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In JoVE (2)
- Microfluídicos Co-cultura de células epiteliais e bactérias para a Investigação Solúvel sinal mediada por interações
- Um dispositivo micro para Quantificar Quimiotaxia bacteriana em gradientes de concentração estável
Other Publications (45)
- Annual Review of Biomedical Engineering
- Proteomics
- Analytical Chemistry
- Electrophoresis
- Tissue Engineering
- Biotechnology and Bioengineering
- Proteomics
- Biomedical Microdevices
- Biotechnology and Bioengineering
- Biotechnology and Bioengineering
- Lab on a Chip
- Journal of Lipid Research
- Applied and Environmental Microbiology
- BMC Microbiology
- Infection and Immunity
- Foodborne Pathogens and Disease
- FEBS Letters
- Lab on a Chip
- Applied Microbiology and Biotechnology
- Foodborne Pathogens and Disease
- The ISME Journal
- BMC Systems Biology
- Annual Review of Biomedical Engineering
- Proteomics
- Expert Review of Proteomics
- Annals of Biomedical Engineering
- Applied and Environmental Microbiology
- Applied Microbiology and Biotechnology
- Journal of Biomechanical Engineering
- The Journal of Surgical Research
- Tissue Engineering. Part A
- Journal of Proteome Research
- Methods in Molecular Biology (Clifton, N.J.)
- Expert Review of Proteomics
- Proceedings of the National Academy of Sciences of the United States of America
- Lab on a Chip
- Molecular BioSystems
- Journal of Bacteriology
- Nature Protocols
- Journal of Bacteriology
- International Journal of Food Microbiology
- BMC Cancer
- Journal of Proteome Research
- Lab on a Chip
- Nature Communications
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Articles by Arul Jayaraman in JoVE
JoVE General
Microfluídicos Co-cultura de células epiteliais e bactérias para a Investigação Solúvel sinal mediada por interações
1McFerrin Department of Chemical Engineering, Texas A&M University, 2Department of Biomedical Engineering, Texas A&M University
Este protocolo descreve um modelo de co-cultura microfluídicos para a cultura simultânea e localizada de células epiteliais e bactérias. Este modelo pode ser usado para investigar o papel dos diferentes sinais moleculares solúveis na patogênese, bem como tela a eficácia do suposto probiótico cepas bacterianas.
JoVE General
Um dispositivo micro para Quantificar Quimiotaxia bacteriana em gradientes de concentração estável
1McFerrin Department of Chemical Engineering, Texas A&M University, 2Department of Biology, Texas A&M University, 3Department of Biomedical Engineering, Texas A&M University
Este protocolo descreve o desenvolvimento de um dispositivo micro para investigar quimiotaxia bacteriana em gradientes de concentração estável de chemoeffectors.
Other articles by Arul Jayaraman on PubMed
Advances in Proteomic Technologies
Proteomics is a rapidly emerging set of key technologies that are being used to identify proteins and map their interactions in a cellular context. With the sequencing of the human genome, the scope of proteomics has shifted from protein identification and characterization to include protein structure, function and protein-protein interactions. Technologies used in proteomic research include two-dimensional gel electrophoresis, mass spectrometry, yeast two-hybrids screens, and computational prediction programs. While some of these technologies have been in use for a long time, they are currently being applied to study physiology and cellular processes in high-throughput formats. It is the high-throughput approach that defines and characterizes modern proteomics. In this review, we discuss the current status of these experimental and computational technologies relevant to the three major aspects of proteomics-characterization of proteomes, identification of proteins, and determination of protein function. We also briefly discuss the development of new proteomic technologies that are based on recent advances in analytical and biochemical techniques, engineering, microfabrication, and computational prowess. The integration of these advances with established technologies is invaluable for the drive toward a comprehensive understanding of protein structure and function in the cellular milieu.
Dispensable Role for Interferon-gamma in the Burn-induced Acute Phase Response: a Proteomic Analysis
We examined the role of the pleiotropic cytokine interferon-gamma (IFN-gamma) in initiating the burn injury-induced acute phase response (APR). Two-dimensional (2-D) electrophoresis was used to obtain serum protein profiles from wild-type (WT) and IFN-gamma knockout mice following sham-burn or 20% burn injury. Serum 2-D images from both groups of burn-injured mice were characterized by the upregulation of a similar panel of protein spots. These included the three major murine acute phase proteins haptoglobin, serum amyloid A, and serum amyloid P, that were identified by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF)-mass spectrometry. Furthermore, the changes in the levels of these protein spots were very similar between these two groups of mice, as determined by image analysis. Other features of burn-induced APR such as a decrease in total serum protein concentration, an elevated circulation level of the cytokine interleukin-6 (IL-6), and activation of the IL-6 signal transduction protein STAT3 were also evaluated and found to be similar between wild-type and IFN-gamma knockout mice. These results suggest a dispensable role of IFN-gamma in the induction of the hepatic APR in mice following burn injury.
Dynamic Gene Expression Profiling Using a Microfabricated Living Cell Array
We describe the development of a microfluidic platform for continuous monitoring of gene expression in live cells. This optically transparent microfluidic device integrates high-throughput molecular stimulation with nondestructive monitoring of expression events in individual living cells, hence, a living cell array (LCA). Several concentrations of a soluble molecular stimulus are generated in an upstream microfluidic network and used to stimulate downstream reporter cells, each containing a green fluorescence reporter plasmid for a gene of interest. Cellular fluorescence is continuously monitored and quantified to infer the expression dynamics of the gene being studied. We demonstrate this approach by profiling the activation of the transcription factor NF-kappaB in HeLa S3 cells in response to varying doses of the inflammatory cytokine TNF-alpha. The LCA platform offers a unique opportunity to simultaneously control dynamic inputs and measure dynamic outputs from adherent mammalian cells in a high-throughput fashion. This approach to profiling expression dynamics, in conjunction with complementary techniques such as DNA microarrays, will help provide a more complete picture of the dynamic cellular response to diverse soluble stimuli.
A Mouse Serum Two-dimensional Gel Map: Application to Profiling Burn Injury and Infection
With the importance of mouse as a model to study human diseases and the human and rat plasma/serum two-dimensional (2-D) maps being extensively annotated, this study was aimed at constructing a detailed mouse serum 2-D map. Serum proteins from two different inbred strains of mice (BALB/cJ and C57BL/6J) and mice subjected to two different inflammatory stimuli (20% burn injury and lipopolysaccharide (LPS) injection) were separated on overlapping gels covering pH 3-8 and stained with SYPRO Ruby dye. The tryptic peptides from the resolved spots were analyzed by mass spectrometry, leading to the identification of 38 different gene products. With the exception of major urinary proteins found in abundance in male C57BL/6J mice, little strain difference of the mouse serum 2-D was observed. Many proteins detected in the mouse serum 2-D map were not reported in human or rat serum 2-D maps including epidermal growth factor receptor. Three major murine acute-phase proteins (APPs), haptoglobin, serum amyloid A, and serum amyloid P, were highly induced by both inflammatory stimuli. Image analysis shows that the variations of APPs between these two inflammatory models were not uniform although LPS (100 microg/animal) in general was more effective than 20% burn injury in inducing APPs. Serum amyloid A, much more sensitive to endotoxin than burn injury, may represent a sensitive marker to differentiate these two different inflammatory states.
