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Ligand-conjugated quantum dots for fast sub-diffraction protein tracking in acute brain slices.
Thal LB, Mann VR, Sprinzen D, McBride JR, Reid KR, Tomlinson ID, McMahon DG, Cohen BE, Rosenthal SJ
(2020) Biomater Sci 8: 837-845
MeSH Terms: Animals, Brain, Brain Chemistry, Ligands, Mice, Microscopy, Fluorescence, Microtomy, Proteins, Quantum Dots, Selenium Compounds, Staining and Labeling, Zinc Compounds
Show Abstract · Added March 18, 2020
Semiconductor quantum dots (QDs) have demonstrated utility in long-term single particle tracking of membrane proteins in live cells in culture. To extend the superior optical properties of QDs to more physiologically relevant cell platforms, such as acute brain slices, we examine the photophysics of compact ligand-conjugated CdSe/CdS QDs using both ensemble and single particle analysis in brain tissue media. We find that symmetric core passivation is critical for both photostability in oxygenated media and for prolonged single particle imaging in brain slices. We then demonstrate the utility of these QDs by imaging single dopamine transporters in acute brain slices, achieving 20 nm localization precision at 10 Hz frame rates. These findings detail design requirements needed for new QD probes in complex living environments, and open the door to physiologically relevant studies that capture the utility of QD probes in acute brain slices.
0 Communities
2 Members
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12 MeSH Terms
Automated cell boundary and 3D nuclear segmentation of cells in suspension.
Kesler B, Li G, Thiemicke A, Venkat R, Neuert G
(2019) Sci Rep 9: 10237
MeSH Terms: Algorithms, Biological Phenomena, Cell Nucleus, Computational Biology, Image Processing, Computer-Assisted, Microscopy, Optical Imaging, Single-Cell Analysis, Staining and Labeling, Suspensions
Show Abstract · Added February 5, 2020
To characterize cell types, cellular functions and intracellular processes, an understanding of the differences between individual cells is required. Although microscopy approaches have made tremendous progress in imaging cells in different contexts, the analysis of these imaging data sets is a long-standing, unsolved problem. The few robust cell segmentation approaches that exist often rely on multiple cellular markers and complex time-consuming image analysis. Recently developed deep learning approaches can address some of these challenges, but they require tremendous amounts of data and well-curated reference data sets for algorithm training. We propose an alternative experimental and computational approach, called CellDissect, in which we first optimize specimen preparation and data acquisition prior to image processing to generate high quality images that are easier to analyze computationally. By focusing on fixed suspension and dissociated adherent cells, CellDissect relies only on widefield images to identify cell boundaries and nuclear staining to automatically segment cells in two dimensions and nuclei in three dimensions. This segmentation can be performed on a desktop computer or a computing cluster for higher throughput. We compare and evaluate the accuracy of different nuclear segmentation approaches against manual expert cell segmentation for different cell lines acquired with different imaging modalities.
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10 MeSH Terms
Sulfenylation of Human Liver and Kidney Microsomal Cytochromes P450 and Other Drug-Metabolizing Enzymes as a Response to Redox Alteration.
Albertolle ME, Phan TTN, Pozzi A, Guengerich FP
(2018) Mol Cell Proteomics 17: 889-900
MeSH Terms: Animals, Biocatalysis, Cysteine, Cytochrome P-450 Enzyme System, Humans, Hydrogen Peroxide, Kidney, Mice, Transgenic, Microsomes, Liver, Oxidation-Reduction, Pharmaceutical Preparations, Recombinant Proteins, Staining and Labeling, Sulfenic Acids, Sulfhydryl Compounds
Show Abstract · Added March 14, 2018
The lumen of the endoplasmic reticulum (ER) provides an oxidizing environment to aid in the formation of disulfide bonds, which is tightly regulated by both antioxidant proteins and small molecules. On the cytoplasmic side of the ER, cytochrome P450 (P450) proteins have been identified as a superfamily of enzymes that are important in the formation of endogenous chemicals as well as in the detoxication of xenobiotics. Our previous report described oxidative inhibition of P450 Family 4 enzymes via oxidation of the heme-thiolate cysteine to a sulfenic acid (-SOH) (Albertolle, M. E. (2017) 292, 11230-11242). Further proteomic analyses of murine kidney and liver microsomes led to the finding that a number of other drug-metabolizing enzymes located in the ER are also redox-regulated in this manner. We expanded our analysis of sulfenylated enzymes to human liver and kidney microsomes. Evaluation of the sulfenylation, catalytic activity, and spectral properties of P450s 1A2, 2C8, 2D6, and 3A4 led to the identification of two classes of redox sensitivity in P450 enzymes: heme-thiolate-sensitive and thiol-insensitive. These findings provide evidence for a mammalian P450 regulatory mechanism, which may also be relevant to other drug-metabolizing enzymes. (Data are available via ProteomeXchange with identifier PXD007913.).
