超分辨远场生物荧光成像——突破光学衍射极限

长期以来,远场光学荧光显微镜凭借其非接触、无损伤、可探测样品内部等优点,一直是生命科学中最常用的观测工具。但由于衍射极限的存在,使传统的宽场光学显微镜横向和纵向的分辨率分别仅约为230 nm和1000 nm。为了揭示细胞内分子尺度的动态和结构特征,提高光学显微镜分辨率成为生命科学发展的迫切要求,在远场荧光显微镜的基础上,科学家们已经发展出许多实用的提高分辨率甚至超越分辨率极限的成像技术。例如,采用横向结构光照明提高横向分辨率到约100 nm,利用纵向驻波干涉效应将纵向分辨率提高5~10倍。然而,直到在光学荧光显微镜中引入非线性效应后,衍射极限才被真正突破,如受激荧光损耗显微镜利用非线性效应实现了30~50 nm的三维分辨率。另外应用荧光分子之间能量转移共振原理以及单荧光分子定位技术也可以突破衍射极限,甚至可以将分子定位精度提高到几个纳米的量级。

Dinâmica de crescimento de Cedrela odorata L. (Meliaceae) na Floresta Atlântica do Estado do Rio de Janeiro: fenologia, atividade cambial e dendrocronologia

Ao longo do século XX, poucos estudos de dendrocronologia foram desenvolvidos com espécies de ambientes tropicais, em função da crença de que as condições climáticas nessas regiões não apresentavam variações suficientemente marcantes e regulares para induzir um ritmo anual de crescimento radial. A realização de trabalhos sobre esse tema nas últimas décadas revelou que a formação de anéis de crescimento anuais nos trópicos pode estar associada a fatores diversos, como: existência de estação seca bem definida, ocorrência de inundações sazonais, respostas ao comportamento fenológico, respostas ao fotoperíodo e a ritmos endógenos. O presente estudo tem por objetivo compreender a dinâmica de crescimento radial de uma espécie da Mata Atlântica se desenvolvendo em ambiente natural. Para tanto, propôs-se: i) investigar a periodicidade da atividade cambial e dos fatores que a influenciam; ii) estimar a idade e taxa de crescimento diamétrico e iii) correlacionar os fatores ambientais com os anéis de crescimento, em indivíduos de Cedrela odorata L. Para o estudo da atividade cambial, foram obtidas amostras de caule a 1,30 m do solo, contendo periderme, faixa cambial e xilema e floema secundários, por métodos não destrutivos. A fenologia vegetativa e a frutificação dos indivíduos amostrados foram acompanhadas durante todo o período do experimento. O material coletado foi processado segundo técnicas usuais em Anatomia Vegetal e analisado sob microscopia óptica e de fluorescência. Os dados de fotoperíodo, precipitação, temperatura e fenologia vegetativa foram correlacionados à atividade cambial. Para o estudo dos anéis de crescimento, as coletas também foram realizadas a 1,30 m do solo, por meio de sonda de Pressler. As amostras obtidas foram polidas e analisadas sob microscópio estereoscópio, para demarcação e aferição do número de anéis de crescimento, e a largura dos anéis foi mensurada para a determinação das taxas de crescimento radial. A série histórica de temperatura e precipitação foi correlacionada à cronologia dos anéis de crescimento. Os resultados indicaram que a atividade cambial segue um ritmo anual de crescimento, correlacionado à sazonalidade do fotoperíodo, da precipitação e da fenologia vegetativa. A análise dos anéis de crescimento permitiu estimar a idade dos indivíduos e determinar a taxa média de incremento e as taxas de incremento diamétrico acumulado e incremento médio anual para a espécie no sítio de estudo. Os dados de incremento radial evidenciaram a ausência de relação entre a idade e o diâmetro das árvores. A análise da variação na largura dos anéis não apresentou correlações significativas com os fatores climáticos analisados.

