Advances in multimodal mass spectrometry for single-cell analysis and imaging enhancement

Multimodal mass spectrometry (MMS) incorporates an imaging modality with probe-based mass spectrometry (MS) to enable precise, targeted data acquisition and provide additional biological and chemical data not available by MS alone. Two categories of MMS are covered; in the first, an imaging modality guides the MS probe to target individual cells and to reduce acquisition time by automatically defining regions of interest. In the second category, imaging and MS data are coupled in the data analysis pipeline to increase the effective spatial resolution using a higher resolution imaging method, correct for tissue deformation, and incorporate fine morphological features in an MS imaging dataset. Recent methodological and computational developments are covered along with their application to single-cell and imaging analyses.

Regulation of mineral elements in Hordeum brevisubulatum by Epichloë bromicola under Cd stress

In this study, wild barley (Hordeum brevisubulatum) infected (E+) and uninfected (E-) by Epichloë bromicola were used for hydroponic experiments during the seedling stage. Various attributes, such as the effect of fungal endophyte on the growth and development of wild barley, the absorption of cadmium (Cd) and mineral elements (Ca, Mg, Fe, Mn, Cu, Zn), subcellular distribution, and chemical forms were investigated under CdCl2 stress. The results showed that the fungal endophy significantly reduced the Ca content and percentage of plant roots under Cd stress. The Fe and Mn content of roots, the mineral element content of soluble fractions, and the stems in the pectin acid or protein-chelated state increased significantly in response to fungal endophy. Epichloë endophyte helped Cd2+ to enter into plants; and reduced the positive correlation of Ca-Fe and Ca-Mn in roots. In addition, it also decreased the correlation of soluble components Cd-Cu, Cd-Ca, Cd-Mg in roots, and the negative correlation between pectin acid or protein-chelated Cd in stems and mineral elements, to increase the absorbance of host for mineral elements. In conclusion, fungal endophy regulated the concentration and distribution of mineral elements, while storing more Cd2+ to resist the damage caused by Cd stress. The study could provide a ground for revealing the Cd tolerance mechanism of endophytic fungal symbionts.

Hitting the Sweet Spot: How Glucose Metabolism Is Orchestrated in Space and Time by Phosphofructokinase-1

Glycolysis is the central metabolic pathway across all kingdoms of life. Intensive research efforts have been devoted to understanding the tightly orchestrated processes of converting glucose into energy in health and disease. Our review highlights the advances in knowledge of how metabolic and gene networks are integrated through the precise spatiotemporal compartmentalization of rate-limiting enzymes. We provide an overview of technically innovative approaches that have been applied to study phosphofructokinase-1 (PFK1), which represents the fate-determining step of oxidative glucose metabolism. Specifically, we discuss fast-acting chemical biology and optogenetic tools that have delineated new links between metabolite fluxes and transcriptional reprogramming, which operate together to enact tissue-specific processes. Finally, we discuss how recent paradigm-shifting insights into the fundamental basis of glycolytic regulatory control have shed light on the mechanisms of tumorigenesis and could provide insight into new therapeutic vulnerabilities in cancer.

No net utilization of intramuscular lipid droplets during repeated high-intensity intermittent exercise

Intramuscular lipids are stored as subsarcolemmal or intramyofibrillar droplets with potential diverse roles in energy metabolism. We examined intramuscular lipid utilization through transmission electron microscopy during repeated high-intensity intermittent exercise, an aspect that is hitherto unexplored. Seventeen moderately to well-trained males underwent three periods (EX1-EX3) of 10 × 45-s high-intensity cycling [∼100%-120% Wattmax (Wmax)] combined with maximal repeated sprints (∼250%-300% Wmax). M. vastus lateralis biopsies were obtained at baseline, after EX1, and EX3. During the complete exercise session, no net decline in either subsarcolemmal or intermyofibrillar lipid volume density occurred. However, a temporal relationship emerged for subsarcolemmal lipids with an ∼11% increase in droplet size after EX1 (P = 0.024), which reverted to baseline levels after EX3 accompanied by an ∼30% reduction in the numerical density of subsarcolemmal lipid droplets compared with both baseline (P = 0.019) and after EX1 (P = 0.018). Baseline distinctions were demonstrated with an approximately twofold higher intermyofibrillar lipid volume in type 1 versus type 2 fibers (P = 0.008), mediated solely by a higher number rather than the size of lipid droplets (P < 0.001). No fiber-type-specific differences were observed in subsarcolemmal lipid volume although type 2 fibers exhibited ∼17% larger droplets (P = 0.034) but a lower numerical density (main effect; P = 0.010) including 3% less droplets at baseline. Collectively, these findings suggest that intramuscular lipids do not serve as an important substrate during high-intensity intermittent exercise; however, the repeated exercise pattern mediated a temporal remodeling of the subsarcolemmal lipid pool. Furthermore, fiber-type- and compartment-specific differences were found at baseline underscoring the heterogeneity in lipid droplet deposition.NEW & NOTEWORTHY Undertaking a severe repeated high-intensity intermittent exercise protocol led to no net decline in neither subsarcolemmal nor intermyofibrillar lipid content in the thigh muscle of young moderately to well-trained participants. However, a temporal remodeling of the subsarcolemmal pool of lipid droplets did occur indicative of potential transient lipid accumulation. Moreover, baseline fiber-type distinctions in subcellular lipid droplet deposition were present underscoring the diversity in lipid droplet storage among fiber types and subcellular regions.

Rapid and in-depth proteomic profiling of small extracellular vesicles for ultralow samples

The integration of robust single-pot, solid-phase-enhanced sample preparation with powerful liquid chromatography-tandem mass spectrometry (LC-MS/MS) is routinely used to define the extracellular vesicle (EV) proteome landscape and underlying biology. However, EV proteome studies are often limited by sample availability, requiring upscaling cell cultures or larger volumes of biofluids to generate sufficient materials. Here, we have refined data independent acquisition (DIA)-based MS analysis of EV proteome by optimizing both protein enzymatic digestion and chromatography gradient length (ranging from 15 to 44 min). Our short 15 min gradient length can reproducibly quantify 1168 (from as little as 500 pg of EV peptides) to 3882 proteins groups (from 50 ng peptides), including robust quantification of 22 core EV marker proteins. Compared to data-dependent acquisition, DIA achieved significantly greater EV proteome coverage and quantification of low abundant protein species. Moreover, we have achieved optimal magnetic bead-based sample preparation tailored to low quantities of EVs (0.5 to 1 µg protein) to obtain sufficient peptides for MS quantification of 1908-2340 protein groups. We demonstrate the power and robustness of our pipeline in obtaining sufficient EV proteomes granularity of different cell sources to ascertain known EV biology. This underscores the capacity of our optimised workflow to capture precise and comprehensive proteome of EVs, especially from ultra-low sample quantities (sub-nanogram), an important challenge in the field where obtaining in-depth proteome information is essential.

