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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: 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: 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: 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: 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: 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: 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 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: 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: 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: 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: 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: 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: 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: Genetic Dissection of Dual Roles for the Transcription Factor six7 in Photoreceptor Development and Patterning in Zebrafish.
Creator: Sotolongo-Lopez, Mailin, Alvarez-Delfin, Karen, Saade, Carole J., Vera, Daniel L., Fadool, James M.
Abstract/Description: The visual system of a particular species is highly adapted to convey detailed ecological and behavioral information essential for survival. The consequences of structural mutations of opsins upon spectral sensitivity and environmental adaptation have been studied in great detail, but lacking is knowledge of the potential influence of alterations in gene regulatory networks upon the diversity of cone subtypes and the variation in the ratio of rods and cones observed in numerous diurnal and...
Show moreThe visual system of a particular species is highly adapted to convey detailed ecological and behavioral information essential for survival. The consequences of structural mutations of opsins upon spectral sensitivity and environmental adaptation have been studied in great detail, but lacking is knowledge of the potential influence of alterations in gene regulatory networks upon the diversity of cone subtypes and the variation in the ratio of rods and cones observed in numerous diurnal and nocturnal species. Exploiting photoreceptor patterning in cone-dominated zebrafish, we uncovered two independent mechanisms by which the sine oculis homeobox homolog 7 (six7) regulates photoreceptor development. In a genetic screen, we isolated the lots-of-rods-junior (ljr(p23ahub)) mutation that resulted in an increased number and uniform distribution of rods in otherwise normal appearing larvae. Sequence analysis, genome editing using TALENs and knockdown strategies confirm ljr(p23ahub) as a hypomorphic allele of six7, a teleost orthologue of six3, with known roles in forebrain patterning and expression of opsins. Based on the lack of predicted protein-coding changes and a deletion of a conserved element upstream of the transcription start site, a cis-regulatory mutation is proposed as the basis of the reduced expression of six7 in ljr(p23ahub). Comparison of the phenotypes of the hypomorphic and knock-out alleles provides evidence of two independent roles in photoreceptor development. EdU and PH3 labeling show that the increase in rod number is associated with extended mitosis of photoreceptor progenitors, and TUNEL suggests that the lack of green-sensitive cones is the result of cell death of the cone precursor. These data add six7 to the small but growing list of essential genes for specification and patterning of photoreceptors in non-mammalian vertebrates, and highlight alterations in transcriptional regulation as a potential source of photoreceptor variation across species.
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Date Issued: 2016-04
Identifier: FSU_libsubv1_wos_000375231900020, 10.1371/journal.pgen.1005968
Format: Citation

Title: The Genetics Of Venom Ontogeny In The Eastern Diamondback Rattlesnake (crotalus Adamanteus).
Creator: Rokyta, Darin R., Margres, Mark J., Ward, Micaiah J., Sanchez, Elda E.
Abstract/Description: The same selective forces that give rise to rapid inter- and intraspecific divergence in snake venoms can also favor differences in venoms across life-history stages. Ontogenetic changes in venom composition are well known and widespread in snakes but have not been investigated to the level of unambiguously identifying the specific loci involved. The eastern diamondback rattlesnake was previously shown to undergo an ontogenetic shift in venom composition at sexual maturity, and this shift...
Show moreThe same selective forces that give rise to rapid inter- and intraspecific divergence in snake venoms can also favor differences in venoms across life-history stages. Ontogenetic changes in venom composition are well known and widespread in snakes but have not been investigated to the level of unambiguously identifying the specific loci involved. The eastern diamondback rattlesnake was previously shown to undergo an ontogenetic shift in venom composition at sexual maturity, and this shift accounted for more venom variation than (geography. To characterize the genetics underlying the ontogenetic venom compositional change in C. adamanteus, we sequenced adult/juvenile pairs of venom-gland transcriptomes from five populations previously shown to have different adult venom compositions. We identified a total of 59 putative toxin transcripts for C. adamanteus, and 12 of these were involved in the ontogenetic change. Three toxins were downregulated, and nine were upregulated in adults relative to juveniles. Adults and juveniles expressed similar total levels of snake-venom metalloproteinases but differed substantially in their featured paralogs, and adults expressed higher levels of Bradykinin-potentiating and C-type natriuretic peptides, nerve growth factor, and specific paralogs of phospholipases A(2) and snake venom serine proteinases. Juvenile venom was more toxic to mice, indicating that the expression differences resulted in a phenotypically, and therefore potentially ecologically, significant difference in venom function. We also showed that adult and juvenile venom-gland transcriptomes for a species with known ontogenetic venom variation were equally effective at individually providing a full characterization of the venom genes of a species but that any particular individual was likely to lack several toxins in their transcriptome. A full characterization of a species' venom-gene complement therefore requires sequencing more than one individual, although the ages of the individuals are unimportant.
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Date Issued: 2017-04-27
Identifier: FSU_libsubv1_wos_000400305500019, 10.7717/peerj.3249
Format: Citation

Title: Geographic variation in hybridization across a reinforcement contact zone of chorus frogs (Pseudacris).
Creator: Lemmon, Emily Moriarty, Juenger, Thomas E.
Abstract/Description: Reinforcement contact zones, which are secondary contact zones where species are diverging in reproductive behaviors due to selection against hybridization, represent natural laboratories for studying speciation-in-action. Here, we examined replicate localities across the entire reinforcement contact zone between North American chorus frogs Pseudacris feriarum and P. nigrita to investigate geographic variation in hybridization frequencies and to assess whether reinforcement may have...
Show moreReinforcement contact zones, which are secondary contact zones where species are diverging in reproductive behaviors due to selection against hybridization, represent natural laboratories for studying speciation-in-action. Here, we examined replicate localities across the entire reinforcement contact zone between North American chorus frogs Pseudacris feriarum and P. nigrita to investigate geographic variation in hybridization frequencies and to assess whether reinforcement may have contributed to increased genetic divergence within species. Previous work indicated these species have undergone reproductive character displacement (RCD) in male acoustic signals and female preferences due to reinforcement. We also examined acoustic signal variation across the contact zone to assess whether signal characteristics reliably predict hybrid index and to elucidate whether the degree of RCD predicts hybridization rate. Using microsatellites, mitochondrial sequences, and acoustic signal information from >1,000 individuals across >50 localities and ten sympatric focal regions, we demonstrate: (1) hybridization occurs and (2) varies substantially across the geographic range of the contact zone, (3) hybridization is asymmetric and in the direction predicted from observed patterns of asymmetric RCD, (4) in one species, genetic distance is higher between conspecific localities where one or both have been reinforced than between nonreinforced localities, after controlling for geographic distance, (5) acoustic signal characters strongly predict hybrid index, and (6) the degree of RCD does not strongly predict admixture levels. By showing that hybridization occurs in all sympatric localities, this study provides the fifth and final line of evidence that reproductive character displacement is due to reinforcement in the chorus frog contact zone. Furthermore, this work suggests that the dual action of cascade reinforcement and partial geographic isolation is promoting genetic diversification within one of the reinforced species.
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Date Issued: 2017-10-11
Identifier: FSU_libsubv1_scholarship_submission_1518810795_fea4fd92, 10.1002/ece3.3443
Format: Citation