Evaluation of an in Vitro Model of Hepatic Inflammatory Response by Gene Expression Profiling
The body's response to biochemical stress involves coordinated changes in the expression of several sets of genes that regulate its return to homeostasis. Although several cell culture systems have been utilized for studying such complex physiological events in vitro, their assessment has been limited to biochemical assays on individual genes and proteins, limiting interpretation of the results in a systems context. Advances in genomics provide an opportunity to provide a more comprehensive assessment. In this study, we have used DNA microarrays to profile gene expression dynamics during interleukin 6-stimulated inflammation in hepatocytes maintained in a stable, collagen double-gel in vitro model system. The observed expression profile was also compared with that obtained from rat liver tissue after burn injury to determine the extent and nature of responses captured by the in vitro system. Our results indicate that several aspects of the in vivo hepatic inflammatory response can be captured by the in vitro system at the molecular systems level. Statistical analysis of the mRNA profiles was also used to characterize the temporal response in each model system and demonstrate similar behavior. A small panel of molecules involved in the hepatic acute-phase response was also profiled, using quantitative kinetic polymerase chain reaction, to confirm these observations. These results indicate the utility of the stable hepatocyte culture system for expression profiling of inflammatory states and for providing insights into the interplay of changes in gene expression during complex physiological states.
Identification of Neutrophil Gelatinase-associated Lipocalin (NGAL) As a Discriminatory Marker of the Hepatocyte-secreted Protein Response to IL-1beta: a Proteomic Analysis
The liver is the major source of proteins used throughout the body for various functions. Upon injury or infection, an acute phase response (APR) is initiated in the liver that is primarily mediated by inflammatory cytokines such as interleukin-1beta (IL-1beta) and interleukin-6. Among others, the APR is characterized by an altered protein synthetic profile. We used two-dimensional gel electrophoresis to study the dynamics of changes in protein synthesis in hepatocytes exposed to these inflammatory cytokines. Protein profiles were quantified using image analysis and further analyzed using multivariate statistical methods. Our results indicate that IL-1beta and IL-6 each induces secreted protein responses with distinct dynamics and dose-dependence. Parallel stimulation by IL-1beta and IL-6 results in a protein pattern indistinguishable from the IL-1beta pattern, indicating a dominant effect of IL-1beta over IL-6 at the doses tested. Multidimensional scaling (MDS) of correlation distances between protein secretion levels revealed two protein pairs that are robustly co-secreted across the various cytokine stimulation conditions, suggesting shared regulatory pathways. Finally, we also used multivariate alternating conditional expectation (MACE) to identify transformation functions that discriminated the cytokine-stimulated and untreated hepatocyte-secreted protein profiles. Our analysis indicates that the expression of neutrophil gelatinase-associated lipocalin (NGAL) was sufficient to discriminate between IL-1beta and IL-6 stimulation. The combination of proteomics and multivariate analysis is expected to provide new information on the cellular regulatory networks involved in generating specific cellular responses.
Immunodepletion of Albumin for Two-dimensional Gel Detection of New Mouse Acute-phase Protein and Other Plasma Proteins
Immunodepletion of albumin to improve the 2-D gel resolution of human plasma proteins has recently been described. With the importance of mouse models in many studies in which serum or plasma is often analyzed, we have adopted this approach to immunoprecipitate mouse albumin and evaluated its effectiveness for 2-D separation of mouse plasma proteins. Purified polyclonal antibodies against mouse albumin were effective depleting intact albumin as well as its numerous fragments from mouse plasma samples. Removal of albumin resulted in better resolution of mouse plasma proteins. Three proteins, alpha2-macroglobulin, coagulation factor XII, and hemopexin, that were previously either undetectable or poorly resolved, were identified from albumin-depleted 2-D gels by peptide mass fingerprinting. Albumin depletion also led to partial loss of several other proteins such as clusterin and gelsolin. This loss can be attributed to the interaction with albumin itself because the specificity of the antibody was demonstrated by Western blot. When applying this method to the 2-D separation of plasma from inflamed mouse induced by cutaneous burn injury with superimposed Pseudomonas aeruginosa infection, the upregulation of inter alpha-trypsin inhibitor heavy chain 4 (ITIH4) and hemopexin was unambiguously detected along with other mouse acute-phase proteins (APP), including haptoglobin and serum amyloid A. Based on the significant increase of ITIH4, we propose that this protein is a new member of mouse APP that are upregulated during the inflammatory response.
Optimization of Reporter Cells for Expression Profiling in a Microfluidic Device
The emergence of green fluorescence protein (GFP) technologies has enabled non-invasive monitoring of cell function and gene expression. GFP-based expression studies are typically performed in traditional single-dish or multi-well formats to monitor a small number of genes or conditions that do not lend well to scaling, high-throughput analysis, or single-cell measurements. We have recently developed a microfluidic device, the Living Cell Array (LCA), for monitoring GFP-based gene expression in a high-throughput manner. Here, we report the optimization of GFP reporter cell characteristics in this microfluidic device for gene expression profiling. A reporter cell line for the transcription factor NF-kappa B was generated and used as the model cell line. Reporter cells were seeded in the LCA and NF-kappa B activated by addition of the cytokine TNF-alpha . Our studies show that the fluorescence kinetics from the reporter cell line in response to both single and repeated TNF-alpha stimulation in the LCA is similar to that observed in standard tissue culture. In addition, our data also indicate that multiple expression waves can be reliably monitored from a small population of reporter cells. Using reporter cell line subcloning and cell cycle synchronization, we demonstrate that the kinetics and magnitude of induced fluorescence in the reporter cell lines can be further improved to maximize the fluorescence readout from reporter cell lines, thereby improving their applicability to live cell expression profiling. Our studies establish some of the important criteria to be considered when using reporter cell lines for dynamic expression profiling in microfluidic devices.
