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  • 1
    In: Nature Neuroscience, Springer Science and Business Media LLC, Vol. 19, No. 12 ( 2016-12), p. 1569-1582
    Type of Medium: Online Resource
    ISSN: 1097-6256 , 1546-1726
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2016
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  • 2
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 116, No. 36 ( 2019-09-03), p. 17867-17873
    Abstract: Global change drivers (GCDs) are expected to alter community structure and consequently, the services that ecosystems provide. Yet, few experimental investigations have examined effects of GCDs on plant community structure across multiple ecosystem types, and those that do exist present conflicting patterns. In an unprecedented global synthesis of over 100 experiments that manipulated factors linked to GCDs, we show that herbaceous plant community responses depend on experimental manipulation length and number of factors manipulated. We found that plant communities are fairly resistant to experimentally manipulated GCDs in the short term ( 〈 10 y). In contrast, long-term (≥10 y) experiments show increasing community divergence of treatments from control conditions. Surprisingly, these community responses occurred with similar frequency across the GCD types manipulated in our database. However, community responses were more common when 3 or more GCDs were simultaneously manipulated, suggesting the emergence of additive or synergistic effects of multiple drivers, particularly over long time periods. In half of the cases, GCD manipulations caused a difference in community composition without a corresponding species richness difference, indicating that species reordering or replacement is an important mechanism of community responses to GCDs and should be given greater consideration when examining consequences of GCDs for the biodiversity–ecosystem function relationship. Human activities are currently driving unparalleled global changes worldwide. Our analyses provide the most comprehensive evidence to date that these human activities may have widespread impacts on plant community composition globally, which will increase in frequency over time and be greater in areas where communities face multiple GCDs simultaneously.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2019
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  • 3
    In: The Journal of Neuroscience, Society for Neuroscience, Vol. 33, No. 14 ( 2013-04-03), p. 6123-6132
    Abstract: The mechanisms by which natural rewards such as sugar affect synaptic transmission and behavior are largely unexplored. Here, we investigate regulation of nucleus accumbens synapses by sucrose intake. Previous studies have shown that AMPA receptor (AMPAR) trafficking is a major mechanism for regulating synaptic strength, and that in vitro , trafficking of AMPARs containing the GluA1 subunit takes place by a two-step mechanism involving extrasynaptic and then synaptic receptor transport. We report that in rat, repeated daily ingestion of a 25% sucrose solution transiently elevated spontaneous locomotion and potentiated accumbens core synapses through incorporation of Ca 2+ -permeable AMPA receptors (CPARs), which are GluA1-containing, GluA2-lacking AMPARs. Electrophysiological, biochemical, and quantitative electron microscopy studies revealed that sucrose training (7 d) induced a stable ( 〉 24 h) intraspinous GluA1 population, and that in these rats a single sucrose stimulus rapidly (5 min) but transiently ( 〈 24 h) elevated GluA1 at extrasynaptic sites. CPARs and dopamine D1 receptors were required in vivo for elevated locomotion after sucrose ingestion. Significantly, a 7 d protocol of daily ingestion of a 3% solution of saccharin, a noncaloric sweetener, induced synaptic GluA1 similarly to 25% sucrose ingestion. These findings identify multistep GluA1 trafficking, previously described in vitro , as a mechanism for acute regulation of synaptic transmission in vivo by a natural orosensory reward. Trafficking is stimulated by a chemosensory pathway that is not dependent on the caloric value of sucrose.