Title: Glucagon-like peptide 1 receptor activation regulates cocaine actions and dopamine homeostasis in the lateral septum by decreasing arachidonic acid levels.
Creator: Reddy, I. A., Pino, J. A., Weikop, P., Osses, N., Sorensen, G., Bering, T., Valle, C., Bluett, R. J., Erreger, K., Wortwein, G., Reyes, J. G., Graham, D., Stanwood, G. D.,...
Show moreReddy, I. A., Pino, J. A., Weikop, P., Osses, N., Sorensen, G., Bering, T., Valle, C., Bluett, R. J., Erreger, K., Wortwein, G., Reyes, J. G., Graham, D., Stanwood, G. D., Hackett, T. A., Patel, S., Fink-Jensen, A., Torres, G. E., Galli, A.
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Abstract/Description: Agonism of the glucagon-like peptide 1 (GLP-1) receptor (GLP-1R) has been effective at treating aspects of addictive behavior for a number of abused substances, including cocaine. However, the molecular mechanisms and brain circuits underlying the therapeutic effects of GLP-1R signaling on cocaine actions remain elusive. Recent evidence has revealed that endogenous signaling at the GLP-1R within the forebrain lateral septum (LS) acts to reduce cocaine-induced locomotion and cocaine...
Show moreAgonism of the glucagon-like peptide 1 (GLP-1) receptor (GLP-1R) has been effective at treating aspects of addictive behavior for a number of abused substances, including cocaine. However, the molecular mechanisms and brain circuits underlying the therapeutic effects of GLP-1R signaling on cocaine actions remain elusive. Recent evidence has revealed that endogenous signaling at the GLP-1R within the forebrain lateral septum (LS) acts to reduce cocaine-induced locomotion and cocaine conditioned place preference, both considered dopamine (DA)-associated behaviors. DA terminals project from the ventral tegmental area to the LS and express the DA transporter (DAT). Cocaine acts by altering DA bioavailability by targeting the DAT. Therefore, GLP-1R signaling might exert effects on DAT to account for its regulation of cocaine-induced behaviors. We show that the GLP-1R is highly expressed within the LS. GLP-1, in LS slices, significantly enhances DAT surface expression and DAT function. Exenatide (Ex-4), a long-lasting synthetic analog of GLP-1 abolished cocaine-induced elevation of DA. Interestingly, acute administration of Ex-4 reduces septal expression of the retrograde messenger 2-arachidonylglycerol (2-AG), as well as a product of its presynaptic degradation, arachidonic acid (AA). Notably, AA reduces septal DAT function pointing to AA as a novel regulator of central DA homeostasis. We further show that AA oxidation product.-ketoaldehyde (gamma-KA) forms adducts with the DAT and reduces DAT plasma membrane expression and function. These results support a mechanism in which postsynaptic septal GLP-1R activation regulates 2-AG levels to alter presynaptic DA homeostasis and cocaine actions through AA.
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Date Issued: 2016-05-17
Identifier: FSU_libsubv1_wos_000377306000002, 10.1038/tp.2016.86
Format: Citation

Title: Habitat Configuration Affects Spatial Pattern of β Diversity of Insect Communities Breeding in Oyster Mushrooms.
Creator: Inouye, Brian, Kadowaki, Komei
Abstract/Description: Theory predicts that spatial structure can mediate interactions that affect species diversity in a patchy environment. A rarely considered effect of spatial structure on biodiversity is the interplay of spatial habitat arrangement with species interactions at multiple spatial scales. We investigated how spatial habitat arrangement and predation mediate the assembly of the larval communities of fungivorous insects breeding in the oyster mushroom, Pleurotus ostreatus (Jacq. ex Fr.) P.Kumm in a...
Show moreTheory predicts that spatial structure can mediate interactions that affect species diversity in a patchy environment. A rarely considered effect of spatial structure on biodiversity is the interplay of spatial habitat arrangement with species interactions at multiple spatial scales. We investigated how spatial habitat arrangement and predation mediate the assembly of the larval communities of fungivorous insects breeding in the oyster mushroom, Pleurotus ostreatus (Jacq. ex Fr.) P.Kumm in a North American woodland. In a two-way factorial design, we varied the spatial arrangement of mushroom clumps (‘clustered', ‘patchy', and ‘uniform'; 3 levels) crossed with predator exclusion (access allowed or not; 2 levels) to study their joint effects on patterns of α, β and γ diversity of the fungivorous insect communities. Partitioning diversity into these three components suggested that neither spatial nor predation treatments significantly affected α, β and γ diversity. We found that an intermediate inter-clump distance (i.e., the ‘patchy' treatment) increased spatial autocorrelation in insect community composition within experimental blocks, particularly in the mushrooms to which predators had access. The spatial structuring in β diversity indicates that the arrangement of mushroom clumps can structure β diversity of fungivorous larval communities through direct effects on the species themselves (e.g., increased aggregation and habitat choice of ovipositing females of fungivorous insects), as well as effects mediated through the presence and behavior of predators (e.g., spatially structured selective foraging by predators acting as a filter on which species were in the clumps). The naturally patchy nature of mushroom fruiting may transform the spatial pattern of β diversity by altering the behavior of ovipositing females, or by weakening the negative effect of larval competition.
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Date Issued: 2015-05-08
Identifier: FSU_libsubv1_scholarship_submission_1474991511, 10.1890/ES14-00327.1
Format: Citation

Title: Hierarchical regulation of the genome: global changes in nucleosome organization potentiate genome response.
Creator: Sexton, Brittany S., Druliner, Brooke R., Vera, Daniel L., Avey, Denis, Zhu, Fanxiu, Dennis, Jonathan H.
Abstract/Description: Nucleosome occupancy is critically important in regulating access to the eukaryotic genome. Few studies in human cells have measured genome-wide nucleosome distributions at high temporal resolution during a response to a common stimulus. We measured nucleosome distributions at high temporal resolution following Kaposi's-sarcoma-associated herpesvirus (KSHV) reactivation using our newly developed mTSS-seq technology, which maps nucleosome distribution at the transcription start sites (TSS) of...
Show moreNucleosome occupancy is critically important in regulating access to the eukaryotic genome. Few studies in human cells have measured genome-wide nucleosome distributions at high temporal resolution during a response to a common stimulus. We measured nucleosome distributions at high temporal resolution following Kaposi's-sarcoma-associated herpesvirus (KSHV) reactivation using our newly developed mTSS-seq technology, which maps nucleosome distribution at the transcription start sites (TSS) of all human genes. Nucleosomes underwent widespread changes in organization 24 hours after KSHV reactivation and returned to their basal nucleosomal architecture 48 hours after KSHV reactivation. The widespread changes consisted of an indiscriminate remodeling event resulting in the loss of nucleosome rotational phasing signals. Additionally, one in six TSSs in the human genome possessed nucleosomes that are translationally remodeled. 72% of the loci with translationally remodeled nucleosomes have nucleosomes that moved to positions encoded by the underlying DNA sequence. Finally we demonstrated that these widespread alterations in nucleosomal architecture potentiated regulatory factor binding. These descriptions of nucleosomal architecture changes provide a new framework for understanding the role of chromatin in the genomic response, and have allowed us to propose a hierarchical model for chromatin-based regulation of genome response.
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Date Issued: 2016-02-09
Identifier: FSU_libsubv1_wos_000376123100009, 10.18632/oncotarget.6841
Format: Citation

