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Ajeti V.,University of Wisconsin - Madison | Ajeti V.,Laboratory for Optical and Computational Instrumentation | Lien C.-H.,University of Wisconsin - Madison | Chen S.-J.,National Cheng Kung University | And 12 more authors.
Optics Express | Year: 2013

Multiphoton excited photochemistry is a powerful 3D fabrication tool that produces sub-micron feature sizes. Here we exploit the freeform nature of the process to create models of the extracellular matrix (ECM) of several tissues, where the design blueprint is derived directly from high resolution optical microscopy images (e.g. fluorescence and Second Harmonic Generation). To achieve this goal, we implemented a new form of instrument control, termed modulated raster scanning, where rapid laser shuttering (10 MHz) is used to directly map the greyscale image data to the resulting protein concentration in the fabricated scaffold. Fidelity in terms of area coverage and relative concentration relative to the image data is 95%. We compare the results to an STL approach, and find the new scheme provides significantly improved performance. We suggest the method will enable a variety of cell-matrix studies in cancer biology and also provide insight into generating scaffolds for tissue engineering. ©2013 Optical Society of America.


Keles S.,1300 University Avenue
Bioinformatics | Year: 2014

Motivation: ChIP-seq technology enables investigators to study genome-wide binding of transcription factors and mapping of epigenomic marks. Although the availability of basic analysis tools for ChIP-seq data is rapidly increasing, there has not been much progress on the related design issues. A challenging question for designing a ChIP-seq experiment is how deeply should the ChIP and the control samples be sequenced? The answer depends on multiple factors some of which can be set by the experimenter based on pilot/preliminary data. The sequencing depth of a ChIP-seq experiment is one of the key factors that determine whether all the underlying targets (e.g. binding locations or epigenomic profiles) can be identified with a targeted power.Results: We developed a statistical framework named CSSP (ChIP-seq Statistical Power) for power calculations in ChIP-seq experiments by considering a local Poisson model, which is commonly adopted by many peak callers. Evaluations with simulations and data-driven computational experiments demonstrate that this framework can reliably estimate the power of a ChIP-seq experiment at different sequencing depths based on pilot data. Furthermore, it provides an analytical approach for calculating the required depth for a targeted power while controlling the false discovery rate at a user-specified level. Hence, our results enable researchers to use their own or publicly available data for determining required sequencing depths of their ChIP-seq experiments and potentially make better use of the multiplexing functionality of the sequencers. Evaluation of power for multiple public ChIP-seq datasets indicate that, currently, typical ChIP-seq studies are powered well for detecting large fold changes of ChIP enrichment over the control sample, but they have considerably less power for detecting smaller fold changes. © 2013 The Author 2013. Published by Oxford University Press. All rights reserved.


Zuo C.,1300 University Avenue
Bioinformatics (Oxford, England) | Year: 2014

ChIP-seq technology enables investigators to study genome-wide binding of transcription factors and mapping of epigenomic marks. Although the availability of basic analysis tools for ChIP-seq data is rapidly increasing, there has not been much progress on the related design issues. A challenging question for designing a ChIP-seq experiment is how deeply should the ChIP and the control samples be sequenced? The answer depends on multiple factors some of which can be set by the experimenter based on pilot/preliminary data. The sequencing depth of a ChIP-seq experiment is one of the key factors that determine whether all the underlying targets (e.g. binding locations or epigenomic profiles) can be identified with a targeted power. We developed a statistical framework named CSSP (ChIP-seq Statistical Power) for power calculations in ChIP-seq experiments by considering a local Poisson model, which is commonly adopted by many peak callers. Evaluations with simulations and data-driven computational experiments demonstrate that this framework can reliably estimate the power of a ChIP-seq experiment at different sequencing depths based on pilot data. Furthermore, it provides an analytical approach for calculating the required depth for a targeted power while controlling the false discovery rate at a user-specified level. Hence, our results enable researchers to use their own or publicly available data for determining required sequencing depths of their ChIP-seq experiments and potentially make better use of the multiplexing functionality of the sequencers. Evaluation of power for multiple public ChIP-seq datasets indicate that, currently, typical ChIP-seq studies are powered well for detecting large fold changes of ChIP enrichment over the control sample, but they have considerably less power for detecting smaller fold changes. Available at www.stat.wisc.edu/~zuo/CSSP. keles@stat.wisc.edu Supplementary data are available at Bioinformatics online.


