The plant cell cycle: Pre-Replication complex formation and controls

PubMed Central

Brasil, Juliana Nogueira; Costa, Carinne N. Monteiro; Cabral, Luiz Mors; Ferreira, Paulo C. G.; Hemerly, Adriana S.

2017-01-01

Abstract The multiplication of cells in all living organisms requires a tight regulation of DNA replication. Several mechanisms take place to ensure that the DNA is replicated faithfully and just once per cell cycle in order to originate through mitoses two new daughter cells that contain exactly the same information from the previous one. A key control mechanism that occurs before cells enter S phase is the formation of a pre-replication complex (pre-RC) that is assembled at replication origins by the sequential association of the origin recognition complex, followed by Cdt1, Cdc6 and finally MCMs, licensing DNA to start replication. The identification of pre-RC members in all animal and plant species shows that this complex is conserved in eukaryotes and, more importantly, the differences between kingdoms might reflect their divergence in strategies on cell cycle regulation, as it must be integrated and adapted to the niche, ecosystem, and the organism peculiarities. Here, we provide an overview of the knowledge generated so far on the formation and the developmental controls of the pre-RC mechanism in plants, analyzing some particular aspects in comparison to other eukaryotes. PMID:28304073

Calcium ions and osteoclastogenesis initiate the induction of bone formation by coral-derived macroporous constructs

PubMed Central

Klar, Roland M; Duarte, Raquel; Dix-Peek, Therese; Dickens, Caroline; Ferretti, Carlo; Ripamonti, Ugo

2013-01-01

Coral-derived calcium carbonate/hydroxyapatite macroporous constructs of the genus Goniopora with limited hydrothermal conversion to hydroxyapatite (7% HA/CC) initiate the induction of bone formation. Which are the molecular signals that initiate pattern formation and the induction of bone formation? To evaluate the role of released calcium ions and osteoclastogenesis, 7% HA/CC was pre-loaded with either 500 μg of the calcium channel blocker, verapamil hydrochloride, or 240 μg of the osteoclast inhibitor, biphosphonate zoledronate, and implanted in the rectus abdominis muscle of six adult Chacma baboons Papio ursinus. Generated tissues on days 15, 60 and 90 were analysed by histomorphometry and qRT-PCR. On day 15, up-regulation of type IV collagen characterized all the implanted constructs correlating with vascular invasion. Zoledronate-treated specimens showed an important delay in tissue patterning and morphogenesis with limited bone formation. Osteoclastic inhibition yielded minimal, if any, bone formation by induction. 7% HA/CC pre-loaded with the Ca++ channel blocker verapamil hydrochloride strongly inhibited the induction of bone formation. Down-regulation of bone morphogenetic protein-2 (BMP-2) together with up-regulation of Noggin genes correlated with limited bone formation in 7% HA/CC pre-loaded with either verapamil or zoledronate, indicating that the induction of bone formation by coral-derived macroporous constructs is via the BMPs pathway. The spontaneous induction of bone formation is initiated by a local peak of Ca++ activating stem cell differentiation and the induction of bone formation. PMID:24106923

The formation mechanisms of turbidity maximum in the Pearl River estuary, China.

PubMed

Wai, O W H; Wang, C H; Li, Y S; Li, X D

2004-03-01

The formation and dynamics of turbidity maxima (TM) in the Pearl River estuary (PRE) are not well understood but the existence of TM in the estuary have great potential engineering and environmental impacts. Based on the measurements of two large-scale field surveys conducted in the wet season of 1978 (July of 1978) and the dry season of 1979 (March of 1979), the existence and seasonal variations of TM in the PRE focusing on the two major natural navigation channels have been studied. The sediment transport fluxes over two consecutive tidal cycles have been analyzed in detail. The analysis results reveal that the formation mechanisms of TM in the estuary are rather complex. In general, gravitational circulation, tidal trapping, and sediment resuspension and deposition processes are the primary TM formation mechanisms in the PRE. The clockwise back flow pattern around Lingding Island also leads to the formation of TM in the West channel of the PRE. The occurrence of TM far upstream of the salt water wedge is the result of the complex hydrodynamic and sediment transport processes generated by the runoff of the major rivers.

Nucleosome occupancy as a novel chromatin parameter for replication origin functions

PubMed Central

Rodriguez, Jairo; Lee, Laura; Lynch, Bryony; Tsukiyama, Toshio

2017-01-01

Eukaryotic DNA replication initiates from multiple discrete sites in the genome, termed origins of replication (origins). Prior to S phase, multiple origins are poised to initiate replication by recruitment of the pre-replicative complex (pre-RC). For proper replication to occur, origin activation must be tightly regulated. At the population level, each origin has a distinct firing time and frequency of activation within S phase. Many studies have shown that chromatin can strongly influence initiation of DNA replication. However, the chromatin parameters that affect properties of origins have not been thoroughly established. We found that nucleosome occupancy in G1 varies greatly around origins across the S. cerevisiae genome, and nucleosome occupancy around origins significantly correlates with the activation time and efficiency of origins, as well as pre-RC formation. We further demonstrate that nucleosome occupancy around origins in G1 is established during transition from G2/M to G1 in a pre-RC-dependent manner. Importantly, the diminished cell-cycle changes in nucleosome occupancy around origins in the orc1-161 mutant are associated with an abnormal global origin usage profile, suggesting that proper establishment of nucleosome occupancy around origins is a critical step for regulation of global origin activities. Our work thus establishes nucleosome occupancy as a novel and key chromatin parameter for proper origin regulation. PMID:27895110

MMSET is dynamically regulated during cell-cycle progression and promotes normal DNA replication.

