A methanotrophic bacterium to enable methane removal for climate mitigation.

The rapid increase of the potent greenhouse gas methane in the atmosphere creates great urgency to develop and deploy technologies for methane mitigation. One approach to removing methane is to use bacteria for which methane is their carbon and energy source (methanotrophs). Such bacteria naturally convert methane to CO2 and biomass, a value-added product and a cobenefit of methane removal. Typically, methanotrophs grow best at around 5,000 to 10,000 ppm methane, but methane in the atmosphere is 1.9 ppm. Air above emission sites such as landfills, anaerobic digestor effluents, rice paddy effluents, and oil and gas wells contains elevated methane in the 500 ppm range. If such sites are targeted for methane removal, technology harnessing aerobic methanotroph metabolism has the potential to become economically and environmentally viable. The first step in developing such methane removal technology is to identify methanotrophs with enhanced ability to grow and consume methane at 500 ppm and lower. We report here that some existing methanotrophic strains grow well at 500 ppm methane, and one of them, Methylotuvimicrobium buryatense 5GB1C, consumes such low methane at enhanced rates compared to previously published values. Analyses of bioreactor-based performance and RNAseq-based transcriptomics suggest that this ability to utilize low methane is based at least in part on extremely low non-growth-associated maintenance energy and on high methane specific affinity. This bacterium is a candidate to develop technology for methane removal at emission sites. If appropriately scaled, such technology has the potential to slow global warming by 2050.

In vivo quantification of polyhydroxybutyrate (PHB) in the alphaproteobacterial methanotroph, Methylocystis sp. Rockwell.

Methane is a common industrial by-product that can be used as feedstock for production of the biopolymer polyhydroxybutyrate (PHB) by alphaproteobacterial methanotrophs. In vivo assessment of PHB production would shed light on the biosynthesis process and guide design of improved production strategies, but it is currently difficult to perform efficiently. In this study, the alphaproteobacterial methanotroph Methylocystis sp. Rockwell was grown on methane with three different nitrogen sources (ammonium, nitrate, and atmospheric nitrogen), and biomass samples were harvested at defined time points during lag, exponential, and stationary growth phases. PHB cell content was analyzed at these sampling points via a standard gas chromatography-flame ionization detector method, which requires hydrolysis of PHB and esterification of the resulting monomer under acidic conditions, and a novel, rapid, cost-effective approach based on fixation and staining of bacterial cells via Nile Blue A fluorescent dye enabling differential staining of cell membranes and intracellular PHB granules for single-cell analysis through fluorescence microscopy. Overall, the two PHB quantification approaches were in agreement at all stages of growth and in all three growing conditions tested. The PHB cell content was greatest with atmospheric nitrogen as a nitrogen source, followed by ammonium and nitrate. Under atmospheric nitrogen and ammonium conditions, PHB cell content decreased with growth progression, while under nitrate conditions PHB cell content remained unchanged in all growth phases. In addition to presenting a rapid, efficient method enabling in vivo quantification of PHB production, the present study highlights the impact of nitrogen source on PHB production by Methylocystis sp. Rockwell. KEY POINTS: • A novel fluorescence microscopy method to quantify PHB in single cells was developed • The microscopy method was validated by the derivation/gas chromatography method • Methylocystis sp. Rockwell synthesizes PHB granules without nutrient stress.

NIR-emitting styryl dyes with large Stokes' shifts for imaging application: From cellular plasma membrane, mitochondria to Zebrafish neuromast.

Near-infrared (NIR) emitting probes with very large Stokes' shifts play a crucial role in bioimaging applications, as the optical signals in this region exhibit high signal to background ratio and allow deeper tissue penetration. Herein we illustrate NIR-emitting probe 2 with very large Stokes' shifts (Δλ ≈ 260 - 272 nm) by integrating the excited-state intramolecular proton transfer (ESIPT) unit 2-(2'-hydroxyphenyl)benzoxazole (HBO) into a pyridinium derived cyanine. The ESIPT not only enhances the Stokes' shifts but also improves the quantum efficiency of the probe 2 (фfl = 0.27 - 0.40 in DCM). The application of 2 in live cells imaging reveals that compound 2 stains mitochondria in eukaryotic cells, normal human lungs fibroblast (NHLF), Zebrafish's neuromast hair cells, and support cells, and inner plasma membrane in prokaryotic cells, Escherichia coli (E. coli).