© 2018 by The American Society for Biochemistry and Molecular Biology, Inc.
1 Communities
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15 MeSH Terms
Cavernous Nerve Injury by Radiation Therapy May Potentiate Erectile Dysfunction in Rats.
Mahmood J, Connors CQ, Alexander AA, Pavlovic R, Samanta S, Soman S, Matsui H, Sopko NA, Bivalacqua TJ, Weinreich D, Ho CY, Eley J, Sawant A, Jackson IL, Vujaskovic Z
(2017) Int J Radiat Oncol Biol Phys 99: 680-688
MeSH Terms: Animals, Disease Models, Animal, Erectile Dysfunction, Male, Neural Conduction, Parasympathetic Fibers, Postganglionic, Penile Erection, Penis, Prostate, Radiation Injuries, Experimental, Random Allocation, Rats, Rats, Sprague-Dawley, Staining and Labeling
Show Abstract · Added March 30, 2020
PURPOSE/OBJECTIVES - Radiation-induced erectile-dysfunction (RiED) is one of the most common side effects of radiation therapy (RT) and significantly reduces the quality of life (QoL) of cancer patients. Approximately 50% of prostate cancer patients experience RiED within 3 to 5 years after completion of RT. A series of vascular, muscular, and neurogenic injuries after prostate RT lead to RiED; however, the precise role of RT-induced neurogenic injury in RiED has not been fully established. The cavernous nerves (CN) are postganglionic parasympathetic nerves located beside the prostate gland that assist in penile erection. This study was designed to investigate the role of CN injury, tissue damage, and altered signaling pathways in an RiED rat model.
METHODS AND MATERIALS - Male rats were exposed to a single dose of 25 Gy prostate-confined RT. Erectile function was evaluated by intracavernous pressure (ICP) measurements conducted both 9 and 14 weeks after RT. Neuronal injury was evaluated in the CN using quantitative polymerase chain reaction, conduction studies, transmission electron microscopy, and immunoblotting. Masson trichrome staining was performed to elucidate fibrosis level in penile tissues.
RESULTS - There were significant alterations in the ICP (P<.0001) of RT rats versus non-RT rats. TEM analysis showed decreased myelination, increased microvascular damage, and progressive axonal atrophy of the CN fibers after RT. Electrophysiologic analysis showed significant impairment of the CN conduction velocity after RT. RT also significantly increased RhoA/Rho-associated protein kinase 1 (ROCK1) mRNA and protein expression. In addition, penile tissue showed increased apoptosis and fibrosis 14 weeks after RT.
CONCLUSIONS - RT-induced CN injury may contribute to RiED; this is therefore a rationale for developing novel therapeutic strategies to mitigate CN and tissue damage. Moreover, further investigation of the RhoA/ROCK pathway's role in mitigating RiED is necessary.
Copyright © 2017 Elsevier Inc. All rights reserved.
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MeSH Terms
Isotopically nonstationary C flux analysis of cyanobacterial isobutyraldehyde production.