PubMed

Evans, Debra L; Zhang, Haoxing; Ham, Hyoungjun; Pei, Huadong; Lee, SeungBaek; Kim, JungJin; Billadeau, Daniel D; Lou, Zhenkun

2016-01-01

The timely and precise duplication of cellular DNA is essential for maintaining genome integrity and is thus tightly-regulated. During mitosis and G1, the Origin Recognition Complex (ORC) binds to future replication origins, coordinating with multiple factors to load the minichromosome maintenance (MCM) complex onto future replication origins as part of the pre-replication complex (pre-RC). The pre-RC machinery, in turn, remains inactive until the subsequent S phase when it is required for replication fork formation, thereby initiating DNA replication. Multiple myeloma SET domain-containing protein (MMSET, a.k.a. WHSC1, NSD2) is a histone methyltransferase that is frequently overexpressed in aggressive cancers and is essential for normal human development. Several studies have suggested a role for MMSET in cell-cycle regulation; however, whether MMSET is itself regulated during cell-cycle progression has not been examined. In this study, we report that MMSET is degraded during S phase in a cullin-ring ligase 4-Cdt2 (CRL4(Cdt2)) and proteasome-dependent manner. Notably, we also report defects in DNA replication and a decreased association of pre-RC factors with chromatin in MMSET-depleted cells. Taken together, our results suggest a dynamic regulation of MMSET levels throughout the cell cycle, and further characterize the role of MMSET in DNA replication and cell-cycle progression.

Structure of a human cap-dependent 48S translation pre-initiation complex

PubMed Central

Eliseev, Boris; Yeramala, Lahari; Leitner, Alexander; Karuppasamy, Manikandan; Raimondeau, Etienne; Huard, Karine; Alkalaeva, Elena; Aebersold, Ruedi

2018-01-01

Abstract Eukaryotic translation initiation is tightly regulated, requiring a set of conserved initiation factors (eIFs). Translation of a capped mRNA depends on the trimeric eIF4F complex and eIF4B to load the mRNA onto the 43S pre-initiation complex comprising 40S and initiation factors 1, 1A, 2, 3 and 5 as well as initiator-tRNA. Binding of the mRNA is followed by mRNA scanning in the 48S pre-initiation complex, until a start codon is recognised. Here, we use a reconstituted system to prepare human 48S complexes assembled on capped mRNA in the presence of eIF4B and eIF4F. The highly purified h-48S complexes are used for cross-linking/mass spectrometry, revealing the protein interaction network in this complex. We report the electron cryo-microscopy structure of the h-48S complex at 6.3 Å resolution. While the majority of eIF4B and eIF4F appear to be flexible with respect to the ribosome, additional density is detected at the entrance of the 40S mRNA channel which we attribute to the RNA-recognition motif of eIF4B. The eight core subunits of eIF3 are bound at the 40S solvent-exposed side, as well as the subunits eIF3d, eIF3b and eIF3i. elF2 and initiator-tRNA bound to the start codon are present at the 40S intersubunit side. This cryo-EM structure represents a molecular snap-shot revealing the h-48S complex following start codon recognition. PMID:29401259

Mechanisms of excitatory synapse maturation by trans-synaptic organizing complexes

PubMed Central

McMahon, Samuel A.; Díaz, Elva

2011-01-01

Synapses are specialized cell-cell adhesion contacts that mediate communication within neural networks. During development, excitatory synapses are generated by step-wise recruitment of pre- and postsynaptic proteins to sites of contact. Several classes of synaptic organizing complexes have been identified that function during the initial stages of synapse formation. However, mechanisms underlying the later stages of synapse development are less well understood. In recent years, molecules have been discovered that appear to play a role in synapse maturation. In this review, we highlight recent findings that have provided key insights for understanding postsynaptic maturation of developing excitatory synapses with a focus on recruitment of AMPA receptors to developing synapses. PMID:21242087

Pre-cometary ice composition from hot core chemistry.

PubMed

Tornow, Carmen; Kührt, Ekkehard; Motschmann, Uwe

2005-10-01

Pre-cometary ice located around star-forming regions contains molecules that are pre-biotic compounds or pre-biotic precursors. Molecular line surveys of hot cores provide information on the composition of the ice since it sublimates near these sites. We have combined a hydrostatic hot core model with a complex network of chemical reactions to calculate the time-dependent abundances of molecules, ions, and radicals. The model considers the interaction between the ice and gas phase. It is applied to the Orion hot core where high-mass star formation occurs, and to the solar-mass binary protostar system IRAS 16293-2422. Our calculations show that at the end of the hot core phase both star-forming sites produce the same prebiotic CN-bearing molecules. However, in the Orion hot core these molecules are formed in larger abundances. A comparison of the calculated values with the abundances derived from the observed line data requires a chemically unprocessed molecular cloud as the initial state of hot core evolution. Thus, it appears that these objects are formed at a much younger cloud stage than previously thought. This implies that the ice phase of the young clouds does not contain CN-bearing molecules in large abundances before the hot core has been formed. The pre-biotic molecules synthesized in hot cores cause a chemical enrichment in the gas phase and in the pre-cometary ice. This enrichment is thought to be an important extraterrestrial aspect of the formation of life on Earth and elsewhere.

