Total Cellular Volume Research Articles

Defocus Corrected Large Area Cryo-EM (DeCo-LACE) for label-free detection of molecules across entire cell sections.

A major goal of biological imaging is localization of biomolecules inside a cell. Fluorescence microscopy can localize biomolecules inside whole cells and tissues, but its ability to count biomolecules and accuracy of the spatial coordinates is limited by the wavelength of visible light. Cryo-electron microscopy (cryo-EM) provides highly accurate position and orientation information of biomolecules but is often confined to small fields of view inside a cell, limiting biological context. In this study, we use a new data-acquisition scheme called Defocus-Corrected Large-Area cryo-EM (DeCo-LACE) to collect high-resolution images of entire sections (100- to 250-nm-thick lamellae) of neutrophil-like mouse cells, representing 1-2% of the total cellular volume. We use 2D template matching (2DTM) to determine localization and orientation of the large ribosomal subunit in these sections. These data provide maps of ribosomes across entire sections of mammalian cells. This high-throughput cryo-EM data collection approach together with 2DTM will advance visual proteomics and provide biological insight that cannot be obtained by other methods.

Physical properties of the cytoplasm modulate the rates of microtubule polymerization and depolymerization.

The cytoplasm is a crowded, visco-elastic environment whose physical properties change according to physiological or developmental states. How the physical properties of the cytoplasm impact cellular functions invivo remains poorly understood. Here, we probe the effects of cytoplasmic concentration on microtubules by applying osmotic shifts to fission yeast, moss, and mammalian cells. We show that the rates of both microtubule polymerization and depolymerization scale linearly and inversely with cytoplasmic concentration; an increase in cytoplasmic concentration decreases the rates of microtubule polymerization and depolymerization proportionally, whereas a decrease in cytoplasmic concentration leads to the opposite. Numerous lines of evidence indicate that these effects are due to changes in cytoplasmic viscosity rather than cellular stress responses or macromolecular crowding per se. We reconstituted these effects on microtubules invitro by tuning viscosity. Our findings indicate that, even in normal conditions, the viscosity of the cytoplasm modulates the reactions that underlie microtubule dynamic behaviors.

Oncogene-regulated release of extracellular vesicles.

Oncogenes can alter metabolism by changing the balance between anabolic and catabolic processes. However, how oncogenes regulate tumor cell biomass remains poorly understood. Using isogenic MCF10A cells transformed with nine different oncogenes, we show that specific oncogenes reduce the biomass of cancer cells by promoting extracellular vesicle (EV) release. While MYC and AURKB elicited the highest number of EVs, each oncogene selectively altered the protein composition of released EVs. Likewise, oncogenes alter secreted miRNAs. MYC-overexpressing cells require ceramide, whereas AURKB requires ESCRT to release high levels of EVs. We identify an inverse relationship between MYC upregulation and activation of the RAS/MEK/ERK signaling pathway for regulating EV release in some tumor cells. Finally, lysosome genes and activity are downregulated in the context of MYC and AURKB, suggesting that cellular contents, instead of being degraded, were released via EVs. Thus, oncogene-mediated biomass regulation via differential EV release is a new metabolic phenotype.

Adherens junction engagement regulates functional patterning of the cardiac pacemaker cell lineage.

Cardiac pacemaker cells (CPCs) rhythmically initiate the electrical impulses that drive heart contraction. CPCs display the highest rate of spontaneous depolarization in the heart despite being subjected to inhibitory electrochemical conditions that should theoretically suppress their activity. While several models have been proposed to explain this apparent paradox, the actual molecular mechanisms that allow CPCs to overcome electrogenic barriers to their function remain poorly understood. Here, we have traced CPC development at single-cell resolution and uncovered a series of cytoarchitectural patterning events that are critical for proper pacemaking. Specifically, our data reveal that CPCs dynamically modulate adherens junction (AJ) engagement to control characteristics including surface area, volume, and gap junctional coupling. This allows CPCs to adopt a structural configuration that supports their overall excitability. Thus, our data have identified a direct role for local cellular mechanics in patterning critical morphological features that are necessary for CPC electrical activity.

Lysosomal Stress Response (LSR): Physiological Importance and Pathological Relevance.