A Fluorescent Flavonoid for Lysosome Imaging: the Effect of Substituents on Selectivity and Optical Properties.

Lysosome selective bright orange-red emitting flavonoid (2) was synthesized by attaching a strong donor (NPh2) group into flavonoid skeleton. As a result of efficient intra molecular charge transfer due to the strong donor group, a significant bathochromic shift was observed from the emission of 2b (with a -NPh2 group, λem ≈ 590 nm), in comparison that of 1b (with a -NMe2 group, λem ≈ 519 nm). The role of the substituent effect towards ICT was further studied by low temperature spectral analysis. Fluorescence spectra at low temperature confirmed that large Stokes shift for probe 2 (Δλ ≈ 150 nm) was due to strong ICT. Probe 2b exhibited exceptional selectivity towards cellular lysosomes in live cells studies thus generating bright orange-red emission upon localization. Intra-cellular pH analysis results confirmed that probe 2b did not participate in the elevation of lysosomal pH upon staining with different probe concentrations (0.5 µM - 2.0 µM) which is a potential advantage compared to acidotropic commercial LysoTracker® probes. This study further illustrated that the substituents in probe 2 play a significant role towards probe's organelle selectivity since probe 2a (R = OH) did not show any lysosomal localization compared with 2b. In addition, the calculated cytotoxicity data further revealed that this new probe design is highly biocompatible (LC50 > 50 µM) and suitable for long term imaging. Graphical Abstract.

An NIR emitting styryl dye with large Stokes shift to enable co-staining study on zebrafish neuromast hair cells.

Hearing loss is a significant public health problem, and the "loss of sensory hair cells" is one of two leading causes in humans. Advanced imaging reagents are desirable for understanding the role of the surrounding support cells in the loss or regeneration of the hair cells. A styryl dye was found to exhibit NIR emission (λem ≈ 684 nm) with a very large Stokes shift (Δν ≈ 9190 cm-1), due to the incorporation of excited state intramolecular proton transfer (ESIPT) mechanism. When used to stain live zebrafish embryos, the probe was found to exhibit good selectivity in targeting neuromasts, which are sensory organs on the surface of the fish's body. The finding was verified by direct comparison with the known neuromast-labeling reagent, 4-Di-2-ASP. In contrast to the existing styryl dyes that label neuromast hair cells, the new probe labeled both neuromast hair cells and the surrounding support cells, while giving discernable signals. The study thus illustrated a useful tool to aid the developmental study of two closely related cell types on the mechanosensory sensory organ of zebrafish, which is a powerful animal model for hearing loss research.

NIR-emitting benzothiazolium cyanines with an enhanced stokes shift for mitochondria imaging in live cells.

A series of benzothiazolium-based hemicyanines (3a-3f) have been synthesized. Evaluation of their photophysical properties shows that they exhibit improved photophysical characteristics. In comparison with the available commercial MitoTrackers, the new probes revealed an enhanced Stokes shift (Δλ ∼ 80 nm) and minimized aggregation for increased sensitivity. The synthesized probes are found to exhibit excellent selectivity for mitochondrial staining in an oligodendrocyte cell line. Probes show almost no fluorescence in aqueous environments, while the fluorescence is increased by ∼10-fold in organic solvents, making it possible for mitochondrial imaging without the need for post-staining washing. Since the absorption peaks of probes are close to the laser wavelengths of 561 and 640 nm on a commercial confocal microscope, e.g.3a exhibits λabs ∼ 620 nm and λem ∼ 702 nm, they could be useful probes for mitochondrial tracking in live cells.

Synthesis, characterization, in vitro SAR and in vivo evaluation of N,N'bisnaphthylmethyl 2-alkyl substituted imidazolium salts against NSCLC.

