Indole is an inter-species biofilm signal mediated by SdiA

<p>Abstract</p> <p>Background</p> <p>As a stationary phase signal, indole is secreted in large quantities into rich medium by <it>Escherichia coli </it>and has been shown to control several genes (e.g., <it>astD</it>, <it>tnaB</it>, <it>gabT</it>), multi-drug exporters, and the pathogenicity island of <it>E. coli</it>; however, its impact on biofilm formation has not been well-studied.</p> <p>Results</p> <p>Through a series of global transcriptome analyses, confocal microscopy, isogenic mutants, and dual-species biofilms, we show here that indole is a non-toxic signal that controls <it>E. coli </it>biofilms by repressing motility, inducing the sensor of the quorum sensing signal autoinducer-1 (SdiA), and influencing acid resistance (e.g., <it>hdeABD, gadABCEX</it>). Isogenic mutants showed these associated proteins are directly related to biofilm formation (e.g., the <it>sdiA </it>mutation increased biofilm formation 50-fold), and SdiA-mediated transcription was shown to be influenced by indole. The reduction in motility due to indole addition results in the biofilm architecture changing from scattered towers to flat colonies. Additionally, there are 12-fold more <it>E. coli </it>cells in dual-species biofilms grown in the presence of <it>Pseudomonas </it>cells engineered to express toluene <it>o-</it>monooxygenase (TOM, which converts indole to an insoluble indigoid) than in biofilms with pseudomonads that do not express TOM due to a 22-fold reduction in extracellular indole. Also, indole stimulates biofilm formation in pseudomonads. Further evidence that the indole effects are mediated by SdiA and homoserine lactone quorum sensing is that the addition of <it>N</it>-butyryl-, <it>N</it>-hexanoyl-, and <it>N</it>-octanoyl-<it>L</it>-homoserine lactones repress <it>E. coli </it>biofilm formation in the wild-type strain but not with the <it>sdiA </it>mutant.</p> <p>Conclusion</p> <p>Indole is an interspecies signal that decreases <it>E. coli </it>biofilms through SdiA and increases those of pseudomonads. Indole may be manipulated to control biofilm formation by oxygenases of bacteria that do not synthesize it in a dual-species biofilm. Furthermore, <it>E. coli </it>changes its biofilm in response to signals it cannot synthesize (homoserine lactones), and pseudomonads respond to signals they do not synthesize (indole).</p

Integrated modeling and experimental approach for determining transcription factor profiles from fluorescent reporter data

<p>Abstract</p> <p>Background</p> <p>The development of quantitative models of signal transduction, as well as parameter estimation to improve existing models, depends on the ability to obtain quantitative information about various proteins that are part of the signaling pathway. However, commonly-used measurement techniques such as Western blots and mobility shift assays provide only qualitative or semi-quantitative data which cannot be used for estimating parameters. Thus there is a clear need for techniques that enable quantitative determination of signal transduction intermediates.</p> <p>Results</p> <p>This paper presents an integrated modeling and experimental approach for quantitatively determining transcription factor profiles from green fluorescent protein (GFP) reporter data. The technique consists of three steps: (1) creating data sets for green fluorescent reporter systems upon stimulation, (2) analyzing the fluorescence images to determine fluorescence intensity profiles using principal component analysis (PCA) and K-means clustering, and (3) computing the transcription factor concentration from the fluorescence intensity profiles by inverting a model describing transcription, translation, and activation of green fluorescent proteins.</p> <p>We have used this technique to quantitatively characterize activation of the transcription factor NF-κB by the cytokine TNF-α. In addition, we have applied the quantitative NF-κB profiles obtained from our technique to develop a model for TNF-α signal transduction where the parameters were estimated from the obtained data.</p> <p>Conclusion</p> <p>The technique presented here for computing transcription factor profiles from fluorescence microscopy images of reporter cells generated quantitative data on the magnitude and dynamics of NF-κB activation by TNF-α. The obtained results are in good agreement with qualitative descriptions of NF-κB activation as well as semi-quantitative experimental data from the literature. The profiles computed from the experimental data have been used to re-estimate parameters for a NF-κB model and the results of additional experiments are predicted very well by the model with the new parameter values. While the presented approach has been applied to NF-κB and TNF-α signaling, it can be used to determine the profile of any transcription factor as long as GFP reporter fluorescent profiles are available.</p

Keratitis due to Chaetomium sp.