RNA trafficking and subcellular localization-a review of mechanisms, experimental and predictive methodologies

RNA localization is essential for regulating spatial translation, where RNAs are trafficked to their target locations via various biological mechanisms. In this review, we discuss RNA localization in the context of molecular mechanisms, experimental techniques and machine learning-based prediction tools. Three main types of molecular mechanisms that control the localization of RNA to distinct cellular compartments are reviewed, including directed transport, protection from mRNA degradation, as well as diffusion and local entrapment. Advances in experimental methods, both image and sequence based, provide substantial data resources, which allow for the design of powerful machine learning models to predict RNA localizations. We review the publicly available predictive tools to serve as a guide for users and inspire developers to build more effective prediction models. Finally, we provide an overview of multimodal learning, which may provide a new avenue for the prediction of RNA localization.

Sub-Cellular Dynamic Analysis of BGC823 Cells after Treatment with the Multi-Component Drug CKI Using Raman Spectroscopy

Multi-component drugs (MCDs) can induce various cellular changes covering multiple levels, from molecular and subcellular structure to cell morphology. A "non-invasive" method for comprehensively detecting the dynamic changes of cellular fine structure and chemical components on the subcellular level is highly desirable for MCD studies. In this study, the subcellular dynamic processes of gastric cancer BGC823 cells after treatment with a multi-component drug, Compound Kushen Injection (CKI), were investigated using a homemade, high-resolution, confocal Raman spectroscopy (RS) device combined with bright-field imaging. The Raman spectra of the nucleus, cytoplasm and intracellular vesicles (0.4-1 μm) were collected simultaneously for each cell treated with CKI at different times and doses. The RS measurements showed that CKI decreased the DNA signatures, which the drug is known to inhibit. Meanwhile, the CKI-induced subcellular dynamic changes in the appearance of numerous intracellular vesicles and the deconstruction of cytoplasm components were observed and discussed. The results demonstrated that high-resolution subcellular micro-Raman spectroscopy has potential for detecting fine cellular dynamic variation induced by drugs and the screening of MCDs in cancer therapy.

Subcellular Proteomics to Elucidate Soybean Response to Abiotic Stress

Climate change jeopardizes soybean production by declining seed yield and quality. In this review, the morphophysiological alterations of soybean in response to abiotic stress are summarized, followed by illustrations of cellular metabolisms and regulatory mechanisms to organellar stress based on subcellular proteomics. This highlights the communications associated with reactive oxygen species scavenging, molecular chaperones, and phytohormone signals among subcellular compartments. Given the complexity of climate change and the limitations of plants in coping with multiple abiotic stresses, a generic response to environmental constraints is proposed between calcium and abscisic acid signals in subcellular organelles. This review summarizes the findings of subcellular proteomics in stressed soybean and discusses the future prospects of subcellular proteomics for promoting the improvement of climate-tolerant crops.

Abrupt and acclimation responses to changing temperature elicit divergent physiological effects in the diatom Phaeodactylum tricornutum

Growth rates and other biomass traits of phytoplankton are strongly affected by temperature. We hypothesized that resulting phenotypes originate from deviating temperature sensitivities of underlying physiological processes. We used membrane-inlet mass spectrometry to assess photosynthetic and respiratory O₂ and CO₂ fluxes in response to abrupt temperature changes as well as after acclimation periods in the diatom Phaeodactylum tricornutum. Abrupt temperature changes caused immediate over- or undershoots in most physiological processes, that is, photosynthetic oxygen release ( PS O 2 $$ {\mathrm{PS}}_{{\mathrm{O}}_2} $$ ), photosynthetic carbon uptake ( PS CO 2 $$ {\mathrm{PS}}_{{\mathrm{CO}}_2} $$ ), and respiratory oxygen release ( R O 2 $$ {\mathrm{R}}_{{\mathrm{O}}_2} $$ ). Over acclimation timescales, cells were, however, able to re-adjust their physiology and revert to phenotypic 'sweet spots'. Respiratory CO₂ release ( R CO 2 $$ {\mathrm{R}}_{{\mathrm{CO}}_2} $$ ) was generally inhibited under high temperature and stimulated under low-temperature settings, on abrupt as well as acclimation timescales. Such behavior may help mitochondria to stabilize plastidial ATP : NADPH ratios and thus maximize photosynthetic carbon assimilation.

Fibre type- and localisation-specific muscle glycogen utilisation during repeated high-intensity intermittent exercise

Glycogen particles are situated in key areas of the muscle cell in the vicinity of the main energy-consumption sites and may be utilised heterogeneously dependent on the nature of the metabolic demands. The present study aimed to investigate the time course of fibre type-specific utilisation of muscle glycogen in three distinct subcellular fractions (intermyofibrillar, IMF; intramyofibrillar, Intra; and subsarcolemmal, SS) during repeated high-intensity intermittent exercise. Eighteen moderately to well-trained male participants performed three periods of 10 × 45 s cycling at ∼105% watt max (EX1-EX3) coupled with 5 × 6 s maximal sprints at baseline and after each period. Muscle biopsies were sampled at baseline and after EX1 and EX3. A higher glycogen breakdown rate in type 2 compared to type 1 fibres was found during EX1 for the Intra (-72 vs. -45%) and IMF (-59 vs. -35%) glycogen fractions (P < 0.001) but with no differences for SS glycogen (-52 vs. -40%). In contrast, no fibre type differences were observed during EX2-EX3, where the utilisation of Intra and IMF glycogen in type 2 fibres was reduced, resulting in depletion of all three subcellular fractions to very low levels post-exercise within both fibre types. Importantly, large heterogeneity in single-fibre glycogen utilisation was present with an early depletion of especially Intra glycogen in individual type 2 fibres. In conclusion, there is a clear fibre type- and localisation-specific glycogen utilisation during high-intensity intermittent exercise, which varies with time course of exercise and is characterised by exacerbated pool-specific glycogen depletion at the single-fibre level. KEY POINTS: Muscle glycogen is the major fuel during high-intensity exercise and is stored in distinct subcellular areas of the muscle cell in close vicinity to the main energy consumption sites. In the present study quantitative electron microscopy imaging was used to investigate the utilisation pattern of three distinct subcellular muscle glycogen fractions during repeated high-intensity intermittent exercise. It is shown that the utilisation differs dependent on fibre type, subcellular localisation and time course of exercise and with large single-fibre heterogeneity. These findings expand on our understanding of subcellular muscle glycogen metabolism during exercise and may help us explain how reductions in muscle glycogen can attenuate muscle function even at only moderately lowered whole-muscle glycogen concentrations.

Harnessing Oxidative Microenvironment for In Vivo Synthesis of Subcellular Conductive Polymer Microesicles Enhances Nerve Reconstruction

Conductive polymers (CPs) are promising biomaterials to address signal connection at biointerfaces for tissue regeneration. However, regulating material microstructure at the subcellular scale to provide a more seamless interface between conductive substrates and cells remains a great challenge. Here, we demonstrate that chemical factors and enzyme-carried subcellular structures at lesion site provide a natural bioreactor to self-assemble conductive microvesicles (CMVs) for improving bioelectrical signal reconstruction. The synthesized CMVs contribute to the electrical conduction of the injured nerve in the early stage. Moreover, CMVs are eventually expelled via lymphatic capillary to minimize space-occupying and chronic inflammation. Therefore, we provide a prototype to integrate specific physiological microenvironments and polymer chemistry to manufacture subcellular functional materials with self-adaptive interface in vivo for biomedical applications.

