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Wolter S, Löschberger A, Holm T, Aufmkolk S, Dabauvalle MC, van de Linde S, Sauer M. rapidSTORM: accurate, fast open-source software for localization microscopy. Nat Methods 2012; 9:1040-1. [DOI: 10.1038/nmeth.2224] [Citation(s) in RCA: 297] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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227
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Owen DM, Sauer M, Gaus K. Fluorescence localization microscopy: The transition from concept to biological research tool. Commun Integr Biol 2012; 5:345-9. [PMID: 23060958 PMCID: PMC3460839 DOI: 10.4161/cib.20348] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Localization microscopy techniques are super-resolution fluorescence imaging methods based on the detection of individual molecules. Despite the relative simplicity of the microscope setups and the availability of commercial instruments, localization microscopy faces unique challenges. While achieving super-resolution is now routine, issues concerning data analysis and interpretation mean that revealing novel biological insights is not. Here, we outline why data analysis and the design of robust test samples may hold the key to harness the full potential of localization microscopy.
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228
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Andronic J, Bobak N, Bittner S, Ehling P, Kleinschnitz C, Herrmann AM, Zimmermann H, Sauer M, Wiendl H, Budde T, Meuth SG, Sukhorukov VL. Identification of two-pore domain potassium channels as potent modulators of osmotic volume regulation in human T lymphocytes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1828:699-707. [PMID: 23041580 DOI: 10.1016/j.bbamem.2012.09.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 09/21/2012] [Accepted: 09/27/2012] [Indexed: 11/17/2022]
Abstract
Many functions of T lymphocytes are closely related to cell volume homeostasis and regulation, which utilize a complex network of membrane channels for anions and cations. Among the various potassium channels, the voltage-gated K(V)1.3 is well known to contribute greatly to the osmoregulation and particularly to the potassium release during the regulatory volume decrease (RVD) of T cells faced with hypotonic environment. Here we address a putative role of the newly identified two-pore domain (K(2P)) channels in the RVD of human CD4(+) T lymphocytes, using a series of potent well known channel blockers. In the present study, the pharmacological profiles of RVD inhibition revealed K(2P)5.1 and K(2P)18.1 as the most important K(2P) channels involved in the RVD of both naïve and stimulated T cells. The impact of chemical inhibition of K(2P)5.1 and K(2P)18.1 on the RVD was comparable to that of K(V)1.3. K(2P)9.1 also notably contributed to the RVD of T cells but the extent of this contribution and its dependence on the activation status could not be unambiguously resolved. In summary, our data provide first evidence that the RVD-related potassium efflux from human T lymphocytes relies on K(2P) channels.
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229
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Löschberger A, van de Linde S, Dabauvalle MC, Rieger B, Heilemann M, Krohne G, Sauer M. Super-resolution imaging visualizes the eightfold symmetry of gp210 proteins around the nuclear pore complex and resolves the central channel with nanometer resolution. J Cell Sci 2012; 125:570-5. [PMID: 22389396 DOI: 10.1242/jcs.098822] [Citation(s) in RCA: 239] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
One of the most complex molecular machines of cells is the nuclear pore complex (NPC), which controls all trafficking of molecules in and out of the nucleus. Because of their importance for cellular processes such as gene expression and cytoskeleton organization, the structure of NPCs has been studied extensively during the last few decades, mainly by electron microscopy. We have used super-resolution imaging by direct stochastic optical reconstruction microscopy (dSTORM) to investigate the structure of NPCs in isolated Xenopus laevis oocyte nuclear envelopes, with a lateral resolution of ~15 nm. By generating accumulated super-resolved images of hundreds of NPCs we determined the diameter of the central NPC channel to be 41 ± 7 nm and demonstrate that the integral membrane protein gp210 is distributed in an eightfold radial symmetry. Two-color dSTORM experiments emphasize the highly symmetric NPCs as ideal model structures to control the quality of corrections to chromatic aberration and to test the capability and reliability of super-resolution imaging methods.
