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Title: Thrombopoietin Signaling To Chromatin Elicits Rapid And Pervasive Epigenome Remodeling Within Poised Chromatin Architectures.
Creator: Comoglio, Federico, Park, Hyun Jung, Schoenfelder, Stefan, Barozzi, Iros, Bode, Daniel, Fraser, Peter, Green, Anthony R.
Abstract/Description: Thrombopoietin (TPO) is a critical cytokine regulating hematopoietic stem cell maintenance and differentiation into the megakaryocytic lineage. However, the transcriptional and chromatin dynamics elicited by TPO signaling are poorly understood. Here, we study the immediate early transcriptional and cis-regulatory responses to TPO in hematopoietic stem/progenitor cells (HSPCs) and use this paradigm of cytokine signaling to chromatin to dissect the relationship between cis-regulatory activity...
Show moreThrombopoietin (TPO) is a critical cytokine regulating hematopoietic stem cell maintenance and differentiation into the megakaryocytic lineage. However, the transcriptional and chromatin dynamics elicited by TPO signaling are poorly understood. Here, we study the immediate early transcriptional and cis-regulatory responses to TPO in hematopoietic stem/progenitor cells (HSPCs) and use this paradigm of cytokine signaling to chromatin to dissect the relationship between cis-regulatory activity and chromatin architecture. We show that TPO profoundly alters the transcriptome of HSPCs, with key hematopoietic regulators being transcriptionally repressed within 30 min of TPO. By examining cis-regulatory dynamics and chromatin architectures, we demonstrate that these changes are accompanied by rapid and extensive epigenome remodeling of cis-regulatory landscapes that is spatially coordinated within topologically associating domains (TADs). Moreover, TPO-responsive enhancers are spatially clustered and engage in preferential homotypic intra-and inter-TAD interactions that are largely refractory to TPO signaling. By further examining the link between cis-regulatory dynamics and chromatin looping, we show that rapid modulation of cis-regulatory activity is largely independent of chromatin looping dynamics. Finally, we show that, although activated and repressed cis-regulatory elements share remarkably similar DNA sequence compositions, transcription factor binding patterns accurately predict rapid cis-regulatory responses to TPO.
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Date Issued: 2018-03
Identifier: FSU_libsubv1_wos_000426355600003, 10.1101/gr.227272.117
Format: Citation

Title: Atomic Resolution Structures Of Human Bufaviruses Determined By Cryo-electron Microscopy.
Creator: Ilyas, Maria, Mietzsch, Mario, Kailasan, Shweta, Vaisanen, Elina, Luo, Mengxiao, Chipman, Paul, Smith, J. Kennon, Kurian, Justin, Sousa, Duncan, McKenna, Robert, Soderlund...
Show moreIlyas, Maria, Mietzsch, Mario, Kailasan, Shweta, Vaisanen, Elina, Luo, Mengxiao, Chipman, Paul, Smith, J. Kennon, Kurian, Justin, Sousa, Duncan, McKenna, Robert, Soderlund-Venermo, Maria, Agbandje-McKenna, Mavis
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Abstract/Description: Bufavirus strain 1 (BuV1), a member of the Protoparvovirus genus of the Parvoviridae, was first isolated from fecal samples of children with acute diarrhea in Burkina Faso. Since this initial discovery, BuVs have been isolated in several countries, including Finland, the Netherlands, and Bhutan, in pediatric patients exhibiting similar symptoms. Towards their characterization, the structures of virus-like particles of BuV1, BuV2, and BuV3, the current known genotypes, have been determined by...
Show moreBufavirus strain 1 (BuV1), a member of the Protoparvovirus genus of the Parvoviridae, was first isolated from fecal samples of children with acute diarrhea in Burkina Faso. Since this initial discovery, BuVs have been isolated in several countries, including Finland, the Netherlands, and Bhutan, in pediatric patients exhibiting similar symptoms. Towards their characterization, the structures of virus-like particles of BuV1, BuV2, and BuV3, the current known genotypes, have been determined by cryo-electron microscopy and image reconstruction to 2.84, 3.79, and 3.25 angstrom, respectively. The BuVs, 65-73% identical in amino acid sequence, conserve the major viral protein, VP2, structure and general capsid surface features of parvoviruses. These include a core -barrel (B-I), -helix A, and large surface loops inserted between these elements in VP2. The capsid contains depressions at the icosahedral 2-fold and around the 5-fold axes, and has three separated protrusions surrounding the 3-fold axes. Structure comparison among the BuVs and to available parvovirus structures revealed capsid surface variations and capsid 3-fold protrusions that depart from the single pinwheel arrangement of the animal protoparvoviruses. These structures provide a platform to begin the molecular characterization of these potentially pathogenic viruses.
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Date Issued: 2018-01
Identifier: FSU_libsubv1_wos_000424414900022, 10.3390/v10010022
Format: Citation

Title: Synchrotron-generated Microbeams Induce Hippocampal Transections In Rats.
Creator: Fardone, Erminia, Pouyatos, Benoit, Brauer-Krisch, Elke, Bartzsch, Stefan, Mathieu, Herve, Requardt, Herwig, Bucci, Domenico, Barbone, Giacomo, Coan, Paola, Battaglia, Giuseppe,...
Show moreFardone, Erminia, Pouyatos, Benoit, Brauer-Krisch, Elke, Bartzsch, Stefan, Mathieu, Herve, Requardt, Herwig, Bucci, Domenico, Barbone, Giacomo, Coan, Paola, Battaglia, Giuseppe, Le Duc, Geraldine, Bravin, Alberto, Romanelli, Pantaleo
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Abstract/Description: Synchrotron-generated microplanar beams (microbeams) provide the most stereo-selective irradiation modality known today. This novel irradiation modality has been shown to control seizures originating from eloquent cortex causing no neurological deficit in experimental animals. To test the hypothesis that application of microbeams in the hippocampus, the most common source of refractory seizures, is safe and does not induce severe side effects, we used microbeams to induce transections to the...
Show moreSynchrotron-generated microplanar beams (microbeams) provide the most stereo-selective irradiation modality known today. This novel irradiation modality has been shown to control seizures originating from eloquent cortex causing no neurological deficit in experimental animals. To test the hypothesis that application of microbeams in the hippocampus, the most common source of refractory seizures, is safe and does not induce severe side effects, we used microbeams to induce transections to the hippocampus of healthy rats. An array of parallel microbeams carrying an incident dose of 600 Gy was delivered to the rat hippocampus. Immunohistochemistry of phosphorylated gamma-H2AX showed cell death along the microbeam irradiation paths in rats 48 hours after irradiation. No evident behavioral or neurological deficits were observed during the 3-month period of observation. MR imaging showed no signs of radio-induced edema or radionecrosis 3 months after irradiation. Histological analysis showed a very well preserved hippocampal cytoarchitecture and confirmed the presence of clear-cut microscopic transections across the hippocampus. These data support the use of synchrotron-generated microbeams as a novel tool to slice the hippocampus of living rats in a minimally invasive way, providing (i) a novel experimental model to study hippocampal function and (ii) a new treatment tool for patients affected by refractory epilepsy induced by mesial temporal sclerosis.
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Date Issued: 2018-01-09
Identifier: FSU_libsubv1_wos_000419659800019, 10.1038/s41598-017-18000-x
Format: Citation

Title: Single-cell Replication Profiling To Measure Stochastic Variation In Mammalian Replication Timing.
Creator: Dileep, Vishnu, Gilbert, David M.
Abstract/Description: Mammalian DNA replication is regulated via multi-replicon segments that replicate in a defined temporal order during S-phase. Further, early/late replication of RDs corresponds to active/inactive chromatin interaction compartments. Although replication origins are selected stochastically, variation in replication timing is poorly understood. Here we devise a strategy to measure variation in replication timing using DNA copy number in single mouse embryonic stem cells. We find that borders...
Show moreMammalian DNA replication is regulated via multi-replicon segments that replicate in a defined temporal order during S-phase. Further, early/late replication of RDs corresponds to active/inactive chromatin interaction compartments. Although replication origins are selected stochastically, variation in replication timing is poorly understood. Here we devise a strategy to measure variation in replication timing using DNA copy number in single mouse embryonic stem cells. We find that borders between replicated and unreplicated DNA are highly conserved between cells, demarcating active and inactive compartments of the nucleus. Fifty percent of replication events deviated from their average replication time by +/- 15% of S phase. This degree of variation is similar between cells, between homologs within cells and between all domains genomewide, regardless of their replication timing. These results demonstrate that stochastic variation in replication timing is independent of elements that dictate timing or extrinsic environmental variation.
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Date Issued: 2018-01-30
Identifier: FSU_libsubv1_wos_000423510600004, 10.1038/s41467-017-02800-w
Format: Citation

Title: Impacts Of The Deepwater Horizon Oil Spill Evaluated Using An End-to-end Ecosystem Model.
Creator: Ainsworth, Cameron H., Paris, Claire B., Perlin, Natalie, Dornberger, Lindsey N., Patterson, William F., Chancellor, Emily, Murawski, Steve, Hollander, David, Daly, Kendra,...
Show moreAinsworth, Cameron H., Paris, Claire B., Perlin, Natalie, Dornberger, Lindsey N., Patterson, William F., Chancellor, Emily, Murawski, Steve, Hollander, David, Daly, Kendra, Romero, Isabel C., Coleman, Felicia, Perryman, Holly
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Abstract/Description: We use a spatially explicit biogeochemical end-to-end ecosystem model, Atlantis, to simulate impacts from the Deepwater Horizon oil spill and subsequent recovery of fish guilds. Dose-response relationships with expected oil concentrations were utilized to estimate the impact on fish growth and mortality rates. We also examine the effects of fisheries closures and impacts on recruitment. We validate predictions of the model by comparing population trends and age structure before and after the...
Show moreWe use a spatially explicit biogeochemical end-to-end ecosystem model, Atlantis, to simulate impacts from the Deepwater Horizon oil spill and subsequent recovery of fish guilds. Dose-response relationships with expected oil concentrations were utilized to estimate the impact on fish growth and mortality rates. We also examine the effects of fisheries closures and impacts on recruitment. We validate predictions of the model by comparing population trends and age structure before and after the oil spill with fisheries independent data. The model suggests that recruitment effects and fishery closures had little influence on biomass dynamics. However, at the assumed level of oil concentrations and toxicity, impacts on fish mortality and growth rates were large and commensurate with observations. Sensitivity analysis suggests the biomass of large reef fish decreased by 25% to 50% in areas most affected by the spill, and biomass of large demersal fish decreased even more, by 40% to 70%. Impacts on reef and demersal forage caused starvation mortality in predators and increased reliance on pelagic forage. Impacts on the food web translated effects of the spill far away from the oiled area. Effects on age structure suggest possible delayed impacts on fishery yields. Recovery of high-turnover populations generally is predicted to occur within 10 years, but some slower-growing populations may take 30+ years to fully recover.
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Date Issued: 2018-01-25
Identifier: FSU_libsubv1_wos_000423416600024, 10.1371/journal.pone.0190840
Format: Citation

Title: A Second Specimen Of Citipati Osmolskae Associated With A Nest Of Eggs From Ukhaa Tolgod, Omnogov Aimag, Mongolia.
Creator: Norell, Mark A., Balanoff, Amy M., Barta, Daniel E., Erickson, Gregory M.
Abstract/Description: Adult dinosaurs preserved attending their nests in brooding positions are among the rarest vertebrate fossils. By far the most common occurrences are members of the dinosaur group Oviraptorosauria. The first finds of these were specimens recovered from the Djadokhta Formation at the Mongolian locality of Ukhaa Tolgod and the Chinese locality of Bayan Mandahu. Since the initial discovery of these specimens, a few more occurrences of nesting oviraptors have been found at other Asian localities....
Show moreAdult dinosaurs preserved attending their nests in brooding positions are among the rarest vertebrate fossils. By far the most common occurrences are members of the dinosaur group Oviraptorosauria. The first finds of these were specimens recovered from the Djadokhta Formation at the Mongolian locality of Ukhaa Tolgod and the Chinese locality of Bayan Mandahu. Since the initial discovery of these specimens, a few more occurrences of nesting oviraptors have been found at other Asian localities. Here we report on a second nesting oviraptorid specimen (IGM 100/1004) sitting in a brooding position atop a nest of eggs from Ukhaa Tolgod, Omnogov, Mongolia. This is a large specimen of the ubiquitous Ukhaa Tolgod taxon Citipati osmolskae. It is approximately 11% larger based on humeral length than the original Ukhaa Tolgod nesting Citipati osmolskae specimen (IGM 100/979), yet eggshell structure and egg arrangement are identical. No evidence for colonial breeding of these animals has been recovered. Reexamination of another "nesting" oviraptorosaur, the holotype of Oviraptor philoceratops (AMNH FARB 6517) indicates that in addition to the numerous partial eggs associated with the original skeleton that originally led to its referral as a protoceratopsian predator, there are the remains of a tiny theropod. This hind limb can be provisionally assigned to Oviraptoridae. It is thus at least possible that some of the eggs associated with the holotype had hatched and the perinates had not left the nest.
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Date Issued: 2018-04-26
Identifier: FSU_libsubv1_wos_000430953800001
Format: Citation

