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Gorczyza M, Schoepke N, Krause K, Hawro T, Maurer M. Patients with chronic cold urticaria may benefit from doxycycline therapy. Br J Dermatol 2016; 176:259-261. [DOI: 10.1111/bjd.14820] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Franz F, Weidinger C, Krause K, Gimm O, Dralle H, Führer D. The Transcriptional Regulation of FOXO Genes in Thyrocytes. Horm Metab Res 2016; 48:601-6. [PMID: 27258970 DOI: 10.1055/s-0042-105153] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
FOXO transcription factors are key regulators of DNA damage repair, proliferation and apoptosis in thyrocytes. Thyroid malignancies show impaired FOXO function. In this study, we investigated the transcriptional regulation of FOXO isoforms in thyroid epithelial cells. mRNA expression of FOXO isoforms (FOXO1, 3 and 4) was determined in FRTL-5 cells stimulated with different growth factors and H2O2. Furthermore, the impact of PI3K/AKT signalling on FOXO transcription was investigated in PI3K p110α mutant FRTL-5 cells and regulatory dependence of FOXO transcription on FOXO was studied in FRTL-5 cells with hFOXO3 overexpression. Finally, mRNA expression levels of FOXO isoforms were determined in human epithelial thyroid tumours. Growth factor deprivation induced transcription of FOXO1, 3 and 4, whereas insulin stimulation decreased FOXO1 and FOXO4 transcription in FRTL-5 cells. Inhibition of the PI3K/AKT cascade amplified FOXO1 and FOXO4 expression. In contrast, H2O2 and TSH did not influence FOXO transcription in thyrocytes. Overexpression of PI3K p110α inhibited FOXO3 and induced FOXO4 transcription. In human thyroid tumours, FOXO1 and FOXO3 mRNA levels were significantly downregulated in papillary thyroid carcinoma when compared to normal tissues. In contrast, follicular thyroid carcinomas showed significant upregulation of FOXO4 mRNA.In this paper, we demonstrate an influence of PI3K signalling on FOXO transcription in thyrocytes. Moreover, we show that thyroid cancers exhibit alterations in FOXO transcription besides the previously reported alterations in posttranslational FOXO3 regulation. These findings may add to the concept of targeting the PI3K pathway in advanced thyroid cancers.
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Krüger J, Scholz M, Gross A, Krause K, Marzi C, Grallert H, Ladenvall C, Schleinitz D, Kirsten H, Heyne H, Laurila E, Kriebel J, Thorand B, Rathmann W, Groop L, Prokopenko I, Isomaa B, Beutner F, Kratzsch J, Thiery J, Klöting N, Fischer-Rosinský A, Pfeiffer A, Spranger J, Gieger C, Blüher M, Stumvoll M, Kovacs P, Tönjes A. Genome wide meta-analysis identifies novel regulators of circulating serum progranulin. DIABETOL STOFFWECHS 2016. [DOI: 10.1055/s-0036-1580916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Olsen S, Striberny B, Hollmann J, Schwacke R, Popper Z, Krause K. Getting ready for host invasion: elevated expression and action of xyloglucan endotransglucosylases/hydrolases in developing haustoria of the holoparasitic angiosperm Cuscuta. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:695-708. [PMID: 26561437 PMCID: PMC4737069 DOI: 10.1093/jxb/erv482] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Changes in cell walls have been previously observed in the mature infection organ, or haustorium, of the parasitic angiosperm Cuscuta, but are not equally well charted in young haustoria. In this study, we focused on the molecular processes in the early stages of developing haustoria; that is, before the parasite engages in a physiological contact with its host. We describe first the identification of differentially expressed genes in young haustoria whose development was induced by far-red light and tactile stimuli in the absence of a host plant by suppression subtractive hybridization. To improve sequence information and to aid in the identification of the obtained candidates, reference transcriptomes derived from two species of Cuscuta, C. gronovii and C. reflexa, were generated. Subsequent quantitative gene expression analysis with different tissues of C. reflexa revealed that among the genes that were up-regulated in young haustoria, two xyloglucan endotransglucosylase/hydrolase (XTH) genes were highly expressed almost exclusively at the onset of haustorium development. The same expression pattern was also found for the closest XTH homologues from C. gronovii. In situ assays for XTH-specific action suggested that xyloglucan endotransglucosylation was most pronounced in the cell walls of the swelling area of the haustorium facing the host plant, but was also detectable in later stages of haustoriogenesis. We propose that xyloglucan remodelling by Cuscuta XTHs prepares the parasite for host infection and possibly aids the invasive growth of the haustorium.
