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Title: Spatio-temporal re-organization of replication foci accompanies replication domain consolidation during human pluripotent stem cell lineage specification.
Creator: Wilson, Korey A, Elefanty, Andrew G, Stanley, Edouard G, Gilbert, David M
Abstract/Description: Lineage specification of both mouse and human pluripotent stem cells (PSCs) is accompanied by spatial consolidation of chromosome domains and temporal consolidation of their replication timing. Replication timing and chromatin organization are both established during G1 phase at the timing decision point (TDP). Here, we have developed live cell imaging tools to track spatio-temporal replication domain consolidation during differentiation. First, we demonstrate that the fluorescence...
Show moreLineage specification of both mouse and human pluripotent stem cells (PSCs) is accompanied by spatial consolidation of chromosome domains and temporal consolidation of their replication timing. Replication timing and chromatin organization are both established during G1 phase at the timing decision point (TDP). Here, we have developed live cell imaging tools to track spatio-temporal replication domain consolidation during differentiation. First, we demonstrate that the fluorescence ubiquitination cell cycle indicator (Fucci) system is incapable of demarcating G1/S or G2/M cell cycle transitions. Instead, we employ a combination of fluorescent PCNA to monitor S phase progression, cytokinesis to demarcate mitosis, and fluorescent nucleotides to label early and late replication foci and track their 3D organization into sub-nuclear chromatin compartments throughout all cell cycle transitions. We find that, as human PSCs differentiate, the length of S phase devoted to replication of spatially clustered replication foci increases, coincident with global compartmentalization of domains into temporally clustered blocks of chromatin. Importantly, re-localization and anchorage of domains was completed prior to the onset of S phase, even in the context of an abbreviated PSC G1 phase. This approach can also be employed to investigate cell fate transitions in single PSCs, which could be seen to differentiate preferentially from G1 phase. Together, our results establish real-time, live-cell imaging methods for tracking cell cycle transitions during human PSC differentiation that can be applied to study chromosome domain consolidation and other aspects of lineage specification.
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Date Issued: 2016-09-16
Identifier: FSU_pmch_27433885, 10.1080/15384101.2016.1203492, PMC5026818, 27433885, 27433885
Format: Citation

Title: Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture.
Creator: Darrow, Emily M, Huntley, Miriam H, Dudchenko, Olga, Stamenova, Elena K, Durand, Neva C, Sun, Zhuo, Huang, Su-Chen, Sanborn, Adrian L, Machol, Ido, Shamim, Muhammad, Seberg,...
Show moreDarrow, Emily M, Huntley, Miriam H, Dudchenko, Olga, Stamenova, Elena K, Durand, Neva C, Sun, Zhuo, Huang, Su-Chen, Sanborn, Adrian L, Machol, Ido, Shamim, Muhammad, Seberg, Andrew P, Lander, Eric S, Chadwick, Brian P, Aiden, Erez Lieberman
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Abstract/Description: During interphase, the inactive X chromosome (Xi) is largely transcriptionally silent and adopts an unusual 3D configuration known as the "Barr body." Despite the importance of X chromosome inactivation, little is known about this 3D conformation. We recently showed that in humans the Xi chromosome exhibits three structural features, two of which are not shared by other chromosomes. First, like the chromosomes of many species, Xi forms compartments. Second, Xi is partitioned into two huge...
Show moreDuring interphase, the inactive X chromosome (Xi) is largely transcriptionally silent and adopts an unusual 3D configuration known as the "Barr body." Despite the importance of X chromosome inactivation, little is known about this 3D conformation. We recently showed that in humans the Xi chromosome exhibits three structural features, two of which are not shared by other chromosomes. First, like the chromosomes of many species, Xi forms compartments. Second, Xi is partitioned into two huge intervals, called "superdomains," such that pairs of loci in the same superdomain tend to colocalize. The boundary between the superdomains lies near DXZ4, a macrosatellite repeat whose Xi allele extensively binds the protein CCCTC-binding factor. Third, Xi exhibits extremely large loops, up to 77 megabases long, called "superloops." DXZ4 lies at the anchor of several superloops. Here, we combine 3D mapping, microscopy, and genome editing to study the structure of Xi, focusing on the role of DXZ4 We show that superloops and superdomains are conserved across eutherian mammals. By analyzing ligation events involving three or more loci, we demonstrate that DXZ4 and other superloop anchors tend to colocate simultaneously. Finally, we show that deleting DXZ4 on Xi leads to the disappearance of superdomains and superloops, changes in compartmentalization patterns, and changes in the distribution of chromatin marks. Thus, DXZ4 is essential for proper Xi packaging.
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Date Issued: 2016-08-02
Identifier: FSU_pmch_27432957, 10.1073/pnas.1609643113, PMC4978254, 27432957, 27432957, 1609643113
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_pmch_27467759, 10.1371/journal.pone.0160022, PMC4965136, 27467759, 27467759, PONE-D-15-54558
Format: Citation

