Search results

Title: Advancing Behavioural Genomics By Considering Timescale.
Creator: Rittschof, Clare C., Hughes, Kimberly A.
Abstract/Description: Animal behavioural traits often covary with gene expression, pointing towards a genomic constraint on organismal responses to environmental cues. This pattern highlights a gap in our understanding of the time course of environmentally responsive gene expression, and moreover, how these dynamics are regulated. Advances in behavioural genomics explore how gene expression dynamics are correlated with behavioural traits that range from stable to highly labile. We consider the idea that certain...
Show moreAnimal behavioural traits often covary with gene expression, pointing towards a genomic constraint on organismal responses to environmental cues. This pattern highlights a gap in our understanding of the time course of environmentally responsive gene expression, and moreover, how these dynamics are regulated. Advances in behavioural genomics explore how gene expression dynamics are correlated with behavioural traits that range from stable to highly labile. We consider the idea that certain genomic regulatory mechanisms may predict the timescale of an environmental effect on behaviour. This temporally minded approach could inform both organismal and evolutionary questions ranging from the remediation of early life social trauma to understanding the evolution of trait plasticity.
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Date Issued: 2018-02-12
Identifier: FSU_libsubv1_wos_000424747100001, 10.1038/s41467-018-02971-0
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: 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: Anchored Enrichment Dataset For True Flies (order Diptera) Reveals Insights Into The Phylogeny Of Flower Flies (family Syrphidae).
Creator: Young, Andrew Donovan, Lemmon, Alan R., Skevington, Jeffrey H., Mengual, Ximo, Stahls, Gunilla, Reemer, Menno, Jordaens, Kurt, Kelso, Scott, Lemmon, Emily Moriarty, Hauser,...
Show moreYoung, Andrew Donovan, Lemmon, Alan R., Skevington, Jeffrey H., Mengual, Ximo, Stahls, Gunilla, Reemer, Menno, Jordaens, Kurt, Kelso, Scott, Lemmon, Emily Moriarty, Hauser, Martin, De Meyer, Marc, Misof, Bernhard, Wiegmann, Brian M.
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Abstract/Description: Background: Anchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid enrichment is superior to traditional PCR-based Sanger sequencing in terms of both the amount of genomic data that can be recovered and effective cost. Due to their incredibly...
Show moreBackground: Anchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid enrichment is superior to traditional PCR-based Sanger sequencing in terms of both the amount of genomic data that can be recovered and effective cost. Due to their incredibly diverse nature, importance as pollinators, and historical instability with regard to subfamilial and tribal classification, Syrphidae (flower flies or hoverflies) are an ideal candidate for anchored hybrid enrichment-based phylogenetics, especially since recent molecular phylogenies of the syrphids using only a few markers have resulted in highly unresolved topologies. Over 6200 syrphids are currently known and uncovering their phylogeny will help us to understand how these species have diversified, providing insight into an array of ecological processes, from the development of adult mimicry, the origin of adult migration, to pollination patterns and the evolution of larval resource utilization. Results: We present the first use of anchored hybrid enrichment in insect phylogenetics on a dataset containing 30 flower fly species from across all four subfamilies and 11 tribes out of 15. To produce a phylogenetic hypothesis, 559 loci were sampled to produce a final dataset containing 217,702 sites. We recovered a well resolved topology with bootstrap support values that were almost universally >95 %. The subfamily Eristalinae is recovered as paraphyletic, with the strongest support for this hypothesis to date. The ant predators in the Microdontinae are sister to all other syrphids. Syrphinae and Pipizinae are monophyletic and sister to each other. Larval predation on soft-bodied hemipterans evolved only once in this family. Conclusions: Anchored hybrid enrichment was successful in producing a robustly supported phylogenetic hypothesis for the syrphids. Subfamilial reconstruction is concordant with recent phylogenetic hypotheses, but with much higher support values. With the newly designed probe kit this analysis could be rapidly expanded with further sampling, opening the door to more comprehensive analyses targeting problem areas in syrphid phylogenetics and ecology.
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Date Issued: 2016-06-29
Identifier: FSU_libsubv1_wos_000378675500003, 10.1186/s12862-016-0714-0
Format: Citation

Title: Anchored enrichment dataset for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae).
Creator: Young, Andrew Donovan, Lemmon, Alan R, Skevington, Jeffrey H, Mengual, Ximo, Ståhls, Gunilla, Reemer, Menno, Jordaens, Kurt, Kelso, Scott, Lemmon, Emily Moriarty, Hauser, Martin...
Show moreYoung, Andrew Donovan, Lemmon, Alan R, Skevington, Jeffrey H, Mengual, Ximo, Ståhls, Gunilla, Reemer, Menno, Jordaens, Kurt, Kelso, Scott, Lemmon, Emily Moriarty, Hauser, Martin, De Meyer, Marc, Misof, Bernhard, Wiegmann, Brian M
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Abstract/Description: Anchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid enrichment is superior to traditional PCR-based Sanger sequencing in terms of both the amount of genomic data that can be recovered and effective cost. Due to their incredibly diverse...
Show moreAnchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid enrichment is superior to traditional PCR-based Sanger sequencing in terms of both the amount of genomic data that can be recovered and effective cost. Due to their incredibly diverse nature, importance as pollinators, and historical instability with regard to subfamilial and tribal classification, Syrphidae (flower flies or hoverflies) are an ideal candidate for anchored hybrid enrichment-based phylogenetics, especially since recent molecular phylogenies of the syrphids using only a few markers have resulted in highly unresolved topologies. Over 6200 syrphids are currently known and uncovering their phylogeny will help us to understand how these species have diversified, providing insight into an array of ecological processes, from the development of adult mimicry, the origin of adult migration, to pollination patterns and the evolution of larval resource utilization. We present the first use of anchored hybrid enrichment in insect phylogenetics on a dataset containing 30 flower fly species from across all four subfamilies and 11 tribes out of 15. To produce a phylogenetic hypothesis, 559 loci were sampled to produce a final dataset containing 217,702 sites. We recovered a well resolved topology with bootstrap support values that were almost universally >95 %. The subfamily Eristalinae is recovered as paraphyletic, with the strongest support for this hypothesis to date. The ant predators in the Microdontinae are sister to all other syrphids. Syrphinae and Pipizinae are monophyletic and sister to each other. Larval predation on soft-bodied hemipterans evolved only once in this family. Anchored hybrid enrichment was successful in producing a robustly supported phylogenetic hypothesis for the syrphids. Subfamilial reconstruction is concordant with recent phylogenetic hypotheses, but with much higher support values. With the newly designed probe kit this analysis could be rapidly expanded with further sampling, opening the door to more comprehensive analyses targeting problem areas in syrphid phylogenetics and ecology.
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Date Issued: 2016-06-29
Identifier: FSU_pmch_27357120, 10.1186/s12862-016-0714-0, PMC4928351, 27357120, 27357120, 10.1186/s12862-016-0714-0
Format: Citation