Spectroscopic Study of NGC 281 West

NASA Astrophysics Data System (ADS)

Hasan, Priya

2018-04-01

NGC 281 is a complex region of star formation at 2.8 kpc. This complex is situated 300 pc above the Galactic plane, and appears to be part of a 270 pc diameter ring of atomic and molecular clouds expanding at 22 km/s (Megeath et al. 2003). It appears that two modes of triggered star formation are at work here: an initial supernova to trigger the ring complex and the initial O stars and the subsequent triggering of low mass star formation by photoevaporation driven molecular core compression. To get a complete census of the young stellar population, we use observations from Chandra ACIS 100 ksec coupled with data from 2MASS and Spitzer. The Master X-ray catalog has 446 sources detected in different bandpasses. We present the spatial distribution of Class I, II and III sources to study the progress of star formation. We also determine the gas to dust ratio NH/AK to be 1.93 ± 0.47 ×1022 cm‑2 mag‑1 for this region. In this article, we present NGC 281 as a good target to study with the 3.6-m Devasthal Optical Telescope (DOT) in spectroscopy. With these spectra, we look for evidence for the pre-main-sequence (PMS) nature of the objects, study the properties of the detected emission lines as a function of evolutionary class, and obtain spectral types for the observed young stellar objects (YSOs). The temperatures implied by the spectral types can be combined with luminosities determined from the near-infrared (NIR) photometry to construct Hertzsprung–Russell (HR) diagrams for the clusters. By comparing the positions of the YSOs in the HR diagrams with the PMS tracks, we can determine the ages of the embedded sources and study the relative ages of the YSOs with and without optically thick circumstellar disks.

The Evolutionarily Conserved Protein LAS1 Is Required for Pre-rRNA Processing at Both Ends of ITS2

PubMed Central

Schillewaert, Stéphanie; Wacheul, Ludivine; Lhomme, Frédéric

2012-01-01

Ribosome synthesis entails the formation of mature rRNAs from long precursor molecules, following a complex pre-rRNA processing pathway. Why the generation of mature rRNA ends is so complicated is unclear. Nor is it understood how pre-rRNA processing is coordinated at distant sites on pre-rRNA molecules. Here we characterized, in budding yeast and human cells, the evolutionarily conserved protein Las1. We found that, in both species, Las1 is required to process ITS2, which separates the 5.8S and 25S/28S rRNAs. In yeast, Las1 is required for pre-rRNA processing at both ends of ITS2. It is required for Rrp6-dependent formation of the 5.8S rRNA 3′ end and for Rat1-dependent formation of the 25S rRNA 5′ end. We further show that the Rat1-Rai1 5′-3′ exoribonuclease (exoRNase) complex functionally connects processing at both ends of the 5.8S rRNA. We suggest that pre-rRNA processing is coordinated at both ends of 5.8S rRNA and both ends of ITS2, which are brought together by pre-rRNA folding, by an RNA processing complex. Consistently, we note the conspicuous presence of ∼7- or 8-nucleotide extensions on both ends of 5.8S rRNA precursors and at the 5′ end of pre-25S RNAs suggestive of a protected spacer fragment of similar length. PMID:22083961

Early Paleozoic development of the Maine-Quebec boundary Mountains region

USGS Publications Warehouse

Gerbi, C.C.; Johnson, S.E.; Aleinikoff, J.N.; Bedard, J.H.; Dunning, G.R.; Fanning, C.M.

2006-01-01

Pre-Silurian bedrock units played key roles in the early Paleozoic history of the Maine-Quebec Appalachians. These units represent peri-Laurentian material whose collision with the craton deformed the Neoproteozoic passive margin and initiated the Appalachian mountain-building cycle. We present new field, petrological, geochronological, and geochemical data to support the following interpretations related to these units. (1) The Boil Mountain Complex and Jim Pond Formation do not represent part of a coherent ophiolite. (2) Gabbro and tonalite of the Boil Mountain Complex intruded the Chain Lakes massif at ca. 477 Ma. (3) The Skinner pluton, an arc-related granodiorite, intruded the Chain Lakes massif at ca. 472 Ma. (4) The Attean pluton, with a reconfirmed age of ca. 443 Ma, is unrelated to Early Ordovician orogenesis. (5) The most likely timing for the juxtaposition of the Jim Pond Formation and the Boil Mountain Complex was during regional Devonian deformation. These interpretations suggest that the Boundary Mountains were once part of a series of arcs extending at least from central New England through Newfoundland. ?? 2006 NRC Canada.

Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex.

PubMed

Robinson, Philip J; Trnka, Michael J; Bushnell, David A; Davis, Ralph E; Mattei, Pierre-Jean; Burlingame, Alma L; Kornberg, Roger D

2016-09-08

A complete, 52-protein, 2.5 million dalton, Mediator-RNA polymerase II pre-initiation complex (Med-PIC) was assembled and analyzed by cryo-electron microscopy and by chemical cross-linking and mass spectrometry. The resulting complete Med-PIC structure reveals two components of functional significance, absent from previous structures, a protein kinase complex and the Mediator-activator interaction region. It thereby shows how the kinase and its target, the C-terminal domain of the polymerase, control Med-PIC interaction and transcription. Copyright © 2016 Elsevier Inc. All rights reserved.

Thinning of heterogeneous lithosphere: insights from field observations and numerical modelling

NASA Astrophysics Data System (ADS)

Petri, B.; Duretz, T.; Mohn, G.; Schmalholz, S. M.