    Type of Medium: Online Resource
    ISSN: 0270-6474 , 1529-2401
    Language: English
    Publisher: Society for Neuroscience
    Publication Date: 2013
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  • 4
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 109, No. 43 ( 2012-10-23), p. 17501-17506
    Abstract: Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the “button mushroom” forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and β-etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor . A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2012
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  • 5
    In: The Journal of Neuroscience, Society for Neuroscience, Vol. 21, No. 18 ( 2001-09-15), p. 7089-7098
    Type of Medium: Online Resource
    ISSN: 0270-6474 , 1529-2401
    Language: English
    Publisher: Society for Neuroscience
    Publication Date: 2001
    detail.hit.zdb_id: 1475274-8
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  • 6
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 1999
    In:  Proceedings of the National Academy of Sciences Vol. 96, No. 2 ( 1999-01-19), p. 657-662
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 96, No. 2 ( 1999-01-19), p. 657-662
    Abstract: NO ⋅ is a free radical that modulates heart function and metabolism. We report that a neuronal-type NO synthase (NOS) is located on cardiac sarcoplasmic reticulum (SR) membrane vesicles and that endogenous NO ⋅ produced by SR-associated NOS inhibits SR Ca 2+ uptake. Ca 2+ -dependent biochemical conversion of l -arginine to l -citrulline was observed from isolated rabbit cardiac SR vesicles in the presence of NOS substrates and cofactors. Endogenous NO ⋅ was generated from the vesicles and detected by electron paramagnetic resonance spin-trapping measurements. Immunoelectron microscopy demonstrated labeling of cardiac SR vesicles by using anti-neuronal NOS (nNOS), but not anti-endothelial NOS (eNOS) or anti-inducible NOS (iNOS) antibodies, whereas skeletal muscle SR vesicles had no nNOS immunoreactivity. The nNOS immunoreactivity also displayed a pattern consistent with SR localization in confocal micrographs of sections of human myocardium. Western blotting demonstrated that cardiac SR NOS is larger than brain NOS (160 vs. 155 kDa). No immunodetection was observed in cardiac SR vesicles from nNOS knockout mice or with an anti-nNOSμ antibody, suggesting the possibility of a new nNOS-type isoform. 45 Ca uptake by cardiac SR vesicles, catalyzed by Ca 2+ -ATPase, was inhibited by NO ⋅ produced endogenously from cardiac SR NOS, and 7-nitroindazole, a selective nNOS inhibitor, completely prevented this inhibition. These results suggest that a cardiac muscle nNOS isoform is located on SR of cardiac myocytes, where it may respond to intracellular Ca 2+ concentration and modulate SR Ca 2+ ion active transport in the heart.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 1999
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
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  • 7
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2000
    In:  Proceedings of the National Academy of Sciences Vol. 97, No. 7 ( 2000-03-28), p. 3136-3141
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 97, No. 7 ( 2000-03-28), p. 3136-3141
    Abstract: The single-stranded region of DNA within the open complex of transcriptionally active genes provides a unique target for the design of gene-specific transcription inhibitors. Using the Escherichia coli lac UV5 and trp EDCBA promoters as in vitro models of open complex formation, we have identified the sites inside these transcription bubbles that are accessible for hybridization by short, nuclease-resistant, nonextendible oligoribonucleotides (ORNs). Binding of ORNs inside the open complex was determined by linking the chemical nuclease bis(1,10-phenanthroline) cuprous chelate [(OP) 2 Cu + ] to the ORN and demonstrating template-specific DNA scission. In addition, these experiments were supported by in vitro transcription inhibition. We find that the most effective inhibitors are 5 nt long and have sequences that are complementary to the DNA template strand in the region near the transcription start site. The ORNs bind to the DNA template strand, forming an antiparallel heteroduplex inside the open complex. In this system, RNA polymerase is essential not only to melt the duplex DNA but also to facilitate hybridization of the incoming ORN. This paradigm for gene-specific inactivation relies on the base complementarity of the ORN and the catalytic activity and sequence specificity of RNA polymerase for the site- and sequence-specific recognition and inhibition of transcriptionally active DNA.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2000
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
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  • 8
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 109, No. 17 ( 2012-04-24)