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230
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Bar-On D, Wolter S, van de Linde S, Heilemann M, Nudelman G, Nachliel E, Gutman M, Sauer M, Ashery U. Super-resolution imaging reveals the internal architecture of nano-sized syntaxin clusters. J Biol Chem 2012; 287:27158-67. [PMID: 22700970 DOI: 10.1074/jbc.m112.353250] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Key synaptic proteins from the soluble SNARE (N-ethylmaleimide-sensitive factor attachment protein receptor) family, among many others, are organized at the plasma membrane of cells as clusters containing dozens to hundreds of protein copies. However, the exact membranal distribution of proteins into clusters or as single molecules, the organization of molecules inside the clusters, and the clustering mechanisms are unclear due to limitations of the imaging and analytical tools. Focusing on syntaxin 1 and SNAP-25, we implemented direct stochastic optical reconstruction microscopy together with quantitative clustering algorithms to demonstrate a novel approach to explore the distribution of clustered and nonclustered molecules at the membrane of PC12 cells with single-molecule precision. Direct stochastic optical reconstruction microscopy images reveal, for the first time, solitary syntaxin/SNAP-25 molecules and small clusters as well as larger clusters. The nonclustered syntaxin or SNAP-25 molecules are mostly concentrated in areas adjacent to their own clusters. In the clusters, the density of the molecules gradually decreases from the dense cluster core to the periphery. We further detected large clusters that contain several density gradients. This suggests that some of the clusters are formed by unification of several clusters that preserve their original organization or reorganize into a single unit. Although syntaxin and SNAP-25 share some common distributional features, their clusters differ markedly from each other. SNAP-25 clusters are significantly larger, more elliptical, and less dense. Finally, this study establishes methodological tools for the analysis of single-molecule-based super-resolution imaging data and paves the way for revealing new levels of membranal protein organization.
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231
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Hoseini S, Hapke M, Herbst J, Heinz N, Schiedlmeyer B, Krüger A, Sauer M. Timely controlled T cell receptor expression against a leukemia-associated antigen for the co-transplantation of MHC-mismatched T-cell precursors into hematopoietic stem cell (HCT) recipients. KLINISCHE PADIATRIE 2012. [DOI: 10.1055/s-0032-1310489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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232
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Yahiatène I, Doose S, Huser T, Sauer M. Correlation-Matrix Analysis of Two-Color Coincidence Events in Single-Molecule Fluorescence Experiments. Anal Chem 2012; 84:2729-36. [DOI: 10.1021/ac2030283] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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233
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van de Linde S, Heilemann M, Sauer M. Live-cell super-resolution imaging with synthetic fluorophores. Annu Rev Phys Chem 2012; 63:519-40. [PMID: 22404589 DOI: 10.1146/annurev-physchem-032811-112012] [Citation(s) in RCA: 201] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Super-resolution imaging methods now can provide spatial resolution that is well below the diffraction limit approaching virtually molecular resolution. They can be applied to biological samples and provide new and exciting views on the structural organization of cells and the dynamics of biomolecular assemblies on wide timescales. These revolutionary developments come with novel requirements for fluorescent probes, labeling techniques, and data interpretation strategies. Synthetic fluorophores have a small size, are available in many colors spanning the whole spectrum, and can easily be chemically modified and used for stoichiometric labeling of proteins in live cells. Because of their brightness, their photostability, and their ability to be operated as photoswitchable fluorophores even in living cells under physiological conditions, synthetic fluorophores have the potential to substantially accelerate the broad application of live-cell super-resolution imaging methods.
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234
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Löschberger A, van de Linde S, Dabauvalle MC, Rieger B, Heilemann M, Krohne G, Sauer M. The Nuclear Pore Complex as seen by Dstorm. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.3923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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235
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Bollmann S, Burgert A, Plattner C, Nagel L, Sewald N, Löllmann M, Sauer M, Doose S. Conformational Flexibility of Glycosylated Unstructured Peptides. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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236
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Bollmann S, Burgert A, Plattner C, Nagel L, Sewald N, Löllmann M, Sauer M, Doose S. Conformational Flexibility of Glycosylated Peptides. Chemphyschem 2011; 12:2907-11. [DOI: 10.1002/cphc.201100650] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Indexed: 11/08/2022]
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237
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Kaminski Schierle GS, van de Linde S, Erdelyi M, Esbjörner EK, Klein T, Rees E, Bertoncini CW, Dobson CM, Sauer M, Kaminski CF. In situ measurements of the formation and morphology of intracellular β-amyloid fibrils by super-resolution fluorescence imaging. J Am Chem Soc 2011; 133:12902-5. [PMID: 21793568 DOI: 10.1021/ja201651w] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Misfolding and aggregation of peptides and proteins is a characteristic of many neurodegenerative disorders, including Alzheimer's disease (AD). In AD the β-amyloid peptide (Aβ) aggregates to form characteristic fibrillar structures, which are the deposits found as plaques in the brains of patients. We have used direct stochastic optical reconstruction microscopy, dSTORM, to probe the process of in situ Aβ aggregation and the morphology of the ensuing aggregates with a resolution better than 20 nm. We are able to distinguish different types of structures, including oligomeric assemblies and mature fibrils, and observe a number of morphological differences between the species formed in vitro and in vivo, which may be significant in the context of disease. Our data support the recent view that intracellular Aβ could be associated with Aβ pathogenicity in AD, although the major deposits are extracellular, and suggest that this approach will be widely applicable to studies of the molecular mechanisms of protein deposition diseases.