Toops K.A.,University of Wisconsin - Madison | Hagemann T.L.,University of Wisconsin - Madison | Messing A.,University of Wisconsin - Madison | Nickells R.W.,University of Wisconsin - Madison | Nickells R.W.,1300 University Avenue
BMC Research Notes | Year: 2012

Background: Increased expression of glial fibrillary acidic protein (GFAP) within macroglia is commonly seen as a hallmark of glial activation after damage within the central nervous system, including the retina. The increased expression of GFAP in glia is also considered part of the pathologically inhibitory environment for regeneration of axons from damaged neurons. Recent studies have raised the possibility that reactive gliosis and increased GFAP cannot automatically be assumed to be negative events for the surrounding neurons and that the context of the reactive gliosis is critical to whether neurons benefit or suffer. We utilized transgenic mice expressing a range of Gfap to titrate the amount of GFAP in retinal explants to investigate the relationship between GFAP concentration and the regenerative potential of retinal ganglion cells. Findings. Explants from Gfap -/- and Gfap +/- mice did not have increased neurite outgrowth compared with Gfap +/+ or Gfap over-expressing mice as would be expected if GFAP was detrimental to axon regeneration. In fact, Gfap over-expressing explants had the most neurite outgrowth when treated with a neurite stimulatory media. Transmission electron microscopy revealed that neurites formed bundles, which were surrounded by larger cellular processes that were GFAP positive indicating a close association between growing axons and glial cells in this regeneration paradigm. Conclusions: We postulate that glial cells with increased Gfap expression support the elongation of new neurites from retinal ganglion cells possibly by providing a scaffold for outgrowth. © 2012 Toops et al.; licensee BioMed Central Ltd.


Thein-Nissenbaum J.M.,University of Wisconsin - Madison | Thein-Nissenbaum J.M.,1300 University Avenue | Carr K.E.,University of Wisconsin - Madison
Physical Therapy in Sport | Year: 2011

Female sports participation at the high school level has significantly increased since the 1970s. Physical activity in females has numerous positive benefits, including improved body image and overall health. Unfortunately, a select population of exercising females may experience symptoms related to the " female athlete triad," which refers to the interrelationships among energy availability, menstrual function, and bone mineral density. Clinically, these conditions can manifest as disordered eating behaviors, menstrual irregularity, and stress fractures. Athletes with conditions related to the triad are distributed along a spectrum between optimal health and disease and may not experience all conditions simultaneously.Previous research related to the triad has primarily focused on collegiate and elite athletes. However, mounting evidence demonstrates that the triad is present in the high school population. High school athletes should be assessed for triad components at preparticipation physicals. In addition, parents, coaches, and health care professionals should be educated and informed about the female athlete triad syndrome. In the presence of triad symptoms, further evaluation and treatment by a multidisciplinary team is strongly recommended for the athlete. © 2011.


King W.J.,550 Engineering Drive | Murphy W.L.,550 Engineering Drive | Murphy W.L.,1300 University Avenue
Polymer Chemistry | Year: 2011

Hydrogels that respond to their environment have been extensively used as controlled drug delivery devices. An emerging trend is to form these "dynamic" hydrogels from polymers that undergo conformational changes. Indeed, nanometer scale polymer conformational changes have translated to macroscopic changes in hydrogel properties and controlled the release of encapsulated drugs. This review will focus on the mechanisms that control protein release from dynamic hydrogels. Specifically, we will highlight emerging mechanisms to form dynamic hydrogels, whose functional nature is derived from nature-inspired polymer conformational changes. Pertinent results from the literature will be examined to illustrate how these nanometer scale polymer conformational changes influence therapeutic protein release from dynamic hydrogels. © The Royal Society of Chemistry 2011.


