{"title":"Active cytoskeletal force and chromatin condensation independently modulate intranuclear network fluctuations.","authors":"Stephen T Spagnol, Kris Noel Dahl","doi":"10.1039/c3ib40226f","DOIUrl":"https://doi.org/10.1039/c3ib40226f","url":null,"abstract":"<p><p>Chromatin remodeling, including the movement of genes and regulatory factors, precedes or accompanies stimulated changes in gene expression. Here we quantify chromatin fluctuations in primary human cells using particle-tracking microrheology and determine the physical mechanisms which influence chromatin reorganization. We find that intranuclear movements are enhanced beyond thermal motion by active force generation from cytoskeletal motor activity propagated through the LINC complex; intranuclear movements are also dependent on the viscoelasticity of the DNA-protein polymer network. Chromatin movements were dramatically altered by modulation of chromatin condensation state, which we independently verified using fluorescence lifetime imaging microscopy (FLIM). These findings suggest that chromatin condensation and cytoskeletal force generation play distinct functional roles in regulating intranuclear movements, and these effects are decoupled as measured by particle tracking. We further utilize this approach in identifying the nuclear responsiveness of primary human endothelial cells to vascular endothelial growth factor (VEGF): early in the response chromatin movements increase and are dominated by cytoskeletal force, which transitions at later times to a chromatin decondensation event. Given the hierarchical genome organization in primary cells, our work generally suggests an important role for force generation and chromatin mechanics in altered gene expression kinetics. </p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"523-31"},"PeriodicalIF":2.5,"publicationDate":"2014-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c3ib40226f","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40301246","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Seyong Kwon, Minseok S Kim, Eun Sook Lee, Jang Sihn Sohn, Je-Kyun Park
{"title":"A quantum dot-based microfluidic multi-window platform for quantifying the biomarkers of breast cancer cells.","authors":"Seyong Kwon, Minseok S Kim, Eun Sook Lee, Jang Sihn Sohn, Je-Kyun Park","doi":"10.1039/c3ib40224j","DOIUrl":"https://doi.org/10.1039/c3ib40224j","url":null,"abstract":"<p><p>Conventional molecular profiling methods using immunochemical assays have limits in terms of multiplexity and the quantification of biomarkers in investigation of cancer cells. In this paper, we demonstrate a quantum dot (QD)-based microfluidic multiple biomarker quantification (QD-MMBQ) method that enables labeling of more than eight proteins immunochemically on cell blocks within 1 h, in a quantitative manner. An internal reference, β-actin, was used as a loading control to compensate for differences in not only the cell number but also in staining quality among specimens. Furthermore, the microfluidic blocking method exhibited less nonspecific binding of QDs than the conventional static blocking method. </p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"430-7"},"PeriodicalIF":2.5,"publicationDate":"2014-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c3ib40224j","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40287200","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Predicting essential genes in prokaryotic genomes using a linear method: ZUPLS.","authors":"Kai Song, Tuopong Tong, Fang Wu","doi":"10.1039/c3ib40241j","DOIUrl":"https://doi.org/10.1039/c3ib40241j","url":null,"abstract":"<p><p>An effective linear method, ZUPLS, was developed to improve the accuracy and speed of prokaryotic essential gene identification. ZUPLS only uses the Z-curve and other sequence-based features. Such features can be calculated readily from the DNA/amino acid sequences. Therefore, no well-studied biological network knowledge is required for using ZUPLS. This significantly simplifies essential gene identification, especially for newly sequenced species. ZUPLS can also select necessary features automatically by embedding the uninformative variable elimination tool into the partial least squares classifier. No optimized modelling parameters are needed. ZUPLS has been used, herein, to predict essential genes of 12 remotely related prokaryotes to test its performance. The cross-organism predictions yielded AUC (Area Under the Curve) scores between 0.8042 and 0.9319 by using E. coli genes as the training samples. Similarly, ZUPLS achieved AUC scores between 0.8111 and 0.9371 by using B. subtilis genes as the training samples. We also compared it with the best available results of the existing approaches for further testing. The improvement of the AUC score in predicting B. subtilis essential genes using E. coli genes was 