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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: Automatic stage identification of Drosophila egg chamber based on DAPI images.
Creator: Jia, Dongyu, Xu, Qiuping, Xie, Qian, Mio, Washington, Deng, Wu-Min
Abstract/Description: The Drosophila egg chamber, whose development is divided into 14 stages, is a well-established model for developmental biology. However, visual stage determination can be a tedious, subjective and time-consuming task prone to errors. Our study presents an objective, reliable and repeatable automated method for quantifying cell features and classifying egg chamber stages based on DAPI images. The proposed approach is composed of two steps: 1) a feature extraction step and 2) a statistical...
Show moreThe Drosophila egg chamber, whose development is divided into 14 stages, is a well-established model for developmental biology. However, visual stage determination can be a tedious, subjective and time-consuming task prone to errors. Our study presents an objective, reliable and repeatable automated method for quantifying cell features and classifying egg chamber stages based on DAPI images. The proposed approach is composed of two steps: 1) a feature extraction step and 2) a statistical modeling step. The egg chamber features used are egg chamber size, oocyte size, egg chamber ratio and distribution of follicle cells. Methods for determining the on-site of the polytene stage and centripetal migration are also discussed. The statistical model uses linear and ordinal regression to explore the stage-feature relationships and classify egg chamber stages. Combined with machine learning, our method has great potential to enable discovery of hidden developmental mechanisms.
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Date Issued: 2016-01-06
Identifier: FSU_pmch_26732176, 10.1038/srep18850, PMC4702167, 26732176, 26732176, srep18850
Format: Citation

Title: Expression Differentiation Is Constrained to Low-Expression Proteins over Ecological Timescales.
Creator: Margres, Mark J, Wray, Kenneth P, Seavy, Margaret, McGivern, James J, Herrera, Nathanael D, Rokyta, Darin R
Abstract/Description: Protein expression level is one of the strongest predictors of protein sequence evolutionary rate, with high-expression protein sequences evolving at slower rates than low-expression protein sequences largely because of constraints on protein folding and function. Expression evolutionary rates also have been shown to be negatively correlated with expression level across human and mouse orthologs over relatively long divergence times (i.e., ∼100 million years). Long-term evolutionary patterns,...
Show moreProtein expression level is one of the strongest predictors of protein sequence evolutionary rate, with high-expression protein sequences evolving at slower rates than low-expression protein sequences largely because of constraints on protein folding and function. Expression evolutionary rates also have been shown to be negatively correlated with expression level across human and mouse orthologs over relatively long divergence times (i.e., ∼100 million years). Long-term evolutionary patterns, however, often cannot be extrapolated to microevolutionary processes (and vice versa), and whether this relationship holds for traits evolving under directional selection within a single species over ecological timescales (i.e., <5000 years) is unknown and not necessarily expected. Expression is a metabolically costly process, and the expression level of a particular protein is predicted to be a tradeoff between the benefit of its function and the costs of its expression. Selection should drive the expression level of all proteins close to values that maximize fitness, particularly for high-expression proteins because of the increased energetic cost of production. Therefore, stabilizing selection may reduce the amount of standing expression variation for high-expression proteins, and in combination with physiological constraints that may place an upper bound on the range of beneficial expression variation, these constraints could severely limit the availability of beneficial expression variants. To determine whether rapid-expression evolution was restricted to low-expression proteins owing to these constraints on highly expressed proteins over ecological timescales, we compared venom protein expression levels across mainland and island populations for three species of pit vipers. We detected significant differentiation in protein expression levels in two of the three species and found that rapid-expression differentiation was restricted to low-expression proteins. Our results suggest that various constraints on high-expression proteins reduce the availability of beneficial expression variants relative to low-expression proteins, enabling low-expression proteins to evolve and potentially lead to more rapid adaptation.
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Date Issued: 2016-01-01
Identifier: FSU_pmch_26546003, 10.1534/genetics.115.180547, PMC4701091, 26546003, 26546003, genetics.115.180547
Format: Citation

Title: Comparative analysis of glucagonergic cells, glia, and the circumferential marginal zone in the reptilian retina.
Creator: Todd, Levi, Suarez, Lilianna, Squires, Natalie, Zelinka, Christopher Paul, Gribbins, Kevin, Fischer, Andy J
Abstract/Description: Retinal progenitors in the circumferential marginal zone (CMZ) and Müller glia-derived progenitors have been well described for the eyes of fish, amphibians, and birds. However, there is no information regarding a CMZ and the nature of retinal glia in species phylogenetically bridging amphibians and birds. The purpose of this study was to examine the retinal glia and investigate whether a CMZ is present in the eyes of reptilian species. We used immunohistochemical analyses to study retinal...
Show moreRetinal progenitors in the circumferential marginal zone (CMZ) and Müller glia-derived progenitors have been well described for the eyes of fish, amphibians, and birds. However, there is no information regarding a CMZ and the nature of retinal glia in species phylogenetically bridging amphibians and birds. The purpose of this study was to examine the retinal glia and investigate whether a CMZ is present in the eyes of reptilian species. We used immunohistochemical analyses to study retinal glia, neurons that could influence CMZ progenitors, the retinal margin, and the nonpigmented epithelium of ciliary body of garter snakes, queen snakes, anole lizards, snapping turtles, and painted turtles. We compare our observations on reptile eyes to the CMZ and glia of fish, amphibians, and birds. In all species, Sox9, Pax6, and the glucocorticoid receptor are expressed by Müller glia and cells at the retinal margin. However, proliferating cells were found only in the CMZ of turtles and not in the eyes of anoles and snakes. Similar to eyes of chickens, the retinal margin in turtles contains accumulations of GLP1/glucagonergic neurites. We find that filamentous proteins, vimentin and GFAP, are expressed by Müller glia, but have different patterns of subcellular localization in the different species of reptiles. We provide evidence that the reptile retina may contain nonastrocytic inner retinal glial cells, similar to those described in the avian retina. We conclude that the retinal glia, glucagonergic neurons, and CMZ of turtles appear to be most similar to those of fish, amphibians, and birds.
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Date Issued: 2016-01-01
Identifier: FSU_pmch_26053997, 10.1002/cne.23823, PMC4659723, 26053997, 26053997
Format: Citation

