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1.
Annu Int Conf IEEE Eng Med Biol Soc ; 2020: 1895-1898, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-33018371

RESUMO

We present a robust, precise image binarization technique for automatically detecting filamentous microorganisms from digital fluorescence microscopy scans, with application to finding the pseudohyphae that are fungal pathogens responsible for Candida vaginitis. This method employs a hybrid constant false positive rate processor that integrates cell average and order statistic detectors, with linear windows at multiple orientation angles. The hypothesis test rule incorporates elongation enhancement and region of interest masking. Our approach achieves the adaptivity to local noise and all possible object orientations. The designed processor is evaluated theoretically and experimentally using clinical images. Successful detection results are demonstrated.


Assuntos
Vaginite , Feminino , Humanos , Microscopia de Fluorescência , Cintilografia , Vaginite/diagnóstico
2.
Annu Int Conf IEEE Eng Med Biol Soc ; 2020: 4385-4389, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-33018967

RESUMO

In vivo fluorescence miniature microscopy has recently proven a major advance, enabling cellular imaging in freely behaving animals. However, fluorescence imaging suffers from autofluorescence, phototoxicity, photobleaching and non- homogeneous illumination artifacts. These factors limit the quality and time course of data collection. Bioluminescence provides an alternative kind of activity-dependent light indicator. Bioluminescent calcium indicators do not require light input, instead generating photons through chemiluminescence. As such, limitations inherent to the requirement for light presentation are eliminated. Further, bioluminescent indicators also do not require excitation light optics: the removal of these components should make a lighter and lower cost microscope with fewer assembly parts. While there has been significant recent progress in making brighter and faster bioluminescence indicators, the advances in imaging hardware have not yet been realized. A hardware challenge is that despite potentially higher signal-to-noise of bioluminescence, the signal strength is lower than that of fluorescence. An open question we address in this report is whether fluorescent miniature microscopes can be rendered sensitive enough to detect bioluminescence. We demonstrate this possibility in vitro and in vivo by implementing optimizations of the UCLA fluorescent miniscope v3.2. These optimizations yielded a miniscope (BLmini) which is 22% lighter in weight, has 45% fewer components, is up to 58% less expensive, offers up to 15 times stronger signal and is sensitive enough to capture spatiotemporal dynamics of bioluminescence in the brain with a signal-to-noise ratio of 34 dB.


Assuntos
Encéfalo , Testes Imunológicos , Animais , Testes Diagnósticos de Rotina , Microscopia de Fluorescência , Fotodegradação
3.
Annu Int Conf IEEE Eng Med Biol Soc ; 2020: 1428-1431, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-33018258

RESUMO

Segmentation of cell nuclei in fluorescence microscopy images provides valuable information about the shape and size of the nuclei, its chromatin texture and DNA content. It has many applications such as cell tracking, counting and classification. In this work, we extended our recently proposed approach for nuclei segmentation based on deep learning, by adding to its input handcrafted features. Our handcrafted features introduce additional domain knowledge that nuclei are expected to have an approximately round shape. For round shapes the gradient vector of points at the border point to the center. To convey this information, we compute a map of gradient convergence to be used by the CNN as a new channel, in addition to the fluorescence microscopy image. We applied our method to a dataset of microscopy images of cells stained with DAPI. Our results show that with this approach we are able to decrease the number of missdetections and, therefore, increase the F1-Score when compared to our previously proposed approach. Moreover, the results show that faster convergence is obtained when handcrafted features are combined with deep learning.


Assuntos
Algoritmos , Aprendizado Profundo , Núcleo Celular , Cromatina , Microscopia de Fluorescência
4.
Annu Int Conf IEEE Eng Med Biol Soc ; 2020: 1828-1831, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-33018355

RESUMO

We propose a new framework for super-resolution structured illumination microscopy (SR-SIM) based on compressed sensing (CS). Our framework addresses several key problems in SIM, including long readout time and photobleaching. CS has the potential to eliminate these problems because it allows the reduction of the number of measurements, can record an image faster, and excites fluorochromes with less excitation light. Key contribution of our proposed method is that sampling and down-modulation of an object scene are simultaneously performed. The impact of our contribution is demonstrated by simulation-based experiments involving computer-generated super-resolution microscopy images, considering reductions in both data quality and quantity.


