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

{"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}

{"title":"Personalised treatment of haematological malignancies through systems medicine based on single molecules in single cells.","authors":"Ehsan Ghayoor Karimiani,&nbsp;Philip Day","doi":"10.1039/c3ib20258e","DOIUrl":"https://doi.org/10.1039/c3ib20258e","url":null,"abstract":"<p><p>Molecular diagnostics in haematological malignancies continues to advance towards more personalized treatment and accordingly demand is increasing for procedures providing quantitative analyses of heterogeneous tissue in malignancies. Circulating leukaemic cells are diverse and comprise discrete clonal populations arising from a common progenitor cell. Some of the current diagnostic techniques possess an attenuated dynamic quantitative range that prevents a clear comprehension of intercellular interactions. Quantitative measurements will facilitate an accurate appreciation of holistic cellular processes, assist with predictions pertaining to perturbations and reveal functional moieties that are truly a facet of the disease, and thus add to current biomarker discovery which often lack assessment of functional involvement in disease mechanisms and processes. This review focuses on quantitative studies related to peripheral blood and haematological malignancies. Data retrieval for either of these diseases is hampered by the high and unchartered degree of heterogeneity typically existing within clinical samples. The likelihood of analysis across single cell populations is highly probable in the near future. This will allow a patient to be readily screened for malignancies and assigned to a risk group based on a quantitative profile of a complex of molecules related to disease. The future analysis of molecular pathology based on detailed molecular dissection looks promising, requiring the integration of various disciplines encompassing morphology, genetics, expression profiling and new and evolving predictive modeling via systems medicine. From this detailed view into patient health, an increasingly personalized treatment plan can be administered, commencing with stratified medicine.</p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"759-67"},"PeriodicalIF":2.5,"publicationDate":"2013-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c3ib20258e","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40228645","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":"Conserved host-pathogen PPIs. Globally conserved inter-species bacterial PPIs based conserved host-pathogen interactome derived novel target in C. pseudotuberculosis, C. diphtheriae, M. tuberculosis, C. ulcerans, Y. pestis, and E. coli targeted by Piper betel compounds.","authors":"Debmalya Barh,&nbsp;Krishnakant Gupta,&nbsp;Neha Jain,&nbsp;Gourav Khatri,&nbsp;Nidia León-Sicairos,&nbsp;Adrian Canizalez-Roman,&nbsp;Sandeep Tiwari,&nbsp;Ankit Verma,&nbsp;Sachin Rahangdale,&nbsp;Syed Shah Hassan,&nbsp;Anderson Rodrigues dos Santos,&nbsp;Amjad Ali,&nbsp;Luis Carlos Guimarães,&nbsp;Rommel Thiago Jucá Ramos,&nbsp;Pratap Devarapalli,&nbsp;Neha Barve,&nbsp;Marriam Bakhtiar,&nbsp;Ranjith Kumavath,&nbsp;Preetam Ghosh,&nbsp;Anderson Miyoshi,&nbsp;Artur Silva,&nbsp;Anil Kumar,&nbsp;Amarendra Narayan Misra,&nbsp;Kenneth Blum,&nbsp;Jan Baumbach,&nbsp;Vasco Azevedo","doi":"10.1039/c2ib20206a","DOIUrl":"https://doi.org/10.1039/c2ib20206a","url":null,"abstract":"<p><p>Although attempts have been made to unveil protein-protein and host-pathogen interactions based on molecular insights of important biological events and pathogenesis in various organisms, these efforts have not yet been reported in Corynebacterium pseudotuberculosis (Cp), the causative agent of Caseous Lymphadenitis (CLA). In this study, we used computational approaches to develop common conserved intra-species protein-protein interaction (PPI) networks first time for four Cp strains (Cp FRC41, Cp 316, Cp 3/99-5, and Cp P54B96) followed by development of a common conserved inter-species bacterial PPI using conserved proteins in multiple pathogens (Y. pestis, M. tuberculosis, C. diphtheriae, C. ulcerans, E. coli, and all four Cp strains) and E. Coli based experimentally validated PPI data. Furthermore, the interacting proteins in the common conserved inter-species bacterial PPI were used to generate a conserved host-pathogen interaction (HP-PPI) network considering human, goat, sheep, bovine, and horse as hosts. The HP-PPI network was validated, and acetate kinase (Ack) was identified as a novel broad spectrum target. Ceftiofur, penicillin, and two natural compounds derived from Piper betel were predicted to inhibit Ack activity. One of these Piper betel compounds found to inhibit E. coli O157:H7 growth similar to penicillin. The target specificity of these betel compounds, their effects on other studied pathogens, and other in silico results are currently being validated and the results are promising.