椭偏光学生物传感器及生物医学应用

椭偏光学生物传感器是识别和检测蛋白质的一种新型的高通量、快速生物分子分析技术.它可以实现无标记多元生物分子自动化检测、静态或动态测量及定性和定量测量等,已应用于生物医学与临床检测等方面,如肿瘤标志蛋白检测、乙肝五项同时检测、蛋白质竞争吸附以及多元蛋白质相互作用动态测量等,显示出了广阔的应用前景.

Geometric optimization methods for the analysis of gene expression data

DNA microarrays provide such a huge amount of data that unsupervised methods are required to reduce the dimension of the data set and to extract meaningful biological information. This work shows that Independent Component Analysis (ICA) is a promising approach for the analysis of genome-wide transcriptomic data. The paper first presents an overview of the most popular algorithms to perform ICA. These algorithms are then applied on a microarray breast-cancer data set. Some issues about the application of ICA and the evaluation of biological relevance of the results are discussed. This study indicates that ICA significantly outperforms Principal Component Analysis (PCA).

蛋白质芯片用表面改性剂的合成——蛋白质偶联剂与蛋白质非特异吸附抑制剂的合成

以巯丙基三乙氧基硅烷和单取代三聚乙二醇为原料，先把巯基转换成巯钠，把醇羟基转换成对甲苯磺酰基，利用巯钠和对甲苯磺酰基间的亲核取代反应，在温和条件下合成了标题试剂。

Support for Integrated Ecosystem Assessments of NOAA’s National Estuarine Research Reserves System (NERRS), Volume I: The Impacts of Coastal Development on the Ecology and Human Well-being of Tidal Creek Ecosystems of the US Southeast

A study was conducted, in association with the Sapelo Island and North Carolina National Estuarine Research Reserves (NERRs), to evaluate the impacts of coastal development on sentinel habitats (e.g., tidal creek ecosystems), including potential impacts to human health and well-being. Uplands associated with southeastern tidal creeks and the salt marshes they drain are popular locations for building homes, resorts, and recreational facilities because of the high quality of life and mild climate associated with these environments. Tidal creeks form part of the estuarine ecosystem characterized by high biological productivity, great ecological value, complex environmental gradients, and numerous interconnected processes. This research combined a watershed-level study integrating ecological, public health and human dimension attributes with watershed-level land use data. The approach used for this research was based upon a comparative watershed and ecosystem approach that sampled tidal creek networks draining developed watersheds (e.g., suburban, urban, and industrial) as well as undeveloped sites. The primary objective of this work was to clearly define the relationships between coastal development with its concomitant land use changes and non-point source pollution loading and the ecological and human health and well-being status of tidal creek ecosystems. Nineteen tidal creek systems, located along the southeastern United States coast from southern North Carolina to southern Georgia, were sampled during summer (June-August), 2005 and 2006. Within each system, creeks were divided into two primary segments based upon tidal zoning: intertidal (i.e., shallow, narrow headwater sections) and subtidal (i.e., deeper and wider sections), and watersheds were delineated for each segment. In total, we report findings on 24 intertidal and 19 subtidal creeks. Indicators sampled throughout each creek included water quality (e.g., dissolved oxygen concentration, salinity, nutrients, chlorophyll-a levels), sediment quality (e.g., characteristics, contaminants levels including emerging contaminants), pathogen and viral indicators, and abundance and genetic responses of biological resources (e.g., macrobenthic and nektonic communities, shellfish tissue contaminants, oyster microarray responses). For many indicators, the intertidally-dominated or headwater portions of tidal creeks were found to respond differently than the subtidally-dominated or larger and deeper portions of tidal creeks. Study results indicate that the integrity and productivity of headwater tidal creeks were impaired by land use changes and associated non-point source pollution, suggesting these habitats are valuable early warning sentinels of ensuing ecological impacts and potential public health threats. For these headwater creeks, this research has assisted the validation of a previously developed conceptual model for the southeastern US region. This conceptual model identified adverse changes that generally occurred in the physical and chemical environment (e.g., water quality indicators such as indicator bacteria for sewage pollution or sediment chemical contamination) when impervious cover levels in the watershed reach 10-20%. Ecological characteristics responded and were generally impaired when impervious cover levels exceed 20-30%. Estimates of impervious cover levels defining where human uses are impaired are currently being determined, but it appears that shellfish bed closures and the flooding vulnerability of headwater regions become a concern when impervious cover values exceed 10-30%. This information can be used to forecast the impacts of changing land use patterns on tidal creek environmental quality as well as associated human health and well-being. In addition, this study applied tools and technologies that are adaptable, transferable, and repeatable among the high quality NERRS sites as comparable reference entities to other nearby developed coastal watersheds. The findings herein will be of value in addressing local, regional and national needs for understanding multiple stressor (anthropogenic and human impacts) effects upon estuarine ecosystems and response trends in ecosystem condition with changing coastal impacts (i.e., development, climate change). (PDF contaions 88 pages)

