[{"day":"01","author":[{"full_name":"Tang, Yong","first_name":"Yong","last_name":"Tang"},{"first_name":"Shutang","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan"},{"full_name":"Xue, Hongwei","first_name":"Hongwei","last_name":"Xue"}],"page":"549-560","volume":45,"quality_controlled":"1","article_type":"original","pmid":1,"publication":"Acta Biochimica et Biophysica Sinica","publication_status":"published","fulldoi":"https://doi.org/10.1093/abbs/gmt039","date_published":"2013-07-01T00:00:00Z","date_created":"2020-03-21T16:06:36Z","issue":"7","type":"journal_article","intvolume":"        45","extern":"1","year":"2013","status":"public","month":"07","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","citation":{"ieee":"Y. Tang, S. Tan, and H. Xue, “Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development,” <i>Acta Biochimica et Biophysica Sinica</i>, vol. 45, no. 7. Oxford University Press, pp. 549–560, 2013.","ista":"Tang Y, Tan S, Xue H. 2013. Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development. Acta Biochimica et Biophysica Sinica. 45(7), 549–560.","short":"Y. Tang, S. Tan, H. Xue, Acta Biochimica et Biophysica Sinica 45 (2013) 549–560.","chicago":"Tang, Yong, Shutang Tan, and Hongwei Xue. “Arabidopsis Inositol 1,3,4-Trisphosphate 5/6 Kinase 2 Is Required for Seed Coat Development.” <i>Acta Biochimica et Biophysica Sinica</i>. Oxford University Press, 2013. <a href=\"https://doi.org/10.1093/abbs/gmt039\">https://doi.org/10.1093/abbs/gmt039</a>.","ama":"Tang Y, Tan S, Xue H. Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development. <i>Acta Biochimica et Biophysica Sinica</i>. 2013;45(7):549-560. doi:<a href=\"https://doi.org/10.1093/abbs/gmt039\">10.1093/abbs/gmt039</a>","mla":"Tang, Yong, et al. “Arabidopsis Inositol 1,3,4-Trisphosphate 5/6 Kinase 2 Is Required for Seed Coat Development.” <i>Acta Biochimica et Biophysica Sinica</i>, vol. 45, no. 7, Oxford University Press, 2013, pp. 549–60, doi:<a href=\"https://doi.org/10.1093/abbs/gmt039\">10.1093/abbs/gmt039</a>.","apa":"Tang, Y., Tan, S., &#38; Xue, H. (2013). Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development. <i>Acta Biochimica et Biophysica Sinica</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/abbs/gmt039\">https://doi.org/10.1093/abbs/gmt039</a>"},"doi":"10.1093/abbs/gmt039","abstract":[{"lang":"eng","text":"Inositol 1,3,4-trisphosphate 5/6 kinase (ITPK) phosphorylates inositol 1,3,4-trisphosphate to form inositol 1,3,4,5-tetrakisphosphate and inositol 1,3,4,6-tetrakisphosphate which can be finally transferred to inositol hexaphosphate (IP6) and play important roles during plant growth and development. There are 4 putative ITPK members in Arabidopsis. Expression pattern analysis showed that ITPK2 is constitutively expressed in various tissues. A T-DNA knockout mutant of ITPK2 was identified and scanning electron microscopy (SEM) analysis showed that the epidermis structure of seed coat was irregularly formed in seeds of itpk2-1 mutant, resulting in the increased permeability of seed coat to tetrazolium salts. Further analysis by gas chromatography coupled with mass spectrometry of lipid polyester monomers in cell wall confirmed a dramatic decrease in composition of suberin and cutin, which relate to the permeability of seed coat and the formation of which is accompanied with seed coat development. These results indicate that ITPK2 plays an essential role in seed coat development and lipid polyester barrier formation."}],"publication_identifier":{"issn":["1745-7270","1672-9145"]},"article_processing_charge":"No","title":"Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development","external_id":{"pmid":["23595027"]},"_id":"7595","publisher":"Oxford University Press","date_updated":"2021-01-12T08:14:23Z"},{"oa_version":"None","language":[{"iso":"eng"}],"month":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["23897926"]},"date_updated":"2021-01-12T08:14:24Z","_id":"7596","publisher":"American Society of Plant Biologists","title":"Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling","abstract":[{"text":"Casein kinase1 (CK1) plays crucial roles in regulating growth and development via phosphorylating various substrates throughout the eukaryote kingdom. Blue light is crucial for normal growth of both plants and animals, and blue light receptor cryptochrome2 (CRY2) undergoes blue light–dependent phosphorylation and degradation in planta. To study the function of plant CK1s, systematic genetic analysis showed that deficiency of two paralogous Arabidopsis thaliana CK1s, CK1.3 and CK1.4, caused shortened hypocotyls, especially under blue light, while overexpression of either CK1.3 or CK1.4 resulted in the insensitive response to blue light and delayed flowering under long-day conditions. CK1.3 or CK1.4 act dependently on CRY2, and overexpression of CK1.3 or CK1.4 significantly suppresses the hypersensitive response to blue light by CRY2 overexpression. Biochemical studies showed that CK1.3 and CK1.4 directly phosphorylate CRY2 at Ser-587 and Thr-603 in vitro and negatively regulate CRY2 stability in planta, which are stimulated by blue light, further confirming the crucial roles of CK1.3 and CK1.4 in blue light responses through phosphorylating CRY2. Interestingly, expression of CK1.3 and CK1.4 is stimulated by blue light and feedback regulated by CRY2-mediated signaling. These results provide direct evidence for CRY2 phosphorylation and informative clues on the mechanisms of CRY2-mediated light responses.","lang":"eng"}],"publication_identifier":{"issn":["1040-4651","1532-298X"]},"doi":"10.1105/tpc.113.114322","citation":{"mla":"Tan, Shutang, et al. “Arabidopsis Casein Kinase1 Proteins CK1.3 and CK1.4 Phosphorylate Cryptochrome2 to Regulate Blue Light Signaling.” <i>The Plant Cell</i>, vol. 25, no. 7, American Society of Plant Biologists, 2013, pp. 2618–32, doi:<a href=\"https://doi.org/10.1105/tpc.113.114322\">10.1105/tpc.113.114322</a>.","apa":"Tan, S., Dai, C., Liu, H.-T., &#38; Xue, H.-W. (2013). Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling. <i>The Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.113.114322\">https://doi.org/10.1105/tpc.113.114322</a>","chicago":"Tan, Shutang, C. Dai, H.-T. Liu, and H.-W. Xue. “Arabidopsis Casein Kinase1 Proteins CK1.3 and CK1.4 Phosphorylate Cryptochrome2 to Regulate Blue Light Signaling.” <i>The Plant Cell</i>. American Society of Plant Biologists, 2013. <a href=\"https://doi.org/10.1105/tpc.113.114322\">https://doi.org/10.1105/tpc.113.114322</a>.","short":"S. Tan, C. Dai, H.-T. Liu, H.-W. Xue, The Plant Cell 25 (2013) 2618–2632.","ama":"Tan S, Dai C, Liu H-T, Xue H-W. Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling. <i>The Plant Cell</i>. 2013;25(7):2618-2632. doi:<a href=\"https://doi.org/10.1105/tpc.113.114322\">10.1105/tpc.113.114322</a>","ieee":"S. Tan, C. Dai, H.-T. Liu, and H.-W. Xue, “Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling,” <i>The Plant Cell</i>, vol. 25, no. 7. American Society of Plant Biologists, pp. 2618–2632, 2013.","ista":"Tan S, Dai C, Liu H-T, Xue H-W. 2013. Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling. The Plant Cell. 25(7), 2618–2632."},"article_processing_charge":"No","quality_controlled":"1","pmid":1,"article_type":"original","volume":25,"page":"2618-2632","day":"26","author":[{"last_name":"Tan","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","full_name":"Tan, Shutang"},{"full_name":"Dai, C.","first_name":"C.","last_name":"Dai"},{"last_name":"Liu","first_name":"H.-T.","full_name":"Liu, H.-T."},{"last_name":"Xue","first_name":"H.-W.","full_name":"Xue, H.-W."}],"type":"journal_article","issue":"7","extern":"1","status":"public","year":"2013","intvolume":"        25","date_published":"2013-08-26T00:00:00Z","date_created":"2020-03-21T16:06:55Z","publication":"The Plant Cell","fulldoi":"https://doi.org/10.1105/tpc.113.114322","publication_status":"published"},{"oa_version":"None","page":"200 - 209","day":"01","author":[{"last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian"},{"first_name":"James","full_name":"Aspnes, James","last_name":"Aspnes"},{"first_name":"George","full_name":"Giakkoupis, George","last_name":"Giakkoupis"},{"last_name":"Woelfel","full_name":"Woelfel, Philipp","first_name":"Philipp"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","language":[{"iso":"eng"}],"citation":{"chicago":"Alistarh, Dan-Adrian, James Aspnes, George Giakkoupis, and Philipp Woelfel. “Randomized Loose Renaming in O(Loglogn) Time,” 200–209. ACM, 2013. <a href=\"https://doi.org/10.1145/2484239.2484240\">https://doi.org/10.1145/2484239.2484240</a>.","short":"D.-A. Alistarh, J. Aspnes, G. Giakkoupis, P. Woelfel, in:, ACM, 2013, pp. 200–209.","ama":"Alistarh D-A, Aspnes J, Giakkoupis G, Woelfel P. Randomized loose renaming in O(loglogn) time. In: ACM; 2013:200-209. doi:<a href=\"https://doi.org/10.1145/2484239.2484240\">10.1145/2484239.2484240</a>","ieee":"D.-A. Alistarh, J. Aspnes, G. Giakkoupis, and P. Woelfel, “Randomized loose renaming in O(loglogn) time,” presented at the PODC: Principles of Distributed Computing, 2013, pp. 200–209.","ista":"Alistarh D-A, Aspnes J, Giakkoupis G, Woelfel P. 2013. Randomized loose renaming in O(loglogn) time. PODC: Principles of Distributed Computing, 200–209.","mla":"Alistarh, Dan-Adrian, et al. <i>Randomized Loose Renaming in O(Loglogn) Time</i>. ACM, 2013, pp. 200–09, doi:<a href=\"https://doi.org/10.1145/2484239.2484240\">10.1145/2484239.2484240</a>.","apa":"Alistarh, D.-A., Aspnes, J., Giakkoupis, G., &#38; Woelfel, P. (2013). Randomized loose renaming in O(loglogn) time (pp. 200–209). Presented at the PODC: Principles of Distributed Computing, ACM. <a href=\"https://doi.org/10.1145/2484239.2484240\">https://doi.org/10.1145/2484239.2484240</a>"},"doi":"10.1145/2484239.2484240","abstract":[{"text":"Renaming is a classic distributed coordination task in which a set of processes must pick distinct identifiers from a small namespace. In this paper, we consider the time complexity of this problem when the namespace is linear in the number of participants, a variant known as loose renaming. We give a non-adaptive algorithm with O(log log n) (individual) step complexity, where n is a known upper bound on contention, and an adaptive algorithm with step complexity O((log log k)2), where k is the actual contention in the execution. We also present a variant of the adaptive algorithm which requires O(k log log k) total process steps. All upper bounds hold with high probability against a strong adaptive adversary. We complement the algorithms with an ω(log log n) expected time lower bound on the complexity of randomized renaming using test-and-set operations and linear space. The result is based on a new coupling technique, and is the first to apply to non-adaptive randomized renaming. Since our algorithms use O(n) test-and-set objects, our results provide matching bounds on the cost of loose renaming in this setting.","lang":"eng"}],"publication_status":"published","article_processing_charge":"No","fulldoi":"https://doi.org/10.1145/2484239.2484240","publist_id":"6889","conference":{"name":"PODC: Principles of Distributed Computing"},"acknowledgement":"Dan Alistarh - This author was supported by the SNF Postdoctoral Fellows Program, NSF grant CCF-1217921, DoE ASCR grant\r\nER26116/DE-SC0008923,  and  by  grants  from  the  Oracle\r\nand Intel corporations.\r\nJames Aspnes - Supported in part by NSF grant CCF-0916389.\r\nGeorge Giakkoupis - This work was funded in part by INRIA Associate Team\r\nRADCON, and ERC Starting Grant GOSSPLE 204742.