Title: ORF33 and ORF38 of Kaposi's Sarcoma-Associated Herpesvirus Interact and Are Required for Optimal Production of Infectious Progeny Viruses.
Creator: Wu, Jian-Jun, Avey, Denis, Li, Wenwei, Gillen, Joseph, Fu, Bishi, Miley, Wendell, Whitby, Denise, Zhu, Fanxiu
Abstract/Description: We recently showed that the interaction between Kaposi's sarcoma-associated herpesvirus (KSHV) tegument proteins ORF33 and ORF45 is crucial for progeny virion production, but the exact functions of KSHV ORF33 during lytic replication were unknown (J. Gillen, W. Li, Q. Liang, D. Avey, J. Wu, F. Wu, J. Myoung, and F. Zhu, J Virol 89:4918-4931, 2015, http://dx.doi.org/10.1128/JVI.02925-14). Therefore, here we investigated the relationship between ORF33 and ORF38, whose counterparts in both alpha...
Show moreWe recently showed that the interaction between Kaposi's sarcoma-associated herpesvirus (KSHV) tegument proteins ORF33 and ORF45 is crucial for progeny virion production, but the exact functions of KSHV ORF33 during lytic replication were unknown (J. Gillen, W. Li, Q. Liang, D. Avey, J. Wu, F. Wu, J. Myoung, and F. Zhu, J Virol 89:4918-4931, 2015, http://dx.doi.org/10.1128/JVI.02925-14). Therefore, here we investigated the relationship between ORF33 and ORF38, whose counterparts in both alpha- and betaherpesviruses interact with each other. Using specific monoclonal antibodies, we found that both proteins are expressed during the late lytic cycle with similar kinetics and that both are present in mature virions as components of the tegument. Furthermore, we confirmed that ORF33 interacts with ORF38. Interestingly, we observed that ORF33 tightly associates with the capsid, whereas ORF38 associates with the envelope. We generated ORF33-null, ORF38-null, and double-null mutants and found that these mutants apparently have identical phenotypes: the mutations caused no apparent effect on viral gene expression but reduced the yield of progeny virion by about 10-fold. The progeny virions also lack certain virion component proteins, including ORF45. During viral lytic replication, the virions associate with cytoplasmic vesicles. We also observed that ORF38 associates with the membranes of vesicles and colocalizes with the Golgi membrane or early endosome membrane. Further analyses of ORF33/ORF38 mutants revealed the reduced production of virion-containing vesicles, suggesting that ORF33 and ORF38 are involved in the transport of newly assembled viral particles into cytoplasmic vesicles, a process important for viral maturation and egress. Herpesvirus assembly is an essential step in virus propagation that leads to the generation of progeny virions. It is a complicated process that depends on the delicate regulation of interactions among virion proteins. We previously revealed an essential role of ORF45-ORF33 binding for virus assembly. Here, we report that ORF33 and its binding partner, ORF38, are required for infectious virus production due to their important role in the tegumentation process. Moreover, we found that both ORF33 and ORF38 are involved in the transportation of virions through vesicles during maturation and egress. Our results provide new insights into the important roles of ORF33 and ORF38 during viral assembly, a process critical for virus propagation that is intimately linked to KSHV pathobiology.
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Date Issued: 2015-12-04
Identifier: FSU_pmch_26637455, 10.1128/JVI.02738-15, PMC4734004, 26637455, 26637455, JVI.02738-15
Format: Citation

Title: Emergence and evolution of Zfp36l3.
Creator: Gingerich, Timothy J, Stumpo, Deborah J, Lai, Wi S, Randall, Thomas A, Steppan, Scott J, Blackshear, Perry J
Abstract/Description: In most mammals, the Zfp36 gene family consists of three conserved members, with a fourth member, Zfp36l3, present only in rodents. The ZFP36 proteins regulate post-transcriptional gene expression at the level of mRNA stability in organisms from humans to yeasts, and appear to be expressed in all major groups of eukaryotes. In Mus musculus, Zfp36l3 expression is limited to the placenta and yolk sac, and is important for overall fecundity. We sequenced the Zfp36l3 gene from more than 20...
Show moreIn most mammals, the Zfp36 gene family consists of three conserved members, with a fourth member, Zfp36l3, present only in rodents. The ZFP36 proteins regulate post-transcriptional gene expression at the level of mRNA stability in organisms from humans to yeasts, and appear to be expressed in all major groups of eukaryotes. In Mus musculus, Zfp36l3 expression is limited to the placenta and yolk sac, and is important for overall fecundity. We sequenced the Zfp36l3 gene from more than 20 representative species, from members of the Muridae, Cricetidae and Nesomyidae families. Zfp36l3 was not present in Dipodidae, or any families that branched earlier, indicating that this gene is exclusive to the Muroidea superfamily. We provide evidence that Zfp36l3 arose by retrotransposition of an mRNA encoded by a related gene, Zfp36l2 into an ancestral rodent X chromosome. Zfp36l3 has evolved rapidly since its origin, and numerous modifications have developed, including variations in start codon utilization, de novo intron formation by mechanisms including a nested retrotransposition, and the insertion of distinct repetitive regions. One of these repeat regions, a long alanine rich-sequence, is responsible for the full-time cytoplasmic localization of Mus musculus ZFP36L3. In contrast, this repeat sequence is lacking in Peromyscus maniculatus ZFP36L3, and this protein contains a novel nuclear export sequence that controls shuttling between the nucleus and cytosol. Zfp36l3 is an example of a recently acquired, rapidly evolving gene, and its various orthologues illustrate several different mechanisms by which new genes emerge and evolve.
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Date Issued: 2016-01-01
Identifier: FSU_pmch_26493225, 10.1016/j.ympev.2015.10.016, PMC4663143, 26493225, 26493225, S1055-7903(15)00319-X
Format: Citation

Title: IgE epitope proximity determines immune complex shape and effector cell activation capacity.
Creator: Gieras, Anna, Linhart, Birgit, Roux, Kenneth H, Dutta, Moumita, Khodoun, Marat, Zafred, Domen, Cabauatan, Clarissa R, Lupinek, Christian, Weber, Milena, Focke-Tejkl, Margarete,...
Show moreGieras, Anna, Linhart, Birgit, Roux, Kenneth H, Dutta, Moumita, Khodoun, Marat, Zafred, Domen, Cabauatan, Clarissa R, Lupinek, Christian, Weber, Milena, Focke-Tejkl, Margarete, Keller, Walter, Finkelman, Fred D, Valenta, Rudolf
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Abstract/Description: IgE-allergen complexes induce mast cell and basophil activation and thus immediate allergic inflammation. They are also important for IgE-facilitated allergen presentation to T cells by antigen-presenting cells. To investigate whether the proximity of IgE binding sites on an allergen affects immune complex shape and subsequent effector cell activation in vitro and in vivo. We constructed artificial allergens by grafting IgE epitopes in different numbers and proximity onto a scaffold protein....
Show moreIgE-allergen complexes induce mast cell and basophil activation and thus immediate allergic inflammation. They are also important for IgE-facilitated allergen presentation to T cells by antigen-presenting cells. To investigate whether the proximity of IgE binding sites on an allergen affects immune complex shape and subsequent effector cell activation in vitro and in vivo. We constructed artificial allergens by grafting IgE epitopes in different numbers and proximity onto a scaffold protein. The shape of immune complexes formed between artificial allergens and the corresponding IgE was studied by negative-stain electron microscopy. Allergenic activity was determined using basophil activation assays. Mice were primed with IgE, followed by injection of artificial allergens to evaluate their in vivo allergenic activity. Severity of systemic anaphylaxis was measured by changes in body temperature. We could demonstrate simultaneous binding of 4 IgE antibodies in close vicinity to each other. The proximity of IgE binding sites on allergens influenced the shape of the resulting immune complexes and the magnitude of effector cell activation and in vivo inflammation. Our results demonstrate that the proximity of IgE epitopes on an allergen affects its allergenic activity. We thus identified a novel mechanism by which IgE-allergen complexes regulate allergic inflammation. This mechanism should be important for allergy and other immune complex-mediated diseases.
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Date Issued: 2016-05-01
Identifier: FSU_pmch_26684291, 10.1016/j.jaci.2015.08.055, PMC4890651, 26684291, 26684291, S0091-6749(15)01422-0
Format: Citation