Transcription Factor Movement and Exercise-Induced Mitochondrial Biogenesis in Human Skeletal Muscle: Current Knowledge and Future Perspectives

In response to exercise, the oxidative capacity of mitochondria within skeletal muscle increases through the coordinated expression of mitochondrial proteins in a process termed mitochondrial biogenesis. Controlling the expression of mitochondrial proteins are transcription factors—a group of proteins that regulate messenger RNA transcription from DNA in the nucleus and mitochondria. To fulfil other functions or to limit gene expression, transcription factors are often localised away from DNA to different subcellular compartments and undergo rapid movement or accumulation only when required. Although many transcription factors involved in exercise-induced mitochondrial biogenesis have been identified, numerous conflicting findings and gaps exist within our knowledge of their subcellular movement. This review aims to summarise and provide a critical analysis of the published literature regarding the exercise-induced movement of transcription factors involved in mitochondria biogenesis in skeletal muscle.

Quantitative subcellular acyl-CoA analysis reveals distinct nuclear metabolism and isoleucine-dependent histone propionylation

Quantitative subcellular metabolomic measurements can explain the roles of metabolites in cellular processes but are subject to multiple confounding factors. We developed stable isotope labeling of essential nutrients in cell culture-subcellular fractionation (SILEC-SF), which uses isotope-labeled internal standard controls that are present throughout fractionation and processing to quantify acyl-coenzyme A (acyl-CoA) thioesters in subcellular compartments by liquid chromatography-mass spectrometry. We tested SILEC-SF in a range of sample types and examined the compartmentalized responses to oxygen tension, cellular differentiation, and nutrient availability. Application of SILEC-SF to the challenging analysis of the nuclear compartment revealed a nuclear acyl-CoA profile distinct from that of the cytosol, with notable nuclear enrichment of propionyl-CoA. Using isotope tracing, we identified the branched chain amino acid isoleucine as a major metabolic source of nuclear propionyl-CoA and histone propionylation, thus revealing a new mechanism of crosstalk between metabolism and the epigenome.

[Accumulation, subcellular distribution, and chemical forms of zinc in three tree species]

In order to explore the mechanism underlying zinc (Zn) accumulation and tolerance in woody garden species, the effects of different Zn concentrations (0, 250, 500, 1000, 2000 mg·kg^-1) on leaf, branch, root biomass and leaf ultrastructure of Koelreuteria paniculata, Ailanthus altissima, and Ginkgo biloba were studied in a pot pollution simulation experiment. The concentration of Zn in plant organs, the subcellular distribution and chemical forms of Zn in leaves and roots were further analyzed. The results showed that all the three species could survive under diffe-rent Zn concentrations, but the biomass of leaves, stems and roots decreased compared with the control. Excessive Zn could lead to cell deformation, cell wall rupture and organelle disintegration of leaves in K. paniculata and A. altissima, while the cells in leaves of G. biloba could maintain normal morphology, indicating that G. biloba had a better tolerance to Zn than K. paniculata and A. altissima. With the increases of Zn concentration, Zn concentration in the organs of the three species showed an increasing trend, and the Zn concentration in K. paniculata and A. altissima was significantly higher than that in G. biloba, indicating that the Zn accumulation ability of K. paniculata and A. altissima was stronger than that of G. biloba. Zn was mainly distributed in the cell walls of leaves and roots, accounting for 26.9%-71.8% and 28.1%-82.6%, respectively. Under the treatment with the highest Zn concentration (2000 mg·kg^-1), Zn concentration in the soluble components (mainly vacuoles) could be higher than that in the cell walls. In addition, Zn mainly existed in NaCl-, HAc- and HCl-extracted forms in leaves, accounting for 57.4%-82.7%, and Zn mainly existed in NaCl- and HAc-extracted forms in roots, accounting for 42.8%-67.2%, all of which were forms with relatively low activity. Therefore, cell wall retention, vacuoles segregation and accumulating Zn in less active forms might be important mechanisms underlying Zn accumulation and tolerance in the three trees.

Long noncoding RNA and protein abundance in lncRNPs

Although long noncoding RNAs (lncRNAs) are generally expressed at low levels, emerging evidence has revealed that many play important roles in gene regulation by a variety of mechanisms as they engage with proteins. Given that the abundance of proteins often greatly exceeds that of their interacting lncRNAs, quantification of the relative abundance, or even the exact stoichiometry in some cases, within lncRNA-protein complexes is helpful for understanding of the mechanism(s) of action of lncRNAs. We discuss methods used to examine lncRNA and protein expression at the single cell, subcellular, and suborganelle levels, the average and local lncRNA concentration in cells, as well as how lncRNAs can modulate the functions of their interacting proteins even at a low stoichiometric concentration.

Single Molecule RNA Localization and Translation in the Mammalian Oocyte and Embryo

During oocyte growth the cell accumulates RNAs to contribute to oocyte and embryo development which progresses with ceased transcription. To investigate the subcellular distribution of specific RNAs and their translation we developed a technique revealing several instances of localized translation with distinctive regulatory implications. We analyzed the localization and expression of candidate non-coding and mRNAs in the mouse oocyte and embryo. Furthermore, we established simultaneous visualization of mRNA and in situ translation events validated with polysomal occupancy. We discovered that translationally dormant and abundant mRNAs CyclinB1 and Mos are localized in the cytoplasm of the fully grown GV oocyte forming cloud-like structures with consequent abundant translation at the center of the MII oocyte. Coupling detection of the localization of specific single mRNA molecules with their translation at the subcellular context is a valuable tool to quantitatively study temporal and spatial translation of specific target mRNAs to understand molecular processes in the developing cell.

Algae to angiosperms: Autofluorescence for rapid visualization of plant anatomy among diverse taxa

PREMISE

Fluorescence microscopy is an effective tool for viewing plant internal anatomy. However, using fluorescent antibodies or labels hinders throughput. We present a minimal protocol that takes advantage of inherent autofluorescence and aldehyde-induced fluorescence in plant cellular and subcellular structures to markedly increase throughput in cellular and ultrastructural visualization.

METHODS AND RESULTS

Twelve species distributed across the plant phylogeny were each subjected to five fixative treatments: 1% paraformaldehyde and 2% glutaraldehyde, 2% paraformaldehyde, 2% glutaraldehyde, formalin-acid-alcohol (FAA), and 70% ethanol. Samples were prepared by embedding and mechanically sectioning or via whole mount. A confocal laser scanning system was used to collect micrographs. We evaluated and compared fixative influence on sample structural preservation and tissue autofluorescence.

CONCLUSIONS

Formaldehyde fixation of Viridiplantae taxa samples generates useful structural data while requiring no additional histological staining or clearing. In addition, a fluorescence-capable microscope is the only specialized equipment required for image acquisition. The minimal protocol developed in this experiment enables high-throughput sample processing by eliminating the need for multi-day preparations.

Mitochondrial isolation: when size matters

Mitochondrial vitality is critical to cellular function, with mitochondrial dysfunction linked to a growing number of human diseases. Tissue and cellular heterogeneity, in terms of genetics, dynamics and function means that increasingly mitochondrial research is conducted at the single cell level. Whilst there are several technologies that are currently available for single-cell analysis, each with their advantages, they cannot be easily adapted to study mitochondria with subcellular resolution. Here we review the current techniques and strategies for mitochondrial isolation, critically discussing each technology's limitations for future mitochondrial research. Finally, we highlight and discuss the recent breakthroughs in sub-cellular isolation techniques, with a particular focus on nanotechnologies that enable the isolation of mitochondria from subcellular compartments. This allows isolation of mitochondria with unprecedented spatial precision with minimal disruption to mitochondria and their immediate cellular environment.