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Olsen S, Popper ZA, Krause K. Two sides of the same coin: Xyloglucan endotransglucosylases/hydrolases in host infection by the parasitic plant Cuscuta. PLANT SIGNALING & BEHAVIOR 2016; 11:e1145336. [PMID: 26852915 PMCID: PMC4883916 DOI: 10.1080/15592324.2016.1145336] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 01/18/2016] [Indexed: 05/29/2023]
Abstract
The holoparasitic angiosperm Cuscuta develops haustoria that enable it to feed on other plants. Recent findings corroborate the long-standing theory that cell wall modifications are required in order for the parasite to successfully infect a host, and further suggest that changes to xyloglucan through the activity of xyloglucan endotransglucosylases/hydrolases (XTHs) are essential. On the other hand, XTH expression was also detected in resistant tomato upon an attack by Cuscuta, which suggests that both host and parasite use these enzymes in their "arms race." Here, we summarize existing data on the cell wall-modifying activities of XTHs during parasitization and present a model suggesting how XTHs might function to make the host's resources accessible to Cuscuta.
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Bonnekoh H, Maurer M, Krause K. Interleukin-1-related cytokines as potential biomarkers in autoinflammatory skin diseases. Pediatr Rheumatol Online J 2015. [PMCID: PMC4599984 DOI: 10.1186/1546-0096-13-s1-p197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
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Kuemmerle-Deschner J, Hofer F, Endres T, Kortus-Goetze B, Blank N, Weißbarth-Riedel E, Schuetz C, Kallinich T, Krause K, Rietschel C, Horneff G, Benseler SM. Canakinumab treat-to target strategies increase complete response rate in CAPS. Pediatr Rheumatol Online J 2015. [PMCID: PMC4599896 DOI: 10.1186/1546-0096-13-s1-p173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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58
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Meyer C, Gürtler D, Krause K, Freyer-Adam J, Ulbricht S, Bischof G, Rumpf HJ, Batra A, Stiegler A, Chenot JF, Grabe HJ, John U. Entwicklung und Evaluation einer computergestützten Beratung für Patienten mit gesundheitsriskantem Alkoholkonsum und depressiven Symptomen. DAS GESUNDHEITSWESEN 2015. [DOI: 10.1055/s-0035-1562972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Krause K, Gürtler D, Bischof G, Rumpf HJ, Meyer C, John U. Verfügbarkeit von Internet-, computer- und smartphonebasierten Interventionen bei Depressionen. DAS GESUNDHEITSWESEN 2015. [DOI: 10.1055/s-0035-1563048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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60
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Johnsen HR, Striberny B, Olsen S, Vidal-Melgosa S, Fangel JU, Willats WGT, Rose JKC, Krause K. Cell wall composition profiling of parasitic giant dodder (Cuscuta reflexa) and its hosts: a priori differences and induced changes. THE NEW PHYTOLOGIST 2015; 207:805-16. [PMID: 25808919 DOI: 10.1111/nph.13378] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 02/16/2015] [Indexed: 05/02/2023]
Abstract
Host plant penetration is the gateway to survival for holoparasitic Cuscuta and requires host cell wall degradation. Compositional differences of cell walls may explain why some hosts are amenable to such degradation while others can resist infection. Antibody-based techniques for comprehensive profiling of cell wall epitopes and cell wall-modifying enzymes were applied to several susceptible hosts and a resistant host of Cuscuta reflexa and to the parasite itself. Infected tissue of Pelargonium zonale contained high concentrations of de-esterified homogalacturonans in the cell walls, particularly adjacent to the parasite's haustoria. High pectinolytic activity in haustorial extracts and high expression levels of pectate lyase genes suggest that the parasite contributes directly to wall remodeling. Mannan and xylan concentrations were low in P. zonale and in five susceptible tomato introgression lines, but high in the resistant Solanum lycopersicum cv M82, and in C. reflexa itself. Knowledge of the composition of resistant host cell walls and the parasite's own cell walls is useful in developing strategies to prevent infection by parasitic plants.