Title: Role of cardiac troponin I carboxy terminal mobile domain and linker sequence in regulating cardiac contraction.
Creator: Meyer, Nancy L, Chase, P Bryant
Abstract/Description: Inhibition of striated muscle contraction at resting Ca(2+) depends on the C-terminal half of troponin I (TnI) in thin filaments. Much focus has been on a short inhibitory peptide (Ip) sequence within TnI, but structural studies and identification of disease-associated mutations broadened emphasis to include a larger mobile domain (Md) sequence at the C-terminus of TnI. For Md to function effectively in muscle relaxation, tight mechanical coupling to troponin's core-and thus tropomyosin-is...
Show moreInhibition of striated muscle contraction at resting Ca(2+) depends on the C-terminal half of troponin I (TnI) in thin filaments. Much focus has been on a short inhibitory peptide (Ip) sequence within TnI, but structural studies and identification of disease-associated mutations broadened emphasis to include a larger mobile domain (Md) sequence at the C-terminus of TnI. For Md to function effectively in muscle relaxation, tight mechanical coupling to troponin's core-and thus tropomyosin-is presumably needed. We generated recombinant, human cardiac troponins containing one of two TnI constructs: either an 8-amino acid linker between Md and the rest of troponin (cTnILink8), or an Md deletion (cTnI1-163). Motility assays revealed that Ca(2+)-sensitivity of reconstituted thin filament sliding was markedly increased with cTnILink8 (∼0.9 pCa unit leftward shift of speed-pCa relation compared to WT), and increased further when Md was missing entirely (∼1.4 pCa unit shift). Cardiac Tn's ability to turn off filament sliding at diastolic Ca(2+) was mostly (61%), but not completely eliminated with cTnI1-163. TnI's Md is required for full inhibition of unloaded filament sliding, although other portions of troponin-presumably including Ip-are also necessary. We also confirm that TnI's Md is not responsible for superactivation of actomyosin cycling by troponin.
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Date Issued: 2016-07-01
Identifier: FSU_pmch_26971468, 10.1016/j.abb.2016.03.010, PMC4899117, 26971468, 26971468, S0003-9861(16)30062-5
Format: Citation

Title: Sliding of centrosome-unattached microtubules defines key features of neuronal phenotype.
Creator: Rao, Anand N, Falnikar, Aditi, O'Toole, Eileen T, Morphew, Mary K, Hoenger, Andreas, Davidson, Michael W, Yuan, Xiaobing, Baas, Peter W
Abstract/Description: Contemporary models for neuronal migration are grounded in the view that virtually all functionally relevant microtubules (MTs) in migrating neurons are attached to the centrosome, which occupies a position between the nucleus and a short leading process. It is assumed that MTs do not undergo independent movements but rather transduce forces that enable movements of the centrosome and nucleus. The present results demonstrate that although this is mostly true, a small fraction of the MTs are...
Show moreContemporary models for neuronal migration are grounded in the view that virtually all functionally relevant microtubules (MTs) in migrating neurons are attached to the centrosome, which occupies a position between the nucleus and a short leading process. It is assumed that MTs do not undergo independent movements but rather transduce forces that enable movements of the centrosome and nucleus. The present results demonstrate that although this is mostly true, a small fraction of the MTs are centrosome-unattached, and this permits limited sliding of MTs. When this sliding is pharmacologically inhibited, the leading process becomes shorter, migration of the neuron deviates from its normal path, and the MTs within the leading process become buckled. Partial depletion of ninein, a protein that attaches MTs to the centrosome, leads to greater numbers of centrosome-unattached MTs as well as greater sliding of MTs. Concomitantly, the soma becomes less mobile and the leading process acquires an elongated morphology akin to an axon.
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Date Issued: 2016-05-09
Identifier: FSU_pmch_27138250, 10.1083/jcb.201506140, PMC4862329, 27138250, 27138250, jcb.201506140
Format: Citation

