High-dimensional super-resolution imaging reveals heterogeneity and dynamics of subcellular lipid membranes

Ultra-high spatio-temporal resolution imaging with parallel acquisition-readout structured illumination microscopy (PAR-SIM)

Structured illumination microscopy (SIM) has emerged as a promising super-resolution fluorescence imaging technique, offering diverse configurations and computational strategies to mitigate phototoxicity during real-time imaging of biological specimens. Traditional efforts to enhance system frame rates have concentrated on processing algorithms, like rolling reconstruction or reduced frame reconstruction, or on investments in costly sCMOS cameras with accelerated row readout rates. In this article, we introduce an approach to elevate SIM frame rates and region of interest (ROI) coverage at the hardware level, without necessitating an upsurge in camera expenses or intricate algorithms. Here, parallel acquisition-readout SIM (PAR-SIM) achieves the highest imaging speed for fluorescence imaging at currently available detector sensitivity. By using the full frame-width of the detector through synchronizing the pattern generation and image exposure-readout process, we have achieved a fundamentally stupendous information spatial-temporal flux of 132.9 MPixels · s-1, 9.6-fold that of the latest techniques, with the lowest SNR of -2.11 dB and 100 nm resolution. PAR-SIM demonstrates its proficiency in successfully reconstructing diverse cellular organelles in dual excitations, even under conditions of low signal due to ultra-short exposure times. Notably, mitochondrial dynamic tubulation and ongoing membrane fusion processes have been captured in live COS-7 cell, recorded with PAR-SIM at an impressive 408 Hz. We posit that this novel parallel exposure-readout mode not only augments SIM pattern modulation for superior frame rates but also holds the potential to benefit other complex imaging systems with a strategic controlling approach.

Probing the heterogeneity of molecular level organization of ionic liquids: a comparative study using neutral Nile red and cationic Nile blue sulfate as fluorescent probes for butyrolactam-based protic ionic liquids

Ionic liquids (ILs) are liquid salts composed of cations and anions, known for their significant local heterogeneity at the molecular level. To understand the microheterogeneity with regard to their local polarity and local viscosity, we have used two structurally similar but chemically distinguishable fluorescent probes: Nile red (NR), a neutral molecule, and Nile blue sulfate (NBS), a charged molecule. A comparative study of the response of the two probes to the molecular level heterogeneity of ILs is expected to provide a better clarity of understanding regarding the charged polar domain and the uncharged hydrophobic domain of ILs. Towards this, we synthesized two butyrolactam-based protic ionic liquids (PILs), i.e., BTF and BTD, with the same ionic headgroup ([BT]+) and different alkyl tails ([RCOO]-), where {R = H, C11H23}. BTF has no significant hydrophobic domain, whereas BTD has a larger hydrophobic domain. Temperature-dependent fluorescence parameters such as fluorescence intensity, lifetime, and anisotropy were measured for both NR and NBS molecules. The use of a pair of structurally similar but ionically different probes enables differential estimation of parameters like the microviscosity of a domain using the fluorescence anisotropy parameter (r). The absorption and emission spectra of both probe molecules are observed to be blue shifted upon going from BTF to BTD. NR showed a significant blue shift in absorption and emission band maxima. Conversely, NBS exhibited a small wavelength shift, possibly influenced by the preferred location of their charged head group domain. Temperature-dependent rotational relaxation time (θ) of NR in BTD is smaller than that of NBS by 60-70%, indicating that stronger charge-charge interactions exist between the polar domain of BTD and NBS. Moreover, it is observed that the local viscosity of the BTF IL around both probes is similar, whereas there is a considerable difference for the BTD IL. These results are an indication that NBS being charged prefers to locate itself in the charged head group region of the IL, whereas NR being neutral tends to reside both in the hydrophobic domain and in the head group but is predominantly located in the hydrophobic domain.

Quantitative mass spectrometry imaging: therapeutics & biomolecules

Mass spectrometry imaging (MSI) has become increasingly utilized in the analysis of biological molecules. MSI grants the ability to spatially map thousands of molecules within one experimental run in a label-free manner. While MSI is considered by most to be a qualitative method, recent advancements in instrumentation, sample preparation, and development of standards has made quantitative MSI (qMSI) more common. In this feature article, we present a tailored review of recent advancements in qMSI of therapeutics and biomolecules such as lipids and peptides/proteins. We also provide detailed experimental considerations for conducting qMSI studies on biological samples, aiming to advance the methodology.

Fluorescent Probes Based on Charge and Proton Transfer for Probing Biomolecular Environment

Fluorescent probes for sensing fundamental properties of biomolecular environment, such as polarity and hydration, help to study assembly of lipids into biomembranes, sensing interactions of biomolecules and imaging physiological state of the cells. Here, we summarize major efforts in the development of probes based on two photophysical mechanisms: (i) an excited-state intramolecular charge transfer (ICT), which is represented by fluorescent solvatochromic dyes that shift their emission band maximum as a function of environment polarity and hydration; (ii) excited-state intramolecular proton transfer (ESIPT), with particular focus on 5-membered cyclic systems, represented by 3-hydroxyflavones, because they exhibit dual emission sensitive to the environment. For both ICT and ESIPT dyes, the design of the probes and their biological applications are summarized. Thus, dyes bearing amphiphilic anchors target lipid membranes and report their lipid organization, while targeting ligands direct them to specific organelles for sensing their local environment. The labels, amino acid and nucleic acid analogues inserted into biomolecules enable monitoring their interactions with membranes, proteins and nucleic acids. While ICT probes are relatively simple and robust environment-sensitive probes, ESIPT probes feature high information content due their dual emission. They constitute a powerful toolbox for addressing multitude of biological questions.

Biosynthesized Silver Nanoparticles from Cyperus conglomeratus Root Extract Inhibit Osteogenic Differentiation of Immortalized Mesenchymal Stromal Cells

BACKGROUND

Silver nanoparticles (AgNPs) are a focus of huge interest in biological research, including stem cell research. AgNPs synthesized using Cyperus conglomeratus root extract have been previously reported but their effects on mesenchymal stromal cells have yet to be investigated.