2017-12-01

The nature and mechanisms of formation of extremely thinned continental crust (< 10 km) and lithosphere during rifting remain debated. Observations from present-day and fossil continental passive margins document the heterogeneous nature of the lithosphere characterized, among others, by lithological variations and structural inheritance. This contribution aims at investigating the mechanisms of extreme lithospheric thinning by exploring in particular the role of initial heterogeneities by coupling field observations from fossil passive margins and numerical models of lithospheric extension. Two field examples from the Alpine Tethys margins outcropping in the Eastern Alps (E Switzerland and N Italy) and in the Southern Alps (N Italy) were selected for their exceptional level of preservation of rift-related structures. This situation enables us to characterize (1) the pre-rift architecture of the continental lithosphere, (2) the localization of rift-related deformation in distinct portion of the lithosphere and (3) the interaction between initial heterogeneities of the lithosphere and rift-related structures. In a second stage, these observations are integrated in high-resolution, two-dimensional thermo-mechanical models taking into account various patterns of initial mechanical heterogeneities. Our results show the importance of initial pre-rift architecture of the continental lithosphere during rifting. Key roles are given to high-angle and low-angle normal faults, anastomosing shear-zones and decoupling horizons. We propose that during the first stages of thinning, deformation is strongly controlled by the complex pre-rift architecture of the lithosphere, localized along major structures responsible for the lateral extrusion of mid to lower crustal levels. This extrusion juxtaposes mechanically stronger levels in the hyper-thinned continental crust, being exhumed by subsequent low-angle normal faults. Altogether, these results highlight the critical role of the extraction of mechanically strong layers of the lithosphere during the extreme thinning of the continental lithosphere and allows to propose a new model for the formation of continental passive margins.

Morphology of Dbx1 respiratory neurons in the preBötzinger complex and reticular formation of neonatal mice.

PubMed

Akins, Victoria T; Weragalaarachchi, Krishanthi; Picardo, Maria Cristina D; Revill, Ann L; Del Negro, Christopher A

2017-08-01

The relationship between neuron morphology and function is a perennial issue in neuroscience. Information about synaptic integration, network connectivity, and the specific roles of neuronal subpopulations can be obtained through morphological analysis of key neurons within a microcircuit. Here we present morphologies of two classes of brainstem respiratory neurons. First, interneurons derived from Dbx1-expressing precursors (Dbx1 neurons) in the preBötzinger complex (preBötC) of the ventral medulla that generate the rhythm for inspiratory breathing movements. Second, Dbx1 neurons of the intermediate reticular formation that influence the motor pattern of pharyngeal and lingual movements during the inspiratory phase of the breathing cycle. We describe the image acquisition and subsequent digitization of morphologies of respiratory Dbx1 neurons from the preBötC and the intermediate reticular formation that were first recorded in vitro. These data can be analyzed comparatively to examine how morphology influences the roles of Dbx1 preBötC and Dbx1 reticular interneurons in respiration and can also be utilized to create morphologically accurate compartmental models for simulation and modeling of respiratory circuits.

Concise review: preleukemic stem cells: molecular biology and clinical implications of the precursors to leukemia stem cells.

PubMed

Pandolfi, Ashley; Barreyro, Laura; Steidl, Ulrich

2013-02-01

Recent experimental evidence has shown that acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) arise from transformed immature hematopoietic cells following the accumulation of multiple stepwise genetic and epigenetic changes in hematopoietic stem cells and committed progenitors. The series of transforming events initially gives rise to preleukemic stem cells (pre-LSC), preceding the formation of fully transformed leukemia stem cells (LSC). Despite the established use of poly-chemotherapy, relapse continues to be the most common cause of death in AML and MDS. The therapeutic elimination of all LSC, as well as pre-LSC, which provide a silent reservoir for the re-formation of LSC, will be essential for achieving lasting cures. Conventional sequencing and next-generation genome sequencing have allowed us to describe many of the recurrent mutations in the bulk cell populations in AML and MDS, and recent work has also focused on identifying the initial molecular changes contributing to leukemogenesis. Here we review recent and ongoing advances in understanding the roles of pre-LSC, and the aberrations that lead to pre-LSC formation and subsequent LSC transformation.

Sleep-disordered breathing after targeted ablation of preBötzinger complex neurons.

PubMed

McKay, Leanne C; Janczewski, Wiktor A; Feldman, Jack L

2005-09-01

Ablation of preBötzinger complex (preBötC) neurons, critical for respiratory rhythm generation, resulted in a progressive, increasingly severe disruption of respiratory pattern, initially during sleep and then also during wakefulness in adult rats. Sleep-disordered breathing is highly prevalent in elderly humans and in some patients with neurodegenerative disease. We propose that sleep-disordered breathing results from loss of preBötC neurons and could underlie death during sleep in these populations.

Sleep-disordered breathing after targeted ablation of preBötzinger complex neurons

PubMed Central

McKay, Leanne C; Janczewski, Wiktor A; Feldman, Jack L

2010-01-01

Ablation of preBötzinger complex (preBötC) neurons, critical for respiratory rhythm generation, resulted in a progressive, increasingly severe disruption of respiratory pattern, initially during sleep and then also during wakefulness in adult rats. Sleep-disordered breathing is highly prevalent in elderly humans and in some patients with neurodegenerative disease. We propose that sleep-disordered breathing results from loss of preBötC neurons and could underlie death during sleep in these populations. PMID:16116455

Complex interactions amongst N-cadherin, DLAR, and Liprin-α regulate Drosophila photoreceptor axon targeting

PubMed Central

Prakash, Saurabh; Maclendon, Helen; Dubreuil, Catherine I.; Ghose, Aurnab; Hwa, Jennifer; Dennehy, Kelly A.; Tomalty, Katharine M.H.; Clark, Kelsey; Van Vactor, David; Clandinin, Thomas R.