Title: Anti-Inflammatory Mechanism of Neural Stem Cell Transplantation in Spinal Cord Injury.
Creator: Cheng, Zhijian, Zhu, Wen, Cao, Kai, Wu, Fei, Li, Jin, Wang, Guoyu, Li, Haopen, Lu, Ming, Ren, Yi, He, Xijing
Abstract/Description: Neural stem cell (NSC) transplantation has been proposed to promote functional recovery after spinal cord injury. However, a detailed understanding of the mechanisms of how NSCs exert their therapeutic plasticity is lacking. We transplanted mouse NSCs into the injured spinal cord seven days after SCI, and the Basso Mouse Scale (BMS) score was performed to assess locomotor function. The anti-inflammatory effects of NSC transplantation was analyzed by immunofluorescence staining of neutrophil...
Show moreNeural stem cell (NSC) transplantation has been proposed to promote functional recovery after spinal cord injury. However, a detailed understanding of the mechanisms of how NSCs exert their therapeutic plasticity is lacking. We transplanted mouse NSCs into the injured spinal cord seven days after SCI, and the Basso Mouse Scale (BMS) score was performed to assess locomotor function. The anti-inflammatory effects of NSC transplantation was analyzed by immunofluorescence staining of neutrophil and macrophages and the detection of mRNA levels of tumor necrosis factor- (TNF-), interleukin-1 (IL-1), interleukin-6 (IL-6) and interleukin-12 (IL-12). Furthermore, bone marrow-derived macrophages (BMDMs) were co-cultured with NSCs and followed by analyzing the mRNA levels of inducible nitric oxide synthase (iNOS), TNF-, IL-1, IL-6 and IL-10 with quantitative real-time PCR. The production of TNF- and IL-1 by BMDMs was examined using the enzyme-linked immunosorbent assay (ELISA). Transplanted NSCs had significantly increased BMS scores (p < 0.05). Histological results showed that the grafted NSCs migrated from the injection site toward the injured area. NSCs transplantation significantly reduced the number of neutrophils and iNOS+/Mac-2+ cells at the epicenter of the injured area (p < 0.05). Meanwhile, mRNA levels of TNF-, IL-1, IL-6 and IL-12 in the NSCs transplantation group were significantly decreased compared to the control group. Furthermore, NSCs inhibited the iNOS expression of BMDMs and the release of inflammatory factors by macrophages in vitro (p < 0.05). These results suggest that NSC transplantation could modulate SCI-induced inflammatory responses and enhance neurological function after SCI via reducing M1 macrophage activation and infiltrating neutrophils. Thus, this study provides a new insight into the mechanisms responsible for the anti-inflammatory effect of NSC transplantation after SCI.
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Date Issued: 2016-09
Identifier: FSU_libsubv1_wos_000385525500008, 10.3390/ijms17091380
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: 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_libsubv1_wos_000368658200001, 10.1038/srep18850
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: Bacterial Artificial Chromosomes Establish Replication Timing And Sub-nuclear Compartment De Novo As Extra-chromosomal Vectors.
Creator: Sima, Jiao, Bartlett, Daniel A., Gordon, Molly R., Gilbert, David M.
Abstract/Description: The role of DNA sequence in determining replication timing (RT) and chromatin higher order organization remains elusive. To address this question, we have developed an extra-chromosomal replication system (E-BACs) consisting of similar to 200 kb human bacterial artificial chromosomes (BACs) modified with Epstein-Barr virus (EBV) stable segregation elements. E-BACs were stably maintained as autonomous mini-chromosomes in EBNA1-expressing HeLa or human induced pluripotent stem cells (hiP-SCs)...
Show moreThe role of DNA sequence in determining replication timing (RT) and chromatin higher order organization remains elusive. To address this question, we have developed an extra-chromosomal replication system (E-BACs) consisting of similar to 200 kb human bacterial artificial chromosomes (BACs) modified with Epstein-Barr virus (EBV) stable segregation elements. E-BACs were stably maintained as autonomous mini-chromosomes in EBNA1-expressing HeLa or human induced pluripotent stem cells (hiP-SCs) and established distinct RT patterns. An E-BAC harboring an early replicating chromosomal region replicated early during S phase, while E-BACs derived from RT transition regions (TTRs) and late replicating regions replicated in mid to late S phase. Analysis of E-BAC interactions with cellular chromatin (4C-seq) revealed that the early replicating E-BAC interacted broadly throughout the genome and preferentially with the early replicating compartment of the nucleus. In contrast, mid-to late-replicating E-BACs interacted with more specific late replicating chromosomal segments, some of which were shared between different E-BACs. Together, we describe a versatile system in which to study the structure and function of chromosomal segments that are stably maintained separately from the influence of cellular chromosome context.
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Date Issued: 2018-02-28
Identifier: FSU_libsubv1_wos_000426293300025, 10.1093/nar/gkx1265
Format: Citation

Title: The Biomechanics Behind Extreme Osteophagy In Tyrannosaurus Rex.
Creator: Gignac, Paul M., Erickson, Gregory M.
Abstract/Description: Most carnivorous mammals can pulverize skeletal elements by generating tooth pressures between occluding teeth that exceed cortical bone shear strength, thereby permitting access to marrow and phosphatic salts. Conversely, carnivorous reptiles have non-occluding dentitions that engender negligible bone damage during feeding. As a result, most reptilian predators can only consume bones in their entirety. Nevertheless, North American tyrannosaurids, including the giant (13 metres [m]) theropod...
Show moreMost carnivorous mammals can pulverize skeletal elements by generating tooth pressures between occluding teeth that exceed cortical bone shear strength, thereby permitting access to marrow and phosphatic salts. Conversely, carnivorous reptiles have non-occluding dentitions that engender negligible bone damage during feeding. As a result, most reptilian predators can only consume bones in their entirety. Nevertheless, North American tyrannosaurids, including the giant (13 metres [m]) theropod dinosaur Tyrannosaurus rex stand out for habitually biting deeply into bones, pulverizing and digesting them. How this mammal-like capacity was possible, absent dental occlusion, is unknown. Here we analyzed T. rex feeding behaviour from trace evidence, estimated bite forces and tooth pressures, and studied tooth-bone contacts to provide the answer. We show that bone pulverization was made possible through a combination of: (1) prodigious bite forces (8,526-34,522 newtons [N]) and tooth pressures (718-2,974 megapascals [MPa]) promoting crack propagation in bones, (2) tooth form and dental arcade configurations that concentrated shear stresses, and (3) repetitive, localized biting. Collectively, these capacities and behaviors allowed T. rex to finely fragment bones and more fully exploit large dinosaur carcasses for sustenance relative to competing carnivores.
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Date Issued: 2017-05-17
Identifier: FSU_libsubv1_wos_000401511100019, 10.1038/s41598-017-02161-w
Format: Citation

Title: Bioturbation By The Fungus-gardening Ant, Trachymyrmex Septentrionalis.
Creator: Tschinkel, Walter R., Seal, Jon N.
Abstract/Description: Soil invertebrates such as ants are thought to be important manipulators of soils in temperate and tropical ecosystems. The fungus gardening ant, Trachymyrmex septentrionalis, is an important agent of biomantling, that is, of depositing soil excavated from below onto the surface, and has been suggested as an agent of bioturbation (moving soil below ground) as well. The amount of bioturbation by this ant was quantified by planting queenright colonies in sand columns consisting of 5 layers of...
Show moreSoil invertebrates such as ants are thought to be important manipulators of soils in temperate and tropical ecosystems. The fungus gardening ant, Trachymyrmex septentrionalis, is an important agent of biomantling, that is, of depositing soil excavated from below onto the surface, and has been suggested as an agent of bioturbation (moving soil below ground) as well. The amount of bioturbation by this ant was quantified by planting queenright colonies in sand columns consisting of 5 layers of different colored sand. The amount of each color of sand deposited on the surface was determined from April to November 2015. In November, colonies were excavated and the color and amount of sand deposited below ground (mostly as backfill in chambers) was determined. Extrapolated to one ha, T. septentrionalis deposited 800 kg of sand per annum on the surface, and an additional 200 kg (17% of the total excavated) below ground. On average, this mixes 1.3% of the sand from other layers within the top meter of soil per millennium, but this mixing is unlikely to be homogeneous, and probably occurs as "hotspots" in both horizontal and vertical space. Such mixing is discussed as a challenge to sediment dating by optically stimulated luminescence (OSL).
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Date Issued: 2016-07-08
Identifier: FSU_libsubv1_wos_000380005400162, 10.1371/journal.pone.0158920
Format: Citation