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

Title: Historical baselines and the future of shell calcification for a foundation species in a changing ocean.
Creator: Pfister, Catherine A, Roy, Kaustuv, Wootton, J Timothy, McCoy, Sophie J, Paine, Robert T, Suchanek, Thomas H, Sanford, Eric
Abstract/Description: Seawater pH and the availability of carbonate ions are decreasing due to anthropogenic carbon dioxide emissions, posing challenges for calcifying marine species. Marine mussels are of particular concern given their role as foundation species worldwide. Here, we document shell growth and calcification patterns in Mytilus californianus, the California mussel, over millennial and decadal scales. By comparing shell thickness across the largest modern shells, the largest mussels collected in the...
Show moreSeawater pH and the availability of carbonate ions are decreasing due to anthropogenic carbon dioxide emissions, posing challenges for calcifying marine species. Marine mussels are of particular concern given their role as foundation species worldwide. Here, we document shell growth and calcification patterns in Mytilus californianus, the California mussel, over millennial and decadal scales. By comparing shell thickness across the largest modern shells, the largest mussels collected in the 1960s-1970s and shells from two Native American midden sites (∼1000-2420 years BP), we found that modern shells are thinner overall, thinner per age category and thinner per unit length. Thus, the largest individuals of this species are calcifying less now than in the past. Comparisons of shell thickness in smaller individuals over the past 10-40 years, however, do not show significant shell thinning. Given our sampling strategy, these results are unlikely to simply reflect within-site variability or preservation effects. Review of environmental and biotic drivers known to affect shell calcification suggests declining ocean pH as a likely explanation for the observed shell thinning. Further future decreases in shell thickness could have significant negative impacts on M. californianus survival and, in turn, negatively impact the species-rich complex that occupies mussel beds.
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Date Issued: 2016-06-15
Identifier: FSU_pmch_27306049, 10.1098/rspb.2016.0392, PMC4920315, 27306049, 27306049, rspb.2016.0392
Format: Citation

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

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

Title: GABAergic mechanisms contributing to categorical amygdala responses to chemosensory signals.
Creator: Westberry, Jenne M, Meredith, Michael
Abstract/Description: Chemosensory stimuli from conspecific and heterospecific animals, elicit categorically different immediate-early gene response-patterns in medial amygdala in male hamsters and mice. We previously showed that conspecific signals activate posterior (MeP) as well as anterior medial amygdala (MeA), and especially relevant heterospecific signals such as chemosensory stimuli from potential predators also activate MeP in mice. Other heterospecific chemosignals activate MeA, but not MeP. Here we show...
Show moreChemosensory stimuli from conspecific and heterospecific animals, elicit categorically different immediate-early gene response-patterns in medial amygdala in male hamsters and mice. We previously showed that conspecific signals activate posterior (MeP) as well as anterior medial amygdala (MeA), and especially relevant heterospecific signals such as chemosensory stimuli from potential predators also activate MeP in mice. Other heterospecific chemosignals activate MeA, but not MeP. Here we show that male hamster amygdala responds significantly differentially to different conspecific signals, by activating different proportions of cells of different phenotype, possibly leading to differential activation of downstream circuits. Heterospecific signals that fail to activate MeP do activate GABA-immunoreactive cells in the adjacent caudal main intercalated nucleus (mICNc) and elicit selective suppression of MeP cells bearing GABA-Receptors, suggesting GABA inhibition in MeP by GABAergic cells in mICNc. Overall, work presented here suggests that medial amygdala may discriminate between important conspecific social signals, distinguish them from the social signals of other species and convey that information to brain circuits eliciting appropriate social behavior.
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Date Issued: 2016-09-07
Identifier: FSU_pmch_27329335, 10.1016/j.neuroscience.2016.06.020, PMC4955787, 27329335, 27329335, S0306-4522(16)30250-0
Format: Citation

