The Impact of Entropy on the Spatial Organization of Synaptonemal Complexes within the Cell Nucleus
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{"title"=>"The impact of entropy on the spatial organization of synaptonemal complexes within the cell nucleus", "type"=>"journal", "authors"=>[{"first_name"=>"Miriam", "last_name"=>"Fritsche", "scopus_author_id"=>"23027731500"}, {"first_name"=>"Laura G.", "last_name"=>"Reinholdt", "scopus_author_id"=>"6508052962"}, {"first_name"=>"Mark", "last_name"=>"Lessard", "scopus_author_id"=>"7006169842"}, {"first_name"=>"Mary Ann", "last_name"=>"Handel", "scopus_author_id"=>"7005488445"}, {"first_name"=>"Jörg", "last_name"=>"Bewersdorf", "scopus_author_id"=>"6506277447"}, {"first_name"=>"Dieter W.", "last_name"=>"Heermann", "scopus_author_id"=>"7006305689"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"364730672", "scopus"=>"2-s2.0-84860544026", "isbn"=>"10.1371/journal.pone.0036282", "pmid"=>"22574147", "sgr"=>"84860544026", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0036282"}, "id"=>"4ecf56cb-9989-31fc-8572-1044beb024a3", "abstract"=>"We employ 4Pi-microscopy to study SC organization in mouse spermatocyte nuclei allowing for the three-dimensional reconstruction of the SC's backbone arrangement. Additionally, we model the SCs in the cell nucleus by confined, self-avoiding polymers, whose chain ends are attached to the envelope of the confining cavity and diffuse along it. This work helps to elucidate the role of entropy in shaping pachytene SC organization. The framework provided by the complex interplay between SC polymer rigidity, tethering and confinement is able to qualitatively explain features of SC organization, such as mean squared end-to-end distances, mean squared center-of-mass distances, or SC density distributions. However, it fails in correctly assessing SC entanglement within the nucleus. In fact, our analysis of the 4Pi-microscopy images reveals a higher ordering of SCs within the nuclear volume than what is expected by our numerical model. This suggests that while effects of entropy impact SC organization, the dedicated action of proteins or actin cables is required to fine-tune the spatial ordering of SCs within the cell nucleus.", "link"=>"http://www.mendeley.com/research/impact-entropy-spatial-organization-synaptonemal-complexes-within-cell-nucleus", "reader_count"=>13, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>3, "Student > Ph. D. Student"=>7, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>3, "Student > Ph. D. Student"=>7, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>6, "Medicine and Dentistry"=>1, "Physics and Astronomy"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>6}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"United States"=>1, "Mexico"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/642666"], "description"=>"<p>Summary of values obtained from 4Pi data.</p>", "links"=>[], "tags"=>["4pi"], "article_id"=>313154, "categories"=>["Physics", "Biological Sciences", "Genetics", "Biophysics"], "users"=>["Miriam Fritsche", "Laura G. Reinholdt", "Mark Lessard", "Mary Ann Handel", "Jörg Bewersdorf", "Dieter W. Heermann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036282.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_values_obtained_from_4Pi_data_/313154", "title"=>"Summary of values obtained from 4Pi data.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-04 00:52:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/642289"], "description"=>"<p>At low bending rigidity, double tethered SC polymers effectively form a “polymer brush”, leading to stronger segregation between them in contrast to the intermingling of free polymers. The shaded region indicates the range of bending rigidity that generates the experimentally observed mean squared center of mass distance of .</p>", "links"=>[], "tags"=>["squared", "interchain", "rigidity", "double-tethered", "sc", "polymer", "polymers"], "article_id"=>312772, "categories"=>["Physics", "Biological Sciences", "Genetics", "Biophysics"], "users"=>["Miriam Fritsche", "Laura G. Reinholdt", "Mark Lessard", "Mary Ann Handel", "Jörg Bewersdorf", "Dieter W. Heermann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036282.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mean_squared_interchain_center_of_mass_distance_as_a_function_of_chain_rigidity_for_the_double_tethered_SC_polymer_model_Two_tethers_as_well_as_for_the_null_model_of_free_polymers_Untethered_/312772", "title"=>"Mean squared interchain center of mass distance as a function of chain rigidity for the double-tethered SC polymer model (“Two tethers”) as well as for the “null” model of free polymers (“Untethered”).