Title: Spindly Is Required For Rapid Migration Of Human Cells.
Creator: Conte, Claudia, Baird, Michelle A., Davidson, Michael W., Griffis, Eric R.
Abstract/Description: Dynein is the sole processive minus-end-directed microtubule motor found in animals. It has roles in cell division, membrane trafficking, and cell migration. Together with dynactin, dynein regulates centrosomal orientation to establish and maintain cell polarity, controls focal adhesion turnover and anchors microtubules at the leading edge. In higher eukaryotes, dynein/dynactin requires additional components such as Bicaudal D to form an active motor complex and for regulating its cellular...
Show moreDynein is the sole processive minus-end-directed microtubule motor found in animals. It has roles in cell division, membrane trafficking, and cell migration. Together with dynactin, dynein regulates centrosomal orientation to establish and maintain cell polarity, controls focal adhesion turnover and anchors microtubules at the leading edge. In higher eukaryotes, dynein/dynactin requires additional components such as Bicaudal D to form an active motor complex and for regulating its cellular localization. Spindly is a protein that targets dynein/dynactin to kinetochores in mitosis and can activate its motility in vitro. However, no role for Spindly in interphase dynein/dynactin function has been found. We show that Spindly binds to the cell cortex and microtubule tips and colocalizes with dynein/dynactin at the leading edge of migrating U2OS cells and primary fibroblasts. U2OS cells that lack Spindly migrated slower in 2D than control cells, although centrosome polarization appeared to happen properly in the absence of Spindly. Re-expression of Spindly rescues migration, but the expression of a mutant, which is defective for dynactin binding, failed to rescue this defect. Taken together, these data demonstrate that Spindly plays an important role in mediating a subset of dynein/dynactin's function in cell migration.
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Date Issued: 2018-05-01
Identifier: FSU_libsubv1_wos_000434210800009, 10.1242/bio.033233
Format: Citation

Title: Promoter Capture Hi-c: High-resolution, Genome-wide Profiling Of Promoter Interactions.
Creator: Schoenfelder, Stefan, Javierre, Biola-Maria, Furlan-Magaril, Mayra, Wingett, Steven W., Fraser, Peter
Abstract/Description: The three-dimensional organization of the genome is linked to its function. For example, regulatory elements such as transcriptional enhancers control the spatio-temporal expression of their target genes through physical contact, often bridging considerable (in some cases hundreds of kilobases) genomic distances and bypassing nearby genes. The human genome harbors an estimated one million enhancers, the vast majority of which have unknown gene targets. Assigning distal regulatory regions to...
Show moreThe three-dimensional organization of the genome is linked to its function. For example, regulatory elements such as transcriptional enhancers control the spatio-temporal expression of their target genes through physical contact, often bridging considerable (in some cases hundreds of kilobases) genomic distances and bypassing nearby genes. The human genome harbors an estimated one million enhancers, the vast majority of which have unknown gene targets. Assigning distal regulatory regions to their target genes is thus crucial to understand gene expression control. We developed Promoter Capture Hi-C (PCHi-C) to enable the genome-wide detection of distal promoter-interacting regions (PIRs), for all promoters in a single experiment. In PCHi-C, highly complex Hi-C libraries are specifically enriched for promoter sequences through in-solution hybrid selection with thousands of biotinylated RNA baits complementary to the ends of all promoter-containing restriction fragments. The aim is to then pull-down promoter sequences and their frequent interaction partners such as enhancers and other potential regulatory elements. After high-throughput paired-end sequencing, a statistical test is applied to each promoter-ligated restriction fragment to identify significant PIRs at the restriction fragment level. We have used PCHi-C to generate an atlas of long-range promoter interactions in dozens of human and mouse cell types. These promoter interactome maps have contributed to a greater understanding of mammalian gene expression control by assigning putative regulatory regions to their target genes and revealing preferential spatial promoter-promoter interaction networks. This information also has high relevance to understanding human genetic disease and the identification of potential disease genes, by linking non-coding disease-associated sequence variants in or near control sequences to their target genes.
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Date Issued: 2018-06-01
Identifier: FSU_libsubv1_wos_000444752100043, 10.3791/57320
Format: Citation

Title: Interactive Effects Of Precipitation And Nitrogen Enrichment On Multi-trophic Dynamics In Plant-arthropod Communities.
Creator: Griffith, Kaitlin A., Grinath, Joshua B.
Abstract/Description: Patterns of precipitation and nitrogen (N) deposition are changing in ecosystems worldwide. Simultaneous increases in precipitation and N deposition can relieve co-limiting soil resource conditions for plants and result in synergistic plant responses, which may affect animals and plant responses to higher trophic levels. However, the potential for synergistic effects of precipitation and N deposition on animals and plant responses to herbivores and predators (via trophic cascades) is unclear....
Show morePatterns of precipitation and nitrogen (N) deposition are changing in ecosystems worldwide. Simultaneous increases in precipitation and N deposition can relieve co-limiting soil resource conditions for plants and result in synergistic plant responses, which may affect animals and plant responses to higher trophic levels. However, the potential for synergistic effects of precipitation and N deposition on animals and plant responses to herbivores and predators (via trophic cascades) is unclear. We investigated the influence of precipitation and N enrichment on ecological dynamics across three trophic levels, hypothesizing that herbivores and plants would exhibit synergistic responses to the combined influence of precipitation, N amendments and predators. To test this, we conducted a field experiment with arthropods on two model plant species, Nicotiana tabacum and Nicotiana rustica. First, we characterized the plant-arthropod assemblages, finding that N.tabacum hosted greater abundances of caterpillars, while N. rustica hosted more sap-sucking herbivores. Next, we evaluated the effects of rainwater, soil N, and predatory spider manipulations for both plantarthropod assemblages. On N. tabacum, water and N availability had an interactive effect on caterpillars, where caterpillars were most abundant with rainwater additions and least abundant when both rainwater and N were added. For N. rustica, foliar chemistry had a synergistic response to all three experimental factors. Compared to spider-absent conditions, leaf N concentration increased and C/N decreased when spiders were present, but this response only occurred under high water and N availability. Spiders indirectly altered plant chemistry via a facilitative effect of spiders on sap-sucking herbivores, potentially due to intra-guild predation, and a positive effect of sap-suckers on foliar N concentration. Our study suggests that predictions of the ecological impacts of altered precipitation and N deposition may need to account for the effects of resource co-limitation on dynamics across trophic levels.
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Date Issued: 2018-08-02
Identifier: FSU_libsubv1_wos_000440778600029, 10.1371/journal.pone.0201219
Format: Citation

Title: The Half-bridge Component Kar1 Promotes Centrosome Separation And Duplication During Budding Yeast Meiosis.
Creator: Agarwal, Meenakshi, Jin, Hui, McClain, Melainia, Fan, Jinbo, Koch, Bailey A., Jaspersen, Sue L., Yu, Hong-Guo
Abstract/Description: The budding yeast centrosome, often called the spindle pole body (SPB), nudeates microtubules for chromosome segregation during cell division. An appendage, called the half bridge, attaches to one side of the SPB and regulates SPB duplication and separation. Like DNA, the SPB is duplicated only once per cell cycle. During meiosis, however, after one round of DNA replication, two rounds of SPB duplication and separation are coupled with homologue segregation in meiosis I and sister-chromatid...
Show moreThe budding yeast centrosome, often called the spindle pole body (SPB), nudeates microtubules for chromosome segregation during cell division. An appendage, called the half bridge, attaches to one side of the SPB and regulates SPB duplication and separation. Like DNA, the SPB is duplicated only once per cell cycle. During meiosis, however, after one round of DNA replication, two rounds of SPB duplication and separation are coupled with homologue segregation in meiosis I and sister-chromatid segregation in meiosis II. How SPB duplication and separation are regulated during meiosis remains to be elucidated, and whether regulation in meiosis differs from that in mitosis is unclear. Here we show that overproduction of the half-bridge component Kar1 leads to premature SPB separation during meiosis. Furthermore, excessive Kar1 induces SPB overduplication to form supernumerary SPBs, leading to chromosome missegregation and erroneous ascospore formation. Kar1-mediated SPB duplication bypasses the requirement of dephosphorylation of Sfi1, another half-bridge component previously identified as a licensing factor. Our results therefore reveal an unexpected role of Kar1 in licensing meiotic SPB duplication and suggest a unique mechanism of SPB regulation during budding yeast meiosis.
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Date Issued: 2018-08-01
Identifier: FSU_libsubv1_wos_000446089500003, 10.1091/mbc.E18-03-0163
Format: Citation

Title: Phylogenomics Uncovers Early Hybridization And Adaptive Loci Shaping The Radiation Of Lake Tanganyika Cichlid Fishes.
Creator: Irisarri, Iker, Singh, Pooja, Koblmuller, Stephan, Torres-Dowdall, Julian, Henning, Frederico, Franchini, Paolo, Fischer, Christoph, Lemmon, Alan R., Lemmon, Emily Moriarty,...
Show moreIrisarri, Iker, Singh, Pooja, Koblmuller, Stephan, Torres-Dowdall, Julian, Henning, Frederico, Franchini, Paolo, Fischer, Christoph, Lemmon, Alan R., Lemmon, Emily Moriarty, Thallinger, Gerhard G., Sturmbauer, Christian, Meyer, Axel
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Abstract/Description: Lake Tanganyika is the oldest and phenotypically most diverse of the three East African cichlid fish adaptive radiations. It is also the cradle for the younger parallel haplochromine cichlid radiations in Lakes Malawi and Victoria. Despite its evolutionary significance, the relationships among the main Lake Tanganyika lineages remained unresolved, as did the general timescale of cichlid evolution. Here, we disentangle the deep phylogenetic structure of the Lake Tanganyika radiation using...
Show moreLake Tanganyika is the oldest and phenotypically most diverse of the three East African cichlid fish adaptive radiations. It is also the cradle for the younger parallel haplochromine cichlid radiations in Lakes Malawi and Victoria. Despite its evolutionary significance, the relationships among the main Lake Tanganyika lineages remained unresolved, as did the general timescale of cichlid evolution. Here, we disentangle the deep phylogenetic structure of the Lake Tanganyika radiation using anchored phylogenomics and uncover hybridization at its base, as well as early in the haplochromine radiation. This suggests that hybridization might have facilitated these speciation bursts. Time-calibrated trees support that the radiation of Tanganyika cichlids coincided with lake formation and that Gondwanan vicariance concurred with the earliest splits in the cichlid family tree. Genes linked to key innovations show signals of introgression or positive selection following colonization of lake habitats and species' dietary adaptations are revealed as major drivers of colour vision evolution. These findings shed light onto the processes shaping the evolution of adaptive radiations.
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Date Issued: 2018-08-08
Identifier: FSU_libsubv1_wos_000440982800001, 10.1038/s41467-018-05479-9
Format: Citation

Title: Loss Of Setdb1 Decompacts The Inactive X Chromosome In Part Through Reactivation Of An Enhancer In The Il1rapl1 Gene.
Creator: Sun, Zhuo, Chadwick, Brian P.
Abstract/Description: Background: The product of dosage compensation in female mammals is the inactive X chromosome (Xi). Xi facultative heterochromatin is organized into two different types, one of which is defined by histone H3 trimethylated at lysine 9 (H3K9me3). The rationale for this study was to assess SET domain bifurcated 1 (SETDB1) as a candidate for maintaining this repressive modification at the human Xi. Results: Here, we show that loss of SETDB1 does not result in large-scale H3K9me3 changes at the Xi...
Show moreBackground: The product of dosage compensation in female mammals is the inactive X chromosome (Xi). Xi facultative heterochromatin is organized into two different types, one of which is defined by histone H3 trimethylated at lysine 9 (H3K9me3). The rationale for this study was to assess SET domain bifurcated 1 (SETDB1) as a candidate for maintaining this repressive modification at the human Xi. Results: Here, we show that loss of SETDB1 does not result in large-scale H3K9me3 changes at the Xi, but unexpectedly we observed striking decompaction of the Xi territory. Close examination revealed a 0.5 Mb region of the Xi that transitioned from H3K9me3 heterochromatin to euchromatin within the 3' end of the IL1RAPL1 gene that is part of a common chromosome fragile site that is frequently deleted or rearranged in patients afflicted with intellectual disability and other neurological ailments. Centrally located within this interval is a powerful enhancer adjacent to an ERVL-MaLR element. In the absence of SETDB1, the enhancer is reactivated on the Xi coupled with bidirectional transcription from the ERVL-MaLR element. Xa deletion of the enhancer/ERVL-MaLR resulted in loss of full-length IL1RAPL1 transcript in cis, coupled with trans decompaction of the Xi chromosome territory, whereas Xi deletion increased detection of full-length IL1RAPL1 transcript in trans, but did not impact Xi compaction. Conclusions: These data support a critical role for SETDB1 in maintaining the ERVL-MaLR element and adjacent enhancer in the 3' end of the IL1RAPL1 gene in a silent state to facilitate Xi compaction.
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Date Issued: 2018-08-13
Identifier: FSU_libsubv1_wos_000441459500001, 10.1186/s13072-018-0218-9
Format: Citation