Assuntos
Processamento de Imagem Assistida por Computador , Iluminação , Corantes Fluorescentes , Microscopia de Fluorescência
5.
Annu Int Conf IEEE Eng Med Biol Soc ; 2020: 1887-1890, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-33018369

RESUMO

Automatic identification of subcellular compartments of proteins in fluorescence microscopy images is an important task to quantitatively evaluate cellular processes. A common problem for the development of deep learning based classifiers is that there is only a limited number of labeled images available for training. To address this challenge, we propose a new approach for subcellular organelles classification combining an effective and efficient architecture based on a compact Convolutional Neural Network and deep embedded clustering algorithm. We validate our approach on a benchmark of HeLa cell microscopy images. The network both yields high accuracy that outperforms state of the art methods and has significantly small number of parameters. More interestingly, experimental results show that our method is strongly robust against limited labeled data for training, requiring four times less annotated data than usual while maintaining the high accuracy of 93.9%.


Assuntos
Algoritmos , Redes Neurais de Computação , Células HeLa , Humanos , Microscopia de Fluorescência , Organelas
6.
Nat Commun ; 11(1): 4902, 2020 09 29.
Artigo em Inglês | MEDLINE | ID: mdl-32994402

RESUMO

Living cells and tissues experience various complex modes of forces that are important in physiology and disease. However, how different force modes impact gene expression is elusive. Here we apply local forces of different modes via a magnetic bead bound to the integrins on a cell and quantified cell stiffness, chromatin deformation, and DHFR (dihydrofolate reductase) gene transcription. In-plane stresses result in lower cell stiffness than out-of-plane stresses that lead to bead rolling along the cell long axis (i.e., alignment of actin stress fibers) or at different angles (90° or 45°). However, chromatin stretching and ensuing DHFR gene upregulation by the in-plane mode are similar to those induced by the 45° stress mode. Disrupting stress fibers abolishes differences in cell stiffness, chromatin stretching, and DHFR gene upregulation under different force modes and inhibiting myosin II decreases cell stiffness, chromatin deformation, and gene upregulation. Theoretical modeling using discrete anisotropic stress fibers recapitulates experimental results and reveals underlying mechanisms of force-mode dependence. Our findings suggest that forces impact biological responses of living cells such as gene transcription via previously underappreciated means.


Assuntos
Cromatina/química , Fibras de Estresse/química , Tetra-Hidrofolato Desidrogenase/genética , Transcrição Genética/fisiologia , Regulação para Cima/fisiologia , Animais , Anisotropia , Fenômenos Biomecânicos/genética , Células CHO , Cromatina/metabolismo , Cricetulus , Compostos Heterocíclicos de 4 ou mais Anéis/farmacologia , Microscopia Intravital , Microscopia de Fluorescência , Miosina Tipo II/antagonistas & inibidores , Miosina Tipo II/metabolismo , Fibras de Estresse/efeitos dos fármacos , Fibras de Estresse/metabolismo , Estresse Mecânico , Transcrição Genética/efeitos dos fármacos , Regulação para Cima/efeitos dos fármacos
7.
PLoS Comput Biol ; 16(9): e1008179, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32898132

RESUMO

Detection and segmentation of macrophage cells in fluorescence microscopy images is a challenging problem, mainly due to crowded cells, variation in shapes, and morphological complexity. We present a new deep learning approach for cell detection and segmentation that incorporates previously learned nucleus features. A novel fusion of feature pyramids for nucleus detection and segmentation with feature pyramids for cell detection and segmentation is used to improve performance on a microscopic image dataset created by us and provided for public use, containing both nucleus and cell signals. Our experimental results indicate that cell detection and segmentation performance significantly benefit from the fusion of previously learned nucleus features. The proposed feature pyramid fusion architecture clearly outperforms a state-of-the-art Mask R-CNN approach for cell detection and segmentation with relative mean average precision improvements of up to 23.88% and 23.17%, respectively.