2009-01-01

The formation of stable adhesive contacts between pre- and post-synaptic neurons represents the initial step in synapse assembly. The cell adhesion molecule N-cadherin, the receptor tyrosine phosphatase DLAR, and the scaffolding molecule Liprin-α play critical, evolutionarily conserved roles in this process. However, how these proteins signal to the growth cone, and are themselves regulated, remains poorly understood. Using Drosophila photoreceptors (R cells) as a model, we evaluate genetic and physical interactions among these three proteins. We demonstrate that DLAR function in this context is independent of phosphatase activity, but requires interactions mediated by its intracellular domain. Genetic studies reveal both positive and, surprisingly, inhibitory interactions amongst all three genes. These observations are corroborated by biochemical studies demonstrating that DLAR physically associates via its phosphatase domain with N-cadherin in Drosophila embryos. Together, these data demonstrate that N-cadherin, DLAR, and Liprin-α function in a complex to regulate adhesive interactions between pre- and post-synaptic cells, and provide a novel mechanism for controlling the activity of liprin-α in the developing growth cone. PMID:19766621

Deuterated methanol map towards L1544

NASA Astrophysics Data System (ADS)

Chacón-Tanarro, A.; Caselli, P.; Bizzocchi, L.; Pineda, J. E.; Spezzano, S.; Giuliano, B. M.; Lattanzi, V.; Punanova, A.

Pre-stellar cores are self-gravitating starless dense cores with clear signs of contraction and chemical evolution (Crapsi et al. 2005), considered to represent the initial conditions in the process of star formation (Caselli & Ceccarelli 2012). Theoretical studies predict that CO is one of the precursors of complex organic molecules (COMs) during this cold and dense phase (Tielens et al. 1982; Watanabe et al. 2002). Moreover, when CO starts to deplete onto dust grains (at densities of a few 104 cm-3), the formation of deuterated species is enhanced, as CO accelerates the destruction of important precursors of deuterated molecules (Dalgarno & Lepp 1984). Here, we present the CH_2DOH/CH_3OH column density map toward the pre-stellar core L1544 (Chacón-Tanarro et al., in prep.), taken with the IRAM 30 m antenna. The results are compared with the C17O (1-0) distribution across L1544. As methanol is formed on dust grains via hydrogenation of frozen-out CO, this work allows us to measure the deuteration on surfaces and compared it with gas phase deuteration, as well as CO freeze-out and dust properties. This is important to shed light on the basic chemical processes just before the formation of a stellar system.

The pre-autophagosomal structure organized by concerted functions of APG genes is essential for autophagosome formation.

PubMed

Suzuki, K; Kirisako, T; Kamada, Y; Mizushima, N; Noda, T; Ohsumi, Y

2001-11-01

Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Several key reactions performed by these proteins have been described, but a comprehensive understanding of the overall network is still lacking. Based on Apg protein localization, we have identified a novel structure that functions in autophagosome formation. This pre-autophagosomal structure, containing at least five Apg proteins, i.e. Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p, is localized in the vicinity of the vacuole. Analysis of apg mutants revealed that the formation of both a phosphatidylethanolamine-conjugated Aut7p and an Apg12p- Apg5p conjugate is essential for the localization of Aut7p to the pre-autophagosomal structure. Vps30p/Apg6p and Apg14p, components of an autophagy- specific phosphatidylinositol 3-kinase complex, Apg9p and Apg16p are all required for the localization of Apg5p and Aut7p to the structure. The Apg1p protein kinase complex functions in the late stage of autophagosome formation. Here, we present the classification of Apg proteins into three groups that reflect each step of autophagosome formation.

The pre-autophagosomal structure organized by concerted functions of APG genes is essential for autophagosome formation

PubMed Central

Suzuki, Kuninori; Kirisako, Takayoshi; Kamada, Yoshiaki; Mizushima, Noboru; Noda, Takeshi; Ohsumi, Yoshinori

2001-01-01

Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Several key reactions performed by these proteins have been described, but a comprehensive understanding of the overall network is still lacking. Based on Apg protein localization, we have identified a novel structure that functions in autophagosome formation. This pre-autophagosomal structure, containing at least five Apg proteins, i.e. Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p, is localized in the vicinity of the vacuole. Analysis of apg mutants revealed that the formation of both a phosphatidylethanolamine-conjugated Aut7p and an Apg12p– Apg5p conjugate is essential for the localization of Aut7p to the pre-autophagosomal structure. Vps30p/Apg6p and Apg14p, components of an autophagy- specific phosphatidylinositol 3-kinase complex, Apg9p and Apg16p are all required for the localization of Apg5p and Aut7p to the structure. The Apg1p protein kinase complex functions in the late stage of autophagosome formation. Here, we present the classification of Apg proteins into three groups that reflect each step of autophagosome formation. PMID:11689437

Mammalian splicing factor SF1 interacts with SURP domains of U2 snRNP-associated proteins

PubMed Central

Crisci, Angela; Raleff, Flore; Bagdiul, Ivona; Raabe, Monika; Urlaub, Henning; Rain, Jean-Christophe; Krämer, Angela