Jazmin LJ, Xu Y, Cheah YE, Adebiyi AO, Johnson CH, Young JD
(2017) Metab Eng 42: 9-18
MeSH Terms: Aldehydes, Bacterial Proteins, Carbon Isotopes, Malate Dehydrogenase, Phosphoenolpyruvate Carboxylase, Pyruvate Kinase, Staining and Labeling, Synechococcus
Show Abstract · Added September 11, 2017
We applied isotopically nonstationary C metabolic flux analysis (INST-MFA) to compare the pathway fluxes of wild-type (WT) Synechococcus elongatus PCC 7942 to an engineered strain (SA590) that produces isobutyraldehyde (IBA). The flux maps revealed a potential bottleneck at the pyruvate kinase (PK) reaction step that was associated with diversion of flux into a three-step PK bypass pathway involving the enzymes PEP carboxylase (PEPC), malate dehydrogenase (MDH), and malic enzyme (ME). Overexpression of pk in SA590 led to a significant improvement in IBA specific productivity. Single-gene overexpression of the three enzymes in the proposed PK bypass pathway also led to improvements in IBA production, although to a lesser extent than pk overexpression. Combinatorial overexpression of two of the three genes in the proposed PK bypass pathway (mdh and me) led to improvements in specific productivity that were similar to those achieved by single-gene pk overexpression. Our work demonstrates how C flux analysis can be used to identify potential metabolic bottlenecks and novel metabolic routes, and how these findings can guide rational metabolic engineering of cyanobacteria for increased production of desired molecules.
Copyright © 2017 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.
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8 MeSH Terms
Intracellular Staining and Flow Cytometry to Identify Lymphocyte Subsets within Murine Aorta, Kidney and Lymph Nodes in a Model of Hypertension.
Laroumanie F, Dale BL, Saleh MA, Madhur MS
(2017) J Vis Exp :
MeSH Terms: Angiotensin II, Animals, Aorta, Cytokines, Disease Models, Animal, Flow Cytometry, Hypertension, Kidney, Lymph Nodes, Mice, Staining and Labeling, T-Lymphocyte Subsets
Show Abstract · Added September 7, 2017
It is now well known that T lymphocytes play a critical role in the development of several cardiovascular diseases. For example, studies from our group have shown that hypertension is associated with an excessive accumulation of T cells in the vessels and kidney during the development of experimental hypertension. Once in these tissues, T cells produce several cytokines that affect both vascular and renal function leading to vasoconstriction and sodium and water retention. To fully understand how T cells cause cardiovascular and renal diseases, it is important to be able to identify and quantify the specific T cell subsets present in these tissues. T cell subsets are defined by a combination of surface markers, the cytokines they secrete, and the transcription factors they express. The complexity of the T cell population makes flow cytometry and intracellular staining an invaluable technique to dissect the phenotypes of the lymphocytes present in tissues. Here, we provide a detailed protocol to identify the surface and intracellular markers (cytokines and transcription factors) in T cells isolated from murine kidney, aorta and aortic draining lymph nodes in a model of angiotensin II induced hypertension. The following steps are described in detail: isolation of the tissues, generation of the single cell suspensions, ex vivo stimulation, fixation, permeabilization and staining. In addition, several fundamental principles of flow cytometric analyses including choosing the proper controls and appropriate gating strategies are discussed.
1 Communities
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12 MeSH Terms
The use of fluorescently-tagged apoptolidins in cellular uptake and response studies.
Chong KM, Leelatian N, Deguire SM, Brockman AA, Earl D, Ihrie RA, Irish JM, Bachmann BO, Sulikowski GA
(2016) J Antibiot (Tokyo) 69: 327-30
MeSH Terms: A549 Cells, Biological Transport, Cell Line, Tumor, Flow Cytometry, Fluorescent Dyes, Humans, Macrolides, Staining and Labeling
Show Abstract · Added March 12, 2016
The apoptolidins are glycomacrolide microbial metabolites reported to be selectively cytotoxic against tumor cells. Using fluorescently tagged active derivatives we demonstrate selective uptake of these four tagged glycomacrolides in cancer cells over healthy human blood cells. We also demonstrate the utility of these five fluorescently tagged glycomacrolides in fluorescent flow cytometry to monitor cellular uptake of the six glycomacrolides and cellular response.