Modeling Regulatory Mechanisms in IL-6 Signal Transduction in Hepatocytes
Cytokines like interleukin-6 (IL-6) play an important role in triggering the acute phase response of the body to injury or inflammation. Signaling by IL-6 involves two pathways: Janus-associated kinases (JAK) and signal transducers and activators of transcription (STAT 3) are activated in the first pathway while the second pathway involves the activation of mitogen-activated protein kinases (MAPK). While it is recognized that both pathways play a major role in IL-6 signal transduction, a majority of studies have focused on signaling through either one of the pathways. However, simultaneous signaling through both JAK/STAT and MAPK pathways is still poorly understood. In this work, a mathematical model has been developed that integrates signaling through both the JAK/STAT and the MAPK pathway. The presented model is used to analyze the effect of three molecules that are involved in the regulation of IL-6 signaling-SHP-2 (domain containing tyrosine phosphatase 2), SOCS3 (suppressor of cytokine signaling 3), and a STAT3 nuclear phosphatase (PP2)-on the dynamics of IL-6 signal transduction in hepatocytes. The obtained results suggest that interactions between SHP-2 and SOCS3 influence signaling through the JAK/STAT and the MAPK pathways. It is shown that SHP-2 and SOCS3 do not just regulate the pathway that they are known to be associated with, (SHP-2 with MAPK and SOCS3 with JAK/STAT), but also have a strong effect on the other pathway. Several simulations with SOCS3, SHP-2, and PP2 knockout cells, that is, where the signaling pathway is unable to produce these proteins, have been performed to characterize the effect of these regulatory proteins on IL-6 signal transduction in hepatocytes.
Contribution of Gene Expression to Metabolic Fluxes in Hypermetabolic Livers Induced Through Burn Injury and Cecal Ligation and Puncture in Rats
Severe injury activates many stress-related and inflammatory pathways that can lead to a systemic hypermetabolic state. Prior studies using perfused hypermetabolic rat livers have identified intrinsic metabolic flux changes that were not dependent upon the continual presence of elevated stress hormones and substrate loads. We investigated the hypothesis that such changes may be due to persistent alterations in gene expression. A systemic hypermetabolic response was induced in rats by applying a moderate burn injury followed 2 days later by cecum ligation and puncture (CLP) to produce sepsis. Control animals received a sham-burn followed by CLP, or a sham-burn followed by sham-CLP. Two days after CLP, livers were analyzed for gene expression changes using DNA microarrays and for metabolism alterations by ex vivo perfusion coupled with Metabolic Flux Analysis. Burn injury prior to CLP increased fluxes while decreases in gene expression levels were observed. Conversely, CLP alone significantly increased metabolic gene expression, but decreased many of the corresponding metabolic fluxes. Burn injury combined with CLP led to the most dramatic changes, where concurrent changes in fluxes and gene expression levels occurred in about 1/3 of the reactions. The data are consistent with the notion that in this model, burn injury prior to CLP increased fluxes through post-translational mechanisms with little contribution of gene expression, while CLP treatment up-regulated the metabolic machinery by transcriptional mechanisms. Overall, these data show that mRNA changes measured at a single time point by DNA microarray analysis do not reliably predict metabolic flux changes in perfused livers.
A High-throughput Microfluidic Real-time Gene Expression Living Cell Array
The dynamics of gene expression are fundamental to the coordination of cellular responses. Measurement of temporal gene expression patterns is currently limited to destructive low-throughput techniques such as northern blotting, reverse transcription polymerase chain reaction (RT-PCR), and DNA microarrays. We report a scalable experimental platform that combines microfluidic addressability with quantitative live cell imaging of fluorescent protein transcriptional reporters to achieve real-time characterization of gene expression programs in living cells. Integrated microvalve arrays control row-seeding and column-stimulation of 256 nanoliter-scale bioreactors to create a high density matrix of stimulus-response experiments. We demonstrate the approach in the context of hepatic inflammation by acquiring approximately 5000 single-time-point measurements in each automated and unattended experiment. Experiments can be assembled in hours and perform the equivalent of months of conventional experiments. By enabling efficient investigation of dynamic gene expression programs, this technology has the potential to make significant impacts in basic science, drug development, and clinical medicine.
Effects of Forced Uncoupling Protein 1 Expression in 3T3-L1 Cells on Mitochondrial Function and Lipid Metabolism
Obesity-related increase in body fat mass is a risk factor for many diseases, including type 2 diabetes. Controlling adiposity by targeted modulation of adipocyte enzymes could offer an attractive alternative to current dietary approaches. Brown adipose tissue, which is present in rodents but not in adult humans, expresses the mitochondrial uncoupling protein 1 (UCP1) that promotes cellular energy dissipation as heat. Here, we report on the direct metabolic effects of forced UCP1 expression in white adipocytes derived from a murine (3T3-L1) preadipocyte cell line. After stable integration, the ucp1 gene product was continuously expressed during differentiation and reduced the total lipid accumulation by approximately 30% without affecting other adipocyte markers, such as cytosolic glycerol-3-phosphate dehydrogenase activity and leptin production. The expression of UCP1 also decreased glycerol output and increased glucose uptake, lactate output, and the sensitivity of cellular ATP content to nutrient removal. However, oxygen consumption and beta-oxidation were minimally affected. Together, our results suggest that the reduction in intracellular lipid by constitutive expression of UCP1 reflects a downregulation of fat synthesis rather than an upregulation of fatty acid oxidation.
Enterohemorrhagic Escherichia Coli Biofilms Are Inhibited by 7-hydroxyindole and Stimulated by Isatin
Since indole is present at up to 500 microM in the stationary phase and is an interspecies biofilm signal (J. Lee, A. Jayaraman, and T. K. Wood, BMC Microbiol. 7:42, 2007), we investigated hydroxyindoles as biofilm signals and found them also to be nontoxic interspecies biofilm signals for enterohemorrhagic Escherichia coli O157:H7 (EHEC), E. coli K-12, and Pseudomonas aeruginosa. The genetic basis of EHEC biofilm formation was also explored, and notably, virulence genes in biofilm cells were repressed compared to those in planktonic cells. In Luria-Bertani medium (LB) on polystyrene with quiescent conditions, 7-hydroxyindole decreased EHEC biofilm formation 27-fold and decreased K-12 biofilm formation 8-fold without affecting the growth of planktonic cells. 5-Hydroxyindole also decreased biofilm formation 11-fold for EHEC and 6-fold for K-12. In contrast, isatin (indole-2,3-dione) increased biofilm formation fourfold for EHEC, while it had no effect for K-12. When continuous-flow chambers were used, confocal microscopy revealed that EHEC biofilm formation was reduced 6-fold by indole and 10-fold by 7-hydroxyindole in LB. Whole-transcriptome analysis revealed that isatin represses indole synthesis by repressing tnaABC 7- to 37-fold in EHEC, and extracellular indole levels were found to be 20-fold lower. Furthermore, isatin repressed the AI-2 transporters lsrABCDFGKR, while significantly inducing the flagellar genes flgABCDEFGHIJK and fliAEFGILMNOPQ (which led to a 50% increase in motility). 7-Hydroxyindole induces the biofilm inhibitor/stress regulator ycfR and represses cysADIJPU/fliC (which led to a 50% reduction in motility) and purBCDEFHKLMNRT. Isogenic mutants showed that 7-hydroxyindole inhibits E. coli biofilm through cysteine metabolism. 7-Hydroxyindole (500 microM) also stimulates P. aeruginosa PAO1 biofilm formation twofold; therefore, hydroxyindoles are interspecies bacterial signals, and 7-hydroxyindole is a potent EHEC biofilm inhibitor.