Title: Venom Complexity In A Pitviper Produced By Facultative Parthenogenesis.
Creator: Calvete, J. J., Casewell, N. R., Hernandez-Guzman, U., Quesada-Bernat, S., Sanz, L., Rokyta, D. R., Storey, D., Albulescu, L.-O., Wuster, W., Smith, C. F., Schuett, G. W., Booth...
Show moreCalvete, J. J., Casewell, N. R., Hernandez-Guzman, U., Quesada-Bernat, S., Sanz, L., Rokyta, D. R., Storey, D., Albulescu, L.-O., Wuster, W., Smith, C. F., Schuett, G. W., Booth, W.
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Abstract/Description: Facultative parthenogenesis (FP) is asexual reproduction in plant and animal species that would otherwise reproduce sexually. This process in vertebrates typically results from automictic development (likely terminal fusion) and is phylogenetically widespread. In squamate reptiles and chondrichthyan fishes, FP has been reported to occur in nature and can result in the production of reproductively viable offspring; suggesting that it is of ecological and evolutionary significance. However,...
Show moreFacultative parthenogenesis (FP) is asexual reproduction in plant and animal species that would otherwise reproduce sexually. This process in vertebrates typically results from automictic development (likely terminal fusion) and is phylogenetically widespread. In squamate reptiles and chondrichthyan fishes, FP has been reported to occur in nature and can result in the production of reproductively viable offspring; suggesting that it is of ecological and evolutionary significance. However, terminal fusion automixis is believed to result in near genome-wide reductions in heterozygosity; thus, FP seems likely to affect key phenotypic characters, yet this remains almost completely unstudied. Snake venom is a complex phenotypic character primarily used to subjugate prey and is thus tightly linked to individual fitness. Surprisingly, the composition and function of venom produced by a parthenogenetic pitviper exhibits a high degree of similarity to that of its mother and conspecifics from the same population. Therefore, the apparent loss of allelic diversity caused by FP appears unlikely to have a significant impact on the prey-capturing ability of this snake. Accordingly, the pitviper offspring produced by FP retained complex phenotypic characteristics associated with fitness. This result reinforces the potential ecological and evolutionary importance of FP and questions our understanding of the inheritance of venom-associated genes.
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Date Issued: 2018-08-01
Identifier: FSU_libsubv1_wos_000440411300024, 10.1038/s41598-018-29791-y
Format: Citation

Title: Improved Estimates Of Net Primary Production, Growth, And Standing Crop Of Macrocystis Pyrifera In Southern California.
Creator: Rassweiler, Andrew, Reed, Daniel C., Harrer, Shannon L., Nelson, J. Clint
Abstract/Description: The giant kelp Macrocystis pyrifera forms subtidal forests on shallow reefs in temperate regions of the world. It is one of the fastest-growing multicellular autotrophs on Earth and its high productivity supports diverse marine food webs. In 2008, we published a method for estimating biomass and net primary production (NPP) of giant kelp along with five years of data, to provide a more integrated measure of NPP than those yielded by previous methods. Our method combines monthly field...
Show moreThe giant kelp Macrocystis pyrifera forms subtidal forests on shallow reefs in temperate regions of the world. It is one of the fastest-growing multicellular autotrophs on Earth and its high productivity supports diverse marine food webs. In 2008, we published a method for estimating biomass and net primary production (NPP) of giant kelp along with five years of data, to provide a more integrated measure of NPP than those yielded by previous methods. Our method combines monthly field measurements of standing crop and loss rates with a model of kelp biomass dynamics to estimate instantaneous mass-specific growth rates and NPP for each season of each year. We have since improved our approach to account for several previously unresolved sources of biomass loss. These improvements have led to a near doubling of our prior estimates of growth and NPP. At our site with the most persistent stand of giant kelp, NPP averages similar to 5.2 kg dry mass.m(-2).yr(-1) and results from the rapid growth (similar to 3.5% per d) of a relatively small standing biomass (similar to 0.4 kg dry mass/m(2) on average) that turns over similar to 12 times annually. Here we provide revised estimates of seasonal biomass, growth, and NPP for the five years covered by our previous publication (2002-2006), along with more than a decade of additional data (2007-2017). We also present updated relationships for predicting giant kelp biomass and NPP from much more easily obtained measurements of frond density. These data can be used to understand the mechanisms that drive variation in giant kelp NPP at a wide range of temporal scales. No copyright or proprietary restrictions are associated with the use of this data set other than citation of this Data Paper.
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Date Issued: 2018-09-01
Identifier: FSU_libsubv1_wos_000443558200024, 10.1002/ecy.2440
Format: Citation

Title: The Role Of Geography In Adaptive Radiation.
Creator: Schenk, John J., Steppan, Scott J.
Abstract/Description: Although the importance of biogeography in the speciation process is well recognized, the fundamental role of geographic diversification during adaptive radiations has not been studied to determine its importance during the adaptive radiation process. We examined the relationship between lineage and regional diversification patterns in the South American rodent subfamily Sigmodontinae, one of the best candidates for an adaptive radiation in mammals, to propose a conceptual framework for...
Show moreAlthough the importance of biogeography in the speciation process is well recognized, the fundamental role of geographic diversification during adaptive radiations has not been studied to determine its importance during the adaptive radiation process. We examined the relationship between lineage and regional diversification patterns in the South American rodent subfamily Sigmodontinae, one of the best candidates for an adaptive radiation in mammals, to propose a conceptual framework for geographic transitions during adaptive radiations. We reconstructed a time-calibrated phylogeny from four nuclear genes and one mitochondrial gene for 77% of sigmodontine diversity. Historical biogeography was reconstructed among 14 regions, for which we applied a sliding-window approach to estimate regional transition rates through time. We compared these rate patterns and measured whether regions consisted of species that were more phylogenetically related than expected by chance. Following the initial South American colonization around 7 million years ago, multiple expansions from northern regions correlated with a burst of speciation. Subsequently, both diversification and regional transition rates decreased overall and within the majority of regions. Despite high regional transition rates, nearly all regional assemblages were phylogenetically clustered, indicating that within-region diversification was common. We conclude that biogeographic complexity and partitioning played a profound role in the adaptive radiation of the South American Sigmodontinae (Oryzomyalia), the degree to which is determined by the relative scales of spatial variation and dispersal abilities.
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Date Issued: 2018-10-01
Identifier: FSU_libsubv1_wos_000444262900004, 10.1086/699221
Format: Citation

Title: Distinct Tissue-specific Transcriptional Regulation Revealed By Gene Regulatory Networks In Maize.
Creator: Huang, Ji, Zheng, Juefei, Yuan, Hui, McGinnis, Karen
Abstract/Description: Background: Transcription factors (TFs) are proteins that can bind to DNA sequences and regulate gene expression. Many TFs are master regulators in cells that contribute to tissue-specific and cell-type-specific gene expression patterns in eukaryotes. Maize has been a model organism for over one hundred years, but little is known about its tissue-specific gene regulation through TFs. In this study, we used a network approach to elucidate gene regulatory networks (GRNs) in four tissues (leaf,...
Show moreBackground: Transcription factors (TFs) are proteins that can bind to DNA sequences and regulate gene expression. Many TFs are master regulators in cells that contribute to tissue-specific and cell-type-specific gene expression patterns in eukaryotes. Maize has been a model organism for over one hundred years, but little is known about its tissue-specific gene regulation through TFs. In this study, we used a network approach to elucidate gene regulatory networks (GRNs) in four tissues (leaf, root, SAM and seed) in maize. We utilized GENIE3, a machine-learning algorithm combined with large quantity of RNA-Seq expression data to construct four tissue-specific GRNs. Unlike some other techniques, this approach is not limited by high-quality Position Weighed Matrix (PWM), and can therefore predict GRNs for over 2000 TFs in maize. Results: Although many TFs were expressed across multiple tissues, a multi-tiered analysis predicted tissue-specific regulatory functions for many transcription factors. Some well-studied TFs emerged within the four tissue-specific GRNs, and the GRN predictions matched expectations based upon published results for many of these examples. Our GRNs were also validated by ChIP-Seq datasets (KN1, FEA4 and O2). Key TFs were identified for each tissue and matched expectations for key regulators in each tissue, including GO enrichment and identity with known regulatory factors for that tissue. We also found functional modules in each network by clustering analysis with the MCL algorithm. Conclusions: By combining publicly available genome-wide expression data and network analysis, we can uncover GRNs at tissue-level resolution in maize. Since ChIP-Seq and PWMs are still limited in several model organisms, our study provides a uniform platform that can be adapted to any species with genome-wide expression data to construct GRNs. We also present a publicly available database, maize tissue-specific GRN (mGRN, https://www.bio.fsu.edu/mcginnislab/mgrn/), for easy querying. All source code and data are available at Github (https://github.com/timedreamer/maize_tissue-specific_GRN).
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Date Issued: 2018-06-07
Identifier: FSU_libsubv1_wos_000434971800002, 10.1186/s12870-018-1329-y
Format: Citation

Title: Emetine Inhibits Zika And Ebola Virus Infections Through Two Molecular Mechanisms: Inhibiting Viral Replication And Decreasing Viral Entry.
Creator: Yang, Shu, Xu, Miao, Lee, Emily M., Gorshkov, Kirill, Shiryaev, Sergey A., He, Shihua, Sun, Wei, Cheng, Yu-Shan, Hu, Xin, Tharappel, Anil Mathew, Lu, Billy, Pinto, Antonella,...
Show moreYang, Shu, Xu, Miao, Lee, Emily M., Gorshkov, Kirill, Shiryaev, Sergey A., He, Shihua, Sun, Wei, Cheng, Yu-Shan, Hu, Xin, Tharappel, Anil Mathew, Lu, Billy, Pinto, Antonella, Farhy, Chen, Huang, Chun-Teng, Zhang, Zirui, Zhu, Wenjun, Wu, Yuying, Zhou, Yi, Song, Guang, Zhu, Heng, Shamim, Khalida, Martinez-Romero, Carles, Garcia-Sastre, Adolfo, Preston, Richard A., Jayaweera, Dushyantha T., Huang, Ruili, Huang, Wenwei, Xia, Menghang, Simeonov, Anton, Ming, Guoli, Qiu, Xiangguo, Terskikh, Alexey, Tang, Hengli, Song, Hongjun, Zheng, Wei
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Abstract/Description: The re-emergence of Zika virus (ZIKV) and Ebola virus (EBOV) poses serious and continued threats to the global public health. Effective therapeutics for these maladies is an unmet need. Here, we show that emetine, an anti-protozoal agent, potently inhibits ZIKV and EBOV infection with a low nanomolar half maximal inhibitory concentration (IC50) in vitro and potent activity in vivo. Two mechanisms of action for emetine are identified: the inhibition of ZIKV NS5 polymerase activity and...
Show moreThe re-emergence of Zika virus (ZIKV) and Ebola virus (EBOV) poses serious and continued threats to the global public health. Effective therapeutics for these maladies is an unmet need. Here, we show that emetine, an anti-protozoal agent, potently inhibits ZIKV and EBOV infection with a low nanomolar half maximal inhibitory concentration (IC50) in vitro and potent activity in vivo. Two mechanisms of action for emetine are identified: the inhibition of ZIKV NS5 polymerase activity and disruption of lysosomal function. Emetine also inhibits EBOV entry. Cephaeline, a desmethyl analog of emetine, which may be better tolerated in patients than emetine, exhibits a similar efficacy against both ZIKV and EBOV infections. Hence, emetine and cephaeline offer pharmaceutical therapies against both ZIKV and EBOV infection.
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Date Issued: 2018-06-05
Identifier: FSU_libsubv1_wos_000434231100001, 10.1038/s41421-018-0034-1
Format: Citation

