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

{"title":"Resolving brain regions using nanostructure initiator mass spectrometry imaging of phospholipids.","authors":"Do Yup Lee,&nbsp;Virginia Platt,&nbsp;Ben Bowen,&nbsp;Katherine Louie,&nbsp;Christie A Canaria,&nbsp;Cynthia T McMurray,&nbsp;Trent Northen","doi":"10.1039/c2ib20043k","DOIUrl":"https://doi.org/10.1039/c2ib20043k","url":null,"abstract":"<p><p>In a variety of neurological diseases, pathological progression is cell type and region specific. Previous reports suggest that mass spectrometry imaging has the potential to differentiate between brain regions enriched in specific cell types. Here, we utilized a matrix-free surface mass spectrometry approach, nanostructure initiator mass spectrometry (NIMS), to show that spatial distributions of multiple lipids can be used as a 'fingerprint' to discriminate between neuronal- and glial- enriched brain regions. In addition, glial cells from different brain regions can be distinguished based on unique lipid profiles. NIMS images were generated from sagittal brain sections and were matched with immunostained serial sections to define glial cell enriched areas. Tandem mass spectrometry (LC-MS/MS QTOF) on whole brain extracts was used to identify 18 phospholipids. Multivariate statistical analysis (Nonnegative Matrix Factorization) enhanced differentiation of brain regions and cell populations compared to single ion imaging methods. This analysis resolved brain regions that are difficult to distinguish using conventional stains but are known to have distinct physiological functions. This method accurately distinguished the frontal (or somatomotor) and dorsal (or retrosplenial) regions of the cortex from each other and from the pons region.</p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"693-9"},"PeriodicalIF":2.5,"publicationDate":"2012-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c2ib20043k","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40190879","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":"Surface mobility regulates skeletal stem cell differentiation.","authors":"Cristina González-García, David Moratal, Richard O C Oreffo, Matthew J Dalby, Manuel Salmerón-Sánchez","doi":"10.1039/c2ib00139j","DOIUrl":"10.1039/c2ib00139j","url":null,"abstract":"<p><p>A family of polymer substrates which consists of a vinyl backbone chain with the side groups -COO(CH(2))(x)H, with x = 1, 2, 4, was prepared. Substrates with similar chemical groups but decreasing stiffness, characterized by their elastic modulus at 37 °C, as well as surface mobility, characterized by the glass transition temperature, were obtained. We have investigated whether these subtle variations in polymer chemistry lead to alterations in fibronectin (FN) adsorption and mesenchymal stem cell response. The same FN density was adsorbed on every substrate (∼450 ng cm(-2)) although the supramolecular organization of the protein at the material interface, as obtained with AFM, was different for x = 1 and the other two surfaces (x = 2, 4). Consequently, this allows one to investigate the effect of physical properties of the matrix on stem cell differentiation after ruling out any influence of protein activity. Cell adhesion was quantified by calculating the size distribution of focal adhesions. Mesenchymal stem cell differentiation to the osteoblastic lineage was determined by quantifying protein levels for osteocalcin, osteopontin and Runx2, in the absence of any additional osteogenic soluble factors in the culture media, but as a direct effect of material properties. The findings indicate the potential to modulate skeletal progenitor cell commitment to the osteoblastic lineage through surface mobility of the underlying material surface.</p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"531-9"},"PeriodicalIF":0.0,"publicationDate":"2012-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40144510","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":"Glycation of plasma proteins in type II diabetes lowers the non-covalent interaction affinities for dietary polyphenols.","authors":"Yixie Xie,&nbsp;Jianbo Xiao,&nbsp;Guoyin Kai,&nbsp;Xiaoqing Chen","doi":"10.1039/c2ib00185c","DOIUrl":"https://doi.org/10.1039/c2ib00185c","url":null,"abstract":"<p><p>Diabetes is characterized by an elevated level of glucose in the blood. This glucose can form covalent adducts with plasma proteins through a non-enzymatic process known as glycation. It has been suggested that the increasing glycation can influence the ability of plasma proteins to bind to small molecules. Herein, the difference between healthy human plasma proteins (HPP) and type II diabetes plasma proteins (TPP) in binding small molecules was investigated. TPP showed about 1-10 times lower affinities for polyphenols than HPP. The values of lg K(a)(HPP) are positive proportional to the values of lg K(a)(TPP) with excellent linear relationship. The glycation of HPP decreased the affinities for HPP by about 1.17 to 16.6 times. The difference between HPP-polyphenol interaction and TPP-polyphenol interaction was bigger for the more lipophilic polyphenols. The affinities for TPP or HPP slightly decreased with increasing hydrogen bond donor numbers of polyphenols and hardly changed with hydrogen bond acceptor numbers.