Mitochondrial isolation: when size matters

Mitochondrial vitality is critical to cellular function, with mitochondrial dysfunction linked to a growing number of human diseases. Tissue and cellular heterogeneity, in terms of genetics, dynamics and function means that increasingly mitochondrial research is conducted at the single cell level. Whilst there are several technologies that are currently available for single-cell analysis, each with their advantages, they cannot be easily adapted to study mitochondria with subcellular resolution. Here we review the current techniques and strategies for mitochondrial isolation, critically discussing each technology's limitations for future mitochondrial research. Finally, we highlight and discuss the recent breakthroughs in sub-cellular isolation techniques, with a particular focus on nanotechnologies that enable the isolation of mitochondria from subcellular compartments. This allows isolation of mitochondria with unprecedented spatial precision with minimal disruption to mitochondria and their immediate cellular environment.

A Comprehensive Subcellular Atlas of the Toxoplasma Proteome via hyperLOPIT Provides Spatial Context for Protein Functions

Apicomplexan parasites cause major human disease and food insecurity. They owe their considerable success to highly specialized cell compartments and structures. These adaptations drive their recognition, nondestructive penetration, and elaborate reengineering of the host's cells to promote their growth, dissemination, and the countering of host defenses. The evolution of unique apicomplexan cellular compartments is concomitant with vast proteomic novelty. Consequently, half of apicomplexan proteins are unique and uncharacterized. Here, we determine the steady-state subcellular location of thousands of proteins simultaneously within the globally prevalent apicomplexan parasite Toxoplasma gondii. This provides unprecedented comprehensive molecular definition of these unicellular eukaryotes and their specialized compartments, and these data reveal the spatial organizations of protein expression and function, adaptation to hosts, and the underlying evolutionary trajectories of these pathogens.

Coordinated crosstalk between microtubules and actin by a spectraplakin regulates lumen formation and branching

Subcellular lumen formation by single-cells involves complex cytoskeletal remodelling. We have previously shown that centrosomes are key players in the initiation of subcellular lumen formation in Drosophila melanogaster, but not much is known on the what leads to the growth of these subcellular luminal branches or makes them progress through a particular trajectory within the cytoplasm. Here, we have identified that the spectraplakin Short-stop (Shot) promotes the crosstalk between MTs and actin, which leads to the extension and guidance of the subcellular lumen within the tracheal terminal cell (TC) cytoplasm. Shot is enriched in cells undergoing the initial steps of subcellular branching as a direct response to FGF signalling. An excess of Shot induces ectopic acentrosomal luminal branching points in the embryonic and larval tracheal TC leading to cells with extra-subcellular lumina. These data provide the first evidence for a role for spectraplakins in single-cell lumen formation and branching.

Near-Infrared-Activated Lysosome Pathway Death Induced by ROS Generated from Layered Double Hydroxide-Copper Sulfide Nanocomposites

The overdeveloped lysosomes in cancer cells are gaining increasing attention toward more precise and effective organelle-targeted cancer therapy. It is suggested that rod/plate-like nanomaterials with an appropriate size exhibited a greater quantity and longer-term lysosomal enrichment, as the shape plays a notable role in the nanomaterial transmembrane process and subcellular behaviors. Herein, a biodegradable platform based on layered double hydroxide-copper sulfide nanocomposites (LDH-CuS NCs) is successfully prepared via in situ growth of CuS nanodots on LDH nanoplates. The as-prepared LDH-CuS NCs exhibited not only high photothermal conversion and near-infrared (NIR)-induced chemodynamic and photodynamic therapeutic efficacies, but also could achieve real-time in vivo photoacoustic imaging (PAI) of the entire tumor. LDH-CuS NCs accumulated in lysosomes would then generate extensive subcellular reactive oxygen species (ROS) in situ, leading to lysosomal membrane permeabilization (LMP) pathway-associated cell death both in vitro and in vivo.

Lights up on organelles: Optogenetic tools to control subcellular structure and organization

Since the neurobiological inception of optogenetics, light-controlled molecular perturbations have been applied in many scientific disciplines to both manipulate and observe cellular function. Proteins exhibiting light-sensitive conformational changes provide researchers with avenues for spatiotemporal control over the cellular environment and serve as valuable alternatives to chemically inducible systems. Optogenetic approaches have been developed to target proteins to specific subcellular compartments, allowing for the manipulation of nuclear translocation and plasma membrane morphology. Additionally, these tools have been harnessed for molecular interrogation of organelle function, location, and dynamics. Optogenetic approaches offer novel ways to answer fundamental biological questions and to improve the efficiency of bioengineered cell factories by controlling the assembly of synthetic organelles. This review first provides a summary of available optogenetic systems with an emphasis on their organelle-specific utility. It then explores the strategies employed for organelle targeting and concludes by discussing our perspective on the future of optogenetics to control subcellular structure and organization. This article is categorized under: Metabolic Diseases > Molecular and Cellular Physiology.

Transmission Fourier Transform Infrared Spectroscopic Imaging, Mapping, and Synchrotron Scanning Microscopy with Zinc Sulfide Hemispheres on Living Mammalian Cells at Sub-Cellular Resolution

Fourier transform infrared (FT-IR) spectroscopic imaging and microscopy of single living cells are established label-free technique for the study of cell biology. The constant driver to improve the spatial resolution of the technique is due to the diffraction limit given by infrared (IR) wavelength making subcellular study challenging. Recently, we have reported, with the use of a prototype zinc sulfide (ZnS) transmission cell made of two hemispheres, that the spatial resolution is improved by the factor of the refractive index of ZnS, achieving a λ/2.7 spatial resolution using the synchrotron-IR microscopy with a 36× objective with numerical aperture of 0.5. To refine and to demonstrate that the ZnS hemisphere transmission device can be translated to standard bench-top FT-IR imaging systems, we have, in this work, modified the device to achieve a more precise path length, which has improved the spectral quality of the living cells, and showed for the first time that the device can be applied to study live cells with three different bench-top FT-IR imaging systems. We applied focal plane array (FPA) imaging, linear array, and a synchrotron radiation single-point scanning method and demonstrated that in all cases, subcellular details of individual living cells can be obtained. Results have shown that imaging with the FPA detector can measure the largest area in a given time, while measurements from the scanning methods produced a smoother image. Synchrotron radiation single-point mapping produced the best quality image and has the flexibility to introduce over sampling to produce images of cells with great details, but it is time consuming in scanning mode. In summary, this work has demonstrated that the ZnS hemispheres can be applied in all three spectroscopic approaches to improve the spatial resolution without any modification to the existing microscopes.