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-04 00:46:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/642517"], "description"=>"<p>The behavior of the experimental PDF fits qualitatively to our (double-tethered) SC polymer model, where the probability density is high for middle-chain regions and drops quickly towards the polymer end regions. This is in contrast to the untethered model, where random coil formation induces a less steep decrease of the probability density function towards both polymer end regions.</p>", "links"=>[], "tags"=>["calculated", "sites", "backbone", "scs", "4pi-microscopy", "samples", "sc", "sytems", "bending"], "article_id"=>312997, "categories"=>["Physics", "Biological Sciences", "Genetics", "Biophysics"], "users"=>["Miriam Fritsche", "Laura G. Reinholdt", "Mark Lessard", "Mary Ann Handel", "Jörg Bewersdorf", "Dieter W. Heermann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036282.g005", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Probability_density_function_PDF_calculated_for_b_sites_along_the_backbone_of_each_SCs_within_the_nuclear_volume_for_various_4Pi_microscopy_samples_as_well_as_a_for_our_SC_model_sytems_at_high_and_low_bending_rigidity_and_respectively_/312997", "title"=>"Probability density function (PDF) calculated for (b) sites along the backbone of each SCs within the nuclear volume for various 4Pi-microscopy samples as well as (a) for our SC model sytems at high and low bending rigidity, and , respectively.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-04 00:49:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/642371"], "description"=>"<p>(a) Intrachain entanglement (“self-entanglement”) and (b) interchain entanglement measured by the mean average crossing number mACN as a function of chain rigidity . Tethering the SC polymer's ends to the borders of the confining cavity induces fewer chain overcrossings than the “null model” consisting of free semiflexible polymers in confinement, which suggests that the interplay between tethering and confinement might help to prevent an excess of chain overcrossings. However, semiflexibility induces a trade-off in both polymer systems between the amount of intrachain- and interchain-entanglement which has to be balanced with respect to interlock resolution. Notably, we find a surprisingly low amount of both types of chain overcrossings for the 4Pi microscopy dataset, mACN and mACN, which cannot be explained within our SC polymer model.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "biophysics", "physics"], "article_id"=>312857, "categories"=>["Physics", "Biological Sciences", "Genetics", "Biophysics"], "users"=>["Miriam Fritsche", "Laura G. Reinholdt", "Mark Lessard", "Mary Ann Handel", "Jörg Bewersdorf", "Dieter W. Heermann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036282.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Figure_4_/312857", "title"=>"Figure 4", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-04 00:47:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/642212"], "description"=>"<p>The insets show the probability density function (PDF) of the end-to-end distance for the flexible regime as well as for the stiff case . Semiflexible end-tethered polymers are forces to stretch out between the (moving) attachment sites, leading to larger mean end-to-end distances in agreement with visual inspection of the SC's end-to-end distances in 4Pi-microscopy images. The shaded region indicates the range of bending rigidity that generates the experimentally observed mean squared end-to-end distance of .</p>", "links"=>[], "tags"=>["squared", "end-to-end", "rigidity", "double-tethered", "sc", "polymer", "polymers"], "article_id"=>312692, "categories"=>["Physics", "Biological Sciences", "Genetics", "Biophysics"], "users"=>["Miriam Fritsche", "Laura G. Reinholdt", "Mark Lessard", "Mary Ann Handel", "Jörg Bewersdorf", "Dieter W. Heermann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036282.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mean_squared_end_to_end_distance_as_a_function_of_chain_rigidity_for_the_double_tethered_SC_polymer_model_Two_tethers_as_well_as_for_the_null_model_of_free_polymers_Untethered_/312692", "title"=>"Mean squared end-to-end distance <b> as a function of chain rigidity </b> for the double-tethered SC polymer model (“Two tethers”) as well as for the “null” model of free polymers (“Untethered”).