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

Title: The DEAD-box Protein Rok1 Orchestrates 40S and 60S Ribosome Assembly by Promoting the Release of Rrp5 from Pre-40S Ribosomes to Allow for 60S Maturation.
Creator: Khoshnevis, Sohail, Askenasy, Isabel, Johnson, Matthew C, Dattolo, Maria D, Young-Erdos, Crystal L, Stroupe, M Elizabeth, Karbstein, Katrin
Abstract/Description: DEAD-box proteins are ubiquitous regulators of RNA biology. While commonly dubbed "helicases," their activities also include duplex annealing, adenosine triphosphate (ATP)-dependent RNA binding, and RNA-protein complex remodeling. Rok1, an essential DEAD-box protein, and its cofactor Rrp5 are required for ribosome assembly. Here, we use in vivo and in vitro biochemical analyses to demonstrate that ATP-bound Rok1, but not adenosine diphosphate (ADP)-bound Rok1, stabilizes Rrp5 binding to 40S...
Show moreDEAD-box proteins are ubiquitous regulators of RNA biology. While commonly dubbed "helicases," their activities also include duplex annealing, adenosine triphosphate (ATP)-dependent RNA binding, and RNA-protein complex remodeling. Rok1, an essential DEAD-box protein, and its cofactor Rrp5 are required for ribosome assembly. Here, we use in vivo and in vitro biochemical analyses to demonstrate that ATP-bound Rok1, but not adenosine diphosphate (ADP)-bound Rok1, stabilizes Rrp5 binding to 40S ribosomes. Interconversion between these two forms by ATP hydrolysis is required for release of Rrp5 from pre-40S ribosomes in vivo, thereby allowing Rrp5 to carry out its role in 60S subunit assembly. Furthermore, our data also strongly suggest that the previously described accumulation of snR30 upon Rok1 inactivation arises because Rrp5 release is blocked and implicate a previously undescribed interaction between Rrp5 and the DEAD-box protein Has1 in mediating snR30 accumulation when Rrp5 release from pre-40S subunits is blocked.
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Date Issued: 2016-06-09
Identifier: FSU_pmch_27280440, 10.1371/journal.pbio.1002480, PMC4900678, 27280440, 27280440, PBIOLOGY-D-16-00944
Format: Citation

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

Title: Label-Free Relative Quantitation of Isobaric and Isomeric Human Histone H2A and H2B Variants by Fourier Transform Ion Cyclotron Resonance Top-Down MS/MS.
Creator: Dang, Xibei, Singh, Amar, Spetman, Brian D, Nolan, Krystal D, Isaacs, Jennifer S, Dennis, Jonathan H, Dalton, Stephen, Marshall, Alan G, Young, Nicolas L
Abstract/Description: Histone variants are known to play a central role in genome regulation and maintenance. However, many variants are inaccessible by antibody-based methods or bottom-up tandem mass spectrometry due to their highly similar sequences. For many, the only tractable approach is with intact protein top-down tandem mass spectrometry. Here, ultra-high-resolution FT-ICR MS and MS/MS yield quantitative relative abundances of all detected HeLa H2A and H2B isobaric and isomeric variants with a label-free...
Show moreHistone variants are known to play a central role in genome regulation and maintenance. However, many variants are inaccessible by antibody-based methods or bottom-up tandem mass spectrometry due to their highly similar sequences. For many, the only tractable approach is with intact protein top-down tandem mass spectrometry. Here, ultra-high-resolution FT-ICR MS and MS/MS yield quantitative relative abundances of all detected HeLa H2A and H2B isobaric and isomeric variants with a label-free approach. We extend the analysis to identify and relatively quantitate 16 proteoforms from 12 sequence variants of histone H2A and 10 proteoforms of histone H2B from three other cell lines: human embryonic stem cells (WA09), U937, and a prostate cancer cell line LaZ. The top-down MS/MS approach provides a path forward for more extensive elucidation of the biological role of many previously unstudied histone variants and post-translational modifications.
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Date Issued: 2016-09-02
Identifier: FSU_pmch_27431976, 10.1021/acs.jproteome.6b00414, PMC6261780, 27431976, 27431976
Format: Citation

