The Experts below are selected from a list of 111393 Experts worldwide ranked by ideXlab platform
Christopher A Schmitt - One of the best experts on this subject based on the ideXlab platform.
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Predation risk sensitivity and the Spatial Organization of primate groups: a case study using GIS in lowland Woolly Monkeys (Lagothrix lagotricha poeppigii).
American Journal of Physical Anthropology, 2014Co-Authors: Christopher A Schmitt, Anthony Di FioreAbstract:Predation risk is thought to be a potent force influencing intragroup cohesion, and the level of risk experienced by an individual is expected to vary with both group size and Spatial position within a group. Smaller-bodied and less-experienced individuals are presumed to be more vulnerable to predators, suggesting that within-group Spatial Organization should show size- and age-dependent patterns in predator sensitive positioning. However, such effects have been difficult to evaluate for arboreal primates living in large groups. We conducted a preliminary study using a novel, Spatially explicit method of assessing group Spatial Organization using GIS data in two groups of wild lowland Woolly monkeys, in which one group had a membership roughly twice as large as the second. In the larger group, group spread was more diffuse and large adult males were more frequently on the outskirts of the group than other age/sex classes, while immatures and females with dependents were more often in the center. Leaf cover around an individual—presumed to index an animal's perception of risk—increased significantly with distance from the group center for all immatures, although they were typically under lower leaf cover than adults; the number of groupmates in proximity also had an effect, but nearest neighbor distance did not. These differences were not detectable in the smaller group. This preliminary study suggests that thorough studies of Spatial Organization and predation risk sensitivity in arboreal primates are possible and could yield valuable information on how gregarious individuals offset ecological risks through social spacing. Am J Phys Anthropol 156:158–165, 2015 © 2014 Wiley Periodicals, Inc.
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brief communication predation risk sensitivity and the Spatial Organization of primate groups a case study using gis in lowland woolly monkeys lagothrix lagotricha poeppigii
American Journal of Physical Anthropology, 2014Co-Authors: Christopher A Schmitt, Anthony Di FioreAbstract:Predation risk is thought to be a potent force influencing intragroup cohesion, and the level of risk experienced by an individual is expected to vary with both group size and Spatial position within a group. Smaller-bodied and less-experienced individuals are pre- sumed to be more vulnerable to predators, suggesting that within-group Spatial Organization should show size- and age-dependent patterns in predator sensitive posi- tioning. However, such effects have been difficult to eval- uate for arboreal primates living in large groups. We conducted a preliminary study using a novel, Spatially explicit method of assessing group Spatial Organization using GIS data in two groups of wild lowland Woolly monkeys, in which one group had a membership roughly twice as large as the second. In the larger group, group spread was more diffuse and large adult males were more frequently on the outskirts of the group than other age/sex classes, while immatures and females with dependents were more often in the center. Leaf cover around an individual—presumed to index an animal's perception of risk—increased significantly with distance from the group center for all immatures, although they were typically under lower leaf cover than adults; the number of groupmates in proximity also had an effect, but nearest neighbor distance did not. These differences were not detectable in the smaller group. This prelimi- nary study suggests that thorough studies of Spatial Organization and predation risk sensitivity in arboreal primates are possible and could yield valuable informa- tion on how gregarious individuals offset ecological risks through social spacing. Am J Phys Anthropol 000:000-
Anthony Di Fiore - One of the best experts on this subject based on the ideXlab platform.
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Predation risk sensitivity and the Spatial Organization of primate groups: a case study using GIS in lowland Woolly Monkeys (Lagothrix lagotricha poeppigii).
American Journal of Physical Anthropology, 2014Co-Authors: Christopher A Schmitt, Anthony Di FioreAbstract:Predation risk is thought to be a potent force influencing intragroup cohesion, and the level of risk experienced by an individual is expected to vary with both group size and Spatial position within a group. Smaller-bodied and less-experienced individuals are presumed to be more vulnerable to predators, suggesting that within-group Spatial Organization should show size- and age-dependent patterns in predator sensitive positioning. However, such effects have been difficult to evaluate for arboreal primates living in large groups. We conducted a preliminary study using a novel, Spatially explicit method of assessing group Spatial Organization using GIS data in two groups of wild lowland Woolly monkeys, in which one group had a membership roughly twice as large as the second. In the larger group, group spread was more diffuse and large adult males were more frequently on the outskirts of the group than other age/sex classes, while immatures and females with dependents were more often in the center. Leaf cover around an individual—presumed to index an animal's perception of risk—increased significantly with distance from the group center for all immatures, although they were typically under lower leaf cover than adults; the number of groupmates in proximity also had an effect, but nearest neighbor distance did not. These differences were not detectable in the smaller group. This preliminary study suggests that thorough studies of Spatial Organization and predation risk sensitivity in arboreal primates are possible and could yield valuable information on how gregarious individuals offset ecological risks through social spacing. Am J Phys Anthropol 156:158–165, 2015 © 2014 Wiley Periodicals, Inc.