[Tolerance Mechanism and Cadmium Enrichment Abilities in Two Brassica napus L. Cultivars]

A hydroponic experiment was conducted to explore the differences in growth status and Cd accumulation characteristics of two Brassica napus L. cultivars (QY-1 and SYH) under different concentrations of cadmium (Cd) stress (0, 2, and 5 mg·L^-1). The Cd subcellular compartmentalization and antioxidant enzyme activities were determined to elucidate the intrinsic mechanism of the differences in the Cd accumulation capacity between the two cultivars of Brassica napus L. Furthermore, field trials were conducted to further verify the differences in phytoremediation of the two cultivars. Results show that neither of the cultivars exhibited obvious growth inhibition under Cd stress. Under the 2 mg·L^-1 Cd condition, there were no significant differences in shoot Cd concentrations between the two cultivars. Under 5 mg·L^-1 Cd condition, however, the Cd concentrations in both shoot and root of SYH were significantly higher than that of QY-1, which increased by 32.05% and 99.57%, respectively. In addition, the bioconcentration factor (BCF) of the root in SYH is significantly higher than that of QY-1. The subcellular Cd distribution in leaves of the two cultivars of Brassica napus L. showed that, with an increase of Cd stress, Cd concentrations of heat stable protein (HSP) and metal-rich granule (MRG) fractions in leaves significantly increased by 143.69% and 118.91% for QY-1, and by 63.34% and 118.91% for SYH. Thus, the segregation of Cd in HSP and MRG, which was reported to be biological detoxified metal fractions (BDM), might play an important role in the detoxification of Brassica napus L. at a subcellular level under Cd stress. Moreover, the distribution of Cd in the cellular debris fraction might be another important factor contributing to the differences in Cd accumulation of the two Brassica napus L. cultivars, which was 4.41 times higher in SYH than in QY-1 under Cd stress. The results of the antioxidant enzyme activities of two Brassica napus L. cultivars showed that, under the 5 mg·L^-1 Cd condition, the antioxidant enzyme system may represent an important detoxification mechanism for QY-1 to cope with stress induced by high concentrations of Cd, while SYH is more effective in reducing the toxicity of Cd by separation of Cd into BDM fractions. The results of the field trial confirmed that the Cd concentrations in the above- and underground parts of SYH were 2.34 and 1.43 times higher than in QY-1, respectively. Therefore, SYH possess a higher Cd phytoextraction capacity than QY-1, and might be a good candidate for the remediation of moderate and mildly Cd-contaminated farmland.

Active Cellular and Subcellular Targeting of Nanoparticles for Drug Delivery

Nanoparticle (NP)-mediated drug delivery (NMDD) for active targeting of diseases is a primary goal of nanomedicine. NPs have much to offer in overcoming the limitations of traditional drug delivery approaches, including off-target drug toxicity and the need for the administration of repetitive doses. In the last decade, one of the main foci in NMDD has been the realization of NP-mediated drug formulations for active targeted delivery to diseased tissues, with an emphasis on cellular and subcellular targeting. Advances on this front have included the intricate design of targeted NP-drug constructs to navigate through biological barriers, overcome multidrug resistance (MDR), decrease side effects, and improve overall drug efficacy. In this review, we survey advancements in NP-mediated drug targeting over the last five years, highlighting how various NP-drug constructs have been designed to achieve active targeted delivery and improved therapeutic outcomes for critical diseases including cancer, rheumatoid arthritis, and Alzheimer's disease. We conclude with a survey of the current clinical trial landscape for active targeted NP-drug delivery and how we envision this field will progress in the near future.

Multilevel heterogeneity of mitochondrial respiratory chain deficiency

Mitochondrial diseases are heterogeneous multisystem disorders that show a mosaic pattern of mitochondrial respiratory chain dysfunction. The mitochondrial DNA (mtDNA) mutation load is heterogeneous at multiple levels: across organs, between cells, and between subcellular compartments. Such heterogeneity poses a diagnostic challenge, but also provides a scientific opportunity to explore the biological mechanisms underlying the onset and progression of these disorders. A recent article in The Journal of Pathology described a novel histochemical technique - nitro blue tetrazolium exclusion assay (NBTx) - to quantify mitochondrial cytochrome c oxidase (COX, or complex IV) deficiency. This technique is rapid, cost-effective, and quantitative, and is more sensitive than previous histochemical methods. It can also be applied across model organisms and human tissues. The NBTx method should therefore be a useful diagnostic tool, and may catalyze research examining the cellular and subcellular mechanisms that drive the onset and progression of inherited and acquired mtDNA disorders. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Identification of VAPA and VAPB as Kv2 Channel-Interacting Proteins Defining Endoplasmic Reticulum-Plasma Membrane Junctions in Mammalian Brain Neurons

Membrane contacts between endoplasmic reticulum (ER) and plasma membrane (PM), or ER-PM junctions, are ubiquitous in eukaryotic cells and are platforms for lipid and calcium signaling and homeostasis. Recent studies have revealed proteins crucial to the formation and function of ER-PM junctions in non-neuronal cells, but little is known of the ER-PM junctions prominent in aspiny regions of mammalian brain neurons. The Kv2.1 voltage-gated potassium channel is abundantly clustered at ER-PM junctions in brain neurons and is the first PM protein that functions to organize ER-PM junctions. However, the molecular mechanism whereby Kv2.1 localizes to and remodels these junctions is unknown. We used affinity immunopurification and mass spectrometry-based proteomics on brain samples from male and female WT and Kv2.1 KO mice and identified the resident ER vesicle-associated membrane protein-associated proteins isoforms A and B (VAPA and VAPB) as prominent Kv2.1-associated proteins. Coexpression with Kv2.1 or its paralog Kv2.2 was sufficient to recruit VAPs to ER-PM junctions. Multiplex immunolabeling revealed colocalization of Kv2.1 and Kv2.2 with endogenous VAPs at ER-PM junctions in brain neurons from male and female mice in situ and in cultured rat hippocampal neurons, and KO of VAPA in mammalian cells reduces Kv2.1 clustering. The association of VAPA with Kv2.1 relies on a "two phenylalanines in an acidic tract" (FFAT) binding domain on VAPA and a noncanonical phosphorylation-dependent FFAT motif comprising the Kv2-specific clustering or PRC motif. These results suggest that Kv2.1 localizes to and organizes neuronal ER-PM junctions through an interaction with VAPs.SIGNIFICANCE STATEMENT Our study identified the endoplasmic reticulum (ER) proteins vesicle-associated membrane protein-associated proteins isoforms A and B (VAPA and VAPB) as proteins copurifying with the plasma membrane (PM) Kv2.1 ion channel. We found that expression of Kv2.1 recruits VAPs to ER-PM junctions, specialized membrane contact sites crucial to distinct aspects of cell function. We found endogenous VAPs at Kv2.1-mediated ER-PM junctions in brain neurons and other mammalian cells and that knocking out VAPA expression disrupts Kv2.1 clustering. We identified domains of VAPs and Kv2.1 necessary and sufficient for their association at ER-PM junctions. Our study suggests that Kv2.1 expression in the PM can affect ER-PM junctions via its phosphorylation-dependent association to ER-localized VAPA and VAPB.

Application of the Mesolens for subcellular resolution imaging of intact larval and whole adult Drosophila

In a previous paper, we showed a new giant lens called the Mesolens and presented performance data and images from whole fixed and intact fluorescently‐stained 12.5‐day old mouse embryos. Here, we show that using the Mesolens we can image an entire Drosophila larva or adult fly in confocal epifluorescence and show subcellular detail in all tissues. By taking several hundreds of optical sections through the entire volume of the specimen, we show cells and nuclear details within the gut, brain, salivary glands and reproductive system that normally require dissection for study. Organs are imaged in situ in correct 3D arrangement. Imaginal discs are imaged in mature larvae and it proved possible to image pachytene chromosomes in cells within ovarian follicles in intact female flies. Methods for fixing, staining and clearing are given.