2015-01-01

Splicing factor 1 (SF1) recognizes the branch point sequence (BPS) at the 3′ splice site during the formation of early complex E, thereby pre-bulging the BPS adenosine, thought to facilitate subsequent base-pairing of the U2 snRNA with the BPS. The 65-kDa subunit of U2 snRNP auxiliary factor (U2AF65) interacts with SF1 and was shown to recruit the U2 snRNP to the spliceosome. Co-immunoprecipitation experiments of SF1-interacting proteins from HeLa cell extracts shown here are consistent with the presence of SF1 in early splicing complexes. Surprisingly almost all U2 snRNP proteins were found associated with SF1. Yeast two-hybrid screens identified two SURP domain-containing U2 snRNP proteins as partners of SF1. A short, evolutionarily conserved region of SF1 interacts with the SURP domains, stressing their role in protein–protein interactions. A reduction of A complex formation in SF1-depleted extracts could be rescued with recombinant SF1 containing the SURP-interaction domain, but only partial rescue was observed with SF1 lacking this sequence. Thus, SF1 can initially recruit the U2 snRNP to the spliceosome during E complex formation, whereas U2AF65 may stabilize the association of the U2 snRNP with the spliceosome at later times. In addition, these findings may have implications for alternative splicing decisions. PMID:26420826

The Populus class III HD ZIP, popREVOLUTA, influences cambium initiation and patterning of woody stems.

PubMed

Robischon, Marcel; Du, Juan; Miura, Eriko; Groover, Andrew

2011-03-01

The secondary growth of a woody stem requires the formation of a vascular cambium at an appropriate position and proper patterning of the vascular tissues derived from the cambium. Class III homeodomain-leucine zipper (HD ZIP) transcription factors have been implicated in polarity determination and patterning in lateral organs and primary vascular tissues and in the initiation and function of shoot apical meristems. We report here the functional characterization of a Populus class III HD ZIP gene, popREVOLUTA (PRE), that demonstrates another role for class III HD ZIPs in regulating the development of cambia and secondary vascular tissues. PRE is orthologous to Arabidopsis (Arabidopsis thaliana) REVOLUTA and is expressed in both the shoot apical meristem and in the cambial zone and secondary vascular tissues. Transgenic Populus expressing a microRNA-resistant form of PRE presents unstable phenotypic abnormalities affecting both primary and secondary growth. Surprisingly, phenotypic changes include abnormal formation of cambia within cortical parenchyma that can produce secondary vascular tissues in reverse polarity. Genes misexpressed in PRE mutants include transcription factors and auxin-related genes previously implicated in class III HD ZIP functions during primary growth. Together, these results suggest that PRE plays a fundamental role in the initiation of the cambium and in regulating the patterning of secondary vascular tissues.

Mutations in CDC45, Encoding an Essential Component of the Pre-initiation Complex, Cause Meier-Gorlin Syndrome and Craniosynostosis.

PubMed

Fenwick, Aimee L; Kliszczak, Maciej; Cooper, Fay; Murray, Jennie; Sanchez-Pulido, Luis; Twigg, Stephen R F; Goriely, Anne; McGowan, Simon J; Miller, Kerry A; Taylor, Indira B; Logan, Clare; Bozdogan, Sevcan; Danda, Sumita; Dixon, Joanne; Elsayed, Solaf M; Elsobky, Ezzat; Gardham, Alice; Hoffer, Mariette J V; Koopmans, Marije; McDonald-McGinn, Donna M; Santen, Gijs W E; Savarirayan, Ravi; de Silva, Deepthi; Vanakker, Olivier; Wall, Steven A; Wilson, Louise C; Yuregir, Ozge Ozalp; Zackai, Elaine H; Ponting, Chris P; Jackson, Andrew P; Wilkie, Andrew O M; Niedzwiedz, Wojciech; Bicknell, Louise S

2016-07-07

DNA replication precisely duplicates the genome to ensure stable inheritance of genetic information. Impaired licensing of origins of replication during the G1 phase of the cell cycle has been implicated in Meier-Gorlin syndrome (MGS), a disorder defined by the triad of short stature, microtia, and a/hypoplastic patellae. Biallelic partial loss-of-function mutations in multiple components of the pre-replication complex (preRC; ORC1, ORC4, ORC6, CDT1, or CDC6) as well as de novo stabilizing mutations in the licensing inhibitor, GMNN, cause MGS. Here we report the identification of mutations in CDC45 in 15 affected individuals from 12 families with MGS and/or craniosynostosis. CDC45 encodes a component of both the pre-initiation (preIC) and CMG helicase complexes, required for initiation of DNA replication origin firing and ongoing DNA synthesis during S-phase itself, respectively, and hence is functionally distinct from previously identified MGS-associated genes. The phenotypes of affected individuals range from syndromic coronal craniosynostosis to severe growth restriction, fulfilling diagnostic criteria for Meier-Gorlin syndrome. All mutations identified were biallelic and included synonymous mutations altering splicing of physiological CDC45 transcripts, as well as amino acid substitutions expected to result in partial loss of function. Functionally, mutations reduce levels of full-length transcripts and protein in subject cells, consistent with partial loss of CDC45 function and a predicted limited rate of DNA replication and cell proliferation. Our findings therefore implicate the preIC as an additional protein complex involved in the etiology of MGS and connect the core cellular machinery of genome replication with growth, chondrogenesis, and cranial suture homeostasis. Copyright © 2016 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Temporal evolution of ion spectral structures during a geomagnetic storm: Observations and modeling

NASA Astrophysics Data System (ADS)

Ferradas, C.; Zhang, J.; Spence, H. E.; Kistler, L. M.; Larsen, B.; Reeves, G. D.; Skoug, R. M.; Funsten, H. O.