Title: Histone Posttranslational Modifications Predict Specific Alternative Exon Subtypes In Mammalian Brain.
Creator: Hu, Qiwen, Kim, Eun Ji, Feng, Jian, Grant, Gregory R., Heller, Elizabeth A.
Abstract/Description: A compelling body of literature, based on next generation chromatin immunoprecipitation and RNA sequencing of reward brain regions indicates that the regulation of the epigenetic landscape likely underlies chronic drug abuse and addiction. It is now critical to develop highly innovative computational strategies to reveal the relevant regulatory transcriptional mechanisms that may underlie neuropsychiatric disease. We have analyzed chromatin regulation of alternative splicing, which is...
Show moreA compelling body of literature, based on next generation chromatin immunoprecipitation and RNA sequencing of reward brain regions indicates that the regulation of the epigenetic landscape likely underlies chronic drug abuse and addiction. It is now critical to develop highly innovative computational strategies to reveal the relevant regulatory transcriptional mechanisms that may underlie neuropsychiatric disease. We have analyzed chromatin regulation of alternative splicing, which is implicated in cocaine exposure in mice. Recent literature has described chromatin-regulated alternative splicing, suggesting a novel function for drug-induced neuroepigenetic remodeling. However, the extent of the genome-wide association between particular histone modifications and alternative splicing remains unexplored. To address this, we have developed novel computational approaches to model the association between alternative splicing and histone posttranslational modifications in the nucleus accumbens (NAc), a brain reward region. Using classical statistical methods and machine learning to combine ChIP-Seq and RNA-Seq data, we found that specific histone modifications are strongly associated with various aspects of differential splicing. H3K36me3 and H3K4me1 have the strongest association with splicing indicating they play a significant role in alternative splicing in brain reward tissue.
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Date Issued: 2017-06
Identifier: FSU_libsubv1_wos_000404565400051, 10.1371/journal.pcbi.1005602
Format: Citation

Title: How Plant Neighborhood Composition Influences Herbivory: Testing Four Mechanisms Of Associational Resistance And Susceptibility.
Creator: Kim, Tania N.
Abstract/Description: Neighboring plants can decrease or increase each other's likelihood of damage from herbivores through associational resistance or susceptibility, respectively. Associational effects (AE) can transpire through changes in herbivore or plant traits that affect herbivore movement, densities, and feeding behaviors to ultimately affect plant damage. While much work has focused on understanding the mechanisms that underlie associational effects, we know little about how these mechanisms are...
Show moreNeighboring plants can decrease or increase each other's likelihood of damage from herbivores through associational resistance or susceptibility, respectively. Associational effects (AE) can transpire through changes in herbivore or plant traits that affect herbivore movement, densities, and feeding behaviors to ultimately affect plant damage. While much work has focused on understanding the mechanisms that underlie associational effects, we know little about how these mechanisms are influenced by neighborhood composition, i.e., plant density or relative frequency which is necessary to make predictions about when AE should occur in nature. Using a series of field and greenhouse experiments, I examined how plant density and relative frequency affected plant damage to Solanum carolinense and four mechanisms that underlie AE; (i) accumulation of insect herbivores and arthropod predators, (ii) microclimate conditions, (iii) plant resistance, and (iv) specialist herbivore preference. I found a positive relationship between S. carolinense damage and the relative frequency of a non-focal neighbor (Solidago altissima) and all four AE mechanisms were influenced by one or multiple neighborhood components. Frequency-dependence in S. carolinense damage is most likely due to greater generalist herbivore load on S. carolinense (through spillover from S. altissima) with microclimate variables, herbivore preference, predation pressures, and plant resistance having relatively weaker effects. Associational effects may have long-term consequences for these two plant species during plant succession and understanding context-dependent herbivory has insect pest management implication for other plant species in agriculture and forestry.
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Date Issued: 2017-05-09
Identifier: FSU_libsubv1_wos_000401314000013, 10.1371/journal.pone.0176499
Format: Citation

Title: An improved smaller biotin ligase for BioID proximity labeling.
Creator: Kim, Dae In, Jensen, Samuel C., Noble, Kyle A., Birendra, K. C., Roux, Kenneth H., Motamedchaboki, Khatereh, Roux, Kyle J.
Abstract/Description: The BioID method uses a promiscuous biotin ligase to detect protein-protein associations as well as proximate proteins in living cells. Here we report improvements to the BioID method centered on BioID2, a substantially smaller promiscuous biotin ligase. BioID2 enables more-selective targeting of fusion proteins, requires less biotin supplementation, and exhibits enhanced labeling of proximate proteins. Thus BioID2 improves the efficiency of screening for protein-protein associations. We also...
Show moreThe BioID method uses a promiscuous biotin ligase to detect protein-protein associations as well as proximate proteins in living cells. Here we report improvements to the BioID method centered on BioID2, a substantially smaller promiscuous biotin ligase. BioID2 enables more-selective targeting of fusion proteins, requires less biotin supplementation, and exhibits enhanced labeling of proximate proteins. Thus BioID2 improves the efficiency of screening for protein-protein associations. We also demonstrate that the biotinylation range of BioID2 can be considerably modulated using flexible linkers, thus enabling application-specific adjustment of the biotin-labeling radius.
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Date Issued: 2016-04-15
Identifier: FSU_libsubv1_wos_000375753600003, 10.1091/mbc.E15-12-0844
Format: Citation

Title: Influence Of Repressive Histone And Dna Methylation Upon D4z4 Transcription In Non-myogenic Cells.
Creator: Das, Sunny, Chadwick, Brian P.
Abstract/Description: We looked at a disease-associated macrosatellite array D4Z4 and focused on epigenetic factors influencing its chromatin state outside of the disease-context. We used the HCT116 cell line that contains the non-canonical polyadenylation (poly-A) signal required to stabilize somatic transcripts of the human double homeobox gene DUX4, encoded from D4Z4. In HCT116, D4Z4 is packaged into constitutive heterochromatin, characterized by DNA methylation and histone H3 tri-methylation at lysine 9 ...
Show moreWe looked at a disease-associated macrosatellite array D4Z4 and focused on epigenetic factors influencing its chromatin state outside of the disease-context. We used the HCT116 cell line that contains the non-canonical polyadenylation (poly-A) signal required to stabilize somatic transcripts of the human double homeobox gene DUX4, encoded from D4Z4. In HCT116, D4Z4 is packaged into constitutive heterochromatin, characterized by DNA methylation and histone H3 tri-methylation at lysine 9 (H3K9me3), resulting in low basal levels of D4Z4-derived transcripts. However, a double knockout (DKO) of DNA methyltransferase genes, DNMT1 and DNMT3B, but not either alone, results in significant loss of DNA and H3K9 methylation. This is coupled with upregulation of transcript levels from the array, including DUX4 isoforms (DUX4-fl) that are abnormally expressed in somatic muscle in the disease Facioscapulohumeral muscular dystrophy (FSHD) along with DUX4 protein, as indicated indirectly by upregulation of bondafide targets of DUX4 in DKO but not HCT116 cells. Results from treatment with a chemical inhibitor of histone methylation in HCT116 suggest that in the absence of DNA hypomethylation, H3K9me3 loss alone is sufficient to facilitate DUX4-fl transcription. Additionally, characterization of a cell line from a patient with Immunodeficiency, Centromeric instability and Facial anomalies syndrome 1 (ICF1) possessing a non-canonical poly-A signal and DNA hypomethylation at D4Z4 showed DUX4 target gene upregulation in the patient when compared to controls in spite of retention of H3K9me3. Taken together, these data suggest that both DNA methylation and H3K9me3 are determinants of D4Z4 silencing. Moreover, we show that in addition to testis, there is appreciable expression of spliced and polyadenylated D4Z4 derived transcripts that contain the complete DUX4 open reading frame (ORF) along with DUX4 target gene expression in the thymus, suggesting that DUX4 may provide normal function in this somatic tissue.
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Date Issued: 2016-07-28
Identifier: FSU_libsubv1_wos_000381516100091, 10.1371/journal.pone.0160022
Format: Citation