Aim. To describe keratitis due to Chaetomium sp. occurring in a 65-year-old woman who presented with a corneal ulcer with hypopyon of the right eye with a history of trauma by vegetable matter. Method. Multiple scrapings were obtained from the ulcer. A lactophenol cotton blue wet mount and a Gram-stained smear of the scrapings were made. Scrapings were also inoculated onto various culture media. Results. Direct microscopy of corneal scrapings revealed moderate numbers of septate fungal hyphae. Greenish-yellow-coloured fungal colonies with aerial mycelium were observed in culture of the corneal scrapes. On the basis of colony characteristics and conidial structure, the fungal isolate was identified as Chaetomium sp. The patient was treated with topical natamycin (5%) hourly and cyclopentolate 1% drops 3 times a day. After 4 weeks of therapy, the hypopyon had disappeared, the epithelial defect had healed, and the stromal infiltration had almost completely resolved; the visual acuity of the eye improved from hand movements to (1/2)/60. Conclusion. Fungi of the genus Chaetomium, which are rare causes of human disease (systemic mycosis, endocarditis, subcutaneous lesions), may also cause ocular lesions

Parallel screening of FDA-approved antineoplastic drugs for identifying sensitizers of TRAIL-induced apoptosis in cancer cells

<p>Abstract</p> <p>Background</p> <p>Tumor Necrosis Factor-α Related Apoptosis Inducing Ligand (TRAIL) and agonistic antibodies to death receptor 4 and 5 are promising candidates for cancer therapy due to their ability to induce apoptosis selectively in a variety of human cancer cells, while demonstrating little cytotoxicity in normal cells. Although TRAIL and agonistic antibodies to DR4 and DR5 are considered safe and promising candidates in cancer therapy, many malignant cells are resistant to DR-mediated, TRAIL-induced apoptosis. In the current work, we screened a small library of fifty-five FDA and foreign-approved anti-neoplastic drugs in order to identify candidates that sensitized resistant prostate and pancreatic cancer cells to TRAIL-induced apoptosis.</p> <p>Methods</p> <p>FDA-approved drugs were screened for their ability to sensitize TRAIL resistant prostate cancer cells to TRAIL using an MTT assay for cell viability. Analysis of variance was used to identify drugs that exhibited synergy with TRAIL. Drugs demonstrating the highest synergy were selected as leads and tested in different prostate and pancreatic cancer cell lines, and one immortalized human pancreatic epithelial cell line. Sequential and simultaneous dosing modalities were investigated and the annexin V/propidium iodide assay, in concert with fluorescence microscopy, was employed to visualize cells undergoing apoptosis.</p> <p>Results</p> <p>Fourteen drugs were identified as having synergy with TRAIL, including those whose TRAIL sensitization activities were previously unknown in either prostate or pancreatic cancer cells or both. Five leads were tested in additional cancer cell lines of which, doxorubicin, mitoxantrone, and mithramycin demonstrated synergy in all lines. In particular, mitoxantrone and mithramycin demonstrated significant synergy with TRAIL and led to reduction of cancer cell viability at concentrations lower than 1 μM. At these low concentrations, mitoxantrone demonstrated selectivity toward malignant cells over normal pancreatic epithelial cells.</p> <p>Conclusions</p> <p>The identification of a number of FDA-approved drugs as TRAIL sensitizers can expand chemotherapeutic options for combination treatments in prostate and pancreatic cancer diseases.</p

A chalcone synthase-like bacterial protein catalyzes heterocyclic c-ring cleavage of naringenin to alter bioactivity against nuclear receptors in colonic epithelial cells