OBJECTIVES

The aim of this study is to investigate the effects of C. conglomeratus-derived AgNPs on adipogenesis and osteogenesis of mesenchymal stromal cells.

METHODS

AgNPs were synthesized using C. conglomeratus root extract, and the phytochemicals involved in AgNPs synthesis were analyzed using gas chromatography-mass spectrometry (GCMS). The cytotoxicity of the AgNPs was tested on telomerase-transformed immortalized human bone marrow-derived MSCs-hTERT (iMSC3) and human osteosarcoma cell line (MG-63) using MTT and apoptosis assays. The uptake of AgNPs by both cells was confirmed using inductively coupled plasma-optical emission spectrometry (ICP-OES). Furthermore, the effect of AgNPs on iMSC3 adipogenesis and osteogenesis was analyzed using stain quantification and reverse transcription- quantitative polymerase chain reaction (RT-qPCR).

RESULTS

The phytochemicals predominately identified in both the AgNPs and C. conglomeratus root extract were carbohydrates. The AgNP concentrations tested using MTT and apoptosis assays (0.5-64 µg/ml and 1,4 and 32 µg/ml, respectively) showed no significant cytotoxicity on iMSC3 and MG-63. The AgNPs were internalized in a concentration-dependent manner in both cell types. Additionally, the AgNPs exhibited a significant negative effect on osteogenesis but not on adipogenesis.

CONCLUSION

C. conglomeratus-derived AgNPs had an impact on the differentiation capacity of iMSC3. Our results indicated that C. conglomeratus AgNPs and the associated phytochemicals could exhibit potential medical applications.

Xanthene, cyanine, oxazine and BODIPY: the four pillars of the fluorophore empire for super-resolution bioimaging

In the realm of biological research, the invention of super-resolution microscopy (SRM) has enabled the visualization of ultrafine sub-cellular structures and their functions in live cells at the nano-scale level, beyond the diffraction limit, which has opened up a new window for advanced biomedical studies to unravel the complex unknown details of physiological disorders at the sub-cellular level with unprecedented resolution and clarity. However, most of the SRM techniques are highly reliant on the personalized special photophysical features of the fluorophores. In recent times, there has been an unprecedented surge in the development of robust new fluorophore systems with personalized features for various super-resolution imaging techniques. To date, xanthene, cyanine, oxazine and BODIPY cores have been authoritatively utilized as the basic fluorophore units in most of the small-molecule-based organic fluorescent probe designing strategies for SRM owing to their excellent photophysical characteristics and easy synthetic acquiescence. Since the future of next-generation SRM studies will be decided by the availability of advanced fluorescent probes and these four fluorescent building blocks will play an important role in progressive new fluorophore design, there is an urgent need to review the recent advancements in designing fluorophores for different SRM methods based on these fluorescent dye cores. This review article not only includes a comprehensive discussion about the recent developments in designing fluorescent probes for various SRM techniques based on these four important fluorophore building blocks with special emphasis on their effective integration into live cell super-resolution bio-imaging applications but also critically evaluates the background of each of the fluorescent dye cores to highlight their merits and demerits towards developing newer fluorescent probes for SRM.

Microfluidic Aqueous Two-Phase Focusing of Chemical Species for In Situ Subcellular Stimulation

Confinement of chemical species in a controllable micrometer-level (several to a dozen micrometers) space in an aqueous environment is essential for precisely manipulating chemical events in subcellular regions. However, rapid diffusion and hard-to-control micrometer-level fluids make it a tough challenge. Here, a versatile open microfluidic method based on an aqueous two-phase system (ATPS) is developed to restrict species inside an open space with micron-level width. Unequal standard chemical potentials of the chemical species in two phases and space-time correspondence in the microfluidic system prevent outward diffusion across the phase interface, retaining the target species inside its preferred phase flow and creating a sharp boundary with a dramatic concentration change. Then, the chemical flow (the preferred phase with target chemical species) is precisely manipulated by a microfluidic probe, which can be compressed to a micron-level width and aimed at an arbitrary position of the sample. As a demonstration of the feasibility and versatility of the strategy, chemical flow is successfully applied to subcellular regions of various kinds of living single cells. Subcellular regions are successfully labeled (cytomembrane and mitochondria) and damaged. Healing-regeneration behaviors of living single cells are triggered by subcellular damage and analyzed. The method is relatively general regarding the species of chemicals and biosamples, which could promote deeper cell research.

Design and fabrication of intracellular therapeutic cargo delivery systems based on nanomaterials: current status and future perspectives

Intracellular cargo delivery, the introduction of small molecules, proteins, and nucleic acids into a specific targeted site in a biological system, is an important strategy for deciphering cell function, directing cell fate, and reprogramming cell behavior. With the advancement of nanotechnology, many researchers use nanoparticles (NPs) to break through biological barriers to achieving efficient targeted delivery in biological systems, bringing a new way to realize efficient targeted drug delivery in biological systems. With a similar size to many biomolecules, NPs possess excellent physical and chemical properties and a certain targeting ability after functional modification on the surface of NPs. Currently, intracellular cargo delivery based on NPs has emerged as an important strategy for genome editing regimens and cell therapy. Although researchers can successfully deliver NPs into biological systems, many of them are delivered very inefficiently and are not specifically targeted. Hence, the development of efficient, target-capable, and safe nanoscale drug delivery systems to deliver therapeutic substances to cells or organs is a major challenge today. In this review, on the basis of describing the research overview and classification of NPs, we focused on the current research status of intracellular cargo delivery based on NPs in biological systems, and discuss the current problems and challenges in the delivery process of NPs in biological systems.