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-04 00:44:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/331377"], "description"=>"<div><p>We employ 4Pi-microscopy to study SC organization in mouse spermatocyte nuclei allowing for the three-dimensional reconstruction of the SC's backbone arrangement. Additionally, we model the SCs in the cell nucleus by confined, self-avoiding polymers, whose chain ends are attached to the envelope of the confining cavity and diffuse along it. This work helps to elucidate the role of entropy in shaping pachytene SC organization. The framework provided by the complex interplay between SC polymer rigidity, tethering and confinement is able to qualitatively explain features of SC organization, such as mean squared end-to-end distances, mean squared center-of-mass distances, or SC density distributions. However, it fails in correctly assessing SC entanglement within the nucleus. In fact, our analysis of the 4Pi-microscopy images reveals a higher ordering of SCs within the nuclear volume than what is expected by our numerical model. This suggests that while effects of entropy impact SC organization, the dedicated action of proteins or actin cables is required to fine-tune the spatial ordering of SCs within the cell nucleus.</p> </div>", "links"=>[], "tags"=>["entropy", "spatial", "synaptonemal", "complexes", "nucleus"], "article_id"=>125419, "categories"=>["Physics", "Biological Sciences", "Genetics", "Biophysics"], "users"=>["Miriam Fritsche", "Laura G. Reinholdt", "Mark Lessard", "Mary Ann Handel", "Jörg Bewersdorf", "Dieter W. Heermann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036282", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Impact_of_Entropy_on_the_Spatial_Organization_of_Synaptonemal_Complexes_within_the_Cell_Nucleus/125419", "title"=>"The Impact of Entropy on the Spatial Organization of Synaptonemal Complexes within the Cell Nucleus", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-04 01:30:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/642127"], "description"=>"<p>(a) Sketch of the applied SC polymer model with the tethered polymer ends being able to diffuse along the envelope of the confining geometry. (b) “Snapshot” of SC polymers in confinement based on the double-tethered SC polymer model. (c) “Snapshot” of synaptonemal complexes in spermatocyte nuclei based on 4Pi-microscopy data. Visual inspection of structural characteristics between the 4Pi-microscopy images and the SC model results such as their end-to-end distance as well as their orientation with respect to each other and the confining cavity indicate that entropy might be one driving force for structural SC organization complementing the dedicated action of specific proteins or actin cables <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036282#pone.0036282-Kleckner1\" target=\"_blank\">[2]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036282#pone.0036282-Koszul1\" target=\"_blank\">[10]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036282#pone.0036282-Storlazzi1\" target=\"_blank\">[25]</a>.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "biophysics", "physics"], "article_id"=>312613, "categories"=>["Physics", "Biological Sciences", "Genetics", "Biophysics"], "users"=>["Miriam Fritsche", "Laura G. Reinholdt", "Mark Lessard", "Mary Ann Handel", "Jörg Bewersdorf", "Dieter W. Heermann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036282.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Figure_1_/312613", "title"=>"Figure 1", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-04 00:43:33"}

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Relative Metric

{"start_date"=>"2012-01-01T00:00:00Z", "end_date"=>"2012-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[322, 550, 671, 773, 864, 955, 1048, 1135, 1223, 1308, 1387, 1465, 1534, 1602, 1673, 1744, 1813, 1885, 1955, 2026, 2093, 2160, 2228, 2290, 2349]}, {"subject_area"=>"/Biology and life sciences/Biochemistry", "average_usage"=>[316, 541, 663, 766, 856, 950, 1041, 1128, 1218, 1302, 1382, 1456, 1526, 1593, 1657, 1729, 1796, 1862, 1930, 1999, 2065, 2132, 2202, 2261, 2319]}, {"subject_area"=>"/Biology and life sciences/Cell biology", "average_usage"=>[319, 556, 679, 785, 881, 970, 1062, 1149, 1236, 1323, 1402, 1474, 1545, 1617, 1681, 1754, 1822, 1892, 1963, 2031, 2099, 2165, 2233, 2299, 2359]}, {"subject_area"=>"/Physical sciences/Mathematics", "average_usage"=>[325, 522, 627, 718, 804, 884, 969, 1052, 1131, 1207, 1277, 1346, 1415, 1478, 1542, 1605, 1663, 1723, 1776, 1839, 1895, 1955, 2008, 2066, 2123]}, {"subject_area"=>"/Physical sciences/Physics", "average_usage"=>[298, 476, 578, 665, 743, 821, 891, 962, 1036, 1108, 1174, 1240, 1312, 1371, 1430, 1494, 1551, 1609, 1673, 1736, 1795, 1857, 1913, 1976, 2035]}]}
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