Wide Screening of Phage-Displayed Libraries Identifies Immune Targets in Planta

Microbe-Associated Molecular Patterns and virulence effectors are recognized by plants as a first step to mount a defence response against potential pathogens. This recognition involves a large family of extracellular membrane receptors and other immune proteins located in different sub-cellular compartments. We have used phage-display technology to express and select for Arabidopsis proteins able to bind bacterial pathogens. To rapidly identify microbe-bound phage, we developed a monitoring method based on microarrays. This combined strategy allowed for a genome-wide screening of plant proteins involved in pathogen perception. Two phage libraries for high-throughput selection were constructed from cDNA of plants infected with Pseudomonas aeruginosa PA14, or from combined samples of the virulent isolate DC3000 of Pseudomonas syringae pv. tomato and its avirulent variant avrRpt2. These three pathosystems represent different degrees in the specificity of plant-microbe interactions. Libraries cover up to 26107 different plant transcripts that can be displayed as functional proteins on the surface of T7 bacteriophage. A number of these were selected in a bio-panning assay for binding to Pseudomonas cells. Among the selected clones we isolated the ethylene response factor ATERF-1, which was able to bind the three bacterial strains in competition assays. ATERF-1 was rapidly exported from the nucleus upon infiltration of either alive or heat-killed Pseudomonas. Moreover, aterf-1 mutants exhibited enhanced susceptibility to infection. These findings suggest that ATERF-1 contains a microbe-recognition domain with a role in plant defence. To identify other putative pathogen-binding proteins on a genome-wide scale, the copy number of selected-vs.-total clones was compared by hybridizing phage cDNAs with Arabidopsis microarrays. Microarray analysis revealed a set of 472 candidates with significant fold change. Within this set defence-related genes, including well-known targets of bacterial effectors, are over-represented. Other genes non-previously related to defence can be associated through this study with general or strain-specific recognition of Pseudomonas.

Preprocess and data analysis techniques for affymetrix DNA microarrays using bioconductor: a case study in Alzheimer disease

DNA microarray, or DNA chip, is a technology that allows us to obtain the expression level of many genes in a single experiment. The fact that numerical expression values can be easily obtained gives us the possibility to use multiple statistical techniques of data analysis. In this project microarray data is obtained from Gene Expression Omnibus, the repository of National Center for Biotechnology Information (NCBI). Then, the noise is removed and data is normalized, also we use hypothesis tests to find the most relevant genes that may be involved in a disease and use machine learning methods like KNN, Random Forest or Kmeans. For performing the analysis we use Bioconductor, packages in R for the analysis of biological data, and we conduct a case study in Alzheimer disease. The complete code can be found in https://github.com/alberto-poncelas/ bioc-alzheimer

Genomotipificación de Camylobacter jejuni mediante microarrays de ADN

354 p. (Bibliogr. 271-303) - Correo electrónico de la autora: andrea.guridi@gmail.com

Phage M13Ko7 Detection With Biosensor Based On Imaging Ellipsometry And Afm Microscopic Confirmation

A rapid detection and identification of pathogens is important for minimizing transfer and spread of disease. A label-free and multiplex biosensor based on imaging ellipsometry (BIE) had been developed for the detection of phage M13KO7. The surface of silicon wafer is modified with aldehyde, and proteins can be patterned homogeneously and simultaneously on the surface of silicon wafer in an array format by a microfluidic system. Avidin is immobilized on the surface for biotin-anti-M13 immobilization by means of interaction between avidin and biotin, which will serve as ligand against phage M13KO7. Phages M13KO7 are specifically captured by the ligand when phage M13KO7 solution passes over the surface, resulting in a significant increase of mass surface concentration of the anti-M13 binding phage M13KO7 layer, which could be detected by imaging ellipsometry with a sensitivity of 10(9) pfu/ml. Moreover, atomic force microscopy is also used to confirm the fact that phage M13KO7 has been directly captured by ligands on the surface. It indicates that BIE is competent for direct detection of phage M13KO7 and has potential in the field of virus detection. (C) 2008 Elsevier B.V. All rights reserved.