Alkyl- and N,N'-bisnaphthyl-substituted imidazolium salts were tested in vitro for their anti-cancer activity against four non-small cell lung cancer cell lines (NCI-H460, NCI-H1975, HCC827, A549). All compounds had potent anticancer activity with 2 having IC50 values in the nanomolar range for three of the four cell lines, a 17-fold increase in activity against NCI-H1975 cells when compared to cisplatin. Compounds 1-4 also showed high anti-cancer activity against nine NSCLC cell lines in the NCI-60 human tumor cell line screen. In vitro studies performed using the Annexin V and JC-1 assays suggested that NCI-H460 cells treated with 2 undergo an apoptotic cell death pathway and that mitochondria could be the cellular target of 2 with the mechanism of action possibly related to a disruption of the mitochondrial membrane potential. The water solubilities of 1-4 was over 4.4mg/mL using 2-hydroxypropyl-ß-cyclodextrin as a chemical excipient, thereby providing sufficient solubility for systemic administration.

The role of physiological heterogeneity in microbial population behavior.

As the ability to analyze individual cells in microbial populations expands, it is becoming apparent that isogenic microbial populations contain substantial cell-to-cell differences in physiological parameters such as growth rate, resistance to stress and regulatory circuit output. Subpopulations exist that are manyfold different in these parameters from the population average, and these differences arise by stochastic processes. Such differences can dramatically affect the response of cells to perturbations, especially stress, which in turn dictates overall population response. Defining the role of cell-to-cell heterogeneity in population behavior is important for understanding population-based research problems, including those involving infecting populations, normal flora and bacterial populations in water and soils. Emerging technological breakthroughs are poised to transform single-cell analysis and are critical for the next phase of insights into physiological heterogeneity in the near future. These include technologies for multiparameter analysis of live cells, with downstream processing and analysis.

Therapeutic Targeting of Stromal-Tumor HGF-MET Signaling in an Organotypic Triple-Negative Breast Tumor Model.

The tumor microenvironment (TME) promotes proliferation, drug resistance, and invasiveness of cancer cells. Therapeutic targeting of the TME is an attractive strategy to improve outcomes for patients, particularly in aggressive cancers such as triple-negative breast cancer (TNBC) that have a rich stroma and limited targeted therapies. However, lack of preclinical human tumor models for mechanistic understanding of tumor-stromal interactions has been an impediment to identify effective treatments against the TME. To address this need, we developed a three-dimensional organotypic tumor model to study interactions of patient-derived cancer-associated fibroblasts (CAF) with TNBC cells and explore potential therapy targets. We found that CAFs predominantly secreted hepatocyte growth factor (HGF) and activated MET receptor tyrosine kinase in TNBC cells. This tumor-stromal interaction promoted invasiveness, epithelial-to-mesenchymal transition, and activities of multiple oncogenic pathways in TNBC cells. Importantly, we established that TNBC cells become resistant to monotherapy and demonstrated a design-driven approach to select drug combinations that effectively inhibit prometastatic functions of TNBC cells. Our study also showed that HGF from lung fibroblasts promotes colony formation by TNBC cells, suggesting that blocking HGF-MET signaling potentially could target both primary TNBC tumorigenesis and lung metastasis. Overall, we established the utility of our organotypic tumor model to identify and therapeutically target specific mechanisms of tumor-stromal interactions in TNBC toward the goal of developing targeted therapies against the TME. IMPLICATIONS: Leveraging a state-of-the-art organotypic tumor model, we demonstrated that CAFs-mediated HGF-MET signaling drive tumorigenic activities in TNBC and presents a therapeutic target.

Osmoregulatory Role of Betaine and Betaine/γ-Aminobutyric Acid Transporter 1 in Post-Traumatic Syringomyelia.