Emprego de microscopia de fluorescência para a quantificação microbiana em amostras salinas da indústria do petróleo

Os micro-organismos constituem um grande problema em termos econômicos para a indústria petrolífera. Estes são responsáveis pela produção de substâncias corrosivas e a formação de biofilmes, que causam deterioração dos materiais metálicos. Os principais grupos microbianos presentes em amostras ambientais da indústria do petróleo são as bactérias anaeróbias heterotróficas totais (BANHT) e as bactérias redutoras de sulfato (BRS). Atualmente, a quantificação desses grupos microbianos é realizada através da técnica do Número Mais Provável (NMP) que estima o resultado em aproximadamente 28 dias. Neste trabalho foi otimizada uma metodologia para a microscopia de fluorescência de amostras salinas provenientes de tanques de armazenamento de água/óleo. As condições testadas foram o tipo de óleo de imersão, o tipo de diluente, o volume do corante, o volume da amostra corada e a concentração do fixador (glutaraldeído) numa tentativa de correlacionar com resultados de quantificação de BANHT e BRS através da técnica convencional do NMP. Nesse caso, as células totais foram quantificadas por microscopia de fluorescência utilizando o corante fluorescente laranja de acridina (AO). Verificou-se que houve uma correlação entre os resultados da quantificação de células totais por microscopia de fluorescência e os resultados de BANHT pela técnica do NMP, devido a pouca variação de valores expressos em ambas as quantificações. Entretanto, não foi possível correlacionar os resultados da quantificação de células totais com os resultados de BRS por NMP devido à grande variação dos valores de quantificação de BRS. Na microscopia de fluorescência, foi possível, quantificar os micro-organismos em aproximadamente 30 minutos e através das fotografias, verificou-se ainda que as amostras apresentaram-se nítidas e os micro-organismos com uma boa fluorescência

Towards in situ Single Cell Systems Biology

Systems-level studies of biological systems rely on observations taken at a resolution lower than the essential unit of biology, the cell. Recent technical advances in DNA sequencing have enabled measurements of the transcriptomes in single cells excised from their environment, but it remains a daunting technical problem to reconstruct in situ gene expression patterns from sequencing data. In this thesis I develop methods for the routine, quantitative in situ measurement of gene expression using fluorescence microscopy.

The number of molecular species that can be measured simultaneously by fluorescence microscopy is limited by the pallet of spectrally distinct fluorophores. Thus, fluorescence microscopy is traditionally limited to the simultaneous measurement of only five labeled biomolecules at a time. The two methods described in this thesis, super-resolution barcoding and temporal barcoding, represent strategies for overcoming this limitation to monitor expression of many genes in a single cell. Super-resolution barcoding employs optical super-resolution microscopy (SRM) and combinatorial labeling via-smFISH (single molecule fluorescence in situ hybridization) to uniquely label individual mRNA species with distinct barcodes resolvable at nanometer resolution. This method dramatically increases the optical space in a cell, allowing a large numbers of barcodes to be visualized simultaneously. As a proof of principle this technology was used to study the S. cerevisiae calcium stress response. The second method, sequential barcoding, reads out a temporal barcode through multiple rounds of oligonucleotide hybridization to the same mRNA. The multiplexing capacity of sequential barcoding increases exponentially with the number of rounds of hybridization, allowing over a hundred genes to be profiled in only a few rounds of hybridization.

The utility of sequential barcoding was further demonstrated by adapting this method to study gene expression in mammalian tissues. Mammalian tissues suffer both from a large amount of auto-fluorescence and light scattering, making detection of smFISH probes on mRNA difficult. An amplified single molecule detection technology, smHCR (single molecule hairpin chain reaction), was developed to allow for the quantification of mRNA in tissue. This technology is demonstrated in combination with light sheet microscopy and background reducing tissue clearing technology, enabling whole-organ sequential barcoding to monitor in situ gene expression directly in intact mammalian tissue.

The methods presented in this thesis, specifically sequential barcoding and smHCR, enable multiplexed transcriptional observations in any tissue of interest. These technologies will serve as a general platform for future transcriptomic studies of complex tissues.