Title: Postsynaptic Fmrp Regulates Synaptogenesis In Vivo In The Developing Cochlear Nucleus.
Creator: Wang, Xiaoyu, Zorio, Diego A. R., Schecterson, Leslayann, Lu, Yong, Wang, Yuan
Abstract/Description: A global loss of the fragile X mental retardation protein (FMRP; encoded by the Fmr1 gene) leads to sensory dysfunction and intellectual disabilities. One underlying mechanism of these phenotypes is structural and functional deficits in synapses. Here, we determined the autonomous function of postsynaptic FMRP in circuit formation, synaptogenesis, and synaptic maturation. In normal cochlea nucleus, presynaptic auditory axons form large axosomatic endbulb synapses on cell bodies of...
Show moreA global loss of the fragile X mental retardation protein (FMRP; encoded by the Fmr1 gene) leads to sensory dysfunction and intellectual disabilities. One underlying mechanism of these phenotypes is structural and functional deficits in synapses. Here, we determined the autonomous function of postsynaptic FMRP in circuit formation, synaptogenesis, and synaptic maturation. In normal cochlea nucleus, presynaptic auditory axons form large axosomatic endbulb synapses on cell bodies of postsynaptic bushy neurons. In ovo electroporation of drug-inducible Fmr1-shRNA constructs produced a mosaicism of FMRP expression in chicken (either sex) bushy neurons, leading to reduced FMRP levels in transfected, but not neighboring nontransfected, neurons. Structural analyses revealed that postsynaptic FMRP reduction led to smaller size and abnormal morphology of individual presynaptic endbulbs at both early and later developmental stages. We further examined whether FMRP reduction affects dendritic development, as a potential mechanism underlying defective endbulb formation. Normally, chicken bushy neurons grow extensive dendrites at early stages and retract these dendrites when endbulbs begin to form. Neurons transfected with Fmr1 shRNA exhibited a remarkable delay in branch retraction, failing to provide necessary somatic surface for timely formation and growth of large endbulbs. Patch-clamp recording verified functional consequences of dendritic and synaptic deficits on neurotransmission, showing smaller amplitudes and slower kinetics of spontaneous and evoked EPSCs. Together, these data demonstrate that proper levels of postsynaptic FMRP are required for timely maturation of somatodendritic morphology, a delay of which may affect synaptogenesis and thus contribute to long-lasting deficits of excitatory synapses.
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Date Issued: 2018-07-18
Identifier: FSU_libsubv1_wos_000439698400004, 10.1523/JNEUROSCI.0665-18.2018
Format: Citation

Title: Open chromatin reveals the functional maize genome.
Creator: Rodgers-Melnick, Eli, Vera, Daniel L, Bass, Hank W, Buckler, Edward S
Abstract/Description: Cellular processes mediated through nuclear DNA must contend with chromatin. Chromatin structural assays can efficiently integrate information across diverse regulatory elements, revealing the functional noncoding genome. In this study, we use a differential nuclease sensitivity assay based on micrococcal nuclease (MNase) digestion to discover open chromatin regions in the maize genome. We find that maize MNase-hypersensitive (MNase HS) regions localize around active genes and within...
Show moreCellular processes mediated through nuclear DNA must contend with chromatin. Chromatin structural assays can efficiently integrate information across diverse regulatory elements, revealing the functional noncoding genome. In this study, we use a differential nuclease sensitivity assay based on micrococcal nuclease (MNase) digestion to discover open chromatin regions in the maize genome. We find that maize MNase-hypersensitive (MNase HS) regions localize around active genes and within recombination hotspots, focusing biased gene conversion at their flanks. Although MNase HS regions map to less than 1% of the genome, they consistently explain a remarkably large amount (∼40%) of heritable phenotypic variance in diverse complex traits. MNase HS regions are therefore on par with coding sequences as annotations that demarcate the functional parts of the maize genome. These results imply that less than 3% of the maize genome (coding and MNase HS regions) may give rise to the overwhelming majority of phenotypic variation, greatly narrowing the scope of the functional genome.
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Date Issued: 2016-05-31
Identifier: FSU_pmch_27185945, 10.1073/pnas.1525244113, PMC4896728, 27185945, 27185945, 1525244113
Format: Citation