Title: Do Sperm Really Compete And Do Eggs Ever Have A Choice? Adult Distribution And Gamete Mixing Influence Sexual Selection, Sexual Conflict, And The Evolution Of Gamete Recognition Proteins In The Sea.
Creator: Levitan, Don R.
Abstract/Description: The evolution of gametic compatibility and the effectiveness of compatibility, within and across species, depend on whether sperm from different males directly compete for an egg and whether eggs ever have a choice. Direct sperm competition and egg choice depend on whether sperm from different males arrive at an egg in the brief interval between first sperm contact and fertilization. Although this process may be relevant for all sexually reproducing organisms, it is most easily examined in...
Show moreThe evolution of gametic compatibility and the effectiveness of compatibility, within and across species, depend on whether sperm from different males directly compete for an egg and whether eggs ever have a choice. Direct sperm competition and egg choice depend on whether sperm from different males arrive at an egg in the brief interval between first sperm contact and fertilization. Although this process may be relevant for all sexually reproducing organisms, it is most easily examined in aquatic external fertilizers. When sperm are released into the sea, packets of seawater at the spatial scale relevant to single eggs might contain sperm from only one male, eliminating the potential for direct sperm competition and egg choice. Field experiments and a simple heuristic model examining the degree of sperm mixing for the sea urchin Strongylocentrotus franciscanus indicate that degree of competitive fertilization depends on density and distribution of competing males and that the nature of this competition influences whether males with high- or low-affinity gamete recognition protein genotypes have higher reproductive success. These results provide a potential explanation for the generation and maintenance of variation in gamete recognition proteins and why effectiveness of conspecific sperm precedence can be density dependent.
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Date Issued: 2018-01
Identifier: FSU_libsubv1_wos_000418197900009, 10.1086/694780
Format: Citation

Title: Stereocilia-staircase spacing is influenced by myosin III motors and their cargos espin-1 and espin-like.
Creator: Ebrahim, Seham, Avenarius, Matthew R, Grati, M'hamed, Krey, Jocelyn F, Windsor, Alanna M, Sousa, Aurea D, Ballesteros, Angela, Cui, Runjia, Millis, Bryan A, Salles, Felipe T,...
Show moreEbrahim, Seham, Avenarius, Matthew R, Grati, M'hamed, Krey, Jocelyn F, Windsor, Alanna M, Sousa, Aurea D, Ballesteros, Angela, Cui, Runjia, Millis, Bryan A, Salles, Felipe T, Baird, Michelle A, Davidson, Michael W, Jones, Sherri M, Choi, Dongseok, Dong, Lijin, Raval, Manmeet H, Yengo, Christopher M, Barr-Gillespie, Peter G, Kachar, Bechara
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Abstract/Description: Hair cells tightly control the dimensions of their stereocilia, which are actin-rich protrusions with graded heights that mediate mechanotransduction in the inner ear. Two members of the myosin-III family, MYO3A and MYO3B, are thought to regulate stereocilia length by transporting cargos that control actin polymerization at stereocilia tips. We show that eliminating espin-1 (ESPN-1), an isoform of ESPN and a myosin-III cargo, dramatically alters the slope of the stereocilia staircase in a...
Show moreHair cells tightly control the dimensions of their stereocilia, which are actin-rich protrusions with graded heights that mediate mechanotransduction in the inner ear. Two members of the myosin-III family, MYO3A and MYO3B, are thought to regulate stereocilia length by transporting cargos that control actin polymerization at stereocilia tips. We show that eliminating espin-1 (ESPN-1), an isoform of ESPN and a myosin-III cargo, dramatically alters the slope of the stereocilia staircase in a subset of hair cells. Furthermore, we show that espin-like (ESPNL), primarily present in developing stereocilia, is also a myosin-III cargo and is essential for normal hearing. ESPN-1 and ESPNL each bind MYO3A and MYO3B, but differentially influence how the two motors function. Consequently, functional properties of different motor-cargo combinations differentially affect molecular transport and the length of actin protrusions. This mechanism is used by hair cells to establish the required range of stereocilia lengths within a single cell.
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Date Issued: 2016-03-01
Identifier: FSU_pmch_26926603, 10.1038/ncomms10833, PMC4773517, 26926603, 26926603, ncomms10833
Format: Citation

Title: Quantitative Multiscale Cell Imaging in Controlled 3D Microenvironments.
Creator: Welf, Erik S, Driscoll, Meghan K, Dean, Kevin M, Schäfer, Claudia, Chu, Jun, Davidson, Michael W, Lin, Michael Z, Danuser, Gaudenz, Fiolka, Reto
Abstract/Description: The microenvironment determines cell behavior, but the underlying molecular mechanisms are poorly understood because quantitative studies of cell signaling and behavior have been challenging due to insufficient spatial and/or temporal resolution and limitations on microenvironmental control. Here we introduce microenvironmental selective plane illumination microscopy (meSPIM) for imaging and quantification of intracellular signaling and submicrometer cellular structures as well as large-scale...
Show moreThe microenvironment determines cell behavior, but the underlying molecular mechanisms are poorly understood because quantitative studies of cell signaling and behavior have been challenging due to insufficient spatial and/or temporal resolution and limitations on microenvironmental control. Here we introduce microenvironmental selective plane illumination microscopy (meSPIM) for imaging and quantification of intracellular signaling and submicrometer cellular structures as well as large-scale cell morphological and environmental features. We demonstrate the utility of this approach by showing that the mechanical properties of the microenvironment regulate the transition of melanoma cells from actin-driven protrusion to blebbing, and we present tools to quantify how cells manipulate individual collagen fibers. We leverage the nearly isotropic resolution of meSPIM to quantify the local concentration of actin and phosphatidylinositol 3-kinase signaling on the surfaces of cells deep within 3D collagen matrices and track the many small membrane protrusions that appear in these more physiologically relevant environments.
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Date Issued: 2016-02-22
Identifier: FSU_pmch_26906741, 10.1016/j.devcel.2016.01.022, PMC4784259, 26906741, 26906741, S1534-5807(16)00089-7
Format: Citation

Title: The functional significance of the last 5 residues of the C-terminus of cardiac troponin I.
Creator: Gilda, Jennifer E, Xu, Qian, Martinez, Margaret E, Nguyen, Susan T, Chase, P Bryant, Gomes, Aldrin V
Abstract/Description: The C-terminal region of cardiac troponin I (cTnI) is known to be important in cardiac function, as removal of the last 17 C-terminal residues of human cTnI has been associated with myocardial stunning. To investigate the C-terminal region of cTnI, three C-terminal deletion mutations in human cTnI were generated: Δ1 (deletion of residue 210), Δ3 (deletion of residues 208-210), and Δ5 (deletion of residues 206-210). Mammalian two-hybrid studies showed that the interactions between cTnI mutants...
Show moreThe C-terminal region of cardiac troponin I (cTnI) is known to be important in cardiac function, as removal of the last 17 C-terminal residues of human cTnI has been associated with myocardial stunning. To investigate the C-terminal region of cTnI, three C-terminal deletion mutations in human cTnI were generated: Δ1 (deletion of residue 210), Δ3 (deletion of residues 208-210), and Δ5 (deletion of residues 206-210). Mammalian two-hybrid studies showed that the interactions between cTnI mutants and cardiac troponin C (cTnC) or cardiac troponin T (cTnT) were impaired in Δ3 and Δ5 mutants when compared to wild-type cTnI. Troponin complexes containing 2-[4'-(iodoacetamido) anilino] naphthalene-6-sulfonic acid (IAANS) labeled cTnC showed that the troponin complex containing cTnI Δ5 had a small increase in Ca(2+) affinity (P < 0.05); while the cTnI Δ1- and Δ3 troponin complexes showed no difference in Ca(2+) affinity when compared to wild-type troponin. In vitro motility assays showed that all truncation mutants had increased Ca(2+) dependent motility relative to wild-type cTnI. These results suggest that the last 5 C-terminal residues of cTnI influence the binding of cTnI with cTnC and cTnT and affect the Ca(2+) dependence of filament sliding, and demonstrate the importance of this region of cTnI.
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Date Issued: 2016-07-01
Identifier: FSU_pmch_26919894, 10.1016/j.abb.2016.02.023, PMC4899223, 26919894, 26919894, S0003-9861(16)30042-X
Format: Citation