Efeitos de raios-X de baixa energia em células mamárias

Doses de radiação de baixa energia podem induzir quebras de dupla fita no DNA assim como também produzir perfis alterados de expressão de genes relacionados a estas lesões. Os danos não reparados ou mal reparados levam a uma maior suscetibilidade à transformação oncogênica já que os efeitos biológicos mais importantes causados pela radiação ionizante são mutação e carcinogênese. As lesões no DNA provocadas pela radiação podem também ocasionar o surgimento micronúcleos e as células podem ser induzidas à apoptose. O objetivo deste trabalho é estudar in vitro a presença de micronúcleos e a apoptose ocasionados por Raios-X de baixa energia. Pretende-se analisar estes efeitos biológicos em relação à energia equivalente à utilizada em exames mamográficos usando duas linhagens estabelecias de células de mama: a MCF-7 (tumoral) e a HB-2 (não-tumoral). As células, em crescimento exponencial, foram irradiadas no equipamento de arranjo experimental de mamografia do LCR/UERJ. A dose de 5Gy na energia de 30 kV foi aplicada com taxa de 0,1 Gy/seg utilizando filtro de 0,03 mm de molibdênio. As irradiações foram realizadas duas vezes, após as irradiações, as células foram incubadas por 4, 24 ou 48 horas e posteriormente coradas com o corante Hoechst33258 para análise em microscopia de fluorescência. Para cada análise, 1000 células foram categorizadas pela morfologia do núcleo. Os resultados mostraram que a HB-2, utilizada neste estudo como célula mamária normal, apresentou maior sensibilidade aos efeitos da radiação, com 37 % das células em apoptose após 4 hs de incubação, enquanto a MCF-7 apresentou 6,5 %. Nas análises após 24 hs foi possível confirmar a radioresistência da MCF-7 tendo sido observadas 11% de células em apoptose no grupo irradiado. Houve um aumento crescente de micronúcleos radioinduzidos nas duas linhagens de acordo com os tempos de incubação. Na análise de 4 hs a HB-2 apresentou 3%, em 24 hs, 8,5% e 48 hs, 11,5 %. Diante destes resultados, foi possível concluir que a energia do feixe de raios-X utilizada na mamografia pode ser capaz de ocasionar aumento de ocorrência de apoptose e geração de micronúcleos nas duas linhagens estudadas

Avaliação da ação antitumoral in vitro da pterocarpanoquinona LQB 118 e estudo de alguns mecanismos de ação

Tem sido descrito que o acúmulo de mutações em proto-oncogenes e genes supressores de tumor contribui para o direcionamento da célula à carcinogênese. Na maioria dos casos de câncer, as células apresentam proliferação descontrolada devido a alterações na expressão e/ou mutações de ciclinas, quinases dependentes de ciclinas e/ou inibidores do ciclo celular. Os tumores sólidos figuram entre o tipo de câncer mais incidente no mundo, sendo a quimioterapia e/ou hormônio-terapia, radioterapia e cirurgia os tratamentos mais indicados para estes tipos de tumores. Entretanto, o tratamento quimioterápico apresenta diversos efeitos colaterais e muitas vezes é ineficaz. Portanto, a busca por novas moléculas capazes de conter a proliferação destas células e com baixa toxicidade para o organismo se faz necessário. Este trabalho teve por objetivo avaliar a ação antitumoral in vitro de um novo composto sintético, a pterocarpanoquinona LQB118, sobre algumas linhagens tumorais humanas de alta prevalência e estudar alguns dos seus mecanismos de ação. As linhagens tumorais estudadas neste trabalho foram os adenocarcinomas de mama (MCF7) e próstata (PC-3), e carcinoma de pulmão (A549). A citotoxicidade foi avaliada pelo ensaio do MTT e a proliferação celular pela contagem de células vivas (exclusão do corante azul de tripan) e análise do ciclo celular (citometria de fluxo). A expressão gênica foi avaliada por RT-PCR e a apoptose foi avaliada por condensação da cromatina (microscopia de fluorescência-DAPI), fragmentação de DNA (eletroforese) e marcação com anexina V (citometria de fluxo). Das linhagens tumorais testadas, a de próstata (PC3) foi a que se mostrou mais sensível ao LQB 118, e em função deste resultado, os demais experimentos foram realizados com esta linhagem tumoral. O efeito citotóxico do LQB 118 se mostrou tempo e concentração dependente. Esta substância inibiu a proliferação celular e prejudicou a progressão do ciclo celular, acumulando células nas fases S e G2/M. Buscando esclarecer os mecanismos desta ação antitumoral, demonstrou-se que o LQB 118 inibe a expressão do mRNA do fator de transcrição c-Myc e das ciclinas D1 e B1, e induz a apoptose de tais células tumorais. Em suma, o LQB 118 é capaz de inibir a proliferação das células tumorais de próstata, alterando a expressão do mRNA de alguns genes reguladores do ciclo celular, resultando em interrupção do ciclo celular e indução de apoptose, indicando este composto como um potencial candidato a futuro medicamento no tratamento do câncer de próstata.