Extensive work has characterized endoplasmic reticulum (ER) and mitochondrial stress responses. In contrast, very little has been published about stress responses in lysosomes; subcellular acidic organelles that are physiologically important and are of pathological relevance. The greater lysosomal system is dynamic and is comprised of endosomes, lysosomes, multivesicular bodies, autophagosomes, and autophagolysosomes. They are important regulators of cellular physiology, they represent about 5% of the total cellular volume, they are heterogeneous in their sizes and distribution patterns, they are electron dense, and their subcellular positioning within cells varies in response to stimuli, insults and pH. These organelles are also integral to the pathogenesis of lysosomal storage diseases and it is increasingly recognized that lysosomes play important roles in the pathogenesis of such diverse conditions as neurodegenerative disorders and cancer. The purpose of this review is to focus attention on lysosomal stress responses (LSR), compare LSR with better characterized stress responses in ER and mitochondria, and form a framework for future characterizations of LSR. We synthesized data into the concept of LSR and present it here such that the definition of LSR can be modified as new knowledge is added and specific therapeutics are developed.

New Method for Quantitation of Lipid Droplet Volume From Light Microscopic Images With an Application to Determination of PAT Protein Density on the Droplet Surface.

Determination of lipid droplet (LD) volume has depended on direct measurement of the diameter of individual LDs, which is not possible when LDs are small or closely apposed. To overcome this problem, we describe a new method in which a volume-fluorescence relationship is determined from automated analysis of calibration samples containing well-resolved LDs. This relationship is then used to estimate total cellular droplet volume in experimental samples, where the LDs need not be individually resolved, or to determine the volumes of individual LDs. We describe quantitatively the effects of various factors, including image noise, LD crowding, and variation in LD composition on the accuracy of this method. We then demonstrate this method by utilizing it to address a scientifically interesting question, to determine the density of green fluorescent protein (GFP)-tagged Perilipin-Adipocyte-Tail (PAT) proteins on the LD surface. We find that PAT proteins cover only a minority of the LD surface, consistent with models in which they primarily serve as scaffolds for binding of regulatory proteins and enzymes, but inconsistent with models in which their major function is to sterically block access to the droplet surface.

Effect of candesartan and metoprolol on myocardial tissue composition during anthracycline treatment: the PRADA trial.

Anthracycline treatment may cause myocyte loss and expansion of the myocardial extracellular volume (ECV) fraction by oedema and fibrosis. We tested the hypotheses that adjuvant treatment for early breast cancer with the anthracycline epirubicin is dose dependently associated with increased ECV fraction and total ECV, as well as reduced total myocardial cellular volume, and that these changes could be prevented by concomitant angiotensin or beta-adrenergic blockade. PRevention of cArdiac Dysfunction during Adjuvant breast cancer therapy (PRADA) was a 2 × 2 factorial, placebo-controlled, double-blinded trial of candesartan and metoprolol. Sixty-nine women had valid ECV measurements. ECV fraction, total ECV, and total cellular volume were measured by cardiovascular magnetic resonance before and at the completion of anthracycline therapy. ECV fraction increased from 27.5 ± 2.7% to 28.6 ± 2.9% (P = 0.002). A cumulative doxorubicin equivalent dose of 268 mg/m2 was associated with greater increase in ECV fraction than doses <268 mg/m2 (mean change 3.4% [95% confidence interval (CI) 1.2, 5.5] vs. 0.7% [95% CI 0.0, 1.5], P = 0.006), as well as greater increase in total ECV (1.9 mL [95% CI 0.4, 3.5] vs. 0.1 mL [95% CI -0.6, 0.8], P = 0.04). In patients receiving candesartan, total cellular volume decreased (-3.5 mL [95% CI - 4.7, -2.2], P < 0.001) while in patients not receiving candesartan, it remained unchanged (P = 0.45; between group difference P = 0.003). Anthracycline therapy is associated with dose-dependent increase in ECV fraction and total ECV. Concomitant treatment with candesartan reduces left ventricular total cellular volume.