Mitochondrial heterogeneity in diseases

As key organelles involved in cellular metabolism, mitochondria frequently undergo adaptive changes in morphology, components and functions in response to various environmental stresses and cellular demands. Previous studies of mitochondria research have gradually evolved, from focusing on morphological change analysis to systematic multiomics, thereby revealing the mitochondrial variation between cells or within the mitochondrial population within a single cell. The phenomenon of mitochondrial variation features is defined as mitochondrial heterogeneity. Moreover, mitochondrial heterogeneity has been reported to influence a variety of physiological processes, including tissue homeostasis, tissue repair, immunoregulation, and tumor progression. Here, we comprehensively review the mitochondrial heterogeneity in different tissues under pathological states, involving variant features of mitochondrial DNA, RNA, protein and lipid components. Then, the mechanisms that contribute to mitochondrial heterogeneity are also summarized, such as the mutation of the mitochondrial genome and the import of mitochondrial proteins that result in the heterogeneity of mitochondrial DNA and protein components. Additionally, multiple perspectives are investigated to better comprehend the mysteries of mitochondrial heterogeneity between cells. Finally, we summarize the prospective mitochondrial heterogeneity-targeting therapies in terms of alleviating mitochondrial oxidative damage, reducing mitochondrial carbon stress and enhancing mitochondrial biogenesis to relieve various pathological conditions. The possibility of recent technological advances in targeted mitochondrial gene editing is also discussed.

Mammalian lipid droplets: structural, pathological, immunological and anti-toxicological roles

Mammalian lipid droplets (LDs) are specialized cytosolic organelles consisting of a neutral lipid core surrounded by a membrane made up of a phospholipid monolayer and a specific population of proteins that varies according to the location and function of each LD. Over the past decade, there have been significant advances in the understanding of LD biogenesis and functions. LDs are now recognized as dynamic organelles that participate in many aspects of cellular homeostasis plus other vital functions. LD biogenesis is a complex, highly-regulated process with assembly occurring on the endoplasmic reticulum although aspects of the underpinning molecular mechanisms remain elusive. For example, it is unclear how many enzymes participate in the biosynthesis of the neutral lipid components of LDs and how this process is coordinated in response to different metabolic cues to promote or suppress LD formation and turnover. In addition to enzymes involved in the biosynthesis of neutral lipids, various scaffolding proteins play roles in coordinating LD formation. Despite their lack of ultrastructural diversity, LDs in different mammalian cell types are involved in a wide range of biological functions. These include roles in membrane homeostasis, regulation of hypoxia, neoplastic inflammatory responses, cellular oxidative status, lipid peroxidation, and protection against potentially toxic intracellular fatty acids and lipophilic xenobiotics. Herein, the roles of mammalian LDs and their associated proteins are reviewed with a particular focus on their roles in pathological, immunological and anti-toxicological processes.

A novel CRISPR/Cas9-based iduronate-2-sulfatase (IDS) knockout human neuronal cell line reveals earliest pathological changes

Multiple complex intracellular cascades contributing to Hunter syndrome (mucopolysaccharidosis type II) pathogenesis have been recognized and documented in the past years. However, the hierarchy of early cellular abnormalities leading to irreversible neuronal damage is far from being completely understood. To tackle this issue, we have generated two novel iduronate-2-sulfatase (IDS) loss of function human neuronal cell lines by means of genome editing. We show that both neuronal cell lines exhibit no enzymatic activity and increased GAG storage despite a completely different genotype. At a cellular level, they display reduced differentiation, significantly decreased LAMP1 and RAB7 protein levels, impaired lysosomal acidification and increased lipid storage. Moreover, one of the two clones is characterized by a marked decrease of the autophagic marker p62, while none of the two mutants exhibit marked oxidative stress and mitochondrial morphological changes. Based on our preliminary findings, we hypothesize that neuronal differentiation might be significantly affected by IDS functional impairment.

Multi-omics analysis of a drug-induced model of bipolar disorder in zebrafish

Emerging studies demonstrate that inflammation plays a crucial role in the pathogenesis of bipolar disorder (BD), but the underlying mechanism remains largely unclear. Given the complexity of BD pathogenesis, we performed high-throughput multi-omic profiling (metabolomics, lipidomics, and transcriptomics) of the BD zebrafish brain to comprehensively unravel the molecular mechanism. Our research proved that in BD zebrafish, JNK-mediated neuroinflammation altered metabolic pathways involved in neurotransmission. On one hand, disturbed metabolism of tryptophan and tyrosine limited the participation of the monoamine neurotransmitters serotonin and dopamine in synaptic vesicle recycling. On the other hand, dysregulated metabolism of the membrane lipids sphingomyelin and glycerophospholipids altered the synaptic membrane structure and neurotransmitter receptors (chrnα7, htr1b, drd5b, and gabra1) activity. Our findings revealed that disturbance of serotonergic and dopaminergic synaptic transmission mediated by the JNK inflammatory cascade was the key pathogenic mechanism in a zebrafish model of BD, provides critical biological insights into the pathogenesis of BD.

High-throughput microfluidic droplets in biomolecular analytical system: A review

Droplet microfluidic technology has revolutionized biomolecular analytical research, as it has the capability to reserve the genotype-to-phenotype linkage and assist for revealing the heterogeneity. Massive and uniform picolitre droplets feature dividing solution to the level that single cell and single molecule in each droplet can be visualized, barcoded, and analyzed. Then, the droplet assays can unfold intensive genomic data, offer high sensitivity, and screen and sort from a large number of combinations or phenotypes. Based on these unique advantages, this review focuses on up-to-date research concerning diverse screening applications utilizing droplet microfluidic technology. The emerging progress of droplet microfluidic technology is first introduced, including efficient and scaling-up in droplets encapsulation, and prevalent batch operations. Then the new implementations of droplet-based digital detection assays and single-cell muti-omics sequencing are briefly examined, along with related applications such as drug susceptibility testing, multiplexing for cancer subtype identification, interactions of virus-to-host, and multimodal and spatiotemporal analysis. Meanwhile, we specialize in droplet-based large-scale combinational screening regarding desired phenotypes, with an emphasis on sorting for immune cells, antibodies, enzymatic properties, and proteins produced by directed evolution methods. Finally, some challenges, deployment and future perspective of droplet microfluidics technology in practice are also discussed.