Title: An improved smaller biotin ligase for BioID proximity labeling.
Creator: Kim, Dae In, Jensen, Samuel C, Noble, Kyle A, Kc, Birendra, Roux, Kenneth H, Motamedchaboki, Khatereh, Roux, Kyle J
Abstract/Description: The BioID method uses a promiscuous biotin ligase to detect protein-protein associations as well as proximate proteins in living cells. Here we report improvements to the BioID method centered on BioID2, a substantially smaller promiscuous biotin ligase. BioID2 enables more-selective targeting of fusion proteins, requires less biotin supplementation, and exhibits enhanced labeling of proximate proteins. Thus BioID2 improves the efficiency of screening for protein-protein associations. We also...
Show moreThe BioID method uses a promiscuous biotin ligase to detect protein-protein associations as well as proximate proteins in living cells. Here we report improvements to the BioID method centered on BioID2, a substantially smaller promiscuous biotin ligase. BioID2 enables more-selective targeting of fusion proteins, requires less biotin supplementation, and exhibits enhanced labeling of proximate proteins. Thus BioID2 improves the efficiency of screening for protein-protein associations. We also demonstrate that the biotinylation range of BioID2 can be considerably modulated using flexible linkers, thus enabling application-specific adjustment of the biotin-labeling radius.
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Date Issued: 2016-04-15
Identifier: FSU_pmch_26912792, 10.1091/mbc.E15-12-0844, PMC4831873, 26912792, 26912792, mbc.E15-12-0844
Format: Citation

Title: RNA helicase Belle/DDX3 regulates transgene expression in Drosophila.
Creator: Lo, Pang-Kuo, Huang, Yi-Chun, Poulton, John S, Leake, Nicholas, Palmer, William H, Vera, Daniel, Xie, Gengqiang, Klusza, Stephen, Deng, Wu-Min
Abstract/Description: Belle (Bel), the Drosophila homolog of the yeast DEAD-box RNA helicase DED1 and human DDX3, has been shown to be required for oogenesis and female fertility. Here we report a novel role of Bel in regulating the expression of transgenes. Abrogation of Bel by mutations or RNAi induces silencing of a variety of P-element-derived transgenes. This silencing effect depends on downregulation of their RNA levels. Our genetic studies have revealed that the RNA helicase Spindle-E (Spn-E), a nuage RNA...
Show moreBelle (Bel), the Drosophila homolog of the yeast DEAD-box RNA helicase DED1 and human DDX3, has been shown to be required for oogenesis and female fertility. Here we report a novel role of Bel in regulating the expression of transgenes. Abrogation of Bel by mutations or RNAi induces silencing of a variety of P-element-derived transgenes. This silencing effect depends on downregulation of their RNA levels. Our genetic studies have revealed that the RNA helicase Spindle-E (Spn-E), a nuage RNA helicase that plays a crucial role in regulating RNA processing and PIWI-interacting RNA (piRNA) biogenesis in germline cells, is required for loss-of-bel-induced transgene silencing. Conversely, Bel abrogation alleviates the nuage-protein mislocalization phenotype in spn-E mutants, suggesting a competitive relationship between these two RNA helicases. Additionally, disruption of the chromatin remodeling factor Mod(mdg4) or the microRNA biogenesis enzyme Dicer-1 (Dcr-1) also alleviates the transgene-silencing phenotypes in bel mutants, suggesting the involvement of chromatin remodeling and microRNA biogenesis in loss-of-bel-induced transgene silencing. Finally we show that genetic inhibition of Bel function leads to de novo generation of piRNAs from the transgene region inserted in the genome, suggesting a potential piRNA-dependent mechanism that may mediate transgene silencing as Bel function is inhibited.
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Date Issued: 2016-04-01
Identifier: FSU_pmch_26900887, 10.1016/j.ydbio.2016.02.014, PMC4814335, 26900887, 26900887, S0012-1606(15)30107-X
Format: Citation

Title: Influence of ATM-Mediated DNA Damage Response on Genomic Variation in Human Induced Pluripotent Stem Cells.
Creator: Lu, Junjie, Li, Hu, Baccei, Anna, Sasaki, Takayo, Gilbert, David M, Lerou, Paul H
Abstract/Description: Genome instability is a potential limitation to the research and therapeutic application of induced pluripotent stem cells (iPSCs). Observed genomic variations reflect the combined activities of DNA damage, cellular DNA damage response (DDR), and selection pressure in culture. To understand the contribution of DDR on the distribution of copy number variations (CNVs) in iPSCs, we mapped CNVs of iPSCs with mutations in the central DDR gene ATM onto genome organization landscapes defined by...
Show moreGenome instability is a potential limitation to the research and therapeutic application of induced pluripotent stem cells (iPSCs). Observed genomic variations reflect the combined activities of DNA damage, cellular DNA damage response (DDR), and selection pressure in culture. To understand the contribution of DDR on the distribution of copy number variations (CNVs) in iPSCs, we mapped CNVs of iPSCs with mutations in the central DDR gene ATM onto genome organization landscapes defined by genome-wide replication timing profiles. We show that following reprogramming the early and late replicating genome is differentially affected by CNVs in ATM-deficient iPSCs relative to wild-type iPSCs. Specifically, the early replicating regions had increased CNV losses during retroviral (RV) reprogramming. This differential CNV distribution was not present after later passage or after episomal reprogramming. Comparison of different reprogramming methods in the setting of defective DDR reveals unique vulnerability of early replicating open chromatin to RV vectors.
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Date Issued: 2016-05-01
Identifier: FSU_pmch_26935587, 10.1089/scd.2015.0393, PMC4854209, 26935587, 26935587
Format: Citation

Title: Zika Virus Infects Human Cortical Neural Progenitors and Attenuates Their Growth.
Creator: Tang, Hengli, Hammack, Christy, Ogden, Sarah C, Wen, Zhexing, Qian, Xuyu, Li, Yujing, Yao, Bing, Shin, Jaehoon, Zhang, Feiran, Lee, Emily M, Christian, Kimberly M, Didier, Ruth...
Show moreTang, Hengli, Hammack, Christy, Ogden, Sarah C, Wen, Zhexing, Qian, Xuyu, Li, Yujing, Yao, Bing, Shin, Jaehoon, Zhang, Feiran, Lee, Emily M, Christian, Kimberly M, Didier, Ruth A, Jin, Peng, Song, Hongjun, Ming, Guo-Li
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Abstract/Description: The suspected link between infection by Zika virus (ZIKV), a re-emerging flavivirus, and microcephaly is an urgent global health concern. The direct target cells of ZIKV in the developing human fetus are not clear. Here we show that a strain of the ZIKV, MR766, serially passaged in monkey and mosquito cells efficiently infects human neural progenitor cells (hNPCs) derived from induced pluripotent stem cells. Infected hNPCs further release infectious ZIKV particles. Importantly, ZIKV infection...
Show moreThe suspected link between infection by Zika virus (ZIKV), a re-emerging flavivirus, and microcephaly is an urgent global health concern. The direct target cells of ZIKV in the developing human fetus are not clear. Here we show that a strain of the ZIKV, MR766, serially passaged in monkey and mosquito cells efficiently infects human neural progenitor cells (hNPCs) derived from induced pluripotent stem cells. Infected hNPCs further release infectious ZIKV particles. Importantly, ZIKV infection increases cell death and dysregulates cell-cycle progression, resulting in attenuated hNPC growth. Global gene expression analysis of infected hNPCs reveals transcriptional dysregulation, notably of cell-cycle-related pathways. Our results identify hNPCs as a direct ZIKV target. In addition, we establish a tractable experimental model system to investigate the impact and mechanism of ZIKV on human brain development and provide a platform to screen therapeutic compounds.
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Date Issued: 2016-05-05
Identifier: FSU_pmch_26952870, 10.1016/j.stem.2016.02.016, PMC5299540, 26952870, 26952870, S1934-5909(16)00106-5
Format: Citation