</p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"502-7"},"PeriodicalIF":2.5,"publicationDate":"2012-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c2ib00185c","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40166217","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":"Identifying core features of adaptive metabolic mechanisms for chronic heat stress attenuation contributing to systems robustness.","authors":"Jenny Gu,&nbsp;Katrin Weber,&nbsp;Elisabeth Klemp,&nbsp;Gidon Winters,&nbsp;Susanne U Franssen,&nbsp;Isabell Wienpahl,&nbsp;Ann-Kathrin Huylmans,&nbsp;Karsten Zecher,&nbsp;Thorsten B H Reusch,&nbsp;Erich Bornberg-Bauer,&nbsp;Andreas P M Weber","doi":"10.1039/c2ib00109h","DOIUrl":"https://doi.org/10.1039/c2ib00109h","url":null,"abstract":"<p><p>The contribution of metabolism to heat stress may play a significant role in defining robustness and recovery of systems; either by providing the energy and metabolites required for cellular homeostasis, or through the generation of protective osmolytes. However, the mechanisms by which heat stress attenuation could be adapted through metabolic processes as a stabilizing strategy against thermal stress are still largely unclear. We address this issue through metabolomic and transcriptomic profiles for populations along a thermal cline where two seagrass species, Zostera marina and Zostera noltii, were found in close proximity. Significant changes captured by these profile comparisons could be detected, with a larger response magnitude observed in northern populations to heat stress. Sucrose, fructose, and myo-inositol were identified to be the most responsive of the 29 analyzed organic metabolites. Many key enzymes in the Calvin cycle, glycolysis and pentose phosphate pathways also showed significant differential expression. The reported comparison suggests that adaptive mechanisms are involved through metabolic pathways to dampen the impacts of heat stress, and interactions between the metabolome and proteome should be further investigated in systems biology to understand robust design features against abiotic stress.</p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"480-93"},"PeriodicalIF":2.5,"publicationDate":"2012-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c2ib00109h","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40151928","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 mechanical memory of lung myofibroblasts.","authors":"Jenna L Balestrini,&nbsp;Sidharth Chaudhry,&nbsp;Vincent Sarrazy,&nbsp;Anne Koehler,&nbsp;Boris Hinz","doi":"10.1039/c2ib00149g","DOIUrl":"https://doi.org/10.1039/c2ib00149g","url":null,"abstract":"<p><p>Fibroblasts differentiate into the highly synthetic and contractile myofibroblast phenotype when exposed to substrates with an elastic modulus corresponding to pathologically stiff fibrotic tissue. Cellular responses to changes in substrate stiffness are typically analyzed after hours or days, which does not enable the monitoring of myofibroblast persistence, a hallmark of fibrosis. To determine long-lasting effects on the fibrotic behavior of lung fibroblasts, we followed a novel approach of explanting and repeatedly passaging fibroblasts on silicone substrates with stiffness representing various states of lung health. Fibrotic activity was determined by assaying for myofibroblast proliferation, cell contractility, expression of α-smooth muscle actin, extracellular matrix and active TGFβ1. As predicted, myofibroblast activity was low on healthy soft substrates and increased with increasing substrate stiffness. However, explanting and mechanically priming lung fibroblasts for 3 weeks on pathologically stiff substrates resulted in sustained myofibroblast activity even after the cells were returned to healthy soft cultures for 2 weeks. Such primed cells retained higher fibrotic activity than cells that had been exclusively cultured on soft substrates, and were not statistically different from cells continuously passaged on stiff surfaces. Inversely, priming lung fibroblasts for 3 weeks on soft substrates partially protected from myofibroblast activation after the shift to stiff substrates. Hence, mechano-sensed information relating to physical conditions of the local cellular environment could permanently induce fibrotic behavior of lung fibroblasts. This priming effect has important implications for the progression and persistence of aggressive fibrotic diseases such as idiopathic pulmonary fibrosis.