Coarse-grained molecular simulation of extracellular vesicle squeezing for drug loading

In recent years, extracellular vesicles have become promising carriers as next-generation drug delivery platforms. Effective loading of exogenous cargos without compromising the extracellular vesicle membrane is a major challenge. Rapid squeezing through nanofluidic channels is a widely used approach to load exogenous cargoes into the EV through the nanopores generated temporarily on the membrane. However, the exact mechanism and dynamics of nanopore opening, as well as cargo loading through nanopores during the squeezing process remains unknown and it is impossible to visualize or quantify it experimentally due to the small size of the EV and the fast transient process. This paper developed a systemic algorithm to simulate nanopore formation and predict drug loading during extracellular vesicle (EV) squeezing by leveraging the power of coarse-grain (CG) molecular dynamics simulations with fluid dynamics. The EV CG beads are coupled with implicit the fluctuating lattice Boltzmann solvent. The effects of EV properties and various squeezing test parameters, such as EV size, flow velocity, channel width, and length, on pore formation and drug loading efficiency are analyzed. Based on the simulation results, a phase diagram is provided as a design guide for nanochannel geometry and squeezing velocity to generate pores on the membrane without damaging the EV. This method can be utilized to optimize the nanofluidic device configuration and flow setup to obtain desired drug loading into EVs.

Fluorescent Probes for Lipid Membranes: From the Cell Surface to Organelles

Biomembranes are ubiquitous lipid structures that delimit the cell surface and organelles and operate as platforms for a multitude of biomolecular processes. The development of chemical tools─fluorescent probes─for the sensing and imaging of biomembranes is a rapidly growing research direction, stimulated by a high demand from cell biologists and biophysicists. This Account focuses on advances in these smart molecules, providing a voyage from the cell frontier─plasma membranes (PM)─toward intracellular membrane compartments─organelles. General classification of the membrane probes can be based on targeting principles, sensing profile, and optical response. Probes for PM and organelle membranes are designed based on multiple targeting principles: conjugation with natural lipids or synthetic targeting ligands and in situ cell labeling by bio-orthogonal chemistry, conjugation to protein tags, and receptor-ligand interactions. Thus, to obtain membrane probes targeting PM with selectivity to one leaflet, we designed membrane anchor ligands based on a charged group and an alkyl chain. According to the sensing profile, we define basic membrane markers with constant emission and probes for biophysical and chemical sensing. The markers are built from classical fluorophores, exemplified by a series of bright cyanines and BODIPY dyes bearing the PM anchors (MemBright). Membrane probes for biophysical sensing are based on environment-sensitive fluorophores: (1) polarity-sensitive solvatochromic dyes; (2) viscosity-sensitive fluorescent molecular rotors; (3) mechanosensitive fluorescent flippers; and (4) voltage-sensitive electrochromic dyes. Our solvatochromic probes based on Nile Red (NR12S, NR12A, NR4A), Laurdan (Pro12A), and 3-hydroxyflavone (F2N12S) through polarity-sensing can visualize liquid ordered and disordered phases of lipid membranes, sense lipid order and its heterogeneity in cell PM, detect apoptosis, etc. Chemically sensitive probes, combining a dye, membrane-targeting ligand, and molecular recognition unit, enable the detection of pH, ions, redox species, lipids, and proteins at the biomembrane surface. In terms of the optical response profile, we can identify (1) fluorogenic (turn-on) probes, allowing background-free imaging; (2) ratiometric probes, e.g., solvatochromic probes, which enable ratiometric imaging by changing their emission/excitation color; (3) fluorescence lifetime-responsive probes, e.g., fluorescence molecular rotors and flippers, suitable for fluorescence lifetime imaging (FLIM); and (4) switchable probes, important for single-molecule localization microscopy. We showed that combining solvatochromic probes with on-off switching through a reversible binding specifically to cell PM enables the mapping of their biophysical properties with superior resolution. While the majority of efforts have been focused on PM, the probes for cellular organelles, such as endoplasmic reticulum, mitochondria, Golgi apparatus, etc., emerge rapidly. Thus, nontargeted solvatochromic probes can distinguish organelles by the emission color. Targeted solvatochromic probes based on Nile Red revealed unique signatures of polarity and lipid order of individual organelles and their different sensitivities to oxidative or mechanical stress. Lipid droplets, which are membraneless lipidic structures, constitute another interesting organelle target for probing the cell stress. Currently, we stand at the beginning of a long route with big challenges ahead, in particular (1) to achieve superior organelle specificity; (2) to label specific biomembrane leaflets, notably the inner leaflet of PM; (3) to detect lipid organization in a proximity of specific proteins; and (4) to probe biomembranes in tissues and animals.

Error analysis of a rotating-metasurface polarimeter

Polarimeters, which measure the polarization states of light directly, are essentially desired in many areas of science and technology. In our previous work, we have constructed a polarimeter based on a rotating-metasurface, and the polarization Stokes parameters of the light were measured with the known Mueller elements of the metasurface. Here, we further perform the error analysis of the metasurface polarimeter. The errors in the measured Stokes parameters have been formulated for the errors in Mueller elements of the metasurface. This analysis can be used to evaluate and minimize the errors of the metasurface polarimeter.

Shrimp miR-965 transfers tumoricidal mitochondria

Background

Micro RNA of Marsupenaeus japonicas has been known to promote apoptosis of tumor cells. However, the detailed mechanisms are not well understood.

Results

Using tomographic microscope, which can detect the internal structure of cells, we observed breast tumor cells following treatment of the miRNA. Intriguingly, we found that mitochondria migrate to an adjacent tumor cells through a tunneling nanotube. To recapitulate this process, we engineered a microfluidic device through which mitochondria were transferred. We show that this mitochondrial transfer process released endonuclease G (Endo G) into tumor cells, which we referred to herein as unsealed mitochondria. Importantly, Endo G depleted mitochondria alone did not have tumoricidal effects. Moreover, unsealed mitochondria had synergistic apoptotic effects with subtoxic dose of doxorubicin thereby mitigating cardiotoxicity.

Conclusions

Together, we show that the mitochondrial transfer through microfluidics can provide potential novel strategies towards tumor cell death.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12575-022-00178-8.

Lipid Expansion Microscopy

Strategies to visualize cellular membranes with light microscopy are restricted by the diffraction limit of light, which far exceeds the dimensions of lipid bilayers. Here, we describe a method for super-resolution imaging of metabolically labeled phospholipids within cellular membranes. Guided by the principles of expansion microscopy, we develop an all-small molecule approach that enables direct chemical anchoring of bioorthogonally labeled phospholipids into a hydrogel network and is capable of super-resolution imaging of cellular membranes. We apply this method, termed lipid expansion microscopy (LExM), to visualize organelle membranes with precision, including a unique class of membrane-bound structures known as nuclear invaginations. Compatible with standard confocal microscopes, LExM will be widely applicable for super-resolution imaging of phospholipids and cellular membranes in numerous physiological contexts.