Title: Integrin-mediated Traction Force Enhances Paxillin Molecular Associations And Adhesion Dynamics That Increase The Invasiveness Of Tumor Cells Into A Three-dimensional Extracellular Matrix.
Creator: Mekhdjian, Armen H., Kai, FuiBoon, Rubashkin, Matthew G., Prahl, Louis S., Przybyla, Laralynne M., McGregor, Alexandra L., Bell, Emily S., Barnes, J. Matthew, DuFort,...
Show moreMekhdjian, Armen H., Kai, FuiBoon, Rubashkin, Matthew G., Prahl, Louis S., Przybyla, Laralynne M., McGregor, Alexandra L., Bell, Emily S., Barnes, J. Matthew, DuFort, Christopher C., Ou, Guanqing, Chang, Alice C., Cassereau, Luke, Tan, Steven J., Pickup, Michael W., Lakins, Jonathan N., Ye, Xin, Davidson, Michael W., Lammerding, Jan, Odde, David J., Dunn, Alexander R., Weaver, Valerie M.
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Abstract/Description: Metastasis requires tumor cells to navigate through a stiff stroma and squeeze through confined microenvironments. Whether tumors exploit unique biophysical properties to metastasize remains unclear. Data show that invading mammary tumor cells, when cultured in a stiffened three-dimensional extracellular matrix that recapitulates the primary tumor stroma, adopt a basal-like phenotype. Metastatic tumor cells and basal-like tumor cells exert higher integrin-mediated traction forces at the bulk...
Show moreMetastasis requires tumor cells to navigate through a stiff stroma and squeeze through confined microenvironments. Whether tumors exploit unique biophysical properties to metastasize remains unclear. Data show that invading mammary tumor cells, when cultured in a stiffened three-dimensional extracellular matrix that recapitulates the primary tumor stroma, adopt a basal-like phenotype. Metastatic tumor cells and basal-like tumor cells exert higher integrin-mediated traction forces at the bulk and molecular levels, consistent with a motor-clutch model in which motors and clutches are both increased. Basal-like nonmalignant mammary epithelial cells also display an altered integrin adhesion molecular organization at the nanoscale and recruit a suite of paxillin-associated proteins implicated in invasion and metastasis. Phosphorylation of paxillin by Src family kinases, which regulates adhesion turnover, is similarly enhanced in the metastatic and basal-like tumor cells, fostered by a stiff matrix, and critical for tumor cell invasion in our assays. Bioinformatics reveals an unappreciated relationship between Src kinases, paxillin, and survival of breast cancer patients. Thus adoption of the basal-like adhesion phenotype may favor the recruitment of molecules that facilitate tumor metastasis to integrin-based adhesions. Analysis of the physical properties of tumor cells and integrin adhesion composition in biopsies may be predictive of patient outcome.
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Date Issued: 2017-06-01
Identifier: FSU_libsubv1_wos_000402330400009, 10.1091/mbc.E16-09-0654
Format: Citation

Title: The M(6)a Pathway Facilitates Sex Determination In Drosophila.
Creator: Kan, Lijuan, Grozhik, Anya V., Vedanayagam, Jeffrey, Patil, Deepak P., Pang, Nan, Lim, Kok-Seong, Huang, Yi-Chun, Joseph, Brian, Lin, Ching-Jung, Despic, Vladimir, Guo, Jian,...
Show moreKan, Lijuan, Grozhik, Anya V., Vedanayagam, Jeffrey, Patil, Deepak P., Pang, Nan, Lim, Kok-Seong, Huang, Yi-Chun, Joseph, Brian, Lin, Ching-Jung, Despic, Vladimir, Guo, Jian, Yan, Dong, Kondo, Shu, Deng, Wu-Min, Dedon, Peter C., Jaffrey, Samie R., Lai, Eric C.
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Abstract/Description: The conserved modification N-6-methyladenosine (m(6)A) modulates mRNA processing and activity. Here, we establish the Drosophila system to study the m(6)A pathway. We first apply miCLIP to map m(6)A across embryogenesis, characterize its m(6)A 'writer' complex, validate its YTH 'readers' CG6422 and YT521-B, and generate mutants in five m(6)A factors. While m(6)A factors with additional roles in splicing are lethal, m(6)A-specific mutants are viable but present certain developmental and...
Show moreThe conserved modification N-6-methyladenosine (m(6)A) modulates mRNA processing and activity. Here, we establish the Drosophila system to study the m(6)A pathway. We first apply miCLIP to map m(6)A across embryogenesis, characterize its m(6)A 'writer' complex, validate its YTH 'readers' CG6422 and YT521-B, and generate mutants in five m(6)A factors. While m(6)A factors with additional roles in splicing are lethal, m(6)A-specific mutants are viable but present certain developmental and behavioural defects. Notably, m(6)A facilitates the master female determinant Sxl, since multiple m(6)A components enhance female lethality in Sxl sensitized backgrounds. The m(6)A pathway regulates Sxl processing directly, since miCLIP data reveal Sxl as a major intronic m(6)A target, and female-specific Sxl splicing is compromised in multiple m(6)A pathway mutants. YT521-B is a dominant m(6)A effector for Sxl regulation, and YT521-B overexpression can induce female-specific Sxl splicing. Overall, our transcriptomic and genetic toolkit reveals in vivo biologic function for the Drosophila m(6)A pathway.
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Date Issued: 2017-07-04
Identifier: FSU_libsubv1_wos_000404640800001, 10.1038/ncomms15737
Format: Citation

Title: Mechanism Of Ribosome Rescue By Arfa And Rf2.
Creator: Demo, Gabriel, Svidritskiy, Egor, Madireddy, Rohini, Diaz-Avalos, Ruben, Grant, Timothy, Grigorieff, Nikolaus, Sousa, Duncan, Korostelev, Andrei A.
Abstract/Description: ArfA rescues ribosomes stalled on truncated mRNAs by recruiting release factor RF2, which normally binds stop codons to catalyze peptide release. We report two 3.2 angstrom resolution cryo-EM structures - determined from a single sample - of the 70S ribosome with ArfA.RF2 in the A site. In both states, the ArfA C-terminus occupies the mRNA tunnel downstream of the A site. One state contains a compact inactive RF2 conformation. Ordering of the ArfA N-terminus in the second state rearranges RF2...
Show moreArfA rescues ribosomes stalled on truncated mRNAs by recruiting release factor RF2, which normally binds stop codons to catalyze peptide release. We report two 3.2 angstrom resolution cryo-EM structures - determined from a single sample - of the 70S ribosome with ArfA.RF2 in the A site. In both states, the ArfA C-terminus occupies the mRNA tunnel downstream of the A site. One state contains a compact inactive RF2 conformation. Ordering of the ArfA N-terminus in the second state rearranges RF2 into an extended conformation that docks the catalytic GGQ motif into the peptidyl-transferase center. Our work thus reveals the structural dynamics of ribosome rescue. The structures demonstrate how ArfA 'senses' the vacant mRNA tunnel and activates RF2 to mediate peptide release without a stop codon, allowing stalled ribosomes to be recycled.
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Date Issued: 2017-03-16
Identifier: FSU_libsubv1_wos_000398146500001, 10.7554/eLife.23687
Format: Citation