Title: Evaluating The Performance Of De Novo Assembly Methods For Venom-gland Transcriptomics.
Creator: Holding, Matthew L., Margres, Mark J., Mason, Andrew J., Parkinson, Christopher L., Rokyta, Darin R.
Abstract/Description: Venom-gland transcriptomics is a key tool in the study of the evolution, ecology, function, and pharmacology of animal venoms. In particular, gene-expression variation and coding sequences gained through transcriptomics provide key information for explaining functional venom variation over both ecological and evolutionary timescales. The accuracy and usefulness of inferences made through transcriptomics, however, is limited by the accuracy of the transcriptome assembly, which is a...
Show moreVenom-gland transcriptomics is a key tool in the study of the evolution, ecology, function, and pharmacology of animal venoms. In particular, gene-expression variation and coding sequences gained through transcriptomics provide key information for explaining functional venom variation over both ecological and evolutionary timescales. The accuracy and usefulness of inferences made through transcriptomics, however, is limited by the accuracy of the transcriptome assembly, which is a bioinformatic problem with several possible solutions. Several methods have been employed to assemble venom-gland transcriptomes, with the Trinity assembler being the most commonly applied among them. Although previous evidence of variation in performance among assembly software exists, particularly regarding recovery of difficult-to-assemble multigene families such as snake venom metalloproteinases, much work to date still employs a single assembly method. We evaluated the performance of several commonly used de novo assembly methods for the recovery of both nontoxin transcripts and complete, high-quality venom-gene transcripts across eleven snake and four scorpion transcriptomes. We varied k-mer sizes used by some assemblers to evaluate the impact of k-mer length on transcript recovery. We showed that the recovery of nontoxin transcripts and toxin transcripts is best accomplished through different assembly software, with SDT at smaller k-mer lengths and Trinity being best for nontoxin recovery and a combination of SeqMan NGen and a seed-and-extend approach implemented in Extender as the best means of recovering a complete set of toxin transcripts. In particular, Extender was the only means tested capable of assembling multiple isoforms of the diverse snake venom metalloproteinase family, while traditional approaches such as Trinity recovered at most one metalloproteinase transcript. Our work demonstrated that traditional metrics of assembly performance are not predictive of performance in the recovery of complete and high quality toxin genes. Instead, effective venom-gland transcriptomic studies should combine and quality-filter the results of several assemblers with varying algorithmic strategies.
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Date Issued: 2018-06-01
Identifier: FSU_libsubv1_wos_000436131800037, 10.3390/toxins10060249
Format: Citation

Title: Unique Maternal And Environmental Effects On The Body Morphology Of The Least Killifish, Heterandria Formosa.
Creator: Landy, J. Alex, Travis, Joseph
Abstract/Description: An important step in diagnosing local adaptation is the demonstration that phenotypic variation among populations is at least in part genetically based. To do this, many methods experimentally minimize the environmental effect on the phenotype to elucidate the genetic effect. Minimizing the environmental effect often includes reducing possible environmental maternal effects. However, maternal effects can be an important factor in patterns of local adaptation as well as adaptive plasticity....
Show moreAn important step in diagnosing local adaptation is the demonstration that phenotypic variation among populations is at least in part genetically based. To do this, many methods experimentally minimize the environmental effect on the phenotype to elucidate the genetic effect. Minimizing the environmental effect often includes reducing possible environmental maternal effects. However, maternal effects can be an important factor in patterns of local adaptation as well as adaptive plasticity. Here, we report the results of an experiment with males from two populations of the poeciliid fish, Heterandria formosa, designed to examine the relative influence of environmental maternal effects and environmental effects experienced during growth and development on body morphology, and, in addition, whether the balance among those effects is unique to each population. We used a factorial design that varied thermal environment and water chemistry experienced by mothers and thermal environment and water chemistry experienced by offspring. We found substantial differences between the two populations in their maternal and offspring norms of reaction of male body morphology to differences in thermal environment and water chemistry. We also found that the balance between maternal effects and postparturition environmental effects differed from one thermal regime to another and among traits. These results indicate that environmental maternal effects can be decidedly population-specific and, as a result, might either contribute to the appearance of or blur evidence for local adaptation. These results also suggest that local adaptation might also occur through the evolution of maternal norms of reaction to important, and varying, environmental factors.
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Date Issued: 2018-06-01
Identifier: FSU_libsubv1_wos_000436799100024, 10.1002/ece3.4166
Format: Citation

Title: Why Does The Magnitude Of Genotype-by-environment Interaction Vary?.
Creator: Saltz, Julia B., Bell, Alison M., Flint, Jonathan, Gomulkiewicz, Richard, Hughes, Kimberly A., Keagy, Jason
Abstract/Description: Genotype-by-environment interaction (GxE), that is, genetic variation in phenotypic plasticity, is a central concept in ecology and evolutionary biology. GxE has wide-ranging implications for trait development and for understanding how organisms will respond to environmental change. Although GxE has been extensively documented, its presence and magnitude vary dramatically across populations and traits. Despite this, we still know little about why GxE is so evident in some traits and...
Show moreGenotype-by-environment interaction (GxE), that is, genetic variation in phenotypic plasticity, is a central concept in ecology and evolutionary biology. GxE has wide-ranging implications for trait development and for understanding how organisms will respond to environmental change. Although GxE has been extensively documented, its presence and magnitude vary dramatically across populations and traits. Despite this, we still know little about why GxE is so evident in some traits and populations, but minimal or absent in others. To encourage synthetic research in this area, we review diverse hypotheses for the underlying biological causes of variation in GxE. We extract common themes from these hypotheses to develop a more synthetic understanding of variation in GxE and suggest some important next steps.
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Date Issued: 2018-06-01
Identifier: FSU_libsubv1_wos_000436799100031, 10.1002/ece3.4128
Format: Citation

Title: Genome Organization And Chromatin Analysis Identify Transcriptional Downregulation Of Insulin-like Growth Factor Signaling As A Hallmark Of Aging In Developing B Cells.
Creator: Koohy, Hashem, Bolland, Daniel J., Matheson, Louise S., Schoenfelder, Stefan, Stellato, Claudia, Dimond, Andrew, Varnai, Csilla, Chovanec, Peter, Chessa, Tamara, Denizot, Jeremy...
Show moreKoohy, Hashem, Bolland, Daniel J., Matheson, Louise S., Schoenfelder, Stefan, Stellato, Claudia, Dimond, Andrew, Varnai, Csilla, Chovanec, Peter, Chessa, Tamara, Denizot, Jeremy, Garcia, Raquel Manzano, Wingett, Steven W., Freire-Pritchett, Paula, Nagano, Takashi, Hawkins, Phillip, Stephens, Len, Elderkin, Sarah, Spivakov, Mikhail, Fraser, Peter, Corcoran, Anne E., Varga-Weisz, Patrick D.
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Abstract/Description: Background: Aging is characterized by loss of function of the adaptive immune system, but the underlying causes are poorly understood. To assess the molecular effects of aging on B cell development, we profiled gene expression and chromatin features genome-wide, including histone modifications and chromosome conformation, in bone marrow pro-B and pre-B cells from young and aged mice. Results: Our analysis reveals that the expression levels of most genes are generally preserved in B cell...
Show moreBackground: Aging is characterized by loss of function of the adaptive immune system, but the underlying causes are poorly understood. To assess the molecular effects of aging on B cell development, we profiled gene expression and chromatin features genome-wide, including histone modifications and chromosome conformation, in bone marrow pro-B and pre-B cells from young and aged mice. Results: Our analysis reveals that the expression levels of most genes are generally preserved in B cell precursors isolated from aged compared with young mice. Nonetheless, age-specific expression changes are observed at numerous genes, including microRNA encoding genes. Importantly, these changes are underpinned by multi-layered alterations in chromatin structure, including chromatin accessibility, histone modifications, long-range promoter interactions, and nuclear compartmentalization. Previous work has shown that differentiation is linked to changes in promoter-regulatory element interactions. We find that aging in B cell precursors is accompanied by rewiring of such interactions. We identify transcriptional downregulation of components of the insulin-like growth factor signaling pathway, in particular downregulation of Irs1 and upregulation of Let-7 microRNA expression, as a signature of the aged phenotype. These changes in expression are associated with specific alterations in H3K27me3 occupancy, suggesting that Polycomb-mediated repression plays a role in precursor B cell aging. Conclusions: Changes in chromatin and 3D genome organization play an important role in shaping the altered gene expression profile of aged precursor B cells. Components of the insulin-like growth factor signaling pathways are key targets of epigenetic regulation in aging in bone marrow B cell precursors.
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Date Issued: 2018-09-05
Identifier: FSU_libsubv1_wos_000443725200001, 10.1186/s13059-018-1489-y
Format: Citation

Title: Characterization Of The Icce Repea In Mammals Reveals An Evolutionary Relationship With The Dxz4 Macrosatellite Through Conserved Ctcf Binding Motifs.
Creator: Westervelt, Natalia, Chadwick, Brian P.
Abstract/Description: Appreciation is growing for how chromosomes are organized in three-dimensional space at interphase. Microscopic and high throughput sequence-based studies have established that the mammalian inactive X chromosome (Xi) adopts an alternate conformation relative to the active X chromosome. The Xi is organized into several multi-megabase chromatin loops called superloops. At the base of these loops are superloop anchors, and in humans three of these anchors are composed of large tandem repeat DNA...
Show moreAppreciation is growing for how chromosomes are organized in three-dimensional space at interphase. Microscopic and high throughput sequence-based studies have established that the mammalian inactive X chromosome (Xi) adopts an alternate conformation relative to the active X chromosome. The Xi is organized into several multi-megabase chromatin loops called superloops. At the base of these loops are superloop anchors, and in humans three of these anchors are composed of large tandem repeat DNA that include DXZ4, Functional Intergenic Repeating RNA Element, and Inactive-X CTCF-binding Contact Element (ICCE). Each repeat contains a high density of binding sites for the architectural organization protein CCCTC-binding factor (CTCF) which exclusively associates with the Xi allele in normal cells. Removal of DXZ4 from the Xi compromises proper folding of the chromosome. In this study, we report the characterization of the ICCE tandem repeat, for which very little is known. ICCE is embedded within an intron of the Nobody (NBDY) gene locus at Xp11.21. We find that primary DNA sequence conservation of ICCE is only retained in higher primates, but that ICCE orthologs exist beyond the primate lineage. Like DXZ4, what is conserved is organization of the underlying DNA into a large tandem repeat, physical location within the NBDY locus and conservation of short DNA sequences corresponding to specific CTCF and Yin Yang 1 binding motifs that correlate with female-specific DNA hypomethylation. Unlike DXZ4, ICCE is not common to all eutherian mammals. Analysis of certain ICCE CTCF motifs reveal striking similarity with the DXZ4 motif and support an evolutionary relationship between DXZ4 and ICCE.
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Date Issued: 2018-09-01
Identifier: FSU_libsubv1_wos_000446102700004, 10.1093/gbe/evy176
Format: Citation

Title: An Hpsc-derived Tissue-resident Macrophage Model Reveals Differential Responses Of Macrophages To Zikv And Deny Infection.
Creator: Lang, Jianshe, Cheng, Yichen, Rolfe, Alyssa, Hammack, Christy, Vera, Daniel, Kyle, Kathleen, Wang, Jingying, Meissner, Torsten B., Ren, Yi, Cowan, Chad, Tang, Hengli
Abstract/Description: Zika virus (ZIKV) and dengue virus (DENV) are two closely related flaviviruses that lead to different clinical outcomes. The mechanism for the distinct pathogenesis of ZIKV and DENV is poorly understood. Here, we investigate ZIKV and DENV infection of macrophages using a human pluripotent stem cell (hPSC)-derived macrophage model and discover key virus-specific responses. ZIKV and DENV productively infect hPSC-derived macrophages. DENV, but not ZIKV, infection of macrophages strongly...
Show moreZika virus (ZIKV) and dengue virus (DENV) are two closely related flaviviruses that lead to different clinical outcomes. The mechanism for the distinct pathogenesis of ZIKV and DENV is poorly understood. Here, we investigate ZIKV and DENV infection of macrophages using a human pluripotent stem cell (hPSC)-derived macrophage model and discover key virus-specific responses. ZIKV and DENV productively infect hPSC-derived macrophages. DENV, but not ZIKV, infection of macrophages strongly activates macrophage migration inhibitory factor (MIF) secretion and decreases macrophage migration. Neutralization of MIF leads to improved migratory ability of DENV-infected macrophages. In contrast, ZIKV-infected macrophages exhibit prolonged migration and express low levels of pro-inflammatory cytokines and chemokines. Mechanistically, ZIKV disrupts the nuclear factor kappa B (NF-kappa B)-MIF positive feedback loop by inhibiting the NF-kappa B signaling pathway. Our results demonstrate the utility of hPSC-derived macrophages in infectious disease modeling and suggest that the distinct impact of ZIKV and DENV on macrophage immune response may underlie different pathogenesis of Zika and dengue diseases.
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Date Issued: 2018-08-14
Identifier: FSU_libsubv1_wos_000441583100006, 10.1016/j.stemcr.2018.06.006
Format: Citation