Syringomyelia (SM) is primarily characterized by the formation of a fluid-filled cyst that forms in the parenchyma of the spinal cord following injury or other pathology. Recent omics studies in animal models have identified dysregulation of solute carriers, channels, transporters, and small molecules associated with osmolyte regulation during syrinx formation/expansion in the spinal cord. However, their connections to syringomyelia etiology are poorly understood. In this study, the biological functions of the potent osmolyte betaine and its associated solute carrier betaine/γ-aminobutyric acid (GABA) transporter 1 (BGT1) were studied in SM. First, a rat post-traumatic SM model was used to demonstrate that the BGT1 was primarily expressed in astrocytes in the vicinity of syrinxes. In an in vitro system, we found that astrocytes uptake betaine through BGT1 to regulate cell size under hypertonic conditions. Treatment with BGT1 inhibitors, especially NNC 05-2090, demonstrated midhigh micromolar range potency in vitro that reversed the osmoprotective effects of betaine. Finally, the specificity of these BGT1 inhibitors in the CNS was demonstrated in vivo, suggesting feasibility for targeting betaine transport in SM. In summary, these data provide an enhanced understanding of the role of betaine and its associated solute carrier BGT1 in cell osmoregulation and implicates the active role of betaine and BGT1 in syringomyelia progression.

Organotypic breast tumor model elucidates dynamic remodeling of tumor microenvironment.

Fibroblasts are a critical component of tumor microenvironments and associate with cancer cells physically and biochemically during different stages of the disease. Existing cell culture models to study interactions between fibroblasts and cancer cells lack native tumor architecture or scalability. We developed a scalable organotypic model by robotically encapsulating a triple negative breast cancer (TNBC) cell spheroid within a natural extracellular matrix containing dispersed fibroblasts. We utilized an established CXCL12 - CXCR4 chemokine-receptor signaling in breast tumors to validate our model. Using imaging techniques and molecular analyses, we demonstrated that CXCL12-secreting fibroblasts have elevated activity of RhoA/ROCK/myosin light chain-2 pathway and rapidly and significantly contract collagen matrices. Signaling between TNBC cells and CXCL12-producing fibroblasts promoted matrix invasion of cancer cells by activating oncogenic mitogen-activated protein kinase signaling, whereas normal fibroblasts significantly diminished TNBC cell invasiveness. We demonstrated that disrupting CXCL12 - CXCR4 signaling using a molecular inhibitor significantly inhibited invasiveness of cancer cells, suggesting blocking of tumor-stromal interactions as a therapeutic strategy especially for cancers such as TNBC that lack targeted therapies. Our organotypic tumor model mimics native solid tumors, enables modular addition of different stromal cells and extracellular matrix proteins, and allows high throughput compound screening against tumor-stromal interactions to identify novel therapeutics.

Cytoplasmic protein mobility in osmotically stressed Escherichia coli.

Facile diffusion of globular proteins within a cytoplasm that is dense with biopolymers is essential to normal cellular biochemical activity and growth. Remarkably, Escherichia coli grows in minimal medium over a wide range of external osmolalities (0.03 to 1.8 osmol). The mean cytoplasmic biopolymer volume fraction ((phi)) for such adapted cells ranges from 0.16 at 0.10 osmol to 0.36 at 1.45 osmol. For cells grown at 0.28 osmol, a similar phi range is obtained by plasmolysis (sudden osmotic upshift) using NaCl or sucrose as the external osmolyte, after which the only available cellular response is passive loss of cytoplasmic water. Here we measure the effective axial diffusion coefficient of green fluorescent protein (D(GFP)) in the cytoplasm of E. coli cells as a function of (phi) for both plasmolyzed and adapted cells. For plasmolyzed cells, the median D(GFP) (D(GFP)(m)) decreases by a factor of 70 as (phi) increases from 0.16 to 0.33. In sharp contrast, for adapted cells, D(GFP)(m) decreases only by a factor of 2.1 as (phi) increases from 0.16 to 0.36. Clearly, GFP diffusion is not determined by (phi) alone. By comparison with quantitative models, we show that the data cannot be explained by crowding theory. We suggest possible underlying causes of this surprising effect and further experiments that will help choose among competing hypotheses. Recovery of the ability of proteins to diffuse in the cytoplasm after plasmolysis may well be a key determinant of the time scale of the recovery of growth.