2016-12-01

During the last decades several missions have recorded the presence of dynamic spectral features of energetic ions in the inner magnetosphere. We present a case study of the temporal evolution of H+, He+, and O+ spectral structures throughout the geomagnetic storm of 2 October 2013. We use data from the Helium, Oxygen, Proton, and Electron (HOPE) mass spectrometer onboard Van Allen Probe A to analyze the spectral structures in the energy range of 1- 50 keV. We find that the characteristics of the ion structures follow a cyclic pattern, the observed features changing dramatically as the storm starts and then returning to its initial pre-storm state. Quiet, pre-storm times are characterized by multiple and often complex flux structures at narrow energy bands. During the storm main phase, the observed features become simple, with no nose structures or only one nose structure present in the energy-time spectrograms. As the inner magnetosphere recovers from the storm, more complex structures appear once again. Additionally, the heavy ion spectral features are generally more complex than the H+ features, with multiple noses being observed more often in the heavy ion spectra. We use a model of ion drift and losses due to charge exchange to understand the formation of the spectral features and their species dependence.

Multiple interactions between RNA polymerase I, TIF-IA and TAF(I) subunits regulate preinitiation complex assembly at the ribosomal gene promoter.

PubMed

Yuan, Xuejun; Zhao, Jian; Zentgraf, Hanswalter; Hoffmann-Rohrer, Urs; Grummt, Ingrid

2002-11-01

In mammals, growth-dependent regulation of rRNA synthesis is brought about by the transcription initiation factor TIF-IA. TIF-IA is associated with a fraction of the TBP-containing factor TIF-IB/SL1 and the initiation-competent form of RNA polymerase I (Pol I). We investigated the mechanisms that down-regulate cellular pre-rRNA synthesis and demonstrate that nutrient starvation, density arrest and protein synthesis inhibitors inactivate TIF-IA and impair the association of TIF-IA with Pol I. Moreover, we used a panel of TIF-IA deletion mutants to map the domains that mediate the interaction of TIF-IA with Pol I and TIF-IB/SL1. We found that amino acids 512-609 interact with two subunits of Pol I, RPA43 and PAF67, whereas a short, conserved motif (LARAK, amino acids 411-415) is required for the association of TIF-IA with TAF(I)95 and TAF(I)68. The results uncover an interphase for essential protein-protein interactions that facilitate Pol I preinitiation complex formation.

The structure of SV40 large T hexameric helicase in complex with AT-rich origin DNA

PubMed Central

Gai, Dahai; Wang, Damian; Li, Shu-Xing; Chen, Xiaojiang S

2016-01-01

DNA replication is a fundamental biological process. The initial step in eukaryotic DNA replication is the assembly of the pre-initiation complex, including the formation of two head-to-head hexameric helicases around the replication origin. How these hexameric helicases interact with their origin dsDNA remains unknown. Here, we report the co-crystal structure of the SV40 Large-T Antigen (LT) hexameric helicase bound to its origin dsDNA. The structure shows that the six subunits form a near-planar ring that interacts with the origin, so that each subunit makes unique contacts with the DNA. The origin dsDNA inside the narrower AAA+ domain channel shows partial melting due to the compression of the two phosphate backbones, forcing Watson-Crick base-pairs within the duplex to flip outward. This structure provides the first snapshot of a hexameric helicase binding to origin dsDNA, and suggests a possible mechanism of origin melting by LT during SV40 replication in eukaryotic cells. DOI: http://dx.doi.org/10.7554/eLife.18129.001 PMID:27921994

SWI/SNF interacts with cleavage and polyadenylation factors and facilitates pre-mRNA 3' end processing.

PubMed

Yu, Simei; Jordán-Pla, Antonio; Gañez-Zapater, Antoni; Jain, Shruti; Rolicka, Anna; Östlund Farrants, Ann-Kristin; Visa, Neus

2018-05-31

SWI/SNF complexes associate with genes and regulate transcription by altering the chromatin at the promoter. It has recently been shown that these complexes play a role in pre-mRNA processing by associating at alternative splice sites. Here, we show that SWI/SNF complexes are involved also in pre-mRNA 3' end maturation by facilitating 3' end cleavage of specific pre-mRNAs. Comparative proteomics show that SWI/SNF ATPases interact physically with subunits of the cleavage and polyadenylation complexes in fly and human cells. In Drosophila melanogaster, the SWI/SNF ATPase Brahma (dBRM) interacts with the CPSF6 subunit of cleavage factor I. We have investigated the function of dBRM in 3' end formation in S2 cells by RNA interference, single-gene analysis and RNA sequencing. Our data show that dBRM facilitates pre-mRNA cleavage in two different ways: by promoting the association of CPSF6 to the cleavage region and by stabilizing positioned nucleosomes downstream of the cleavage site. These findings show that SWI/SNF complexes play a role also in the cleavage of specific pre-mRNAs in animal cells.

The 70 S monosome accumulation and in vitro initiation complex formation by Escherichia coli ribosomes at 5 C. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Broeze, R. J.; Pope, D. H.