Title: Bioturbation by the Fungus-Gardening Ant, Trachymyrmex septentrionalis.
Creator: Tschinkel, Walter R, Seal, Jon N
Abstract/Description: Soil invertebrates such as ants are thought to be important manipulators of soils in temperate and tropical ecosystems. The fungus gardening ant, Trachymyrmex septentrionalis, is an important agent of biomantling, that is, of depositing soil excavated from below onto the surface, and has been suggested as an agent of bioturbation (moving soil below ground) as well. The amount of bioturbation by this ant was quantified by planting queenright colonies in sand columns consisting of 5 layers of...
Show moreSoil invertebrates such as ants are thought to be important manipulators of soils in temperate and tropical ecosystems. The fungus gardening ant, Trachymyrmex septentrionalis, is an important agent of biomantling, that is, of depositing soil excavated from below onto the surface, and has been suggested as an agent of bioturbation (moving soil below ground) as well. The amount of bioturbation by this ant was quantified by planting queenright colonies in sand columns consisting of 5 layers of different colored sand. The amount of each color of sand deposited on the surface was determined from April to November 2015. In November, colonies were excavated and the color and amount of sand deposited below ground (mostly as backfill in chambers) was determined. Extrapolated to one ha, T. septentrionalis deposited 800 kg of sand per annum on the surface, and an additional 200 kg (17% of the total excavated) below ground. On average, this mixes 1.3% of the sand from other layers within the top meter of soil per millennium, but this mixing is unlikely to be homogeneous, and probably occurs as "hotspots" in both horizontal and vertical space. Such mixing is discussed as a challenge to sediment dating by optically stimulated luminescence (OSL).
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Date Issued: 2016-07-08
Identifier: FSU_pmch_27391485, 10.1371/journal.pone.0158920, PMC4938500, 27391485, 27391485, PONE-D-16-06201
Format: Citation

Title: Bottom-up And Top-down Controls On Coral Reef Sponges: Disentangling Within-habitat And Between-habitat Processes.
Creator: Wulff, Janie
Abstract/Description: Polarized debates about top-down vs. bottom-up control have given way to more nuanced understanding of control by both resources and consumers in many systems, but coral reef sponges have recently been asserted to differ from other groups in being controlled exclusively top-down. This assertion has been countered by reports of exclusively bottom-up control, with both conclusions based on studies of the same species. Accelerating deterioration of coral reefs motivates knowing the contexts in...
Show morePolarized debates about top-down vs. bottom-up control have given way to more nuanced understanding of control by both resources and consumers in many systems, but coral reef sponges have recently been asserted to differ from other groups in being controlled exclusively top-down. This assertion has been countered by reports of exclusively bottom-up control, with both conclusions based on studies of the same species. Accelerating deterioration of coral reefs motivates knowing the contexts in which either consumers or nutrients or both control key ecosystem role players like sponges. Accordingly, genotype-and size-controlled individuals of 12 common Caribbean reef sponge species were transplanted, in the field, into five circumstances differing in predators, competitors, and the picoplankton consumed by sponges. Growth and survival of the experimental transplants for periods of 1-9 yr revealed context-dependent control of sponges. Primary control of growth was bottom-up, with more picoplankton resulting in consistent and sustained higher growth rates for all 12 of these ecologically and phylogenetically diverse species. Top-down control was not detected within-habitat, on the coral reef. However, between-habitat control was by predation and competition, with reef sponges excluded from adjacent seagrass meadows by spongivorous starfish, and excluded from mangrove prop roots by faster-growing mangrove sponges. These results highlight the strong importance of experimental design details that consider behavior idiosyncrasies, sufficiently long time scales, and appropriate division of species into categories. Diametrically opposite results from studies of the same species also illustrate the inherently greater difficulty of detecting bottom-up processes and the importance of distinguishing within-habitat vs. between-habitat patterns and processes.
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Date Issued: 2017-04
Identifier: FSU_libsubv1_wos_000398175200024
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: 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

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: Cleavage Of The Sun-domain Protein Mps3 At Its N-terminus Regulates Centrosome Disjunction In Budding Yeast Meiosis.
Creator: Li, Ping, Jin, Hui, Koch, Bailey A., Abblett, Rebecca L., Han, Xuemei, Yates, John R., Yu, Hong-Guo
Abstract/Description: Centrosomes organize microtubules and are essential for spindle formation and chromosome segregation during cell division. Duplicated centrosomes are physically linked, but how this linkage is dissolved remains unclear. Yeast centrosomes are tethered by a nuclear-envelope-attached structure called the half-bridge, whose components have mammalian homologues. We report here that cleavage of the half-bridge protein Mps3 promotes accurate centrosome disjunction in budding yeast. Mps3 is a single...
Show moreCentrosomes organize microtubules and are essential for spindle formation and chromosome segregation during cell division. Duplicated centrosomes are physically linked, but how this linkage is dissolved remains unclear. Yeast centrosomes are tethered by a nuclear-envelope-attached structure called the half-bridge, whose components have mammalian homologues. We report here that cleavage of the half-bridge protein Mps3 promotes accurate centrosome disjunction in budding yeast. Mps3 is a single-pass SUN-domain protein anchored at the inner nuclear membrane and concentrated at the nuclear side of the half-bridge. Using the unique feature in yeast meiosis that centrosomes are linked for hours before their separation, we have revealed that Mps3 is cleaved at its nucleus-localized Nterminal domain, the process of which is regulated by its phosphorylation at serine 70. Cleavage of Mps3 takes place at the yeast centrosome and requires proteasome activity. We show that noncleavable Mps3 (Mps3-nc) inhibits centrosome separation during yeast meiosis. In addition, overexpression of mps3-nc in vegetative yeast cells also inhibits centrosome separation and is lethal. Our findings provide a genetic mechanism for the regulation of SUN-domain protein-mediated activities, including centrosome separation, by irreversible protein cleavage at the nuclear periphery.
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Date Issued: 2017-06
Identifier: FSU_libsubv1_wos_000404512600017, 10.1371/journal.pgen.1006830
Format: Citation

Title: Coevolution Leaves A Weak Signal On Ecological Networks.
Creator: Ponisio, Lauren C., M'Gonigle, Leithen K.
Abstract/Description: One of the major challenges in evolutionary ecology is to understand how coevolution shapes species interaction networks. Important topological properties of networks such as nestedness and modularity are thought to be affected by coevolution. However, there has been no test whether coevolution does, in fact, lead to predictable network structure. Here, we investigate the structure of simulated bipartite networks generated under different modes of coevolution. We ask whether evolutionary...
Show moreOne of the major challenges in evolutionary ecology is to understand how coevolution shapes species interaction networks. Important topological properties of networks such as nestedness and modularity are thought to be affected by coevolution. However, there has been no test whether coevolution does, in fact, lead to predictable network structure. Here, we investigate the structure of simulated bipartite networks generated under different modes of coevolution. We ask whether evolutionary processes influence network structure and, furthermore, whether any emergent trends are influenced by the strength or "intimacy" of the species interactions. We find that coevolution leaves a weak and variable signal on network topology, particularly nestedness and modularity, which was not strongly affected by the intimacy of interactions. Our findings indicate that network metrics, on their own, should not be used to make inferences about processes underlying the evolutionary history of communities. Instead, a more holistic approach that combines network approaches with traditional phylogenetic and biogeographic reconstructions is needed.
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Date Issued: 2017-04
Identifier: FSU_libsubv1_wos_000400985300044, 10.1002/ecs2.1798
Format: Citation