Assuntos
Células Eucarióticas/citologia , Processamento de Imagem Assistida por Computador/métodos , Microscopia de Fluorescência/métodos , Redes Neurais de Computação , Biologia Computacional , Aprendizado Profundo , Humanos , Macrófagos/citologia , Células THP-1
8.
Nat Commun ; 11(1): 4339, 2020 08 28.
Artigo em Inglês | MEDLINE | ID: mdl-32859909

RESUMO

DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) facilitates multiplexing in superresolution microscopy but is practically limited by slow imaging speed. To address this issue, we propose the additions of ethylene carbonate (EC) to the imaging buffer, sequence repeats to the docking strand, and a spacer between the docking strand and the affinity agent. Collectively termed DNA-PAINT-ERS (E = EC, R = Repeating sequence, and S = Spacer), these strategies can be easily integrated into current DNA-PAINT workflows for both accelerated imaging speed and improved image quality through optimized DNA hybridization kinetics and efficiency. We demonstrate the general applicability of DNA-PAINT-ERS for fast, multiplexed superresolution imaging using previously validated oligonucleotide constructs with slight modifications.


Assuntos
Técnicas Citológicas/métodos , DNA/química , Microscopia de Fluorescência/métodos , Simulação de Acoplamento Molecular/métodos , Linhagem Celular , Humanos , Processamento de Imagem Assistida por Computador/métodos , Oligonucleotídeos , Coloração e Rotulagem/métodos
9.
Nat Commun ; 11(1): 3881, 2020 08 04.
Artigo em Inglês | MEDLINE | ID: mdl-32753572

RESUMO

Cells typically respond to chemical or physical perturbations via complex signaling cascades which can simultaneously affect multiple physiological parameters, such as membrane voltage, calcium, pH, and redox potential. Protein-based fluorescent sensors can report many of these parameters, but spectral overlap prevents more than ~4 modalities from being recorded in parallel. Here we introduce the technique, MOSAIC, Multiplexed Optical Sensors in Arrayed Islands of Cells, where patterning of fluorescent sensor-encoding lentiviral vectors with a microarray printer enables parallel recording of multiple modalities. We demonstrate simultaneous recordings from 20 sensors in parallel in human embryonic kidney (HEK293) cells and in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), and we describe responses to metabolic and pharmacological perturbations. Together, these results show that MOSAIC can provide rich multi-modal data on complex physiological responses in multiple cell types.


Assuntos
Técnicas Biossensoriais/métodos , Células-Tronco Pluripotentes Induzidas/metabolismo , Microscopia de Fluorescência/métodos , Miócitos Cardíacos/metabolismo , Imagem Óptica/métodos , Potenciais de Ação/efeitos dos fármacos , Antagonistas Adrenérgicos beta/farmacologia , Técnicas Biossensoriais/instrumentação , Cálcio/química , Proteínas de Fluorescência Verde/metabolismo , Células HEK293 , Humanos , Peróxido de Hidrogênio/farmacologia , Concentração de Íons de Hidrogênio , Células-Tronco Pluripotentes Induzidas/citologia , Mitocôndrias/metabolismo , Miócitos Cardíacos/citologia , Miócitos Cardíacos/fisiologia , Imagem Óptica/instrumentação , Oxidantes/farmacologia , Oxirredução/efeitos dos fármacos , Propanolaminas/farmacologia
10.
Nat Commun ; 11(1): 4070, 2020 08 13.
Artigo em Inglês | MEDLINE | ID: mdl-32792502

RESUMO

Human astroviruses are small non-enveloped viruses with positive-sense single-stranded RNA genomes. Astroviruses cause acute gastroenteritis in children worldwide and have been associated with encephalitis and meningitis in immunocompromised individuals. It is still unknown how astrovirus particles exit infected cells following replication. Through comparative genomic analysis and ribosome profiling we here identify and confirm the expression of a conserved alternative-frame ORF, encoding the protein XP. XP-knockout astroviruses are attenuated and pseudo-revert on passaging. Further investigation into the function of XP revealed plasma and trans Golgi network membrane-associated roles in virus assembly and/or release through a viroporin-like activity. XP-knockout replicons have only a minor replication defect, demonstrating the role of XP at late stages of infection. The discovery of XP advances our knowledge of these important human viruses and opens an additional direction of research into their life cycle and pathogenesis.