Title: Allele-specific Control Of Replication Timing And Genome Organization During Development.
Creator: Rivera-Mulia, Juan Carlos, Dimond, Andrew, Vera, Daniel, Trevilla-Garcia, Claudia, Sasaki, Takayo, Zimmerman, Jared, Dupont, Catherine, Gribnau, Joost, Fraser, Peter, Gilbert,...
Show moreRivera-Mulia, Juan Carlos, Dimond, Andrew, Vera, Daniel, Trevilla-Garcia, Claudia, Sasaki, Takayo, Zimmerman, Jared, Dupont, Catherine, Gribnau, Joost, Fraser, Peter, Gilbert, David M.
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Abstract/Description: DNA replication occurs in a defined temporal order known as the replication-timing (RT) program. RT is regulated during development in discrete chromosomal units, coordinated with transcriptional activity and 3D genome organization. Here, we derived distinct cell types from F1 hybrid musculus x castaneus mouse crosses and exploited the high single-nucleotide polymorphism (SNP) density to characterize allelic differences in RT (Repli-seq), genome organization (Hi-C and promoter-capture Hi-C),...
Show moreDNA replication occurs in a defined temporal order known as the replication-timing (RT) program. RT is regulated during development in discrete chromosomal units, coordinated with transcriptional activity and 3D genome organization. Here, we derived distinct cell types from F1 hybrid musculus x castaneus mouse crosses and exploited the high single-nucleotide polymorphism (SNP) density to characterize allelic differences in RT (Repli-seq), genome organization (Hi-C and promoter-capture Hi-C), gene expression (total nuclear RNA-seq), and chromatin accessibility (ATAC-seq). We also present HARP, a new computational tool for sorting SNPs in phased genomes to efficiently measure allele-specific genome-wide data. Analysis of six different hybrid mESC clones with different genomes (C57BL/ 6,129 /sv, and CAST/ Ei), parental configurations, and gender revealed significant RT asynchrony between alleles across similar to 12% of the autosomal genome linked to subspecies genomes but not to parental origin, growth conditions, or gender. RT asynchrony in mESCs strongly correlated with changes in Hi-C compartments between alleles but not as strongly with SNP density, gene expression, imprinting, or chromatin accessibility. We then tracked mESC RT asynchronous regions during development by analyzing differentiated cell types, including extraembryonic endoderm stem (XEN) cells, four male and female primary mouse embryonic fibroblasts (MEFs), and neural precursor cells (NPCs) differentiated in vitro from mESCs with opposite parental configurations. We found that RT asynchrony and allelic discordance in Hi-C compartments seen in mESCs were largely lost in all differentiated cell types, accompanied by novel sites of allelic asynchrony at a considerably smaller proportion of the genome, suggesting that genome organization of homologs converges to similar folding patterns during cell fate commitment.
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Date Issued: 2018-06-01
Identifier: FSU_libsubv1_wos_000436084800005, 10.1101/gr.232561.117
Format: Citation

Title: Dinosaur incubation periods directly determined from growth-line counts in embryonic teeth show reptilian-grade development.
Creator: Erickson, Gregory M, Zelenitsky, Darla K, Kay, David Ian, Norell, Mark A
Abstract/Description: Birds stand out from other egg-laying amniotes by producing relatively small numbers of large eggs with very short incubation periods (average 11-85 d). This aspect promotes high survivorship by limiting exposure to predation and environmental perturbation, allows for larger more fit young, and facilitates rapid attainment of adult size. Birds are living dinosaurs; their rapid development has been considered to reflect the primitive dinosaurian condition. Here, nonavian dinosaurian incubation...
Show moreBirds stand out from other egg-laying amniotes by producing relatively small numbers of large eggs with very short incubation periods (average 11-85 d). This aspect promotes high survivorship by limiting exposure to predation and environmental perturbation, allows for larger more fit young, and facilitates rapid attainment of adult size. Birds are living dinosaurs; their rapid development has been considered to reflect the primitive dinosaurian condition. Here, nonavian dinosaurian incubation periods in both small and large ornithischian taxa are empirically determined through growth-line counts in embryonic teeth. Our results show unexpectedly slow incubation (2.8 and 5.8 mo) like those of outgroup reptiles. Developmental and physiological constraints would have rendered tooth formation and incubation inherently slow in other dinosaur lineages and basal birds. The capacity to determine incubation periods in extinct egg-laying amniotes has implications for dinosaurian embryology, life history strategies, and survivorship across the Cretaceous-Paleogene mass extinction event.
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Date Issued: 2017-01-17
Identifier: FSU_pmch_28049837, 10.1073/pnas.1613716114, PMC5255600, 28049837, 28049837, 1613716114
Format: Citation

Title: Fluorescent Protein-Based Ca2+ Sensor Reveals Global, Divalent Cation-Dependent Conformational Changes in Cardiac Troponin C.
Creator: Badr, Myriam A., Pinto, Jose R., Davidson, Michael W., Chase, P. Bryant
Abstract/Description: Cardiac troponin C (cTnC) is a key effector in cardiac muscle excitation-contraction coupling as the Ca2+ sensing subunit responsible for controlling contraction. In this study, we generated several FRET sensors for divalent cations based on cTnC flanked by a donor fluorescent protein (CFP) and an acceptor fluorescent protein (YFP). The sensors report Ca2+ and Mg2+ binding, and relay global structural information about the structural relationship between cTnC's N- and C-domains. The sensors...
Show moreCardiac troponin C (cTnC) is a key effector in cardiac muscle excitation-contraction coupling as the Ca2+ sensing subunit responsible for controlling contraction. In this study, we generated several FRET sensors for divalent cations based on cTnC flanked by a donor fluorescent protein (CFP) and an acceptor fluorescent protein (YFP). The sensors report Ca2+ and Mg2+ binding, and relay global structural information about the structural relationship between cTnC's N- and C-domains. The sensors were first characterized using end point titrations to decipher the response to Ca2+ binding in the presence or absence of Mg2+. The sensor that exhibited the largest responses in end point titrations, CTV-TnC, (Cerulean, TnC, and Venus) was characterized more extensively. Most of the divalent cation-dependent FRET signal originates from the high affinity C-terminal EF hands. CTV-TnC reconstitutes into skinned fiber preparations indicating proper assembly of troponin complex, with only similar to 0.2 pCa unit rightward shift of Ca2+-sensitive force development compared to WT-cTnC. Affinity of CTV-TnC for divalent cations is in agreement with known values for WT-cTnC. Analytical ultracentrifugation indicates that CTV-TnC undergoes compaction as divalent cations bind. C-terminal sites induce ion-specific (Ca2+ versus Mg2+) conformational changes in cTnC. Our data also provide support for the presence of additional, non-EF-hand sites on cTnC for Mg2+ binding. In conclusion, we successfully generated a novel FRET-Ca2+ sensor based on full length cTnC with a variety of cellular applications. Our sensor reveals global structural information about cTnC upon divalent cation binding.
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Date Issued: 2016-10-13
Identifier: FSU_libsubv1_wos_000385505800046, 10.1371/journal.pone.0164222, PMC5063504
Format: Citation

Title: Nanoscale architecture of cadherin-based cell adhesions.
Creator: Bertocchi, Cristina, Wang, Yilin, Ravasio, Andrea, Hara, Yusuke, Wu, Yao, Sailov, Talgat, Baird, Michelle A, Davidson, Michael W, Zaidel-Bar, Ronen, Toyama, Yusuke, Ladoux,...
Show moreBertocchi, Cristina, Wang, Yilin, Ravasio, Andrea, Hara, Yusuke, Wu, Yao, Sailov, Talgat, Baird, Michelle A, Davidson, Michael W, Zaidel-Bar, Ronen, Toyama, Yusuke, Ladoux, Benoit, Mege, Rene-Marc, Kanchanawong, Pakorn
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Abstract/Description: Multicellularity in animals requires dynamic maintenance of cell-cell contacts. Intercellularly ligated cadherins recruit numerous proteins to form supramolecular complexes that connect with the actin cytoskeleton and support force transmission. However, the molecular organization within such structures remains unknown. Here we mapped protein organization in cadherin-based adhesions by super-resolution microscopy, revealing a multi-compartment nanoscale architecture, with the plasma-membrane...
Show moreMulticellularity in animals requires dynamic maintenance of cell-cell contacts. Intercellularly ligated cadherins recruit numerous proteins to form supramolecular complexes that connect with the actin cytoskeleton and support force transmission. However, the molecular organization within such structures remains unknown. Here we mapped protein organization in cadherin-based adhesions by super-resolution microscopy, revealing a multi-compartment nanoscale architecture, with the plasma-membrane-proximal cadherin-catenin compartment segregated from the actin cytoskeletal compartment, bridged by an interface zone containing vinculin. Vinculin position is determined by α-catenin, and following activation, vinculin can extend ∼30 nm to bridge the cadherin-catenin and actin compartments, while modulating the nanoscale positions of the actin regulators zyxin and VASP. Vinculin conformational activation requires tension and tyrosine phosphorylation, regulated by Abl kinase and PTP1B phosphatase. Such modular architecture provides a structural framework for mechanical and biochemical signal integration by vinculin, which may differentially engage cadherin-catenin complexes with the actomyosin machinery to regulate cell adhesions.
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Date Issued: 2017-01-01
Identifier: FSU_pmch_27992406, 10.1038/ncb3456, PMC5421576, 27992406, 27992406, ncb3456
Format: Citation

Title: Variation In Plant-mediated Intra- And Interspecific Interactions Among Insect Herbivores: Effects Of Host Genotype.
Creator: McNutt, David W., Underwood, Nora
Abstract/Description: Many studies show that indirect interactions between insect herbivores via shared host plants are common and often mediated by plant-induced responses to damage. However, we lack some types of data that will be needed to model how plant-mediated interactions on individual plants contribute to the population dynamics of interacting herbivores. Specifically, there are few simultaneous characterizations of both the intra- and interspecific effects that are mediated by the host plant, as well as...
Show moreMany studies show that indirect interactions between insect herbivores via shared host plants are common and often mediated by plant-induced responses to damage. However, we lack some types of data that will be needed to model how plant-mediated interactions on individual plants contribute to the population dynamics of interacting herbivores. Specifically, there are few simultaneous characterizations of both the intra- and interspecific effects that are mediated by the host plant, as well as host plant constitutive resistance. Additionally, as herbivores are likely to move among plants that differ in quality, we must consider how this set of intra- and interspecific effects differs among plant genotypes-that is, how plant-mediated effects genetically vary or covary. We examined how the set of intra- and interspecific indirect effects involving the insect folivores Leptinotarsa juncta and Manduca sexta varies across different genotypes of a shared host plant, Solanum carolinense. We damaged 12 plant genotypes using both herbivore species, then measured effects on the growth of both con- and heterospecifics, as well as constitutive resistance to each herbivore. We then tested for genetic variation and covariation in plant-mediated effects and constitutive resistance among plant genotypes. We found that on average, there were significant negative intraspecific plant-mediated effects on the growth rate of both herbivores, as well as asymmetric negative interspecific effects of M. sexta on L. juncta. Both intra- and interspecific effects varied across plant genotypes. For example, the interspecific effect of M. sexta on L. juncta ranged from significantly negative to significantly positive. Additionally, there were strong correlations among the individual effects mediated by S. carolinense, particularly between constitutive resistance and both intra- and interspecific effects. We find that these genetic correlations might limit the types and strength of interactions that take place across multiple genotypes of the same plant species. Our results suggest that future models of plant-mediated interactions between herbivores should account for patterns of genetic variation and covariation when scaling from individual interactions to population-level processes.
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Date Issued: 2016-10
Identifier: FSU_libsubv1_wos_000387216300050, 10.1002/ecs2.1520
Format: Citation