Indole is an Inter-species Biofilm Signal Mediated by SdiA
As a stationary phase signal, indole is secreted in large quantities into rich medium by Escherichia coli and has been shown to control several genes (e.g., astD, tnaB, gabT), multi-drug exporters, and the pathogenicity island of E. coli; however, its impact on biofilm formation has not been well-studied.
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.
Proteomic Analysis to Identify the Role of LuxS/AI-2 Mediated Protein Expression in Escherichia Coli O157:H7
Microorganisms employ autoinducer molecules to modulate various bacterial processes including virulence expression, biofilm development, and bioluminescence. The universal autoinducer molecule AI-2 is hypothesized to mediate cell signaling in Escherichia coli O157:H7. We investigated the role of AI-2 on the E. coli O157:H7 cellular proteins using a two-dimensional (2D) gel electrophoresis-based proteomic approach. The protein expression patterns between two experimental comparisons were studied namely, 1) a wild type E. coli O157:H7 and its isogenic luxS mutant, and 2) the luxS mutant and the luxS mutant supplemented with AI-2 molecules. Eleven proteins were differentially expressed between the wild type and the luxS mutant strain, whereas 18 proteins were differentially expressed in the luxS mutant strain when supplemented with AI-2. The tryptophan repressor binding protein (WrbA), phosphoglycerate mutase (GpmA), and a putative protein YbbN were found to be differentially expressed under both experimental comparisons. The FliC protein which is involved in flagellar synthesis and motility was up-regulated in the wild type strain but was not influenced by the addition of synthetic AI-2 molecules to the luxS mutant suggesting the involvement of signaling molecules other than AI-2 on flagellar synthesis and motility.
Effect of Uncoupling Protein-1 Expression on 3T3-L1 Adipocyte Gene Expression
The mitochondrial respiratory uncoupling protein 1 (UCP1) partially uncouples substrate oxidation and oxidative phosphorylation to promote the dissipation of cellular biochemical energy as heat in brown adipose tissue. We have recently shown that expression of UCP1 in 3T3-L1 white adipocytes reduces the accumulation of triglycerides. Here, we investigated the molecular basis underlying UCP1 expression in 3T3-L1 adipocytes. Gene expression data showed that forced UCP1 expression down-regulated several energy metabolism pathways; but ATP levels were constant. A metabolic flux analysis model was used to reflect the gene expression changes onto metabolic processes and concordance was observed in the down-regulation of energy consuming pathways. Our data suggest that adipocytes respond to long-term mitochondrial uncoupling by minimizing ATP utilization.
Microfluidic Flow-encoded Switching for Parallel Control of Dynamic Cellular Microenvironments
The temporal pattern of a biological stimulus is an important determinant of the resulting cellular response. We present a microfluidic parallel perfusion culture system for controlling the dynamics of soluble cell microenvironments while simultaneously performing live-cell imaging of cellular responses. A "Flow-encoded Switching" (FES) design strategy is developed to simultaneously deliver many different temporal profiles of stimuli, including pulse train widths, lengths, and frequencies, to downstream adherent cells using a single input control. The design strategy uses principles of laminar flow and diffusion-limited mixing to encode the state of the network (the instantaneous stimulus concentrations in each channel) into the ratio of two flow rates, which is controlled by a single differential pressure. To demonstrate the utility of this experimental system, we investigated the effect of dynamic stimuli on NFkappaB transcriptional activation and cell fate determination. Our results illustrate that transcriptional responses and cell fate decisions depend both quantitatively and qualitatively on the timing of the stimulus. In summary, by encoding dynamic stimuli in a single input pressure, microfluidic flow-encoded switching offers a scalable experimental method for systematically probing the functional significance of temporally patterned cellular environments.
Temporal Regulation of Enterohemorrhagic Escherichia Coli Virulence Mediated by Autoinducer-2
The autoinducer-2 (AI-2) molecule is produced by many bacterial species, including various human gastrointestinal (GI) tract commensal bacteria, and has been proposed to be involved in interspecies communication. Because pathogens are likely to encounter AI-2 in the GI tract, we studied the effects of AI-2 on various phenotypes associated with enterohemorrhagic Escherichia coli (EHEC) infections. AI-2 attracted EHEC in agarose plug chemotaxis assays and also increased swimming motility, as well as increased EHEC attachment to HeLa cells. The molecular basis underlying the stimulation of EHEC chemotaxis, motility, and colonization by AI-2 was investigated at the transcriptome level using DNA microarrays. We found that exposure to AI-2 altered the expression of 23 locus of enterocyte effacement (LEE) genes directly involved in the production of virulence determinants, as well as other genes associated with virulence (e.g., 46 flagellar/fimbrial genes, 24 iron-related genes), in a temporally defined manner. To our knowledge, this is the first study to report AI-2-mediated regulation of EHEC chemotaxis and colonization, as well as temporal regulation of EHEC transcriptome by AI-2. Our results suggest that AI-2 is an important signal in EHEC infections of the human GI tract.
Autoinducer AI-2 is Involved in Regulating a Variety of Cellular Processes in Salmonella Typhimurium
Salmonella Typhimurium is known to exhibit LuxS/AI-2-mediated cell signaling. We investigated the role of LuxS/AI-2 system on Salmonella Typhimurium protein expression using a proteomics approach based on two-dimensional gel electrophoresis (2DGE)-MALDI-MS. The global protein expression profiles of the wild-type, a luxS mutant, and a luxS mutant strain supplemented with AI-2 were compared. Seven proteins were differentially expressed when comparing the wild-type and luxS mutant strains, whereas 13 proteins were differentially expressed when comparisons were made between luxS mutant strains with and without AI-2 supplementation. The seven proteins that were differentially expressed between the wild-type and the luxS mutant strain were also differentially expressed in the luxS mutant strain supplemented with AI-2. The level of PhoP, a virulence determinant, was higher in the presence of AI-2. Proteins associated with the carbohydrate metabolism (pfkA, gpmI, and talB) and ATP synthesis (Pta gene product) were up-regulated by the presence of AI-2 molecules. These results provide experimental evidence that AI-2 molecules regulate a variety of cellular processes in Salmonella Typhimurium.