2 Communities
2 Members
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8 MeSH Terms
Fluorescent Protein Approaches in Alpha Herpesvirus Research.
Hogue IB, Bosse JB, Engel EA, Scherer J, Hu JR, Del Rio T, Enquist LW
(2015) Viruses 7: 5933-61
MeSH Terms: Alphaherpesvirinae, Biomedical Research, Host-Pathogen Interactions, Luminescent Proteins, Recombinant Fusion Proteins, Staining and Labeling, Virology
Show Abstract · Added April 6, 2019
In the nearly two decades since the popularization of green fluorescent protein (GFP), fluorescent protein-based methodologies have revolutionized molecular and cell biology, allowing us to literally see biological processes as never before. Naturally, this revolution has extended to virology in general, and to the study of alpha herpesviruses in particular. In this review, we provide a compendium of reported fluorescent protein fusions to herpes simplex virus 1 (HSV-1) and pseudorabies virus (PRV) structural proteins, discuss the underappreciated challenges of fluorescent protein-based approaches in the context of a replicating virus, and describe general strategies and best practices for creating new fluorescent fusions. We compare fluorescent protein methods to alternative approaches, and review two instructive examples of the caveats associated with fluorescent protein fusions, including describing several improved fluorescent capsid fusions in PRV. Finally, we present our future perspectives on the types of powerful experiments these tools now offer.
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Analysis of the Phosphoinositide Composition of Subcellular Membrane Fractions.
Sarkes DA, Rameh LE
(2016) Methods Mol Biol 1376: 213-27
MeSH Terms: Cell Fractionation, Cell Membrane, Chromatography, High Pressure Liquid, Phosphatidylinositols, Staining and Labeling, Subcellular Fractions, Tritium
Show Abstract · Added November 26, 2018
Phosphoinositides play critical roles in the transduction of extracellular signals through the plasma membrane and also in endomembrane events important for vesicle trafficking and organelle function (Di Paolo and De Camilli, Nature 443(7112):651-657, 2006). The response triggered by these lipids is heavily dependent on the microenvironment in which they are found. HPLC analysis of labeled phosphoinositides allows quantification of the levels of each phosphoinositide species relative to their precursor, phosphatidylinositol. When combined with subcellular fractionation techniques, this strategy allows measurement of the relative phosphoinositide composition of each membrane fraction or organelle and determination of the microenvironment in which each species is enriched. Here, we describe the steps to separate and quantify total or localized phosphoinositides from cultured cells.
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Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping.
Treweek JB, Chan KY, Flytzanis NC, Yang B, Deverman BE, Greenbaum A, Lignell A, Xiao C, Cai L, Ladinsky MS, Bjorkman PJ, Fowlkes CC, Gradinaru V
(2015) Nat Protoc 10: 1860-1896
MeSH Terms: Animals, Detergents, Histocytochemistry, Lipids, Mice, Optical Imaging, Pathology, Rats, Specimen Handling, Staining and Labeling, Time Factors, Tissue Embedding, Tissue Fixation
Show Abstract · Added July 20, 2016
To facilitate fine-scale phenotyping of whole specimens, we describe here a set of tissue fixation-embedding, detergent-clearing and staining protocols that can be used to transform excised organs and whole organisms into optically transparent samples within 1-2 weeks without compromising their cellular architecture or endogenous fluorescence. PACT (passive CLARITY technique) and PARS (perfusion-assisted agent release in situ) use tissue-hydrogel hybrids to stabilize tissue biomolecules during selective lipid extraction, resulting in enhanced clearing efficiency and sample integrity. Furthermore, the macromolecule permeability of PACT- and PARS-processed tissue hybrids supports the diffusion of immunolabels throughout intact tissue, whereas RIMS (refractive index matching solution) grants high-resolution imaging at depth by further reducing light scattering in cleared and uncleared samples alike. These methods are adaptable to difficult-to-image tissues, such as bone (PACT-deCAL), and to magnified single-cell visualization (ePACT). Together, these protocols and solutions enable phenotyping of subcellular components and tracing cellular connectivity in intact biological networks.
1 Communities
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13 MeSH Terms