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

Title: Collective epithelial cell sheet adhesion and migration on polyelectrolyte multilayers with uniform and gradients of compliance.
Creator: Martinez, Jessica S, Schlenoff, Joseph B, Keller, Thomas C S
Abstract/Description: Polyelectrolyte multilayers (PEMUs) are tunable thin films that could serve as coatings for biomedical implants. PEMUs built layer by layer with the polyanion poly(acrylic acid) (PAA) modified with a photosensitive 4-(2-hydroxyethoxy) benzophenone (PAABp) group and the polycation poly(allylamine hydrochloride) (PAH) are mechanically tunable by UV irradiation, which forms covalent bonds between the layers and increases PEMU stiffness. PAH-terminated PEMUs (PAH-PEMUs) that were uncrosslinked,...
Show morePolyelectrolyte multilayers (PEMUs) are tunable thin films that could serve as coatings for biomedical implants. PEMUs built layer by layer with the polyanion poly(acrylic acid) (PAA) modified with a photosensitive 4-(2-hydroxyethoxy) benzophenone (PAABp) group and the polycation poly(allylamine hydrochloride) (PAH) are mechanically tunable by UV irradiation, which forms covalent bonds between the layers and increases PEMU stiffness. PAH-terminated PEMUs (PAH-PEMUs) that were uncrosslinked, UV-crosslinked to a uniform stiffness, or UV-crosslinked with an edge mask or through a neutral density optical gradient filter to form continuous compliance gradients were used to investigate how differences in PEMU stiffness affect the adhesion and migration of epithelial cell sheets from scales of the fish Poecilia sphenops (Black Molly) and Carassius auratus (Comet Goldfish). During the progressive collective cell migration, the edge cells (also known as 'leader' cells) in the sheets on softer uncrosslinked PEMUs and less crosslinked regions of the gradient formed more actin filaments and vinculin-containing adherens junctions and focal adhesions than formed in the sheet cells on stiffer PEMUs or glass. During sheet migration, the ratio of edge cell to internal cell (also known as 'follower' cells) motilities were greater on the softer PEMUs than on the stiffer PEMUs or glass, causing tension to develop across the sheet and periods of retraction, during which the edge cells lost adhesion to the substrate and regions of the sheet retracted toward the more adherent internal cell region. These retraction events were inhibited by the myosin II inhibitor Blebbistatin, which reduced the motility velocity ratios to those for sheets on the stiffer PEMUs. Blebbistatin also caused disassembly of actin filaments, reorganization of focal adhesions, increased cell spreading at the leading edge, as well as loss of edge cell-cell connections in epithelial cell sheets on all surfaces. Interestingly, cells throughout the interior region of the sheets on uncrosslinked PEMUs retained their actin and vinculin organization at adherens junctions after treatment with Blebbistatin. Like Blebbistatin, a Rho-kinase (ROCK) inhibitor, Y27632, promoted loss of cell-cell connections between edge cells, whereas a Rac1 inhibitor, NSC23766, primarily altered the lamellipodial protrusion in edge cells. Compliance gradient PAH-PEMUs promoted durotaxis of the cell sheets but not of individual keratocytes, demonstrating durotaxis, like plithotaxis, is an emergent property of cell sheet organization.
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Date Issued: 2016-08-01
Identifier: FSU_pmch_27292313, 10.1016/j.yexcr.2016.06.002, PMC4967014, 27292313, 27292313, S0014-4827(16)30143-4
Format: Citation

Title: Commentary: Epigenetic Regulation of Phosphodiesterases 2A and 3A Underlies Compromised beta-Adrenergic Signaling in an iPSC Model of Dilated Cardiomyopatyh.
Creator: Cole, Lauren A., Dennis, Jonathan H., Chase, P. Bryant
Date Issued: 2016-09-23
Identifier: FSU_libsubv1_wos_000383760700001, 10.3389/fphys.2016.00418
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: Comparative Genotype-phenotype Mapping Reveals Distinct Modes of Venom Expression Evolution in the Sympatric Eastern Diamondback Rattlesnake (Crotalus adamanteus) and Eastern Coral SSnake (Micrurus fulvius).
Creator: Margres, Mark, McGivern, James J., Seavy, Margaret, Wray, Kenneth, Facente, Jack, Rokyta, Darin
Abstract/Description: Selection is predicted to drive diversification within species and lead to local adaptation, but understanding the mechanistic details underlying this process, and thus the genetic basis of adaptive evolution, requires the mapping of genotype to phenotype. Venom is complex and involves many genes, but the specialization of the venom-gland towards toxin production allows specific transcripts to be correlated with specific toxic proteins, establishing a direct link from genotype to phenotype....
Show moreSelection is predicted to drive diversification within species and lead to local adaptation, but understanding the mechanistic details underlying this process, and thus the genetic basis of adaptive evolution, requires the mapping of genotype to phenotype. Venom is complex and involves many genes, but the specialization of the venom-gland towards toxin production allows specific transcripts to be correlated with specific toxic proteins, establishing a direct link from genotype to phenotype. To determine the extent of expression variation and identify the processes driving patterns of phenotypic diversity, we constructed genotype-phenotype maps and compared range-wide toxin-protein expression variation for two species of snake with nearly identical ranges: the eastern diamondback rattlesnake (Crotalus adamanteus) and the eastern coral snake (Micrurus fulvius). We detected significant expression variation in C. adamanteus, identified the specific loci associated with population differentiation, and found that loci expressed at all levels contributed to this divergence. Contrary to expectations, we found no expression variation in M. fulvius, suggesting that M. fulvius populations are not locally adapted. Our results not only linked expression variation at specific loci to divergence in a polygenic, complex trait, but also have extensive conservation and biomedical implications. Crotalus adamanteus is currently a candidate for Federal listing under the Endangered Species Act, and the loss of any major population would result in the irrevocable loss of a unique venom phenotype. The lack of variation in M. fulvius has significant biomedical application because our data will assist in the development of effective antivenom for this species.
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Date Issued: 2014
Identifier: FSU_migr_bio_faculty_publications-0001, 10.1534/genetics.114.172437
Format: Citation

Title: Comprehensive Nucleosome Mapping Of The Human Genome In Cancer Progression.
Creator: Druliner, Brooke R., Vera, Daniel, Johnson, Ruth, Ruan, Xiaoyang, Apone, Lynn M., Dimalanta, Eileen T., Stewart, Fiona J., Boardman, Lisa, Dennis, Jonathan H.
Abstract/Description: Altered chromatin structure is a hallmark of cancer, and inappropriate regulation of chromatin structure may represent the origin of transformation. Important studies have mapped human nucleosome distributions genome wide, but the role of chromatin structure in cancer progression has not been addressed. We developed a MNase-Transcription Start Site Sequence Capture method (mTSS-seq) to map the nucleosome distribution at human transcription start sites genome-wide in primary human lung and...
Show moreAltered chromatin structure is a hallmark of cancer, and inappropriate regulation of chromatin structure may represent the origin of transformation. Important studies have mapped human nucleosome distributions genome wide, but the role of chromatin structure in cancer progression has not been addressed. We developed a MNase-Transcription Start Site Sequence Capture method (mTSS-seq) to map the nucleosome distribution at human transcription start sites genome-wide in primary human lung and colon adenocarcinoma tissue. Here, we confirm that nucleosome redistribution is an early, widespread event in lung (LAC) and colon (CRC) adenocarcinoma. These altered nucleosome architectures are consistent between LAC and CRC patient samples indicating that they may serve as important early adenocarcinoma markers. We demonstrate that the nucleosome alterations are driven by the underlying DNA sequence and potentiate transcription factor binding. We conclude that DNA-directed nucleosome redistributions are widespread early in cancer progression. We have proposed an entirely new hierarchical model for chromatin-mediated genome regulation.
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Date Issued: 2016-03-22
Identifier: FSU_libsubv1_wos_000375687200013, 10.1101/021618
Format: Citation