\r\nPhilipp Woelfel - This research was undertaken, in part, thanks to funding\r\nfrom the Canada Research Chairs program and the HP Labs\r\nInnovation Research Program.","type":"conference","publisher":"ACM","_id":"765","extern":"1","status":"public","year":"2013","date_updated":"2023-02-23T13:13:14Z","title":"Randomized loose renaming in O(loglogn) time","date_published":"2013-01-01T00:00:00Z","date_created":"2018-12-11T11:48:23Z"},{"publication_status":"published","fulldoi":"https://doi.org/10.1111/mec.12375","article_processing_charge":"No","publication":"Molecular Ecology","citation":{"apa":"Robinson, M. R., Santure, A. W., DeCauwer, I., Sheldon, B. C., &#38; Slate, J. (2013). Partitioning of genetic variation across the genome using multimarker methods in a wild bird population. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.12375\">https://doi.org/10.1111/mec.12375</a>","mla":"Robinson, Matthew Richard, et al. “Partitioning of Genetic Variation across the Genome Using Multimarker Methods in a Wild Bird Population.” <i>Molecular Ecology</i>, vol. 22, no. 15, Wiley, 2013, pp. 3963–80, doi:<a href=\"https://doi.org/10.1111/mec.12375\">10.1111/mec.12375</a>.","ista":"Robinson MR, Santure AW, DeCauwer I, Sheldon BC, Slate J. 2013. Partitioning of genetic variation across the genome using multimarker methods in a wild bird population. Molecular Ecology. 22(15), 3963–3980.","ieee":"M. R. Robinson, A. W. Santure, I. DeCauwer, B. C. Sheldon, and J. Slate, “Partitioning of genetic variation across the genome using multimarker methods in a wild bird population,” <i>Molecular Ecology</i>, vol. 22, no. 15. Wiley, pp. 3963–3980, 2013.","ama":"Robinson MR, Santure AW, DeCauwer I, Sheldon BC, Slate J. Partitioning of genetic variation across the genome using multimarker methods in a wild bird population. <i>Molecular Ecology</i>. 2013;22(15):3963-3980. doi:<a href=\"https://doi.org/10.1111/mec.12375\">10.1111/mec.12375</a>","chicago":"Robinson, Matthew Richard, Anna W. Santure, Isabelle DeCauwer, Ben C. Sheldon, and Jon Slate. “Partitioning of Genetic Variation across the Genome Using Multimarker Methods in a Wild Bird Population.” <i>Molecular Ecology</i>. Wiley, 2013. <a href=\"https://doi.org/10.1111/mec.12375\">https://doi.org/10.1111/mec.12375</a>.","short":"M.R. Robinson, A.W. Santure, I. DeCauwer, B.C. Sheldon, J. Slate, Molecular Ecology 22 (2013) 3963–3980."},"doi":"10.1111/mec.12375","publication_identifier":{"issn":["0962-1083"]},"abstract":[{"lang":"eng","text":"The underlying basis of genetic variation in quantitative traits, in terms of the number of causal variants and the size of their effects, is largely unknown in natural populations. The expectation is that complex quantitative trait variation is attributable to many, possibly interacting, causal variants, whose effects may depend upon the sex, age and the environment in which they are expressed. A recently developed methodology in animal breeding derives a value of relatedness among individuals from high‐density genomic marker data, to estimate additive genetic variance within livestock populations. Here, we adapt and test the effectiveness of these methods to partition genetic variation for complex traits across genomic regions within ecological study populations where individuals have varying degrees of relatedness. We then apply this approach for the first time to a natural population and demonstrate that genetic variation in wing length in the great tit (Parus major) reflects contributions from multiple genomic regions. We show that a polygenic additive mode of gene action best describes the patterns observed, and we find no evidence of dosage compensation for the sex chromosome. Our results suggest that most of the genomic regions that influence wing length have the same effects in both sexes. We found a limited amount of genetic variance in males that is attributed to regions that have no effects in females, which could facilitate the sexual dimorphism observed for this trait. Although this exploratory work focuses on one complex trait, the methodology is generally applicable to any trait for any laboratory or wild population, paving the way for investigating sex‐, age‐ and environment‐specific genetic effects and thus the underlying genetic architecture of phenotype in biological study systems."}],"publisher":"Wiley","_id":"7745","intvolume":"        22","status":"public","extern":"1","date_updated":"2021-01-12T08:15:14Z","year":"2013","issue":"15","type":"journal_article","date_created":"2020-04-30T11:00:15Z","title":"Partitioning of genetic variation across the genome using multimarker methods in a wild bird population","date_published":"2013-08-01T00:00:00Z","oa_version":"None","page":"3963-3980","author":[{"last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard"},{"last_name":"Santure","first_name":"Anna W.","full_name":"Santure, Anna W."},{"first_name":"Isabelle","full_name":"DeCauwer, Isabelle","last_name":"DeCauwer"},{"full_name":"Sheldon, Ben C.","first_name":"Ben C.","last_name":"Sheldon"},{"full_name":"Slate, Jon","first_name":"Jon","last_name":"Slate"}],"month":"08","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","article_type":"original","quality_controlled":"1","volume":22},{"oa_version":"None","page":"3949-3962","author":[{"last_name":"Santure","first_name":"Anna W.","full_name":"Santure, Anna W."},{"last_name":"De Cauwer","full_name":"De Cauwer, Isabelle","first_name":"Isabelle"},{"full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"full_name":"Poissant, Jocelyn","first_name":"Jocelyn","last_name":"Poissant"},{"last_name":"Sheldon","first_name":"Ben C.","full_name":"Sheldon, Ben C."},{"last_name":"Slate","full_name":"Slate, Jon","first_name":"Jon"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"month":"08","day":"01","article_type":"original","quality_controlled":"1","volume":22,"publication_status":"published","article_processing_charge":"No","fulldoi":"https://doi.org/10.1111/mec.12376","publication":"Molecular Ecology","doi":"10.1111/mec.12376","citation":{"mla":"Santure, Anna W., et al. “Genomic Dissection of Variation in Clutch Size and Egg Mass in a Wild Great Tit (Parus Major) Population.” <i>Molecular Ecology</i>, vol. 22, no. 15, Wiley, 2013, pp. 3949–62, doi:<a href=\"https://doi.org/10.1111/mec.12376\">10.1111/mec.12376</a>.","apa":"Santure, A. W., De Cauwer, I., Robinson, M. R., Poissant, J., Sheldon, B. C., &#38; Slate, J. (2013). Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.12376\">https://doi.org/10.1111/mec.12376</a>","ieee":"A. W. Santure, I. De Cauwer, M. R. Robinson, J. Poissant, B. C. Sheldon, and J. Slate, “Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population,” <i>Molecular Ecology</i>, vol. 22, no. 15. Wiley, pp. 3949–3962, 2013.","ista":"Santure AW, De Cauwer I, Robinson MR, Poissant J, Sheldon BC, Slate J. 2013. Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population. Molecular Ecology. 22(15), 3949–3962.","short":"A.W. Santure, I. De Cauwer, M.R. Robinson, J. Poissant, B.C. Sheldon, J. Slate, Molecular Ecology 22 (2013) 3949–3962.","chicago":"Santure, Anna W., Isabelle De Cauwer, Matthew Richard Robinson, Jocelyn Poissant, Ben C. Sheldon, and Jon Slate. “Genomic Dissection of Variation in Clutch Size and Egg Mass in a Wild Great Tit (Parus Major) Population.” <i>Molecular Ecology</i>. Wiley, 2013. <a href=\"https://doi.org/10.1111/mec.12376\">https://doi.org/10.1111/mec.12376</a>.","ama":"Santure AW, De Cauwer I, Robinson MR, Poissant J, Sheldon BC, Slate J. Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population. <i>Molecular Ecology</i>. 2013;22(15):3949-3962. doi:<a href=\"https://doi.org/10.1111/mec.12376\">10.1111/mec.12376</a>"},"abstract":[{"lang":"eng","text":"Clutch size and egg mass are life history traits that have been extensively studied in wild bird populations, as life history theory predicts a negative trade‐off between them, either at the phenotypic or at the genetic level. Here, we analyse the genomic architecture of these heritable traits in a wild great tit (Parus major) population, using three marker‐based approaches – chromosome partitioning, quantitative trait locus (QTL) mapping and a genome‐wide association study (GWAS). The variance explained by each great tit chromosome scales with predicted chromosome size, no location in the genome contains genome‐wide significant QTL, and no individual SNPs are associated with a large proportion of phenotypic variation, all of which may suggest that variation in both traits is due to many loci of small effect, located across the genome. There is no evidence that any regions of the genome contribute significantly to both traits, which combined with a small, nonsignificant negative genetic covariance between the traits, suggests the absence of genetic constraints on the independent evolution of these traits. Our findings support the hypothesis that variation in life history traits in natural populations is likely to be determined by many loci of small effect spread throughout the genome, which are subject to continued input of variation by mutation and migration, although we cannot exclude the possibility of an additional input of major effect genes influencing either trait."}],"publication_identifier":{"issn":["0962-1083"]},"_id":"7746","intvolume":"        22","publisher":"Wiley","extern":"1","date_updated":"2021-01-12T08:15:14Z","status":"public","year":"2013","issue":"15","type":"journal_article","date_created":"2020-04-30T11:00:32Z","title":"Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population","date_published":"2013-08-01T00:00:00Z"},{"article_type":"original","quality_controlled":"1","volume":16,"page":"281-290","oa_version":"None","month":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"author":[{"last_name":"Robinson","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard"},{"last_name":"Beckerman","full_name":"Beckerman, Andrew P.","first_name":"Andrew P."}],"day":"01","status":"public","extern":"1","year":"2013","date_updated":"2021-01-12T08:15:15Z","intvolume":"        16","_id":"7747","publisher":"Wiley","type":"journal_article","issue":"3","date_created":"2020-04-30T11:00:49Z","date_published":"2013-03-01T00:00:00Z","title":"Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history","fulldoi":"https://doi.org/10.1111/ele.12047","article_processing_charge":"No","publication_status":"published","publication_identifier":{"issn":["1461-023X"]},"abstract":[{"text":"Acquisition and allocation of resources are central to life‐history theory. However, empirical work typically focuses only on allocation despite the fact that relationships between fitness components may be governed by differences in the ability of individuals to acquire resources across environments. Here, we outline a statistical framework to partition the genetic basis of multivariate plasticity into independent axes of genetic variation, and quantify for the first time, the extent to which specific traits drive multitrait genotype–environment interactions. Our framework generalises to analyses of plasticity, growth and ageing. We apply this approach to a unique, large‐scale, multivariate study of acquisition, allocation and plasticity in the life history of the cricket, Gryllus firmus. We demonstrate that resource acquisition and allocation are genetically correlated, and that plasticity in trade‐offs between allocation to components of fitness is 90% dependent on genetic variance for total resource acquisition. These results suggest that genotype–environment effects for resource acquisition can maintain variation in life‐history components that are typically observed in the wild.","lang":"eng"}],"citation":{"apa":"Robinson, M. R., &#38; Beckerman, A. P. (2013). Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history. <i>Ecology Letters</i>. Wiley. <a href=\"https://doi.org/10.1111/ele.12047\">https://doi.org/10.1111/ele.12047</a>","mla":"Robinson, Matthew Richard, and Andrew P. Beckerman. “Quantifying Multivariate Plasticity: Genetic Variation in Resource Acquisition Drives Plasticity in Resource Allocation to Components of Life History.” <i>Ecology Letters</i>, vol. 16, no. 3, Wiley, 2013, pp. 281–90, doi:<a href=\"https://doi.org/10.1111/ele.12047\">10.1111/ele.12047</a>.","ama":"Robinson MR, Beckerman AP. Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history. <i>Ecology Letters</i>. 2013;16(3):281-290. doi:<a href=\"https://doi.org/10.1111/ele.12047\">10.1111/ele.12047</a>","chicago":"Robinson, Matthew Richard, and Andrew P. Beckerman. “Quantifying Multivariate Plasticity: Genetic Variation in Resource Acquisition Drives Plasticity in Resource Allocation to Components of Life History.” <i>Ecology Letters</i>. Wiley, 2013. <a href=\"https://doi.org/10.1111/ele.12047\">https://doi.org/10.1111/ele.12047</a>.","short":"M.R. Robinson, A.P. Beckerman, Ecology Letters 16 (2013) 281–290.","ista":"Robinson MR, Beckerman AP. 2013. Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history. Ecology Letters. 16(3), 281–290.","ieee":"M. R. Robinson and A. P. Beckerman, “Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history,” <i>Ecology Letters</i>, vol. 16, no. 3. Wiley, pp. 281–290, 2013."},"publication":"Ecology Letters","doi":"10.1111/ele.12047"},{"citation":{"apa":"Goodrich, C. P., Ellenbroek, W. G., &#38; Liu, A. J. (2013). Stability of jammed packings I: The rigidity length scale. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c3sm51095f\">https://doi.org/10.1039/c3sm51095f</a>","mla":"Goodrich, Carl Peter, et al. “Stability of Jammed Packings I: The Rigidity Length Scale.” <i>Soft Matter</i>, vol. 9, no. 46, 10993, Royal Society of Chemistry, 2013, doi:<a href=\"https://doi.org/10.1039/c3sm51095f\">10.1039/c3sm51095f</a>.","ista":"Goodrich CP, Ellenbroek WG, Liu AJ. 2013. Stability of jammed packings I: The rigidity length scale. Soft Matter. 9(46), 10993.","ieee":"C. P. Goodrich, W. G. Ellenbroek, and A. J. Liu, “Stability of jammed packings I: The rigidity length scale,” <i>Soft Matter</i>, vol. 9, no. 46. Royal Society of Chemistry, 2013.","ama":"Goodrich CP, Ellenbroek WG, Liu AJ. Stability of jammed packings I: The rigidity length scale. <i>Soft Matter</i>. 2013;9(46). doi:<a href=\"https://doi.org/10.1039/c3sm51095f\">10.1039/c3sm51095f</a>","short":"C.P. Goodrich, W.G. Ellenbroek, A.J. Liu, Soft Matter 9 (2013).","chicago":"Goodrich, Carl Peter, Wouter G. Ellenbroek, and Andrea J. Liu. “Stability of Jammed Packings I: The Rigidity Length Scale.” <i>Soft Matter</i>. Royal Society of Chemistry, 2013. <a href=\"https://doi.org/10.1039/c3sm51095f\">https://doi.org/10.1039/c3sm51095f</a>."},"publication":"Soft Matter","doi":"10.1039/c3sm51095f","abstract":[{"text":"In 2005, Wyart et al. [Europhys. Lett., 2005, 72, 486] showed that the low frequency vibrational properties of jammed amorphous sphere packings can be understood in terms of a length scale, called l*, that diverges as the system becomes marginally unstable. Despite the tremendous success of this theory, it has been difficult to connect the counting argument that defines l* to other length scales that diverge near the jamming transition. We present an alternate derivation of l* based on the onset of rigidity. This phenomenological approach reveals the physical mechanism underlying the length scale and is relevant to a range of systems for which the original argument breaks down. It also allows us to present the first direct numerical measurement of l*.","lang":"eng"}],"publication_identifier":{"issn":["1744-683X","1744-6848"]},"publication_status":"published","fulldoi":"https://doi.org/10.1039/c3sm51095f","article_processing_charge":"No","issue":"46","type":"journal_article","_id":"7774","intvolume":"         9","publisher":"Royal Society of Chemistry","status":"public","year":"2013","extern":"1","date_updated":"2021-01-12T08:15:27Z","title":"Stability of jammed packings I: The rigidity length scale","date_published":"2013-10-08T00:00:00Z","date_created":"2020-04-30T11:43:42Z","oa_version":"None","day":"08","author":[{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","orcid":"0000-0002-1307-5074","first_name":"Carl Peter","full_name":"Goodrich, Carl Peter"},{"full_name":"Ellenbroek, Wouter G.","first_name":"Wouter G.","last_name":"Ellenbroek"},{"full_name":"Liu, Andrea J.","first_name":"Andrea J.","last_name":"Liu"}],"month":"10","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","article_type":"original","volume":9,"article_number":"10993"},{"abstract":[{"lang":"eng","text":"As a function of packing fraction at zero temperature and applied stress, an amorphous packing of spheres exhibits a jamming transition where the system is sensitive to boundary conditions even in the thermodynamic limit. Upon further compression, the system should become insensitive to boundary conditions provided it is sufficiently large. Here we explore the linear response to a large class of boundary perturbations in 2 and 3 dimensions. We consider each finite packing with periodic-boundary conditions as the basis of an infinite square or cubic lattice and study properties of vibrational modes at arbitrary wave vector. We find that the stability of such modes can be understood in terms of a competition between plane waves and the anomalous vibrational modes associated with the jamming transition; infinitesimal boundary perturbations become irrelevant for systems that are larger than a length scale that characterizes the transverse excitations. This previously identified length diverges at the jamming transition."}],"publication_identifier":{"issn":["1744-683X","1744-6848"]},"publication":"Soft Matter","citation":{"ama":"Schoenholz SS, Goodrich CP, Kogan O, Liu AJ, Nagel SR. Stability of jammed packings II: The transverse length scale. <i>Soft Matter</i>. 2013;9(46). doi:<a href=\"https://doi.org/10.1039/c3sm51096d\">10.1039/c3sm51096d</a>","chicago":"Schoenholz, Samuel S., Carl Peter Goodrich, Oleg Kogan, Andrea J. Liu, and Sidney R. Nagel. “Stability of Jammed Packings II: The Transverse Length Scale.” <i>Soft Matter</i>. Royal Society of Chemistry, 2013. <a href=\"https://doi.org/10.1039/c3sm51096d\">https://doi.org/10.1039/c3sm51096d</a>.","short":"S.S. Schoenholz, C.P. Goodrich, O. Kogan, A.J. Liu, S.R. Nagel, Soft Matter 9 (2013).","ista":"Schoenholz SS, Goodrich CP, Kogan O, Liu AJ, Nagel SR. 2013. Stability of jammed packings II: The transverse length scale. Soft Matter. 9(46), 11000.","ieee":"S. S. Schoenholz, C. P. Goodrich, O. Kogan, A. J. Liu, and S. R. Nagel, “Stability of jammed packings II: The transverse length scale,” <i>Soft Matter</i>, vol. 9, no. 46. Royal Society of Chemistry, 2013.","apa":"Schoenholz, S. S., Goodrich, C. P., Kogan, O., Liu, A. J., &#38; Nagel, S. R. (2013). Stability of jammed packings II: The transverse length scale. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c3sm51096d\">https://doi.org/10.1039/c3sm51096d</a>","mla":"Schoenholz, Samuel S., et al. “Stability of Jammed Packings II: The Transverse Length Scale.” <i>Soft Matter</i>, vol. 9, no. 46, 11000, Royal Society of Chemistry, 2013, doi:<a href=\"https://doi.org/10.1039/c3sm51096d\">10.1039/c3sm51096d</a>."},"doi":"10.1039/c3sm51096d","fulldoi":"https://doi.org/10.1039/c3sm51096d","article_processing_charge":"No","publication_status":"published","type":"journal_article","issue":"46","extern":"1","date_updated":"2021-01-12T08:15:27Z","status":"public","year":"2013","_id":"7775","intvolume":"         9","publisher":"Royal Society of Chemistry","date_published":"2013-10-08T00:00:00Z","title":"Stability of jammed packings II: The transverse length scale","date_created":"2020-04-30T11:43:58Z","oa_version":"None","day":"08","language":[{"iso":"eng"}],"month":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Schoenholz, Samuel S.","first_name":"Samuel S.","last_name":"Schoenholz"},{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter","first_name":"Carl Peter"},{"full_name":"Kogan, Oleg","first_name":"Oleg","last_name":"Kogan"},{"full_name":"Liu, Andrea J.","first_name":"Andrea J.","last_name":"Liu"},{"first_name":"Sidney R.","full_name":"Nagel, Sidney R.","last_name":"Nagel"}],"quality_controlled":"1","article_type":"original","volume":9,"article_number":"11000"},{"article_type":"original","quality_controlled":"1","volume":78,"page":"673-686","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"month":"05","author":[{"last_name":"Joo","full_name":"Joo, William J.","first_name":"William J."},{"orcid":"0000-0001-9242-5601","last_name":"Sweeney","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","first_name":"Lora Beatrice Jaeger","full_name":"Sweeney, Lora Beatrice Jaeger"},{"first_name":"Liang","full_name":"Liang, Liang","last_name":"Liang"},{"last_name":"Luo","full_name":"Luo, Liqun","first_name":"Liqun"}],"day":"22","status":"public","date_updated":"2024-01-31T10:15:25Z","extern":"1","year":"2013","publisher":"Elsevier","_id":"7785","intvolume":"        78","type":"journal_article","issue":"4","date_created":"2020-04-30T13:19:59Z","title":"Linking cell fate, trajectory choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting","date_published":"2013-05-22T00:00:00Z","article_processing_charge":"No","fulldoi":"https://doi.org/10.1016/j.neuron.2013.03.022","publication_status":"published","abstract":[{"text":"Neural circuit assembly requires selection of specific cell fates, axonal trajectories, and synaptic targets. By analyzing the function of a secreted semaphorin, Sema-2b, in Drosophila olfactory receptor neuron (ORN) development, we identified multiple molecular and cellular mechanisms that link these events. Notch signaling limits Sema-2b expression to ventromedial ORN classes, within which Sema-2b cell-autonomously sensitizes ORN axons to external semaphorins. Central-brain-derived Sema-2a and Sema-2b attract Sema-2b-expressing axons to the ventromedial trajectory. In addition, Sema-2b/PlexB-mediated axon-axon interactions consolidate this trajectory choice and promote ventromedial axon-bundle formation. Selecting the correct developmental trajectory is ultimately essential for proper target choice. These findings demonstrate that Sema-2b couples ORN axon guidance to postsynaptic target neuron dendrite patterning well before the final target selection phase, and exemplify how a single guidance molecule can drive consecutive stages of neural circuit assembly with the help of sophisticated spatial and temporal regulation.","lang":"eng"}],"publication_identifier":{"issn":["0896-6273"]},"citation":{"ama":"Joo WJ, Sweeney LB, Liang L, Luo L. Linking cell fate, trajectory choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting. <i>Neuron</i>. 2013;78(4):673-686. doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.03.022\">10.1016/j.neuron.2013.03.022</a>","chicago":"Joo, William J., Lora B. Sweeney, Liang Liang, and Liqun Luo. “Linking Cell Fate, Trajectory Choice, and Target Selection: Genetic Analysis of Sema-2b in Olfactory Axon Targeting.” <i>Neuron</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.neuron.2013.03.022\">https://doi.org/10.1016/j.neuron.2013.03.022</a>.","short":"W.J. Joo, L.B. Sweeney, L. Liang, L. Luo, Neuron 78 (2013) 673–686.","ista":"Joo WJ, Sweeney LB, Liang L, Luo L. 2013. Linking cell fate, trajectory choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting. Neuron. 