Sodium Channel Remodeling in Subcellular Microdomains of Murine Failing Cardiomyocytes

Background

Cardiac sodium channel (NaV1.5) dysfunction contributes to arrhythmogenesis during pathophysiological conditions. Nav1.5 localizes to distinct subcellular microdomains within the cardiomyocyte, where it associates with region‐specific proteins, yielding complexes whose function is location specific. We herein investigated sodium channel remodeling within distinct cardiomyocyte microdomains during heart failure.

Methods and Results

Mice were subjected to 6 weeks of transverse aortic constriction (TAC; n=32) to induce heart failure. Sham–operated on mice were used as controls (n=20). TAC led to reduced left ventricular ejection fraction, QRS prolongation, increased heart mass, and upregulation of prohypertrophic genes. Whole‐cell sodium current (I_Na) density was decreased by 30% in TAC versus sham–operated on cardiomyocytes. On macropatch analysis, I_Na in TAC cardiomyocytes was reduced by 50% at the lateral membrane (LM) and by 40% at the intercalated disc. Electron microscopy and scanning ion conductance microscopy revealed remodeling of the intercalated disc (replacement of [inter‐]plicate regions by large foldings) and LM (less identifiable T tubules and reduced Z‐groove ratios). Using scanning ion conductance microscopy, cell‐attached recordings in LM subdomains revealed decreased I_Na and increased late openings specifically at the crest of TAC cardiomyocytes, but not in groove/T tubules. Failing cardiomyocytes displayed a denser, but more stable, microtubule network (demonstrated by increased α‐tubulin and Glu‐tubulin expression). Superresolution microscopy showed reduced average Na_V1.5 cluster size at the LM of TAC cells, in line with reduced I_Na.

Conclusions

Heart failure induces structural remodeling of the intercalated disc, LM, and microtubule network in cardiomyocytes. These adaptations are accompanied by alterations in Na_V1.5 clustering and I_Na within distinct subcellular microdomains of failing cardiomyocytes.

Compartmentalized Signaling in Neurons: From Cell Biology to Neuroscience

Neurons are the largest known cells, with complex and highly polarized morphologies. As such, neuronal signaling is highly compartmentalized, requiring sophisticated transfer mechanisms to convey and integrate information within and between sub-neuronal compartments. Here, we survey different modes of compartmentalized signaling in neurons, highlighting examples wherein the fundamental cell biological processes of protein synthesis and degradation, membrane trafficking, and organelle transport are employed to enable the encoding and integration of information, locally and globally within a neuron. Comparisons to other cell types indicate that neurons accentuate widely shared mechanisms, providing invaluable models for the compartmentalization and transfer mechanisms required and used by most eukaryotic cells.

Compartment-Dependent Degradation of Mutant Huntingtin Accounts for Its Preferential Accumulation in Neuronal Processes

In neurodegenerative diseases caused by misfolded proteins, including Huntington's disease (HD), the neuronal processes and terminals are particularly prone to the accumulation of misfolded proteins, leading to axonal and synaptic dysfunction. This compartment-dependent accumulation can result from either the altered transport of misfolded proteins or impaired protein degradation. Mutant huntingtin (mHtt), the HD protein, is known to affect intracellular transport and can be degraded by the proteasome and autophagy, but how mHtt accumulates in the neuronal processes, an early pathological event in the brains of HD patients, still remains unclear. Using an "optical pulse-chase" assay that can quantify protein degradation in specific subcellular regions, we found that neuronal mHtt is removed faster in the cell body than in neurites. Furthermore, mHtt is cleared more rapidly in astrocytes than in neurons. The ubiquitin-proteasome system plays a much bigger role than autophagy in degrading soluble mHtt via K48 ubiquitination in both the cytoplasm and processes of neurons and astrocytes. By injecting adenoviral vectors expressing mHtt into the mouse brain, we confirmed that mHtt is removed more slowly in neurites than in the cytoplasm of the cell body of neurons. Our findings provide evidence for the cell type- and compartment-dependent degradation of mHtt and explain why mHtt preferentially accumulates and aggregates in the neuropils of vulnerable neurons. In addition, our findings suggest that enhancing proteasomal activity could be an effective way to reduce the preferential accumulation of soluble mHtt in neuronal processes.

SIGNIFICANCE STATEMENT

The clearance of misfolded proteins is key to preventing neurodegeneration in Huntington's disease, but how mutant huntingtin (mHtt) accumulates differentially in different cell types and subcellular regions remains unclear. We found mHtt is cleared slowly in neuronal processes compared with the cytoplasm and is cleared more efficiently in astrocytes than in neurons. Moreover, this compartment-dependent degradation of soluble mHtt is mediated primarily by the ubiquitin-proteasome system rather than autophagy. Our findings imply that enhancing proteasome activity could be an efficient way to clear soluble misfolded proteins in the neuronal processes.

Recent advances in proteomics of cereals

Cereals contribute a major part of human nutrition and are considered as an integral source of energy for human diets. With genomic databases already available in cereals such as rice, wheat, barley, and maize, the focus has now moved to proteome analysis. Proteomics studies involve the development of appropriate databases based on developing suitable separation and purification protocols, identification of protein functions, and can confirm their functional networks based on already available data from other sources. Tremendous progress has been made in the past decade in generating huge data-sets for covering interactions among proteins, protein composition of various organs and organelles, quantitative and qualitative analysis of proteins, and to characterize their modulation during plant development, biotic, and abiotic stresses. Proteomics platforms have been used to identify and improve our understanding of various metabolic pathways. This article gives a brief review of efforts made by different research groups on comparative descriptive and functional analysis of proteomics applications achieved in the cereal science so far.

An NMDA receptor-dependent mechanism for subcellular segregation of sensory inputs in the tadpole optic tectum

In the vertebrate CNS, afferent sensory inputs are targeted to specific depths or layers of their target neuropil. This patterning exists ab initio, from the very beginning, and therefore has been considered an activity-independent process. However, here we report that, during circuit development, the subcellular segregation of the visual and mechanosensory inputs to specific regions of tectal neuron dendrites in the tadpole optic tectum requires NMDA receptor activity. Blocking NMDARs during the formation of these sensory circuits, or removing the visual set of inputs, leads to less defined segregation, and suggests a correlation-based mechanism in which correlated inputs wire to common regions of dendrites. This can account for how two sets of inputs form synapses onto different regions of the same dendrite. Blocking NMDA receptors during later stages of circuit development did not disrupt segregation, indicating a critical period for activity-dependent shaping of patterns of innervation.