Title: Mitochondrial Ultrastructure And Glucose Signaling Pathways Attributed To The Kv1.3 Ion Channel.
Creator: Kovach, Christopher P., Al Koborssy, Dolly, Huang, Zhenbo, Chelette, Brandon M., Fadool, James M., Fadool, Debra A.
Abstract/Description: Gene-targeted deletion of the potassium channel Kv1.3 (Kv1.3(-/-)) results in "Super-smeller" mice with a sensory phenotype that includes an increased olfactory ability linked to changes in olfactory circuitry, increased abundance of olfactory cilia, and increased expression of odorant receptors and the G-protein, G(olf). Kv1.3(-/-) mice also have a metabolic phenotype including lower body weight and decreased adiposity, increased total energy expenditure (TEE), increased locomotor activity,...
Show moreGene-targeted deletion of the potassium channel Kv1.3 (Kv1.3(-/-)) results in "Super-smeller" mice with a sensory phenotype that includes an increased olfactory ability linked to changes in olfactory circuitry, increased abundance of olfactory cilia, and increased expression of odorant receptors and the G-protein, G(olf). Kv1.3(-/-) mice also have a metabolic phenotype including lower body weight and decreased adiposity, increased total energy expenditure (TEE), increased locomotor activity, and resistance to both diet- and genetic-induced obesity. We explored two cellular aspects to elucidate the mechanism by which loss of Kv1.3 channel in the olfactory bulb (OB) may enhance glucose utilization and metabolic rate. First, using in situ hybridization we find that Kv1.3 and the insulin-dependent glucose transporter type 4 (GLUT4) are co-localized to the mitral cell layer of the OB. Disruption of Kv1.3 conduction via construction of a pore mutation (W386F Kv1.3) was sufficient to independently translocate GLUT4 to the plasma membrane in HEK 293 cells. Because olfactory sensory perception and the maintenance of action potential (AP) firing frequency by mitral cells of the OB is highly energy demanding and Kv1.3 is also expressed in mitochondria, we next explored the structure of this organelle in mitral cells. We challenged wildtype (WT) and Kv1.3(-/-) male mice with a moderately high-fat diet (MHF, 31.8 % kcal fat) for 4 months and then examined OB ultrastructure using transmission electron microscopy. In WT mice, mitochondria were significantly enlarged following diet-induced obesity (DIO) and there were fewer mitochondria, likely due to mitophagy. Interestingly, mitochondria were significantly smaller in Kv1.3(-/-) mice compared with that of WT mice. Similar to their metabolic resistance to DIO, the Kv1.3(-/-) mice had unchanged mitochondria in terms of cross sectional area and abundance following a challenge with modified diet. We are very interested to understand how targeted disruption of the Kv1.3 channel in the OB can modify TEE. Our study demonstrates that Kv1.3 regulates mitochondrial structure and alters glucose utilization; two important metabolic changes that could drive whole system changes in metabolism initiated at the OB.
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Date Issued: 2016-05-19
Identifier: FSU_libsubv1_wos_000376059000001, 10.3389/fphys.2016.00178
Format: Citation

Title: Molecular signatures associated with ZIKV exposure in human cortical neural progenitors.
Creator: Zhang, Feiran, Hammack, Christy, Ogden, Sarah C., Cheng, Yichen, Lee, Emily M., Wen, Zhexing, Qian, Xuyu, Nguyen, Ha Nam, Li, Yujing, Yao, Bing, Xu, Miao, Xu, Tianlei, Chen, Li,...
Show moreZhang, Feiran, Hammack, Christy, Ogden, Sarah C., Cheng, Yichen, Lee, Emily M., Wen, Zhexing, Qian, Xuyu, Nguyen, Ha Nam, Li, Yujing, Yao, Bing, Xu, Miao, Xu, Tianlei, Chen, Li, Wang, Zhiqin, Feng, Hao, Huang, Wei-Kai, Yoon, Ki-jun, Shan, Chao, Huang, Luoxiu, Qin, Zhaohui, Christian, Kimberly M., Shi, Pei-Yong, Xu, Mingjiang, Xia, Menghang, Zheng, Wei, Wu, Hao, Song, Hongjun, Tang, Hengli, Ming, Guo-Li, Jin, Peng
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Abstract/Description: Zika virus (ZIKV) infection causes microcephaly and has been linked to other brain abnormalities. How ZIKV impairs brain development and function is unclear. Here we systematically profiled transcriptomes of human neural progenitor cells exposed to Asian ZIKV(C), African ZIKV(M), and dengue virus (DENV). In contrast to the robust global transcriptome changes induced by DENV, ZIKV has a more selective and larger impact on expression of genes involved in DNA replication and repair. While...
Show moreZika virus (ZIKV) infection causes microcephaly and has been linked to other brain abnormalities. How ZIKV impairs brain development and function is unclear. Here we systematically profiled transcriptomes of human neural progenitor cells exposed to Asian ZIKV(C), African ZIKV(M), and dengue virus (DENV). In contrast to the robust global transcriptome changes induced by DENV, ZIKV has a more selective and larger impact on expression of genes involved in DNA replication and repair. While overall expression profiles are similar, ZIKV(C), but not ZIKV(M), induces upregulation of viral response genes and TP53. P53 inhibitors can block the apoptosis induced by both ZIKV(C) and ZIKV(M) in hNPCs, with higher potency against ZIKV(C)-induced apoptosis. Our analyses reveal virus- and strain-specific molecular signatures associated with ZIKV infection. These datasets will help to investigate ZIKV-host interactions and identify neurovirulence determinants of ZIKV.
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Date Issued: 2016-10-14
Identifier: FSU_libsubv1_wos_000386945000012, 10.1093/nar/gkw765
Format: Citation

Title: Muroid rodent phylogenetics: 900-species tree reveals increasing diversification rates.
Creator: Steppan, Scott J., Schenk, John J.
Abstract/Description: We combined new sequence data for more than 300 muroid rodent species with our previously published sequences for up to five nuclear and one mitochondrial genes to generate the most widely and densely sampled hypothesis of evolutionary relationships across Muroidea. An exhaustive screening procedure for publically available sequences was implemented to avoid the propagation of taxonomic errors that are common to supermatrix studies. The combined data set of carefully screened sequences...
Show moreWe combined new sequence data for more than 300 muroid rodent species with our previously published sequences for up to five nuclear and one mitochondrial genes to generate the most widely and densely sampled hypothesis of evolutionary relationships across Muroidea. An exhaustive screening procedure for publically available sequences was implemented to avoid the propagation of taxonomic errors that are common to supermatrix studies. The combined data set of carefully screened sequences derived from all available sequences on GenBank with our new data resulted in a robust maximum likelihood phylogeny for 900 of the approximately 1,620 muroids. Several regions that were equivocally resolved in previous studies are now more decisively resolved, and we estimated a chronogram using 28 fossil calibrations for the most integrated age and topological estimates to date. The results were used to update muroid classification and highlight questions needing additional data. We also compared the results of multigene supermatrix studies like this one with the principal published supertrees and concluded that the latter are unreliable for any comparative study in muroids. In addition, we explored diversification patterns as an explanation for why muroid rodents represent one of the most species-rich groups of mammals by detecting evidence for increasing net diversification rates through time across the muroid tree. We suggest the observation of increasing rates may be due to a combination of parallel increases in rate across clades and high average extinction rates. Five increased diversification-rate-shifts were inferred, suggesting that multiple, but perhaps not independent, events have led to the remarkable species diversity in the superfamily. Our results provide a phylogenetic framework for comparative studies that is not highly dependent upon the signal from any one gene.
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Date Issued: 2017-08-16
Identifier: FSU_libsubv1_scholarship_submission_1520869888_479c6b5a, doi.org/10.1371/journal.pone.0183070
Format: Citation