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Krause K. Grand-scale theft: kleptoplasty in parasitic plants? TRENDS IN PLANT SCIENCE 2015; 20:196-198. [PMID: 25795238 DOI: 10.1016/j.tplants.2015.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 03/04/2015] [Accepted: 03/05/2015] [Indexed: 06/04/2023]
Abstract
The angiosperm Rafflesia lives as an obligate holoparasite in intimate contact with its hosts, vines in the genus Tetrastigma. The hosts are forced to supply the parasite with all the necessary nutrients. Novel data tentatively suggest that the thievery may happen on a larger scale and include entire organellar genomes.
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Krause K, Kranz M, Weiner J, Klöting N, Rijntjes E, Köhrle J, Zeisig V, Steinhoff K, Deuther-Conrad W, Fasshauer M, Stumvoll M, Sabri O, Blüher M, Hesse S, Brust P, Tönjes A. Influence of thyroid hormones on brown adipose tissue activity and browning of white adipose tissues in mice. Exp Clin Endocrinol Diabetes 2015. [DOI: 10.1055/s-0035-1549076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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63
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Striberny B, Krause K. Cell wall glycoproteins at interaction sites between parasitic giant dodder (Cuscuta reflexa) and its host Pelargonium zonale. PLANT SIGNALING & BEHAVIOR 2015; 10:e1086858. [PMID: 26367804 PMCID: PMC4883938 DOI: 10.1080/15592324.2015.1086858] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 08/20/2015] [Accepted: 08/20/2015] [Indexed: 05/21/2023]
Abstract
The process of host plant penetration by parasitic dodder (genus Cuscuta) is accompanied by molecular and structural changes at the host/parasite interface. Recently, changes in pectin methyl esterification levels in the host cell walls abutting parasitic cells in established infection sites were reported. In addition to that, we show here that the composition of cell wall glycoproteins in Cuscuta-infected Pelargonium zonale undergoes substantial changes. While several arabinogalactan protein epitopes exhibit decreased abundances in the vicinity of the Cuscuta reflexa haustorium, extensins tend to increase in the infected areas.
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Hankir M, Krause K, Tönjes A, Fenske WK, Sabri O, Hesse S, Steinhoff KG. Interaction of thyroid hormone with brown adipose tissue. Nuklearmedizin 2015. [DOI: 10.1055/s-0037-1616608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
SummaryBrown adipose tissue (BAT) plays an important role in regulating core-body temperature in various species including man. [18F]FDGPET/ CT imaging first revealed the presence of metabolically active BAT depots and that decreased BAT function is associated with various metabolic conditions. Thyroid hormone (TH) in concert with sympathetic nervous system signalling (SNS) stimulates BAT thermogenesis and thyroid disorders result in dysfunctional BAT. Currently, research is focussing not only on BAT regulation but also on browning of white adipose tissue (WAT) to BAT beige adipose tissue (BeAT) in order to develop novel treatments for human obesity and related conditions. While [18F]FDG-PET/ CT imaging is continuing to provide valuable insights into BAT and BeAT function in health and disease, there is a pressing need to develop alternative radiotracers that reliably track their activity in vivo. As a result it is expected that preclinical micro PET/CT investigations of BAT and BeAT will gain in prominence.The aim of this short review is to i) describe fundamentals in BAT biology, ii) highlight some of the clinical and preclinical studies performed on humans and rodents with a focus on TH, BAT and PET/CT, and iii) bridge these data with our own studies within the DFG thyroid transact priority program.