    Abstract: Our results have broad clinical implications. Small-molecule inhibitors targeting the Smo signaling molecule are being evaluated currently for the treatment of pancreatic cancer ( 5 ). However, the activity of these Smo inhibitors likely is limited to the stromal compartment, having no effect on epithelial cells. Our genetic data identifying an alternative genetic pathway involving Gli argue strongly for the clinical development of Gli inhibitors, because these molecules contribute critical function in the tumor epithelium as well as the tumor stroma. We next investigated which downstream genes mediated Gli-driven phenotypes in pancreatic cancer cells. We performed gene-expression profiling analysis in human pancreatic ductal adenocarcinoma cells in which Gli-mediated transcription had been inhibited by Gli3T. Interestingly, we found that Gli activation in pancreatic cancer cells imposed a unique transcriptional program. Specifically, we found that the expression of the IκB kinase IKBKE (IKKε) was regulated by Gli proteins. These results suggest that IKBKE may play a critical role in pancreatic tumorigenesis. In general, kinases are enzymes that affect other proteins by adding phosphate molecules to these proteins. IKBKE is a noncanonical IkB kinase involved in stimulating the NF-κB signaling pathway. We showed that IKBKE is highly expressed in pancreatic tumors that are characterized by both Kras and Gli activation. We also found that Gli regulates NF-κB activity in vitro and in vivo. Furthermore, we demonstrated that Gli-dependent IKBKE expression in pancreatic cancer cells is essential for maintaining their cell survival and transformation characteristics, which are fundamental properties of cancerous cells. These data establish a connection between Gli transcription factors and the IKBKE and NF-κB activity in tumorigenesis, providing a molecular basis for the observed requirement of Gli transcription in the development of pancreatic ductal adenocarcinoma in vivo. In addition, we evaluated the tumorigenic potential of Gli1 in pancreatic cancer by ectopically expressing Gli1 in the mouse pancreas. We found that Gli1 activation significantly enhanced the ability of Kras to promote tumor development. Thus, both our loss-of-function and gain-of-function analyses highlight the functional importance of epithelial Gli activity in Kras-induced pancreatic tumorigenesis in vivo. However, using a primary pancreatic ductal epithelial cell (PDEC) culture, we showed that Gli-mediated transcription activation is required for Kras-induced PDEC proliferation and survival. Additionally, we combined this model with another in which oncogenic Kras activation in the mouse pancreatic epithelium drove tumor initiation and progression, mimicking the pathogenesis of human pancreatic cancer. Significantly, when these mice were genetically modified to exhibit both activation of Kras and inhibition of Gli transcription in the pancreatic epithelium, we found that the development of pancreatic precursor lesions and pancreatic ductal adenocarcinoma initiated by Kras activation was blocked. This inhibition happened even when the p53 tumor suppressor, which commonly is inactivated in this disease, was deleted. These results provide genetic evidence that Gli activity is required for Kras-driven transformation of the pancreatic epithelium. To investigate the role of Gli in pancreatic tumorigenesis, we generated a mouse model of pancreatic epithelium-specific inhibition of Gli-mediated transcription. This model was achieved by the ectopic expression of a dominant Gli3 repressor allele, Gli3T, which is capable of inhibiting Gli1- and Gli2-mediated activation of transcription. We found that inhibition of Gli transcriptional activity did not affect differentiation of the pancreatic epithelial cell lineages. This lack of effect suggests that epithelial Gli activity is largely dispensable for the proper development of the mouse pancreas. The Gli proteins Gli1, Gli2, and Gli3 are transcription factors. They operate in a cellular signaling pathway called the “Hedgehog” (Hh) pathway that often is activated in human tumors. The Hh pathway is mediated by activation of a cell-surface molecule, Smoothened (Smo) ( 3 ). Stimulation of the Hh pathway results in the activation of Gli proteins. However, Gli proteins may be regulated by other oncogenic pathways. For example, Gli1 gene expression is maintained in pancreatic cancer cells despite deletion of the Smo gene and is regulated in part by Kras independently of Hh ligand input ( 4 ). However, Gli's role in pancreatic tumorigenesis in vivo remains unexplored. Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer-related mortality in the United States ( 1 ). This disease arises from precursor lesions in pancreatic epithelium, characterized by mutations in a potential cancer-causing gene called the “ KRAS oncogene” ( 1 , 2 ). However, limited understanding of the molecular and genetic mechanisms underlying Kras-dependent pancreatic tumorigenesis has impeded the development of early diagnostic and treatment tools. Here, using mouse genetics and cellular biology, we demonstrated that the ability of Gli proteins to activate gene transcription is critical for the development of Kras-driven pancreatic cancer ( Fig. P1 ). Significantly, we identified a key mechanism that operates after Gli transcription activity during pancreatic tumorigenesis: the induction of the expression of the atypical IkB kinase IKBKE and the activity of the NF-κB pathway in the tumor epithelium ( Fig. P1 ).