Title: Native grouper indirectly ameliorates the negative effects of invasive lionfish.
Creator: Ellis, Robert D., Faletti, Meaghan E.
Abstract/Description: Non-trophic interactions between Indo-Pacific lionfish Pterois volitans and P. miles and Atlantic and Caribbean reef fishes are not yet well understood. To determine the effects of potential competitive and behavioral interactions between native predators and invasive lionfish, we experimentally altered the presence of lionfish and red grouper Epinephelus morio in karst solution holes in Florida Bay, USA, and then tracked subsequent changes in the juvenile reef fish and motile...
Show moreNon-trophic interactions between Indo-Pacific lionfish Pterois volitans and P. miles and Atlantic and Caribbean reef fishes are not yet well understood. To determine the effects of potential competitive and behavioral interactions between native predators and invasive lionfish, we experimentally altered the presence of lionfish and red grouper Epinephelus morio in karst solution holes in Florida Bay, USA, and then tracked subsequent changes in the juvenile reef fish and motile macroinvertebrate communities for 6 wk. Relative to solution holes where we excluded both predators, mean juvenile reef fish abundance declined 83.7% in solution holes with a lionfish but increased by 154% in solution holes with a red grouper. There was no difference in juvenile reef fish abundance in solution holes with both lionfish and red grouper compared to holes where we excluded both predators. The composition of lionfish stomach contents shifted from mostly teleost fishes when lionfish were present in solution holes alone, to mostly crustaceans when in the presence of a red grouper. Concurrently, the abundance of 2 species of cleaner shrimp (Ancylomenes pedersoni and Periclimenes yucatanicus) decreased by 14.7% when lionfish were present but increased by 56.2% at holes where lionfish were excluded. We suggest that these results are due to altered lionfish predatory behavior in the presence of red grouper and highlight the importance of maintaining intact native predator communities for ameliorating the negative effects of the lionfish invasion.
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Date Issued: 2016-10-25
Identifier: FSU_libsubv1_wos_000387116200022, 10.3354/meps11808
Format: Citation

Title: A new Arctic hadrosaurid from the Prince Creek Formation (lower Maastrichtian) of northern Alaska.
Creator: Mori, Hirotsugu, Druckenmiller, Patrick S., Erickson, Gregory M.
Abstract/Description: The Liscomb bonebed in the Price Creek Formation of northern Alaska has produced thousands of individual bones of a saurolophine hadrosaurid similar to Edmontosaurus; however, the specific identity of this taxon has been unclear, in part because the vast majority of the remains represent immature individuals. In this study, we address the taxonomic status of the Alaskan material through a comparative and quantitative morphological analysis of juvenile as well several near adult-sized...
Show moreThe Liscomb bonebed in the Price Creek Formation of northern Alaska has produced thousands of individual bones of a saurolophine hadrosaurid similar to Edmontosaurus; however, the specific identity of this taxon has been unclear, in part because the vast majority of the remains represent immature individuals. In this study, we address the taxonomic status of the Alaskan material through a comparative and quantitative morphological analysis of juvenile as well several near adult-sized specimens with particular reference to the two known species of Edmontosaurus, as well as a cladistic analysis using two different matrices for Hadrosauroidea. In the comparative morphological analysis, we introduce a quantitative method using bivariate plots to address ontogenetic variation. Our comparative anatomical analysis reveals that the Alaskan saurolophine possesses a unique suite of characters that distinguishes it from Edmontosaurus, including a premaxillary circumnarial ridge that projects posterolaterally without a premaxillary vestibular promontory, a shallow groove lateral to the posterodorsal premaxillary foramen, a relatively narrow jugal process of the postorbital lacking a postorbital pocket, a relatively tall maxilla, a relatively gracile jugal, a more strongly angled posterior margin of the anterior process of the jugal, wide lateral exposure of the quadratojugal, and a short symphyseal process of the dentary. The cladistic analyses consistently recover the Alaskan saurolophine as the sister taxon to Edmontosaurus annectens + Edmontosaurus regalis. This phylogenetic assessment is robust even when accounting for ontogenetically variable characters. Based on these results, we erect a new taxon, Ugrunaaluk kuukpikensis gen. et sp. nov. that contributes to growing evidence for a distinct, early Maastrichtian Arctic dinosaur community that existed at the northernmost extent of Laramidia during the Late Cretaceous.
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Date Issued: 2016
Identifier: FSU_libsubv1_wos_000371323000002, 10.4202/app.00152.2015
Format: Citation

Title: Ocean Acidification Changes The Male Fitness Landscape.
Creator: Campbell, Anna L., Levitan, Don R., Hosken, David J., Lewis, Ceri
Abstract/Description: Sperm competition is extremely common in many ecologically important marine taxa. Ocean acidification (OA) is driving rapid changes to the marine environments in which freely spawned sperm operate, yet the consequences of OA on sperm performance are poorly understood in the context of sperm competition. Here, we investigated the impacts of OA (+ 1000 mu atm pCO(2)) on sperm competitiveness for the sea urchin Paracentrotus lividus. Males with faster sperm had greater competitive fertilisation...
Show moreSperm competition is extremely common in many ecologically important marine taxa. Ocean acidification (OA) is driving rapid changes to the marine environments in which freely spawned sperm operate, yet the consequences of OA on sperm performance are poorly understood in the context of sperm competition. Here, we investigated the impacts of OA (+ 1000 mu atm pCO(2)) on sperm competitiveness for the sea urchin Paracentrotus lividus. Males with faster sperm had greater competitive fertilisation success in both seawater conditions. Similarly, males with more motile sperm had greater sperm competitiveness, but only under current pCO(2) levels. Under OA the strength of this association was significantly reduced and there were male sperm performance rank changes under OA, such that the best males in current conditions are not necessarily best under OA. Therefore OA will likely change the male fitness landscape, providing a mechanism by which environmental change alters the genetic landscape of marine species.
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Date Issued: 2016-08-17
Identifier: FSU_libsubv1_wos_000381496800001, 10.1038/srep31250
Format: Citation

Title: Pathways For Effects Of Small-scale Disturbances On A Rare Plant: How Mimulus Angustatus Benefits From Gopher Mounds.
Creator: Underwood, Nora, Inouye, Brian D.
Abstract/Description: Small-scale soil disturbances such as soil mounds produced by gophers are known to influence local plant communities. A variety of mechanisms might account for the influence of gopher disturbances on individual plant success, but understanding of these mechanisms is not well developed. Disturbances are often assumed to affect plants through changing competition or the abiotic environment, but disturbances might also influence plant size, which in turn influences other biotic interactions,...
Show moreSmall-scale soil disturbances such as soil mounds produced by gophers are known to influence local plant communities. A variety of mechanisms might account for the influence of gopher disturbances on individual plant success, but understanding of these mechanisms is not well developed. Disturbances are often assumed to affect plants through changing competition or the abiotic environment, but disturbances might also influence plant size, which in turn influences other biotic interactions, including pollination. In this study, we tested for effects of soil disturbance on the density, flower size, and reproduction of an annual plant, Mimulus angustatus. We used soil disturbance manipulations, observational data, and a pollination experiment to examine two possible pathways for effects of disturbance on M. angustatus: competition and pollination. We also considered how effects of gopher mounds change with years since initial disturbance. We found that disturbance strongly increased the local density and flower size of M. angustatus, but the strength of these effects decays quickly. We found no support for these effects being mediated by competition with other plant species. We also found that M. angustatus with larger flowers receive more natural pollination. Our pollination experiment suggests that M. angustatus benefits from pollination (seed set increases with hand pollination or access to pollinators), and suggests that pollen limitation may occur. Taken together, our results indicate that increased pollination and seed set is an alternative response to disturbance that should receive further consideration. Regardless of the exact mechanism, it appears that in the absence of frequent small-scale soil disturbance, M. angustatus would not persist at our field site, as a large majority of plant recruitment and seed set occurs on recent disturbances.
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Date Issued: 2017-06
Identifier: FSU_libsubv1_wos_000405626700005, 10.1002/ecs2.1838
Format: Citation