Indole Cell Signaling Occurs Primarily at Low Temperatures in Escherichia Coli
We have shown that the quorum-sensing signals acylhomoserine lactones, autoinducer-2 (AI-2) and indole influence the biofilm formation of Escherichia coli. Here, we investigate how the environment, that is, temperature, affects indole and AI-2 signaling in E. coli. We show in biofilms that indole addition leads to more extensive differential gene expression at 30 degrees C (186 genes) than at 37 degrees C (59 genes), that indole reduces biofilm formation (without affecting growth) more significantly at 25 and 30 degrees C than at 37 degrees C and that the effect is associated with the quorum-sensing protein SdiA. The addition of indole at 30 degrees C compared to 37 degrees C most significantly repressed genes involved in uridine monophosphate (UMP) biosynthesis (carAB, pyrLBI, pyrC, pyrD, pyrF and upp) and uracil transport (uraA). These uracil-related genes are also repressed at 30 degrees C by SdiA, which confirms SdiA is involved in indole signaling. Also, compared to 37 degrees C, indole more significantly decreased flagella-related qseB, flhD and fliA promoter activity, enhanced antibiotic resistance and inhibited cell division at 30 degrees C. In contrast to indole and SdiA, the addition of (S)-4,5-dihydroxy-2,3-pentanedione (the AI-2 precursor) leads to more extensive differential gene expression at 37 degrees C (63 genes) than at 30 degrees C (11 genes), and, rather than repressing UMP synthesis genes, AI-2 induces them at 37 degrees C (but not at 30 degrees C). Also, the addition of AI-2 induces the transcription of virulence genes in enterohemorrhagic E. coli O157:H7 at 37 degrees C but not at 30 degrees C. Hence, cell signals cause diverse responses at different temperatures, and indole- and AI-2-based signaling are intertwined.
Integrated Modeling and Experimental Approach for Determining Transcription Factor Profiles from Fluorescent Reporter Data
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.
Bacterial Quorum Sensing: Signals, Circuits, and Implications for Biofilms and Disease
Communication between bacteria, belonging to the same species or to different species, is mediated through different chemical signals that are synthesized and secreted by bacteria. These signals can either be cell-density related (autoinducers) or be produced by bacteria at different stages of growth, and they allow bacteria to monitor their environment and alter gene expression to derive a competitive advantage. The properties of these signals and the response elicited by them are important in ensuring bacterial survival and propagation in natural environments (e.g., human oral cavity) where hundreds of bacterial species coexist. First, the interaction between a signal and its receptor is very specific, which underlies intraspecies communication and quorum sensing. Second, when multiple signals are synthesized by the same bacterium, the signaling circuits utilized by the different signals are coordinately regulated with distinct overall circuit architecture so as to maximize the overall response. Third, the recognition of a universal communication signal synthesized by different bacterial species (interspecies communication), as well that of signals produced by eukaryotic cells (interkingdom communication), is also integral to the formation of multispecies biofilm communities that are important in infection and disease. The focus of this review is on the principles underlying signal-mediated bacterial communication, with specific emphasis on the potential for using them in two applications-development of synthetic biology modules and circuits, and the control of biofilm formation and infection.
Identification of Proteins to Predict the Molecular Basis for the Observed Gender Susceptibility in a Rat Model of Alcoholic Steatohepatitis by 2-D Gel Proteomics
Females are reported to be highly susceptible to alcoholic steatohepatitis (ASH) compared to the males. Although a variety of mechanisms have been proposed to explain this higher sensitivity of females, the precise mechanism is not well understood. The objective of this study was to identify changes in global protein expression in liver tissues of male and female rats with pathologically evident ASH by 2-DE (dimensional electrophoresis). ASH was induced in the SD (Sprague-Dawley) rats by feeding ethanol (EtOH) containing Lieber-DeCarli diet for 6 wk followed by a single injection of lipopolysaccharide (LPS, 10 mg/kg, i.p.). Higher liver injury in females in the ASH group as compared to the males was confirmed by HE stained liver sections. As identified by 2-DE, 22 protein-spots were differentially expressed in the females in the ASH group as compared to the males. Following identification of these proteins by MALDI-MS, they were mainly categorized into metabolism and oxidative stress-related proteins. The expression pattern of a few of these oxidative stress-related proteins like Ferritin Heavy chain (Ferritin-H chain), ER stress protein 60 (ER 60) and Heat-shock protein-60 (HSP 60) were verified by Western blotting. To conclude, the current study has identified a set of proteins that highlights potential novel mechanisms associated with higher liver injury noted in the female rat ASH model.
Proteomics: Technology Development and Applications
Technology development in, and the application of, proteomics are emerging areas among chemical engineers and others who presented at the 2008 American Institute of Chemical Engineers (AIChE) Annual Meeting. Overall, the centennial meeting offered a broad current perspective on the discipline of chemical engineering as it enters its second century. Biomedical and biochemical engineering continue to grow as important facets of the discipline. Within these, the value and applicability of proteomics were demonstrated in a number of interesting presentations. This year, as in the recent past, the AIChE Annual Meeting was held in conjunction with the American Electrophoresis Society Annual Meeting. American Electrophoresis Society presenters offered further academic and industrial viewpoints on the still-developing role of proteomics and proteomic technologies in biological and clinical analyses.
Modeling Growth and Quorum Sensing in Biofilms Grown in Microfluidic Chambers
Biofilms are highly organized structures coordinately formed by multiple species of bacteria. Quorum sensing (QS) is one cell-cell communication mechanism that is used by bacteria during biofilm formation. Biofilm formation is widely acknowledged to occur through a sequence of spatially and temporally regulated colonization events. While several mathematical models exist for describing biofilm development, these have been developed for open systems and are not applicable to closed systems where biofilm development and hydrodynamics are interlinked. Here, we report the development of a mathematical model describing QS and biofilm formation in a closed system such as a microfluidic channel. The model takes into account the effect of the external environment viz the mass and momentum transport in the microfluidic channel on QS and biofilm development. Model predictions of biofilm thickness were verified experimentally by developing Pseudomonas aeruginosa PA14 biofilms in microfluidic chambers and reflect the interplay between the dynamics of biofilm community development, mass transport, and hydrodynamics. Our QS model is expected to guide the design of experiments in closed systems to address spatio-temporal aspects of QS in biofilm development and can lead to novel approaches for controlling biofilm formation through disruption of QS spatio-temporal dynamics.