Cloning and expression of zebra fish ferroportin and investigating its influence on anemia

Iron is required for many microbes and pathogens for their survival and proliferation including Leishmania which cause leishmaniasis. Leishmaniasis is an increasingly serious infectious disease with a wide spectrum of clinical manifestations. These range from localized cutaneous leishmaniasis (CL) lesions to a lethal visceral form. Certain strains such as BALB/c mice fail to control L. major infection and develop progressive lesions and systemic disease. These mice are thought to be a model of non-healing forms of the human disease such as kala-azar or diffuse cutaneous leishmaniasis. Progression of disease in BALB/c mice has been associated with the anemia, in last days of their survival, the progressive anemia is considered to be one of the reasons of their death. Ferroportin (Fpn), a key regulator of iron homeostasis is a conserved membrane protein that exports iron across the duodenal enterocytes as well as macrophages and hepatocytes into the blood circulation. Fpn has also critical influence on survival and proliferation of many microorganisms whose growth is dependent upon iron, thus preparation of Fpn is needed to study the role of iron in immune responses and pathogenesis of micoorganisms. To prepare and characterize a recombinant ferroportin, total RNA was extracted from Indian zebrafish duodenum, and used to synthesize cDNA by RT-PCR. PCR product was first cloned in Topo TA vector and then subcloned into the GFP expression vector pEGFP–N1. The final resulted plasmid (pEGFP-ZFpn) was used for expression of FPN-EGFP protein in Hek 293T cells. The expression was confirmed by fluorescence microscopy and flow cytometery. Recombinant Fpn was further characterized by submission of its predicted amino acid sequences to the TMHMM V2.0 prediction server (hidden Markov model), NetOGlyc 3.1 server and NetNGlyc 3.1 server. Data emphasised that obtained Fpn from indian zebrafish contained eight transmembrane domains with N- and C-termini inside the cytoplasm and harboured 78 mucin-type glycosylated amino acid. The results indicate that the prepared and characterized recombinant Fpn protein has no membrane topology difference compared to other Fpn described by other researcher. Our next aim was to deliver recombinant plasmid (pEGFP-ZFpn) to entrocyte cells. However, naked therapeutic genes are rapidly degraded by nucleases, showing poor cellular uptake, nonspecificity to the target cells, and low transfection efficiency. The development of safe and efficient gene carriers is one of the prerequisites for the success of gene therapy. Chitosan and alginate 139 polymers were used for oral gene carrier because of their biodegradability, biocompatibility and their mucoadhesive and permeability-enhancing properties in the gut. Nanoparticles comprising Alginate/Chitosan polymers were prepared by pregel preparation method. The resulting nanoparticles had a loading efficiency of 95% and average size of 188 nm as confirmed by PCS method and SEM images had showed spherical particles. BALB/c mice were divided to three groups. The first and second group were fed with chitosan/alginate nanoparticles containing the pEGFP-ZFpn and pEGFP plasmid, respectively (30 μgr/mice) and the third group (control) didn’t get any nanoparticles. The result showed BALB/c mice infected by L.major, resulted in higher hematocryte and iron level in pEGFP-ZFpn fed mice than that in other groups. Consentration of cytokines determined by ELISA showed lower levels of IL-4 and IL-10 and higher levels of IFN-γ/IL-4 and IFN-γ/IL-10 ratios in pEGFP-ZFpn fed mice than that in other groups. Morover more limited increase of footpad thickness and significant reduction of viable parasites in lymph node was seen in pEGFP-ZFpn fed mice. The results showed the first group exhibited a highr hematocryte and iron compared to the other groups. These data strongly suggests the in vivo administration of chitosan/alginate nanoparticles containing pEGFP-ZFpn suppress Th2 response and may be used to control the leishmaniasis .