Raster-scanning Donut simplifies MINFLUX and provides alternative implement on other scanning-based microscopes

A donut excitation moves around a single molecule with a zigzag configuration lattice by lattice. Such a method implemented in scanning fluorescence microscopy simplifies the conventional MINFLUX process. Consisting of hollow zero-intensity excitation, single-pixel detection, time-correlated single photon counting, and drift stabilization, the system achieves localization precision and resolution very close to conventional MINFLUX theoretically and experimentally. An averaged high-SNR reference, and pixel-registered intensity from a single molecule is essential to reconstruct localization in maximum likelihood estimation. With performance reaching nearly conventional MINFLUX's, the proposed raster-scanning MINFLUX can inspire researchers expertized in STED or confocal setup to quickly transform to MINFLUX and develop for further exploring on bio-specimens or optical applications.

A multicomponent reaction platform towards multimodal near-infrared BODIPY dyes for STED and fluorescence lifetime imaging

We report a platform combining multicomponent reaction synthesis and automated cell-based screening to develop biocompatible NIR-BODIPY fluorophores. From a library of over 60 fluorophores, we optimised compound NIRBD-62c as a multimodal probe with suitable properties for STED super-resolution and fluorescence lifetime imaging. Furthermore, we employed NIRBD-62c for imaging trafficking inside cells and to examine how pharmacological inhibitors can alter the vesicular traffic between intracellular compartments and the plasma membrane.

An ultra-small nine-color spectrometer with a two-layer biparted ten-dichroic-mirror array and an image sensor

An ultra-small (54 × 58 × 8.5 mm) and large aperture (1 × 7 mm) nine-color spectrometer-using an array of ten dichroic mirrors "biparted" as two layers-was developed and used for snapshot spectral imaging. Incident-light flux with a cross section smaller than the aperture size is split into nine color fluxes with 20-nm-width contiguous wavelength bands and central wavelengths of 530, 550, 570, 590, 610, 630, 650, 670, and 690 nm. Images of the nine color fluxes are simultaneously and efficiently measured by an image sensor. Unlike a conventional dichroic-mirror array, the developed dichroic-mirror array has a unique biparted configuration that not only increases the number of colors that can be measured simultaneously but also improves the image resolution of each color flux. The developed nine-color spectrometer was used for four-capillary-array electrophoresis. Eight dyes concurrently migrating in each capillary were simultaneously quantified by nine-color laser-induced fluorescence detection. Since the nine-color spectrometer is not only ultra-small and inexpensive but also has high light throughput and sufficient spectral resolution for most spectral-imaging applications, it has the potential to be widely used in various fields.

SERINC5-Mediated Restriction of HIV-1 Infectivity Correlates with Resistance to Cholesterol Extraction but Not with Lipid Order of Viral Membrane

Serine incorporator 5 (SER5) is a protein that upon incorporation into virions inhibits HIV-1 infectivity by interfering with the ability of the Env glycoprotein to promote viral fusion. The mechanisms by which SER5 antagonizes HIV-1 fusion are not well understood. A recent study of SER5's structure revealed a lipid-binding pocket, suggesting the ability to sequester lipids. This finding, along with the well-documented modulation of HIV-1 infectivity by viral lipids, especially cholesterol, prompted our examination of SER5's effect on the general lipid order of the HIV-1 membrane. Pseudoviruses bearing the SER5-sensitive HXB2-Env and containing SER5 or SER2, a control protein that lacks antiviral activity, were analyzed using two distinct lipid-order probes. We show that SER5 incorporation does not noticeably affect the lipid order of pseudoviruses. Although viral cholesterol extraction reduces HIV-1 infectivity, SER5+ viruses are less sensitive to cholesterol extraction than the control samples. In contrast, the virus' sensitivity to cholesterol oxidation was not affected by SER5 incorporation. The hydrolytic release of sphingomyelin-sequestered cholesterol had a minimal impact on the apparent resistance to cholesterol extraction. Based on these results, we propose that a subpopulation of more stable Env glycoproteins responsible for the residual infectivity of SER5+ viruses is less sensitive to the cholesterol content of the viral membrane.

Simultaneous super-resolution estimation of single-molecule position and orientation with minimal photon fluxes

The orientation of a single molecule provides valuable information on fundamental biological processes. We report a technique for the simultaneous estimation of single-molecule 2D position and 2D orientation with ultra-high localization precision (∼2-nm precision with ∼500 photons under a typical 100-nm diameter of excitation beam pattern), which is also compatible with tracking in living cells. In the proposed method, the theoretical precision limits are calculated, and the localization and orientation performance along with potential applications are explored using numerical simulations. Compared to other camera-based orientation measurement methods, it is confirmed that the proposed method can obtain reasonable estimates even under very weak signals (∼15 photons). Moreover, the maximum likelihood estimator (MLE) is found to converge to the theoretical limit when the total number of photons is less than 100.

Lipidomic and Membrane Mechanical Signatures in Triple-Negative Breast Cancer: Scope for Membrane-Based Theranostics

Triple-negative breast cancer (TNBC) is a highly aggressive form of breast cancer associated with poor prognosis, higher grade, and a high rate of metastatic occurrence. Limited therapeutic interventions and the compounding issue of drug resistance in triple-negative breast cancer warrants the discovery of novel therapeutic targets and diagnostic modules. To this view, in addition to proteins, lipids also regulate cellular functions via the formation of membranes that modulate membrane protein function, diffusion, and their localization; thus, orchestrating signaling hot spots enriched in specific lipids/proteins on cell membranes. Lipid deregulation in cancer leads to reprogramming of the membrane dynamics and functions impacting cell proliferation, metabolism, and metastasis, providing exciting starting points for developing lipid-based approaches for treating TNBC. In this review, we provide a detailed account of specific lipidic changes in breast cancer, link the altered lipidome with membrane structure and mechanical properties, and describe how these are linked to subsequent downstream functions implicit in cancer progression, metastasis, and chemoresistance. At the fundamental level, we discuss how the lipid-centric findings in TNBC are providing cues for developing lipid-inspired theranostic strategies while bridging existing gaps in our understanding of the functional involvement of lipid membranes in cancer.