0.13. Additionally, in predicting E. coli essential genes using P. aeruginosa genes, the significant improvement was 0.10. Similarly, the exceptional improvement of the average accuracy of M. pulmonis using M. genitalium and M. pulmonis genes was 14.7%. The combined superior feature extraction and selection power of ZUPLS enable it to give reliable prediction of essential genes for both Gram-positive/negative organisms and rich/poor culture media. </p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"460-9"},"PeriodicalIF":2.5,"publicationDate":"2014-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c3ib40241j","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40289951","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Laura M McLaughlin, Hui Xu, Sarah E Carden, Samantha Fisher, Monique Reyes, Sarah C Heilshorn, Denise M Monack
{"title":"A microfluidic-based genetic screen to identify microbial virulence factors that inhibit dendritic cell migration.","authors":"Laura M McLaughlin, Hui Xu, Sarah E Carden, Samantha Fisher, Monique Reyes, Sarah C Heilshorn, Denise M Monack","doi":"10.1039/c3ib40177d","DOIUrl":"https://doi.org/10.1039/c3ib40177d","url":null,"abstract":"<p><p>Microbial pathogens are able to modulate host cells and evade the immune system by multiple mechanisms. For example, Salmonella injects effector proteins into host cells and evades the host immune system in part by inhibiting dendritic cell (DC) migration. The identification of microbial factors that modulate normal host functions should lead to the development of new classes of therapeutics that target these pathways. Current screening methods to identify either host or pathogen genes involved in modulating migration towards a chemical signal are limited because they do not employ stable, precisely controlled chemical gradients. Here, we develop a positive selection microfluidic-based genetic screen that allows us to identify Salmonella virulence factors that manipulate DC migration within stable, linear chemokine gradients. Our screen identified 7 Salmonella effectors (SseF, SifA, SspH2, SlrP, PipB2, SpiC and SseI) that inhibit DC chemotaxis toward CCL19. This method is widely applicable for identifying novel microbial factors that influence normal host cell chemotaxis as well as revealing new mammalian genes involved in directed cell migration. </p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"438-49"},"PeriodicalIF":2.5,"publicationDate":"2014-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c3ib40177d","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40287327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"T cells sense biophysical cues using lamellipodia and filopodia to optimize intraluminal path finding.","authors":"Kwang Hoon Song, Keon Woo Kwon, Jong-Cheol Choi, Jaehwang Jung, Yongkeun Park, Kahp-Yang Suh, Junsang Doh","doi":"10.1039/c4ib00021h","DOIUrl":"https://doi.org/10.1039/c4ib00021h","url":null,"abstract":"<p><p>Intraluminal crawling is considered to be important for extravasation of leukocytes in blood vessels, but biochemical/biophysical cues guiding the crawling of leukocytes have not been clearly understood. Here we provide evidence that T cells sense the topography of luminal surfaces and the nuclei of endothelial cells (ECs) using lamellipodia and filopodia, respectively, to optimize path finding during intraluminal crawling. Well-aligned EC layers or replicas of EC layers, which exhibit topography similar to that of EC layers, were fabricated, and flow was applied either parallel or perpendicular to the orientation of EC alignment. T cells crawled along the valleys of the topographical landscapes of the EC layers, while avoiding nuclei of ECs regardless of flow direction. Pharmacological inhibitor treatments revealed that sensing of topography and nuclei of EC layers was mediated by lamellipodia and filopodia, respectively. Lamellipodia or filopodia-inhibited T cells crawled significantly longer distances for extravasation than did normal T cells, indicating that sensing biophysical cues are critical for optimizing routes for extravasation. </p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"450-9"},"PeriodicalIF":2.5,"publicationDate":"2014-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c4ib00021h","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40286573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bano Subia, Sourov Chandra, Sarmistha Talukdar, Subhas C Kundu