Developing A Microfluidic-Based System To Quantify Cell Capture Efficiency

Micro-fabrication technology has substantial potential for identifying molecular markers expressed on the surfaces of tissue cells and viruses. It has been found in several conceptual prototypes that cells with such markers are able to be captured by their antibodies immobilized on microchannel substrates and unbound cells are flushed out by a driven flow. The feasibility and reliability of such a microfluidic-based assay, however, remains to be further tested. In the current work, we developed a microfluidic-based system consisting of a microfluidic chip, an image grabbing unit, data acquisition and analysis software, as well as a supporting base. Specific binding of CD59-expressed or BSA-coupled human red blood cells (RBCs) to anti-CD59 or anti-BSA antibody-immobilized chip surfaces was quantified by capture efficiency and by the fraction of bound cells. Impacts of respective flow rate, cell concentration, antibody concentration and site density were tested systematically. The measured data indicated that the assay was robust. The robustness was further confirmed by capture efficiencies measured from an independent ELISA-based cell binding assay. These results demonstrated that the system developed provided a new platform to effectively quantify cellular surface markers effectively, which promoted the potential applications in both biological studies and clinical diagnoses.

Biomolecule storage on non-modified thermoplastic microfluidic chip by ink-jet printing of ionogels

[EN] This paper reports an innovative technique for reagents storage in microfluidic devices by means of a one-step UV-photoprintable ionogel-based microarray on non-modified polymeric substrates. Although the ionogel and the ink-jet printing technology are well published, this is the first study where both are used for long-term reagent storage in lab-on-a-chip devices. This technology for reagent storage is perfectly compatible with mass production fabrication processes since pre-treatment of the device substrate is not necessary and inkjet printing allows for an efficient reagent deposition process. The functionality of this microarray is demonstrated by testing the release of biotin-647 after being stored for 1 month at room temperature. Analysis of the fluorescence of the ionogel-based microarray that contains biotin-647 demonstrated that 90% of the biotin-647 present was released from the ionogel-based microarray after pumping PBS 0.1% Tween at 37 °C. Moreover, the activity of biotin-647 after being released from the ionogel-based microarray was investigated trough the binding capability of this biotin to a microcontact printed chip surface with avidin. These findings pave the way for a novel, one-step, cheap and mass production on-chip reagents storage method applicable to other reagents such as antibodies and proteins and enzymes.

Altered expression of Alzheimer's disease-related genes in the cerebellum of autistic patients: a model for disrupted brain connectome and therapy

Autism and Alzheimer's disease (AD) are, respectively, neurodevelopmental and degenerative diseases with an increasing epidemiological burden. The AD-associated amyloid-beta precursor protein-alpha has been shown to be elevated in severe autism, leading to the 'anabolic hypothesis' of its etiology. Here we performed a focused microarray analysis of genes belonging to NOTCH and WNT signaling cascades, as well as genes related to AD and apoptosis pathways in cerebellar samples from autistic individuals, to provide further evidence for pathological relevance of these cascades for autism. By using the limma package from R and false discovery rate, we demonstrated that 31% (116 out of 374) of the genes belonging to these pathways displayed significant changes in expression (corrected P-values <0.05), with mitochondria- related genes being the most downregulated. We also found upregulation of GRIN1, the channel-forming subunit of NMDA glutamate receptors, and MAP3K1, known activator of the JNK and ERK pathways with anti-apoptotic effect. Expression of PSEN2 (presinilin 2) and APBB1 (or F65) were significantly lower when compared with control samples. Based on these results, we propose a model of NMDA glutamate receptor-mediated ERK activation of alpha-secretase activity and mitochondrial adaptation to apoptosis that may explain the early brain overgrowth and disruption of synaptic plasticity and connectome in autism. Finally, systems pharmacology analyses of the model that integrates all these genes together (NOWADA) highlighted magnesium (Mg2+) and rapamycin as most efficient drugs to target this network model in silico. Their potential therapeutic application, in the context of autism, is therefore discussed.