In vivo dynamics of the internal fibrous structure in smooth adhesive pads of insects.

Many insects with smooth adhesive pads can rapidly enlarge their contact area by centripetal pulls on the legs, allowing them to cope with sudden mechanical perturbations such as gusts of wind or raindrops. The short time scale of this reaction excludes any neuromuscular control; it is thus more likely to be caused by mechanical properties of the pad's specialized cuticle. This soft cuticle contains numerous branched fibrils oriented almost perpendicularly to the surface. Assuming a fixed volume of the water-filled cuticle, we hypothesized that pulls could decrease the fibril angle, thereby helping the contact area to expand laterally and longitudinally. Three-dimensional fluorescence microscopy on the cuticle of smooth stick insect pads confirmed that pulls significantly reduced the fibril angle. However, the fibril angle variation appeared insufficient to explain the observed increase in contact area. Direct strain measurements in the contact zone demonstrated that pulls not only expand the cuticle laterally, but also add new contact area at the pad's outer edge.

Quantification of the effects of antibodies on the extra- and intracellular dynamics of Salmonella enterica.

Antibodies are known to be essential in controlling Salmonella infection, but their exact role remains elusive. We recently developed an in vitro model to investigate the relative efficiency of four different human immunoglobulin G (IgG) subclasses in modulating the interaction of the bacteria with human phagocytes. Our results indicated that different IgG subclasses affect the efficacy of Salmonella uptake by human phagocytes. In this study, we aim to quantify the effects of IgG on intracellular dynamics of infection by combining distributions of bacterial numbers per phagocyte observed by fluorescence microscopy with a mathematical model that simulates the in vitro dynamics. We then use maximum likelihood to estimate the model parameters and compare them across IgG subclasses. The analysis reveals heterogeneity in the division rates of the bacteria, strongly suggesting that a subpopulation of intracellular Salmonella, while visible under the microscope, is not dividing. Clear differences in the observed distributions among the four IgG subclasses are best explained by variations in phagocytosis and intracellular dynamics. We propose and compare potential factors affecting the replication and death of bacteria within phagocytes, and we discuss these results in the light of recent findings on dormancy of Salmonella.

Morphological and ultrastructural changes in tobacco BY-2 cells exposed to microcystin-RR

Tobacco BY-2 cells were exposed to microcystin-RR (MC-RR) at two concentrations, 60 mu g mL(-1) and 120 mu g mL(-1), to study the changes in morphology and ultrastructure of cells as a result of the exposure. Exposure to the lower concentration for 5 d led to typical apoptotic morphological changes including condensation of nuclear chromatin, creation of a characteristic 'half moon' structure, and cytoplasm shrinkage and decreased cell volume, as revealed through light microscopy. fluorescence microscopy, and transmission electron microscopy, respectively. Exposure to the higher concentration, on the other hand, led to morphological and ultrastructural changes typical of necrosis, such as rupture of the plasma membrane and the nuclear membrane and a marked swelling of cells. The presence of many vacuoles containing unusual deposits points to the involvement of vacuoles in detoxifying MC-RR. Results of the present study indicate that exposure of tobacco BY-2 cells to MC-RR at a lower concentration (60 mu g mL(-1)) results in apoptosis and that to a higher concentration (120 mu g mL(-1)), in necrosis. (C) 2009 Elsevier Ltd. All rights reserved.

Constitutive expression of thymidylate synthase from LCDV-C induces a transformed phenotype in fish cells

Thymidylate synthase (TS), an essential enzyme in DNA synthesis and repair, plays a key role in the events of cell cycle regulation and tumor formation. Here, an investigation was presented about subcellular location and biological function of viral TS from lymphocystis disease virus from China (LCDV-C) in fish cells. Fluorescence microscopy revealed that LCDV-C TS was predominantly localized in the cytoplasm in fish cells. Cell cycle analysis demonstrated that LCDV-C TS promoted cell cycle progression into S and G2/M phase in the constitutive expressed cells. As a result, the cells have a faster growth rate compared with the control cells as revealed by cell growth curves. For foci assay, the TS-expressed cells gave rise to foci 4-5 weeks after incubation. Microscopic examination of the TS-induced foci revealed multilayered growth and crisscross morphology characteristic of transformed cells. Moreover, LCDV-C TS predisposed the transfected cells to acquire an anchorage-independent phenotype and could grow in 0.3% soft agar. So the data reveal LCDV-C TS is sufficient to induce a transformed phenotype in fish cells in vitro and exhibits its potential ability in cell transformation. To our knowledge, it is the first report on viral TS sequences associated with transforming activity. (C) 2007 Elsevier Inc. All rights reserved.