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brief communication predation risk sensitivity and the Spatial Organization of primate groups a case study using gis in lowland woolly monkeys lagothrix lagotricha poeppigii
American Journal of Physical Anthropology, 2014Co-Authors: Christopher A Schmitt, Anthony Di FioreAbstract:Predation risk is thought to be a potent force influencing intragroup cohesion, and the level of risk experienced by an individual is expected to vary with both group size and Spatial position within a group. Smaller-bodied and less-experienced individuals are pre- sumed to be more vulnerable to predators, suggesting that within-group Spatial Organization should show size- and age-dependent patterns in predator sensitive posi- tioning. However, such effects have been difficult to eval- uate for arboreal primates living in large groups. We conducted a preliminary study using a novel, Spatially explicit method of assessing group Spatial Organization using GIS data in two groups of wild lowland Woolly monkeys, in which one group had a membership roughly twice as large as the second. In the larger group, group spread was more diffuse and large adult males were more frequently on the outskirts of the group than other age/sex classes, while immatures and females with dependents were more often in the center. Leaf cover around an individual—presumed to index an animal's perception of risk—increased significantly with distance from the group center for all immatures, although they were typically under lower leaf cover than adults; the number of groupmates in proximity also had an effect, but nearest neighbor distance did not. These differences were not detectable in the smaller group. This prelimi- nary study suggests that thorough studies of Spatial Organization and predation risk sensitivity in arboreal primates are possible and could yield valuable informa- tion on how gregarious individuals offset ecological risks through social spacing. Am J Phys Anthropol 000:000-
Shaun Mahony - One of the best experts on this subject based on the ideXlab platform.
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alignment and quantification of chip exo crosslinking patterns reveal the Spatial Organization of protein dna complexes
Nucleic Acids Research, 2020Co-Authors: Naomi Yamada, Matthew J Rossi, Nina Farrell, Franklin B Pugh, Shaun MahonyAbstract:The ChIP-exo assay precisely delineates protein-DNA crosslinking patterns by combining chromatin immunoprecipitation with 5' to 3' exonuclease digestion. Within a regulatory complex, the physical distance of a regulatory protein to DNA affects crosslinking efficiencies. Therefore, the Spatial Organization of a protein-DNA complex could potentially be inferred by analyzing how crosslinking signatures vary between its subunits. Here, we present a computational framework that aligns ChIP-exo crosslinking patterns from multiple proteins across a set of coordinately bound regulatory regions, and which detects and quantifies protein-DNA crosslinking events within the aligned profiles. By producing consistent measurements of protein-DNA crosslinking strengths across multiple proteins, our approach enables characterization of relative Spatial Organization within a regulatory complex. Applying our approach to collections of ChIP-exo data, we demonstrate that it can recover aspects of regulatory complex Spatial Organization at yeast ribosomal protein genes and yeast tRNA genes. We also demonstrate the ability to quantify changes in protein-DNA complex Organization across conditions by applying our approach to analyze Drosophila Pol II transcriptional components. Our results suggest that principled analyses of ChIP-exo crosslinking patterns enable inference of Spatial Organization within protein-DNA complexes.
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alignment and quantification of chip exo crosslinking patterns reveal the Spatial Organization of protein dna complexes
bioRxiv, 2019Co-Authors: Naomi Yamada, Matthew J Rossi, Nina Farrell, Franklin B Pugh, Shaun MahonyAbstract:Abstract The ChIP-exo assay precisely delineates protein-DNA crosslinking patterns by combining chromatin immunoprecipitation with 5′ to 3′ exonuclease digestion. Within a regulatory complex, the physical distance of a regulatory protein to DNA affects crosslinking efficiencies. Therefore, the Spatial Organization of a protein-DNA complex could potentially be inferred by analyzing how crosslinking signatures vary between the subunits of a regulatory complex. Here, we present a computational framework that aligns ChIP-exo crosslinking patterns from multiple proteins across a set of coordinately bound regulatory regions, and which detects and quantifies protein-DNA crosslinking events within the aligned profiles. By producing consistent measurements of protein-DNA crosslinking strengths across multiple proteins, our approach enables characterization of relative Spatial Organization within a regulatory complex. We demonstrate that our approach can recover aspects of regulatory complex Spatial Organization when applied to collections of ChIP-exo data that profile regulatory machinery at yeast ribosomal protein genes and yeast tRNA genes. We also demonstrate the ability to quantify changes in protein-DNA complex Organization across conditions by applying our approach to data profiling Drosophila Pol II transcriptional components. Our results suggest that principled analyses of ChIP-exo crosslinking patterns enable inference of Spatial Organization within protein-DNA complexes.
Naomi Yamada - One of the best experts on this subject based on the ideXlab platform.