Filla M.S.,1300 University Avenue | Clark R.,1300 University Avenue | Peters D.M.,1300 University Avenue
Experimental Cell Research | Year: 2014

In this study, we examined the role(s) of syndecan-4 in regulating the formation of an actin geodesic dome structure called a cross-linked actin network (CLAN) in which syndecan-4 has previously been localized. CLANs have been described in several different cell types, but they have been most widely studied in human trabecular meshwork (HTM) cells where they may play a key role in controlling intraocular pressure by regulating aqueous humor outflow from the eye. In this study we show that a loss of cell surface synedcan-4 significantly reduces CLAN formation in HTM cells. Analysis of HTM cultures treated with or without dexamethasone shows that laminin 5 deposition within the extracellular matrix is increased by glucocorticoid treatment and that a laminin 5-derived, syndecan-4-binding peptide (PEP75), induces CLAN formation in TM cells. This PEP75-induced CLAN formation was inhibited by heparin and the broad spectrum PKC inhibitor Ro-31-7549. In contrast, the more specific PKCα inhibitor Gö 6976 had no effect, thus excluding PKCα as a downstream effector of syndecan-4 signaling. Analysis of PKC isozyme expression showed that HTM cells also expressed both PKCγ and PKCε. Cells treated with a PKCε agonist formed CLANs while a PKCα{plus 45 degree rule}γ agonist had no effect. These data suggest that syndecan-4 is essential for CLAN formation in HTM cells and that a novel PKCε-mediated signaling pathway can regulate formation of this unique actin structure. © 2014 Elsevier Inc.


PubMed | University of Wisconsin - Madison and 1300 University Avenue
Type: Journal Article | Journal: Trends in cancer | Year: 2016

Phosphoinositide 3-kinase (PI3K) generation of PI(3,4,5)P


PubMed | University of Wisconsin - Madison, 1300 University Avenue and Texas A&M University
Type: Journal Article | Journal: Preventive veterinary medicine | Year: 2014

Enterohemorrhagic Escherichia coli (EHEC) O157 are important foodborne pathogens whose major reservoir are asymptomatic cattle. There is evidence suggesting that nonpathogenic E. coli and bacteriophages in the gastro-intestinal tract can influence the pathogenicity of EHEC O157. The factors contributing to the onset and persistence of shedding EHEC O157 in cattle are not completely elucidated. This study used Bayesian network analysis to identify genetic markers of generic E. coli associated with shedding of EHEC O157 in cattle from data generated during an oral experimental challenge study in 4 groups of 6 steers inoculated with three different EHEC O157 strains. The quantification of these associations was accomplished using mixed effects logistic regression. The results showed that the concurrent presence of generic E. coli carrying the prophage marker R4-N and the virulence marker stx2 increased the odds of the onset of EHEC O157 shedding. The presence of prophage markers z2322 and X011C increased, while C1.N decreased the odds of shedding EHEC O157 two days later. A significant antagonist interaction effect between the presence of the virulence marker stx2 on the day of shedding EHEC O157 and two days before shedding was also found. In terms of the persistence of EHEC O157 shedding, the presence of prophage marker R4-N (OR=16, and 95% confidence interval (CI): 1.1, 252) was found to increase the odds of stopping EHEC O157 shedding, whereas prophage marker C1.N (OR=0.16, CI: 0.03, 0.7) and the enterohemolysin gene hly (OR=0.03, CI: 0.001, 0.8) were found to significantly decrease the odds of stopping EHEC O157 shedding. In conclusion, the study found that the presence of certain genetic markers in the generic E. coli genome can influence the pathogenicity of EHEC O157.


Zhang Q.,300 University Avenue | Keles S.,1300 University Avenue
Bioinformatics (Oxford, England) | Year: 2014

MOTIVATION: In chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) and other short-read sequencing experiments, a considerable fraction of the short reads align to multiple locations on the reference genome (multi-reads). Inferring the origin of multi-reads is critical for accurately mapping reads to repetitive regions. Current state-of-the-art multi-read allocation algorithms rely on the read counts in the local neighborhood of the alignment locations and ignore the variation in the copy numbers of these regions. Copy-number variation (CNV) can directly affect the read densities and, therefore, bias allocation of multi-reads.RESULTS: We propose cnvCSEM (CNV-guided ChIP-Seq by expectation-maximization algorithm), a flexible framework that incorporates CNV in multi-read allocation. cnvCSEM eliminates the CNV bias in multi-read allocation by initializing the read allocation algorithm with CNV-aware initial values. Our data-driven simulations illustrate that cnvCSEM leads to higher read coverage with satisfactory accuracy and lower loss in read-depth recovery (estimation). We evaluate the biological relevance of the cnvCSEM-allocated reads and the resultant peaks with the analysis of several ENCODE ChIP-seq datasets.AVAILABILITY AND IMPLEMENTATION: Available at http://www.stat.wisc.edu/∼qizhang/CONTACT: : qizhang@stat.wisc.edu or keles@stat.wisc.eduSUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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