78(4), 673–686.","ieee":"W. J. Joo, L. B. Sweeney, L. Liang, and L. Luo, “Linking cell fate, trajectory choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting,” <i>Neuron</i>, vol. 78, no. 4. Elsevier, pp. 673–686, 2013.","apa":"Joo, W. J., Sweeney, L. B., Liang, L., &#38; Luo, L. (2013). Linking cell fate, trajectory choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2013.03.022\">https://doi.org/10.1016/j.neuron.2013.03.022</a>","mla":"Joo, William J., et al. “Linking Cell Fate, Trajectory Choice, and Target Selection: Genetic Analysis of Sema-2b in Olfactory Axon Targeting.” <i>Neuron</i>, vol. 78, no. 4, Elsevier, 2013, pp. 673–86, doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.03.022\">10.1016/j.neuron.2013.03.022</a>."},"publication":"Neuron","doi":"10.1016/j.neuron.2013.03.022"},{"article_number":"119","oa_version":"Published Version","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","_id":"8030","publisher":"Frontiers Media","date_updated":"2021-01-12T08:16:38Z","ddc":["570"],"external_id":{"pmid":["23882186"]},"title":"Inhibitory synaptic plasticity: Spike timing-dependence and putative network function","article_processing_charge":"No","citation":{"ama":"Vogels TP, Froemke RC, Doyon N, et al. Inhibitory synaptic plasticity: Spike timing-dependence and putative network function. <i>Frontiers in Neural Circuits</i>. 2013;7. doi:<a href=\"https://doi.org/10.3389/fncir.2013.00119\">10.3389/fncir.2013.00119</a>","short":"T.P. Vogels, R.C. Froemke, N. Doyon, M. Gilson, J.S. Haas, R. Liu, A. Maffei, P. Miller, C.J. Wierenga, M.A. Woodin, F. Zenke, H. Sprekeler, Frontiers in Neural Circuits 7 (2013).","chicago":"Vogels, Tim P, R. C. Froemke, N. Doyon, M. Gilson, J. S. Haas, R. Liu, A. Maffei, et al. “Inhibitory Synaptic Plasticity: Spike Timing-Dependence and Putative Network Function.” <i>Frontiers in Neural Circuits</i>. Frontiers Media, 2013. <a href=\"https://doi.org/10.3389/fncir.2013.00119\">https://doi.org/10.3389/fncir.2013.00119</a>.","ista":"Vogels TP, Froemke RC, Doyon N, Gilson M, Haas JS, Liu R, Maffei A, Miller P, Wierenga CJ, Woodin MA, Zenke F, Sprekeler H. 2013. Inhibitory synaptic plasticity: Spike timing-dependence and putative network function. Frontiers in Neural Circuits. 7, 119.","ieee":"T. P. Vogels <i>et al.</i>, “Inhibitory synaptic plasticity: Spike timing-dependence and putative network function,” <i>Frontiers in Neural Circuits</i>, vol. 7. Frontiers Media, 2013.","apa":"Vogels, T. P., Froemke, R. C., Doyon, N., Gilson, M., Haas, J. S., Liu, R., … Sprekeler, H. (2013). Inhibitory synaptic plasticity: Spike timing-dependence and putative network function. <i>Frontiers in Neural Circuits</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fncir.2013.00119\">https://doi.org/10.3389/fncir.2013.00119</a>","mla":"Vogels, Tim P., et al. “Inhibitory Synaptic Plasticity: Spike Timing-Dependence and Putative Network Function.” <i>Frontiers in Neural Circuits</i>, vol. 7, 119, Frontiers Media, 2013, doi:<a href=\"https://doi.org/10.3389/fncir.2013.00119\">10.3389/fncir.2013.00119</a>."},"doi":"10.3389/fncir.2013.00119","file_date_updated":"2020-07-16T11:23:40Z","publication_identifier":{"eissn":["1662-5110"]},"abstract":[{"text":"While the plasticity of excitatory synaptic connections in the brain has been widely studied, the plasticity of inhibitory connections is much less understood. Here, we present recent experimental and theoretical findings concerning the rules of spike timing-dependent inhibitory plasticity and their putative network function. This is a summary of a workshop at the COSYNE conference 2012.","lang":"eng"}],"has_accepted_license":"1","article_type":"original","pmid":1,"quality_controlled":"1","file":[{"file_name":"2013_FrontNeurCirc_Vogels.pdf","date_created":"2020-07-16T11:23:40Z","access_level":"open_access","date_updated":"2020-07-16T11:23:40Z","relation":"main_file","checksum":"9c321cb12977d84048712eefa7f0c497","success":1,"content_type":"application/pdf","file_id":"8123","creator":"cziletti","file_size":1530469}],"volume":7,"license":"https://creativecommons.org/licenses/by/3.0/","author":[{"orcid":"0000-0003-3295-6181","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","full_name":"Vogels, Tim P","first_name":"Tim P"},{"first_name":"R. C.","full_name":"Froemke, R. C.","last_name":"Froemke"},{"last_name":"Doyon","first_name":"N.","full_name":"Doyon, N."},{"last_name":"Gilson","first_name":"M.","full_name":"Gilson, M."},{"first_name":"J. S.","full_name":"Haas, J. S.","last_name":"Haas"},{"first_name":"R.","full_name":"Liu, R.","last_name":"Liu"},{"last_name":"Maffei","full_name":"Maffei, A.","first_name":"A."},{"last_name":"Miller","first_name":"P.","full_name":"Miller, P."},{"last_name":"Wierenga","first_name":"C. J.","full_name":"Wierenga, C. J."},{"last_name":"Woodin","first_name":"M. A.","full_name":"Woodin, M. A."},{"first_name":"F.","full_name":"Zenke, F.","last_name":"Zenke"},{"first_name":"H.","full_name":"Sprekeler, H.","last_name":"Sprekeler"}],"day":"18","intvolume":"         7","year":"2013","extern":"1","status":"public","type":"journal_article","date_created":"2020-06-25T13:23:50Z","oa":1,"date_published":"2013-07-18T00:00:00Z","publication_status":"published","fulldoi":"https://doi.org/10.3389/fncir.2013.00119","publication":"Frontiers in Neural Circuits","tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"}},{"page":"394 - 400","month":"12","author":[{"full_name":"Florian Schur","first_name":"Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","last_name":"Schur"},{"last_name":"Hagen","first_name":"Wim","full_name":"Hagen, Wim J"},{"full_name":"De Marco, Alex","first_name":"Alex","last_name":"De Marco"},{"full_name":"Briggs, John A","first_name":"John","last_name":"Briggs"}],"day":"01","quality_controlled":0,"volume":184,"fulldoi":"https://doi.org/10.1016/j.jsb.2013.10.015","publication_status":"published","abstract":[{"text":"Cryo-electron tomography combined with image processing by sub-tomogram averaging is unique in its power to resolve the structures of proteins and macromolecular complexes in situ. Limitations of the method, including the low signal to noise ratio within individual images from cryo-tomographic datasets and difficulties in determining the defocus at which the data was collected, mean that to date the very best structures obtained by sub-tomogram averaging are limited to a resolution of approximately 15. Å. Here, by optimizing data collection and defocus determination steps, we have determined the structure of assembled Mason-Pfizer monkey virus Gag protein using sub-tomogram averaging to a resolution of 8.5. Å. At this resolution alpha-helices can be directly and clearly visualized. These data demonstrate for the first time that high-resolution structural information can be obtained from cryo-electron tomograms using sub-tomogram averaging. Sub-tomogram averaging has the potential to allow detailed studies of unsolved and biologically relevant structures under biologically relevant conditions.","lang":"eng"}],"doi":"10.1016/j.jsb.2013.10.015","citation":{"mla":"Schur, Florian KM, et al. “Determination of Protein Structure at 8.5Å Resolution Using Cryo-Electron Tomography and Sub-Tomogram Averaging.” <i>Journal of Structural Biology</i>, vol. 184, no. 3, Academic Press, 2013, pp. 394–400, doi:<a href=\"https://doi.org/10.1016/j.jsb.2013.10.015\">10.1016/j.jsb.2013.10.015</a>.","apa":"Schur, F. K., Hagen, W., De Marco, A., &#38; Briggs, J. (2013). Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging. <i>Journal of Structural Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jsb.2013.10.015\">https://doi.org/10.1016/j.jsb.2013.10.015</a>","ieee":"F. K. Schur, W. Hagen, A. De Marco, and J. Briggs, “Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging,” <i>Journal of Structural Biology</i>, vol. 184, no. 3. Academic Press, pp. 394–400, 2013.","ista":"Schur FK, Hagen W, De Marco A, Briggs J. 2013. Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging. Journal of Structural Biology. 184(3), 394–400.","chicago":"Schur, Florian KM, Wim Hagen, Alex De Marco, and John Briggs. “Determination of Protein Structure at 8.5Å Resolution Using Cryo-Electron Tomography and Sub-Tomogram Averaging.” <i>Journal of Structural Biology</i>. Academic Press, 2013. <a href=\"https://doi.org/10.1016/j.jsb.2013.10.015\">https://doi.org/10.1016/j.jsb.2013.10.015</a>.","short":"F.K. Schur, W. Hagen, A. De Marco, J. Briggs, Journal of Structural Biology 184 (2013) 394–400.","ama":"Schur FK, Hagen W, De Marco A, Briggs J. Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging. <i>Journal of Structural Biology</i>. 2013;184(3):394-400. doi:<a href=\"https://doi.org/10.1016/j.jsb.2013.10.015\">10.1016/j.jsb.2013.10.015</a>"},"publication":"Journal of Structural Biology","publist_id":"6839","date_updated":"2021-01-12T08:16:54Z","year":"2013","extern":1,"status":"public","publisher":"Academic Press","_id":"810","intvolume":"       184","type":"journal_article","acknowledgement":"The M-PMV ΔPro CANC tubes imaged in this study were a kind gift from Pavel Ulbrich and Tomas Ruml, Institute of Chemical Technology, Prague. The cryo-EM grids were prepared by Tanmay Bharat. This study was technically supported by EMBL’s IT services unit and by Frank Thommen. We thank Martin Schorb and Svetlana Dodonova for discussions and advice; Khanh Huy Bui for advice and scripts to streamline tomogram reconstruction; and Giulia Zanetti, Tanmay Bharat, and Martin Beck for comments on the manuscript. This study was supported by Deutsche Forschungsgemeinschaft grant BR 3635/2-1 to JAGB.","issue":"3","date_created":"2018-12-11T11:48:37Z","date_published":"2013-12-01T00:00:00Z","title":"Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging"},{"quality_controlled":0,"volume":126,"page":"4572 - 4588","month":"01","author":[{"first_name":"Anika","full_name":"Steffen, Anika","last_name":"Steffen"},{"full_name":"Ladwein, Markus","first_name":"Markus","last_name":"Ladwein"},{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev","first_name":"Georgi A","full_name":"Georgi Dimchev"},{"first_name":"Anke","full_name":"Hein, Anke","last_name":"Hein"},{"last_name":"Schwenkmezger","first_name":"Lisa","full_name":"Schwenkmezger, Lisa"},{"last_name":"Arens","first_name":"Stefan","full_name":"Arens, Stefan"},{"last_name":"Ladwein","full_name":"Ladwein, Kathrin I","first_name":"Kathrin"},{"first_name":"J.","full_name":"Holleboom, J. Margit","last_name":"Holleboom"},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian","full_name":"Florian Schur"},{"full_name":"Small, John V","first_name":"John","last_name":"Small"},{"last_name":"Schwarz","full_name":"Schwarz, Janett","first_name":"Janett"},{"full_name":"Gerhard, Ralf","first_name":"Ralf","last_name":"Gerhard"},{"last_name":"Faix","first_name":"Jan","full_name":"Faix, Jan"},{"full_name":"Stradal, Theresia E","first_name":"Theresia","last_name":"Stradal"},{"first_name":"Cord","full_name":"Brakebusch, Cord H","last_name":"Brakebusch"},{"first_name":"Klemens","full_name":"Rottner, Klemens","last_name":"Rottner"}],"day":"01","status":"public","extern":1,"date_updated":"2021-01-12T08:16:57Z","year":"2013","publisher":"Company of Biologists","_id":"811","intvolume":"       126","type":"journal_article","issue":"20","acknowledgement":"This work was supported in part by the Deutsche Forschungsgemeinschaft [grants within programs SFB621 to K.R., and FOR629 and SFB629 to T.E.B.S.]. Deposited in PMC for immediate release.