{"title":"Folate conjugated silk fibroin nanocarriers for targeted drug delivery.","authors":"Bano Subia, Sourov Chandra, Sarmistha Talukdar, Subhas C Kundu","doi":"10.1039/c3ib40184g","DOIUrl":"https://doi.org/10.1039/c3ib40184g","url":null,"abstract":"<p><p>Disease treatment processes mainly focus on the development of nontoxic, biodegradable, non-immunogenic, biocompatible materials capable of controlled and long-term release of biomolecules. In this work silk protein fibroin from non-mulberry tropical tasar silkworm, Antheraea mylitta, is used to prepare nanoparticles as a drug delivery system. Folate is a vitamin, which is brought into healthy and cancerous cells by folate receptors. The efficiency of silk fibroin-folate nanoparticles loaded with anticancer drug doxorubicin was evaluated by analysing the cell viability, proliferation and endocytosis. Consequently the effects of pro-inflammatory responses by cytokines such as TNF-α, IL-1β and nitric oxide were checked by stimulating the macrophages with folate conjugated silk fibroin nanoparticles. The fibroin-folate nanocarriers are nontoxic, easily taken up by cells and capable of sustained drug release. Nanoparticles loaded with anticancer drug doxorubicin target cancer cells. The results show that silk fibroin-folate nanoparticles may serve as promising nanocarriers for different biomedical and nanotechnology applications in cancer research. </p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"203-14"},"PeriodicalIF":2.5,"publicationDate":"2014-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c3ib40184g","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31961122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bashar Hamza, Elisabeth Wong, Sachin Patel, Hansang Cho, Joseph Martel, Daniel Irimia
{"title":"Retrotaxis of human neutrophils during mechanical confinement inside microfluidic channels.","authors":"Bashar Hamza, Elisabeth Wong, Sachin Patel, Hansang Cho, Joseph Martel, Daniel Irimia","doi":"10.1039/c3ib40175h","DOIUrl":"https://doi.org/10.1039/c3ib40175h","url":null,"abstract":"<p><p>The current paradigm of unidirectional migration of neutrophils from circulation to sites of injury in tissues has been recently challenged by observations in zebrafish showing that neutrophils can return from tissues back into the circulation. However, the relevance of these observations to human neutrophils remains unclear, the forward and reverse migration of neutrophils is difficult to quantify, and the precise conditions modulating the reverse migration cannot be isolated. Here, we designed a microfluidic platform inside which we observed human neutrophil migration in response to chemoattractant sources inside channels, simulating the biochemical and mechanical confinement conditions at sites of injury in tissues. We observed that, after initially following the direction of chemoattractant gradients, more than 90% of human neutrophils can reverse their direction and migrate persistently and for distances longer than one thousand micrometers away from chemoattractant sources (retrotaxis). Retrotaxis is enhanced in the presence of lipoxin A4 (LXA4), a well-established mediator of inflammation resolution, or Tempol, a standard antioxidant. Retrotaxis stops after neutrophils encounter targets which they phagocytise or on surfaces presenting high concentrations of fibronectin. Our microfluidic model suggests a new paradigm for neutrophil accumulation at sites of inflammation, which depends on the balance of three simultaneous processes: chemotaxis along diffusion gradients, retrotaxis following mechanical guides, and stopping triggered by phagocytosis. </p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"175-83"},"PeriodicalIF":2.5,"publicationDate":"2014-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c3ib40175h","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32024304","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xiangdan Jiang, Yu Kang, Xingjie Pan, Jun Yu, Qi Ouyang, Chunxiong Luo
{"title":"Studies of the drug resistance response of sensitive and drug-resistant strains in a microfluidic system.","authors":"Xiangdan Jiang, Yu Kang, Xingjie Pan, Jun Yu, Qi Ouyang, Chunxiong Luo","doi":"10.1039/c3ib40164b","DOIUrl":"https://doi.org/10.1039/c3ib40164b","url":null,"abstract":"Since the discovery of bacterial drug resistance, its dynamics have been the focus in biophysics studies. In this paper, we used a new microfluidic system to monitor the responses of sensitive and drug-resistant strains of E. coli in different β-lactam ceftriaxone concentrations at the single cell level and traced each individual cell's states such as cell length, GFP protein expression and growth rate. The β-lactamase production of the drug-resistant strain is quantified by fluorescence intensity, as the GFP gene co-transcribes with the enzyme expression gene. Our results show that the drug-resistant strain can endure a much higher concentration of antibiotics than the sensitive strain and has an antibiotic concentration ratio from the cell death state to the cell elongation state that is much larger than that of the sensitive strain. The single cell data and simulation suggest that bacteria with slower growth rates have higher drug resistance both in the sensitive and drug-resistant strains. The drug-resistant strain shows adaptation behavior, but no adaptation is found in the sensitive strain after changing to a high antibiotic concentration. A mathematical model of cell growth can qualitatively explain the observed behavior. The quantitative measurement of single-cell phenotype changes and dynamic analysis presented in this study should shed light on the antibiotic process of different bacteria.","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"143-51"},"PeriodicalIF":2.5,"publicationDate":"2014-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c3ib40164b","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32033500","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