NIR-Emitting Hemicyanines with Large Stokes' Shifts for Live Cell Imaging: from Lysosome to Mitochondria Selectivity by Substituent Effect.

Lysosome imaging without perturbing intracellular activity remains challenging, as the current commercial lysosome probes contain weakly basic amino groups that could perturb lysosome pH. Herein, we illustrate NIR-emitting dyes 2 and 3 (λem ≈ 700 nm) with very large Stokes' shifts (Δλ = 231-246 nm), attributing to the presence of a 2-hydroxyphenyl(benzo[d]oxazol) (HBO) unit that undergoes excited-state intramolecular proton transfer (ESIPT). The structures of 2 and 3 also contain a hemicyanine unit with benzothiazolium and indolium as a terminal group, respectively. Although the fluorescent probe 2 (Φfl ≈ 0.28-0.35 in CH2Cl2) does not contain any basic amino functional group, it exhibits excellent selectivity for staining intracellular lysosomes, showing the potential for long-term in vivo lysosome imaging without "alkalinizing effect." However, probe 3 (Φfl ≈ 0.27, in CH2Cl2) exhibits excellent selectivity toward mitochondria. The observation showed that the terminal group in the hemicyanine unit played an essential role in guiding the intracellular selectivity to different organelles. In addition, the probes also displayed a transparent optical window between 520 and 590 nm, which is useful to achieve multicolor co-staining study, without fluorescence crosstalk that is a common problem on fluorescence microscopes.

Fluorescence-based analysis of the intracytoplasmic membranes of type I methanotrophs.

Most methanotrophic bacteria maintain intracytoplasmic membranes which house the methane-oxidizing enzyme, particulate methane monooxygenase. Previous studies have primarily used transmission electron microscopy or cryo-electron microscopy to look at the structure of these membranes or lipid extraction methods to determine the per cent of cell dry weight composed of lipids. We show an alternative approach using lipophilic membrane probes and other fluorescent dyes to assess the extent of intracytoplasmic membrane formation in living cells. This fluorescence method is sensitive enough to show not only the characteristic shift in intracytoplasmic membrane formation that is present when methanotrophs are grown with or without copper, but also differences in intracytoplasmic membrane levels at intermediate copper concentrations. This technique can also be employed to monitor dynamic intracytoplasmic membrane changes in the same cell in real time under changing growth conditions. We anticipate that this approach will be of use to researchers wishing to visualize intracytoplasmic membranes who may not have access to electron microscopes. It will also have the capability to relate membrane changes in individual living cells to other measurements by fluorescence labelling or other single-cell analysis methods.

A NIR-emitting cyanine with large Stokes shifts for live cell imaging: large impact of the phenol group on emission.

There are a limited number of near-infrared (NIR) emitting (λem = 700-900 nm) molecular probes for imaging applications. A NIR-emitting probe that exhibits emission at ∼800 nm with a large Stokes shift was synthesized and found to exhibit excellent selectivity towards mitochondria for live-cell imaging. The photophysical properties were attributed to an excited "cyanine structure" via intramolecular charge transfer (ICT) involving a phenol group.

Synthesis of highly selective lysosomal markers by coupling 2-(2'-hydroxyphenyl)benzothiazole (HBT) with benzothiazolium cyanine (Cy): the impact of substituents on selectivity and optical properties.

