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

{"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}

{"title":"From swimming to swarming: Escherichia coli cell motility in two-dimensions.","authors":"Jean-Marie Swiecicki,&nbsp;Olesksii Sliusarenko,&nbsp;Douglas B Weibel","doi":"10.1039/c3ib40130h","DOIUrl":"https://doi.org/10.1039/c3ib40130h","url":null,"abstract":"<p><p>Escherichia coli swarmer cells coordinate their movement when confined in thin layers of fluid on agar surfaces. The motion and dynamics of cells, pairs of cells, and packs of cells can be recapitulated and studied in polymer microfluidic systems that are designed to constrain swarmer cell movement in thin layers of fluid between no-slip surfaces. The motion of elongated, smooth swimming E. coli cells in these environments reproduces the behavior of packs of cells observed at the leading edge of swarming communities and demonstrates the delicate balance between the physical dimensions of fluids and bacterial cell behavior. </p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"1490-4"},"PeriodicalIF":2.5,"publicationDate":"2013-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c3ib40130h","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40254855","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":"Probing subcellular organic hydroperoxide formation via a genetically encoded ratiometric and reversible fluorescent indicator.","authors":"Boxuan Simen Zhao,&nbsp;Gong Zhang,&nbsp;Shizhe Zeng,&nbsp;Chuan He,&nbsp;Peng R Chen","doi":"10.1039/c3ib40209f","DOIUrl":"https://doi.org/10.1039/c3ib40209f","url":null,"abstract":"<p><p>A ratiometric and reversible organic hydroperoxide (OHP) sensor, rOHSer, was developed with high sensitivity and selectivity for subcellular OHP visualization. Through targeting rOHSer to the nucleus, we demonstrated that high levels of D-glucose cause elevated OHP production in this compartment. Further utilization of rOHSer probe may allow more elucidation of unique roles of OHPs in diverse biological processes.</p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"1485-9"},"PeriodicalIF":2.5,"publicationDate":"2013-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c3ib40209f","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39973842","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":"Anodic aluminium oxide membranes for immunoisolation with sufficient oxygen supply for pancreatic islets.","authors":"Siwoo Cho,&nbsp;Sangmin Lee,&nbsp;Seong Hee Jeong,&nbsp;Yeongae Kim,&nbsp;Song Cheol Kim,&nbsp;Woonbong Hwang,&nbsp;Jaesung Park","doi":"10.1039/c3ib20226g","DOIUrl":"https://doi.org/10.1039/c3ib20226g","url":null,"abstract":"<p><p>Immunoisolation membranes have been developed for various cell encapsulations for therapeutic purposes. However effective encapsulation systems have been hindered by low oxygen (O2) permeability or imperfect immunoisolation caused by either low porosity or non-uniform pore geometry. Here, we report an encapsulation method that uses an anodic aluminum oxide membrane formed by polyethylene oxide self-assembly to obtain nanochannels with both high selectivity in excluding immune molecules and high permeability of nutrients such as glucose, insulin, and O2. The extracorporeal encapsulation system composed of these membranes allows O2 flux to meet the O2 demand of pancreatic islets of Langerhans and provides excellent in vitro viability and functionality of islets.</p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"828-34"},"PeriodicalIF":2.5,"publicationDate":"2013-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c3ib20226g","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40241014","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}