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238
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Sauer M, Graham D, Tinnefeld P. Advanced markers and labels for life science and biomedical applications. JOURNAL OF BIOPHOTONICS 2011; 4:375-376. [PMID: 21612017 DOI: 10.1002/jbio.201100506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
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239
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Vogel B, Löschberger A, Sauer M, Hock R. Cross-linking of DNA through HMGA1 suggests a DNA scaffold. Nucleic Acids Res 2011; 39:7124-33. [PMID: 21596776 PMCID: PMC3167630 DOI: 10.1093/nar/gkr396] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Binding of proteins to DNA is usually considered 1D with one protein bound to one DNA molecule. In principle, proteins with multiple DNA binding domains could also bind to and thereby cross-link different DNA molecules. We have investigated this possibility using high-mobility group A1 (HMGA1) proteins, which are architectural elements of chromatin and are involved in the regulation of multiple DNA-dependent processes. Using direct stochastic optical reconstruction microscopy (dSTORM), we could show that overexpression of HMGA1a-eGFP in Cos-7 cells leads to chromatin aggregation. To investigate if HMGA1a is directly responsible for this chromatin compaction we developed a DNA cross-linking assay. We were able to show for the first time that HMGA1a can cross-link DNA directly. Detailed analysis using point mutated proteins revealed a novel DNA cross-linking domain. Electron microscopy indicates that HMGA1 proteins are able to create DNA loops and supercoils in linearized DNA confirming the cross-linking ability of HMGA1a. This capacity has profound implications for the spatial organization of DNA in the cell nucleus and suggests cross-linking activities for additional nuclear proteins.
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240
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Wolter S, Endesfelder U, van de Linde S, Heilemann M, Sauer M. Measuring localization performance of super-resolution algorithms on very active samples. OPTICS EXPRESS 2011; 19:7020-33. [PMID: 21503016 DOI: 10.1364/oe.19.007020] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Super-resolution fluorescence imaging based on single-molecule localization relies critically on the availability of efficient processing algorithms to distinguish, identify, and localize emissions of single fluorophores. In multiple current applications, such as three-dimensional, time-resolved or cluster imaging, high densities of fluorophore emissions are common. Here, we provide an analytic tool to test the performance and quality of localization microscopy algorithms and demonstrate that common algorithms encounter difficulties for samples with high fluorophore density. We demonstrate that, for typical single-molecule localization microscopy methods such as dSTORM and the commonly used rapidSTORM scheme, computational precision limits the acceptable density of concurrently active fluorophores to 0.6 per square micrometer and that the number of successfully localized fluorophores per frame is limited to 0.2 per square micrometer.
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241
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Lummer M, Humpert F, Steuwe C, Caesar K, Schüttpelz M, Sauer M, Staiger D. Reversible Photoswitchable DRONPA-s Monitors Nucleocytoplasmic Transport of an RNA-Binding Protein in Transgenic Plants. Traffic 2011; 12:693-702. [DOI: 10.1111/j.1600-0854.2011.01180.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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242
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Dertinger T, Heilemann M, Vogel R, Sauer M, Weiss S. Superresolution optical fluctuation imaging with organic dyes. Angew Chem Int Ed Engl 2011; 49:9441-3. [PMID: 21031383 DOI: 10.1002/anie.201004138] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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243
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Noé F, Doose S, Daidone I, Löllmann M, Sauer M, Chodera JD, Smith JC. Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments. Proc Natl Acad Sci U S A 2011; 108:4822-7. [PMID: 21368203 PMCID: PMC3064371 DOI: 10.1073/pnas.1004646108] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
There is a gap between kinetic experiment and simulation in their views of the dynamics of complex biomolecular systems. Whereas experiments typically reveal only a few readily discernible exponential relaxations, simulations often indicate complex multistate behavior. Here, a theoretical framework is presented that reconciles these two approaches. The central concept is "dynamical fingerprints" which contain peaks at the time scales of the dynamical processes involved with amplitudes determined by the experimental observable. Fingerprints can be generated from both experimental and simulation data, and their comparison by matching peaks permits assignment of structural changes present in the simulation to experimentally observed relaxation processes. The approach is applied here to a test case interpreting single molecule fluorescence correlation spectroscopy experiments on a set of fluorescent peptides with molecular dynamics simulations. The peptides exhibit complex kinetics shown to be consistent with the apparent simplicity of the experimental data. Moreover, the fingerprint approach can be used to design new experiments with site-specific labels that optimally probe specific dynamical processes in the molecule under investigation.