Protein diffusion along DNA: on the effect of roadblocks and crowders

Rapid recognition by a protein of its DNA target site is achieved through a combination of one- and three-dimensional (1D and 3D) diffusion, which allows efficient scanning of the many alternative sites. This facilitated diffusion mechanism is expected to be affected by cellular conditions, particularly crowding, given that up to 40% of the total cellular volume may by occupied by macromolecules. Both experimental and theoretical studies showed that crowding particles can enhance facilitated diffusion and accelerate search kinetics. This effect may originate from crowding forcing a trade-off between 3D and 1D diffusion. In this study, using coarse-grained molecular dynamic simulations, we investigate how the molecular properties of the crowders may modulate the effect exerted by crowding on a searcher protein. We show that crowders with an affinity to the DNA are less effective search facilitators than particles whose contribution is solely entropic. Crowders that have affinity to DNA may occupy DNA sites and thereby function as obstacles or roadblocks that slow down the searcher protein, and they may also produce a smaller excluded volume effect and so reduce usage of the hopping searching mode in favor of less-effective 3D diffusion in the bulk. We discuss how strong repulsive interactions between the crowding particles themselves may affect the overall dynamics of the crowders and their excluded volume effect. Our study shows that search kinetics and its mechanism are modulated not only by salt concentration and crowding occupancy, but also by the properties of the crowding particles.

Mechanism of Facilitated Diffusion during a DNA Search in Crowded Environments.

The key feature explaining the rapid recognition of a DNA target site by its protein lies in the combination of one- and three-dimensional (1D and 3D) diffusion, which allows efficient scanning of the many alternative sites. This facilitated diffusion mechanism is expected to be affected by cellular conditions, particularly crowding, given that up to 40% of the total cellular volume may by occupied by macromolecules. Using coarse-grained molecular dynamics and Monte Carlo simulations, we show that the crowding particles can enhance facilitated diffusion and accelerate search kinetics. This effect originates from a trade-off between 3D and 1D diffusion. The 3D diffusion coefficient is lower under crowded conditions, but it has little influence because the excluded volume effect of molecular crowding restricts its use. Largely prevented from using 3D diffusion, the searching protein dramatically increases its use of the hopping search mode, which results in a higher linear diffusion coefficient. The coefficient of linear diffusion also increases under crowded conditions as a result of increased collisions between the crowding particles and the searching protein. Overall, less 3D diffusion coupled with an increase in the use of the hopping and speed of 1D diffusion results in faster search kinetics under crowded conditions. Our study shows that the search kinetics and mechanism are modulated not only by the crowding occupancy but also by the properties of the crowding particles and the salt concentration.

Macromolecular Crowding Enhances the Efficiency of the Chemical Chaperone, Betaine in Inhibiting Protein Aggregation

Presently, protein aggregation is of intense medical interest since the deposition of protein aggregates in vivo is related to the pathogenesis of many diseases. Interestingly, chemical chaperones accumulated by organisms during stress have been shown to assist in proper protein folding thereby preventing aggregation. However, most of these studies have been performed under dilute conditions as compared to the crowded intracellular environment where proteins perform their function. Indeed, the cell interior is known to be crowded due to the presence of soluble and insoluble macromolecules, which occupy ~40% of the total cellular volume. The degree of volume occupancy by these macromolecules is expected to have significant effect on protein aggregation. It is, thus, important to understand the protective role of chemical chaperones against protein aggregation under conditions mimicking crowded intracellular environment to have a real insight of the in vivo scenario. In this spirit, we have investigated the aggregation behavior of carbonic anhydrase in the presence of betaine, a chemical chaperone under crowded conditions using various spectroscopic techniques and electron microscopy. The results suggest a dramatic increase in the efficiency of betaine in preventing protein aggregation under crowded conditions which is speculated to result from the additive effect of preferential hydration by betaine and excluded volume effect encountered under crowded conditions. It is concluded that chemical chaperones are much more efficient than expected in maintaining protein homeostasis under crowded in vivo conditions. This work is supported by grant from DST, India. Authors acknowledge CSIR, India for providing research fellowship.

Soraphen A: A Probe for Investigating the Role of de Novo Lipogenesis during Viral Infection.