\nWe thank Brigitte Denker and Gerd Landsberg for excellent technical assistance. We are grateful to Robert Geffers (HZI Braunschweig, Germany) for microarray analyses and to Mirko Himmel (UKE Hamburg, Germany) for valuable advice on FRAP analysis.","date_created":"2018-12-11T11:48:38Z","date_published":"2013-01-01T00:00:00Z","title":"Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation","fulldoi":"https://doi.org/10.1242/jcs.118232","publication_status":"published","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"text":"Cell migration is commonly accompanied by protrusion of membrane ruffles and lamellipodia. In two-dimensional migration, protrusion of these thin sheets of cytoplasm is considered relevant to both exploration of new space and initiation of nascent adhesion to the substratum. Lamellipodium formation can be potently stimulated by Rho GTPases of the Rac subfamily, but alsoby RhoG or Cdc42. Here we describe viable fibroblast cell lines geneticallydeficient for Rac1 that lack detectable levels of Rac2 and Rac3. Rac-deficient cells were devoid of apparent lamellipodia, but these structures were restored by expression of either Rac subfamily member, but not by Cdc42 or RhoG. Cells deficient in Rac showed strong reduction in wound closure and random cell migration and a notable loss of sensitivity to a chemotactic gradient. Despite these defects, Rac-deficient cells were able to spread, formed filopodia and established focal adhesions. Spreading in these cells was achieved by the extension of filopodia followed by the advancement of cytoplasmic veils between them. The number and size of focal adhesions as well as their intensity were largely unaffected by genetic removal of Rac1. However, Rac deficiency increased the mobility of different components in focal adhesions, potentially explaining how Rac - although not essential - can contribute to focal adhesion assembly. Together, our data demonstrate that Rac signaling is essential for lamellipodium protrusion and for efficient cell migration, but not for spreading or filopodium formation. Our findings also suggest that Rac GTPases are crucial to the establishment or maintenance of polarity in chemotactic migration.","lang":"eng"}],"doi":"10.1242/jcs.118232","citation":{"apa":"Steffen, A., Ladwein, M., Dimchev, G. A., Hein, A., Schwenkmezger, L., Arens, S., … Rottner, K. (2013). Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.118232\">https://doi.org/10.1242/jcs.118232</a>","mla":"Steffen, Anika, et al. “Rac Function Is Crucial for Cell Migration but Is Not Required for Spreading and Focal Adhesion Formation.” <i>Journal of Cell Science</i>, vol. 126, no. 20, Company of Biologists, 2013, pp. 4572–88, doi:<a href=\"https://doi.org/10.1242/jcs.118232\">10.1242/jcs.118232</a>.","ama":"Steffen A, Ladwein M, Dimchev GA, et al. Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation. <i>Journal of Cell Science</i>. 2013;126(20):4572-4588. doi:<a href=\"https://doi.org/10.1242/jcs.118232\">10.1242/jcs.118232</a>","chicago":"Steffen, Anika, Markus Ladwein, Georgi A Dimchev, Anke Hein, Lisa Schwenkmezger, Stefan Arens, Kathrin Ladwein, et al. “Rac Function Is Crucial for Cell Migration but Is Not Required for Spreading and Focal Adhesion Formation.” <i>Journal of Cell Science</i>. Company of Biologists, 2013. <a href=\"https://doi.org/10.1242/jcs.118232\">https://doi.org/10.1242/jcs.118232</a>.","short":"A. Steffen, M. Ladwein, G.A. Dimchev, A. Hein, L. Schwenkmezger, S. Arens, K. Ladwein, J. Holleboom, F.K. Schur, J. Small, J. Schwarz, R. Gerhard, J. Faix, T. Stradal, C. Brakebusch, K. Rottner, Journal of Cell Science 126 (2013) 4572–4588.","ista":"Steffen A, Ladwein M, Dimchev GA, Hein A, Schwenkmezger L, Arens S, Ladwein K, Holleboom J, Schur FK, Small J, Schwarz J, Gerhard R, Faix J, Stradal T, Brakebusch C, Rottner K. 2013. Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation. Journal of Cell Science. 126(20), 4572–4588.","ieee":"A. Steffen <i>et al.</i>, “Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation,” <i>Journal of Cell Science</i>, vol. 126, no. 20. Company of Biologists, pp. 4572–4588, 2013."},"publication":"Journal of Cell Science","publist_id":"6840"},{"quality_controlled":0,"volume":24,"page":"2861 - 2875","month":"09","author":[{"last_name":"Koestler","first_name":"Stefan","full_name":"Koestler, Stefan A"},{"last_name":"Steffen","first_name":"Anika","full_name":"Steffen, Anika"},{"full_name":"Maria Nemethova","first_name":"Maria","last_name":"Nemethova","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Winterhoff","full_name":"Winterhoff, Moritz","first_name":"Moritz"},{"first_name":"Ningning","full_name":"Luo, Ningning","last_name":"Luo"},{"last_name":"Holleboom","first_name":"J.","full_name":"Holleboom, J. Margit"},{"full_name":"Krupp, Jessica","first_name":"Jessica","last_name":"Krupp"},{"first_name":"Sonja","full_name":"Jacob, Sonja","last_name":"Jacob"},{"last_name":"Vinzenz","full_name":"Vinzenz, Marlene","first_name":"Marlene"},{"full_name":"Florian Schur","first_name":"Florian","orcid":"0000-0003-4790-8078","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schlüter","first_name":"Kai","full_name":"Schlüter, Kai"},{"first_name":"Peter","full_name":"Gunning, Peter W","last_name":"Gunning"},{"first_name":"Christoph","full_name":"Winkler, Christoph","last_name":"Winkler"},{"first_name":"Christian","full_name":"Schmeiser, Christian","last_name":"Schmeiser"},{"last_name":"Faix","first_name":"Jan","full_name":"Faix, Jan"},{"first_name":"Theresia","full_name":"Stradal, Theresia E","last_name":"Stradal"},{"first_name":"John","full_name":"Small, John V","last_name":"Small"},{"last_name":"Rottner","first_name":"Klemens","full_name":"Rottner, Klemens"}],"day":"15","status":"public","extern":1,"date_updated":"2021-01-12T08:17:00Z","year":"2013","_id":"812","publisher":"American Society for Biology","intvolume":"        24","type":"journal_article","issue":"18","acknowledgement":"This work was supported in part by Deutsche Forschungsgemeinschaft Grants RO2414/3-1 (to K.R.) and FA330/6-1 (to J.F.), Austrian \nScience Fund Projects FWF 1516-B09 and FWF P21292-B09 (to  J.V.S.),  the Vienna  Science  and  Technology  Fund  (WWTF,  to \nJ.V.S.  and  C.S.),  and  Australian  National  Health  and  Medical \nResearch Council Grant APP1004175 (to P.W.G.). We thank J. Adams, \nR. Chisholm, A. Hall, L. Machesky, H. G. Mannherz, D. Schafer, and \nR.   Wedlich-Söldner   for   expression   constructs   and   B.   Denker, \nP. Hagendorff, and G. Landsberg for technical assistance.","date_created":"2018-12-11T11:48:38Z","title":"Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin","date_published":"2013-09-15T00:00:00Z","fulldoi":"https://doi.org/10.1091/mbc.E12-12-0857","publication_status":"published","abstract":[{"text":"Lamellipodia are sheet-like protrusions formed during migration or phagocytosis and comprise a network of actin filaments. Filament formation in this network is initiated by nucleation/branching through the actin-related protein 2/3 (Arp2/3) complex downstream of its activator, suppressor of cAMP receptor/WASP-family verprolin homologous (Scar/WAVE), but the relative relevance of Arp2/3-mediated branching versus actin filament elongation is unknown. Here we use instantaneous interference with Arp2/3 complex function in live fibroblasts with established lamellipodia. This allows direct examination of both the fate of elongating filaments upon instantaneous suppression of Arp2/3 complex activity and the consequences of this treatment on the dynamics of other lamellipodial regulators. We show that Arp2/3 complex is an essential organizer of treadmilling actin filament arrays but has little effect on the net rate of actin filament turnover at the cell periphery. In addition, Arp2/3 complex serves as key upstream factor for the recruitment of modulators of lamellipodia formation such as capping protein or cofilin. Arp2/3 complex is thus decisive for filament organization and geometry within the network not only by generating branches and novel filament ends, but also by directing capping or severing activities to the lamellipodium. Arp2/3 complex is also crucial to lamellipodia-based migration of keratocytes.","lang":"eng"}],"publication":"Molecular Biology of the Cell","citation":{"apa":"Koestler, S., Steffen, A., Nemethova, M., Winterhoff, M., Luo, N., Holleboom, J., … Rottner, K. (2013). Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin. <i>Molecular Biology of the Cell</i>. American Society for Biology. <a href=\"https://doi.org/10.1091/mbc.E12-12-0857\">https://doi.org/10.1091/mbc.E12-12-0857</a>","mla":"Koestler, Stefan, et al. “Arp2/3 Complex Is Essential for Actin Network Treadmilling as Well as for Targeting of Capping Protein and Cofilin.” <i>Molecular Biology of the Cell</i>, vol. 24, no. 18, American Society for Biology, 2013, pp. 2861–75, doi:<a href=\"https://doi.org/10.1091/mbc.E12-12-0857\">10.1091/mbc.E12-12-0857</a>.","ama":"Koestler S, Steffen A, Nemethova M, et al. Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin. <i>Molecular Biology of the Cell</i>. 2013;24(18):2861-2875. doi:<a href=\"https://doi.org/10.1091/mbc.E12-12-0857\">10.1091/mbc.E12-12-0857</a>","chicago":"Koestler, Stefan, Anika Steffen, Maria Nemethova, Moritz Winterhoff, Ningning Luo, J. Holleboom, Jessica Krupp, et al. “Arp2/3 Complex Is Essential for Actin Network Treadmilling as Well as for Targeting of Capping Protein and Cofilin.” <i>Molecular Biology of the Cell</i>. American Society for Biology, 2013. <a href=\"https://doi.org/10.1091/mbc.E12-12-0857\">https://doi.org/10.1091/mbc.E12-12-0857</a>.","short":"S. Koestler, A. Steffen, M. Nemethova, M. Winterhoff, N. Luo, J. Holleboom, J. Krupp, S. Jacob, M. Vinzenz, F.K. Schur, K. Schlüter, P. Gunning, C. Winkler, C. Schmeiser, J. Faix, T. Stradal, J. Small, K. Rottner, Molecular Biology of the Cell 24 (2013) 2861–2875.","ista":"Koestler S, Steffen A, Nemethova M, Winterhoff M, Luo N, Holleboom J, Krupp J, Jacob S, Vinzenz M, Schur FK, Schlüter K, Gunning P, Winkler C, Schmeiser C, Faix J, Stradal T, Small J, Rottner K. 2013. Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin. Molecular Biology of the Cell. 24(18), 2861–2875.","ieee":"S. Koestler <i>et al.</i>, “Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin,” <i>Molecular Biology of the Cell</i>, vol. 24, no. 18. American Society for Biology, pp. 2861–2875, 2013."},"doi":"10.1091/mbc.E12-12-0857","publist_id":"6841"},{"pmid":1,"file":[{"relation":"main_file","date_updated":"2020-08-10T13:45:19Z","file_name":"2013_JoTM_Petricevic.pdf","access_level":"open_access","date_created":"2020-08-10T13:45:19Z","creator":"dernst","file_size":777311,"success":1,"file_id":"8247","content_type":"application/pdf"}],"quality_controlled":"1","volume":11,"author":[{"last_name":"Petricevic","first_name":"Branka","full_name":"Petricevic, Branka"},{"full_name":"Laengle, Johannes","first_name":"Johannes","last_name":"Laengle"},{"full_name":"Singer, Josef","first_name":"Josef","last_name":"Singer"},{"full_name":"Sachet, Monika","first_name":"Monika","last_name":"Sachet"},{"last_name":"Fazekas","id":"36432834-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8777-3502","first_name":"Judit","full_name":"Fazekas, Judit"},{"last_name":"Steger","full_name":"Steger, Guenther","first_name":"Guenther"},{"last_name":"Bartsch","first_name":"Rupert","full_name":"Bartsch, Rupert"},{"full_name":"Jensen-Jarolim, Erika","first_name":"Erika","last_name":"Jensen-Jarolim"},{"first_name":"Michael","full_name":"Bergmann, Michael","last_name":"Bergmann"}],"day":"12","year":"2013","status":"public","extern":"1","intvolume":"        11","type":"journal_article","date_created":"2020-08-10T11:54:34Z","date_published":"2013-12-12T00:00:00Z","oa":1,"fulldoi":"https://doi.org/10.1186/1479-5876-11-307","publication_status":"published","tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"publication":"Journal of Translational Medicine","article_number":"307","oa_version":"None","month":"12","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2022-08-25T14:52:39Z","ddc":["570"],"_id":"8245","publisher":"Springer Nature","external_id":{"pmid":["24330813"]},"title":"Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients","article_processing_charge":"No","abstract":[{"text":"Background: Monoclonal antibodies (mAb), such as trastuzumab are a valuable addition to breast cancer therapy.