Assuntos
Canais Iônicos/metabolismo , Mamastrovirus/metabolismo , Proteínas não Estruturais Virais/metabolismo , Animais , Linhagem Celular , Cricetinae , Eletroforese em Gel de Poliacrilamida , Genômica/métodos , Células HeLa , Humanos , Immunoblotting , Imunoprecipitação , Canais Iônicos/genética , Mamastrovirus/genética , Microscopia de Fluorescência , Plasmídeos/genética , Ribossomos , Proteínas não Estruturais Virais/genética , Replicação Viral/genética , Replicação Viral/fisiologia
11.
Nat Commun ; 11(1): 4117, 2020 08 17.
Artigo em Inglês | MEDLINE | ID: mdl-32807785

RESUMO

Strategies for eradicating cancer stem cells (CSCs) are urgently required because CSCs are resistant to anticancer drugs and cause treatment failure, relapse and metastasis. Here, we show that photoactive functional nanocarbon complexes exhibit unique characteristics, such as homogeneous particle morphology, high water dispersibility, powerful photothermal conversion, rapid photoresponsivity and excellent photothermal stability. In addition, the present biologically permeable second near-infrared (NIR-II) light-induced nanocomplexes photo-thermally trigger calcium influx into target cells overexpressing the transient receptor potential vanilloid family type 2 (TRPV2). This combination of nanomaterial design and genetic engineering effectively eliminates cancer cells and suppresses stemness of cancer cells in vitro and in vivo. Finally, in molecular analyses of mechanisms, we show that inhibition of cancer stemness involves calcium-mediated dysregulation of the Wnt/ß-catenin signalling pathway. The present technological concept may lead to innovative therapies to address the global issue of refractory cancers.


Assuntos
Raios Infravermelhos , Nanotecnologia/métodos , Células-Tronco Neoplásicas/efeitos da radiação , Animais , Apoptose/efeitos da radiação , Western Blotting , Cálcio/metabolismo , Canais de Cálcio/metabolismo , Linhagem Celular Tumoral , Feminino , Citometria de Fluxo , Humanos , Imuno-Histoquímica , Células MCF-7 , Camundongos , Camundongos Endogâmicos BALB C , Microscopia de Fluorescência , Células-Tronco Neoplásicas/citologia , Células-Tronco Neoplásicas/metabolismo , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Canais de Cátion TRPV/metabolismo , Via de Sinalização Wnt
12.
Nat Commun ; 11(1): 4124, 2020 08 17.
Artigo em Inglês | MEDLINE | ID: mdl-32807787

RESUMO

In response to DNA damage, a synthetic lethal relationship exists between the cell cycle checkpoint kinase MK2 and the tumor suppressor p53. Here, we describe the concept of augmented synthetic lethality (ASL): depletion of a third gene product enhances a pre-existing synthetic lethal combination. We show that loss of the DNA repair protein XPA markedly augments the synthetic lethality between MK2 and p53, enhancing anti-tumor responses alone and in combination with cisplatin chemotherapy. Delivery of siRNA-peptide nanoplexes co-targeting MK2 and XPA to pre-existing p53-deficient tumors in a highly aggressive, immunocompetent mouse model of lung adenocarcinoma improves long-term survival and cisplatin response beyond those of the synthetic lethal p53 mutant/MK2 combination alone. These findings establish a mechanism for co-targeting DNA damage-induced cell cycle checkpoints in combination with repair of cisplatin-DNA lesions in vivo using RNAi nanocarriers, and motivate further exploration of ASL as a generalized strategy to improve cancer treatment.


Assuntos
Pontos de Checagem do Ciclo Celular/fisiologia , Reparo do DNA/fisiologia , Animais , Pontos de Checagem do Ciclo Celular/genética , Linhagem Celular Tumoral , Dano ao DNA/genética , Dano ao DNA/fisiologia , Reparo do DNA/genética , Células HCT116 , Humanos , Immunoblotting , Camundongos , Microscopia Eletrônica de Transmissão , Microscopia de Fluorescência , Nanomedicina/métodos , Interferência de RNA , RNA Interferente Pequeno/genética , RNA Interferente Pequeno/metabolismo
13.
Nat Commun ; 11(1): 3850, 2020 07 31.
Artigo em Inglês | MEDLINE | ID: mdl-32737322

RESUMO

Resolving the distribution of specific proteins at the nanoscale in the ultrastructural context of the cell is a major challenge in fluorescence microscopy. We report the discovery of a new principle for an optical contrast equivalent to electron microscopy (EM) which reveals the ultrastructural context of the cells with a conventional confocal microscope. By decrowding the intracellular space through 13 to 21-fold physical expansion while simultaneously retaining the proteins, bulk (pan) labeling of the proteome resolves local protein densities and reveals the cellular nanoarchitecture by standard light microscopy.