Many viruses including the hepatitis C virus (HCV) induce changes to the infected host cell metabolism that include the up-regulation of lipogenesis to create a favorable environment for the virus to propagate. The enzyme acetyl-CoA carboxylase (ACC) polymerizes to form a supramolecular complex that catalyzes the rate-limiting step of de novo lipogenesis. The small molecule natural product Soraphen A (SorA) acts as a nanomolar inhibitor of acetyl-CoA carboxylase activity through disruption of the formation of long highly active ACC polymers from less active ACC dimers. We have shown that SorA inhibits HCV replication in HCV cell culture models expressing subgenomic and full-length replicons (IC50 = 5 nM) as well as a cell culture adapted virus. Using coherent anti-Stokes Raman scattering (CARS) microscopy, we have shown that SorA lowers the total cellular lipid volume in hepatoma cells, consistent with a reduction in de novo lipogenesis. Furthermore, SorA treatment was found to depolymerize the ACC complexes into less active dimers. Taken together, our results suggest that SorA treatment reverses HCV-induced lipid accumulation and demonstrate that SorA is a valuable probe to study the roles of ACC polymerization and enzymatic activity in viral pathogenesis.

Mechanism of Nutrient Deprivation Induced Triacylglyceride Accumulation in Alga Indicated by Fluorescence Hyperspectral Imaging

Microalgae have been identified as a promising renewable feedstock for production of lipids for feeds and fuels. For a wide variety of algal species, depletion of major nutrients from the growth medium results in dramatically increased biosynthesis of triacylglycerides, in some cases exceeding 70% of the dry weight of the biomass. In recent work, we explored this process in a number of promising algal production strains (Chlorophyceae and Eustigmophyceae) using hyperspectral confocal fluorescence imaging with multivariate spectral unmixing. By coupling intensity modulation of the excitation laser and attenuation of the dominant chlorophyll fluorescence emission, we identified a distinct spectral component composed of chlorophyll fluorescence and resonance Raman emission for lipid-solubilized carotenoids allowing label-free projections of lipid bodies in addition to plastids. Furthermore, cells exposed to the lipophilic dye, Nile Red, exhibited distinct spectral components corresponding to the polar and neutral lipid fractions. Combining these capabilities for analysis of nutrient deprivation time courses revealed increases in the lipid fraction of the cellular volume of ∼500%, as well as a correlated decrease in the plastid fraction of the total cellular volume. Additionally, diffraction limited tubules connecting the lipids bodies to the plastids and the presence of unbound chlorophyll in the lipid bodies provided evidence for direct shuttling of lipids from the chloroplast to the lipid bodies, in opposition to the expected ER to lipid body transfer dictated by the Kennedy pathway. The results suggest that nutrient deprivation-based lipid accumulation in these species is dominated by plastid membrane recycling, independent of acyl-CoA. Finally, an additional spectral component exhibiting high spectral overlap with Nile Red and varying inversely with the chlorophyll emission was detected during senescence, potentially resulting in false positives for lipid enrichment in low spectral resolution assays.

Label-free measurement of algal triacylglyceride production using fluorescence hyperspectral imaging

Microalgae have been identified as a promising renewable feedstock for production of lipids for feeds and fuels. Current methods for identifying algae strains and growth conditions that support high lipid production require a variety of fluorescent chemical indicators, such as Nile Red and more recently, Bodipy. Despite notable successes using these approaches, chemical indicators exhibit several drawbacks, including non-uniform staining, low lipid specificity, cellular toxicity, and variable permeability based on cell-type, limiting their applicability for high-throughput bioprospecting. In this work, we used in vivo hyperspectral confocal fluorescence microscopy of a variety of potential microalgae production strains (Nannochloropsis sp., Dunaliella salina, Neochloris oleoabundans, and Chlamydomonas reinhardtii) to identify a label-free method for localizing lipid bodies and quantifying the lipid yield on a single-cell basis. By analyzing endogenous fluorescence from chlorophyll and resonance Raman emission from lipid-solubilized carotenoids we deconvolved pure component emission spectra and generated diffraction limited projections of the lipid bodies and chloroplast organelles, respectively. Applying this imaging method to nutrient depletion time-courses from lab-scale and outdoor cultivation systems revealed an additional autofluorescence spectral component that became more prominent over time, and varied inversely with the chlorophyll intensity, indicative of physiological compromise of the algal cell. This signal could result in false-positives for conventional measurements of lipid accumulation (via spectral overlap with Nile Red), however, the additional spectral feature was found to be useful for classification of lipid enrichment and culture crash conditions in the outdoor cultivation system. Under nutrient deprivation, increases in the lipid fraction of the cellular volume of ~500% were observed, as well as a correlated decrease in the chloroplast fraction of the total cellular volume. The results suggest that a membrane recycling mechanism dominates for nutrient deprivation-based lipid accumulation in the microalgae tested.