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244
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Bollmann S, Löllmann M, Sauer M, Doose S. Dimer formation of organic fluorophores reports on biomolecular dynamics under denaturing conditions. Phys Chem Chem Phys 2011; 13:12874-82. [DOI: 10.1039/c1cp21111k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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245
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Abstract
Within only a few years super-resolution fluorescence imaging based on single-molecule localization and image reconstruction has attracted considerable interest because it offers a comparatively simple way to achieve a substantially improved optical resolution down to ∼20 nm in the image plane. Since super-resolution imaging methods such as photoactivated localization microscopy, fluorescence photoactivation localization microscopy, stochastic optical reconstruction microscopy, and direct stochastic optical reconstruction microscopy rely critically on exact fitting of the centre of mass and the shape of the point-spread-function of isolated emitters unaffected by neighbouring fluorophores, controlled photoswitching or photoactivation of fluorophores is the key parameter for resolution improvement. This review will explain the principles and requirements of single-molecule based localization microscopy, and compare different super-resolution imaging concepts and highlight their strengths and limitations with respect to applications in fixed and living cells with high spatio-temporal resolution.
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246
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Seefeldt B, Altenhöner K, Tosic O, Geisler T, Sauer M, Mattay J. Kinetic studies on visible-light-switchable photochromic fluorophores based on diarylethenes. Photochem Photobiol Sci 2011; 10:1488-95. [DOI: 10.1039/c1pp05051f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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247
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van de Linde S, Krstić I, Prisner T, Doose S, Heilemann M, Sauer M. Photoinduced formation of reversible dye radicals and their impact on super-resolution imaging. Photochem Photobiol Sci 2011; 10:499-506. [DOI: 10.1039/c0pp00317d] [Citation(s) in RCA: 171] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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248
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Janík J, Malý V, Lazanská V, Stanek I, Sauer M. [Intrathoracic goitre--undiagnosed--nevertheless operated]. ROZHLEDY V CHIRURGII : MESICNIK CESKOSLOVENSKE CHIRURGICKE SPOLECNOSTI 2010; 89:663-665. [PMID: 21409797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A case review of a female patient, who was indicated for surgery for a goitre with minor bilateral retrosternal spread. The procedure included bilateral thyroidectomy during which the surgeon noticed unusual intrathoracic pathology in the left hemithorax, under the removed lobe. Postoperative chest x-ray and CT examinations revealed intrathoracic goitre, which was then removed during a following procedure. In the article, the authors discuss this uncommon pathology. Because of its uncommon location, the pathology was not detected on standard preoperative endocrinological examination. It was the follow up, postoperative examination, based on which the correct treatment was initiated.
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249
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Glocker EO, Kotlarz D, Boztug K, Gertz EM, Schäffer AA, Noyan F, Perro M, Diestelhorst J, Allroth A, Murugan D, Hätscher N, Pfeifer D, Sykora KW, Sauer M, Kreipe H, Lacher M, Nustede R, Woellner C, Baumann U, Salzer U, Koletzko S, Shah N, Segal AW, Sauerbrey A, Buderus S, Snapper SB, Grimbacher B, Klein C. Early-onset inflammatory bowel disease caused by mutant IL10 receptor. Lab Invest 2010. [PMCID: PMC3007730 DOI: 10.1186/1479-5876-8-s1-i12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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250
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Dertinger T, Heilemann M, Vogel R, Sauer M, Weiss S. Superresolution Optical Fluctuation Imaging with Organic Dyes. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201004138] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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