Title: Critical and direct involvement of the CD23 stalk region in IgE binding.
Creator: Selb, Regina, Eckl-Dorna, Julia, Twaroch, Teresa E, Lupinek, Christian, Teufelberger, Andrea, Hofer, Gerhard, Focke-Tejkl, Margarete, Gepp, Barbara, Linhart, Birgit, Breiteneder...
Show moreSelb, Regina, Eckl-Dorna, Julia, Twaroch, Teresa E, Lupinek, Christian, Teufelberger, Andrea, Hofer, Gerhard, Focke-Tejkl, Margarete, Gepp, Barbara, Linhart, Birgit, Breiteneder, Heimo, Ellinger, Adolf, Keller, Walter, Roux, Kenneth H, Valenta, Rudolf, Niederberger, Verena
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Abstract/Description: The low-affinity receptor for IgE, FcεRII (CD23), contributes to allergic inflammation through allergen presentation to T cells, regulation of IgE responses, and enhancement of transepithelial allergen migration. We sought to investigate the interaction between CD23, chimeric monoclonal human IgE, and the corresponding birch pollen allergen Bet v 1 at a molecular level. We expressed 4 CD23 variants. One variant comprised the full extracellular portion of CD23, including the stalk and head...
Show moreThe low-affinity receptor for IgE, FcεRII (CD23), contributes to allergic inflammation through allergen presentation to T cells, regulation of IgE responses, and enhancement of transepithelial allergen migration. We sought to investigate the interaction between CD23, chimeric monoclonal human IgE, and the corresponding birch pollen allergen Bet v 1 at a molecular level. We expressed 4 CD23 variants. One variant comprised the full extracellular portion of CD23, including the stalk and head domain; 1 variant was identical with the first, except for an amino acid exchange in the stalk region abolishing the N-linked glycosylation site; and 2 variants represented the head domain, 1 complete and 1 truncated. The 4 CD23 variants were purified as monomeric and structurally folded proteins, as demonstrated by gel filtration and circular dichroism. By using a human IgE mAb, the corresponding allergen Bet v 1, and a panel of antibodies specific for peptides spanning the CD23 surface, both binding and inhibition assays and negative stain electron microscopy were performed. A hitherto unknown IgE-binding site was mapped on the stalk region of CD23, and the non-N-glycosylated monomeric version of CD23 was superior in IgE binding compared with glycosylated CD23. Furthermore, we demonstrated that a therapeutic anti-IgE antibody, omalizumab, which inhibits IgE binding to FcεRI, also inhibited IgE binding to CD23. Our results provide a new model for the CD23-IgE interaction. We show that the stalk region of CD23 is crucially involved in IgE binding and that the interaction can be blocked by the therapeutic anti-IgE antibody omalizumab.
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Date Issued: 2017-01-01
Identifier: FSU_pmch_27343203, 10.1016/j.jaci.2016.04.015, PMC5321597, 27343203, 27343203, S0091-6749(16)30261-5
Format: Citation

Title: The Dead-box Protein Rok1 Orchestrates 40s And 60s Ribosome Assembly By Promoting The Release Of Rrp5 From Pre-40s Ribosomes To Allow For 60s Maturation.
Creator: Khoshnevis, Sohail, Askenasy, Isabel, Johnson, Matthew C., Dattolo, Maria D., Young-Erdos, Crystal L., Stroupe, M. Elizabeth, Karbstein, Katrin
Abstract/Description: DEAD-box proteins are ubiquitous regulators of RNA biology. While commonly dubbed "helicases," their activities also include duplex annealing, adenosine triphosphate (ATP)-dependent RNA binding, and RNA-protein complex remodeling. Rok1, an essential DEAD-box protein, and its cofactor Rrp5 are required for ribosome assembly. Here, we use in vivo and in vitro biochemical analyses to demonstrate that ATP-bound Rok1, but not adenosine diphosphate (ADP)-bound Rok1, stabilizes Rrp5 binding to 40S...
Show moreDEAD-box proteins are ubiquitous regulators of RNA biology. While commonly dubbed "helicases," their activities also include duplex annealing, adenosine triphosphate (ATP)-dependent RNA binding, and RNA-protein complex remodeling. Rok1, an essential DEAD-box protein, and its cofactor Rrp5 are required for ribosome assembly. Here, we use in vivo and in vitro biochemical analyses to demonstrate that ATP-bound Rok1, but not adenosine diphosphate (ADP)-bound Rok1, stabilizes Rrp5 binding to 40S ribosomes. Interconversion between these two forms by ATP hydrolysis is required for release of Rrp5 from pre-40S ribosomes in vivo, thereby allowing Rrp5 to carry out its role in 60S subunit assembly. Furthermore, our data also strongly suggest that the previously described accumulation of snR30 upon Rok1 inactivation arises because Rrp5 release is blocked and implicate a previously undescribed interaction between Rrp5 and the DEAD-box protein Has1 in mediating snR30 accumulation when Rrp5 release from pre-40S subunits is blocked.
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Date Issued: 2016-06
Identifier: FSU_libsubv1_wos_000378611200007, 10.1371/journal.pbio.1002480
Format: Citation

Title: The DEAD-box Protein Rok1 Orchestrates 40S and 60S Ribosome Assembly by Promoting the Release of Rrp5 from Pre-40S Ribosomes to Allow for 60S Maturation.
Creator: Khoshnevis, Sohail, Askenasy, Isabel, Johnson, Matthew C, Dattolo, Maria D, Young-Erdos, Crystal L, Stroupe, M Elizabeth, Karbstein, Katrin
Abstract/Description: DEAD-box proteins are ubiquitous regulators of RNA biology. While commonly dubbed "helicases," their activities also include duplex annealing, adenosine triphosphate (ATP)-dependent RNA binding, and RNA-protein complex remodeling. Rok1, an essential DEAD-box protein, and its cofactor Rrp5 are required for ribosome assembly. Here, we use in vivo and in vitro biochemical analyses to demonstrate that ATP-bound Rok1, but not adenosine diphosphate (ADP)-bound Rok1, stabilizes Rrp5 binding to 40S...
Show moreDEAD-box proteins are ubiquitous regulators of RNA biology. While commonly dubbed "helicases," their activities also include duplex annealing, adenosine triphosphate (ATP)-dependent RNA binding, and RNA-protein complex remodeling. Rok1, an essential DEAD-box protein, and its cofactor Rrp5 are required for ribosome assembly. Here, we use in vivo and in vitro biochemical analyses to demonstrate that ATP-bound Rok1, but not adenosine diphosphate (ADP)-bound Rok1, stabilizes Rrp5 binding to 40S ribosomes. Interconversion between these two forms by ATP hydrolysis is required for release of Rrp5 from pre-40S ribosomes in vivo, thereby allowing Rrp5 to carry out its role in 60S subunit assembly. Furthermore, our data also strongly suggest that the previously described accumulation of snR30 upon Rok1 inactivation arises because Rrp5 release is blocked and implicate a previously undescribed interaction between Rrp5 and the DEAD-box protein Has1 in mediating snR30 accumulation when Rrp5 release from pre-40S subunits is blocked.
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Date Issued: 2016-06-09
Identifier: FSU_pmch_27280440, 10.1371/journal.pbio.1002480, PMC4900678, 27280440, 27280440, PBIOLOGY-D-16-00944
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: 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: Do Florida Harvester Ant Colonies (pogonomyrmex Badius) Have A Nest Architecture "plan?".
Creator: Tschinkel, Walter R.
Date Issued: 2017-04
Identifier: FSU_libsubv1_wos_000398175200029, 10.1002/ecy.1739/suppinfo
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: 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: Effects of intraspecific diversity on survivorship, growth, and recruitment of the eastern oyster across sites.
Creator: Hanley, Torrance C., Hughes, A. Randall, Williams, Bethany, Garland, Hanna, Kimbro, David L.
Abstract/Description: Intraspecific diversity, particularly of foundation species, can significantly affect population, community, and ecosystem processes. Examining how genetic diversity relates to demographic traits provides a key mechanistic link from genotypic and phenotypic variation of taxa with complex life histories to their population dynamics. We conducted a field experiment to assess how two metrics of intraspecific diversity (cohort diversity, the number of independent juvenile cohorts created from...
Show moreIntraspecific diversity, particularly of foundation species, can significantly affect population, community, and ecosystem processes. Examining how genetic diversity relates to demographic traits provides a key mechanistic link from genotypic and phenotypic variation of taxa with complex life histories to their population dynamics. We conducted a field experiment to assess how two metrics of intraspecific diversity (cohort diversity, the number of independent juvenile cohorts created from different adult source populations, and genetic relatedness, genetic similarity among individuals within and across cohorts) affect the survivorship, growth, and recruitment of the foundation species Crassostrea virginica. To assess the effects of both cohort diversity and genetic relatedness on oyster demographic traits under different environmental conditions, we manipulated juvenile oyster diversity and predator exposure (presence/absence of a cage) at two sites differing in resource availability and predation intensity. Differences in predation pressure between sites over-whelmingly determined post-settlement survivorship of oysters. However, in the absence of predation (i.e., cage treatment), one or both metrics of intraspecific diversity, in addition to site, influenced long-term survivorship, growth, and recruitment. While both cohort diversity and genetic relatedness were negatively associated with long-term survivorship, genetic relatedness alone showed a positive association with growth and cohort diversity alone showed a positive association with recruitment. Thus, our results demonstrate that in the absence of predation, intraspecific diversity can affect multiple demographic traits of a foundation species, but the relative importance of these effects depends on the environmental context. Moreover, the magnitude and direction of these effects vary depending on the diversity metric, cohort diversity or genetic relatedness, suggesting that although they are inversely related in this system, each captures sufficiently different components of intraspecific diversity. Given the global loss of oyster reef habitat and rapid decline in oyster population size, our results are particularly relevant to management and restoration. In addition, aquaculture, which commonly excludes predators during early life history stages, may benefit from incorporation of oyster cohort diversity into standard practice.
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Date Issued: 2016-06
Identifier: FSU_libsubv1_wos_000377219900015, 10.1890/15-1710.1
Format: Citation