Flow-based Microfluidic Device for Quantifying Bacterial Chemotaxis in Stable, Competing Gradients
Chemotaxis is the migration of cells in gradients of chemoeffector molecules. Although multiple, competing gradients must often coexist in nature, conventional approaches for investigating bacterial chemotaxis are suboptimal for quantifying migration in response to gradients of multiple signals. In this work, we developed a microfluidic device for generating precise and stable gradients of signaling molecules. We used the device to investigate the effects of individual and combined chemoeffector gradients on Escherichia coli chemotaxis. Laminar flow-based diffusive mixing was used to generate gradients, and the chemotactic responses of cells expressing green fluorescent protein were determined using fluorescence microscopy. Quantification of the migration profiles indicated that E. coli was attracted to the quorum-sensing molecule autoinducer-2 (AI-2) but was repelled from the stationary-phase signal indole. Cells also migrated toward higher concentrations of isatin (indole-2,3-dione), an oxidized derivative of indole. Attraction to AI-2 overcame repulsion by indole in equal, competing gradients. Our data suggest that concentration-dependent interactions between attractant and repellent signals may be important determinants of bacterial colonization of the gut.
The Neuroendocrine Hormone Norepinephrine Increases Pseudomonas Aeruginosa PA14 Virulence Through the Las Quorum-sensing Pathway
It has been proposed that the gastrointestinal tract environment containing high levels of neuroendocrine hormones is important for gut-derived Pseudomonas aeruginosa infections. In this study, we report that the hormone norepinephrine increases P. aeruginosa PA14 growth, virulence factor production, invasion of HCT-8 epithelial cells, and swimming motility in a concentration-dependent manner. Transcriptome analysis of P. aeruginosa exposed to 500 microM, but not 50 microM, norepinephrine for 7 h showed that genes involved in the regulation of the virulence determinants pyocyanin, elastase, and the Pseudomonas quinolone signal (PQS, 2-heptyl-3-hydroxy-4-quinolone) were upregulated. The production of rhamnolipids, which are also important in P. aeruginosa infections, was not significantly altered in suspension cultures upon exposure to 500 microM norepinephrine but decreased on semisolid surfaces. Swarming motility, a phenotype that is directly influenced by rhamnolipids, was also decreased upon 500 microM norepinephrine exposure. The increase in the transcriptional activation of lasR but not that of rhlR and the increase in the levels of PQS suggest that the effects of norepinephrine are mediated primarily through the las quorum-sensing pathway. Together, our data strongly suggest that norepinephrine can play an important role in gut-derived infections by increasing the pathogenicity of P. aeruginosa PA14.
Dynamic Effect of Heat Shock Pretreatment on Apoptotic Responses to TNF-alpha in Liver Cells
The heat shock (HS) response is a protective mechanism for cells to protect themselves against subsequent lethal stress. HS upregulated heat shock protein (HSP) expression reduced apoptosis following tumor necrosis factor-alpha (TNF-alpha) stimulation. However, vector-mediated overexpression of HSP70 failed to provide similar protection but rather sensitized cells to TNF-alpha induced apoptosis. This may be due to the fact that the kinetics of vector-mediated HSP overexpression is totally different from that of HSP upregulation by HS. We hypothesized that the response depends on the timing of TNF-alpha challenge relative to HSP expression dynamics after HS. Therefore, we investigated the correlation between the dynamic change of HSP expression and the levels of apoptosis induced by TNF-alpha after HS. Hepatoma cells were subjected to mild heat shock at 42 degrees C for 2 h followed by varied recovery times and then treated with TNF-alpha to induce apoptosis. The results from quantitative apoptosis assays using the TUNEL reaction reveal an optimal HS protection window centered around 5 h post-HS against TNF-alpha induced apoptosis. In addition, we found a window extending up to 2 h after HS where HS sensitized cells to TNF-alpha stress. Importantly, the correlation between apoptosis and HSP expression kinetics demonstrates that both high levels of HSPs and proper timing between HS and TNF-alpha stress were critical for optimal protection. Our study establishes a dynamic experimental model for further investigation of HS as a potential clinical approach to target tissue survival or death.
Gene Expression Profiling of Long-term Changes in Rat Liver Following Burn Injury
The inflammatory response initiated upon burn injury is also associated with extensive metabolic adjustments. While there is a significant body of literature on the characterization of these changes at the metabolite level, little is known on the mechanisms of induction, especially with respect to the role of gene expression. We have comprehensively analyzed changes in gene expression in rat livers during the first 7 d after 20% total body surface area burn injury using Affymetrix microarrays. A total of 740 genes were significantly altered in expression at 1, 2, 4, and 7 d after burn injury compared to sham-burn controls. Functional classification based on gene ontology terms indicated that metabolism, transport, signaling, and defense/inflammation response accounted for more than 70% of the significantly altered genes. Fisher least-significant difference post-hoc testing of the 740 differentially expressed genes indicated that over 60% of the genes demonstrated significant changes in expression either on d 1 or on d 7 postburn. The gene expression trends were corroborated by biochemical measurements of triglycerides and fatty acids 24 h postburn but not at later time points. This suggests that fatty acids are used, at least in part, in the liver as energy substrates for the first 4 d after injury. Our data also suggest that long-term regulation of energy substrate utilization in the liver following burn injury is primarily at the posttranscriptional level. Last, relevance networks of significantly expressed genes indicate the involvement of key small molecules in the hepatic response to 20% total body surface area burn injury.
Enhanced Proliferation of Human Umbilical Vein Endothelial Cells and Differentiation of 3T3-L1 Adipocytes in Coculture
The interactions between adipocytes and endothelial cells in adipose tissue development are poorly understood. In this study, we characterized the growth and differentiation of 3T3-L1 preadipocytes and human umbilical vein endothelial cells (HUVECs) in planar and collagen gel cocultures. In planar coculture, preadipocyte proliferation was up to three times as great as in the control culture with only preadipocytes, where the increase was proportional to the HUVEC fraction in the seeding mixture. In the collagen gel coculture, triglyceride (TG) content (per adipocyte) was up to 3.4 times as much as in the control with only adipocytes. This effect depended on the total density and composition of the seeding mixture, with the largest increase observed at the highest density (2 x 10(6) cells/mL collagen) and preadipocyte:HUVEC ratio (90:10) tested in this study. Immunostaining showed that the collagen gel coculture also supported the elongation of endothelial cells. Blockade of vascular endothelial growth factor receptor 2 (VEGFR2) abolished the adipogenesis- and neovascularization-related effects of the coculture. Taken together, our results indicate that endothelial cell-mediated enhancement of adipocyte differentiation requires the activation of VEGFR2.