SIM reconstruction framework for high-speed multi-dimensional super-resolution imaging

Structured illumination microscopy (SIM) holds great promise for live cell imaging applications due to its potential to obtain multidimensional information such as intensity, spectrum and polarization (I, λ , p) at high spatial-temporal resolution, enabling the observation of more complex dynamic interactions between subcellular structures. However, the reconstruction results of polarized samples are prone to artifacts because all current SIM reconstruction frameworks use incomplete imaging models which neglect polarization modulation. Such polarization-related artifacts are especially prevalent for SIM reconstruction using a reduced number of raw images (RSIM) and severely undermine the ability of SIM to capture multi-dimensional information. Here, we report a new SIM reconstruction framework (PRSIM) that can recover multi-dimensional information (I, λ, p) using a reduced number of raw images. PRSIM adopts a complete imaging model that is versatile for normal and polarized samples and uses a frequency-domain iterative reconstruction algorithm for artifact-free super-resolution (SR) reconstruction. It can simultaneously obtain the SR spatial structure and polarization orientation of polarized samples using 6 raw SIM images and can perform SR reconstruction using 4 SIM images for normal samples. In addition, PRSIM has less spatial computational complexity and achieves reconstruction speeds tens of times higher than that of the state-of-the-art non-iterative RSIM, making it more suitable for large field-of-view imaging. Thus, PRSIM is expected to facilitate the development of SIM into an ultra-high-speed and multi-dimensional SR imaging tool.

Quantitative Jones matrix imaging using vectorial Fourier ptychography

This paper presents a microscopic imaging technique that uses variable-angle illumination to recover the complex polarimetric properties of a specimen at high resolution and over a large field-of-view. The approach extends Fourier ptychography, which is a synthetic aperture-based imaging approach to improve resolution with phaseless measurements, to additionally account for the vectorial nature of light. After images are acquired using a standard microscope outfitted with an LED illumination array and two polarizers, our vectorial Fourier ptychography (vFP) algorithm solves for the complex 2x2 Jones matrix of the anisotropic specimen of interest at each resolved spatial location. We introduce a new sequential Gauss-Newton-based solver that additionally jointly estimates and removes polarization-dependent imaging system aberrations. We demonstrate effective vFP performance by generating large-area (29 mm²), high-resolution (1.24 μm full-pitch) reconstructions of sample absorption, phase, orientation, diattenuation, and retardance for a variety of calibration samples and biological specimens.

Exploiting the Twisted Intramolecular Charge Transfer Effect to Construct a Wash-Free Solvatochromic Fluorescent Lipid Droplet Probe for Fatty Liver Disease Diagnosis

The prominent pathological feature of fatty liver disease lesions is excessive fat accumulation in lipid droplets in hepatocytes. Thus, developing fluorescent lipid droplet-specific probes with high permeability and a high imaging contrast provides a robust tool for diagnosing fatty liver diseases. Herein, we rationally developed a novel donor-acceptor lipophilic fluorescent probe ANI with high photostability for wash-free visualization of lipid droplets and fatty liver disease characteristics. ANI showed a typical twisted intramolecular charge transfer effect with very faint fluorescence in high-polar solvents, but dramatically boosted emissions in low-polar environments. The solvatochromic probe can selectively light up lipid droplets with a high contrast in a wash-free manner. Further use of ANI to reveal the excessive accumulation of lipid droplets with a significantly large size in the liver tissues from the fatty liver disease model mice was successfully demonstrated. The remarkable imaging performances rendered ANI an alternative tool for accurately evaluating fatty liver disease in intraoperative diagnosis.

The stressed life of a lipid in the Zika virus membrane

Protein-lipid interactions modulate a plethora of physiopathologic processes and have been the subject of countless studies. However, these kinds of interactions in the context of viral envelopes have remained relatively unexplored, partially because the intrinsically small dimensions of the molecular systems escape to the current resolution of experimental techniques. However, coarse-grained and multiscale simulations may fill that niche, providing nearly atomistic resolution at an affordable computational price. Here we use multiscale simulations to characterize the lipid-protein interactions in the envelope of the Zika Virus, a prominent member of the Flavivirus genus. Comparisons between the viral envelope and simpler molecular systems indicate that the viral membrane is under extreme pressures and asymmetric forces. Furthermore, the dense net of protein-protein contacts established by the envelope proteins creates poorly solvated regions that destabilize the external leaflet leading to a decoupled dynamics between both membrane layers. These findings lead to the idea that the Flaviviral membrane may store a significant amount of elastic energy, playing an active role in the membrane fusion process.

Super-Multiplex Nonlinear Optical Imaging Unscrambles the Statistical Complexity of Cancer Subtypes and Tumor Microenvironment

Label-free nonlinear optical imaging (NLOI) has made tremendous inroads toward unscrambling the microcosmic complexity of cancers. However, harmonic and Raman microscopy offers throughput without redox information to reveal metabolic differentiation, and fluorescence lifetime microscopy lacks the vibrational response of molecules to visualize specific molecular constituents such as lipid. Here, a flexible, robust simultaneous multi-nonlinear imaging and cross-modality system that combines complementary imaging contrast mechanisms is demonstrated. This system, utilizing multiplexed ultrashort pulses, ingeniously integrates typical nonlinear processes, and high-dimension lifetime extension in a single setup to enhance the imaging dimensions and quality. Using this system, the authors perform label-free comprehensive evaluation of clinicopathological tissues of ovarian carcinoma due to its statistical complexity. The results show that the technology provides statistically rich, insightful information with high accuracy, sensitivity, and specificity, in contrast to standard histopathology, and can potentially be a powerful tool for fundamental cancer research and clinical applications.

