Integrative biology : quantitative biosciences from nano to macro最新文献

{"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}

{"title":"The contractile strength of vascular smooth muscle myocytes is shape dependent.","authors":"George J C Ye,&nbsp;Yvonne Aratyn-Schaus,&nbsp;Alexander P Nesmith,&nbsp;Francesco S Pasqualini,&nbsp;Patrick W Alford,&nbsp;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,&nbsp;Wei Wang,&nbsp;Ping Zheng,&nbsp;Padhmanand Sudhakar,&nbsp;Jibin Sun,&nbsp;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}

{"title":"Bacterial nucleoid structure probed by active drag and resistive pulse sensing.","authors":"Vivek V Thacker,&nbsp;Krystyna Bromek,&nbsp;Benoit Meijer,&nbsp;Jurij Kotar,&nbsp;Bianca Sclavi,&nbsp;Marco Cosentino Lagomarsino,&nbsp;Ulrich F Keyser,&nbsp;Pietro Cicuta","doi":"10.1039/c3ib40147b","DOIUrl":"https://doi.org/10.1039/c3ib40147b","url":null,"abstract":"<p><p>Recent biophysical approaches have provided key insights into the enthalpic and entropic forces that compact the nucleoid in the cell. Our biophysical approach combines two complementary, non-invasive and label-free techniques: a precisely timed steerable optical trap and a high throughput microcapillary Coulter counter. We demonstrate the ability of the latter technique to probe the physical properties and size of many purified nucleoids, at the individual nucleoid level. The DNA-binding protein H-NS is central to the organization of the bacterial genome. Our results show that nucleoids purified from the Δhns strain in the stationary phase expand approximately five fold more than the form observed in WT bacteria. This compaction is consistent with the role played by H-NS in regulating the nucleoid structure and the significant organizational changes that occur as the cell adapts to the stationary phase. We also study the permeability to the flow of ions and find that in the experiment nucleoids behave as solid colloids. </p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"184-91"},"PeriodicalIF":2.5,"publicationDate":"2014-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c3ib40147b","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31942148","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":"Single cell gene expression analysis in injury-induced collective cell migration.","authors":"Reza Riahi,&nbsp;Min Long,&nbsp;Yongliang Yang,&nbsp;Zachary Dean,&nbsp;Donna D Zhang,&nbsp;Marvin J Slepian,&nbsp;Pak Kin Wong","doi":"10.1039/c3ib40095f","DOIUrl":"https://doi.org/10.1039/c3ib40095f","url":null,"abstract":"<p><p>Collective cell behavior in response to mechanical injury is central to various regenerative and pathological processes. Using a double-stranded locked nucleic acid probe for monitoring real-time intracellular gene expression, we examined the spatiotemporal response of epithelial cells during injury-induced collective migration and compared to the blocker assay with minimal injury as control. We showed that cells ∼150 μm from the wound edge exhibit a gradient in response to mechanical injury, expressing different genes depending on the wounding process. While release of contact inhibition is sufficient to trigger the migratory behavior, cell injury additionally induces reactive oxygen species, Nrf2 protein, and stress response genes, including heat shock protein 70 and heme oxygenase-1, in a spatiotemporal manner. Furthermore, we show that Nrf2 has an inhibitory role in injury-induced epithelial-mesenchymal transition, suggesting a potential autoregulatory mechanism in injury-induced response. Taken together, our single-cell gene expression analyses reveal modular cell responses to mechanical injury, manipulation of which may afford novel strategies for tissue repair and prevention of tumor invasion in the future. </p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"192-202"},"PeriodicalIF":2.5,"publicationDate":"2014-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c3ib40095f","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31954619","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":"Response of single leukemic cells to peptidase inhibitor therapy across time and dose using a microfluidic device.","authors":"Michelle L Kovarik,&nbsp;Alexandra J Dickinson,&nbsp;Pourab Roy,&nbsp;Ranjit A Poonnen,&nbsp;Jason P Fine,&nbsp;Nancy L Allbritton","doi":"10.1039/c3ib40249e","DOIUrl":"https://doi.org/10.1039/c3ib40249e","url":null,"abstract":"<p><p>Single-cell methodologies are revealing cellular heterogeneity in numerous biological processes and pathologies. For example, cancer cells are characterized by substantial heterogeneity in basal signaling and in response to perturbations, such as drug treatment. In this work, we examined the response of 678 individual U937 (human acute myeloid leukemia) cells to an aminopeptidase-inhibiting chemotherapeutic