DOI:http://dx.doi.org/10.7554/eLife.20502.001

Regulation of intracellular heme trafficking revealed by subcellular reporters

Heme is an essential prosthetic group in proteins that reside in virtually every subcellular compartment performing diverse biological functions. Irrespective of whether heme is synthesized in the mitochondria or imported from the environment, this hydrophobic and potentially toxic metalloporphyrin has to be trafficked across membrane barriers, a concept heretofore poorly understood. Here we show, using subcellular-targeted, genetically encoded hemoprotein peroxidase reporters, that both extracellular and endogenous heme contribute to cellular labile heme and that extracellular heme can be transported and used in toto by hemoproteins in all six subcellular compartments examined. The reporters are robust, show large signal-to-background ratio, and provide sufficient range to detect changes in intracellular labile heme. Restoration of reporter activity by heme is organelle-specific, with the Golgi and endoplasmic reticulum being important sites for both exogenous and endogenous heme trafficking. Expression of peroxidase reporters in Caenorhabditis elegans shows that environmental heme influences labile heme in a tissue-dependent manner; reporter activity in the intestine shows a linear increase compared with muscle or hypodermis, with the lowest heme threshold in neurons. Our results demonstrate that the trafficking pathways for exogenous and endogenous heme are distinct, with intrinsic preference for specific subcellular compartments. We anticipate our results will serve as a heuristic paradigm for more sophisticated studies on heme trafficking in cellular and whole-animal models.

Diverse and pervasive subcellular distributions for both coding and long noncoding RNAs

Here, Wilk et al. examined ∼8000 mRNA transcripts throughout Drosophila embryogenesis. They found that almost all RNAs, both coding and noncoding RNAs, are subcellularly localized at some stage of development, thus providing an important resource for functional gene analysis.

In a previous analysis of 2300 mRNAs via whole-mount fluorescent in situ hybridization in cellularizing Drosophila embryos, we found that 70% of the transcripts exhibited some form of subcellular localization. To see whether this prevalence is unique to early Drosophila embryos, we examined ∼8000 transcripts over the full course of embryogenesis and ∼800 transcripts in late third instar larval tissues. The numbers and varieties of new subcellular localization patterns are both striking and revealing. In the much larger cells of the third instar larva, virtually all transcripts observed showed subcellular localization in at least one tissue. We also examined the prevalence and variety of localization mechanisms for >100 long noncoding RNAs. All of these were also found to be expressed and subcellularly localized. Thus, subcellular RNA localization appears to be the norm rather than the exception for both coding and noncoding RNAs. These results, which have been annotated and made available on a recompiled database, provide a rich and unique resource for functional gene analyses, some examples of which are provided.

Linking Subcellular Disturbance to Physiological Behavior and Toxicity Induced by Quantum Dots in Caenorhabditis elegans

The wide-ranging applications of fluorescent semiconductor quantum dots (QDs) have triggered increasing concerns about their biosafety. Most QD-related toxicity studies focus on the subcellular processes in cultured cells or global physiological effects on whole animals. However, it is unclear how QDs affect subcellular processes in living organisms, or how the subcellular disturbance contributes to the overall toxicity. Here the behavior and toxicity of QDs of three different sizes in Caenorhabditis elegans (C. elegans) are systematically investigated at both the systemic and the subcellular level. Specifically, clear size-dependent distribution and toxicity of the QDs in the digestive tract are observed. Short-term exposure of QDs leads to acute toxicity on C. elegans, yet incurring no lasting, irreversible damage. In contrast, chronic exposure of QDs severely inhibits development and shortens lifespan. Subcellular analysis reveals that endocytosis and nutrition storage are disrupted by QDs, which likely accounts for the severe deterioration in growth and longevity. This work reveals that QDs invasion disrupts key subcellular processes in living organisms, and may cause permanent damage to the tissues and organs over long-term retention. The findings provide invaluable information for safety evaluations of QD-based applications and offer new opportunities for design of novel nontoxic nanoprobes.

Reciprocal interareal connections to corticospinal neurons in mouse M1 and S2

Primary motor (M1) and secondary somatosensory (S2) cortices, although anatomically and functionally distinct, share an intriguing cellular component: corticospinal neurons (CSP) in layer 5B. Here, we investigated the long-range circuits of CSPs in mouse forelimb-M1 and S2. We found that interareal projections (S2 → M1 and M1 → S2) monosynaptically excited pyramidal neurons across multiple layers, including CSPs. Area-specific differences were observed in the relative strengths of inputs to subsets of CSPs and other cell types, but the general patterns were similar. Furthermore, subcellular mapping of the dendritic distributions of these corticocortical excitatory synapses onto CSPs in both areas also showed similar patterns. Because layer 5B is particularly thick in M1, but not S2, we studied M1-CSPs at different cortical depths, quantifying their dendritic morphology and mapping inputs from additional cortical (M2, contralateral M1, and local layer 2/3) and thalamic (VL nucleus) sources. These results indicated that CSPs exhibit area-specific modifications on an otherwise conserved synaptic organization, and that different afferents innervate M1-CSP dendritic domains in a source-specific manner. In the cervical spinal cord, CSP axons from S2 and M1 partly converged on middle layers, but S2-CSP axons extended further dorsally, and M1-CSP axons ventrally. Thus, our findings identify many shared features in the circuits of M1 and S2 and show that these areas communicate via mutual projections that give each area monosynaptic access to the other area's CSPs. These interareally yoked CSP circuits may enable M1 and S2 to operate in a coordinated yet differentiated manner in the service of sensorimotor integration.

Systems analysis of metabolic phenotypes: what have we learnt?

Flux is one of the most informative measures of metabolic behavior. Its estimation requires integration of experimental and modeling approaches and, thus, is at the heart of metabolic systems biology. In this review, we argue that flux analysis and modeling of a range of plant systems points to the importance of the supply of metabolic inputs and demand for metabolic end-products as key drivers of metabolic behavior. This has implications for metabolic engineering, and the use of in silico models will be important to help design more effective engineering strategies. We also consider the importance of cell type-specific metabolism and the challenges of characterizing metabolism at this resolution. A combination of new measurement technologies and modeling approaches is bringing us closer to integrating metabolic behavior with whole-plant physiology and growth.

Sub-10-nm intracellular bioelectronic probes from nanowire-nanotube heterostructures

The miniaturization of bioelectronic intracellular probes with a wide dynamic frequency range can open up opportunities to study biological structures inaccessible by existing methods in a minimally invasive manner. Here, we report the design, fabrication, and demonstration of intracellular bioelectronic devices with probe sizes less than 10 nm. The devices are based on a nanowire-nanotube heterostructure in which a nanowire field-effect transistor detector is synthetically integrated with a nanotube cellular probe. Sub-10-nm nanotube probes were realized by a two-step selective etching approach that reduces the diameter of the nanotube free-end while maintaining a larger diameter at the nanowire detector necessary for mechanical strength and electrical sensitivity. Quasi-static water-gate measurements demonstrated selective device response to solution inside the nanotube, and pulsed measurements together with numerical simulations confirmed the capability to record fast electrophysiological signals. Systematic studies of the probe bandwidth in different ionic concentration solutions revealed the underlying mechanism governing the time response. In addition, the bandwidth effect of phospholipid coatings, which are important for intracellular recording, was investigated and modeled. The robustness of these sub-10-nm bioelectronics probes for intracellular interrogation was verified by optical imaging and recording the transmembrane resting potential of HL-1 cells. These ultrasmall bioelectronic probes enable direct detection of cellular electrical activity with highest spatial resolution achieved to date, and with further integration into larger chip arrays could provide a unique platform for ultra-high-resolution mapping of activity in neural networks and other systems.