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Steinhoff KG, Hankir M, Krause K, Tönjes A, Fenske WK, Sabri O, Hesse S. Interaction of thyroid hormone with brown adipose tissue. Lessons learned from PET-CT. Nuklearmedizin 2015; 54:82-87. [PMID: 26105715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 05/20/2015] [Indexed: 06/04/2023]
Abstract
Brown adipose tissue (BAT) plays an important role in regulating core-body temperature in various species including man. [18F]FDG-PET/CT imaging first revealed the presence of metabolically active BAT depots and that decreased BAT function is associated with various metabolic conditions. Thyroid hormone (TH) in concert with sympathetic nervous system signalling (SNS) stimulates BAT thermogenesis and thyroid disorders result in dysfunctional BAT. Currently, research is focussing not only on BAT regulation but also on browning of white adipose tissue (WAT) to BAT beige adipose tissue (BeAT) in order to develop novel treatments for human obesity and related conditions. While [18F]FDG-PET/CT imaging is continuing to provide valuable insights into BAT and BeAT function in health and disease, there is a pressing need to develop alternative radiotracers that reliably track their activity in vivo. As a result it is expected that preclinical micro PET/CT investigations of BAT and BeAT will gain in prominence. The aim of this short review is to i) describe fundamentals in BAT biology, ii) highlight some of the clinical and preclinical studies performed on humans and rodents with a focus on TH, BAT and PET/CT, and iii) bridge these data with our own studies within the DFG thyroid transact priority program.
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Jain K, Krause K, Grewe F, Nelson GF, Weber APM, Christensen AC, Mower JP. Extreme features of the Galdieria sulphuraria organellar genomes: a consequence of polyextremophily? Genome Biol Evol 2014; 7:367-80. [PMID: 25552531 PMCID: PMC4316638 DOI: 10.1093/gbe/evu290] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Nuclear genome sequencing from extremophilic eukaryotes has revealed clues about the mechanisms of adaptation to extreme environments, but the functional consequences of extremophily on organellar genomes are unknown. To address this issue, we assembled the mitochondrial and plastid genomes from a polyextremophilic red alga, Galdieria sulphuraria strain 074 W, and performed a comparative genomic analysis with other red algae and more broadly across eukaryotes. The mitogenome is highly reduced in size and genetic content and exhibits the highest guanine–cytosine skew of any known genome and the fastest substitution rate among all red algae. The plastid genome contains a large number of intergenic stem-loop structures but is otherwise rather typical in size, structure, and content in comparison with other red algae. We suggest that these unique genomic modifications result not only from the harsh conditions in which Galdieria lives but also from its unusual capability to grow heterotrophically, endolithically, and in the dark. These conditions place additional mutational pressures on the mitogenome due to the increased reliance on the mitochondrion for energy production, whereas the decreased reliance on photosynthesis and the presence of numerous stem-loop structures may shield the plastome from similar genomic stress.
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Krause K, Güttsches A, Maerkens A, Brady S, Tegenthoff M, Holton J, Marcus K, Vorgerd M, Kley R. G.P.64. Neuromuscul Disord 2014. [DOI: 10.1016/j.nmd.2014.06.078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Magerl M, Abajian M, Krause K, Altrichter S, Siebenhaar F, Church MK. An improved Peltier effect-based instrument for critical temperature threshold measurement in cold- and heat-induced urticaria. J Eur Acad Dermatol Venereol 2014; 29:2043-5. [PMID: 25266078 DOI: 10.1111/jdv.12739] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 08/05/2014] [Indexed: 11/30/2022]
Abstract
BACKGROUND Cold- and heat-induced urticaria are chronic physical urticaria conditions in which wheals, angioedema or both are evoked by skin exposure to cold and heat respectively. The diagnostic work up of both conditions should include skin provocation tests and accurate determination of critical temperature thresholds (CTT) for producing symptoms in order to be able to predict the potential risk that each individual patient faces and how this may be ameliorated by therapy. OBJECTIVE To develop and validate TempTest(®) 4, a simple and relatively inexpensive instrument for the accurate determination of CTT which may be used in clinical practice. METHODS TempTest(®) 4 has a single 2 mm wide 350 mm U-shaped Peltier element generating a temperature gradient from 4 °C to 44 °C along its length. Using a clear plastic guide placed over the skin after provocation, CTT values may be determined with an accuracy of ±1 °C. Here, TempTest(®) 4 was compared with its much more expensive predecessor, TempTest(®) 3, in inducing wheals in 30 cold urticaria patients. RESULTS Both TempTest(®) 4 and TempTest(®) 3 induced wheals in all 30 patients between 8 ° and 28 °C. There was a highly significant (P < 0.0001) correlation between the instruments in the CTT values in individual patients. CONCLUSION The TempTest(®) 4 is a simple, easy to use, licensed, commercially available and affordable instrument for the determination of CTTs in both cold- and heat-induced urticaria.