HBT-Cy 1 has been previously reported as a highly selective fluorescent probe for lysosome visualization in live cells. To further investigate the role of the structural components of HBT-Cy in lysosome selectivity, cyanine based fluorescent probe series (2-5) have been synthesized in good yields by connecting benzothiazolium cyanine (Cy) with 2-hydroxyphenylbenzothiazole (HBT) via a meta phenylene ring. Probes 2-5 exhibited exceptional photophysical properties including bright red-emission (λem≈ 630-650 nm), a large Stokes shift (Δλ > 130 nm) and high fluorescence quantum yields (φfl≈ 0.1-0.5). Probes 2, 3, and 5 exhibited exceptional selectivity towards cellular lysosomes in NHLF and MO3.13 cells. Our further study revealed that the phenyl benzothiazolium cyanine component (6) was the lysosome directing group in the HBT-Cy probe structure. The attachment of the hydroxyphenyl benzothiazole (HBT) component to the HBT-Cy probe structure has significantly improved its photophysical properties. Lysosome probes 2, 3 and 5 exhibited excellent biocompatibility, quick staining, bright red fluorescence, and wash-free application for live cell imaging. These probes further exhibited excellent characteristics for bioimaging experiments including a non-alkalinizing nature, high biocompatibility, high photostability and long-term imaging ability (>4 hours).

A fluorescent flavonoid for lysosome detection in live cells under "wash free" conditions.

Lysosomes are vital organelles in living cells, which have acidic environments (pH 4.0-5.0) where macrobiomolecules and malfunctioning organelles are broken down into monomers by hydrolase activity. The majority of the currently reported fluorescent probes for detecting lysosomes suffer from small Stokes shifts (Δλ < 20 nm) and higher cytotoxicity due to an "alkalinizing effect". An interesting flavonoid-based lysosome probe is synthesized by introducing a morpholine moiety onto the flavonoid skeleton. This new probe has shown excellent selectivity to detect lysosomes in MO3.13 oligodendrocytes and normal human lung fibroblast cell lines. Probes 1a and 1b have shown excellent fluorescence quantum yield (φfl up to 0.43 in non-aqueous solvents) and large Stokes shifts (120-150 nm). These new fluorescent probes also exhibit a large quantum yield difference from an aqueous to organic environment, making them potentially useful as "wash-free" stains for visualizing lysosomes. Cell viability evaluation of these probes shows excellent biocompatibility with the median lethal concentration being LC50 ≈ 50 µM.

Methods of changing biopolymer volume fraction and cytoplasmic solute concentrations for in vivo biophysical studies.

In vitro changes in polymer volume fraction (macromolecular crowding) and changes in solute or salt concentration typically have large effects on protein and nucleic acid processes (e.g., folding, binding, assembly, precipitation, crystallization). However, the large changes in these concentration variables, which occur in vivo as part of cellular responses to osmotic stress, appear to have much less dramatic effects on cellular biopolymer processes. Methods of changing intracellular concentrations by varying the extracellular osmolality or the concentration of a permeable solute or by titrating cells with an impermeable solute (plasmolysis) under conditions where an active response is suppressed are reviewed. The first in vivo biophysical studies of protein folding and protein diffusion performed as a function of these variables are also discussed.

An NIR-emitting lysosome-targeting probe with large Stokes shift via coupling cyanine and excited-state intramolecular proton transfer.

An NIR-emitting probe (λem ∼ 700 nm) with a large Stokes shift (Δλ ≈ 234 nm) is synthesized by using excited-state intramolecular proton transfer (ESIPT). The phenolic proton, which controls ESIPT, acts as a switch to give strong fluorescence at pH ≈ 5. The probe can selectively show lysosome organelles, therefore leading to a lysosome probe without exhibiting "an alkalinizing effect".

Fluorescent flavonoids for endoplasmic reticulum cell imaging.

Visualization of subcellular organelles in vivo is critical for basic biomedical research and clinical applications. Two new flavonoids with an amide substituent were synthesized and characterized. The flavonoids were nearly non-fluorescent in aqueous environment, but exhibited two emission peaks (one λem at 495-536 nm and the other at 570-587 nm) in organic solvents, which were assigned to the excited normal (N*) and tautomer (T*) emission. When the dyes were examined on oligodendrocyte cells, they were found to selectively accumulate in the endoplasmic reticulum (ER), a eukaryotic organelle involved in lipid and protein synthesis, giving fluorescence turn-on. The ER-selective flavonoids could be a valuable tool due to its low molecular mass (<500), large Stokes' shift, low toxicity, and biocompatibility.