drug (Tosedostat) over the course of 95 days. Using a fluorescent reporter peptide and a microfluidic device, we quantified the rate of reporter degradation as a function of dose. While the single-cell measurements reflected ensemble results, they added a layer of detail by revealing unique degradation patterns and outliers within the larger population. Regression modeling of the data allowed us to quantitatively explore the relationships between reporter loading, incubation time, and drug dose on peptidase activity in individual cells. Incubation time was negatively correlated with the number of peptide fragment peaks observed, while peak area (which was proportional to reporter loading) was positively correlated with both the number of fragment peaks observed and the degradation rate. Notably, a statistically significant change in the number of peaks observed was identified as dose increased from 2 to 4 μM. Similarly, a significant difference in degradation rate as a function of reporter loading was observed for doses ≥2 μM compared to the 1 μM dose. These results suggest that additional enzymes may become inhibited at doses >1 μM and >2 μM, demonstrating the utility of single-cell data to yield novel biological hypotheses. </p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"164-74"},"PeriodicalIF":2.5,"publicationDate":"2014-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c3ib40249e","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32020043","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":"Streamlining gene expression analysis: integration of co-culture and mRNA purification.","authors":"Scott M Berry,&nbsp;Chandresh Singh,&nbsp;Jessica D Lang,&nbsp;Lindsay N Strotman,&nbsp;Elaine T Alarid,&nbsp;David J Beebe","doi":"10.1039/c3ib40136g","DOIUrl":"https://doi.org/10.1039/c3ib40136g","url":null,"abstract":"<p><p>Co-culture of multiple cell types within a single device enables the study of paracrine signaling events. However, extracting gene expression endpoints from co-culture experiments is laborious, due in part to pre-PCR processing of the sample (i.e., post-culture cell sorting and nucleic acid purification). Also, a significant loss of nucleic acid may occur during these steps, especially with microfluidic cell culture where lysate volumes are small and difficult to access. Here, we describe an integrated platform for performing microfluidic cell culture and extraction of mRNA for gene expression analysis. This platform was able to recover 30-fold more mRNA than a similar, non-integrated system. Additionally, using a breast cancer/bone marrow stroma co-culture, we recapitulated stromal-dependent, estrogen-independent growth of the breast cancer cells, coincident with transcriptional changes. We anticipate that this platform will be used for streamlined analysis of paracrine signaling events as well as for screening potential drugs and/or patient samples. </p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"224-31"},"PeriodicalIF":2.5,"publicationDate":"2014-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c3ib40136g","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32019837","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":"Cardiac tissue engineering: renewing the arsenal for the battle against heart disease.","authors":"Vassilis Georgiadis, Richard A Knight, Suwan N Jayasinghe, Anastasis Stephanou","doi":"10.1039/c3ib40097b","DOIUrl":"10.1039/c3ib40097b","url":null,"abstract":"<p><p>The development of therapies that lead to the regeneration or functional repair of compromised cardiac tissue is the most important challenge facing translational cardiovascular research today. During the last 25 years huge efforts have been made towards restoring the physiologic functions of the heart by means of delivering cell implants into the insulted heart, initially through 'naked cell' injections and more recently through the principle of cardiac tissue engineering and the use of elaborate delivery systems and priming mechanisms that include scaffolds, bioreactors or ex vivo manipulations of cells and support structures. In this review we summarise various approaches towards cardiac repair and highlight advances in the field of tissue engineering, ranging from a review of cell types used, to advances that attempt to address mechanistic and functional elements that are critical for successful restoration of the heart, including the maintenance of the extracellular matrix through scaffoldless cardiac sheets, strategies that promote neovascularisation and the precise micro-delivery of cell populations to form three-dimensional structures through bioengineering methods such as microfabrication. </p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"111-26"},"PeriodicalIF":0.0,"publicationDate":"2014-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31967504","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":"Complementary