low molecular weight compounds (LMWCs) in the negative ion mode. The PVK achieved excellent matrix action and showed high sensitivity, good salt tolerance, and reproducibility. These results significantly broaden the design rules for new and efficient polymeric MALDI matrices.

Amphiphilic dendritic peptides: Synthesis and behavior as an organogelator and liquid crystal.

New amphiphilic dendritic peptides on dendritic polyaspartic acid were designed and synthesized. The organogel and liquid crystal properties of these amphiphilic dendritic peptides were fully studied by field-emission SEM, temperature dependent FT-IR, differential scanning calorimetry, polarization optical microscopy and X-ray diffraction experiments. Amphiphilic dendritic peptides G3 show good organogel properties with a minimum gelation concentration as low as 1 wt %. Furthermore, amphiphilic dendritic peptides G3 can form a hexagonal columnar liquid crystal assembly over a wide temperature range.

Correction: Enhanced brightness and electron affinity of terrylenediimide with sulfone-bridged substituents on the bay region.

Correction for 'Enhanced brightness and electron affinity of terrylenediimide with sulfone-bridged substituents on the bay region' by Yan Zhang et al., Chem. Commun., 2021, DOI: 10.1039/d0cc06956f.