Assuntos
Imageamento Tridimensional/métodos , Microscopia de Fluorescência/métodos , Proteoma/análise , Coloração e Rotulagem/métodos , Acrilamidas/química , Reagentes para Ligações Cruzadas/química , Corantes Fluorescentes/química , Células HeLa , Humanos , Hidrogéis/química , Espaço Intracelular/química , Succinimidas/química , Inclusão do Tecido/métodos
14.
Proc Natl Acad Sci U S A ; 117(34): 20607-20614, 2020 08 25.
Artigo em Inglês | MEDLINE | ID: mdl-32788360

RESUMO

The mitochondrial contact site and cristae organizing system (MICOS) is a multisubunit protein complex that is essential for the proper architecture of the mitochondrial inner membrane. MICOS plays a key role in establishing and maintaining crista junctions, tubular or slit-like structures that connect the cristae membrane with the inner boundary membrane, thereby ensuring a contiguous inner membrane. MICOS is enriched at crista junctions, but the detailed distribution of its subunits around crista junctions is unclear because such small length scales are inaccessible with established fluorescence microscopy. By targeting individually activated fluorophores with an excitation beam featuring a central zero-intensity point, the nanoscopy method called MINFLUX delivers single-digit nanometer-scale three-dimensional (3D) resolution and localization precision. We employed MINFLUX nanoscopy to investigate the submitochondrial localization of the core MICOS subunit Mic60 in relation to two other MICOS proteins, Mic10 and Mic19. We demonstrate that dual-color 3D MINFLUX nanoscopy is applicable to the imaging of organellar substructures, yielding a 3D localization precision of ∼5 nm in human mitochondria. This isotropic precision facilitated the development of an analysis framework that assigns localization clouds to individual molecules, thus eliminating a source of bias when drawing quantitative conclusions from single-molecule localization microscopy data. MINFLUX recordings of Mic60 indicate ringlike arrangements of multiple molecules with a diameter of 40 to 50 nm, suggesting that Mic60 surrounds individual crista junctions. Statistical analysis of dual-color MINFLUX images demonstrates that Mic19 is generally in close proximity to Mic60, whereas the spatial coordination of Mic10 with Mic60 is less regular, suggesting structural heterogeneity of MICOS.


Assuntos
Proteínas de Membrana/metabolismo , Mitocôndrias/metabolismo , Membranas Mitocondriais/metabolismo , Proteínas Mitocondriais/metabolismo , Células HeLa , Humanos , Microscopia de Fluorescência/métodos
15.
PLoS One ; 15(8): e0237795, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32833989

RESUMO

Extracellular vesicles (EVs) are small membrane-limited structures derived from outward budding of the plasma membrane or endosomal system that participate in cellular communication processes through the transport of bioactive molecules to recipient cells. To date, there are no published methodological works showing step-by-step the isolation, characterization and internalization of small EVs secreted by human primary macrophages derived from circulating monocytes (MDM-derived sEVs). Thus, here we aimed to provide an alternative protocol based on differential ultracentrifugation (dUC) to describe small EVs (sEVs) from these cells. Monocyte-derived macrophages were cultured in EV-free medium during 24, 48 or 72 h and, then, EVs were isolated from culture supernatants by (dUC). Macrophages secreted a large amount of sEVs in the first 24 h, with size ranging from 40-150 nm, peaking at 105 nm, as evaluated by nanoparticle tracking analysis and scanning electron microscopy. The markers Alix, CD63 and CD81 were detected by immunoblotting in EV samples, and the co-localization of CD63 and CD81 after sucrose density gradient ultracentrifugation (S-DGUC) indicated the presence of sEVs from late endosomal origin. Confocal fluorescence revealed that the sEVs were internalized by primary macrophages after three hours of co-culture. The methodology here applied aims to contribute for enhancing reproducibility between the limited number of available protocols for the isolation and characterization of MDM-derived sEVs, thus providing basic knowledge in the area of EV methods that can be useful for those investigators working with sEVs released by human primary macrophages derived from circulating monocytes.