Title: Elevated Anxiety And Impaired Attention In Super-smeller, Kv1.3 Knockout Mice.
Creator: Huang, Zhenbo, Hoffman, Carlie A., Chelette, Brandon M., Thiebaud, Nicolas, Fadool, Debra A.
Abstract/Description: It has long been recognized that olfaction and emotion are linked. While chemosensory research using both human and rodent models have indicated a change in emotion can contribute to olfactory dysfunction, there are few studies addressing the contribution of olfaction to a modulation in emotion. In mice, olfactory deficits have been linked with heightened anxiety levels, suggesting that there could be an inverse relationship between olfaction and anxiety. Furthermore, increased anxiety is...
Show moreIt has long been recognized that olfaction and emotion are linked. While chemosensory research using both human and rodent models have indicated a change in emotion can contribute to olfactory dysfunction, there are few studies addressing the contribution of olfaction to a modulation in emotion. In mice, olfactory deficits have been linked with heightened anxiety levels, suggesting that there could be an inverse relationship between olfaction and anxiety. Furthermore, increased anxiety is often co-morbid with psychiatric conditions such as attention disorders. Our study aimed to investigate the roles of olfaction in modulating anxiety. Voltage-gated potassium ion channel Kv1.3 knockout mice (Kv1.3-/-), which have heightened olfaction, and wild-type (WT) mice were examined for anxiety-like behaviors using marble burying (MB), light-dark box (LDB) and elevated-plus maze (EPM) tests. Because Kv1.3-/- mice have increased locomotor activity, inattentive and hyperactive behaviors were quantified for both genotypes. Kv1.3-/- mice showed increased anxiety levels compared to their WT counterparts and administration of methylphenidate (MPH) via oral gavage alleviated their increased anxiety. Object-based attention testing indicated young and older Kv1.3-/- mice had attention deficits and treatment with MPH also ameliorated this condition. Locomotor testing through use of a metabolic chamber indicated that Kv1.3-/- mice were not significantly hyperactive and MPH treatment failed to modify this activity. Our data suggest that heightened olfaction does not necessarily lead to decreased anxiety levels, and that Kv1.3-/- mice may have behaviors associated with inattentiveness.
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Date Issued: 2018-03-19
Identifier: FSU_libsubv1_wos_000427729100001, 10.3389/fnbeh.2018.00049
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: 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: Epithelial Tumors Originate In Tumor Hotspots, A Tissue-intrinsic Microenvironment.
Creator: Tamori, Yoichiro, Suzuki, Emiko, Deng, Wu-Min
Abstract/Description: Malignant tumors are caused by uncontrolled proliferation of transformed mutant cells that have lost the ability to maintain tissue integrity. Although a number of causative genetic backgrounds for tumor development have been discovered, the initial steps mutant cells take to escape tissue integrity and trigger tumorigenesis remain elusive. Here, we show through analysis of conserved neoplastic tumor-suppressor genes (nTSGs) in Drosophila wing imaginal disc epithelia that tumor initiation...
Show moreMalignant tumors are caused by uncontrolled proliferation of transformed mutant cells that have lost the ability to maintain tissue integrity. Although a number of causative genetic backgrounds for tumor development have been discovered, the initial steps mutant cells take to escape tissue integrity and trigger tumorigenesis remain elusive. Here, we show through analysis of conserved neoplastic tumor-suppressor genes (nTSGs) in Drosophila wing imaginal disc epithelia that tumor initiation depends on tissue-intrinsic local cytoarchitectures, causing tumors to consistently originate in a specific region of the tissue. In this "tumor hotspot" where cells constitute a network of robust structures on their basal side, nTSG-deficient cells delaminate from the apical side of the epithelium and begin tumorigenic overgrowth by exploiting endogenous Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling activity. Conversely, in other regions, the "tumor coldspot" nTSG-deficient cells are extruded toward the basal side and undergo apoptosis. When the direction of delamination is reversed through suppression of RhoGEF2, an activator of the Rho family small GTPases, and JAK/STAT is activated ectopically in these coldspot nTSG-deficient cells, tumorigenesis is induced. These data indicate that two independent processes, apical delamination and JAK/STAT activation, are concurrently required for the initiation of nTSG-deficient-induced tumorigenesis. Given the conservation of the epithelial cytoarchitecture, tumorigenesis may be generally initiated from tumor hotspots by a similar mechanism.
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Date Issued: 2016-09
Identifier: FSU_libsubv1_wos_000386128900002, 10.1371/journal.pbio.1002537
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: Evolution In A Community Context: Trait Responses To Multiple Species Interactions.
Creator: terHorst, Casey P., Zee, Peter C., Heath, Katy D., Miller, Thomas E., Pastore, Abigail I., Patel, Swati, Schreiber, Sebastian J., Wade, Michael J., Walsh, Matthew R.
Abstract/Description: Species that coexist in diverse natural communities interact in complex ways that alter each other's abundances and affect selection on each other's traits. Consequently, predicting trait evolution in natural communities may require understanding ecological and evolutionary dynamics involving a number of species. In August 2016, the American Society of Naturalists sponsored a symposium to explore evolution in a community context, focusing on microevolutionary processes. Here we provide an...
Show moreSpecies that coexist in diverse natural communities interact in complex ways that alter each other's abundances and affect selection on each other's traits. Consequently, predicting trait evolution in natural communities may require understanding ecological and evolutionary dynamics involving a number of species. In August 2016, the American Society of Naturalists sponsored a symposium to explore evolution in a community context, focusing on microevolutionary processes. Here we provide an introduction to our perspectives on this topic by defining the context and describing some examples of when and how microevolutionary responses to multiple species may differ from evolution in isolation or in two-species communities. We find that indirect ecological and evolutionary effects can result in nonadditive selection and evolution that cannot be predicted from pairwise interactions. Genetic correlations of ecological traits in one species can alter trait evolution and adaptation aswell as the abundances of other species. In general, evolution in multispecies communities can change ecological interactions, which then feed back to future evolutionary changes in ways that depend on these indirect effects. We suggest avenues for future research in this field, including determining the circumstances under which pairwise evolution does not adequately describe evolutionary trajectories.
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Date Issued: 2018-03
Identifier: FSU_libsubv1_wos_000427588400013, 10.1086/695835
Format: Citation