Title: Acute Sleep Deprivation Blocks Short- and Long-Term Operant Memory in .
Creator: Krishnan, Harini C, Gandour, Catherine E, Ramos, Joshua L, Wrinkle, Mariah C, Sanchez-Pacheco, Joseph J, Lyons, Lisa C
Abstract/Description: Insufficient sleep in individuals appears increasingly common due to the demands of modern work schedules and technology use. Consequently, there is a growing need to understand the interactions between sleep deprivation and memory. The current study determined the effects of acute sleep deprivation on short and long-term associative memory using the marine mollusk , a relatively simple model system well known for studies of learning and memory. were sleep deprived for 9 hours using context...
Show moreInsufficient sleep in individuals appears increasingly common due to the demands of modern work schedules and technology use. Consequently, there is a growing need to understand the interactions between sleep deprivation and memory. The current study determined the effects of acute sleep deprivation on short and long-term associative memory using the marine mollusk , a relatively simple model system well known for studies of learning and memory. were sleep deprived for 9 hours using context changes and tactile stimulation either prior to or after training for the operant learning paradigm, learning that food is inedible (LFI). The effects of sleep deprivation on short-term (STM) and long-term memory (LTM) were assessed. Acute sleep deprivation prior to LFI training impaired the induction of STM and LTM with persistent effects lasting at least 24 h. Sleep deprivation immediately after training blocked the consolidation of LTM. However, sleep deprivation following the period of molecular consolidation did not affect memory recall. Memory impairments were independent of handling-induced stress, as daytime handled control animals demonstrated no memory deficits. Additional training immediately after sleep deprivation failed to rescue the induction of memory, but additional training alleviated the persistent impairment in memory induction when training occurred 24 h following sleep deprivation. Acute sleep deprivation inhibited the induction and consolidation, but not the recall of memory. These behavioral studies establish as an effective model system for studying the interactions between sleep and memory formation.
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Date Issued: 2016-12-01
Identifier: FSU_pmch_27748243, 10.5665/sleep.6320, PMC5103805, 27748243, 27748243, sp-00313-16
Format: Citation

Title: Advancing Behavioural Genomics By Considering Timescale.
Creator: Rittschof, Clare C., Hughes, Kimberly A.
Abstract/Description: Animal behavioural traits often covary with gene expression, pointing towards a genomic constraint on organismal responses to environmental cues. This pattern highlights a gap in our understanding of the time course of environmentally responsive gene expression, and moreover, how these dynamics are regulated. Advances in behavioural genomics explore how gene expression dynamics are correlated with behavioural traits that range from stable to highly labile. We consider the idea that certain...
Show moreAnimal behavioural traits often covary with gene expression, pointing towards a genomic constraint on organismal responses to environmental cues. This pattern highlights a gap in our understanding of the time course of environmentally responsive gene expression, and moreover, how these dynamics are regulated. Advances in behavioural genomics explore how gene expression dynamics are correlated with behavioural traits that range from stable to highly labile. We consider the idea that certain genomic regulatory mechanisms may predict the timescale of an environmental effect on behaviour. This temporally minded approach could inform both organismal and evolutionary questions ranging from the remediation of early life social trauma to understanding the evolution of trait plasticity.
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Date Issued: 2018-02-12
Identifier: FSU_libsubv1_wos_000424747100001, 10.1038/s41467-018-02971-0
Format: Citation

Title: 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: 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...
Show moreDespite 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. 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. 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_pmch_27733110, 10.1186/s12862-016-0769-y, PMC5062932, 27733110, 27733110, 10.1186/s12862-016-0769-y
Format: Citation