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Differential Effects of Epinephrine, Norepinephrine, and Indole on Escherichia coli O157:H7 Chemotaxis, Colonization, and Gene Expression

During infection in the gastrointestinal tract, enterohemorrhagic Escherichia coli (EHEC) O157:H7 is exposed to a wide range of signaling molecules, including the eukaryotic hormones epinephrine and norepinephrine, and bacterial signal molecules such as indole. Since these signaling molecules have been shown to be involved in the regulation of phenotypes such as motility and virulence that are crucial for EHEC infections, we hypothesized that these molecules also govern the initial recognition of the large intestine environment and attachment to the host cell surface. Here, we report that, compared to indole, epinephrine and norepinephrine exert divergent effects on EHEC chemotaxis, motility, biofilm formation, gene expression, and colonization of HeLa cells. Using a novel two-fluorophore chemotaxis assay, it was found that EHEC is attracted to epinephrine and norepinephrine while it is repelled by indole. In addition, epinephrine and norepinephrine also increased EHEC motility and biofilm formation while indole attenuated these phenotypes. DNA microarray analysis of surface-associated EHEC indicated that epinephrine/norepinephrine up-regulated the expression of genes involved in surface colonization and virulence while exposure to indole decreased their expression. The gene expression data also suggested that autoinducer 2 uptake was repressed upon exposure to epinephrine/norepinephrine but not indole. In vitro adherence experiments confirmed that epinephrine and norepinephrine increased attachment to epithelial cells while indole decreased adherence. Taken together, these results suggest that epinephrine and norepinephrine increase EHEC infection while indole attenuates the process

Embedding Synthetic Microvascular Networks in Poly(Lactic Acid) Substrates with Rounded Cross-Sections for Cell Culture Applications

Synthetic microvascular networks are essential to enable in vitro studies of cell biology, biophysics, hemodynamics, and drug discovery, as well as in applications involving tissue engineering and artificial vasculature. But current limitations make it challenging to construct networks incorporating a hierarchy of microchannel diameters that possess cell-favored circular cross-sectional topographies. We report a new approach that overcomes these limitations by employing pressure-assisted expansion of biocompatible degradable poly(lactic acid) (PLA) substrates. This single-step process is straightforward and highly controllable, making it possible to simultaneously shape the interior topology of branched 3D and pseudo-3D microchannel networks across wide range of diameters. We further demonstrate in vitro culture of confluent endothelial cell monolayers in microchannel networks treated by this process, suggesting potential as a tool to help generate bio-mimicking vascular-like environments