Expressão de marcadores imuno-histoquímicos em biópsias renais de pacientes transplantados

A partir da década de 60, com a utilização do transplante renal em larga escala como terapia substitutiva para pacientes com falência do órgão, surgiu a preocupação quanto ao desenvolvimento do processo de rejeição do enxerto. Tal intercorrência, em geral, cursa com sinais e sintomas clínicos apenas quando o evento está bem estabelecido, ou mesmo quando lesões irreversíveis já se instalaram. Assim, é fundamental um acompanhamento rigoroso, visando detectar os casos subclínicos. O presente trabalho, a fim de fornecer novas ferramentas que auxiliem o diagnóstico precoce de rejeição do enxerto, avaliou a expressão imuno-histoquímica dos anticorpos CD3, CD5, CD20, CD68, CD25, FoxP3 e C4d em biópsias renais realizadas entre os anos de 2007 e 2009 em pacientes transplantados acompanhados pelo Serviço de Nefrologia do Hospital Universitário Pedro Ernesto, UERJ - RJ, correlacionando os resultados obtidos com o diagnóstico histológico. Para tal, as biópsias foram reavaliadas por três médicos patologistas que as classificaram, segundo Critérios de Banff 2007, quanto à presença ou não de rejeição do enxerto e seu tipo, aguda ou crônica. A partir de então, os blocos de parafina foram processados pela técnica Tissue Microarray for all (Pires, ARC. e cols.) e submetidos à imuno-histoquímica. A positividade dos marcadores foi avaliada e graduada e os resultados encontrados foram correlacionados, em um primeiro momento, com a presença ou ausência de rejeição. Posteriormente, os casos com diagnóstico histológico de rejeição tiveram seu perfil imuno-histoquímico analisado em função da positividade para C4d, marcador definidor de rejeição humoral. Neste momento, buscou-se averiguar se os anticorpos estudados seriam úteis em detectar, neste grupo, rejeição humoral e celular. Após a análise estatística, realizada pelo Teste Exato de Fisher, pode-se, então, concluir que o comportamento do marcador CD3 é capaz de inferir a presença de rejeição e que os anticorpos CD5 e CD25 permitem sugerir rejeição celular e humoral, respectivamente. Foi observado também que casos sem diagnóstico histológico de rejeição podem apresentar marcação para C4d em mais de 10% de seus capilares peritubulares.

Expressão da leptina e seu receptor no câncer de próstata

O câncer de próstata é o tumor não cutâneo mais comum entre homens e responsável pela segunda maior mortalidade entre os tumores neste sexo. Diferentes métodos são utilizados com o objetivo de determinar o prognóstico do paciente portador de câncer de próstata, contudo existe grande heterogeneidade quando estes são usados individualmente. A leptina é um hormônio peptídico envolvido na regulação da ingestão alimentar, do metabolismo, do gasto energético, além de função neuroendócrina. Este hormônio parece estar envolvido na patogênese de alguns tipos de tumores, inclusive os adenocarcinomas de próstata. Até o presente não se tem certeza se a leptina e seu receptor possam ser utilizados como fatores prognósticos no cancer de próstata. O objetivo do trabalho foi correlacionar os perfis de imunomarcação da leptina e seu receptor em adenocarcinomas de próstata com diferentes fatores prognósticos e comparar as análises de imunomarcação da leptina e seu receptor em adenocarcinomas de próstata por métodos semiquantitativos e quantitativos (morfometria). Foram analisadas 532 peças cirúrgicas de prostatectomias radicais por câncer prostático. A partir destas amostras, após estudo histopatológico, foi montado um arranjo de matriz tecidual, contendo fragmentos de áreas tumorais e não tumorais (peritumorais) destas amostras. Estas foram imunomarcadas com anticorpos antileptina e antirreceptor de leptina. Análises subjetivas (feitas por dois observadores) e objetivas (através da contagem de pontos) foram realizadas em cada uma das imunomarcações. Estes resultados foram comparados e correlacionados com os seguintes fatores prognósticos: invasão perineural, embolização neoplásica vascular, comprometimento bilateral da próstata, invasão das vesículas seminais, comprometimento de margem vesical, de margem uretral e de margem cirúrgica de ressecção. Houve diferença significativa entre as análises subjetivas dos dois observadores e, portanto, estas não foram utilizadas para as demais comparações. Em relação às análises objetivas, foi verificado que a expressão do receptor de leptina estava diminuída nos tumores com comprometimento de margem cirúrgica, de margem uretral e de vesículas seminais. Ainda foi observado correlação entre a expressão desse receptor e o somátório dos fatores prognósticos analisados. Para as demais análises não foi verificada diferença significativa. Métodos semiquantitativos podem ter grande variação e devem ser preteridos em relação a métodos quantitativos para as análises realizadas neste estudo. Nem a leptina nem o seu receptor apresentaram alterações de sua expressão em amostras neoplásicas de próstata quando comparado àquelas não neoplásicas. O receptor de leptina apresentou uma diminuição da sua expressão em tumores com margem cirúrgica comprometida, margem uretral comprometida e com vesículas seminais comprometidas. Houve correlação negativa entre o percentual de área imunomarcada com o anticorpo antirreceptor de leptina e o somatório dos fatores prognósticos analisados.