Title: Mayans: a Y chromosome perspective..
Creator: Perez-Benedico, David, La Salvia, Joel, Zeng, Zhaoshu, Herrera, Giselle A, Garcia-Bertrand, Ralph, Herrera, Rene J
Abstract/Description: In spite of the wealth of available cultural and archeological information as well as general interest in the Mayans, little is known about their genetics. In this study, for the first time, we attempt to alleviate this lacuna of knowledge by comprehensively investigating the Y chromosome composition of contemporary Mayan populations throughout their domain. To accomplish this, five geographically targeted and ethnically distinct Mayan populations are investigated using Y-SNP and Y-STR...
Show moreIn spite of the wealth of available cultural and archeological information as well as general interest in the Mayans, little is known about their genetics. In this study, for the first time, we attempt to alleviate this lacuna of knowledge by comprehensively investigating the Y chromosome composition of contemporary Mayan populations throughout their domain. To accomplish this, five geographically targeted and ethnically distinct Mayan populations are investigated using Y-SNP and Y-STR markers. overall, the Mayan populations as a group are highly homogeneous, basically made up of only two autochthonous haplogroups, Q1a2a1a1*-M3 and Q1a2a1*-L54. Although the Y-STR data illustrates diversity, this diversity, for the most part, is uniformly distributed among geographically distant Mayan populations. Similar haplotypes among populations, abundance of singletons and absence of population partitioning within networks among Mayan populations suggest recent population expansion and substantial gene flow within the Mayan dominion, possibly due to the development of agriculture, the establishment of interacting City-State systems and commerce.
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Date Issued: 2016-08-01
Identifier: FSU_pmch_26956252, 10.1038/ejhg.2016.18, PMC4989206, 26956252, 26956252, ejhg201618
Format: Citation

Title: The incretin hormone glucagon-like peptide 1 increases mitral cell excitability by decreasing conductance of a voltage-dependent potassium channel.
Creator: Thiebaud, Nicolas, Llewellyn-Smith, Ida J, Gribble, Fiona, Reimann, Frank, Trapp, Stefan, Fadool, Debra Ann
Abstract/Description: The gut hormone called glucagon-like peptide 1 (GLP-1) is a strong moderator of energy homeostasis and communication between the peripheral organs and the brain. GLP-1 signalling occurs in the brain; using a newly developed genetic reporter line of mice, we have discovered GLP-synthesizing cells in the olfactory bulb. GLP-1 increases the firing frequency of neurons (mitral cells) that encode olfactory information by decreasing activity of voltage-dependent K channels (Kv1.3). Modifying GLP-1...
Show moreThe gut hormone called glucagon-like peptide 1 (GLP-1) is a strong moderator of energy homeostasis and communication between the peripheral organs and the brain. GLP-1 signalling occurs in the brain; using a newly developed genetic reporter line of mice, we have discovered GLP-synthesizing cells in the olfactory bulb. GLP-1 increases the firing frequency of neurons (mitral cells) that encode olfactory information by decreasing activity of voltage-dependent K channels (Kv1.3). Modifying GLP-1 levels, either therapeutically or following the ingestion of food, could alter the excitability of neurons in the olfactory bulb in a nutrition or energy state-dependent manner to influence olfactory detection or metabolic sensing. The results of the present study uncover a new function for an olfactory bulb neuron (deep short axon cells, Cajal cells) that could be capable of modifying mitral cell activity through the release of GLP-1. This might be of relevance for the action of GLP-1 mimetics now widely used in the treatment of diabetes. The olfactory system is intricately linked with the endocrine system where it may serve as a detector of the internal metabolic state or energy homeostasis in addition to its classical function as a sensor of external olfactory information. The recent development of transgenic mGLU-yellow fluorescent protein mice that express a genetic reporter under the control of the preproglucagon reporter suggested the presence of the gut hormone, glucagon-like peptide (GLP-1), in deep short axon cells (Cajal cells) of the olfactory bulb and its neuromodulatory effect on mitral cell (MC) first-order neurons. A MC target for the peptide was determined using GLP-1 receptor binding assays, immunocytochemistry for the receptor and injection of fluorescence-labelled GLP-1 analogue exendin-4. Using patch clamp recording of olfactory bulb slices in the whole-cell configuration, we report that GLP-1 and its stable analogue exendin-4 increase the action potential firing frequency of MCs by decreasing the interburst interval rather than modifying the action potential shape, train length or interspike interval. GLP-1 decreases Kv1.3 channel contribution to outward currents in voltage clamp recordings as determined by pharmacological blockade of Kv1.3 or utilizing mice with Kv1.3 gene-targeted deletion as a negative control. Because fluctuations in GLP-1 concentrations monitored by the olfactory bulb can modify the firing frequency of MCs, olfactory coding could change depending upon nutritional or physiological state. As a regulator of neuronal activity, GLP-1 or its analogue may comprise a new metabolic factor with a potential therapeutic target in the olfactory bulb (i.e. via intranasal delivery) for controlling an imbalance in energy homeostasis.
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Date Issued: 2016-05-15
Identifier: FSU_pmch_26931093, 10.1113/JP272322, PMC4865572, 26931093, 26931093
Format: Citation

Title: Genetic Dissection of Dual Roles for the Transcription Factor six7 in Photoreceptor Development and Patterning in Zebrafish.
Creator: Sotolongo-Lopez, Mailin, Alvarez-Delfin, Karen, Saade, Carole J, Vera, Daniel L, Fadool, James M
Abstract/Description: The visual system of a particular species is highly adapted to convey detailed ecological and behavioral information essential for survival. The consequences of structural mutations of opsins upon spectral sensitivity and environmental adaptation have been studied in great detail, but lacking is knowledge of the potential influence of alterations in gene regulatory networks upon the diversity of cone subtypes and the variation in the ratio of rods and cones observed in numerous diurnal and...
Show moreThe visual system of a particular species is highly adapted to convey detailed ecological and behavioral information essential for survival. The consequences of structural mutations of opsins upon spectral sensitivity and environmental adaptation have been studied in great detail, but lacking is knowledge of the potential influence of alterations in gene regulatory networks upon the diversity of cone subtypes and the variation in the ratio of rods and cones observed in numerous diurnal and nocturnal species. Exploiting photoreceptor patterning in cone-dominated zebrafish, we uncovered two independent mechanisms by which the sine oculis homeobox homolog 7 (six7) regulates photoreceptor development. In a genetic screen, we isolated the lots-of-rods-junior (ljrp23ahub) mutation that resulted in an increased number and uniform distribution of rods in otherwise normal appearing larvae. Sequence analysis, genome editing using TALENs and knockdown strategies confirm ljrp23ahub as a hypomorphic allele of six7, a teleost orthologue of six3, with known roles in forebrain patterning and expression of opsins. Based on the lack of predicted protein-coding changes and a deletion of a conserved element upstream of the transcription start site, a cis-regulatory mutation is proposed as the basis of the reduced expression of six7 in ljrp23ahub. Comparison of the phenotypes of the hypomorphic and knock-out alleles provides evidence of two independent roles in photoreceptor development. EdU and PH3 labeling show that the increase in rod number is associated with extended mitosis of photoreceptor progenitors, and TUNEL suggests that the lack of green-sensitive cones is the result of cell death of the cone precursor. These data add six7 to the small but growing list of essential genes for specification and patterning of photoreceptors in non-mammalian vertebrates, and highlight alterations in transcriptional regulation as a potential source of photoreceptor variation across species.
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Date Issued: 2016-04-08
Identifier: FSU_pmch_27058886, 10.1371/journal.pgen.1005968, PMC4825938, 27058886, 27058886, PGENETICS-D-15-02805
Format: Citation