</p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"495-509"},"PeriodicalIF":2.5,"publicationDate":"2013-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c2ib20206a","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40210556","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":"Drug repositioning through incomplete bi-cliques in an integrated drug-target-disease network.","authors":"Simone Daminelli,&nbsp;V Joachim Haupt,&nbsp;Matthias Reimann,&nbsp;Michael Schroeder","doi":"10.1039/c2ib00154c","DOIUrl":"https://doi.org/10.1039/c2ib00154c","url":null,"abstract":"<p><p>Recently, there has been much interest in gene-disease networks and polypharmacology as a basis for drug repositioning. Here, we integrate data from structural and chemical databases to create a drug-target-disease network for 147 promiscuous drugs, their 553 protein targets, and 44 disease indications. Visualizing and analyzing such complex networks is still an open problem. We approach it by mining the network for network motifs of bi-cliques. In our case, a bi-clique is a subnetwork in which every drug is linked to every target and disease. Since the data are incomplete, we identify incomplete bi-cliques, whose completion introduces novel, predicted links from drugs to targets and diseases. We demonstrate the power of this approach by repositioning cardiovascular drugs to parasitic diseases, by predicting the cancer-related kinase PIK3CG as a novel target of resveratrol, and by identifying for five drugs a shared binding site in four serine proteases and novel links to cancer, cardiovascular, and parasitic diseases.</p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"778-88"},"PeriodicalIF":2.5,"publicationDate":"2012-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c2ib00154c","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40186672","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":"Is newer better?--evaluating the effects of data curation on integrated analyses in Saccharomyces cerevisiae.","authors":"Katherine James, Anil Wipat, Jennifer Hallinan","doi":"10.1039/c2ib00123c","DOIUrl":"10.1039/c2ib00123c","url":null,"abstract":"<p><p>Recent high-throughput experiments have produced a wealth of heterogeneous datasets, each of which provides information about different aspects of the cell. Consequently, integration of diverse data types is essential in order to address many biological questions. The quality of any integrated analysis system is dependent upon the quality of its component data, and upon the Gold Standard data used to evaluate it. It is commonly assumed that the quality of data improves as databases grow and change, particularly for manually curated databases. However, the validity of this assumption can be questioned, given the constant changes in the data coupled with the high level of noise associated with high-throughput experimental techniques. One of the most powerful approaches to data integration is the use of Probabilistic Functional Integrated Networks (PFINs). Here, we systematically analyse the changes in four highly-curated and widely-used online databases and evaluate the extent to which these changes affect the protein function prediction performance of PFINs in the yeast Saccharomyces cerevisiae. We find that the global trend in network performance improves over time. Where individual areas of biology are concerned, however, the most recent files do not always produce the best results. Individual datasets have unique biases towards different biological processes and by selecting and integrating relevant datasets performance can be improved. When using any type of integrated system to answer a specific biological question careful selection of raw data and Gold Standard is vital, since the most recent data may not be the most appropriate.</p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"715-27"},"PeriodicalIF":0.0,"publicationDate":"2012-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40177395","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":"Diacylglycerol kinase zeta negatively regulates CXCR4-stimulated T lymphocyte firm arrest to ICAM-1 under shear flow.","authors":"Dooyoung Lee,&nbsp;Jiyeon Kim,&nbsp;Michael T Beste,&nbsp;Gary A Koretzky,&nbsp;Daniel A Hammer","doi":"10.1039/c2ib00002d","DOIUrl":"https://doi.org/10.1039/c2ib00002d","url":null,"abstract":"<p><p>T lymphocyte arrest within microvasculature is an essential process in immune surveillance and the adaptive immune response. Integrins and chemokines coordinately regulate when and where T cells stop under flow via chemokine-triggered inside-out activation of