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Gupta G, Wen Y, Akram M, Krause K, Brogi E, Powell S, Ho A, Petrini J. Low Mre11 Complex Expression Identifies a Subset of Triple Negative Breast Cancer With Excellent Outcomes. Int J Radiat Oncol Biol Phys 2014. [DOI: 10.1016/j.ijrobp.2014.05.229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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70
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Ho A, Morrow M, Krause K, Siu C, Mehrara B, Cordeiro P, Zhang Z, McCormick B, Powell S. The Effect of Radiation Timing in Breast Cancer Patients with Implant-Based Reconstruction. Int J Radiat Oncol Biol Phys 2014. [DOI: 10.1016/j.ijrobp.2014.05.170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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71
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Setton J, Morrow M, Lok B, Krause K, Chun S, Pei X, McCormick B, Powell S, Ho A. Impact of Approximated Biological Subtype on Locoregional Recurrence in Women With Node-Negative Breast Cancer Treated With Mastectomy. Int J Radiat Oncol Biol Phys 2014. [DOI: 10.1016/j.ijrobp.2014.05.228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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72
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Krause K, Kranz M, Zeisig V, Klöting N, Steinhoff K, Deuther-Conrad W, Fasshauer M, Stumvoll M, Sabri O, Hesse S, Brust P, Tönjes A. The influence of thyroid dysfunction on the activity of brown adipose tissue in mice detected by [18F]FDG PET/MR. DIABETOL STOFFWECHS 2014. [DOI: 10.1055/s-0034-1374879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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73
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Holz JB, Sargentini-Maier L, De Bruyn S, Gachályi B, Udvaros I, Rojkovich B, Bruk S, Sramek P, Korkosz M, Krause K, Schoen P, D’Artois J, Verschueren K, Willems W, De Swert K, Arold G. OP0043 Twenty-Four Weeks of Treatment with a Novel Anti-IL-6 Receptor Nanobody® (ALX-0061) Resulted in 84% ACR20 Improvement and 58% DAS28 Remission in a Phase I/Ii Study in RA. Ann Rheum Dis 2014. [DOI: 10.1136/annrheumdis-2013-eular.248] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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74
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Hofer F, Endres T, Kortus-Götze B, Blank N, Weißbarth-Riedel E, Schütz C, Kallinich T, Krause K, Rietschel C, Horneff G, Kuemmerle-Deschner J. PReS-FINAL-2224: Canakinumab treatment regimens in CAPS-patients. Pediatr Rheumatol Online J 2013. [PMCID: PMC4043406 DOI: 10.1186/1546-0096-11-s2-p214] [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] Open
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75
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Fuss J, Liegmann O, Krause K, Rensing SA. Green targeting predictor and ambiguous targeting predictor 2: the pitfalls of plant protein targeting prediction and of transient protein expression in heterologous systems. THE NEW PHYTOLOGIST 2013; 200:1022-33. [PMID: 23915300 DOI: 10.1111/nph.12433] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 07/01/2013] [Indexed: 05/08/2023]
Abstract
The challenges of plant protein targeting prediction are the existence of dual subcellular targets and the bias of experimentally confirmed data towards few and mostly nonplant model species. To assess whether training with proteins from evolutionarily distant species has a negative impact on prediction accuracy, we developed the Green Targeting Predictor tool, which was trained with a species-specific data set for Physcomitrella patens. Its performance was compared with that of the same tool trained with a mixed data set. In addition, we updated the Ambiguous Targeting Predictor. We found that predictions deviated from in vivo observations predominantly for proteins diverging within the green lineage, as well as for dual targeted proteins. To evaluate the usefulness of heterologous expression systems, selected proteins were subjected to localization studies in P. patens, Arabidopsis thaliana and Nicotiana tabacum. Four out of six proteins that show dual targeting in the original plant system were located only in a single compartment in one or both heterologous systems. We conclude that targeting signals of divergent plant species exhibit differences, calling for custom in silico and in vivo approaches when aiming to unravel the actual distribution patterns of proteins within a plant cell.
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