effects of ciclopirox olamine, a prolyl hydroxylase inhibitor and sphingosine 1-phosphate on fibroblasts and endothelial cells in driving capillary sprouting.","authors":"Sei Hien Lim,&nbsp;Choong Kim,&nbsp;Amir R Aref,&nbsp;Roger D Kamm,&nbsp;Michael Raghunath","doi":"10.1039/c3ib40082d","DOIUrl":"https://doi.org/10.1039/c3ib40082d","url":null,"abstract":"<p><p>Capillary sprouting, a key step of neoangiogenesis in wound healing and tumor growth, also represents a therapeutic target for tissue repair. It requires crosstalk between endothelial cells (EC) and other cell types. We studied this process in a microfluidic platform that allows EC to migrate out of a channel across a collagen gel up a gradient of factors produced by a collection of encapsulated fibroblasts. Introduction of a prolyl hydroxylase inhibitor (PHi), ciclopirox olamine (CPX) to stabilize hypoxia inducible factor 1α (HIF-1α) predominantly in fibroblasts induced capillary sprouting in EC, but the most complex tubular networks with true lumina formed after combining CPX with the lysophospholipid sphingosine 1-phosphate (S1P). The enhanced angiogenesis is a possible consequence of the generation of mutually stimulating factors as each cell type responded differently to the compounds. The combination of CPX and S1P induced secretion of vascular endothelial growth factor (VEGF) in fibroblast culture whereas the angiogenic monocyte chemoattractant protein (MCP)-1 was exclusively secreted by fibroblasts, but only in the presence of EC-conditioned medium. Antibody interference with fibroblast-produced VEGF and MCP-1 inhibited the sprouting response. These observations not only demonstrate the collaboration of EC and fibroblasts in inducing capillary sprouting but also suggest that the combination of CPX and S1P enhances angiogenesis and thus might be of therapeutic value for the pharmacological induction of tissue repair and regeneration. </p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"1474-84"},"PeriodicalIF":2.5,"publicationDate":"2013-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c3ib40082d","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39974661","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":"Postulates on electromagnetic activity in biological systems and cancer.","authors":"Jiří Pokorný,&nbsp;Jan Pokorný,&nbsp;Jitka Kobilková","doi":"10.1039/c3ib40166a","DOIUrl":"https://doi.org/10.1039/c3ib40166a","url":null,"abstract":"<p><p>A framework of postulates is formulated to define the existence, nature, and function of a coherent state far from thermodynamic equilibrium in biological systems as an essential condition for the existence of life. This state is excited and sustained by energy supply. Mitochondria producing small packets of energy in the form of adenosine and guanosine triphosphate and strong static electric field around them form boundary elements between biochemical-genetic and physical processes. The transformation mechanism of chemical energy into useful work for biological needs and the excitation of the coherent state far from thermodynamic equilibrium are fundamental problems. The exceptional electrical polarity of biological objects and long-range interactions suggest a basic role of the endogenous electromagnetic field generated by living cells. The formulated postulates encompass generation, properties and function of the electromagnetic field connected with biological activity and its pathological deviations. Excited longitudinal polar oscillations in microtubules in eukaryotic cells generate the endogenous electromagnetic field. The metabolic activity of mitochondria connected with water ordering forms conditions for excitation. The electrodynamic field plays an important role in the establishment of coherence, directional transport, organization of morphological structures, interactions, information transfer, and brain activity. An overview of experimental results and physical models supporting the postulates is included. The existence of the endogenous biological electromagnetic field, its generation by microtubules and supporting effects produced by mitochondria have a reasonable experimental foundation. Cancer transformation is a pathological reduction of the coherent energy state far from thermodynamic equilibrium. Malignancy, i.e. local invasion and metastasis, is a direct consequence of mitochondrial dysfunction, disturbed microtubule polar oscillations and the generated electromagnetic field. </p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"1439-46"},"PeriodicalIF":2.5,"publicationDate":"2013-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c3ib40166a","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40269516","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}