Liver Proteome Analysis in a Rodent Model of Alcoholic Steatosis
Alcoholic steatosis (AS) is the initial pathology associated with early stage alcoholic liver disease (ALD) and is characterized by the accumulation of fat in the liver. AS is considered clinically benign because it is reversible, and the progression of AS to alcoholic steatohepatitis (ASH) is a key step in the development of ALD. A two-dimensional gel electrophoresis (2DE)-mass spectrometry (MS) proteomic approach was used to investigate the protein expression pattern underlying AS, as the first step toward determining liver tissue biomarkers for early stage ALD. Several proteins involved in fatty acid and amino acid metabolism were up-regulated in 3- and 6-week ethanol-fed rats relative to isocaloric controls, which suggest a higher energy demand upon chronic exposure to ethanol. In addition, the expression of two proteins associated with alcohol-induced oxidative stress, peroxiredoxin 6 (PRDX6) and aldehyde dehydrogenase 2 (ALDH2), was down-regulated in ethanol fed rats, and suggests an increase in reactive oxygen species and oxidative stress. To investigate if irreversible protein modification arising from oxidative stress during AS impacts protein levels, the extent of carbonylated proteins in the ethanol and isocaloric groups was identified using mass spectrometry. The detection of modified proteins involved in antioxidant functions further supports the notion that oxidative modification of these proteins leads to protein turnover during AS. In addition, the carbonylation of betaine-homocysteine S-methyltransferase, a protein implicated in fatty liver development, in 3-week and 6-week ethanol exposed samples suggests that this protein could be a marker for early stage AS.
Microfluidic Techniques for the Analysis of Bacterial Chemotaxis
Anton van Leeuwenhoek first observed bacterial motility in the seventeenth century, and Wilhelm Pfeffer described bacterial chemotaxis in the late nineteenth century. A number of methods, briefly summarized here, have been developed over the years to quantify the motility and chemotaxis of bacteria, but none of them is totally satisfactory. In this chapter, we describe two new assays for chemotaxis that are based on microfabrication and microfluidic techniques. With easily culturable and manipulated bacteria like Escherichia coli, fluorescent labeling of the cells with green fluorescent protein (GFP) or red fluorescent protein (RFP) provides a convenient method for visualizing cells and differentiating two strains in the same experiment. The methods can be extended to environmental samples and mixed bacterial populations with suitable modifications of the optical recording system. The methods are equally useful for studying random motility, attractant chemotaxis, or repellent chemotaxis. The microfluidic system also provides a straightforward way to enrich for mutants that lose or gain responses to individual chemicals. The same approaches can presumably be used to isolate bacteria from environmental samples that respond, or do not respond, to particular chemicals or mixtures of chemicals.
Emerging Affinity-based Techniques in Proteomics
Proteomes of interest, such as the human proteome, have such complexity that no single technique is adequate for the complete analysis of the constituents. Depending on the goal (e.g., identification of a novel protein vs measurement of the level of a known protein), the tools required can vary significantly. While existing methods provide valuable information, their limitations drive the development of complementary, innovative methods to achieve greater breadth of coverage, dynamic range or specificity of analysis. We will discuss affinity-based methods and their applications, focusing on their unique advantages. In addition, we will describe emerging methods with potential value to proteomics, as well as the challenges that remain for proteomic studies.
The Bacterial Signal Indole Increases Epithelial-cell Tight-junction Resistance and Attenuates Indicators of Inflammation
Interkingdom signaling is established in the gastrointestinal tract in that human hormones trigger responses in bacteria; here, we show that the corollary is true, that a specific bacterial signal, indole, is recognized as a beneficial signal in intestinal epithelial cells. Our prior work has shown that indole, secreted by commensal Escherichia coli and detected in human feces, reduces pathogenic E. coli chemotaxis, motility, and attachment to epithelial cells. However, the effect of indole on intestinal epithelial cells is not known. Because intestinal epithelial cells are likely to be exposed continuously to indole, we hypothesized that indole may be beneficial for these cells, and investigated changes in gene expression with the human enterocyte cell line HCT-8 upon exposure to indole. Exposure to physiologically relevant amounts of indole increased expression of genes involved in strengthening the mucosal barrier and mucin production, which were consistent with an increase in the transepithelial resistance of HCT-8 cells. Indole also decreased TNF-alpha-mediated activation of NF-kappaB, expression of the proinflammatory chemokine IL-8, and the attachment of pathogenic E. coli to HCT-8 cells, as well as increased expression of the antiinflammatory cytokine IL-10. The changes in transepithelial resistance and NF-kappaB activation were specific to indole: other indole-like molecules did not elicit a similar response. Our results are similar to those observed with probiotic strains and suggest that indole could be important in the intestinal epithelial cells response to gastrointestinal tract pathogens.
Co-culture of Epithelial Cells and Bacteria for Investigating Host-pathogen Interactions
The human gastrointestinal (GI) tract is a unique environment in which intestinal epithelial cells and non-pathogenic (commensal) bacteria co-exist. This equilibrium is perturbed by the entry of pathogens into the GI tract. A key step in the infection process is the navigation of the pathogen through the commensal bacterial layer to attach to epithelial cells. It has been proposed that the microenvironment that the pathogen encounters in the commensal layer plays a significant role in determining the extent of attachment and colonization. Current culture methods for investigating pathogen colonization are not well suited for investigating this hypothesis as they do not enable co-culture of bacteria and epithelial cells in a manner that mimics the GI tract microenvironment. Here we report the development of a microfluidic co-culture model that enables independent culture of eukaryotic cells and bacteria, and testing the effect of the commensal microenvironment on pathogen colonization. A pneumatically-actuated system was developed to form reversible islands that allow development of bacterial biofilm along with culture of an epithelial cell monolayer. The co-culture model used to develop a commensal Escherichia coli biofilm among HeLa cells, followed by introduction of enterohemorrhagic E. coli (EHEC) into the commensal island, in a sequence that mimics the sequence of events in GI tract infection. Using wild-type E. coli and a tnaA mutant (lacks the signal indole) as the commensal bacteria, we demonstrate that the commensal biofilm microenvironment is a key determinant of EHEC infectivity and virulence. Our model has the potential to be used in fundamental studies investigating the effect of GI tract signals on EHEC virulence as well as for screening of different probiotic strains for modulating pathogen infectivity in the GI tract.
Using the Tet-On System to Develop a Procedure for Extracting Transcription Factor Activation Dynamics
The regulation of gene expression by transcription factors through different expression and activation dynamics is an important aspect of genomics and systems biology. Reporter systems using green fluorescent protein (GFP) or luciferase are often used to infer transcription factor dynamics. We recently used an inverse problem solution of GFP reporter profiles to demonstrate that the activation dynamics of a model transcription actor (NF-kappaB) can be reconstructed from GFP data. This approach assumes that the general nature of the transcription factor dynamics is known; however, it is non-trivial to determine the exact nature of the transcription factor dynamics as it often depends upon the cell type and the stimulus used to activate the transcription factor. This, in turn, limits the determination of accurate transcription factor dynamics from reporter data, especially since the model used for solution of an inverse problem needs to be verified. To address this point, we developed a reporter cell line for expressing GFP using an inducible, artificial transcription factor (tTA) and minimal promoter system. The artificial transcription factor can be activated independent of the cellular regulatory machinery through addition of doxycycline. This allows us to directly control the dynamics of the artificial transcription factor, and thereby, develop a model describing its activation dynamics from reporter data. Our experimental data and model predictions are in good agreement, and illustrate the utility of our approach. Future work will focus on using the developed approach, i.e. solution of an inverse problem involving the model describing expression of GFP, to extract the dynamics of transcription factors that are currently uncharacterized.