Title: Kaposi's Sarcoma-Associated Herpesvirus Inhibitor of cGAS (KicGAS), Encoded by ORF52, Is an Abundant Tegument Protein and Is Required for Production of Infectious Progeny Viruses.
Creator: Li, Wenwei, Avey, Denis, Fu, Bishi, Wu, Jian-Jun, Ma, Siming, Liu, Xia, Zhu, Fanxiu
Abstract/Description: Although Kaposi's sarcoma-associated herpesvirus (KSHV) ORF52 (also known as KSHV inhibitor of cGAS [KicGAS]) has been detected in purified virions, the roles of this protein during KSHV replication have not been characterized. Using specific monoclonal antibodies, we revealed that ORF52 displays true late gene expression kinetics and confirmed its cytoplasmic localization in both transfected and KSHV-infected cells. We demonstrated that ORF52 comigrates with other known virion proteins...
Show moreAlthough Kaposi's sarcoma-associated herpesvirus (KSHV) ORF52 (also known as KSHV inhibitor of cGAS [KicGAS]) has been detected in purified virions, the roles of this protein during KSHV replication have not been characterized. Using specific monoclonal antibodies, we revealed that ORF52 displays true late gene expression kinetics and confirmed its cytoplasmic localization in both transfected and KSHV-infected cells. We demonstrated that ORF52 comigrates with other known virion proteins following sucrose gradient centrifugation. We also determined that ORF52 resides inside the viral envelope and remains partially associated with capsid when extracellular virions are treated with various detergents and/or salts. There results indicate that ORF52 is a tegument protein abundantly present in extracellular virions. To characterize the roles of ORF52 in the KSHV life cycle, we engineered a recombinant KSHV ORF52-null mutant virus and found that loss of ORF52 results in reduced virion production and a further defect in infectivity. Upon analysis of the virion composition of ORF52-null viral particles, we observed a decrease in the incorporation of ORF45, as well as other tegument proteins, suggesting that ORF52 is important for the packaging of other virion proteins. In summary, our results indicate that, in addition to its immune evasion function, KSHV ORF52 is required for the optimal production of infectious virions, likely due to its roles in virion assembly as a tegument protein. The tegument proteins of herpesviruses, including Kaposi's sarcoma-associated herpesvirus (KSHV), play key roles in the viral life cycle. Each of the three subfamilies of herpesviruses (alpha, beta, and gamma) encode unique tegument proteins with specialized functions. We recently found that one such gammaherpesvirus-specific protein, ORF52, has an important role in immune evasion during KSHV primary infection, through inhibition of the host cytosolic DNA sensing pathway. In this report, we further characterize ORF52 as a tegument protein with vital roles during KSHV lytic replication. We found that ORF52 is important for the production of infectious viral particles, likely through its role in virus assembly, a critical process for KSHV replication and pathogenesis. More comprehensive investigation of the functions of tegument proteins and their roles in viral replication may reveal novel targets for therapeutic interventions against KSHV-associated diseases.
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Date Issued: 2016-05-12
Identifier: FSU_pmch_27009954, 10.1128/JVI.02675-15, PMC4934757, 27009954, 27009954, JVI.02675-15
Format: Citation

Title: Discovery of a Coregulatory Interaction between Kaposi's Sarcoma-Associated Herpesvirus ORF45 and the Viral Protein Kinase ORF36.
Creator: Avey, Denis, Tepper, Sarah, Pifer, Benjamin, Bahga, Amritpal, Williams, Hunter, Gillen, Joseph, Li, Wenwei, Ogden, Sarah, Zhu, Fanxiu
Abstract/Description: Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent of three human malignancies. KSHV ORF36 encodes a serine/threonine viral protein kinase, which is conserved throughout all herpesviruses. Although several studies have identified the viral and cellular substrates of conserved herpesvirus protein kinases (CHPKs), the precise functions of KSHV ORF36 during lytic replication remain elusive. Here, we report that ORF36 interacts with another lytic protein, ORF45, in a manner...
Show moreKaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent of three human malignancies. KSHV ORF36 encodes a serine/threonine viral protein kinase, which is conserved throughout all herpesviruses. Although several studies have identified the viral and cellular substrates of conserved herpesvirus protein kinases (CHPKs), the precise functions of KSHV ORF36 during lytic replication remain elusive. Here, we report that ORF36 interacts with another lytic protein, ORF45, in a manner dependent on ORF36 kinase activity. We mapped the regions of ORF36 and ORF45 involved in the binding. Their association appears to be mediated by electrostatic interactions, since deletion of either the highly basic N terminus of ORF36 or an acidic patch of ORF45 abolished the binding. In addition, the dephosphorylation of ORF45 protein dramatically reduced its association with ORF36. Importantly, ORF45 enhances both the stability and kinase activity of ORF36. Consistent with previous studies of CHPK homologs, we detected ORF36 protein in extracellular virions. To investigate the roles of ORF36 in the context of KSHV lytic replication, we used bacterial artificial chromosome mutagenesis to engineer both ORF36-null and kinase-dead mutants. We found that ORF36-null/mutant virions are moderately defective in viral particle production and are further deficient in primary infection. In summary, our results uncover a functionally important interaction between ORF36 and ORF45 and indicate a significant role of ORF36 in the production of infectious progeny virions. Kaposi's sarcoma-associated herpesvirus (KSHV) is a human tumor virus with a significant public health burden. KSHV ORF36 encodes a serine/threonine viral protein kinase, whose functions throughout the viral life cycle have not been elucidated. Here, we report that ORF36 interacts with another KSHV protein, ORF45. We mapped the regions of ORF36 and ORF45 involved in their association and further characterized the consequences of this interaction. We engineered ORF36 mutant viruses in order to investigate the functional roles of ORF36 in the context of KSHV lytic replication, and we confirmed that ORF36 is a component of KSHV virions. Moreover, we found that ORF36 mutants are defective in virion production and primary infection. In summary, we discovered and characterized a functionally important interaction between KSHV ORF36 and ORF45, and our results suggest a significant role of ORF36 in the production of infectious progeny virions, a process critical for KSHV pathogenesis.
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Date Issued: 2016-06-10
Identifier: FSU_pmch_27099309, 10.1128/JVI.00516-16, PMC4907238, 27099309, 27099309, JVI.00516-16
Format: Citation