The crowd you're in with: Effects of different types of crowding agents on protein aggregation

The intracellular environment contains high concentrations of macromolecules occupying up to 30% of the total cellular volume. Presence of these macromolecules decreases the effective volume available for the proteins in the cell and thus increases the effective protein concentrations and stabilizes the compact protein conformations. Macromolecular crowding created by various macromolecules such as proteins, nucleic acids, and carbohydrates has been shown to have a significant effect on a variety of cellular processes including protein aggregation. Most studies of macromolecular crowding have used neutral, flexible polysaccharides that function primarily via excluded volume effect as model crowding agents. Here we have examined the effects of more rigid polysaccharides on protein structure and aggregation. Our results indicate that rigid and flexible polysaccharides influence protein aggregation via different mechanisms and suggest that, in addition to excluded volume effect, changes in solution viscosity and non-specific protein–polymer interactions influence the structure and dynamics of proteins in crowded environments.

CARS microscopy of lipid stores in yeast: the impact of nutritional state and genetic background

AbstractWe have developed a protocol for sub‐micrometer resolved and chemically specific imaging of lipid storage in vivo employing coherent anti‐Stokes Raman scattering (CARS) microscopy of one of the most important model organisms Saccharomyces cerevisiae—the yeast cell. By probing the carbon–hydrogen vibration using the nonlinear process of CARS, lipid droplets in the yeast cells clearly appear, as confirmed by comparative studies on relevant labeled organelles using two‐photon fluorescence microscopy. From the images, unique quantitative data can be deduced with high three‐dimensional resolution, such as the volume, shape, number, and intracellular location of the neutral lipid stores. We exemplify the strength and usability of the method for two cases: the impact on lipid storage of the nutritional condition (starvation and type of carbon source available) as well as of genetic modification of two fundamental metabolic regulation pathways involving carbohydrate and lipid storage (BCY1 and DGA1, LRO1, ARE1/2 deletions), respectively. While the impact of carbon source on the total cellular lipid volume was minimal, long‐term starvation induces a significant accumulation of lipid droplets. We also confirm that the lipid‐storage‐deficient mutant is indeed unable to synthesize lipid droplets, and that the inability of the bcy1‐mutant to store carbohydrates is compensated by a two‐fold increase in stored neutral lipids. We note that there is a significant cell‐to‐cell variability in neutral lipid storage in general, i.e. that there is a correspondence to the noise found for gene expression also in lipidomics. Copyright © 2009 John Wiley &amp; Sons, Ltd.

“Nanosized Voltmeter” Enables Cellular-Wide Electric Field Mapping

Previously, all biological measurements of intracellular electric fields (E fields), using voltage dyes or patch/voltage clamps, were confined to cellular membranes, which account for <0.1% of the total cellular volume. These membrane-dependent techniques also frequently require lengthy calibration steps for each cell or cell type measured. A new 30-nm “photonic voltmeter”, 1000-fold smaller than existing voltmeters, enables, to our knowledge, the first complete three-dimensional E field profiling throughout the entire volume of living cells. These nanodevices are calibrated externally and then applied for E field determinations inside any live cell or cellular compartment, with no further calibration steps. The results indicate that the E fields from the mitochondrial membranes penetrate much deeper into the cytosol than previously estimated, indicating that, electrically, the cytoplasm cannot be described as a simple homogeneous solution, as often approximated, but should rather be thought of as a complex, heterogeneous hydrogel, with distinct microdomains.

Enhancing Macroautophagy Protects against Ischemia/Reperfusion Injury in Cardiac Myocytes