</p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"410-21"},"PeriodicalIF":2.5,"publicationDate":"2012-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c2ib00149g","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40159196","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":"Modelling complex biological systems using an agent-based approach.","authors":"Mike Holcombe, Salem Adra, Mesude Bicak, Shawn Chin, Simon Coakley, Alison I Graham, Jeffrey Green, Chris Greenough, Duncan Jackson, Mariam Kiran, Sheila MacNeil, Afsaneh Maleki-Dizaji, Phil McMinn, Mark Pogson, Robert Poole, Eva Qwarnstrom, Francis Ratnieks, Matthew D Rolfe, Rod Smallwood, Tao Sun, David Worth","doi":"10.1039/c1ib00042j","DOIUrl":"10.1039/c1ib00042j","url":null,"abstract":"<p><p>Many of the complex systems found in biology are comprised of numerous components, where interactions between individual agents result in the emergence of structures and function, typically in a highly dynamic manner. Often these entities have limited lifetimes but their interactions both with each other and their environment can have profound biological consequences. We will demonstrate how modelling these entities, and their interactions, can lead to a new approach to experimental biology bringing new insights and a deeper understanding of biological systems.</p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"53-64"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40128464","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":"Limitations of conventional inhibitor classifications.","authors":"Ryan Walsh,&nbsp;Earl Martin,&nbsp;Sultan Darvesh","doi":"10.1039/c1ib00053e","DOIUrl":"https://doi.org/10.1039/c1ib00053e","url":null,"abstract":"<p><p>Enzyme inhibitors are usually classified as competitive, non-competitive or mixed non-competitive. Each of these designations has a serious limitation in that it only describes an extreme of inhibitory behaviour. The non-competitive inhibition equation only considers an approach to complete inhibition of the catalytic turnover rate, while the competitive inhibition equation predicts an infinite increase in the Michaelis-Menten constant (decrease in enzyme affinity for substrate), resulting from increased inhibitor concentration. Both of these models exclude the possibility of a finite inhibitor-induced change in the kinetic parameters of the enzyme they are affecting. They also exclude the possibility of an inhibitor affecting both the substrate affinity and the catalytic turnover at the same time. Mixed non-competitive inhibition describes a hybrid form of inhibition displaying some characteristics of both competitive and non-competitive inhibition. It also suffers from an inability to describe finite changes in activity and to describe concomitant changes in substrate affinity and catalytic turnover. Two inhibitor binding constants are invoked in this equation, suggesting that such inhibitors interact with the enzyme in two completely independent manners. From these considerations, it is suggested here that conventional equations do not adequately describe observed kinetic data due to a lack of distinction between the mass action binding term describing inhibitor-enzyme association and the terms representing the actual effect of the inhibitor on the enzyme. Herein we describe an alternate approach for representing enzyme activity modulation based on a re-examination of conventional inhibition equations. The arguments presented are illustrated using the known competitive inhibition of Kallikrein with benzamidine.</p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"1197-201"},"PeriodicalIF":2.5,"publicationDate":"2011-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c1ib00053e","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40114729","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":"Pattern analysis and spatial distribution of neurons in culture.","authors":"Larry J Millet,&nbsp;Mitchell B Collens,&nbsp;George L W Perry,&nbsp;Rashid Bashir","doi":"10.1039/c1ib00054c","DOIUrl":"https://doi.org/10.1039/c1ib00054c","url":null,"abstract":"<p><p>The nervous system is a complex, highly-ordered, integrated network of cells. Dispersed cultures of neurons enable investigations into intrinsic cellular functions without the complexities inherent in the intact nervous system. This culture process generates a homogeneously dispersed population that is assumed to be spatially random. Despite the vast number of studies utilizing dispersed neurons, few studies address the spatial distribution of large populations of neurons, in vitro. We used ink-jet printing and surface chemistry to define patterned areas of poly-lysine adhesion (∼50 μm spots) juxtaposed against a fluorinated-silane background. We quantitatively analysed populations of patterned neurons on printed protein spots, and unpatterned neurons. Using a microarray scanner, we acquired large images (72 mm × 22 mm) of patterns, and neurons with and without patterns. Fast Fourier transformation (FFT) image analysis was used to