Sub-10-nm intracellular bioelectronic probes from nanowire-nanotube heterostructures

The miniaturization of bioelectronic intracellular probes with a wide dynamic frequency range can open up opportunities to study biological structures inaccessible by existing methods in a minimally invasive manner. Here, we report the design, fabrication, and demonstration of intracellular bioelectronic devices with probe sizes less than 10 nm. The devices are based on a nanowire-nanotube heterostructure in which a nanowire field-effect transistor detector is synthetically integrated with a nanotube cellular probe. Sub-10-nm nanotube probes were realized by a two-step selective etching approach that reduces the diameter of the nanotube free-end while maintaining a larger diameter at the nanowire detector necessary for mechanical strength and electrical sensitivity. Quasi-static water-gate measurements demonstrated selective device response to solution inside the nanotube, and pulsed measurements together with numerical simulations confirmed the capability to record fast electrophysiological signals. Systematic studies of the probe bandwidth in different ionic concentration solutions revealed the underlying mechanism governing the time response. In addition, the bandwidth effect of phospholipid coatings, which are important for intracellular recording, was investigated and modeled. The robustness of these sub-10-nm bioelectronics probes for intracellular interrogation was verified by optical imaging and recording the transmembrane resting potential of HL-1 cells. These ultrasmall bioelectronic probes enable direct detection of cellular electrical activity with highest spatial resolution achieved to date, and with further integration into larger chip arrays could provide a unique platform for ultra-high-resolution mapping of activity in neural networks and other systems.

Spatial profiling of nuclear receptor transcription patterns over the course of Drosophila development

Previous work has shown that many of the 18 family members of Drosophila nuclear receptor transcription factors function in a temporal hierarchy to coordinate developmental progression and growth with the rate limiting process of metabolism. To gain further insight into these interactions and processes, we have undertaken a whole-family analysis of nuclear receptor mRNA spatial expression patterns over the entire process of embryogenesis, as well as the 3rd instar wandering larva stage, by using high-resolution fluorescence in situ hybridization. Overall, the patterns of expression are remarkably consistent with previously mapped spatial activity profiles documented during the same time points, with similar hot spots and temporal profiles in endocrine and metabolically important tissues. Among the more remarkable of the findings is that the majority of mRNA expression patterns observed show striking subcellular distributions, indicating potentially critical roles in the control of protein synthesis and subsequent subcellular distributions. These patterns will serve as a useful reference for future studies on the tissue-specific roles and interactions of nuclear receptor proteins, partners, cofactors and ligands.

KCC2-dependent subcellular E(Cl) difference of ON-OFF retinal ganglion cells in larval zebrafish

Subcellular difference in the reversal potential of Cl(-) (ECl) has been found in many types of neurons. As local ECl largely determines the action of nearby GABAergic/glycinergic synapses, subcellular ECl difference can effectively regulate neuronal computation. The ON-OFF retinal ganglion cell (RGC) processes both ON and OFF visual signals via its ON and OFF dendrites, respectively. It is thus interesting to investigate whether the ON and OFF dendrites of single RGCs exhibit different local ECl. Here, using in vivo gramicidin-perforated patch recording in larval zebrafish ON-OFF RGCs, we examine local ECl at the ON and OFF dendrites, and soma through measuring light-evoked ON and OFF inhibitory responses, and GABA-induced response at the soma, respectively. We find there are subcellular ECl differences between the soma and dendrite, as well as between the ON and OFF dendrites of single RGCs. These somato-dendritic and inter-dendritic ECl differences are dependent on the Cl(-) extruder, K(+)/Cl(-) co-transporter (KCC2), because they are largely diminished by down-regulating kcc2 expression with morpholino oligonucleotides (MOs) or by blocking KCC2 function with furosemide. Thus, our findings indicate that there exists KCC2-dependent ECl difference between the ON and OFF dendrites of individual ON-OFF RGCs that may differentially affect visual processing in the ON and OFF pathways.

Review on recent advances in the analysis of isolated organelles

The analysis of isolated organelles is one of the pillars of modern bioanalytical chemistry. This review describes recent developments on the isolation and characterization of isolated organelles both from living organisms and cell cultures. Salient reports on methods to release organelles focused on reproducibility and yield, membrane isolation, and integrated devices for organelle release. New developments on organelle fractionation after their isolation were on the topics of centrifugation, immunocapture, free flow electrophoresis, flow field-flow fractionation, fluorescence activated organelle sorting, laser capture microdissection, and dielectrophoresis. New concepts on characterization of isolated organelles included atomic force microscopy, optical tweezers combined with Raman spectroscopy, organelle sensors, flow cytometry, capillary electrophoresis, and microfluidic devices.

Capillary electrophoretic analysis reveals subcellular binding between individual mitochondria and cytoskeleton

Interactions between the cytoskeleton and mitochondria are essential for normal cellular function. An assessment of such interactions is commonly based on bulk analysis of mitochondrial and cytoskeletal markers present in a given sample, which assumes complete binding between these two organelle types. Such measurements are biased because they rarely account for nonbound "free" subcellular species. Here we report on the use of capillary electrophoresis with dual laser induced fluorescence detection (CE-LIF) to identify, classify, count, and quantify properties of individual binding events of the mitochondria and cytoskeleton. Mitochondria were fluorescently labeled with DsRed2 while F-actin, a major cytoskeletal component, was fluorescently labeled with Alexa488-phalloidin. In a typical subcellular fraction of L6 myoblasts, 79% of mitochondrial events did not have detectable levels of F-actin, while the rest had on average ~2 zmol of F-actin, which theoretically represents a ~2.5 μm long network of actin filaments per event. Trypsin treatment of L6 subcellular fractions prior to analysis decreased the fraction of mitochondrial events with detectable levels of F-actin, which is expected from digestion of cytoskeletal proteins on the surface of mitochondria. The electrophoretic mobility distributions of the individual events were also used to further distinguish between cytoskeleton-bound from cytoskeleton-free mitochondrial events. The CE-LIF approach described here could be further developed to explore cytoskeleton interactions with other subcellular structures, the effects of cytoskeleton destabilizing drugs, and the progression of viral infections.

Increased RNAi is related to intracellular release of siRNA via a covalently attached signal peptide

In the last decade short interfering RNA (siRNA) became an important means for functional genomics and the development of gene-specific drugs. However, major technical hurdles in the application of siRNA include its cellular delivery followed by its intracellular trafficking and its release in order to enter the RNA interference (RNAi) machinery. The novel phosphorothioate-stimulated cellular uptake of siRNA contrasts other known delivery systems because it involves a caveosomal pathway in which large amounts of siRNA are delivered to the perinuclear environment, leading to measurable though moderate target suppression. Limited efficacy seems to be related to intracellular trapping of siRNA. To study the role of intracellular trafficking of siRNA for biological effectiveness we studied whether a signal peptide for trans-membrane transport of bacterial protein toxins, which is covalently attached to siRNA, can promote its release from the perinuclear space into the cytoplasm and thereby enhance its biological effectiveness. We show that attachment of the peptide TQIENLKEKG to lamin A/C-directed siRNA improves target inhibition after its PS-stimulated delivery. This is related to increased efflux of the siRNA-peptide conjugate from the ER-specific perinuclear sites. In summary, this study strongly suggests that intracellular release of siRNA leads to increased biological effectiveness. Thus covalent peptide-siRNA conjugates are proposed as new tools to study the relationship between intracellular transport and efficacy of siRNA.