\r\nData obtained from neoadjuvant settings revealed that antibody-dependent cell-mediated cytotoxicity (ADCC) is a\r\nmajor mechanism of action for the mAb trastuzumab. Conflicting results still call into question whether disease\r\nprogression, prolonged treatment or concomitant chemotherapy influences ADCC and related immunological\r\nphenomena.\r\nMethods: We analyzed the activity of ADCC and antibody-dependent cell-mediated phagocytosis (ADCP) of\r\nperipheral blood mononuclear cells (PBMCs) from human epidermal growth factor receptor 2 (HER2/neu) positive\r\nbreast cancer patients receiving trastuzumab therapy either in an adjuvant (n = 13) or metastatic (n = 15) setting as\r\nwell as from trastuzumab treatment-naive (t-naive) HER2/neu negative patients (n = 15). PBMCs from healthy volunteers\r\n(n = 24) were used as controls. ADCC and ADCP activity was correlated with the expression of antibody binding\r\nFc-gamma receptor (FcγR)I (CD64), FcγRII (CD32) and FcγRIII (CD16) on CD14+ (monocytes) and CD56+ (NK) cells, as well as the expression of CD107a+ (LAMP-1) on CD56+ cells and the total amount of CD4+CD25+FOXP3+ (Treg) cells. In metastatic patients, markers were correlated with progression-free survival (PFS).\r\nResults: ADCC activity was significantly down regulated in metastatic, adjuvant and t-naive patient cohorts as compared to healthy controls. Reduced ADCC activity was inversely correlated with the expression of CD107a on CD56+\r\ncells in adjuvant patients. ADCC and ADCP activity of the patient cohorts were similar, regardless of treatment duration\r\nor additional chemotherapy. PFS in metastatic patients inversely correlated with the number of peripheral Treg cells.\r\nConclusion: The reduction of ADCC in patients as compared to healthy controls calls for adjuvant strategies, such as\r\nimmune-enhancing agents, to improve the activity of trastuzumab. However, efficacy of trastuzumab-specific ADCC\r\nand ADCP appears not to be affected by treatment duration, disease progression or concomitant chemotherapy. This\r\nfinding supports the application of trastuzumab at any stage of the disease.","lang":"eng"}],"publication_identifier":{"issn":["1479-5876"]},"file_date_updated":"2020-08-10T13:45:19Z","doi":"10.1186/1479-5876-11-307","citation":{"ama":"Petricevic B, Laengle J, Singer J, et al. Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients. <i>Journal of Translational Medicine</i>. 2013;11. doi:<a href=\"https://doi.org/10.1186/1479-5876-11-307\">10.1186/1479-5876-11-307</a>","chicago":"Petricevic, Branka, Johannes Laengle, Josef Singer, Monika Sachet, Judit Singer, Guenther Steger, Rupert Bartsch, Erika Jensen-Jarolim, and Michael Bergmann. “Trastuzumab Mediates Antibody-Dependent Cell-Mediated Cytotoxicity and Phagocytosis to the Same Extent in Both Adjuvant and Metastatic HER2/Neu Breast Cancer Patients.” <i>Journal of Translational Medicine</i>. Springer Nature, 2013. <a href=\"https://doi.org/10.1186/1479-5876-11-307\">https://doi.org/10.1186/1479-5876-11-307</a>.","short":"B. Petricevic, J. Laengle, J. Singer, M. Sachet, J. Singer, G. Steger, R. Bartsch, E. Jensen-Jarolim, M. Bergmann, Journal of Translational Medicine 11 (2013).","ista":"Petricevic B, Laengle J, Singer J, Sachet M, Singer J, Steger G, Bartsch R, Jensen-Jarolim E, Bergmann M. 2013. Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients. Journal of Translational Medicine. 11, 307.","ieee":"B. Petricevic <i>et al.</i>, “Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients,” <i>Journal of Translational Medicine</i>, vol. 11. Springer Nature, 2013.","apa":"Petricevic, B., Laengle, J., Singer, J., Sachet, M., Singer, J., Steger, G., … Bergmann, M. (2013). Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients. <i>Journal of Translational Medicine</i>. Springer Nature. <a href=\"https://doi.org/10.1186/1479-5876-11-307\">https://doi.org/10.1186/1479-5876-11-307</a>","mla":"Petricevic, Branka, et al. “Trastuzumab Mediates Antibody-Dependent Cell-Mediated Cytotoxicity and Phagocytosis to the Same Extent in Both Adjuvant and Metastatic HER2/Neu Breast Cancer Patients.” <i>Journal of Translational Medicine</i>, vol. 11, 307, Springer Nature, 2013, doi:<a href=\"https://doi.org/10.1186/1479-5876-11-307\">10.1186/1479-5876-11-307</a>."},"has_accepted_license":"1"},{"oa_version":"Published Version","language":[{"iso":"eng"}],"month":"11","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","project":[{"call_identifier":"FP7","name":"Hormonal cross-talk in plant organogenesis","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","grant_number":"207362"}],"article_number":"451","article_processing_charge":"No","abstract":[{"text":"As sessile organisms, plants have to be able to adapt to a continuously changing environment. Plants that perceive some of these changes as stress signals activate signaling pathways to modulate their development and to enable them to survive. The complex responses to environmental cues are to a large extent mediated by plant hormones that together orchestrate the final plant response. The phytohormone cytokinin is involved in many plant developmental processes. Recently, it has been established that cytokinin plays an important role in stress responses, but does not act alone. Indeed, the hormonal control of plant development and stress adaptation is the outcome of a complex network of multiple synergistic and antagonistic interactions between various hormones. Here, we review the recent findings on the cytokinin function as part of this hormonal network. We focus on the importance of the crosstalk between cytokinin and other hormones, such as abscisic acid, jasmonate, salicylic acid, ethylene, and auxin in the modulation of plant development and stress adaptation. Finally, the impact of the current research in the biotechnological industry will be discussed.","lang":"eng"}],"doi":"10.3389/fpls.2013.00451","file_date_updated":"2020-07-14T12:48:11Z","citation":{"ista":"O’Brien J, Benková E. 2013. Cytokinin cross talking during biotic and abiotic stress responses. Frontiers in Plant Science. 4, 451.","ieee":"J. O’Brien and E. Benková, “Cytokinin cross talking during biotic and abiotic stress responses,” <i>Frontiers in Plant Science</i>, vol. 4. Frontiers Research Foundation, 2013.","ama":"O’Brien J, Benková E. Cytokinin cross talking during biotic and abiotic stress responses. <i>Frontiers in Plant Science</i>. 2013;4. doi:<a href=\"https://doi.org/10.3389/fpls.2013.00451\">10.3389/fpls.2013.00451</a>","short":"J. O’Brien, E. Benková, Frontiers in Plant Science 4 (2013).","chicago":"O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and Abiotic Stress Responses.” <i>Frontiers in Plant Science</i>. Frontiers Research Foundation, 2013. <a href=\"https://doi.org/10.3389/fpls.2013.00451\">https://doi.org/10.3389/fpls.2013.00451</a>.","apa":"O’Brien, J., &#38; Benková, E. (2013). Cytokinin cross talking during biotic and abiotic stress responses. <i>Frontiers in Plant Science</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fpls.2013.00451\">https://doi.org/10.3389/fpls.2013.00451</a>","mla":"O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and Abiotic Stress Responses.” <i>Frontiers in Plant Science</i>, vol. 4, 451, Frontiers Research Foundation, 2013, doi:<a href=\"https://doi.org/10.3389/fpls.2013.00451\">10.3389/fpls.2013.00451</a>."},"corr_author":"1","department":[{"_id":"EvBe"}],"has_accepted_license":"1","date_updated":"2025-09-29T14:33:09Z","ddc":["580"],"_id":"827","publisher":"Frontiers Research Foundation","external_id":{"isi":["000331445200001"]},"title":"Cytokinin cross talking during biotic and abiotic stress responses","ec_funded":1,"isi":1,"author":[{"first_name":"José","full_name":"O'Brien, José","last_name":"O'Brien"},{"full_name":"Benková, Eva","first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"day":"19","file":[{"relation":"main_file","date_updated":"2020-07-14T12:48:11Z","checksum":"fdc25ddd1bf9a99b99f662cdbafeddd4","date_created":"2019-01-31T10:40:38Z","access_level":"open_access","file_name":"2013_FrontiersPlant_OBrien.pdf","file_size":953299,"creator":"dernst","file_id":"5903","content_type":"application/pdf"}],"quality_controlled":"1","volume":4,"fulldoi":"https://doi.org/10.3389/fpls.2013.00451","publication_status":"published","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"Frontiers in Plant Science","publist_id":"6821","year":"2013","status":"public","intvolume":"         4","type":"journal_article","date_created":"2018-12-11T11:48:43Z","date_published":"2013-11-19T00:00:00Z","oa":1},{"external_id":{"isi":["000331533500002"]},"date_updated":"2025-09-29T14:32:42Z","ddc":["580"],"_id":"828","publisher":"Frontiers Research Foundation","title":"Systems approaches to study root architecture dynamics","abstract":[{"text":"The plant root system is essential for providing anchorage to the soil, supplying minerals and water, and synthesizing metabolites. It is a dynamic organ modulated by external cues such as environmental signals, water and nutrients availability, salinity and others. Lateral roots (LRs) are initiated from the primary root post-embryonically, after which they progress through discrete developmental stages which can be independently controlled, providing a high level of plasticity during root system formation. Within this review, main contributions are presented, from the classical forward genetic screens to the more recent high-throughput approaches, combined with computer model predictions, dissecting how LRs and thereby root system architecture is established and developed.","lang":"eng"}],"file_date_updated":"2020-07-14T12:48:11Z","doi":"10.3389/fpls.2013.00537","citation":{"apa":"Cuesta, C., Wabnik, K. T., &#38; Benková, E. (2013). Systems approaches to study root architecture dynamics. <i>Frontiers in Plant Science</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fpls.2013.00537\">https://doi.org/10.3389/fpls.2013.00537</a>","mla":"Cuesta, Candela, et al. “Systems Approaches to Study Root Architecture Dynamics.” <i>Frontiers in Plant Science</i>, vol. 4, 537, Frontiers Research Foundation, 2013, doi:<a href=\"https://doi.org/10.3389/fpls.2013.00537\">10.3389/fpls.2013.00537</a>.","ista":"Cuesta C, Wabnik KT, Benková E. 2013. Systems approaches to study root architecture dynamics. Frontiers in Plant Science. 4, 537.","ieee":"C. Cuesta, K. T. Wabnik, and E. Benková, “Systems approaches to study root architecture dynamics,” <i>Frontiers in Plant Science</i>, vol. 4. Frontiers Research Foundation, 2013.","ama":"Cuesta C, Wabnik KT, Benková E. Systems approaches to study root architecture dynamics. <i>Frontiers in Plant Science</i>. 