Induction of apoptosis in a carp leucocyte cell line infected with turbot (Scophthalmus maximus L.) rhabdovirus

A rhabdovirus was observed from the diseased turbot (Scophthalmus maximus L.) with lethal syndrome. In this study, a carp leucocyte (CLC) cell line was used to investigate the infection process and cell death mechanism occurring during the virus infection. Strong cytopathogenic effect (CPE) and the morphological changes, such as extreme chromatin condensation, nucleus fragmentation, and apoptotic body formation, were observed under fluorescence microscopy after DAPI staining in the infected CLC cells. Transmission electron microscopy analysis showed cell shrinkage, plasma membrane blebbing, cytoplasm vacuolization, chromatin condensation, nuclear breakdown and formation of discrete apoptotic bodies. The bullet-shaped nucleocapsids were measured and ranged in size from 110 to 150 nm in length and 40 to 60 nm in diameter. And therefore the virus is called Scophthalmus maximus rhabdovirus (SMRV). Agarose gel electrophoresis analysis of the DNA extracted from infected cells showed typical DNA ladder in the course of SMRV infection. Flow cytometry analysis of SMRV infected CLC cells detected apoptotic peak in the virus infected CLC cells. Virus titre analysis and electron microscopic observation revealed that the virus replication fastigium was earlier than that of the apoptosis occurrence. No apoptosis was observed in the CLC infected with UV-inactivated SMRV. All these supported that SMRV infected CLC cells undergo apoptosis and the virus replication is necessary for apoptosis induction of CLC cells. (C) 2004 Published by Elsevier B.V.

High PL-efficiency ZnO nanocrystallites/PPV composite nanofibers

In this paper, we report for the first time on the synthesis of ZnO nanocrystallites in conjugated polymer (PPV) nanofibers by the coupling of the in situ/blend methods and electrospinning. These composite nanofibers were characterized by fluorescence microscopy, atomic force microscope (AFM), field emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), photoluminescence (PL) spectra, Fourier transform infrared (FT-IR) spectroscopy, and X-ray powder diffraction (XRD).

Core Crosslinking of Biodegradable Block Copolymer Micelles Based on Poly(ester carbonate)

A biodegradable amphiphilic block copolymer, PEG-b-P(LA-co-MAC), was used to prepare spherical micelles consisting of a hydrophobic P(LA-co-MAC) core and a hydrophilic PEG shell. To improve their stability, the micelles were crosslinked by radical polymerization of the double bonds in the hydrophobic blocks. The crosslinked micelles had similar sizes and a narrow size distribution compared to their uncrosslinked precursor. The improved stability of the crosslinked micelles was confirmed by measurements of the CMC and a thermodynamic investigation. These micelles can internalize into Hela cells in vitro as demonstrated by inverted fluorescence microscopy and CLSM. These stabilized nanoscale micelles have potential use in biomedical applications such as drug delivery and disease diagnosis.

Rapid self-assembly of oligo(o-phenylenediamine) into one-dimensional structures through a facile reprecipitation route

The self-assembly of oligo(o-phenylenediamine) (OPD) into 1-D nanostructures on a macroscopic length scale was found when they were transferred from N-methyl pyrrolidone to deionized water. Field emission scanning electron microscopy and confocal fluorescence microscopy were used to investigate the morphology of the precipitates. Results showed that large amounts of OPD 1-D supertructures could be obtained through the simple reprecipitation route, and the length of the fibers could be tuned from microscale to macroscale by adjusting the ratio of two solvents. X-ray diffraction patterns and UV-vis spectra revealed that pi-pi interactions between OPD molecules that facilitated the formation of 1-D structures became predominant when they were transferred from a good solvent to a bad one. Accordingly, a possible formation mechanism was proposed.