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2012
    detail.hit.zdb_id: 209104-5
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  • 9
    Online Resource
    Online Resource
    Society for Neuroscience ; 2011
    In:  The Journal of Neuroscience Vol. 31, No. 32 ( 2011-08-10), p. 11537-11546
    In: The Journal of Neuroscience, Society for Neuroscience, Vol. 31, No. 32 ( 2011-08-10), p. 11537-11546
    Abstract: When we applied a single pulse of transcranial magnetic stimulation (TMS) to any part of the human head during a saccadic eye movement, the ongoing eye velocity was reduced as early as 45 ms after the TMS, and lasted ∼32 ms. The perturbation to the saccade trajectory was not due to a mechanical effect of the lid on the eye (e.g., from blinks). When the saccade involved coordinated movements of both the eyes and the lids, e.g., in vertical saccades, TMS produced a synchronized inhibition of the motor commands to both eye and lid muscles. The TMS-induced perturbation of the eye trajectory did not show habituation with repetition, and was present in both pro-saccades and anti-saccades. Despite the perturbation, the eye trajectory was corrected within the same saccade with compensatory motor commands that guided the eyes to the target. This within-saccade correction did not rely on visual input, suggesting that the brain monitored the oculomotor commands as the saccade unfolded, maintained a real-time estimate of the position of the eyes, and corrected for the perturbation. TMS disrupted saccades regardless of the location of the coil on the head, suggesting that the coil discharge engages a nonhabituating startle-like reflex system. This system affects ongoing motor commands upstream of the oculomotor neurons, possibly at the level of the superior colliculus or omnipause neurons. Therefore, a TMS pulse centrally perturbs saccadic motor commands, which are monitored possibly via efference copy and are corrected via internal feedback.
    Type of Medium: Online Resource
    ISSN: 0270-6474 , 1529-2401
    Language: English
    Publisher: Society for Neuroscience
    Publication Date: 2011
    detail.hit.zdb_id: 1475274-8
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  • 10
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2000
    In:  Proceedings of the National Academy of Sciences Vol. 97, No. 7 ( 2000-03-28), p. 3022-3027
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 97, No. 7 ( 2000-03-28), p. 3022-3027
    Abstract: The splicing factor Prp18 is required for the second step of pre-mRNA splicing. We have isolated and determined the crystal structure of a large fragment of the Saccharomyces cerevisiae Prp18 that lacks the N-terminal 79 amino acids. This fragment, called Prp18Δ79, is fully active in yeast splicing in vitro and includes the sequences of Prp18 that have been evolutionarily conserved. The core structure of Prp18Δ79 is compact and globular, consisting of five α-helices that adopt a novel fold that we have designated the five-helix X-bundle. The structure suggests that one face of Prp18 interacts with the splicing factor Slu7, whereas the more evolutionarily conserved amino acids in Prp18 form the opposite face. The most highly conserved region of Prp18, a nearly invariant stretch of 19 aa, forms part of a loop between two α-helices and may interact with the U5 small nuclear ribonucleoprotein particles. The structure is consistent with a model in which Prp18 forms a bridge between Slu7 and the U5 small nuclear ribonucleoprotein particles.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2000
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
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    SSG: 12
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