determine global alignment of neurons to patterns. Through point pattern analysis, we described the spatial organization of dispersed neurons with, or without, patterned substrates. Patterned neurons show spatial organization characteristics reminiscent of printed patterns, with spatial distributions representative of unpatterned neurons. Most notably, both patterned and unpatterned neurons show departure from null models of complete spatial randomness (CSR; a homogeneous Poisson process) at shorter distances with conformity to CSR occurring at longer distances. Cellular morphometrics show that when compared to their unpatterned counterparts, spot-patterned neurons exhibit a significant increase (p < 0.0001) in the mean dendritic circularity and an increase in the number of more circular neurons. Through neurite tracing, we show that dendritic processes are also highly confined to patterned areas, and that they are on average 58% shorter than dendrites of neurons without patterns. Our findings show that patterned areas change the spatial organization of the somata and dendrites of cultured neurons, and that traditional neuronal cultures deviate from CSR.</p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"1167-78"},"PeriodicalIF":2.5,"publicationDate":"2011-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c1ib00054c","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40132870","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":"3D inverted colloidal crystals in realistic cell migration assays for drug screening applications.","authors":"Joakim da Silva,&nbsp;Franziska Lautenschläger,&nbsp;Cheng-Hwa R Kuo,&nbsp;Jochen Guck,&nbsp;Easan Sivaniah","doi":"10.1039/c1ib00065a","DOIUrl":"https://doi.org/10.1039/c1ib00065a","url":null,"abstract":"<p><p>Screening drugs for their specific impact on cell mechanics, in addition to targeting adhesion and proteolysis, will be important for successfully moderating migration in infiltrative disorders including cancer metastasis. We present 3D inverted colloidal crystals made of hydrogel as a realistic cell migration assay, where the geometry and stiffness can be set independently to mimic the tissue requirements in question. We show the utility of this 3D assay for drug screening purposes, specifically in contrast to conventional 2D migration studies, by surveying the effects of commonly used cytoskeletal toxins that impact cell mechanics. This assay allows studying large cell numbers for good statistics but at single-cell resolution.</p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"1202-6"},"PeriodicalIF":2.5,"publicationDate":"2011-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c1ib00065a","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40114786","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":"Direct and cell signaling-based, geometry-induced neuronal differentiation of neural stem cells.","authors":"Sasha Bakhru,&nbsp;Amrinder S Nain,&nbsp;Christopher Highley,&nbsp;Ji Wang,&nbsp;Phil Campbell,&nbsp;Cristina Amon,&nbsp;Stefan Zappe","doi":"10.1039/c1ib00098e","DOIUrl":"https://doi.org/10.1039/c1ib00098e","url":null,"abstract":"<p><p>Neural Stem Cells (NSCs) are multipotent precursors inhabiting the subventricular and hippocampal subgranular regions of the adult mammalian brain, able to self-renew and differentiate into neurons, astrocytes, and oligodendrocytes, the three primary neural cell types of the adult brain. NSC fate is influenced by the physical and chemical microenvironment experienced by the cell, both in vitro and in vivo. Towards characterizing the influence of topographical, geometric cues on NSC fate, we fabricated highly aligned, single- and double-layer polystyrene nanofiber meshes. Seeding of NSCs on laminin-coated fibers induces polarized NSC morphology and cellular elongation in the directions of fiber alignment, with cells extending membranous processes over hundreds of microns along the fiber surfaces. Additionally, these aligned fiber substrates promote neuronal lineage specification of NSCs with an efficiency of 82.3 ± 11.1% within days of seeding. Moreover, not only do cells on fibers yield neurons, but also neighboring cells in close proximity to those differentiating on aligned fibers, with an efficiency of 72.8 ± 9.7%. This neighboring, cell-induced differentiation occurs without cell-cell contact over millimetres away from the fibers, suggesting a paracrine signaling effect not previously reported for NSCs undergoing neurogenesis. In contrast, NSCs farther away from these fiber substrates nearly uniformly yield glia.</p>","PeriodicalId":520649,"journal":{"name":"Integrative biology : quantitative biosciences from nano to macro","volume":" ","pages":"1207-14"},"PeriodicalIF":2.5,"publicationDate":"2011-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/c1ib00098e","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40132880","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}