The role of “omics” technologies for livestock sustainability

Un exitoso programa de seguridad alimentaria de una población en crecimiento necesita una producción más eficiente y sostenible del ganado para asegurar la disponibilidad de alto valor nutritivo, y también la salud y el bienestar de los seres humanos y los animales, y protección del medio ambiente. Innovaciones y avances tecnológicos vendrán de la investigación básica y fundamental. En particular, la integración de la genómica con otros campos de investigación '' OMIC '' y métodos computacionales, posiblemente, facilitar la comprensión de los mecanismos biológicos que son responsables de los atributos físicos o fenotipos de animales. Ejemplos OMIC de diversos métodos y sus aplicaciones se describen para demostrar los avances recientes y cómo estos métodos se pueden aplicar a la producción animal. Los avances en la investigación en genómica y otros campos ómicas se pueden utilizar para aumentar la productividad de los animales, satisfacer la creciente demanda de alimentos de origen animal, aumentar la disponibilidad de nutrientes de alta calidad, garantizar la seguridad alimentaria, mitigar los efectos de la variabilidad climático, y el resultado en nuevas tecnologías que favorezcan un mejor seguridad de los alimentos en todo el mundo.A successful program of food security for a growing population requires the production of livestock in the most efficient and sustainable manner possible to ensure the availability of nutritious foods, the overall health and well-being of humans and animals, and the protection of the environment. Innovative and technological advancements that enhance all aspects of food production will arise from basic, fundamental research. Notably, the integration of genomics with other “’omics” research fields and computational methods will continue to lead to a better understanding of biological mechanisms that are responsible for physical attributes, or phenotypes. Examples of several ‘omics methods and their applications are described to demonstrate recent advances and how these methods can be applied to livestock. Research breakthroughs in genomics and other ‘omics fields can be used to enhance the productivity of food animals, meet the increasing demand for animal-sourced foods, enhance high-quality nutrient availability, ensure nutrient safety, mitigate the effects of climate variability, and result in new technologies that provide continuous improvement in food security worldwide.Um programa bem-sucedido de segurança alimentar para uma população em crescimento necessita de uma produção animal mais eficiente e sustentável para assegurar a disponibilidade de alimentos de alto valor nutricional, e também a saúde e o bem-estar dos humanos e dos animais, e a proteção do ambiente. Inovações e avanços tecnológicos surgirão da pesquisa básica e fundamental. Em especial, a integração da genômica com outros campos de pesquisa ''ômicos '' e com métodos computacionais possivelmente facilitará o entendimento dos mecanismos biológicos que são responsáveis por atributos físicos ou fenótipos dos animais. Exemplos de vários métodos ômicos e suas aplicações são descritos para demonstrar os avanços recentes e como esses métodos podem ser aplicados para produção animal. Os avanços na pesquisa em genômica e em outros campos ômicos podem ser usados para aumentar a produtividade de animais, atender à crescente demanda por alimentos de origem animal, aumentar a disponibilidade de nutrientes de alta qualidade, garantir a segurança nutricional, mitigar os efeitos da variabilidade climática, e resultar em novas tecnologias que favorecem a melhora a segurança alimentar em todo o mundo

Synthetic quorum-sensing circuit to control consortial biofilm formation and dispersal in a microfluidic device

To utilize biofilms for chemical transformations in biorefineries they need to be controlled and replaced. Previously, we engineered the global regulator Hha and cyclic diguanylate-binding BdcA to create proteins that enable biofilm dispersal. Here we report a biofilm circuit that utilizes these two dispersal proteins along with a population-driven quorum-sensing switch. With this synthetic circuit, in a novel microfluidic device, we form an initial colonizer biofilm, introduce a second cell type (dispersers) into this existing biofilm, form a robust dual-species biofilm and displace the initial colonizer cells in the biofilm with an extracellular signal from the disperser cells. We also remove the disperser biofilm with a chemically induced switch, and the consortial population could tune. Therefore, for the first time, cells have been engineered that are able to displace an existing biofilm and then be removed on command allowing one to control consortial biofilm formation for various applications

An optimal multitier resource allocation of cloud RAN in 5G using machine learning

The networks are evolving drastically since last few years in order to meetuser requirements. For example, the 5G is offering most of the available spec-trum under one umbrella. In this work, we will address the resource allocationproblem in fifth-generation (5G) networks, to be exact in the Cloud Radio AccessNetworks (C-RANs). The radio access network mechanisms involve multiplenetwork topologies that are isolated based on the spectrum bands and it shouldbe enhanced with numerous access technology in the deployment of 5G net-work. The C-RAN is one of the optimal technique to combine all the availablespectral bands. However, existing C-RAN mechanisms lacks the intelligence per-spective on choosing the spectral bands. Thus, C-RAN mechanism requires anadvanced tool to identify network topology to allocate the network resources forsubstantial traffic volumes. Therefore, there is a need to propose a frameworkthat handles spectral resources based on user requirements and network behav-ior. In this work, we introduced a new C-RAN architecture modified as multitierHeterogeneous Cloud Radio Access Networks in a 5G environment. This archi-tecture handles spectral resources efficiently. Based on the simulation analysis,the proposed multitier H-CRAN architecture with improved control unit innetwork management perspective enables augmented granularity, end-to-endoptimization, and guaranteed quality of service by 15 percentages over theexisting system