Title: Viral Recombination Blurs Taxonomic Lines: Examination Of Single-stranded Dna Viruses In A Wastewater Treatment Plant.
Creator: Pearson, Victoria M., Caudle, S. Brian, Rokyta, Darin R.
Abstract/Description: Understanding the structure and dynamics of microbial communities, especially those of economic concern, is of paramount importance to maintaining healthy and efficient microbial communities at agricultural sites and large industrial cultures, including bioprocessors. Wastewater treatment plants are large bioprocessors which receive water from multiple sources, becoming reservoirs for the complex collection of many viral families that infect a broad range of hosts. To examine this collection...
Show moreUnderstanding the structure and dynamics of microbial communities, especially those of economic concern, is of paramount importance to maintaining healthy and efficient microbial communities at agricultural sites and large industrial cultures, including bioprocessors. Wastewater treatment plants are large bioprocessors which receive water from multiple sources, becoming reservoirs for the complex collection of many viral families that infect a broad range of hosts. To examine this collection of viruses, full-length genomes of circular ssDNA viruses were isolated from a wastewater treatment facility using a combination of sucrose-gradient size selection and rolling-circle amplification and sequenced on an Illumina MSeq. Single-stranded DNA viruses are among the least understood groups of microbial pathogens due to genomic biases and culturing difficulties, particularly compared to the larger, more often studied dsDNA viruses. However, the group contains several notable well-studied examples, including agricultural pathogens which infect both livestock and crops (Circoviridae and Geminiviridae), and model organisms for genetics and evolution studies (Microviridae). Examination of the collected viral DNA provided evidence for 83 unique genotypic groupings, which were genetically dissimilar to known viral types and exhibited broad diversity within the community. Furthermore, although these genomes express similarities to known viral families, such as Circoviridae, Geminiviridae, and Microviridae, many are so divergent that they may represent new taxonomic groups. This study demonstrated the efficacy of the protocol for separating bacteria and large viruses from the sought after ssDNA viruses and the ability to use this protocol to obtain an in-depth analysis of the diversity within this group.
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Date Issued: 2016-10-18
Identifier: FSU_libsubv1_wos_000385583100006, 10.7717/peerj.2585
Format: Citation

Title: A Dual-Color Reporter Assay of Cohesin-Mediated Gene Regulation in Budding Yeast Meiosis.
Creator: Fan, Jinbo, Jin, Hui, Yu, Hong-Guo
Abstract/Description: In this chapter, we describe a quantitative fluorescence-based assay of gene expression using the ratio of the reporter green fluorescence protein (GFP) to the internal red fluorescence protein (RFP) control. With this dual-color heterologous reporter assay, we have revealed cohesin-regulated genes and discovered a cis-acting DNA element, the Ty1-LTR, which interacts with cohesin and regulates gene expression during yeast meiosis. The method described here provides an effective cytological...
Show moreIn this chapter, we describe a quantitative fluorescence-based assay of gene expression using the ratio of the reporter green fluorescence protein (GFP) to the internal red fluorescence protein (RFP) control. With this dual-color heterologous reporter assay, we have revealed cohesin-regulated genes and discovered a cis-acting DNA element, the Ty1-LTR, which interacts with cohesin and regulates gene expression during yeast meiosis. The method described here provides an effective cytological approach for quantitative analysis of global gene expression in budding yeast meiosis.
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Date Issued: 2017-01-01
Identifier: FSU_pmch_27797078, 10.1007/978-1-4939-6545-8_9, PMC5551346, 27797078, 27797078
Format: Citation

Title: Resolving Cypriniformes relationships using an anchored enrichment approach.
Creator: Stout, Carla C, Tan, Milton, Lemmon, Alan R, Lemmon, Emily Moriarty, Armbruster, Jonathan W
Abstract/Description: Cypriniformes (minnows, carps, loaches, and suckers) is the largest group of freshwater fishes in the world (~4300 described species). Despite much attention, previous attempts to elucidate relationships using molecular and morphological characters have been incongruent. In this study we present the first phylogenomic analysis using anchored hybrid enrichment for 172 taxa to represent the order (plus three out-group taxa), which is the largest dataset for the order to date (219 loci, 315,288...
Show moreCypriniformes (minnows, carps, loaches, and suckers) is the largest group of freshwater fishes in the world (~4300 described species). Despite much attention, previous attempts to elucidate relationships using molecular and morphological characters have been incongruent. In this study we present the first phylogenomic analysis using anchored hybrid enrichment for 172 taxa to represent the order (plus three out-group taxa), which is the largest dataset for the order to date (219 loci, 315,288 bp, average locus length of 1011 bp). Concatenation analysis establishes a robust tree with 97 % of nodes at 100 % bootstrap support. Species tree analysis was highly congruent with the concatenation analysis with only two major differences: monophyly of Cobitoidei and placement of Danionidae. Most major clades obtained in prior molecular studies were validated as monophyletic, and we provide robust resolution for the relationships among these clades for the first time. These relationships can be used as a framework for addressing a variety of evolutionary questions (e.g. phylogeography, polyploidization, diversification, trait evolution, comparative genomics) for which Cypriniformes is ideally suited.
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Date Issued: 2016-11-09
Identifier: FSU_pmch_27829363, 10.1186/s12862-016-0819-5, PMC5103605, 27829363, 27829363, 10.1186/s12862-016-0819-5
Format: Citation

Title: Zika virus and neural developmental defects: building a case for a cause.
Creator: Ogden, Sarah C., Hammack, Christy, Tang, Hengli
Date Issued: 2016-05
Identifier: FSU_libsubv1_wos_000375885300013, 10.1007/s11427-016-5053-2
Format: Citation

Title: Pleiotropy, constraint, and modularity in the evolution of life histories: insights from genomic analyses..
Creator: Hughes, Kimberly A, Leips, Jeff
Abstract/Description: Multicellular organisms display an enormous range of life history (LH) strategies and present an evolutionary conundrum; despite strong natural selection, LH traits are characterized by high levels of genetic variation. To understand the evolution of life histories and maintenance of this variation, the specific phenotypic effects of segregating alleles and the genetic networks in which they act need to be elucidated. In particular, the extent to which LH evolution is constrained by the...
Show moreMulticellular organisms display an enormous range of life history (LH) strategies and present an evolutionary conundrum; despite strong natural selection, LH traits are characterized by high levels of genetic variation. To understand the evolution of life histories and maintenance of this variation, the specific phenotypic effects of segregating alleles and the genetic networks in which they act need to be elucidated. In particular, the extent to which LH evolution is constrained by the pleiotropy of alleles contributing to LH variation is generally unknown. Here, we review recent empirical results that shed light on this question, with an emphasis on studies employing genomic analyses. While genome-scale analyses are increasingly practical and affordable, they face limitations of genetic resolution and statistical power. We describe new research approaches that we believe can produce new insights and evaluate their promise and applicability to different kinds of organisms. Two approaches seem particularly promising: experiments that manipulate selection in multiple dimensions and measure phenotypic and genomic response and analytical approaches that take into account genome-wide associations between markers and phenotypes, rather than applying a traditional marker-by-marker approach.
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Date Issued: 2017-02-01
Identifier: FSU_pmch_27936291, 10.1111/nyas.13256, PMC5318229, 27936291, 27936291
Format: Citation

Title: Reversal Learning Deficits Associated with Increased Frontal Cortical Brain-Derived Neurotrophic Factor Tyrosine Kinase B Signaling in a Prenatal Cocaine Exposure Mouse Model.
Creator: McCarthy, Deirdre M, Bell, Genevieve A, Cannon, Elisa N, Mueller, Kaly A, Huizenga, Megan N, Sadri-Vakili, Ghazaleh, Fadool, Debra A, Bhide, Pradeep G
Abstract/Description: Prenatal cocaine exposure remains a major public health concern because of its adverse impact on cognitive function in children and adults. We report that prenatal cocaine exposure produces significant deficits in reversal learning, a key component of cognitive flexibility, in a mouse model. We used an olfactory reversal learning paradigm and found that the prenatally cocaine-exposed mice showed a marked failure to learn the reversed paradigm. Because brain-derived neurotrophic factor (BDNF)...
Show morePrenatal cocaine exposure remains a major public health concern because of its adverse impact on cognitive function in children and adults. We report that prenatal cocaine exposure produces significant deficits in reversal learning, a key component of cognitive flexibility, in a mouse model. We used an olfactory reversal learning paradigm and found that the prenatally cocaine-exposed mice showed a marked failure to learn the reversed paradigm. Because brain-derived neurotrophic factor (BDNF) is a key regulator of cognitive functions, and because prenatal cocaine exposure increases the expression of BDNF and the phosphorylated form of its receptor, tyrosine kinase B (TrkB), we examined whether BDNF-TrkB signaling is involved in mediating the reversal learning deficit in prenatally cocaine-exposed mice. Systemic administration of a selective TrkB receptor antagonist restored normal reversal learning in prenatally cocaine-exposed mice, suggesting that increased BDNF-TrkB signaling may be an underlying mechanism of reversal learning deficits. Our findings provide novel mechanistic insights into the reversal learning phenomenon and may have significant translational implications because impaired cognitive flexibility is a key symptom in psychiatric conditions of developmental onset.
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Date Issued: 2016-01-01
Identifier: FSU_pmch_27951531, 10.1159/000452739, PMC5360472, 27951531, 27951531, 000452739
Format: Citation

Title: Role of proteasome-dependent protein degradation in long-term operant memory in Aplysia.
Creator: Lyons, Lisa C, Gardner, Jacob S, Gandour, Catherine E, Krishnan, Harini C
Abstract/Description: We investigated the in vivo role of protein degradation during intermediate (ITM) and long-term memory (LTM) in Aplysia using an operant learning paradigm. The proteasome inhibitor MG-132 inhibited the induction and molecular consolidation of LTM with no effect on ITM. Remarkably, maintenance of steady-state protein levels through inhibition of protein synthesis using either anisomycin or rapamycin in conjunction with proteasome inhibition permitted the formation of robust 24 h LTM. Our...
Show moreWe investigated the in vivo role of protein degradation during intermediate (ITM) and long-term memory (LTM) in Aplysia using an operant learning paradigm. The proteasome inhibitor MG-132 inhibited the induction and molecular consolidation of LTM with no effect on ITM. Remarkably, maintenance of steady-state protein levels through inhibition of protein synthesis using either anisomycin or rapamycin in conjunction with proteasome inhibition permitted the formation of robust 24 h LTM. Our studies suggest a primary role for proteasomal activity in facilitation of gene transcription for LTM and raise the possibility that synaptic mechanisms are sufficient to sustain 24 h memory.
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Date Issued: 2016-12-15
Identifier: FSU_pmch_27980077, 10.1101/lm.043794.116, PMC5159658, 27980077, 27980077, 24/1/59
Format: Citation

Title: Extreme warming challenges sentinel status of kelp forests as indicators of climate change.
Creator: Reed, Daniel, Washburn, Libe, Rassweiler, Andrew, Miller, Robert, Bell, Tom, Harrer, Shannon
Abstract/Description: The desire to use sentinel species as early warning indicators of impending climate change effects on entire ecosystems is attractive, but we need to verify that such approaches have sound biological foundations. A recent large-scale warming event in the North Pacific Ocean of unprecedented magnitude and duration allowed us to evaluate the sentinel status of giant kelp, a coastal foundation species that thrives in cold, nutrient-rich waters and is considered sensitive to warming. Here, we...
Show moreThe desire to use sentinel species as early warning indicators of impending climate change effects on entire ecosystems is attractive, but we need to verify that such approaches have sound biological foundations. A recent large-scale warming event in the North Pacific Ocean of unprecedented magnitude and duration allowed us to evaluate the sentinel status of giant kelp, a coastal foundation species that thrives in cold, nutrient-rich waters and is considered sensitive to warming. Here, we show that giant kelp and the majority of species that associate with it did not presage ecosystem effects of extreme warming off southern California despite giant kelp's expected vulnerability. Our results challenge the general perception that kelp-dominated systems are highly vulnerable to extreme warming events and expose the more general risk of relying on supposed sentinel species that are assumed to be very sensitive to climate change.
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Date Issued: 2016-12-13
Identifier: FSU_pmch_27958273, 10.1038/ncomms13757, PMC5159872, 27958273, 27958273, ncomms13757
Format: Citation

Title: Population Variation In The Trophic Niche Of The Trinidadian Guppy From Different Predation Regimes.
Creator: Zandona, Eugenia, Dalton, Christopher M., El-Sabaawi, Rana W., Howard, Jason L., Marshall, Michael C., Kilham, Susan S., Reznick, David N., Travis, Joseph, Kohler, Tyler J.,...
Show moreZandona, Eugenia, Dalton, Christopher M., El-Sabaawi, Rana W., Howard, Jason L., Marshall, Michael C., Kilham, Susan S., Reznick, David N., Travis, Joseph, Kohler, Tyler J., Flecker, Alexander S., Thomas, Steven A., Pringle, Catherine M.
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Abstract/Description: Population variation in trophic niche is widespread among organisms and is of increasing interest given its role in both speciation and adaptation to changing environments. Trinidadian guppies (Poecilia reticulata) inhabiting stream reaches with different predation regimes have rapidly evolved divergent life history traits. Here, we investigated the effects of both predation and resource availability on guppy trophic niches by evaluating their gut contents, resource standing stocks, and delta...
Show morePopulation variation in trophic niche is widespread among organisms and is of increasing interest given its role in both speciation and adaptation to changing environments. Trinidadian guppies (Poecilia reticulata) inhabiting stream reaches with different predation regimes have rapidly evolved divergent life history traits. Here, we investigated the effects of both predation and resource availability on guppy trophic niches by evaluating their gut contents, resource standing stocks, and delta N-15 and delta C-13 stable isotopes across five streams during the wet season. We found that guppies from low predation (LP) sites had a consistently higher trophic position and proportion of invertebrates in their guts and assimilate less epilithon than guppies from high predation (HP) sites. Higher trophic position was also associated with lower benthic invertebrate availability. Our results suggest that LP guppies could be more efficient invertebrate consumers, possibly as an evolutionary response to greater intraspecific competition for higher quality food. This may be intensified by seasonality, as wet season conditions can alter resource availability, feeding rates, and the intensity of intraspecific competition. Understanding how guppy diets vary among communities is critical to elucidating the role of niche shifts in mediating the link between environmental change and the evolution of life histories.
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Date Issued: 2017-07-18
Identifier: FSU_libsubv1_wos_000405746500081, 10.1038/s41598-017-06163-6
Format: Citation