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alignment and quantification of chip exo crosslinking patterns reveal the Spatial Organization of protein dna complexes
Nucleic Acids Research, 2020Co-Authors: Naomi Yamada, Matthew J Rossi, Nina Farrell, Franklin B Pugh, Shaun MahonyAbstract:The ChIP-exo assay precisely delineates protein-DNA crosslinking patterns by combining chromatin immunoprecipitation with 5' to 3' exonuclease digestion. Within a regulatory complex, the physical distance of a regulatory protein to DNA affects crosslinking efficiencies. Therefore, the Spatial Organization of a protein-DNA complex could potentially be inferred by analyzing how crosslinking signatures vary between its subunits. Here, we present a computational framework that aligns ChIP-exo crosslinking patterns from multiple proteins across a set of coordinately bound regulatory regions, and which detects and quantifies protein-DNA crosslinking events within the aligned profiles. By producing consistent measurements of protein-DNA crosslinking strengths across multiple proteins, our approach enables characterization of relative Spatial Organization within a regulatory complex. Applying our approach to collections of ChIP-exo data, we demonstrate that it can recover aspects of regulatory complex Spatial Organization at yeast ribosomal protein genes and yeast tRNA genes. We also demonstrate the ability to quantify changes in protein-DNA complex Organization across conditions by applying our approach to analyze Drosophila Pol II transcriptional components. Our results suggest that principled analyses of ChIP-exo crosslinking patterns enable inference of Spatial Organization within protein-DNA complexes.
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alignment and quantification of chip exo crosslinking patterns reveal the Spatial Organization of protein dna complexes
bioRxiv, 2019Co-Authors: Naomi Yamada, Matthew J Rossi, Nina Farrell, Franklin B Pugh, Shaun MahonyAbstract:Abstract The ChIP-exo assay precisely delineates protein-DNA crosslinking patterns by combining chromatin immunoprecipitation with 5′ to 3′ exonuclease digestion. Within a regulatory complex, the physical distance of a regulatory protein to DNA affects crosslinking efficiencies. Therefore, the Spatial Organization of a protein-DNA complex could potentially be inferred by analyzing how crosslinking signatures vary between the subunits of a regulatory complex. Here, we present a computational framework that aligns ChIP-exo crosslinking patterns from multiple proteins across a set of coordinately bound regulatory regions, and which detects and quantifies protein-DNA crosslinking events within the aligned profiles. By producing consistent measurements of protein-DNA crosslinking strengths across multiple proteins, our approach enables characterization of relative Spatial Organization within a regulatory complex. We demonstrate that our approach can recover aspects of regulatory complex Spatial Organization when applied to collections of ChIP-exo data that profile regulatory machinery at yeast ribosomal protein genes and yeast tRNA genes. We also demonstrate the ability to quantify changes in protein-DNA complex Organization across conditions by applying our approach to data profiling Drosophila Pol II transcriptional components. Our results suggest that principled analyses of ChIP-exo crosslinking patterns enable inference of Spatial Organization within protein-DNA complexes.
Oscar M. Aparicio - One of the best experts on this subject based on the ideXlab platform.
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Conserved forkhead dimerization motif controls DNA replication timing and Spatial Organization of chromosomes in S. cerevisiae
Proceedings of the National Academy of Sciences of the United States of America, 2017Co-Authors: A. Zachary Ostrow, Reza Kalhor, Yan Gan, Sandra K. Villwock, Christian Linke, Matteo Barberis, Lin Chen, Oscar M. AparicioAbstract:Forkhead Box (Fox) proteins share the Forkhead domain, a winged-helix DNA binding module, which is conserved among eukaryotes from yeast to humans. These sequence-specific DNA binding proteins have been primarily characterized as transcription factors regulating diverse cellular processes from cell cycle control to developmental fate, deregulation of which contributes to developmental defects, cancer, and aging. We recently identified Saccharomyces cerevisiae Forkhead 1 (Fkh1) and Forkhead 2 (Fkh2) as required for the clustering of a subset of replication origins in G1 phase and for the early initiation of these origins in the ensuing S phase, suggesting a mechanistic role linking the Spatial Organization of the origins and their activity. Here, we show that Fkh1 and Fkh2 share a unique structural feature of human FoxP proteins that enables FoxP2 and FoxP3 to form domain-swapped dimers capable of bridging two DNA molecules in vitro. Accordingly, Fkh1 self-associates in vitro and in vivo in a manner dependent on the conserved domain-swapping region, strongly suggestive of homodimer formation. Fkh1- and Fkh2-domain-swap-minus (dsm) mutations are functional as transcription factors yet are defective in replication origin timing control. Fkh1-dsm binds replication origins in vivo but fails to cluster them, supporting the conclusion that Fkh1 and Fkh2 dimers perform a structural role in the Spatial Organization of chromosomal elements with functional importance.