Repellent Taxis in Response to Nickel Ion Requires Neither Ni2+ Transport nor the Periplasmic NikA Binding Protein
Ni(2+) and Co(2+) are sensed as repellents by the Escherichia coli Tar chemoreceptor. The periplasmic Ni(2+) binding protein, NikA, has been suggested to sense Ni(2+). We show here that neither NikA nor the membrane-bound NikB and NikC proteins of the Ni(2+) transport system are required for repellent taxis in response to Ni(2+).
Investigation of Bacterial Chemotaxis in Flow-based Microfluidic Devices
The plug-in-pond and capillary assays are convenient methods for measuring attractant and repellent bacterial chemotaxis. However, these assays do not provide quantitative information on the extent of migration and are not well-suited for investigating repellent taxis. Here, we describe a protocol for a flow-based microfluidic system (microFlow) to quantitatively investigate chemotaxis in response to concentration gradients of attractants and repellents. The microFlow device uses diffusive mixing to generate concentration gradients that are stable throughout the chemotaxis chamber and for the duration of the experiment. The gradients may be of any desired absolute concentration and gradient strength. GFP-expressing bacteria immediately encounter a stable concentration gradient when they enter the chemotaxis chamber, and the migration in response to the gradient is monitored by microscopy. The effects of different parameters that influence the extent of migration in the microFlow device-preparation of the motile bacterial population preparation, strength of the concentration gradient and duration of exposure to the gradient-are discussed in the context of repellent taxis of chemotactically wild-type Escherichia coli cells in a gradient of NiSO(4). Fabrication of the microfluidic device takes 1 d while preparing motile cells and carrying out the chemotaxis experiment takes 4-6 h to complete.
Chemotaxis to the Quorum-sensing Signal AI-2 Requires the Tsr Chemoreceptor and the Periplasmic LsrB AI-2-binding Protein
AI-2 is an autoinducer made by many bacteria. LsrB binds AI-2 in the periplasm, and Tsr is the l-serine chemoreceptor. We show that AI-2 strongly attracts Escherichia coli. Both LsrB and Tsr are necessary for sensing AI-2, but AI-2 uptake is not, suggesting that LsrB and Tsr interact directly in the periplasm.
Citrus Flavonoid Represses Salmonella Pathogenicity Island 1 and Motility in S. Typhimurium LT2
Salmonellosis is one of the leading health problems worldwide. With the rise of drug resistance strains, it has become imperative to identify alternative strategies to counter bacterial infection. Natural products were used historically to identify novel compounds with various bioactivities. Citrus species is a rich source of flavonoids. Naringenin, a flavonone, is present predominantly in grapefruit. Previously we have demonstrated that naringenin is potent inhibitor of cell-cell signaling. The current study was undertaken to understand the effect of naringenin on Salmonella Typhimurium LT2. The cDNA microarrays were employed to study the response of S. Typhimurium to naringenin treatment. Naringenin specifically repressed 24 genes in the Salmonella pathogenicity island 1 and down-regulated 17 genes involved in flagellar and motility. Furthermore, phenotypic assays support the result of microarray analysis. In addition, naringenin seems to repress SPI-1 in pstS/hilD-dependent manner. Altogether the data suggest that naringenin attenuated S. Typhimurium virulence and cell motility. This is the first molecular evidence to demonstrate effect of naringenin on bacterial virulence and cell motility.
Parallel Screening of FDA-approved Antineoplastic Drugs for Identifying Sensitizers of TRAIL-induced Apoptosis in Cancer Cells
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.
Proteomic Analysis of 3T3-L1 Adipocyte Mitochondria During Differentiation and Enlargement
The increase in adipose tissue mass arises in part from progressive lipid loading and triglyceride accumulation in adipocytes. Enlarged adipocytes produce the highest levels of pro-inflammatory molecules and reactive oxygen species (ROS). Since mitochondria are the site for major metabolic processes (e.g., TCA cycle) that govern the extent of triglyceride accumulation as well as the primary site of ROS generation, we quantitatively investigated changes in the adipocyte mitochondrial proteome during different stages of differentiation and enlargement. Mitochondrial proteins from 3T3-L1 adipocytes at different stages of lipid accumulation (days 0-18) were digested and labeled using the iTRAQ 8-plex kit. The labeled peptides were fractionated using a liquid phase isoelectric fractionation system (MSWIFT) to increase the depth of proteome coverage and analyzed using LC-MS/MS. A total of 631 proteins in the mitochondrial fraction, including endoplasmic reticulum-associated and golgi-related mitochondrial proteins, were identified and classified into 12 functional categories. A total of 123 proteins demonstrated a statistically significant change in expression in at least one of the time points over the course of the experiment. The identified proteins included enzymes and transporters involved in the TCA cycle, fatty acid oxidation, and ATP synthesis. Our results indicate that cultured adipocytes enter a state of metabolic-overdrive where increased flux through the TCA cycle and increased fatty acid oxidation occur simultaneously. The proteomic data also suggest that accumulation of reduced electron carriers and the resultant oxidative stress may be attractive targets for modulating adipocyte function in metabolic disorders.
A Microfluidic Device for High Throughput Bacterial Biofilm Studies
Bacteria are almost always found in ecological niches as matrix-encased, surface-associated, multi-species communities known as biofilms. It is well established that soluble chemical signals produced by the bacteria influence the organization and structure of the biofilm; therefore, there is significant interest in understanding how different chemical signals are coordinately utilized for community development. Conventional methods for investigating biofilm formation such as macro-scale flow cells are low-throughput, require large volumes, and do not allow spatial and temporal control of biofilm community formation. Here, we describe the development of a PDMS-based two-layer microfluidic flow cell (μFC) device for investigating bacterial biofilm formation and organization in response to different concentrations of soluble signals. The μFC device contains eight separate microchambers for cultivating biofilms exposed to eight different concentrations of signals through a single diffusive mixing-based concentration gradient generator. The presence of pneumatic valves and a separate cell seeding port that is independent from gradient-mixing channels offers complete isolation of the biofilm microchamber from the gradient mixer, and also performs well under continuous, batch or semi-batch conditions. We demonstrate the utility of the μFC by studying the effect of different concentrations of indole-like biofilm signals (7-hydroxyindole and isatin), either individually or in combination, on biofilm development of pathogenic E. coli. This model can be used for developing a fundamental understanding of events leading to bacterial attachment to surfaces that are important in infections and chemicals that influence the biofilm formation or inhibition.
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.