integrins. Diacylglycerol kinases (DGKs) regulate the levels of diacylglycerol (DAG) which in turn determine the activation of guanine nucleotide exchange factors (GEFs) and Ras proximity 1 (Rap1) molecules crucial to the activation of integrin lymphocyte function-associated antigen 1 (LFA-1). However, how the level of DGK regulates chemokine-stimulated LFA-1-mediated T cell arrest under flow is unknown. Using a combination of experiment and computational modeling, we demonstrate that DGKζ is a crucial regulator of CXCL12-triggered T cell arrest on surfaces presenting inter-cellular adhesion molecule 1 (ICAM-1). Using flow chamber assays, we found that the deficiency of DGKζ in T cells significantly increased firm arrest to ICAM-1-coated substrates and shortened the time to stop without altering the rolling velocity. These results suggest that DGKζ levels affect LFA-1-mediated T cell firm arrest, but not P-selectin-mediated rolling during CXCL12 stimulation. We accurately simulated the role of DGKζ in firm arrest of T cells computationally using an Integrated-Signaling Adhesive Dynamics (ISAD). In the absence of DGK catalytic reaction, the model cells rolled for a significantly shorter time before arrest, compared to when DGK molecules were present. Predictions of our model for T cell arrest quantitatively match experimental results. Overall these results demonstrate that DGKζ is a negative regulator of CXCL12-triggered inside-out activation of LFA-1 and firm adhesion of T cells under shear flow.</p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"606-14"},"PeriodicalIF":2.5,"publicationDate":"2012-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c2ib00002d","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40548667","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":"Preparation, characterization, and surface immobilization of native vesicles obtained by mechanical extrusion of mammalian cells.","authors":"Huawen Wu,&nbsp;Ann E Oliver,&nbsp;Viviane N Ngassam,&nbsp;Chanel K Yee,&nbsp;Atul N Parikh,&nbsp;Yin Yeh","doi":"10.1039/c2ib20022h","DOIUrl":"https://doi.org/10.1039/c2ib20022h","url":null,"abstract":"<p><p>Native vesicles or \"reduced protocells\" derived by mechanical extrusion concentrate selected plasma membrane components, while downsizing complexities of whole cells. We illustrate this technique, characterize the physical-chemical properties of these reduced configurations of whole cells, and demonstrate their surface immobilization and patternability. This simple detergent-free vesicularized membrane preparation should prove useful in fundamental studies of cellular membranes, and may provide a means to engineer therapeutic cells and enable high-throughput devices containing near-native, functional proteolipidic assemblies.</p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"685-92"},"PeriodicalIF":2.5,"publicationDate":"2012-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c2ib20022h","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40191670","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":"Regulation of morphogenesis and neural differentiation of human mesenchymal stem cells using carbon nanotube sheets.","authors":"Jeong Ah Kim,&nbsp;Eui Yun Jang,&nbsp;Tae June Kang,&nbsp;Sungjun Yoon,&nbsp;Raquel Ovalle-Robles,&nbsp;Won Jong Rhee,&nbsp;Taewoo Kim,&nbsp;Ray H Baughman,&nbsp;Yong Hyup Kim,&nbsp;Tai Hyun Park","doi":"10.1039/c2ib20017a","DOIUrl":"https://doi.org/10.1039/c2ib20017a","url":null,"abstract":"<p><p>In order to successfully utilize stem cells for therapeutic applications in regenerative medicine, efficient differentiation into a specific cell lineage and guidance of axons in a desired direction is crucial. Here, we used aligned multi-walled carbon nanotube (MWCNT) sheets to differentiate human mesenchymal stem cells (hMSCs) into neural cells. Human MSCs present a preferential adhesion to aligned CNT sheets with longitudinal stretch parallel to the CNT orientation direction. Cell elongation was 2-fold higher than the control and most of the cells were aligned on CNT sheets within 5° from the CNT orientation direction. Furthermore, a significant, synergistic enhancement of neural differentiation was observed in hMSCs cultured on the CNT sheets. Axon outgrowth was also controlled using nanoscale patterning of CNTs. This CNT sheet provides a new cellular scaffold platform that can regulate morphogenesis and differentiation of stem cells, which could open up a new approach for tissue and stem cell regeneration.</p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"587-94"},"PeriodicalIF":2.5,"publicationDate":"2012-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c2ib20017a","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40182246","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}