2013;4. doi:<a href=\"https://doi.org/10.3389/fpls.2013.00537\">10.3389/fpls.2013.00537</a>","chicago":"Cuesta, Candela, Krzysztof T Wabnik, and Eva Benková. “Systems Approaches to Study Root Architecture Dynamics.” <i>Frontiers in Plant Science</i>. Frontiers Research Foundation, 2013. <a href=\"https://doi.org/10.3389/fpls.2013.00537\">https://doi.org/10.3389/fpls.2013.00537</a>.","short":"C. Cuesta, K.T. Wabnik, E. Benková, Frontiers in Plant Science 4 (2013)."},"article_processing_charge":"No","department":[{"_id":"EvBe"}],"has_accepted_license":"1","corr_author":"1","project":[{"grant_number":"207362","name":"Hormonal cross-talk in plant organogenesis","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_number":"537","oa_version":"Published Version","scopus_import":"1","language":[{"iso":"eng"}],"month":"12","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","status":"public","year":"2013","intvolume":"         4","date_published":"2013-12-26T00:00:00Z","oa":1,"date_created":"2018-12-11T11:48:43Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"Frontiers in Plant Science","fulldoi":"https://doi.org/10.3389/fpls.2013.00537","publication_status":"published","publist_id":"6820","file":[{"access_level":"open_access","date_created":"2019-01-31T10:36:43Z","file_name":"2013_FrontiersPlant_Cuesta.pdf","checksum":"0185b3c4d7df9a94bd3ce5a66d213506","date_updated":"2020-07-14T12:48:11Z","relation":"main_file","file_id":"5902","content_type":"application/pdf","file_size":710835,"creator":"dernst"}],"quality_controlled":"1","volume":4,"ec_funded":1,"day":"26","isi":1,"author":[{"full_name":"Cuesta, Candela","first_name":"Candela","orcid":"0000-0003-1923-2410","last_name":"Cuesta","id":"33A3C818-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wabnik","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7263-0560","full_name":"Wabnik, Krzysztof T","first_name":"Krzysztof T"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","last_name":"Benková","full_name":"Benková, Eva","first_name":"Eva"}]},{"title":"An integrative model of the control of ovule primordia formation","date_updated":"2022-03-21T07:17:26Z","_id":"830","publisher":"Wiley-Blackwell","external_id":{"pmid":["23941199"]},"acknowledgement":"The project and F.G. were supported by the CARIPLO Foundation (project 2009-2990) and COST (European Cooperation in Science and Technology) action HAPRECI (Harnessing Plant Reproduction for Crop Improvement). E.B. and C.C. were supported by the European Research Council through a ‘Starting Independent Research’ grant (ERC-2007-Stg-207362-HCPO). We thank A.P. MacCabe (Consejo Superior de Investigaciones Científicas, Valencia, Spain) for critical reading of the manuscript.","article_processing_charge":"No","abstract":[{"text":"Upon hormonal signaling, ovules develop as lateral organs from the placenta. Ovule numbers ultimately determine the number of seeds that develop, and thereby contribute to the final seed yield in crop plants. We demonstrate here that CUP-SHAPED COTYLEDON 1 (CUC1), CUC2 and AINTEGUMENTA (ANT) have additive effects on ovule primordia formation. We show that expression of the CUC1 and CUC2 genes is required to redundantly regulate expression of PINFORMED1 (PIN1), which in turn is required for ovule primordia formation. Furthermore, our results suggest that the auxin response factor MONOPTEROS (MP/ARF5) may directly bind ANT, CUC1 and CUC2 and promote their transcription. Based on our findings, we propose an integrative model to describe the molecular mechanisms of the early stages of ovule development.","lang":"eng"}],"doi":"10.1111/tpj.12309","citation":{"ista":"Galbiati F, Sinha Roy D, Simonini S, Cucinotta M, Ceccato L, Cuesta C, Šimášková M, Benková E, Kamiuchi Y, Aida M, Weijers D, Simon R, Masiero S, Colombo L. 2013. An integrative model of the control of ovule primordia formation. The Plant journal for cell and molecular biology. 76(3), 446–455.","ieee":"F. Galbiati <i>et al.</i>, “An integrative model of the control of ovule primordia formation,” <i>The Plant journal for cell and molecular biology</i>, vol. 76, no. 3. Wiley-Blackwell, pp. 446–455, 2013.","ama":"Galbiati F, Sinha Roy D, Simonini S, et al. An integrative model of the control of ovule primordia formation. <i>The Plant journal for cell and molecular biology</i>. 2013;76(3):446-455. doi:<a href=\"https://doi.org/10.1111/tpj.12309\">10.1111/tpj.12309</a>","chicago":"Galbiati, Francesca, Dola Sinha Roy, Sara Simonini, Mara Cucinotta, Luca Ceccato, Candela Cuesta, Mária Šimášková, et al. “An Integrative Model of the Control of Ovule Primordia Formation.” <i>The Plant Journal for Cell and Molecular Biology</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1111/tpj.12309\">https://doi.org/10.1111/tpj.12309</a>.","short":"F. Galbiati, D. Sinha Roy, S. Simonini, M. Cucinotta, L. Ceccato, C. Cuesta, M. Šimášková, E. Benková, Y. Kamiuchi, M. Aida, D. Weijers, R. Simon, S. Masiero, L. Colombo, The Plant Journal for Cell and Molecular Biology 76 (2013) 446–455.","apa":"Galbiati, F., Sinha Roy, D., Simonini, S., Cucinotta, M., Ceccato, L., Cuesta, C., … Colombo, L. (2013). An integrative model of the control of ovule primordia formation. <i>The Plant Journal for Cell and Molecular Biology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/tpj.12309\">https://doi.org/10.1111/tpj.12309</a>","mla":"Galbiati, Francesca, et al. “An Integrative Model of the Control of Ovule Primordia Formation.” <i>The Plant Journal for Cell and Molecular Biology</i>, vol. 76, no. 3, Wiley-Blackwell, 2013, pp. 446–55, doi:<a href=\"https://doi.org/10.1111/tpj.12309\">10.1111/tpj.12309</a>."},"month":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"scopus_import":"1","oa_version":"None","date_created":"2018-12-11T11:48:44Z","date_published":"2013-09-19T00:00:00Z","extern":"1","status":"public","year":"2013","intvolume":"        76","type":"journal_article","issue":"3","publist_id":"6818","fulldoi":"https://doi.org/10.1111/tpj.12309","publication_status":"published","publication":"The Plant journal for cell and molecular biology","volume":76,"pmid":1,"article_type":"original","quality_controlled":"1","author":[{"first_name":"Francesca","full_name":"Galbiati, Francesca","last_name":"Galbiati"},{"full_name":"Sinha Roy, Dola","first_name":"Dola","last_name":"Sinha Roy"},{"last_name":"Simonini","first_name":"Sara","full_name":"Simonini, Sara"},{"last_name":"Cucinotta","first_name":"Mara","full_name":"Cucinotta, Mara"},{"first_name":"Luca","full_name":"Ceccato, Luca","last_name":"Ceccato"},{"last_name":"Cuesta","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1923-2410","full_name":"Cuesta, Candela","first_name":"Candela"},{"last_name":"Šimášková","first_name":"Mária","full_name":"Šimášková, Mária"},{"orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva"},{"first_name":"Yuri","full_name":"Kamiuchi, Yuri","last_name":"Kamiuchi"},{"full_name":"Aida, Mitsuhiro","first_name":"Mitsuhiro","last_name":"Aida"},{"first_name":"Dolf","full_name":"Weijers, Dolf","last_name":"Weijers"},{"first_name":"Rüdiger","full_name":"Simon, Rüdiger","last_name":"Simon"},{"first_name":"Simona","full_name":"Masiero, Simona","last_name":"Masiero"},{"full_name":"Colombo, Lucia","first_name":"Lucia","last_name":"Colombo"}],"day":"19","page":"446 - 455"},{"publication":"Molecular Systems Biology","doi":"10.1038/msb.2013.43","citation":{"mla":"Péret, Benjamin, et al. “Sequential Induction of Auxin Efflux and Influx Carriers Regulates Lateral Root Emergence.” <i>Molecular Systems Biology</i>, vol. 9, Nature Publishing Group, 2013, doi:<a href=\"https://doi.org/10.1038/msb.2013.43\">10.1038/msb.2013.43</a>.","apa":"Péret, B., Middleton, A., French, A., Larrieu, A., Bishopp, A., Njo, M., … Bennett, M. (2013). Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. <i>Molecular Systems Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/msb.2013.43\">https://doi.org/10.1038/msb.2013.43</a>","chicago":"Péret, Benjamin, Alistair Middleton, Andrew French, Antoine Larrieu, Anthony Bishopp, Maria Njo, Darren Wells, et al. “Sequential Induction of Auxin Efflux and Influx Carriers Regulates Lateral Root Emergence.” <i>Molecular Systems Biology</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/msb.2013.43\">https://doi.org/10.1038/msb.2013.43</a>.","short":"B. Péret, A. Middleton, A. French, A. Larrieu, A. Bishopp, M. Njo, D. Wells, S. Porco, N. Mellor, L. Band, I. Casimiro, J. Kleine Vehn, S. Vanneste, I. Sairanen, R. Mallet, G. Sandberg, K. Ljung, T. Beeckman, E. Benková, J. Friml, E. Kramer, J. King, I. De Smet, T. Pridmore, M. Owen, M. Bennett, Molecular Systems Biology 9 (2013).","ama":"Péret B, Middleton A, French A, et al. Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. <i>Molecular Systems Biology</i>. 2013;9. doi:<a href=\"https://doi.org/10.1038/msb.2013.43\">10.1038/msb.2013.43</a>","ieee":"B. Péret <i>et al.</i>, “Sequential induction of auxin efflux and influx carriers regulates lateral root emergence,” <i>Molecular Systems Biology</i>, vol. 9. Nature Publishing Group, 2013.","ista":"Péret B, Middleton A, French A, Larrieu A, Bishopp A, Njo M, Wells D, Porco S, Mellor N, Band L, Casimiro I, Kleine Vehn J, Vanneste S, Sairanen I, Mallet R, Sandberg G, Ljung K, Beeckman T, Benková E, Friml J, Kramer E, King J, De Smet I, Pridmore T, Owen M, Bennett M. 2013. Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. Molecular Systems Biology. 9."},"abstract":[{"lang":"eng","text":"In Arabidopsis, lateral roots originate from pericycle cells deep within the primary root. New lateral root primordia (LRP) have to emerge through several overlaying tissues. Here, we report that auxin produced in new LRP is transported towards the outer tissues where it triggers cell separation by inducing both the auxin influx carrier LAX3 and cell-wall enzymes. LAX3 is expressed in just two cell files overlaying new LRP. To understand how this striking pattern of LAX3 expression is regulated, we developed a mathematical model that captures the network regulating its expression and auxin transport within realistic three-dimensional cell and tissue geometries. Our model revealed that, for the LAX3 spatial expression to be robust to natural variations in root tissue geometry, an efflux carrier is required--later identified to be PIN3. To prevent LAX3 from being transiently expressed in multiple cell files, PIN3 and LAX3 must be induced consecutively, which we later demonstrated to be the case. Our study exemplifies how mathematical models can be used to direct experiments to elucidate complex developmental processes."