Assuntos
Comunicação Celular , Vesículas Extracelulares/metabolismo , Macrófagos/metabolismo , Buffy Coat/citologia , Diferenciação Celular , Fracionamento Celular/métodos , Centrifugação com Gradiente de Concentração/métodos , Técnicas de Cocultura , Voluntários Saudáveis , Humanos , Microscopia Intravital , Macrófagos/citologia , Macrófagos/ultraestrutura , Microscopia Confocal , Microscopia Eletrônica de Varredura , Microscopia de Fluorescência , Monócitos/fisiologia , Cultura Primária de Células
16.
PLoS One ; 15(8): e0237173, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32845897

RESUMO

Gentian is an important ornamental flower in Japan. The corolla of the majority of cultivated Japanese gentians have green spots, which are rarely encountered in flowers of other angiosperms. Little information is available on the functional traits of the green spots. In this study, we characterized the green spots in the Japanese gentian corolla using a number of microscopic techniques. Opto-digital microscopy revealed that a single visible green spot is composed of approximately 100 epidermal cells. The epidermal cells of a green spot formed a dome-like structure and the cell lumen contained many green structures that were granular and approximately 5 µm in diameter. The green structures emitted red autofluorescence when irradiated with 488 nm excitation light. Transmission electron microscopy revealed that the green structures contained typical thylakoids and grana, thus indicating they are chloroplasts. No grana were observed and the thylakoids had collapsed in the plastids of epidermal cells surrounding green spots. To estimate the rate of photosynthetic electron transfer of the green spots, we measured chlorophyll fluorescence using the MICROSCOPY version of an Imaging-PAM (pulse-amplitude-modulated) fluorometer. Under actinic light of 449 µmol m-2 s-1, substantial electron flow through photosystem II was observed. Observation of green spot formation during corolla development revealed that immature green spots formed at an early bud stage and developed to maturity associated with chloroplast degradation in the surrounding epidermal cells. These results confirmed that the Japanese gentian corolla contains functional chloroplasts in restricted areas of epidermal cells and indicated that a sophisticated program for differential regulation of chloroplast formation and degradation is operative in the epidermis.


Assuntos
Flores/citologia , Flores/metabolismo , Gentiana/anatomia & histologia , Tilacoides/metabolismo , Clorofila/metabolismo , Transporte de Elétrons , Japão , Microscopia Eletrônica de Transmissão , Microscopia de Fluorescência , Fotossíntese , Complexo de Proteína do Fotossistema I/metabolismo , Complexo de Proteína do Fotossistema II/metabolismo , Epiderme Vegetal/citologia , Epiderme Vegetal/metabolismo , Folhas de Planta/metabolismo
17.
Nat Protoc ; 15(9): 2773-2784, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32737465

RESUMO

Spherical aberration (SA) occurs when light rays entering at different points of a spherical lens are not focused to the same point of the optical axis. SA that occurs inside the lens elements of a fluorescence microscope is well understood and corrected for. However, SA is also induced when light passes through an interface of refractive index (RI)-mismatched substances (i.e., a discrepancy between the RI of the immersion medium and the RI of the sample). SA due to RI mismatches has many deleterious effects on imaging. Perhaps most important for 3D imaging is that the distance the image plane moves in a sample is not equivalent to the distance traveled by an objective (or stage) during z-stack acquisition. This non-uniform translation along the z axis gives rise to artifactually elongated images (if the objective is immersed in a medium with a higher RI than that of the sample) or compressed images (if the objective is immersed in a medium with a lower RI than that of the sample) and alters the optimal axial sampling rate. In this tutorial, we describe why this distortion occurs, how it impacts quantitative measurements and axial resolution, and what can be done to avoid SA and thereby prevent distorted images. In addition, this tutorial aims to better inform researchers of how to correct RI mismatch-induced axial distortions and provides a practical ImageJ/Fiji-based tool to reduce the prevalence of volumetric measurement errors and lost axial resolution.