Title: Preservation of Arctic dinosaur remains from the Prince Creek Formation (Alaska, USA): A reply to Fiorillo (2016).
Creator: Mori, Hirotsugu, Druckenmiller, Patrick S., Erickson, Gregory M.
Date Issued: 2016
Identifier: FSU_libsubv1_wos_000371323000014, 10.4202/app.00234.2015
Format: Citation

Title: Transcriptome Dataset Of Halophyte Beach Morning Glory, A Close Wild Relative Of Sweet Potato.
Creator: Reid, Robert W., Luo, Yan, Yan, Sue, Miller, Thomas E., Song, Bao-Hua
Date Issued: 2016-08-24
Identifier: FSU_libsubv1_wos_000381854100001, 10.3389/fpls.2016.01267
Format: Citation

Title: Global patterns of kelp forest change over the past half-century.
Creator: Krumhansl, Kira A, Okamoto, Daniel K, Rassweiler, Andrew, Novak, Mark, Bolton, John J, Cavanaugh, Kyle C, Connell, Sean D, Johnson, Craig R, Konar, Brenda, Ling, Scott D,...
Show moreKrumhansl, Kira A, Okamoto, Daniel K, Rassweiler, Andrew, Novak, Mark, Bolton, John J, Cavanaugh, Kyle C, Connell, Sean D, Johnson, Craig R, Konar, Brenda, Ling, Scott D, Micheli, Fiorenza, Norderhaug, Kjell M, Pérez-Matus, Alejandro, Sousa-Pinto, Isabel, Reed, Daniel C, Salomon, Anne K, Shears, Nick T, Wernberg, Thomas, Anderson, Robert J, Barrett, Nevell S, Buschmann, Alejandro H, Carr, Mark H, Caselle, Jennifer E, Derrien-Courtel, Sandrine, Edgar, Graham J, Edwards, Matt, Estes, James A, Goodwin, Claire, Kenner, Michael C, Kushner, David J, Moy, Frithjof E, Nunn, Julia, Steneck, Robert S, Vásquez, Julio, Watson, Jane, Witman, Jon D, Byrnes, Jarrett E K
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Abstract/Description: Kelp forests (Order Laminariales) form key biogenic habitats in coastal regions of temperate and Arctic seas worldwide, providing ecosystem services valued in the range of billions of dollars annually. Although local evidence suggests that kelp forests are increasingly threatened by a variety of stressors, no comprehensive global analysis of change in kelp abundances currently exists. Here, we build and analyze a global database of kelp time series spanning the past half-century to assess...
Show moreKelp forests (Order Laminariales) form key biogenic habitats in coastal regions of temperate and Arctic seas worldwide, providing ecosystem services valued in the range of billions of dollars annually. Although local evidence suggests that kelp forests are increasingly threatened by a variety of stressors, no comprehensive global analysis of change in kelp abundances currently exists. Here, we build and analyze a global database of kelp time series spanning the past half-century to assess regional and global trends in kelp abundances. We detected a high degree of geographic variation in trends, with regional variability in the direction and magnitude of change far exceeding a small global average decline (instantaneous rate of change = -0.018 y). Our analysis identified declines in 38% of ecoregions for which there are data (-0.015 to -0.18 y), increases in 27% of ecoregions (0.015 to 0.11 y), and no detectable change in 35% of ecoregions. These spatially variable trajectories reflected regional differences in the drivers of change, uncertainty in some regions owing to poor spatial and temporal data coverage, and the dynamic nature of kelp populations. We conclude that although global drivers could be affecting kelp forests at multiple scales, local stressors and regional variation in the effects of these drivers dominate kelp dynamics, in contrast to many other marine and terrestrial foundation species.
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Date Issued: 2016-11-29
Identifier: FSU_pmch_27849580, 10.1073/pnas.1606102113, PMC5137772, 27849580, 27849580, 1606102113
Format: Citation

Title: Margatoxin-bound quantum dots as a novel inhibitor of the voltage-gated ion channel Kv1.3.
Creator: Schwartz, Austin B, Kapur, Anshika, Wang, Wentao, Huang, Zhenbo, Fardone, Erminia, Palui, Goutam, Mattoussi, Hedi, Fadool, Debra Ann
Abstract/Description: Venom-derived ion channel inhibitors have strong channel selectivity, potency, and stability; however, tracking delivery to their target can be challenging. Herein, we utilized luminescent quantum dots (QDs) conjugated to margatoxin (MgTx) as a traceable vehicle to target a voltage-dependent potassium channel, Kv1.3, which has a select distribution and well-characterized role in immunity, glucose metabolism, and sensory ability. We screened both unconjugated (MgTx) and conjugated MgTx (QD...
Show moreVenom-derived ion channel inhibitors have strong channel selectivity, potency, and stability; however, tracking delivery to their target can be challenging. Herein, we utilized luminescent quantum dots (QDs) conjugated to margatoxin (MgTx) as a traceable vehicle to target a voltage-dependent potassium channel, Kv1.3, which has a select distribution and well-characterized role in immunity, glucose metabolism, and sensory ability. We screened both unconjugated (MgTx) and conjugated MgTx (QD-MgTx) for their ability to inhibit Shaker channels Kv1.1 to Kv1.7 using patch-clamp electrophysiology in HEK293 cells. Our data indicate that MgTx inhibits 79% of the outward current in Kv1.3-transfected cells and that the QD-MgTx conjugate is able to achieve a similar level of block, albeit a slightly reduced efficacy (66%) and at a slower time course (50% block by 10.9 ± 1.1 min, MgTx; vs. 15.3 ± 1.2 min, QD-MgTx). Like the unbound peptide, the QD-MgTx conjugate inhibits both Kv1.3 and Kv1.2 at a 1 nM concentration, whereas it does not inhibit other screened Shaker channels. We tested the ability of QD-MgTx to inhibit native Kv1.3 expressed in the mouse olfactory bulb (OB). In brain slices of the OB, the conjugate acted similarly to MgTx to inhibit Kv1.3, causing an increased action potential firing frequency attributed to decreased intraburst duration rather than interspike interval. Our data demonstrate a retention of known biophysical properties associated with block of the vestibule of Kv1.3 by QD-MgTx conjugate compared to that of MgTx, inferring QDs could provide a useful tool to deliver ion channel inhibitors to targeted tissues in vivo.
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Date Issued: 2017-02-01
Identifier: FSU_pmch_27861889, 10.1111/jnc.13891, PMC5250575, 27861889, 27861889
Format: Citation

Title: Diversification In Wild Populations Of The Model Organism Anolis Carolinensis: A Genome-wide Phylogeographic Investigation.
Creator: Manthey, Joseph D., Tollis, Marc, Lemmon, Alan R., Lemmon, Emily Moriarty, Boissinot, Stephane
Abstract/Description: The green anole (Anolis carolinensis) is a lizard widespread throughout the southeastern United States and is a model organism for the study of reproductive behavior, physiology, neural biology, and genomics. Previous phylogeographic studies of A. carolinensis using mitochondrial DNA and small numbers of nuclear loci identified conflicting and poorly supported relationships among geographically structured clades; these inconsistencies preclude confident use of A. carolinensis evolutionary...
Show moreThe green anole (Anolis carolinensis) is a lizard widespread throughout the southeastern United States and is a model organism for the study of reproductive behavior, physiology, neural biology, and genomics. Previous phylogeographic studies of A. carolinensis using mitochondrial DNA and small numbers of nuclear loci identified conflicting and poorly supported relationships among geographically structured clades; these inconsistencies preclude confident use of A. carolinensis evolutionary history in association with morphological, physiological, or reproductive biology studies among sampling localities and necessitate increased effort to resolve evolutionary relationships among natural populations. Here, we used anchored hybrid enrichment of hundreds of genetic markers across the genome of A. carolinensis and identified five strongly supported phylogeographic groups. Using multiple analyses, we produced a fully resolved species tree, investigated relative support for each lineage across all gene trees, and identified mito-nuclear discordance when comparing our results to previous studies. We found fixed differences in only one clade-southern Florida restricted to the Everglades region-while most polymorphisms were shared between lineages. The southern Florida group likely diverged from other populations during the Pliocene, with all other diversification during the Pleistocene. Multiple lines of support, including phylogenetic relationships, a latitudinal gradient in genetic diversity, and relatively more stable long-term population sizes in southern phylogeographic groups, indicate that diversification in A. carolinensis occurred northward from southern Florida.
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Date Issued: 2016-11
Identifier: FSU_libsubv1_wos_000387664500017, 10.1002/ece3.2547
Format: Citation

Title: The Florida Harvester Ant, Pogonomyrmex badius, Relies on Germination to Consume Large Seeds.
Creator: Tschinkel, Walter R, Kwapich, Christina L
Abstract/Description: The Florida harvester ant, Pogonomyrmex badius, is one of many ant species and genera that stores large numbers of seeds in damp, underground chambers for later consumption. A comparison of the sizes of seeds recovered from storage chambers with those of seed husks discarded following consumption revealed that the used seeds are far smaller than stored seeds. This difference in use-rate was confirmed in field and laboratory colonies by offering marked seeds of various sizes and monitoring the...
Show moreThe Florida harvester ant, Pogonomyrmex badius, is one of many ant species and genera that stores large numbers of seeds in damp, underground chambers for later consumption. A comparison of the sizes of seeds recovered from storage chambers with those of seed husks discarded following consumption revealed that the used seeds are far smaller than stored seeds. This difference in use-rate was confirmed in field and laboratory colonies by offering marked seeds of various sizes and monitoring the appearance of size-specific chaff. Because foragers collect a range of seed sizes but only open small seeds, large seeds accumulate, forming 70% or more of the weight of seed stores. Major workers increase the rates at which small and medium seeds are opened, but do not increase the size range of opened seeds. Experiments limiting ant access to portions of natural seed chambers showed that seeds germinate during storage, but that the ants rapidly remove them. When offered alongside non germinating seeds, germinating seeds were preferentially fed to larvae. The rate of germination during the annual cycle was determined by both burial in artificial chambers at various depths and under four laboratory temperatures. The germination rate depends upon the species of seed, the soil/laboratory temperature and/or the elapsed time. The seasonal soil temperature cycle generated germination patterns that vary with the mix of locally-available seeds. Taken together, exploitation of germination greatly increases the resources available to the ants in space and time. While the largest seeds may have the nutritional value of 15 small seeds, the inability of workers to open large seeds at will precludes them from rapid use during catastrophic events. The harvester ant's approach to seed harvesting is therefore two-pronged, with both immediate and delayed payoffs arising from the tendency to forage for a wide variety of seeds sizes.
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Date Issued: 2016-11-28
Identifier: FSU_pmch_27893844, 10.1371/journal.pone.0166907, PMC5125654, 27893844, 27893844, PONE-D-16-33448
Format: Citation

Title: Advances in Zika Virus Research: Stem Cell Models, Challenges, and Opportunities..
Creator: Ming, Guo-Li, Tang, Hengli, Song, Hongjun
Abstract/Description: The re-emergence of Zika virus (ZIKV) and its suspected link with various disorders in newborns and adults led the World Health Organization to declare a global health emergency. In response, the stem cell field quickly established platforms for modeling ZIKV exposure using human pluripotent stem cell-derived neural progenitors and brain organoids, fetal tissues, and animal models. These efforts provided significant insight into cellular targets, pathogenesis, and underlying biological...
Show moreThe re-emergence of Zika virus (ZIKV) and its suspected link with various disorders in newborns and adults led the World Health Organization to declare a global health emergency. In response, the stem cell field quickly established platforms for modeling ZIKV exposure using human pluripotent stem cell-derived neural progenitors and brain organoids, fetal tissues, and animal models. These efforts provided significant insight into cellular targets, pathogenesis, and underlying biological mechanisms of ZIKV infection as well as platforms for drug testing. Here we review the remarkable progress in stem cell-based ZIKV research and discuss current challenges and future opportunities.
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Date Issued: 2016-12-01
Identifier: FSU_pmch_27912090, 10.1016/j.stem.2016.11.014, PMC5218815, 27912090, 27912090, S1934-5909(16)30415-5
Format: Citation