Shedding light on membrane rafts structure and dynamics in living cells

Cellular membranes are fundamental building blocks regulating an extensive repertoire of biological functions. These structures contain lipids and membrane proteins that are known to laterally self-aggregate in the plane of the membrane, forming defined membrane nanoscale domains essential for protein activity. Membrane rafts are described as heterogeneous, dynamic, and short-lived cholesterol- and sphingolipid-enriched membrane nanodomains (10-200 nm) induced by lipid-protein and lipid-lipid interactions. Those membrane nanodomains have been extensively characterized using model membranes and in silico methods. However, despite the development of advanced fluorescence microscopy techniques, undoubted nanoscale visualization by imaging techniques of membrane rafts in the membrane of unperturbed living cells is still uncompleted, increasing the skepticism about their existence. Here, we broadly review recent biochemical and microscopy techniques used to investigate membrane rafts in living cells and we enumerate persistent open questions to answer before unlocking the mystery of membrane rafts in living cells.

Identifying Membrane Lateral Organization by Contrast-Matched Small Angle Neutron Scattering

Lipid domains in model membranes are routinely studied to provide insight into the physical interactions that drive raft formation in cellular membranes. Using small angle neutron scattering, contrast-matching techniques enable the detection of lipid domains ranging from tens to hundreds of nanometers which are not accessible to other techniques without the use of extrinsic probes. Here, we describe a probe-free experimental approach and model-free analysis to identify lipid domains in freely floating vesicles of ternary phase separating lipid mixtures.

Light People: Professor Dayong Jin

He pioneered a new family of nanoscopic probes that can up-convert infrared photons into intense visible light, and won the Australian Museum Eureka Prize for Interdisciplinary Scientific Research in 2015. He created new kinds of microscopes that allow us to watch molecules at work inside living cells, and won the Australian Prime Minister's Prize for Science Malcolm McIntosh Prize for Physical Scientist of the Year 2017. The Australian newspaper identified him among 100 "rock stars of Australia's new economy" as the Knowledge Nation 100. This year, at his age of 42, he won the Australian Laureate Fellowship and was elected to the fellowship of Australian Academy of Technology and Engineering. This is Dayong Jin, a Distinguished Professor at the University of Technology Sydney and a Chair Professor at Southern University of Science and Technology, as well as the editorial manager in Sydney office and the perspective column editor of Light: Science & Applications (LSA). Light People is a featured column of high-end interviews with outstanding scientists. On this issue, it is our great honor to invite Professor Dayong Jin to provide his perspectives on his work, end-user driven research, student mentoring and team building philosophy. In the following, let's take a closer look at the research life of Professor Dayong Jin, and appreciate his style and the story behind his success.

Comparison of Two- and Three-Beam Interference Pattern Generation in Structured Illumination Microscopy

Structured illumination microscopy (SIM) provides wide-field optical sectioning in the focal plane by modulating the imaging information using fringe pattern illumination. For generating the fringe pattern illumination, a digital micro-mirror device (DMD) is commonly used due to its flexibility and fast refresh rate. However, the benefit of different pattern generation, for example, the two-beam interference mode and the three-beam interference mode, has not been clearly investigated. In this study, we systematically analyze the optical sectioning provided by the two-beam inference mode and the three-beam interference mode of DMD. The theoretical analysis and imaging results show that the two-beam interference mode is suitable for fast imaging of the superficial dynamic target due to reduced number of phase shifts needed to form the image, and the three-beam interference mode is ideal for imaging three-dimensional volume due to its superior optical sectioning by the improved modulation of the illumination patterns. These results, we believe, will provide better guidance for the use of DMD for SIM imaging and also for the choice of beam patterns in SIM application in the future.

Polarisation optics for biomedical and clinical applications: a review

Many polarisation techniques have been harnessed for decades in biological and clinical research, each based upon measurement of the vectorial properties of light or the vectorial transformations imposed on light by objects. Various advanced vector measurement/sensing techniques, physical interpretation methods, and approaches to analyse biomedically relevant information have been developed and harnessed. In this review, we focus mainly on summarising methodologies and applications related to tissue polarimetry, with an emphasis on the adoption of the Stokes-Mueller formalism. Several recent breakthroughs, development trends, and potential multimodal uses in conjunction with other techniques are also presented. The primary goal of the review is to give the reader a general overview in the use of vectorial information that can be obtained by polarisation optics for applications in biomedical and clinical research.

Experimental demonstration of the novel "van-Hove integral method (vHI)" for measuring diffusive dynamics by elastic neutron scattering

Quasi-elastic neutron scattering (QENS)-based on the seminal work of Nobel Laureate Brockhouse-has been one of the major methods for studying pico-second to nano-second diffusive dynamics over the past 70 years. This is regarded as an "inelastic" method for dynamics. In contrast, we recently proposed a new neutron-scattering method for dynamics, which uses the elastic line of the scattering to access system dynamics directly in the time domain (Benedetto and Kearley in Sci Rep 9:11284, 2019). This new method has been denoted "vHI" that stands for "van Hove Integral". The reason is that, under certain conditions, the measured elastic intensity corresponds to the running-time integral of the intermediate scattering function, [Formula: see text], up to a time that is inversely proportional to the energy band-width incident on the sample. As a result, [Formula: see text] is accessed from the time derivative of the measured vHI profile. vHI has been supported by numerical and Monte-Carlo simulations, but has been difficult to validate experimentally due to the lack of a suitable instrument. Here we show that vHI works in practice, which we achieved by using a simple modification to the standard QENS backscattering spectrometer methodology. Basically, we varied the neutron-energy band-widths incident at the sample via a step-wise variation of the frequency of the monochromator Doppler-drive. This provides a measurement of the vHI profile at the detectors. The same instrument and sample were also used in standard QENS mode for comparison. The intermediate scattering functions, [Formula: see text], obtained by the two methods-vHI and QENS-are strikingly similar providing a direct experimental validation of the vHI method. Perhaps surprisingly, the counting statistics of the two methods are comparable even though the instrument used was expressly designed for QENS. This shows that the methodology modification adopted here can be used in practice to access vHI profiles at many of the backscattering spectrometers worldwide. We also show that partial integrations of the measured QENS spectrum cannot provide the vHI profile, which clarifies a common misconception. At the same time, we show a novel approach which does access [Formula: see text] from QENS spectra.