George J C Ye, Yvonne Aratyn-Schaus, Alexander P Nesmith, Francesco S Pasqualini, Patrick W Alford, Kevin Kit Parker
{"title":"The contractile strength of vascular smooth muscle myocytes is shape dependent.","authors":"George J C Ye, Yvonne Aratyn-Schaus, Alexander P Nesmith, Francesco S Pasqualini, Patrick W Alford, Kevin Kit Parker","doi":"10.1039/c3ib40230d","DOIUrl":"https://doi.org/10.1039/c3ib40230d","url":null,"abstract":"<p><p>Vascular smooth muscle cells in muscular arteries are more elongated than those in elastic arteries. Previously, we reported changes in the contractility of engineered vascular smooth muscle tissue that appeared to be correlated with the shape of the constituent cells, supporting the commonly held belief that elongated muscle geometry may allow for the better contractile tone modulation required in response to changes in blood flow and pressure. To test this hypothesis more rigorously, we developed an in vitro model by engineering human vascular smooth muscle cells to take on the same shapes as those seen in elastic and muscular arteries and measured their contraction during stimulation with endothelin-1. We found that in the engineered cells, actin alignment and nuclear eccentricity increased as the shape of the cell elongated. Smooth muscle cells with elongated shapes exhibited lower contractile strength but greater percentage increase in contraction after endothelin-1 stimulation. We analysed the relationship between smooth muscle contractility and subcellular architecture and found that changes in contractility were correlated with actin alignment and nuclear shape. These results suggest that elongated smooth muscle cells facilitate muscular artery tone modulation by increasing its dynamic contractile range. </p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"152-63"},"PeriodicalIF":2.5,"publicationDate":"2014-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c3ib40230d","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32013499","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Essential O2-responsive genes of Pseudomonas aeruginosa and their network revealed by integrating dynamic data from inverted conditions.","authors":"Feng Q He, Wei Wang, Ping Zheng, Padhmanand Sudhakar, Jibin Sun, An-Ping Zeng","doi":"10.1039/c3ib40180d","DOIUrl":"https://doi.org/10.1039/c3ib40180d","url":null,"abstract":"<p><p>Identification of the gene network through which Pseudomonas aeruginosa PAO1 (PA) adapts to altered oxygen-availability environments is essential for a better understanding of stress responses and pathogenicity of PA. We performed high-time-resolution (HTR) transcriptome analyses of PA in a continuous cultivation system during the transition from high oxygen tension to low oxygen tension (HLOT) and the reversed transition from low to high oxygen tension (LHOT). From those genes responsive to both transient conditions, we identified 85 essential oxygen-availability responsive genes (EORGs), including the expected ones (arcDABC) encoding enzymes for arginine fermentation. We then constructed the regulatory network for the EORGs of PA by integrating information from binding motif searching, literature and HTR data. Notably, our results show that only the sub-networks controlled by the well-known oxygen-responsive transcription factors show a very high consistency between the inferred network and literature knowledge, e.g. 87.5% and 83.3% of the obtained sub-network controlled by the anaerobic regulator (ANR) and a quorum sensing regulator RhIR, respectively. These results not only reveal stringent EORGs of PA and their transcription regulatory network, but also highlight that achieving a high accuracy of the inferred regulatory network might be feasible only for the apparently affected regulators under the given conditions but not for all the expressed regulators on a genome scale. </p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"215-23"},"PeriodicalIF":2.5,"publicationDate":"2014-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c3ib40180d","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32020819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}