Title: Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life.
Creator: Hamilton, Chris A., Lemmon, Alan R., Lemmon, Emily Moriarty, Bond, Jason E.
Abstract/Description: Background: Despite considerable effort, progress in spider molecular systematics has lagged behind many other comparable arthropod groups, thereby hindering family-level resolution, classification, and testing of important macroevolutionary hypotheses. Recently, alternative targeted sequence capture techniques have provided molecular systematics a powerful tool for resolving relationships across the Tree of Life. One of these approaches, Anchored Hybrid Enrichment (AHE), is designed to...
Show moreBackground: Despite considerable effort, progress in spider molecular systematics has lagged behind many other comparable arthropod groups, thereby hindering family-level resolution, classification, and testing of important macroevolutionary hypotheses. Recently, alternative targeted sequence capture techniques have provided molecular systematics a powerful tool for resolving relationships across the Tree of Life. One of these approaches, Anchored Hybrid Enrichment (AHE), is designed to recover hundreds of unique orthologous loci from across the genome, for resolving both shallow and deep-scale evolutionary relationships within non-model systems. Herein we present a modification of the AHE approach that expands its use for application in spiders, with a particular emphasis on the infraorder Mygalomorphae. Results: Our aim was to design a set of probes that effectively capture loci informative at a diversity of phylogenetic timescales. Following identification of putative arthropod-wide loci, we utilized homologous transcriptome sequences from 17 species across all spiders to identify exon boundaries. Conserved regions with variable flanking regions were then sought across the tick genome, three published araneomorph spider genomes, and raw genomic reads of two mygalomorph taxa. Following development of the 585 target loci in the Spider Probe Kit, we applied AHE across three taxonomic depths to evaluate performance: deep-level spider family relationships (33 taxa, 327 loci); family and generic relationships within the mygalomorph family Euctenizidae (25 taxa, 403 loci); and species relationships in the North American tarantula genus Aphonopelma (83 taxa, 581 loci). At the deepest level, all three major spider lineages (the Mesothelae, Mygalomorphae, and Araneomorphae) were supported with high bootstrap support. Strong support was also found throughout the Euctenizidae, including generic relationships within the family and species relationships within the genus Aptostichus. As in the Euctenizidae, virtually identical topologies were inferred with high support throughout Aphonopelma. Conclusions: The Spider Probe Kit, the first implementation of AHE methodology in Class Arachnida, holds great promise for gathering the types and quantities of molecular data needed to accelerate an understanding of the spider Tree of Life by providing a mechanism whereby different researchers can confidently and effectively use the same loci for independent projects, yet allowing synthesis of data across independent research groups.
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Date Issued: 2016-10-13
Identifier: FSU_libsubv1_wos_000386026100002, 10.1186/s12862-016-0769-y
Format: Citation

Title: Experimental evidence that dispersal drives ant community assembly in human-altered ecosystems.
Creator: King, Joshua R., Tschinkel, Walter R.
Abstract/Description: A key shortcoming in our understanding of exotic species' success is that it is not known how post-introduction dispersal contributes to the success of exotic species and the reassembly of invaded communities. Exotic and native species face poorly understood competition-colonization trade-offs in heterogeneous landscapes of natural and anthropogenic habitats. We conducted three experiments that tested how ant queen behavior during dispersal affects community composition. Using experimental...
Show moreA key shortcoming in our understanding of exotic species' success is that it is not known how post-introduction dispersal contributes to the success of exotic species and the reassembly of invaded communities. Exotic and native species face poorly understood competition-colonization trade-offs in heterogeneous landscapes of natural and anthropogenic habitats. We conducted three experiments that tested how ant queen behavior during dispersal affects community composition. Using experimental plots, we tested whether (1) different types of habitat disturbance and (2) different sizes of habitat disturbance affected the abundance of newly mated queens landing in the plots. The three most abundant species captured were the exotic fire ant Solenopsis invicta, and the native species Brachymyrmex depilis, and S.pergandei, respectively. When queens were considered collectively, more queens landed in plowed, sand-added, and roadside plots than in control or mow plots, in other words, in the more heavily disturbed plots. We also tested (3) the effect of habitat manipulations on the survival of newly mated fire ant queens (Solenopsis invicta). Soil disturbance (tilling), lack of shade, and removal (poisoning) of the ant community resulted in the greatest fire ant colony survivorship. Collectively, experiments revealed that both exotic and native newly mated ant queens select open, human-altered ecosystems for founding new colonies. The selection of such habitats by fire ant queens leads to their successful colony founding and ultimately to their dominance in those habitats. Selection of disturbed habitats is therefore advantageous for exotic species but is an ecological trap for native species because they do not often succeed in founding colonies in these habitats.
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Date Issued: 2016-01
Identifier: FSU_libsubv1_wos_000369852600025, 10.1890/15-1105.1
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: ExtraPEG: A Polyethylene Glycol-Based Method for Enrichment of Extracellular Vesicles.
Creator: Rider, Mark A., Hurwitz, Stephanie N., Meckes, David G.
Abstract/Description: Initially thought to be a means for cells to eliminate waste, secreted extracellular vesicles, known as exosomes, are now understood to mediate numerous healthy and pathological processes. Though abundant in biological fluids, purifying exosomes has been challenging because their biophysical properties overlap with other secreted cell products. Easy-to-use commercial kits for harvesting exosomes are now widely used, but the relative low-purity and high-cost of the preparations restricts their...
Show moreInitially thought to be a means for cells to eliminate waste, secreted extracellular vesicles, known as exosomes, are now understood to mediate numerous healthy and pathological processes. Though abundant in biological fluids, purifying exosomes has been challenging because their biophysical properties overlap with other secreted cell products. Easy-to-use commercial kits for harvesting exosomes are now widely used, but the relative low-purity and high-cost of the preparations restricts their utility. Here we describe a method for purifying exosomes and other extracellular vesicles by adapting methods for isolating viruses using polyethylene glycol. This technique, called ExtraPEG, enriches exosomes from large volumes of media rapidly and inexpensively using low-speed centrifugation, followed by a single small-volume ultracentrifugation purification step. Total protein and RNA harvested from vesicles is sufficient in quantity and quality for proteomics and sequencing analyses, demonstrating the utility of this method for biomarker discovery and diagnostics. Additionally, confocal microscopy studies suggest that the biological activity of vesicles is not impaired. The ExtraPEG method can be easily adapted to enrich for different vesicle populations, or as an efficient precursor to subsequent purification techniques, providing a means to harvest exosomes from many different biological fluids and for a wide variety of purposes.
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Date Issued: 2016-04-12
Identifier: FSU_libsubv1_wos_000373776100001, 10.1038/srep23978
Format: Citation