Title: Differential role of calpain-dependent protein cleavage in intermediate and long-term operant memory in Aplysia.
Creator: Lyons, Lisa C, Gardner, Jacob S, Lentsch, Cassidy T, Gandour, Catherine E, Krishnan, Harini C, Noakes, Eric J
Abstract/Description: In addition to protein synthesis, protein degradation or protein cleavage may be necessary for intermediate (ITM) and long-term memory (LTM) to remove molecular constraints, facilitate persistent kinase activity and modulate synaptic plasticity. Calpains, a family of conserved calcium dependent cysteine proteases, modulate synaptic function through protein cleavage. We used the marine mollusk Aplysia californica to investigate the in vivo role of calpains during intermediate and long-term...
Show moreIn addition to protein synthesis, protein degradation or protein cleavage may be necessary for intermediate (ITM) and long-term memory (LTM) to remove molecular constraints, facilitate persistent kinase activity and modulate synaptic plasticity. Calpains, a family of conserved calcium dependent cysteine proteases, modulate synaptic function through protein cleavage. We used the marine mollusk Aplysia californica to investigate the in vivo role of calpains during intermediate and long-term operant memory formation using the learning that food is inedible (LFI) paradigm. A single LFI training session, in which the animal associates a specific netted seaweed with the failure to swallow, generates short (30min), intermediate (4-6h) and long-term (24h) memory. Using the calpain inhibitors calpeptin and MDL-28170, we found that ITM requires calpain activity for induction and consolidation similar to the previously reported requirements for persistent protein kinase C activity in intermediate-term LFI memory. The induction of LTM also required calpain activity. In contrast to ITM, calpain activity was not necessary for the molecular consolidation of LTM. Surprisingly, six hours after LFI training we found that calpain activity was necessary for LTM, although this is a time at which neither persistent PKC activity nor protein synthesis is required for the maintenance of long-term LFI memory. These results demonstrate that calpains function in multiple roles in vivo during associative memory formation.
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Date Issued: 2017-01-01
Identifier: FSU_pmch_27913293, 10.1016/j.nlm.2016.11.018, PMC6179366, 27913293, 27913293, S1074-7427(16)30358-6
Format: Citation

Title: Promoter Interactome Of Human Embryonic Stem Cell-derived Cardiomyocytes Connects Gwas Regions To Cardiac Gene Networks.
Creator: Choy, Mun-Kit, Javierre, Biola M., Williams, Simon G., Baross, Stephanie L., Liu, Yingjuan, Wingett, Steven W., Akbarov, Artur, Wallace, Chris, Freire-Pritchett, Paula, Rugg...
Show moreChoy, Mun-Kit, Javierre, Biola M., Williams, Simon G., Baross, Stephanie L., Liu, Yingjuan, Wingett, Steven W., Akbarov, Artur, Wallace, Chris, Freire-Pritchett, Paula, Rugg-Gunn, Peter J., Spivakov, Mikhail, Fraser, Peter, Keavney, Bernard D.
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Abstract/Description: Long-range chromosomal interactions bring distal regulatory elements and promoters together to regulate gene expression in biological processes. By performing promoter capture Hi-C (PCHi-C) on human embryonic stem cell-derived cardiomyocytes (hESC-CMs), we show that such promoter interactions are a key mechanism by which enhancers contact their target genes after hESC-CM differentiation from hESCs. We also show that the promoter interactome of hESC-CMs is associated with expression...
Show moreLong-range chromosomal interactions bring distal regulatory elements and promoters together to regulate gene expression in biological processes. By performing promoter capture Hi-C (PCHi-C) on human embryonic stem cell-derived cardiomyocytes (hESC-CMs), we show that such promoter interactions are a key mechanism by which enhancers contact their target genes after hESC-CM differentiation from hESCs. We also show that the promoter interactome of hESC-CMs is associated with expression quantitative trait loci (eQTLs) in cardiac left ventricular tissue; captures the dynamic process of genome reorganisation after hESC-CM differentiation; overlaps genome-wide association study (GWAS) regions associated with heart rate; and identifies new candidate genes in such regions. These findings indicate that regulatory elements in hESC-CMs identified by our approach control gene expression involved in ventricular conduction and rhythm of the heart. The study of promoter interactions in other hESC-derived cell types may be of utility in functional investigation of GWAS-associated regions.
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Date Issued: 2018-06-28
Identifier: FSU_libsubv1_wos_000436548700017, 10.1038/s41467-018-04931-0
Format: Citation

Title: Tet1 in Nucleus Accumbens Opposes Depression- and Anxiety-Like Behaviors.
Creator: Feng, Jian, Pena, Catherine J, Purushothaman, Immanuel, Engmann, Olivia, Walker, Deena, Brown, Amber N, Issler, Orna, Doyle, Marie, Harrigan, Eileen, Mouzon, Ezekiell, Vialou,...
Show moreFeng, Jian, Pena, Catherine J, Purushothaman, Immanuel, Engmann, Olivia, Walker, Deena, Brown, Amber N, Issler, Orna, Doyle, Marie, Harrigan, Eileen, Mouzon, Ezekiell, Vialou, Vincent, Shen, Li, Dawlaty, Meelad M, Jaenisch, Rudolf, Nestler, Eric J
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Abstract/Description: Depression is a leading cause of disease burden, yet current therapies fully treat <50% of affected individuals. Increasing evidence implicates epigenetic mechanisms in depression and antidepressant action. Here we examined a possible role for the DNA dioxygenase, ten-eleven translocation protein 1 (TET1), in depression-related behavioral abnormalities. We applied chronic social defeat stress, an ethologically validated mouse model of depression-like behaviors, and examined Tet1 expression...
Show moreDepression is a leading cause of disease burden, yet current therapies fully treat <50% of affected individuals. Increasing evidence implicates epigenetic mechanisms in depression and antidepressant action. Here we examined a possible role for the DNA dioxygenase, ten-eleven translocation protein 1 (TET1), in depression-related behavioral abnormalities. We applied chronic social defeat stress, an ethologically validated mouse model of depression-like behaviors, and examined Tet1 expression changes in nucleus accumbens (NAc), a key brain reward region. We show decreased Tet1 expression in NAc in stress-susceptible mice only. Surprisingly, selective knockout of Tet1 in NAc neurons of adult mice produced antidepressant-like effects in several behavioral assays. To identify Tet1 targets that mediate these actions, we performed RNAseq on NAc after conditional deletion of Tet1 and found that immune-related genes are the most highly dysregulated. Moreover, many of these genes are also upregulated in the NAc of resilient mice after chronic social defeat stress. These findings reveal a novel role for TET1, an enzyme important for DNA hydroxymethylation, in the brain's reward circuitry in modulating stress responses in mice. We also identify a subset of genes that are regulated by TET1 in this circuitry. These findings provide new insight into the pathophysiology of depression, which can aid in future antidepressant drug discovery efforts.
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Date Issued: 2017-07-01
Identifier: FSU_pmch_28074830, 10.1038/npp.2017.6, PMC5518912, 28074830, 28074830, npp20176
Format: Citation

Title: Structural Heterogeneity in Pre-40S Ribosomes.
Creator: Johnson, Matthew C, Ghalei, Homa, Doxtader, Katelyn A, Karbstein, Katrin, Stroupe, M Elizabeth
Abstract/Description: Late-stage 40S ribosome assembly is a highly regulated dynamic process that occurs in the cytoplasm, alongside the full translation machinery. Seven assembly factors (AFs) regulate and facilitate maturation, but the mechanisms through which they work remain undetermined. Here, we present a series of structures of the immature small subunit (pre-40S) determined by three-dimensional (3D) cryoelectron microscopy with 3D sorting to assess the molecule's heterogeneity. These structures demonstrate...
Show moreLate-stage 40S ribosome assembly is a highly regulated dynamic process that occurs in the cytoplasm, alongside the full translation machinery. Seven assembly factors (AFs) regulate and facilitate maturation, but the mechanisms through which they work remain undetermined. Here, we present a series of structures of the immature small subunit (pre-40S) determined by three-dimensional (3D) cryoelectron microscopy with 3D sorting to assess the molecule's heterogeneity. These structures demonstrate an extensive structural heterogeneity of interface AFs that likely regulates subunit joining during 40S maturation. We also present structural models for the beak and the platform, two regions where the low resolution of previous studies did not allow for localization of AFs and the rRNA, respectively. These models are supported by biochemical analyses using point variants and suggest that maturation of the 18S 3' end is regulated by dissociation of the AF Dim1 from the subunit interface, consistent with previous biochemical analyses.
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Date Issued: 2017-02-07
Identifier: FSU_pmch_28111018, 10.1016/j.str.2016.12.011, PMC5314460, 28111018, 28111018, S0969-2126(16)30401-4
Format: Citation

Title: Evolution In A Community Context: Trait Responses To Multiple Species Interactions.
Creator: terHorst, Casey P., Zee, Peter C., Heath, Katy D., Miller, Thomas E., Pastore, Abigail I., Patel, Swati, Schreiber, Sebastian J., Wade, Michael J., Walsh, Matthew R.
Abstract/Description: Species that coexist in diverse natural communities interact in complex ways that alter each other's abundances and affect selection on each other's traits. Consequently, predicting trait evolution in natural communities may require understanding ecological and evolutionary dynamics involving a number of species. In August 2016, the American Society of Naturalists sponsored a symposium to explore evolution in a community context, focusing on microevolutionary processes. Here we provide an...
Show moreSpecies that coexist in diverse natural communities interact in complex ways that alter each other's abundances and affect selection on each other's traits. Consequently, predicting trait evolution in natural communities may require understanding ecological and evolutionary dynamics involving a number of species. In August 2016, the American Society of Naturalists sponsored a symposium to explore evolution in a community context, focusing on microevolutionary processes. Here we provide an introduction to our perspectives on this topic by defining the context and describing some examples of when and how microevolutionary responses to multiple species may differ from evolution in isolation or in two-species communities. We find that indirect ecological and evolutionary effects can result in nonadditive selection and evolution that cannot be predicted from pairwise interactions. Genetic correlations of ecological traits in one species can alter trait evolution and adaptation aswell as the abundances of other species. In general, evolution in multispecies communities can change ecological interactions, which then feed back to future evolutionary changes in ways that depend on these indirect effects. We suggest avenues for future research in this field, including determining the circumstances under which pairwise evolution does not adequately describe evolutionary trajectories.
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Date Issued: 2018-03
Identifier: FSU_libsubv1_wos_000427588400013, 10.1086/695835
Format: Citation

Title: Collective Dispersal Leads To Variance In Fitness And Maintains Offspring Size Variation Within Marine Populations.
Creator: Burgess, Scott C., Snyder, Robin E., Rountree, Barry
Abstract/Description: Variance in fitness is well known to influence the outcome of evolution but is rarely considered in the theory of marine reproductive strategies. In coastal environments, turbulent mesoscale eddies can collect larvae into packets, resulting in collective dispersal. Larvae in packets return to the coast or are lost offshore in groups, producing variance in fitness. Using a Markov process to calculate fixation probabilities for competing phenotypes, we examine the evolution of offspring size...
Show moreVariance in fitness is well known to influence the outcome of evolution but is rarely considered in the theory of marine reproductive strategies. In coastal environments, turbulent mesoscale eddies can collect larvae into packets, resulting in collective dispersal. Larvae in packets return to the coast or are lost offshore in groups, producing variance in fitness. Using a Markov process to calculate fixation probabilities for competing phenotypes, we examine the evolution of offspring size and spawning duration in species with benthic adults and pelagic offspring. The offspring size that provides mothers with the highest mean fitness also generates the greatest variance in fitness, but pairwise invasion plots show that bet-hedging strategies are not evolutionarily stable; maximizing expected fitness correctly predicts the unique evolutionarily stable strategy. Nonetheless, fixation can take a long time. We find that selection to increase spawning duration as a risk avoidance strategy to reduce the negative impacts of stochastic recruitment success can allow multiple offspring sizes to coexist in a population for extended periods. This has two important consequences for offspring size: (1) coexistence occurs over a broader range of sizes and is longer when spawning duration is longer because longer spawning durations reduce variation in fitness and increase the time to fixation, and (2) longer spawning durations can compensate for having a nonoptimal size and even allow less optimal sizes to reach fixation. Collective dispersal and longer spawning durations could effectively maintain offspring size variation even in the absence of good and bad years or locations. Empirical comparisons of offspring size would therefore not always reflect environment-specific differences in the optimal size.
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Date Issued: 2018-03
Identifier: FSU_libsubv1_wos_000427588400006, 10.1086/695879
Format: Citation

Program in Neuroscience (11)	+ -
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