Serological and Genetic Evidence for Altered Complement System Functionality in Systemic Lupus Erythematosus: Findings of the GAPAID Consortium

Systemic lupus erythematosus is a chronic autoimmune disease with multifactorial ethiopathogenesis. The complement system is involved in both the early and late stages of disease development and organ damage. To better understand autoantibody mediated complement consumption we examined ex vivo immune complex formation on autoantigen arrays. We recruited patients with SLE (n = 211), with other systemic autoimmune diseases (n = 65) and non-autoimmune control subjects (n = 149). Standard clinical and laboratory data were collected and serum complement levels were determined. The genotype of SNP rs1143679 in the ITGAM gene was also determined. Ex vivo formation of immune complexes, with respect to IgM, IgG, complement C4 and C3 binding, was examined using a functional immunoassay on autoantigen microarray comprising nucleic acids, proteins and lipids. Complement consumption of nucleic acids increased upon binding of IgM and IgG even when serum complement levels were decreased due to consumption in SLE patients. A negative correlation between serum complement levels and ex vivo complement deposition on nucleic acid autoantigens is demonstrated. On the contrary, complement deposition on tested protein and lipid autoantigens showed positive correlation with C4 levels. Genetic analysis revealed that the non-synonymous variant rs1143679 in complement receptor type 3 is associated with an increased production of anti-dsDNA IgG antibodies. Notwithstanding, homozygous carriers of the previously reported susceptible allele (AA) had lower levels of dsDNA specific IgM among SLE patients. Both the non-synonymous variant rs1143679 and the high ratio of nucleic acid specific IgG/IgM were associated with multiple organ involvement. In summary, secondary complement deficiency in SLE does not impair opsonization of nucleic-acid-containing autoantigens but does affect other antigens and potentially other complement dependent processes. Dysfunction of the receptor recognizing complement opsonized immune complexes promotes the development of class-switched autoantibodies targeting nucleic acids.

Global analysis of mRNA half-lives and de novo transcription in a dinoflagellate, Karenia brevis

Dinoflagellates possess many physiological processes that appear to be under post-transcriptional control. However, the extent to which their genes are regulated post-transcriptionally remains unresolved. To gain insight into the roles of differential mRNA stability and de novo transcription in dinoflagellates, we biosynthetically labeled RNA with 4-thiouracil to isolate newly transcribed and pre-existing RNA pools in Karenia brevis. These isolated fractions were then used for analysis of global mRNA stability and de novo transcription by hybridization to a K. brevis microarray. Global K. brevis mRNA half-lives were calculated from the ratio of newly transcribed to pre-existing RNA for 7086 array features using the online software HALO (Half-life Organizer). Overall, mRNA half-lives were substantially longer than reported in other organisms studied at the global level, ranging from 42 minutes to greater than 144 h, with a median of 33 hours. Consistent with well-documented trends observed in other organisms, housekeeping processes, including energy metabolism and transport, were significantly enriched in the most highly stable messages. Shorter-lived transcripts included a higher proportion of transcriptional regulation, stress response, and other response/regulatory processes. One such family of proteins involved in post-transcriptional regulation in chloroplasts and mitochondria, the pentatricopeptide repeat (PPR) proteins, had dramatically shorter half-lives when compared to the arrayed transcriptome. As transcript abundances for PPR proteins were previously observed to rapidly increase in response to nutrient addition, we queried the newly synthesized RNA pools at 1 and 4 h following nitrate addition to N-depleted cultures. Transcriptome-wide there was little evidence of increases in the rate of de novo transcription during the first 4 h, relative to that in N-depleted cells, and no evidence for increased PPR protein transcription. These results lend support to the growing consensus of post-transcriptional control of gene expression in dinoflagellates.