Title: Commentary: Epigenetic Regulation of Phosphodiesterases 2A and 3A Underlies Compromised β-Adrenergic Signaling in an iPSC Model of Dilated Cardiomyopathy..
Creator: Cole, Lauren A, Dennis, Jonathan H, Chase, P Bryant
Date Issued: 2016-09-23
Identifier: FSU_pmch_27721795, 10.3389/fphys.2016.00418, PMC5033966, 27721795, 27721795
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: 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: Regulated large-scale nucleosome density patterns and precise nucleosome positioning correlate with V(D)J recombination.
Creator: Pulivarthy, Sandhya R, Lion, Mattia, Kuzu, Guray, Matthews, Adam G W, Borowsky, Mark L, Morris, John, Kingston, Robert E, Dennis, Jonathan H, Tolstorukov, Michael Y, Oettinger,...
Show morePulivarthy, Sandhya R, Lion, Mattia, Kuzu, Guray, Matthews, Adam G W, Borowsky, Mark L, Morris, John, Kingston, Robert E, Dennis, Jonathan H, Tolstorukov, Michael Y, Oettinger, Marjorie A
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Abstract/Description: We show that the physical distribution of nucleosomes at antigen receptor loci is subject to regulated cell type-specific and lineage-specific positioning and correlates with the accessibility of these gene segments to recombination. At the Ig heavy chain locus (IgH), a nucleosome in pro-B cells is generally positioned over each IgH variable (VH) coding segment, directly adjacent to the recombination signal sequence (RSS), placing the RSS in a position accessible to the recombination...
Show moreWe show that the physical distribution of nucleosomes at antigen receptor loci is subject to regulated cell type-specific and lineage-specific positioning and correlates with the accessibility of these gene segments to recombination. At the Ig heavy chain locus (IgH), a nucleosome in pro-B cells is generally positioned over each IgH variable (VH) coding segment, directly adjacent to the recombination signal sequence (RSS), placing the RSS in a position accessible to the recombination activating gene (RAG) recombinase. These changes result in establishment of a specific chromatin organization at the RSS that facilitates accessibility of the genomic DNA for the RAG recombinase. In contrast, in mouse embryonic fibroblasts the coding segment is depleted of nucleosomes, which instead cover the RSS, thereby rendering it inaccessible. Pro-T cells exhibit a pattern intermediate between pro-B cells and mouse embryonic fibroblasts. We also find large-scale variations of nucleosome density over hundreds of kilobases, delineating chromosomal domains within IgH, in a cell type-dependent manner. These findings suggest that developmentally regulated changes in nucleosome location and occupancy, in addition to the known chromatin modifications, play a fundamental role in regulating V(D)J recombination. Nucleosome positioning-which has previously been observed to vary locally at individual enhancers and promoters-may be a more general mechanism by which cells can regulate the accessibility of the genome during development, at scales ranging from several hundred base pairs to many kilobases.
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Date Issued: 2016-10-18
Identifier: FSU_pmch_27698124, 10.1073/pnas.1605543113, PMC5081657, 27698124, 27698124, 1605543113
Format: Citation