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

Title: From Shelf to Shelf: Assessing Historical and Contemporary Genetic Differentiation and Connectivity Across the Gulf of Mexico in Gag, Mycteroperca Microlepis.
Creator: Coleman, Felicia, Jue, Nathaniel K, Brule, Thierry
Abstract/Description: Describing patterns of connectivity among populations of species with widespread distributions is particularly important in understanding the ecology and evolution of marine species. In this study, we examined patterns of population differentiation, migration, and historical population dynamics using microsatellite and mitochondrial loci to test whether populations of the epinephelid fish, Gag, Mycteroperca microlepis, an important fishery species, are genetically connected across the Gulf of...
Show moreDescribing patterns of connectivity among populations of species with widespread distributions is particularly important in understanding the ecology and evolution of marine species. In this study, we examined patterns of population differentiation, migration, and historical population dynamics using microsatellite and mitochondrial loci to test whether populations of the epinephelid fish, Gag, Mycteroperca microlepis, an important fishery species, are genetically connected across the Gulf of Mexico and if so, whether that connectivity is attributable to either contemporary or historical processes. Populations of Gag on the Campeche Bank and the West Florida Shelf show significant, but low magnitude, differentiation. Time since divergence/expansion estimates associated with historical population dynamics indicate that any population or spatial expansions indicated by population genetics would have likely occurred in the late Pleistocene. Using coalescent-based approaches, we find that the best model for explaining observed spatial patterns of contemporary genetic variation is one of asymmetric gene flow, with movement from Campeche Bank to the West Florida Shelf. Both estimated migration rates and ecological data support the hypothesis that Gag populations throughout the Gulf of Mexico are connected via present day larval dispersal. Demonstrating this greatly expanded scale of connectivity for Gag highlights the influence of “ghost” populations (sensu Beerli) on genetic patterns and presents a critical consideration for both fisheries management and conservation of this and other species with similar genetic patterns
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Date Issued: 2015-04-09
Identifier: FSU_libsubv1_scholarship_submission_1475086524, 10.1371/journal.pone.0120676
Format: Citation

Title: Function of Succinoglycan Polysaccharide in Sinorhizobium meliloti Host Plant Invasion Depends on Succinylation, Not Molecular Weight.
Creator: Mendis, Hajeewaka C., Madzima, Thelma F., Queiroux, Clothilde, Jones, Kathryn M.
Abstract/Description: The acidic polysaccharide succinoglycan produced by the rhizobial symbiont Sinorhizobium meliloti 1021 is required for this bacterium to invade the host plant Medicago truncatula and establish a nitrogen-fixing symbiosis. S. meliloti mutants that cannot make succinoglycan cannot initiate invasion structures called infection threads in plant root hairs. S. meliloti exoH mutants that cannot succinylate succinoglycan are also unable to form infection threads, despite the fact that they make...
Show moreThe acidic polysaccharide succinoglycan produced by the rhizobial symbiont Sinorhizobium meliloti 1021 is required for this bacterium to invade the host plant Medicago truncatula and establish a nitrogen-fixing symbiosis. S. meliloti mutants that cannot make succinoglycan cannot initiate invasion structures called infection threads in plant root hairs. S. meliloti exoH mutants that cannot succinylate succinoglycan are also unable to form infection threads, despite the fact that they make large quantities of succinoglycan. Succinoglycan produced by exoH mutants is refractory to cleavage by the glycanases encoded by exoK and exsH, and thus succinoglycan produced by exoH mutants is made only in the high-molecular-weight (HMW) form. One interpretation of the symbiotic defect of exoH mutants is that the low-molecular-weight (LMW) form of succinoglycan is required for infection thread formation. However, our data demonstrate that production of the HMW form of succinoglycan by S. meliloti 1021 is sufficient for invasion of the host M. truncatula and that the LMW form is not required. Here, we show that S. meliloti strains deficient in the exoK- and exsH-encoded glycanases invade M. truncatula and form a productive symbiosis, although they do this with somewhat less efficiency than the wild type. We have also characterized the polysaccharides produced by these double glycanase mutants and determined that they consist of only HMW succinoglycan and no detectable LMW succinoglycan. This demonstrates that LMW succinoglycan is not required for host invasion. These results suggest succinoglycan function is not dependent upon the presence of a small, readily diffusible form. IMPORTANCE Sinorhizobium meliloti is a bacterium that forms a beneficial symbiosis with legume host plants. S. meliloti and other rhizobia convert atmospheric nitrogen to ammonia, a nutrient source for the host plant. To establish the symbiosis, rhizobia must invade plant roots, supplying the proper signals to prevent a plant immune response during invasion. A polysaccharide, succinoglycan, produced by S. meliloti is required for successful invasion. Here, we show that the critical feature of succinoglycan that allows infection to proceed is the attachment of a "succinyl" chemical group and that the chain length of succinoglycan is much less important for its function. We also show that none of the short-chain versions of succinoglycan is produced in the absence of two chain-cleaving enzymes.
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Date Issued: 2016-06
Identifier: FSU_libsubv1_wos_000383440300038, 10.1128/mBio.00606-16
Format: Citation

Title: Function of Succinoglycan Polysaccharide in Sinorhizobium meliloti Host Plant Invasion Depends on Succinylation, Not Molecular Weight.
Creator: Mendis, Hajeewaka C, Madzima, Thelma F, Queiroux, Clothilde, Jones, Kathryn M
Abstract/Description: The acidic polysaccharide succinoglycan produced by the rhizobial symbiont Sinorhizobium meliloti 1021 is required for this bacterium to invade the host plant Medicago truncatula and establish a nitrogen-fixing symbiosis. S. meliloti mutants that cannot make succinoglycan cannot initiate invasion structures called infection threads in plant root hairs. S. meliloti exoH mutants that cannot succinylate succinoglycan are also unable to form infection threads, despite the fact that they make...
Show moreThe acidic polysaccharide succinoglycan produced by the rhizobial symbiont Sinorhizobium meliloti 1021 is required for this bacterium to invade the host plant Medicago truncatula and establish a nitrogen-fixing symbiosis. S. meliloti mutants that cannot make succinoglycan cannot initiate invasion structures called infection threads in plant root hairs. S. meliloti exoH mutants that cannot succinylate succinoglycan are also unable to form infection threads, despite the fact that they make large quantities of succinoglycan. Succinoglycan produced by exoH mutants is refractory to cleavage by the glycanases encoded by exoK and exsH, and thus succinoglycan produced by exoH mutants is made only in the high-molecular-weight (HMW) form. One interpretation of the symbiotic defect of exoH mutants is that the low-molecular-weight (LMW) form of succinoglycan is required for infection thread formation. However, our data demonstrate that production of the HMW form of succinoglycan by S. meliloti 1021 is sufficient for invasion of the host M. truncatula and that the LMW form is not required. Here, we show that S. meliloti strains deficient in the exoK- and exsH-encoded glycanases invade M. truncatula and form a productive symbiosis, although they do this with somewhat less efficiency than the wild type. We have also characterized the polysaccharides produced by these double glycanase mutants and determined that they consist of only HMW succinoglycan and no detectable LMW succinoglycan. This demonstrates that LMW succinoglycan is not required for host invasion. These results suggest succinoglycan function is not dependent upon the presence of a small, readily diffusible form. Sinorhizobium meliloti is a bacterium that forms a beneficial symbiosis with legume host plants. S. meliloti and other rhizobia convert atmospheric nitrogen to ammonia, a nutrient source for the host plant. To establish the symbiosis, rhizobia must invade plant roots, supplying the proper signals to prevent a plant immune response during invasion. A polysaccharide, succinoglycan, produced by S. meliloti is required for successful invasion. Here, we show that the critical feature of succinoglycan that allows infection to proceed is the attachment of a "succinyl" chemical group and that the chain length of succinoglycan is much less important for its function. We also show that none of the short-chain versions of succinoglycan is produced in the absence of two chain-cleaving enzymes.
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Date Issued: 2016-06-21
Identifier: FSU_pmch_27329751, 10.1128/mBio.00606-16, PMC4916376, 27329751, 27329751, mBio.00606-16
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: 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

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