}],"tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"publication_status":"published","fulldoi":"https://doi.org/10.1038/msb.2013.43","publist_id":"6817","acknowledgement":"This work was supported by an FEBS Long‐Term Fellowship (BP), an Intra‐European Fellowship for Career Development under the 7th framework of the European Commission (IEF‐2008‐220506 to BP), an EMBO Long‐Term Fellowship (BP), an European Reintegration Grant under the 7th framework of the European Commission (ERG‐2010‐276662 to BP) and the Swedish Research Council (VR 621‐2010‐5720 to IS, GS and KL). AMM, APF, AL, LRB, SP, NM, DMW, MO, JRK and MJB acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC) and Engineering and Physical Sciences Research Council (EPSRC) funding to the Centre for Plant Integrative Biology (CPIB); BBSRC Professorial Research Fellowship funding to DMW and MJB; Belgian Scientific policy (BELSPO contract MARS) to TB and MJB. We thank Bert de Rybel for his help in Multisite Gateway cloning.","type":"journal_article","publisher":"Nature Publishing Group","_id":"831","intvolume":"         9","year":"2013","status":"public","date_updated":"2021-01-12T08:18:03Z","extern":1,"date_published":"2013-10-22T00:00:00Z","title":"Sequential induction of auxin efflux and influx carriers regulates lateral root emergence","date_created":"2018-12-11T11:48:44Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","day":"22","author":[{"first_name":"Benjamin","full_name":"Péret, Benjamin","last_name":"Péret"},{"last_name":"Middleton","full_name":"Middleton, Alistair M","first_name":"Alistair"},{"first_name":"Andrew","full_name":"French, Andrew P","last_name":"French"},{"first_name":"Antoine","full_name":"Larrieu, Antoine","last_name":"Larrieu"},{"last_name":"Bishopp","full_name":"Bishopp, Anthony","first_name":"Anthony"},{"last_name":"Njo","first_name":"Maria","full_name":"Njo, Maria"},{"last_name":"Wells","full_name":"Wells, Darren M","first_name":"Darren"},{"first_name":"Silvana","full_name":"Porco, Silvana","last_name":"Porco"},{"first_name":"Nathan","full_name":"Mellor, Nathan","last_name":"Mellor"},{"last_name":"Band","first_name":"Leah","full_name":"Band, Leah R"},{"full_name":"Casimiro, Ilda","first_name":"Ilda","last_name":"Casimiro"},{"last_name":"Kleine Vehn","full_name":"Kleine-Vehn, Jürgen","first_name":"Jürgen"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"full_name":"Sairanen, Ilkka","first_name":"Ilkka","last_name":"Sairanen"},{"last_name":"Mallet","first_name":"Romain","full_name":"Mallet, Romain"},{"last_name":"Sandberg","first_name":"Göran","full_name":"Sandberg, Göran"},{"first_name":"Karin","full_name":"Ljung, Karin","last_name":"Ljung"},{"last_name":"Beeckman","full_name":"Beeckman, Tom","first_name":"Tom"},{"first_name":"Eva","full_name":"Eva Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","last_name":"Benková"},{"full_name":"Jirí Friml","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kramer, Eric","first_name":"Eric","last_name":"Kramer"},{"last_name":"King","first_name":"John","full_name":"King, John R"},{"full_name":"De Smet, Ive","first_name":"Ive","last_name":"De Smet"},{"last_name":"Pridmore","first_name":"Tony","full_name":"Pridmore, Tony"},{"last_name":"Owen","full_name":"Owen, Markus","first_name":"Markus"},{"last_name":"Bennett","first_name":"Malcolm","full_name":"Bennett, Malcolm J"}],"month":"10","quality_controlled":0,"volume":9},{"language":[{"iso":"eng"}],"month":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","title":"Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin","date_updated":"2021-01-12T08:19:26Z","publisher":"Springer Nature","_id":"8461","keyword":["Spectroscopy","Biochemistry"],"publication_identifier":{"issn":["0925-2738","1573-5001"]},"abstract":[{"text":"Solid-state NMR provides insight into protein motion over time scales ranging from picoseconds to seconds. While in solution state the methodology to measure protein dynamics is well established, there is currently no such consensus protocol for measuring dynamics in solids. In this article, we perform a detailed investigation of measurement protocols for fast motions, i.e. motions ranging from picoseconds to a few microseconds, which is the range covered by dipolar coupling and relaxation experiments. We perform a detailed theoretical investigation how dipolar couplings and relaxation data can provide information about amplitudes and time scales of local motion. We show that the measurement of dipolar couplings is crucial for obtaining accurate motional parameters, while systematic errors are found when only relaxation data are used. Based on this realization, we investigate how the REDOR experiment can provide such data in a very accurate manner. We identify that with accurate rf calibration, and explicit consideration of rf field inhomogeneities, one can obtain highly accurate absolute order parameters. We then perform joint model-free analyses of 6 relaxation data sets and dipolar couplings, based on previously existing, as well as new data sets on microcrystalline ubiquitin. We show that nanosecond motion can be detected primarily in loop regions, and compare solid-state data to solution-state relaxation and RDC analyses. The protocols investigated here will serve as a useful basis towards the establishment of a routine protocol for the characterization of ps–μs motions in proteins by solid-state NMR.","lang":"eng"}],"citation":{"ista":"Haller JD, Schanda P. 2013. Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. Journal of Biomolecular NMR. 57(3), 263–280.","ieee":"J. D. Haller and P. Schanda, “Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin,” <i>Journal of Biomolecular NMR</i>, vol. 57, no. 3. Springer Nature, pp. 263–280, 2013.","ama":"Haller JD, Schanda P. Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. <i>Journal of Biomolecular NMR</i>. 2013;57(3):263-280. doi:<a href=\"https://doi.org/10.1007/s10858-013-9787-x\">10.1007/s10858-013-9787-x</a>","chicago":"Haller, Jens D., and Paul Schanda. “Amplitudes and Time Scales of Picosecond-to-Microsecond Motion in Proteins Studied by Solid-State NMR: A Critical Evaluation of Experimental Approaches and Application to Crystalline Ubiquitin.” <i>Journal of Biomolecular NMR</i>. Springer Nature, 2013. <a href=\"https://doi.org/10.1007/s10858-013-9787-x\">https://doi.org/10.1007/s10858-013-9787-x</a>.","short":"J.D. Haller, P. Schanda, Journal of Biomolecular NMR 57 (2013) 263–280.","apa":"Haller, J. D., &#38; Schanda, P. (2013). Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. <i>Journal of Biomolecular NMR</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10858-013-9787-x\">https://doi.org/10.1007/s10858-013-9787-x</a>","mla":"Haller, Jens D., and Paul Schanda. “Amplitudes and Time Scales of Picosecond-to-Microsecond Motion in Proteins Studied by Solid-State NMR: A Critical Evaluation of Experimental Approaches and Application to Crystalline Ubiquitin.” <i>Journal of Biomolecular NMR</i>, vol. 57, no. 3, Springer Nature, 2013, pp. 263–80, doi:<a href=\"https://doi.org/10.1007/s10858-013-9787-x\">10.1007/s10858-013-9787-x</a>."},"doi":"10.1007/s10858-013-9787-x","article_processing_charge":"No","volume":57,"quality_controlled":"1","article_type":"original","day":"09","author":[{"last_name":"Haller","first_name":"Jens D.","full_name":"Haller, Jens D."},{"first_name":"Paul","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","last_name":"Schanda"}],"page":"263-280","date_published":"2013-10-09T00:00:00Z","date_created":"2020-09-18T10:09:05Z","type":"journal_article","issue":"3","year":"2013","status":"public","extern":"1","intvolume":"        57","publication":"Journal of Biomolecular NMR","fulldoi":"https://doi.org/10.1007/s10858-013-9787-x","publication_status":"published"},{"date_updated":"2022-08-25T14:56:24Z","_id":"8462","publisher":"Elsevier","title":"Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure","article_processing_charge":"No","abstract":[{"text":"The transition of proteins from their soluble functional state to amyloid fibrils and aggregates is associated with the onset of several human diseases. Protein aggregation often requires some structural reshaping and the subsequent formation of intermolecular contacts. Therefore, the study of the conformation of excited protein states and their ability to form oligomers is of primary importance for understanding the molecular basis of amyloid fibril formation. Here, we investigated the oligomerization processes that occur along the folding of the amyloidogenic human protein β2-microglobulin. The combination of real-time two-dimensional NMR data with real-time small-angle X-ray scattering measurements allowed us to derive thermodynamic and kinetic information on protein oligomerization of different conformational states populated along the folding pathways. In particular, we could demonstrate that a long-lived folding intermediate (I-state) has a higher propensity to oligomerize compared to the native state. Our data agree well with a simple five-state kinetic model that involves only monomeric and dimeric species. The dimers have an elongated shape with the dimerization interface located at the apical side of β2-microglobulin close to Pro32, the residue that has a trans conformation in the I-state and a cis conformation in the native (N) state. Our experimental data suggest that partial unfolding in the apical half of the protein close to Pro32 leads to an excited state conformation with enhanced propensity for oligomerization. This excited state becomes more populated in the transient I-state due to the destabilization of the native conformation by the trans-Pro32 configuration.","lang":"eng"}],"publication_identifier":{"issn":["0022-2836"]},"citation":{"apa":"Rennella, E., Cutuil, T., Schanda, P., Ayala, I., Gabel, F., Forge, V., … Brutscher, B. (2013). Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2013.04.028\">https://doi.org/10.1016/j.jmb.2013.04.028</a>","mla":"Rennella, E., et al. “Oligomeric States along the Folding Pathways of Β2-Microglobulin: Kinetics, Thermodynamics, and Structure.” <i>Journal of Molecular Biology</i>, vol. 425, no. 15, Elsevier, 2013, pp. 2722–36, doi:<a href=\"https://doi.org/10.1016/j.jmb.2013.04.028\">10.1016/j.jmb.2013.04.028</a>.","ista":"Rennella E, Cutuil T, Schanda P, Ayala I, Gabel F, Forge V, Corazza A, Esposito G, Brutscher B. 2013. Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. Journal of Molecular Biology. 425(15), 2722–2736.","ieee":"E. Rennella <i>et al.</i>, “Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure,” <i>Journal of Molecular Biology</i>, vol. 425, no. 15. Elsevier, pp. 2722–2736, 2013.","ama":"Rennella E, Cutuil T, Schanda P, et al. Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. <i>Journal of Molecular Biology</i>. 2013;425(15):2722-2736. doi:<a href=\"https://doi.org/10.1016/j.jmb.2013.04.028\">10.1016/j.jmb.2013.04.028</a>","chicago":"Rennella, E., T. Cutuil, Paul Schanda, I. Ayala, F. Gabel, V. Forge, A. Corazza, G. Esposito, and B. Brutscher. “Oligomeric States along the Folding Pathways of Β2-Microglobulin: Kinetics, Thermodynamics, and Structure.” <i>Journal of Molecular Biology</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.jmb.2013.04.028\">https://doi.org/10.1016/j.jmb.2013.04.028</a>.","short":"E. Rennella, T. Cutuil, P. Schanda, I. Ayala, F. Gabel, V. Forge, A. Corazza, G. Esposito, B. Brutscher, Journal of Molecular Biology 425 (2013) 2722–2736."},"doi":"10.1016/j.jmb.2013.04.028","keyword":["Molecular Biology"],"oa_version":"None","language":[{"iso":"eng"}],"month":"08","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2013","extern":"1","status":"public","intvolume":"       425","type":"journal_article","issue":"15","date_created":"2020-09-18T10:09:12Z","date_published":"2013-08-09T00:00:00Z","fulldoi":"https://doi.org/10.1016/j.jmb.2013.04.028","publication_status":"published","publication":"Journal of Molecular Biology","article_type":"original","quality_controlled":"1","volume":425,"page":"2722-2736","author":[{"full_name":"Rennella, E.","first_name":"E.","last_name":"Rennella"},{"full_name":"Cutuil, T.","first_name":"T.","last_name":"Cutuil"},{"full_name":"Schanda, Paul","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","orcid":"0000-0002-9350-7606"},{"first_name":"I.","full_name":"Ayala, I.","last_name":"Ayala"},{"last_name":"Gabel","full_name":"Gabel, F.","first_name":"F."},{"last_name":"Forge","first_name":"V.","full_name":"Forge, V."},{"full_name":"Corazza, A.","first_name":"A.","last_name":"Corazza"},{"last_name":"Esposito","first_name":"G.","full_name":"Esposito, G."},{"last_name":"Brutscher","first_name":"B.","full_name":"Brutscher, B."}],"day":"09"}]