Development of nanobody-based POLArIS orientation probes enabled multi-color/multi-target orientation imaging in living cells

Fluorescence polarization microscopy (FPM) can visualize the dipole orientation of fluorescent molecules and has been used for analyzing architectural dynamics of biomolecules including cytoskeletal proteins. To monitor the orientation of target molecules by FPM, target molecules need to be labeled with fluorophores in a sterically constrained manner, so that the fluorophores do not freely rotate. Recently, a versatile probe for such labeling using fluorescent proteins, POLArIS (Probe for Orientation and Localization Assessment, recognizing specific Intracellular Structures of interest), was reported. POLArIS is a fusion protein consisting of a non-immunoglobulin-based recombinant binder Affimer and a green fluorescent protein (GFP), where the Affimer and GFP are rigidly connected to each other. POLArIS probe for molecules of interest can be developed through phage display screening of Affimer. This screening is followed by the rigid connection of fluorescent proteins to the selected Affimers. The Affimer-based POLArIS, however, cannot be used with animal immune libraries for selecting specific binder clones. In addition, multi-color FPM by POLArIS was not available due to the lack of color variations of POLArIS. In this study, we have developed new versions of POLArIS with nanobodies, which are compatible with animal immune libraries, and expanded color variations of POLArIS with cyan/green/yellow/red fluorescent proteins, enabling multi-color orientation imaging for multiple targets. Using nanobody-based POLArIS orientation probes, we performed two-color FPM of F-actin and vimentin in living cells. Furthermore, we made nanobody-based POLArIS probes that have different dipole orientations for adjusting the orientation of fluorescence polarization with respect to the target molecules. These nanobody-based POLArIS with options of colors and dipole orientations will enhance the performance of this probe for broader applications of fluorescence polarization imaging in living cells, tissues, and whole organisms.

Unveiling a Hidden Event in Fluorescence Correlative Microscopy by AFM Nanomechanical Analysis

Fluorescent imaging combined with atomic force microscopy (AFM), namely AFM-fluorescence correlative microscopy, is a popular technology in life science. However, the influence of involved fluorophores on obtained mechanical information is normally underestimated, and such subtle changes are still challenging to detect. Herein, we combined AFM with laser light excitation to perform a mechanical quantitative analysis of a model membrane system labeled with a commonly used fluorophore. Mechanical quantification was additionally validated by finite element simulations. Upon staining, we noticed fluorophores forming a diffuse weakly organized overlayer on phospholipid supported membrane, easily detected by AFM mechanics. The laser was found to cause a degradation of mechanical stability of the membrane synergically with presence of fluorophore. In particular, a 30 min laser irradiation, with intensity similar to that in typical confocal scanning microscopy experiment, was found to result in a ∼40% decrease in the breakthrough force of the stained phospholipid bilayer along with a ∼30% reduction in its apparent elastic modulus. The findings highlight the significance of analytical power provided by AFM, which will allow us to “see” the “unseen” in correlative microscopy, as well as the necessity to consider photothermal effects when using fluorescent dyes to investigate, for example, the deformability and permeability of phospholipid membranes.

Investigating Single-Molecule Fluorescence Spectral Heterogeneity of Rhodamines Using High-Throughput Single-Molecule Spectroscopy

We experimentally investigated several intramolecular coordinate and environmental changes as potential causes of single-molecule fluorescence spectral heterogeneities (smFSH). We developed a high-throughput single-molecule spectroscopy method to analyze more than 5000 single-molecule emission spectra from each of 9 commonly used fluorophores with different structural rigidities and deposited on substrates with different polarities. We observed an unexpectedly high smFSH from structurally rigid Rhodamine B compared with a structurally flexible Cyanine dye-Alexa Fluor 647. Based on experimentally measured smFSH, we ruled out the system's noise uncertainty, single-molecule spectral diffusion, and environmental polarity as the primary causes of the high smFSH. We found that the rotational flexibility of N,N-dialkylated groups contributed to the smFSH. With the high smFSH observed in structurally more rigid model fluorophores, we speculated that other intramolecular coordinate and environmental changes might also contribute to the high smFSH in Rhodamines.

Navigating immune cell immunometabolism after liver transplantation

Liver transplantation (LT) is the most effective treatment for end-stage liver diseases. The immunometabolism microenvironment undergoes massive changes at the interface of immune functionalities and metabolic regulations after LT. These changes considerably modify post-transplant complications, and immune cells play an influential role in the hepatic immunometabolism microenvironment after LT. Therefore, adequate studies on the complex pathobiology of immune cells are critical to prevent post-transplant complications, and the interplay between cellular metabolism and immune function is evident. Furthermore, immune cells perform their specified functions, such as activation or differentiation, accompanied by alterations in metabolic pathways, such as metabolic reprogramming. This transformation remarkably affects post-transplant complications like rejection. By targeting different metabolic pathways, regulations of metabolism are employed to shape immune responses. These differences of metabolic pathways allow for selective regulation of immune responses to further develop effective therapies that prevent graft loss after LT. This review examines immune cells in the hepatic immunometabolism microenvironment after LT, summarizes possible mechanisms and potential prevention on rejection to acquire immune tolerance, and offers some insight into references for scientific research along with clinical treatment.

High-dimensional super-resolution imaging reveals heterogeneity and dynamics of subcellular lipid membranes

Lipid membranes are found in most intracellular organelles, and their heterogeneities play an essential role in regulating the organelles' biochemical functionalities. Here we report a Spectrum and Polarization Optical Tomography (SPOT) technique to study the subcellular lipidomics in live cells. Simply using one dye that universally stains the lipid membranes, SPOT can simultaneously resolve the membrane morphology, polarity, and phase from the three optical-dimensions of intensity, spectrum, and polarization, respectively. These high-throughput optical properties reveal lipid heterogeneities of ten subcellular compartments, at different developmental stages, and even within the same organelle. Furthermore, we obtain real-time monitoring of the multi-organelle interactive activities of cell division and successfully reveal their sophisticated lipid dynamics during the plasma membrane separation, tunneling nanotubules formation, and mitochondrial cristae dissociation. This work suggests research frontiers in correlating single-cell super-resolution lipidomics with multiplexed imaging of organelle interactome.