Assuntos
Artefatos , Imageamento Tridimensional , Microscopia de Fluorescência , Espalhamento de Radiação , Corantes Fluorescentes/química , Microesferas
18.
Nat Protoc ; 15(9): 2920-2955, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32788719

RESUMO

Characterization of immune responses is currently hampered by the lack of systems enabling quantitative and dynamic phenotypic characterization of individual cells and, in particular, analysis of secreted proteins such as cytokines and antibodies. We recently developed a simple and robust microfluidic platform, DropMap, to measure simultaneously the kinetics of secretion and other cellular characteristics, including endocytosis activity, viability and expression of cell-surface markers, from tens of thousands of single immune cells. Single cells are compartmentalized in 50-pL droplets and analyzed using fluorescence microscopy combined with an immunoassay based on fluorescence relocation to paramagnetic nanoparticles aligned to form beadlines in a magnetic field. The protocol typically takes 8-10 h after preparation of microfluidic chips and chambers, which can be done in advance. By contrast, enzyme-linked immunospot (ELISPOT), flow cytometry, time-of-flight mass cytometry (CyTOF), and single-cell sequencing enable only end-point measurements and do not enable direct, quantitative measurement of secreted proteins. We illustrate how this system can be used to profile downregulation of tumor necrosis factor-α (TNF-α) secretion by single monocytes in septic shock patients, to study immune responses by measuring rates of cytokine secretion from single T cells, and to measure affinity of antibodies secreted by single B cells.


Assuntos
Sistema Imunitário/citologia , Dispositivos Lab-On-A-Chip , Fenótipo , Análise de Célula Única/instrumentação , Animais , Linfócitos B/citologia , Feminino , Humanos , Processamento de Imagem Assistida por Computador , Camundongos , Microscopia de Fluorescência
19.
Nat Commun ; 11(1): 4226, 2020 08 24.
Artigo em Inglês | MEDLINE | ID: mdl-32839450

RESUMO

Intercellular signaling is indispensable for single cells to form complex biological structures, such as biofilms, tissues and organs. The genetic tools available for engineering intercellular signaling, however, are quite limited. Here we exploit the chemical diversity of biological small molecules to de novo design a genetic toolbox for high-performance, multi-channel cell-cell communications and biological computations. By biosynthetic pathway design for signal molecules, rational engineering of sensing promoters and directed evolution of sensing transcription factors, we obtain six cell-cell signaling channels in bacteria with orthogonality far exceeding the conventional quorum sensing systems and successfully transfer some of them into yeast and human cells. For demonstration, they are applied in cell consortia to generate bacterial colony-patterns using up to four signaling channels simultaneously and to implement distributed bio-computation containing seven different strains as basic units. This intercellular signaling toolbox paves the way for engineering complex multicellularity including artificial ecosystems and smart tissues.


Assuntos
Comunicação Celular/genética , Biologia Computacional/métodos , Transdução de Sinais/genética , Fatores de Transcrição/genética , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Fluorescência Verde/genética , Proteínas de Fluorescência Verde/metabolismo , Células HEK293 , Humanos , Microscopia de Fluorescência , Mutação , Reprodutibilidade dos Testes , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Fatores de Transcrição/metabolismo
20.
Nat Commun ; 11(1): 4271, 2020 08 26.
Artigo em Inglês | MEDLINE | ID: mdl-32848153

RESUMO

Performing multi-color nanoscopy for extended times is challenging due to the rapid photobleaching rate of most fluorophores. Here we describe a new fluorophore (Yale-595) and a bio-orthogonal labeling strategy that enables two-color super-resolution (STED) and 3D confocal imaging of two organelles simultaneously for extended times using high-density environmentally sensitive (HIDE) probes. Because HIDE probes are small, cell-permeant molecules, they can visualize dual organelle dynamics in hard-to-transfect cell lines by super-resolution for over an order of magnitude longer than with tagged proteins. The extended time domain possible using these tools reveals dynamic nanoscale targeting between different organelles.


Assuntos
Corantes Fluorescentes , Microscopia de Fluorescência/métodos , Nanotecnologia/métodos , Organelas/metabolismo , Linhagem Celular , Corantes Fluorescentes/química , Células HeLa , Células Endoteliais da Veia Umbilical Humana , Humanos , Imageamento Tridimensional , Microscopia Confocal , Fotodegradação , Imagem com Lapso de Tempo
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