Title: Anatomy and osteohistology of the basal hadrosaurid dinosaur Eotrachodon from the uppermost Santonian (Cretaceous) of southern Appalachia.
Creator: Prieto-Márquez, Albert, Erickson, Gregory M, Ebersole, Jun A
Abstract/Description: The cranial and postcranial anatomy of the basal hadrosaurid dinosaur Eotrachodon orientalis, from the uppermost Santonian of southern Appalachia (southeastern U.S.A.), is described in detail. This animal is the only known pre-Campanian non-lambeosaurine hadrosaurid, and the most complete hadrosauroid known from Appalachia. E. orientalis possesses a mosaic of plesiomorphic and derived characters in the context of Hadrosauroidea. Characters shared with basal hadrosauroids include a short and...
Show moreThe cranial and postcranial anatomy of the basal hadrosaurid dinosaur Eotrachodon orientalis, from the uppermost Santonian of southern Appalachia (southeastern U.S.A.), is described in detail. This animal is the only known pre-Campanian non-lambeosaurine hadrosaurid, and the most complete hadrosauroid known from Appalachia. E. orientalis possesses a mosaic of plesiomorphic and derived characters in the context of Hadrosauroidea. Characters shared with basal hadrosauroids include a short and sloping maxillary ectopterygoid shelf, caudally prominent maxillary jugal process, one functional tooth per alveolus on the maxillary occlusal plane, a jugal rostral process with a shallow caudodorsal margin and medioventrally facing articular facet, a vertical dentary coronoid process with a poorly expanded apex, and tooth crowns with accessory ridges. Derived characters shared with other hadrosaurids include a circumnarial depression compartmented into three fossae (as in brachylophosaurins and Edmontosaurus), a thin everted premaxillary oral margin (as in Gryposaurus, Prosaurolophus, and Saurolophus), and a maxilla with a deep and rostrocaudally extensive rostrodorsal region with a steeply sloping premaxillary margin (as in Gryposaurus). Eotrachodon orientalis differs primarily from the other hadrosauroid from the Mooreville Chalk of Alabama, Lophorhothon atopus, in having a slender and crestless nasal whose caudodorsal margin is not invaded by the circumnarial depression. Hadrosaurus foulkii, the only other known hadrosaurid from Appalachia, is distinct from E. orientalis in having dentary teeth lacking accessory ridges and a dorsally curved shaft of the ischium. A histological section of the tibia of the E. orientalis holotype (MSC 7949) suggests that this individual was actively growing at the time of death and, thus, had the potential to become a larger animal later in development.
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Date Issued: 2016-04-14
Identifier: FSU_pmch_27114863, 10.7717/peerj.1872, PMC4841272, 27114863, 27114863, 1872
Format: Citation

Title: Brain-Region-Specific Organoids Using Mini-bioreactors for Modeling ZIKV Exposure.
Creator: Qian, Xuyu, Nguyen, Ha Nam, Song, Mingxi M, Hadiono, Christopher, Ogden, Sarah C, Hammack, Christy, Yao, Bing, Hamersky, Gregory R, Jacob, Fadi, Zhong, Chun, Yoon, Ki-Jun, Jeang...
Show moreQian, Xuyu, Nguyen, Ha Nam, Song, Mingxi M, Hadiono, Christopher, Ogden, Sarah C, Hammack, Christy, Yao, Bing, Hamersky, Gregory R, Jacob, Fadi, Zhong, Chun, Yoon, Ki-Jun, Jeang, William, Lin, Li, Li, Yujing, Thakor, Jai, Berg, Daniel A, Zhang, Ce, Kang, Eunchai, Chickering, Michael, Nauen, David, Ho, Cheng-Ying, Wen, Zhexing, Christian, Kimberly M, Shi, Pei-Yong, Maher, Brady J, Wu, Hao, Jin, Peng, Tang, Hengli, Song, Hongjun, Ming, Guo-Li
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Abstract/Description: Cerebral organoids, three-dimensional cultures that model organogenesis, provide a new platform to investigate human brain development. High cost, variability, and tissue heterogeneity limit their broad applications. Here, we developed a miniaturized spinning bioreactor (SpinΩ) to generate forebrain-specific organoids from human iPSCs. These organoids recapitulate key features of human cortical development, including progenitor zone organization, neurogenesis, gene expression, and, notably, a...
Show moreCerebral organoids, three-dimensional cultures that model organogenesis, provide a new platform to investigate human brain development. High cost, variability, and tissue heterogeneity limit their broad applications. Here, we developed a miniaturized spinning bioreactor (SpinΩ) to generate forebrain-specific organoids from human iPSCs. These organoids recapitulate key features of human cortical development, including progenitor zone organization, neurogenesis, gene expression, and, notably, a distinct human-specific outer radial glia cell layer. We also developed protocols for midbrain and hypothalamic organoids. Finally, we employed the forebrain organoid platform to model Zika virus (ZIKV) exposure. Quantitative analyses revealed preferential, productive infection of neural progenitors with either African or Asian ZIKV strains. ZIKV infection leads to increased cell death and reduced proliferation, resulting in decreased neuronal cell-layer volume resembling microcephaly. Together, our brain-region-specific organoids and SpinΩ provide an accessible and versatile platform for modeling human brain development and disease and for compound testing, including potential ZIKV antiviral drugs.
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Date Issued: 2016-05-19
Identifier: FSU_pmch_27118425, 10.1016/j.cell.2016.04.032, PMC4900885, 27118425, 27118425, S0092-8674(16)30467-6
Format: Citation

Title: Replication timing and transcriptional control: beyond cause and effect-part III..
Creator: Rivera-Mulia, Juan Carlos, Gilbert, David M
Abstract/Description: DNA replication is essential for faithful transmission of genetic information and is intimately tied to chromosome structure and function. Genome duplication occurs in a defined temporal order known as the replication-timing (RT) program, which is regulated during the cell cycle and development in discrete units referred to as replication domains (RDs). RDs correspond to topologically-associating domains (TADs) and are spatio-temporally compartmentalized in the nucleus. While improvements in...
Show moreDNA replication is essential for faithful transmission of genetic information and is intimately tied to chromosome structure and function. Genome duplication occurs in a defined temporal order known as the replication-timing (RT) program, which is regulated during the cell cycle and development in discrete units referred to as replication domains (RDs). RDs correspond to topologically-associating domains (TADs) and are spatio-temporally compartmentalized in the nucleus. While improvements in experimental tools have begun to reveal glimpses of causality, they have also unveiled complex context-dependent relationships that challenge long recognized correlations of RT to chromatin organization and gene regulation. In particular, RDs/TADs that switch RT during development march to the beat of a different drummer.
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Date Issued: 2016-06-01
Identifier: FSU_pmch_27115331, 10.1016/j.ceb.2016.03.022, PMC4887323, 27115331, 27115331, S0955-0674(16)30072-2
Format: Citation