Title: Pearson 2018 Associated taxon records parsing R code.
Creator: Pearson, Katelin D
Date Issued: 2017-12-12
Identifier: FSU_libsubv1_scholarship_submission_1513098310_18502571
Format: Downloadable file

Title: Pearson 2018 Combined specimen records and associated taxon records.
Creator: Pearson, Katelin D
Abstract/Description: This dataset is the product of research by Katelin D. Pearson 2018 and consists of herbarium specimen records for the Florida State University R. K. Godfrey Herbarium (FSU) combined with observational records created by parsing the habitat field of these records for scientific names. The downloadable ZIP file contains the CSV dataset and a text file describing the data.
Date Issued: 2017-12-12
Identifier: FSU_libsubv1_scholarship_submission_1513095860_92a1a26b
Format: Downloadable file

Title: Platelet Function Is Modified By Common Sequence Variation In Megakaryocyte Super Enhancers.
Creator: Petersen, Romina, Lambourne, John J., Javierre, Biola M., Grassi, Luigi, Kreuzhuber, Roman, Ruklisa, Dace, Rosa, Isabel M., Tome, Ana R., Elding, Heather, van Geffen, Johanna P....
Show morePetersen, Romina, Lambourne, John J., Javierre, Biola M., Grassi, Luigi, Kreuzhuber, Roman, Ruklisa, Dace, Rosa, Isabel M., Tome, Ana R., Elding, Heather, van Geffen, Johanna P., Jiang, Tao, Farrow, Samantha, Cairns, Jonathan, Al-Subaie, Abeer M., Ashford, Sofie, Attwood, Antony, Batista, Joana, Bouman, Heleen, Burden, Frances, Choudry, Fizzah A., Clarke, Laura, Flicek, Paul, Garner, Stephen F., Haimel, Matthias, Kempster, Carly, Ladopoulos, Vasileios, Lenaerts, An-Sofie, Materek, Paulina M., McKinney, Harriet, Meacham, Stuart, Mead, Daniel, Nagy, Magdolna, Penkett, Christopher J., Rendon, Augusto, Seyres, Denis, Sun, Benjamin, Tuna, Salih, van der Weide, Marie-Elise, Wingett, Steven W., Martens, Joost H., Stegle, Oliver, Richardson, Sylvia, Vallier, Ludovic, Roberts, David J., Freson, Kathleen, Wernisch, Lorenz, Stunnenberg, Hendrik G., Danesh, John, Fraser, Peter, Soranzo, Nicole, Butterworth, Adam S., Heemskerk, Johan W., Turro, Ernest, Spivakov, Mikhail, Ouwehand, Willem H., Astle, William J., Downes, Kate, Kostadima, Myrto, Frontini, Mattia
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Abstract/Description: Linking non-coding genetic variants associated with the risk of diseases or disease-relevant traits to target genes is a crucial step to realize GWAS potential in the introduction of precision medicine. Here we set out to determine the mechanisms underpinning variant association with platelet quantitative traits using cell type-matched epigenomic data and promoter long-range interactions. We identify potential regulatory functions for 423 of 565 (75%) non-coding variants associated with...
Show moreLinking non-coding genetic variants associated with the risk of diseases or disease-relevant traits to target genes is a crucial step to realize GWAS potential in the introduction of precision medicine. Here we set out to determine the mechanisms underpinning variant association with platelet quantitative traits using cell type-matched epigenomic data and promoter long-range interactions. We identify potential regulatory functions for 423 of 565 (75%) non-coding variants associated with platelet traits and we demonstrate, through ex vivo and proof of principle genome editing validation, that variants in super enhancers play an important role in controlling archetypical platelet functions.
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Date Issued: 2017-07-13
Identifier: FSU_libsubv1_wos_000405401600001, 10.1038/ncomms16058
Format: Citation

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

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

Title: A PRIMITIVE HADROSAURID FROM SOUTHEASTERN NORTH AMERICA AND THE ORIGIN AND EARLY EVOLUTION OF 'DUCK- BILLED' DINOSAURS.
Creator: Prieto-Marquez, Albert, Erickson, Gregory M., Ebersole, Jun A.
Abstract/Description: Eotrachodon orientalis gen. et sp. nov. (latest Santonian of Alabama, southeastern U.S.A.) is one of the oldest and most basal hadrosaurid dinosaurs and the only hadrosaurid from Appalachia (present day eastern North America) with a preserved skull. This taxon possesses a relatively derived narial structure that was until now regarded as synapomorphic for saurolophine (solid-crested or crestless) hadrosaurids. Maximum parsimony analysis places E. orientalis as the sister taxon to...
Show moreEotrachodon orientalis gen. et sp. nov. (latest Santonian of Alabama, southeastern U.S.A.) is one of the oldest and most basal hadrosaurid dinosaurs and the only hadrosaurid from Appalachia (present day eastern North America) with a preserved skull. This taxon possesses a relatively derived narial structure that was until now regarded as synapomorphic for saurolophine (solid-crested or crestless) hadrosaurids. Maximum parsimony analysis places E. orientalis as the sister taxon to Saurolophidae (Saurolophinae + Lambeosaurinae). Character optimization on the phylogeny indicates that the saurolophine-like circumnarial structure evolved by the Santonian following the split between saurolophines and lambeosaurines but prior to the major hadrosaurid radiation. Statistical dispersal-vicariance analysis posits an Appalachian ancestral area for Hadrosauridae and subsequent dispersal of their ancestors into Laramidia (present-day western North America) during the Cenomanian.http://zoobank.org/urn:lsid:zoobank.org:pub:3AD914D2-A3A5-45FD-8C94-5EE80461FEBCSUPPLEMENTAL DATASupplemental materials are available for this article for free at www.tandfonline.com/UJVPCitation for this article: Prieto-Marquez, A., G. M. Erickson, and J. A. Ebersole. 2016. A primitive hadrosaurid from southeastern North America and the origin and early evolution of duck-billed' dinosaurs. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2015.1054495
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Date Issued: 2016-03-03
Identifier: FSU_libsubv1_wos_000372953300019, 10.1080/02724634.2015.1054495
Format: Citation

Title: Quantifying The Spatiotemporal Dynamics In A Chorus Frog (pseudacris) Hybrid Zone Over 30 Years.
Creator: Engebretsen, Kristin N., Barrow, Lisa N., Rittmeyer, Eric N., Brown, Jeremy M., Lemmon, Emily Moriarty
Abstract/Description: Although theory suggests that hybrid zones can move or change structure over time, studies supported by direct empirical evidence for these changes are relatively limited. We present a spatiotemporal genetic study of a hybrid zone between Pseudacris nigrita and P.fouquettei across the Pearl River between Louisiana and Mississippi. This hybrid zone was initially characterized in 1980 as a narrow and steep tension zone, in which hybrid populations were inferior to parentals and were maintained...
Show moreAlthough theory suggests that hybrid zones can move or change structure over time, studies supported by direct empirical evidence for these changes are relatively limited. We present a spatiotemporal genetic study of a hybrid zone between Pseudacris nigrita and P.fouquettei across the Pearl River between Louisiana and Mississippi. This hybrid zone was initially characterized in 1980 as a narrow and steep tension zone, in which hybrid populations were inferior to parentals and were maintained through a balance between selection and dispersal. We reanalyzed historical tissue samples and compared them to samples of recently collected individuals using microsatellites. Clinal analyses indicate that the cline has not shifted in roughly 30years but has widened significantly. Anthropogenic and natural changes may have affected selective pressure or dispersal, and our results suggest that the zone may no longer best be described as a tension zone. To the best of our knowledge, this study provides the first evidence of significant widening of a hybrid cline but stasis of its center. Continued empirical study of dynamic hybrid zones will provide insight into the forces shaping their structure and the evolutionary potential they possess for the elimination or generation of species.
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Date Issued: 2016-07
Identifier: FSU_libsubv1_wos_000380033400031, 10.1002/ece3.2232
Format: Citation