Title: Viral recombination blurs taxonomic lines: examination of single-stranded DNA viruses in a wastewater treatment plant..
Creator: Pearson, Victoria M, Caudle, S Brian, Rokyta, Darin R
Abstract/Description: Understanding the structure and dynamics of microbial communities, especially those of economic concern, is of paramount importance to maintaining healthy and efficient microbial communities at agricultural sites and large industrial cultures, including bioprocessors. Wastewater treatment plants are large bioprocessors which receive water from multiple sources, becoming reservoirs for the collection of many viral families that infect a broad range of hosts. To examine this complex collection...
Show moreUnderstanding the structure and dynamics of microbial communities, especially those of economic concern, is of paramount importance to maintaining healthy and efficient microbial communities at agricultural sites and large industrial cultures, including bioprocessors. Wastewater treatment plants are large bioprocessors which receive water from multiple sources, becoming reservoirs for the collection of many viral families that infect a broad range of hosts. To examine this complex collection of viruses, full-length genomes of circular ssDNA viruses were isolated from a wastewater treatment facility using a combination of sucrose-gradient size selection and rolling-circle amplification and sequenced on an Illumina MiSeq. Single-stranded DNA viruses are among the least understood groups of microbial pathogens due to genomic biases and culturing difficulties, particularly compared to the larger, more often studied dsDNA viruses. However, the group contains several notable well-studied examples, including agricultural pathogens which infect both livestock and crops ( and ), and model organisms for genetics and evolution studies (). Examination of the collected viral DNA provided evidence for 83 unique genotypic groupings, which were genetically dissimilar to known viral types and exhibited broad diversity within the community. Furthermore, although these genomes express similarities to known viral families, such as , , and , many are so divergent that they may represent new taxonomic groups. This study demonstrated the efficacy of the protocol for separating bacteria and large viruses from the sought after ssDNA viruses and the ability to use this protocol to obtain an in-depth analysis of the diversity within this group.
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Date Issued: 2016-10-18
Identifier: FSU_pmch_27781171, 10.7717/peerj.2585, PMC5075696, 27781171, 27781171, 2585
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: 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: Global change, life-history complexity and the potential for evolutionary rescue.
Creator: Marshall, Dustin J, Burgess, Scott C, Connallon, Tim
Abstract/Description: Most organisms have complex life cycles, and in marine taxa, larval life-history stages tend to be more sensitive to environmental stress than adult (reproductive) life-history stages. While there are several models of stage-specific adaptation across the life history, the extent to which differential sensitivity to environmental stress (defined here as reductions in absolute fitness across the life history) affects the tempo of adaptive evolution to change remains unclear. We used a...
Show moreMost organisms have complex life cycles, and in marine taxa, larval life-history stages tend to be more sensitive to environmental stress than adult (reproductive) life-history stages. While there are several models of stage-specific adaptation across the life history, the extent to which differential sensitivity to environmental stress (defined here as reductions in absolute fitness across the life history) affects the tempo of adaptive evolution to change remains unclear. We used a heuristic model to explore how commonly observed features associated with marine complex life histories alter a population's capacity to cope with environmental change. We found that increasing the complexity of the life history generally reduces the evolutionary potential of taxa to cope with environmental change. Our model also predicted that genetic correlations in stress tolerance between stages, levels of genetic variance in each stage, and the relative plasticity of different stages, all interact to affect the maximum rate of environmental change that will permit species persistence. Our results suggest that marine organisms with complex life cycles are particularly vulnerable to anthropogenic global change, but we lack empirical estimates of key parameters for most species.
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Date Issued: 2016-06-30
Identifier: FSU_pmch_27695526, 10.1111/eva.12396, PMC5039331, 27695526, 27695526, EVA12396
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: 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: 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: 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: 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: 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: 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: 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: 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: Long-range Enhancer Interactions Are Prevalent In Mouse Embryonic Stem Cells And Are Reorganized Upon Pluripotent State Transition.
Creator: Novo, Clara Lopes, Javierre, Biola-Maria, Cairns, Jonathan, Segonds-Pichon, Anne, Wingett, Steven W., Freire-Pritchett, Paula, Furlan-Magaril, Mayra, Schoenfelder, Stefan,...
Show moreNovo, Clara Lopes, Javierre, Biola-Maria, Cairns, Jonathan, Segonds-Pichon, Anne, Wingett, Steven W., Freire-Pritchett, Paula, Furlan-Magaril, Mayra, Schoenfelder, Stefan, Fraser, Peter, Rugg-Gunn, Peter J.
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Abstract/Description: Transcriptional enhancers, including super-enhancers (SEs), form physical interactions with promoters to regulate cell-type-specific gene expression. SEs are characterized by high transcription factor occupancy and large domains of active chromatin, and they are commonly assigned to target promoters using computational predictions. How promoter-SE interactions change upon cell state transitions, and whether transcription factors maintain SE interactions, have not been reported. Here, we used...
Show moreTranscriptional enhancers, including super-enhancers (SEs), form physical interactions with promoters to regulate cell-type-specific gene expression. SEs are characterized by high transcription factor occupancy and large domains of active chromatin, and they are commonly assigned to target promoters using computational predictions. How promoter-SE interactions change upon cell state transitions, and whether transcription factors maintain SE interactions, have not been reported. Here, we used promoter-capture Hi-C to identify promoters that interact with SEs in mouse embryonic stem cells (ESCs). We found that SEs form complex, spatial networks in which individual SEs contact multiple promoters, and a rewiring of promoter-SE interactions occurs between pluripotent states. We also show that long-range promoter-SE interactions are more prevalent in ESCs than in epiblast stem cells (EpiSCs) or Nanog-deficient ESCs. We conclude that SEs form cell-type-specific interaction networks that are partly dependent on core transcription factors, thereby providing insights into the gene regulatory organization of pluripotent cells.
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Date Issued: 2018-03-06
Identifier: FSU_libsubv1_wos_000427081800012, 10.1016/j.celrep.2018.02.040
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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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

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