Title: The Ecdysone and Notch Pathways Synergistically Regulate Cut at the Dorsal-Ventral Boundary in Drosophila Wing Discs.
Creator: Jia, Dongyu, Bryant, Jamal, Jevitt, Allison, Calvin, Gabriel, Deng, Wu-Min
Abstract/Description: Metazoan development requires coordination of signaling pathways to regulate patterns of gene expression. In Drosophila, the wing imaginal disc provides an excellent model for the study of how signaling pathways interact to regulate pattern formation. The determination of the dorsal-ventral (DV) boundary of the wing disc depends on the Notch pathway, which is activated along the DV boundary and induces the expression of the homeobox transcription factor, Cut. Here, we show that Broad (Br), a...
Show moreMetazoan development requires coordination of signaling pathways to regulate patterns of gene expression. In Drosophila, the wing imaginal disc provides an excellent model for the study of how signaling pathways interact to regulate pattern formation. The determination of the dorsal-ventral (DV) boundary of the wing disc depends on the Notch pathway, which is activated along the DV boundary and induces the expression of the homeobox transcription factor, Cut. Here, we show that Broad (Br), a zinc-finger transcription factor, is also involved in regulating Cut expression in the DV boundary region. However, Br expression is not regulated by Notch signaling in wing discs, while ecdysone signaling is the upstream signal that induces Br for Cut upregulation. Also, we find that the ecdysone-Br cascade upregulates cut-lacZ expression, a reporter containing a 2.7 kb cut enhancer region, implying that ecdysone signaling, similar to Notch, regulates cut at the transcriptional level. Collectively, our findings reveal that the Notch and ecdysone signaling pathways synergistically regulate Cut expression for proper DV boundary formation in the wing disc. Additionally, we show br promotes Delta, a Notch ligand, near the DV boundary to suppress aberrant high Notch activity, indicating further interaction between the two pathways for DV patterning of the wing disc.
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Date Issued: 2016-04-20
Identifier: FSU_pmch_27117286, 10.1016/j.jgg.2016.03.002, PMC5391978, 27117286, 27117286, S1673-8527(16)30017-0
Format: Citation

Title: Replicating Large Genomes: Divide and Conquer..
Creator: Rivera-Mulia, Juan Carlos, Gilbert, David M
Abstract/Description: Complete duplication of large metazoan chromosomes requires thousands of potential initiation sites, only a small fraction of which are selected in each cell cycle. Assembly of the replication machinery is highly conserved and tightly regulated during the cell cycle, but the sites of initiation are highly flexible, and their temporal order of firing is regulated at the level of large-scale multi-replicon domains. Importantly, the number of replication forks must be quickly adjusted in...
Show moreComplete duplication of large metazoan chromosomes requires thousands of potential initiation sites, only a small fraction of which are selected in each cell cycle. Assembly of the replication machinery is highly conserved and tightly regulated during the cell cycle, but the sites of initiation are highly flexible, and their temporal order of firing is regulated at the level of large-scale multi-replicon domains. Importantly, the number of replication forks must be quickly adjusted in response to replication stress to prevent genome instability. Here we argue that large genomes are divided into domains for exactly this reason. Once established, domain structure abrogates the need for precise initiation sites and creates a scaffold for the evolution of other chromosome functions.
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Date Issued: 2016-06-02
Identifier: FSU_pmch_27259206, 10.1016/j.molcel.2016.05.007, PMC4893193, 27259206, 27259206, S1097-2765(16)30144-7
Format: Citation

Title: Functional characterizations of venom phenotypes in the eastern diamondback rattlesnake (Crotalus adamanteus) and evidence for expression-driven divergence in toxic activities among populations.
Creator: Margres, Mark J, Walls, Robert, Suntravat, Montamas, Lucena, Sara, Sánchez, Elda E, Rokyta, Darin R
Abstract/Description: Phenotypes frequently vary across and within species. The connection between specific phenotypic effects and function, however, is less understood despite being essential to our understanding of the adaptive process. Snake venoms are ideal for identifying functionally important phenotypic variation because venom variation is common, and venoms can be functionally characterized through simple assays and toxicity measurements. Previous work with the eastern diamondback rattlesnake (Crotalus...
Show morePhenotypes frequently vary across and within species. The connection between specific phenotypic effects and function, however, is less understood despite being essential to our understanding of the adaptive process. Snake venoms are ideal for identifying functionally important phenotypic variation because venom variation is common, and venoms can be functionally characterized through simple assays and toxicity measurements. Previous work with the eastern diamondback rattlesnake (Crotalus adamanteus) used multivariate statistical approaches to identify six unique venom phenotypes. We functionally characterized hemolytic, gelatinase, fibrinogenolytic, and coagulant activity for all six phenotypes, as well as one additional venom, to determine if the statistically significant differences in toxin expression levels previously documented corresponded to differences in venom activity. In general, statistical differences in toxin expression predicted the identified functional differences, or lack thereof, in toxic activity, demonstrating that the statistical approach used to characterize C. adamanteus venoms was a fair representation of biologically meaningful differences. Minor differences in activity not accounted for by the statistical model may be the result of amino-acid differences and/or post-translational modifications, but overall we were able to link variation in protein expression levels to variation in function as predicted by multivariate statistical approaches.
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Date Issued: 2016-09-01
Identifier: FSU_pmch_27179420, 10.1016/j.toxicon.2016.05.005, PMC5178144, 27179420, 27179420, S0041-0101(16)30134-9
Format: Citation

Title: A bright cyan-excitable orange fluorescent protein facilitates dual-emission microscopy and enhances bioluminescence imaging in vivo.
Creator: Chu, Jun, Oh, Younghee, Sens, Alex, Ataie, Niloufar, Dana, Hod, Macklin, John J, Laviv, Tal, Welf, Erik S, Dean, Kevin M, Zhang, Feijie, Kim, Benjamin B, Tang, Clement Tran, Hu,...
Show moreChu, Jun, Oh, Younghee, Sens, Alex, Ataie, Niloufar, Dana, Hod, Macklin, John J, Laviv, Tal, Welf, Erik S, Dean, Kevin M, Zhang, Feijie, Kim, Benjamin B, Tang, Clement Tran, Hu, Michelle, Baird, Michelle A, Davidson, Michael W, Kay, Mark A, Fiolka, Reto, Yasuda, Ryohei, Kim, Douglas S, Ng, Ho-Leung, Lin, Michael Z
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Abstract/Description: Orange-red fluorescent proteins (FPs) are widely used in biomedical research for multiplexed epifluorescence microscopy with GFP-based probes, but their different excitation requirements make multiplexing with new advanced microscopy methods difficult. Separately, orange-red FPs are useful for deep-tissue imaging in mammals owing to the relative tissue transmissibility of orange-red light, but their dependence on illumination limits their sensitivity as reporters in deep tissues. Here we...
Show moreOrange-red fluorescent proteins (FPs) are widely used in biomedical research for multiplexed epifluorescence microscopy with GFP-based probes, but their different excitation requirements make multiplexing with new advanced microscopy methods difficult. Separately, orange-red FPs are useful for deep-tissue imaging in mammals owing to the relative tissue transmissibility of orange-red light, but their dependence on illumination limits their sensitivity as reporters in deep tissues. Here we describe CyOFP1, a bright, engineered, orange-red FP that is excitable by cyan light. We show that CyOFP1 enables single-excitation multiplexed imaging with GFP-based probes in single-photon and two-photon microscopy, including time-lapse imaging in light-sheet systems. CyOFP1 also serves as an efficient acceptor for resonance energy transfer from the highly catalytic blue-emitting luciferase NanoLuc. An optimized fusion of CyOFP1 and NanoLuc, called Antares, functions as a highly sensitive bioluminescent reporter in vivo, producing substantially brighter signals from deep tissues than firefly luciferase and other bioluminescent proteins.
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Date Issued: 2016-07-01
Identifier: FSU_pmch_27240196, 10.1038/nbt.3550, PMC4942401, 27240196, 27240196, nbt.3550
Format: Citation

Program in Neuroscience (11)	+ -
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