Title: Rescuing macrophage normal function in spinal cord injury with embryonic stem cell conditioned media.
Creator: Guo, Lei, Rolfe, Alyssa J., Wang, Xi, Tai, Wenjiao, Cheng, Zhijian, Cao, Kai, Chen, Xiaoming, Xu, Yunsheng, Sun, Dongming, Li, Jinhua, He, Xijing, Young, Wise, Fan, Jianqing,...
Show moreGuo, Lei, Rolfe, Alyssa J., Wang, Xi, Tai, Wenjiao, Cheng, Zhijian, Cao, Kai, Chen, Xiaoming, Xu, Yunsheng, Sun, Dongming, Li, Jinhua, He, Xijing, Young, Wise, Fan, Jianqing, Ren, Yi
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Abstract/Description: Background: Macrophages play an important role in the inflammatory responses involved with spinal cord injury (SCI). We have previously demonstrated that infiltrated bone marrow-derived macrophages (BMDMs) engulf myelin debris, forming myelin-laden macrophages (mye-M phi). These mye-M phi promote disease progression through their pro-inflammatory phenotype, enhanced neurotoxicity, and impaired phagocytic capacity for apoptotic cells. We thus hypothesize that the excessive accumulation of mye...
Show moreBackground: Macrophages play an important role in the inflammatory responses involved with spinal cord injury (SCI). We have previously demonstrated that infiltrated bone marrow-derived macrophages (BMDMs) engulf myelin debris, forming myelin-laden macrophages (mye-M phi). These mye-M phi promote disease progression through their pro-inflammatory phenotype, enhanced neurotoxicity, and impaired phagocytic capacity for apoptotic cells. We thus hypothesize that the excessive accumulation of mye-M phi is the root of secondary injury, and that targeting mye-M phi represents an efficient strategy to improve the local inflammatory microenvironment in injured spinal cords and to further motor neuron function recovery. In this study, we administer murine embryonic stem cell conditioned media (ESC-M) as a cell-free stem cell based therapy to treat a mouse model of SCI. Results: We showed that BMDMs, but not microglial cells, engulf myelin debris generated at the injury site. Phagocytosis of myelin debris leads to the formation of mye-M phi in the injured spinal cord, which are surrounded by activated microglia cells. These mye-M phi are pro-inflammatory and lose the normal macrophage phagocytic capacity for apoptotic cells. We therefore focus on how to trigger lipid efflux from mye-M phi and thus restore their function. Using ESC-M as an immune modulating treatment for inflammatory damage after SCI, we rescued mye-M phi function and improved functional locomotor recovery. ESC-M treatment on mye-M phi resulted in improved exocytosis of internalized lipids and a normal capacity for apoptotic cell phagocytosis. Furthermore, when ESC-M was administered intraperitoneally after SCI, animals exhibited significant improvements in locomotor recovery. Examination of spinal cords of the ESC-M treated mice revealed similar improvements in macrophage function as well as a shift towards a more anti-inflammatory environment at the lesion and parenchyma. Conclusions: The embryonic stem cell conditioned media can be used as an effective treatment for SCI to resolve inflammation and improve functional recovery while circumventing the complications involved in whole cell transplantation.
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Date Issued: 2016-05-06
Identifier: FSU_libsubv1_wos_000376866000001, 10.1186/s13041-016-0233-3
Format: Citation

Title: Review: Plant G-quadruplex (G4) motifs in DNA and RNA; abundant, intriguing sequences of unknown function.
Creator: Bass, Hank W, Griffin, Brianna D
Abstract/Description: DNA sequences capable of forming G-quadruplex (G4) structures can be predicted and mapped in plant genomes using computerized pattern search programs. Non-telomeric G4 motifs have recently been found to number in the thousands across many plant species and enriched around gene promoters, prompting speculation that they may represent a newly uncovered and ubiquitous family of cis-acting elements. Comparative analysis shows that monocots exhibit five to ten times higher G4 motif density than...
Show moreDNA sequences capable of forming G-quadruplex (G4) structures can be predicted and mapped in plant genomes using computerized pattern search programs. Non-telomeric G4 motifs have recently been found to number in the thousands across many plant species and enriched around gene promoters, prompting speculation that they may represent a newly uncovered and ubiquitous family of cis-acting elements. Comparative analysis shows that monocots exhibit five to ten times higher G4 motif density than eudicots, but the significance of this difference has not been determined. The vast scale and complexity of G4 functions, actual or theoretical, are reviewed in relation to the multiple modes of action and myriad genetic functions for which G4s have been implicated in DNA and RNA. Future experimental strategies and opportunities include identifying plant G4-interactomes, resolving the structures of G4s with and without their binding partners, and defining molecular mechanisms through reporter gene, genetic, or genome editing approaches. Given the global importance of plants for food, clothing, medicine, and energy, together with the potential role of G4 motifs as a widely conserved set of DNA sequences that could coordinate gene regulation, future plant G4 research holds great potential for use in plant improvement strategies.
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Date Issued: 2018-02-08
Identifier: FSU_libsubv1_scholarship_submission_1518188170_bdd4f8ba, 10.1016/j.plantsci.2018.01.011
Format: Citation

Department of Biological Science (57)	+ -
Institute of Molecular Biophysics (2)	+ -
Program in Neuroscience (2)	+ -
Center for Brain Repair (1)	+ -
Center for Genomics and Personalized Medicine (1)	+ -

Department of Mathematics (1)	+ -
Department of Scientific Computing (1)	+ -
Department of Statistics (1)	+ -

text (57)	+ -
journal article (18)	+ -
dataset (1)	+ -
other (1)	+ -

Erickson, Gregory M. (4)	+ -
Lemmon, Emily Moriarty (4)	+ -
Deng, Wu-Min (3)	+ -
Dennis, Jonathan H. (3)	+ -
Tschinkel, Walter R. (3)	+ -

Cao, Kai (2)	+ -
Chase, P. Bryant (2)	+ -
Cheng, Zhijian (2)	+ -
Davidson, Michael W. (2)	+ -
Druckenmiller, Patrick S. (2)	+ -
Druliner, Brooke R. (2)	+ -
Fadool, James M. (2)	+ -
Hammack, Christy (2)	+ -
He, Xijing (2)	+ -
Lemmon, Alan R. (2)	+ -
Mori, Hirotsugu (2)	+ -
Ogden, Sarah C. (2)	+ -
Pearson, Katelin D (2)	+ -
Ren, Yi (2)	+ -
Rokyta, Darin R. (2)	+ -
Sousa, Duncan (2)	+ -
Tang, Hengli (2)	+ -
Underwood, Nora (2)	+ -
Vera, Daniel L. (2)	+ -
Abblett, Rebecca L. (1)	+ -
Agard, David (1)	+ -
Agbandje-McKenna, Mavis (1)	+ -
Al Koborssy, Dolly (1)	+ -
Al-Subaie, Abeer M. (1)	+ -
Alvarez-Delfin, Karen (1)	+ -

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