Cardiac myocytes undergo programmed cell death as a result of ischemia/reperfusion (I/R). One feature of I/R injury is the increased presence of autophagosomes. However, to date it is not known whether macroautophagy functions as a protective pathway, contributes to programmed cell death, or is an irrelevant event during cardiac I/R injury. We employed simulated I/R of cardiac HL-1 cells as an in vitro model of I/R injury to the heart. To assess macroautophagy, we quantified autophagosome generation and degradation (autophagic flux), as determined by steady-state levels of autophagosomes in relation to lysosomal inhibitor-mediated accumulation of autophagosomes. We found that I/R impaired both formation and downstream lysosomal degradation of autophagosomes. Overexpression of Beclin1 enhanced autophagic flux following I/R and significantly reduced activation of pro-apoptotic Bax, whereas RNA interference knockdown of Beclin1 increased Bax activation. Bcl-2 and Bcl-x(L) were protective against I/R injury, and expression of a Beclin1 Bcl-2/-x(L) binding domain mutant resulted in decreased autophagic flux and did not protect against I/R injury. Overexpression of Atg5, a component of the autophagosomal machinery downstream of Beclin1, did not affect cellular injury, whereas expression of a dominant negative mutant of Atg5 increased cellular injury. These results demonstrate that autophagic flux is impaired at the level of both induction and degradation and that enhancing autophagy constitutes a powerful and previously uncharacterized protective mechanism against I/R injury to the heart cell.

Influence of hormonal replacement on the ventral lobe of the prostate of rats ( Rattus norvegicus albinus) submitted to chronic ethanol treatment

The harmful influence of the chronic alcohol ingestion on the male reproductive system leads to important alterations including hypogonadism and feminization, besides the morphological and functional disorganization of the different sexual glands. So, the aim of this study was to analyse the structural changes on the ventral lobe of the prostate of rats with hormonal replacement associated to chronic alcohol ingestion. A total of 30 rats ( Rattus norvegicus albinus) was divided into three groups: control—received water; alcoholic—received ethanol diluted to 20% and hormone-treated alcoholic—received ethanol diluted to 20% associated with the administering of testosterone (5 mg/kg of weight) during the last 30 days of treatment. After 150 days of treatment, the animals were sacrificed, the prostate removed and submitted to transmission and scanning electron microscopies, histochemical analysis for acid phosphatase, testosterone level and stereologic analysis. In the alcoholic group the results demonstrated reduction of the total cellular volume and disorganization of the organelles involved in the secretory process. It was characterized a partial recovery of the cellular volume after treatment with testosterone. It was concluded that the ethanol impaired the cellular morphology and the hormonal replacement by itself did not bring about efficient remodeling of the organelles responsible for the secretory process.

Increased leptin resistance as rats grow to maturity.

Three or eight-month-old Sprague-Dawley rats were treated intracerebroventricularly (ICV) with 5 microg of rat leptin/d for 5 days to determine the effect of age on leptin's actions in ingestive behavior, adipose tissue cellularity, organ weights, body composition, and blood metabolite profile. Effects of leptin on food intake were greater in young immature rats (22.0 vs. 5.7 g/d) than in mature rats (17.4 vs. 9.3 g/d) with a leptin x age interaction (P< 0.01). Leptin results in body weight loss (P < 0.001) by 19% and 9% in young and mature rats, respectively. Water intake was reduced by leptin treatment only in young animals (P< 0.001). The decrease in carcass weight by leptin treatment (P < 0.001) was observed in both young (22%) and mature rats (9%). Leptin treatment greatly reduced retroperitoneal (0.82 vs. 0.11 g, P < 0.05) and epididymal fat weight (1.90 vs. 0.48 g, P < 0.003), associated with a reduction in total adipocyte cell number, DNA content, and cellular volume in young rats; however, there were no effects of leptin in the mature rats. In addition, young rats also displayed a 60% loss of carcass lipid content. An increase in serum fatty acid levels by leptin treatment was observed also only in young rats (P< 0.001). An interaction of leptin by age that was observed for the reduction of serum glucose levels by leptin treatment (P < 0.04) further indicated that mature rats showed a leptin insensitivity compared to young rats. In summary, the data suggest that normal rats become resistant to leptin as they age.

Brain administration of leptin causes deletion of adipocytes by apoptosis.

Leptin, produced in adipocytes, works through the central nervous system (CNS) to modulate food intake and energy expenditure, resulting in rapid loss of body fat depots. It is now shown that this process includes adipocyte apoptosis. Adipocyte deletion by apoptosis occurred after intracerebroventricular (i.c.v.) administration of leptin in rats. Adipose tissue of leptin-treated rats demonstrated characteristic features of apoptosis, including internucleosomal fragmentation of genomic DNA, elevated levels of DNA strand breaks and a reduction in total DNA content and cellular volume. These apoptotic features were absent in control and pair-fed rats and in other tissues of leptin-treated rats.