1978-01-01

The inhibition of translation which is observed after shifting Escherichia coli to low temperature was investigated. 70 S ribosomes were isolated from E. coli 8 hours after a shift to 5 C synthesized protein in the absence of added mRNA (i.e., endogenous protein synthesis by 70 S monosomes) at a rate which was three times greater than the rate of endogenous protein synthesis by 70 S ribosomes which were isolated at the time of the shift to 5 C. Calculations based on the rates of endogenous protein synthesis and polyphenylalanine synthesis indicate that 70 S monosomes comprise only 0.1% of the total E. coli 70 S ribosome population after 8 hours at 5 c. Experiments designed to test initiation complex formation on ApUpG or formaldehyde treated MS-2 viral RNA demonstrated that, although the rate of formation of 30 S initiation complexes was not inhibited, the rate of formation of active 70 S initiation complexes, able to react with puromycin, was inhibited to a great extent at 5 C. A model depicting the effects of low temperature on the E. coli translation system is proposed.

Initial Study of Pre-Service Teachers' Comments on a Reality-Based, Urban-Student Video Streamed within an Online Course

ERIC Educational Resources Information Center

O'Connor, Eileen A.

2009-01-01

The Master of Arts in Teaching program at Empire State College, an alternative teacher certification program focused on bringing career-changing adults to high-needs schools, has an important need in its initial pre-service year. These adult students must be prepared to move into complex, high-needs schools without student teaching and often with…

Interactive effects of compost and pre-planting soil moisture on plant biomass, nutrition and formation of mycorrhizas: a context dependent response.

PubMed

Ngo, H T T; Cavagnaro, T R

2018-01-24

We aimed to investigate the combined impacts of compost addition and pre-planting soil moisture conditions, on plant-available nutrients, and subsequent impacts on the biomass, nutrition and formation of AM by two important crop species. A glasshouse study was undertaken in which wheat and tomato plants were grown in compost amended or un-amended soil that was subjected to different moisture regimes prior to planting. The availability of P was strongly influenced by compost addition, but not pre-planting moisture conditions. In contrast, mineral N pools were affected by compost addition and pre-planting soil moisture conditions in complex ways. These changes in nutrient availability affected plant biomass, nutrient uptake and formation of AM. In general, plant performance was better where pre-planting soil moisture conditions were wet or dry, and worse where they involved a wet/dry cycle, and mycorrhizal colonisation was lower where compost was added to the soil. That pre-planting moisture conditions affect the biomass of subsequent crops is an important finding, the potential implications of which are considered here.

Stimulation of ribosomal RNA gene promoter by transcription factor Sp1 involves active DNA demethylation by Gadd45-NER pathway.

PubMed

Rajput, Pallavi; Pandey, Vijaya; Kumar, Vijay

2016-08-01

The well-studied Pol II transcription factor Sp1 has not been investigated for its regulatory role in rDNA transcription. Here, we show that Sp1 bound to specific sites on rDNA and localized into the nucleoli during the G1 phase of cell cycle to activate rDNA transcription. It facilitated the recruitment of Pol I pre-initiation complex and impeded the binding of nucleolar remodeling complex (NoRC) to rDNA resulting in the formation of euchromatin active state. More importantly, Sp1 also orchestrated the site-specific binding of Gadd45a-nucleotide excision repair (NER) complex resulting in active demethylation and transcriptional activation of rDNA. Interestingly, knockdown of Sp1 impaired rDNA transcription due to reduced engagement of the Gadd45a-NER complex and hypermethylation of rDNA. Thus, the present study unveils a novel role of Sp1 in rDNA transcription involving promoter demethylation. Copyright © 2016 Elsevier B.V. All rights reserved.

Transcription factors PRE3 and WOX11 are involved in the formation of new lateral roots from secondary growth taproot in A. thaliana.

PubMed

Baesso, B; Chiatante, D; Terzaghi, M; Zenga, D; Nieminen, K; Mahonen, A P; Siligato, R; Helariutta, Y; Scippa, G S; Montagnoli, A

2018-05-01

The spatial deployment of lateral roots determines the ability of a plant to interact with the surrounding environment for nutrition and anchorage. This paper shows that besides the pericycle, the vascular cambium becomes active in Arabidopsis thaliana taproot at a later stage of development and is also able to form new lateral roots. To demonstrate the above, we implemented a two-step approach in which the first step leads to development of a secondary structure in A. thaliana taproot, and the second applies a mechanical stress on the vascular cambium to initiate formation of a new lateral root primordium. GUS staining showed PRE3, DR5 and WOX11 signals in the cambial zone of the root during new lateral root formation. An advanced level of wood formation, characterized by the presence of medullar rays, was achieved. Preliminary investigations suggest the involvement of auxin and two transcription factors (PRE3/ATBS1/bHLH135/TMO7 and WOX11) in the transition of some vascular cambium initials from a role as producers of xylem/phloem mother cells to founder cells of a new lateral root primordium. © 2018 German Society for Plant Sciences and The Royal Botanical Society of the Netherlands.

Elevated extracellular [K+] inhibits death-receptor- and chemical-mediated apoptosis prior to caspase activation and cytochrome c release.

PubMed Central

Thompson, G J; Langlais, C; Cain, K; Conley, E C; Cohen, G M

2001-01-01

Efflux of intracellular K(+) and cell shrinkage are features of apoptosis in many experimental systems, and a regulatory role has been proposed for cytoplasmic [K(+)] in initiating apoptosis. We have investigated this in both death-receptor-mediated and chemical-induced apoptosis. Using Jurkat T cells pre-loaded with the K(+) ion surrogate (86)Rb(+), we have demonstrated an efflux of intracellular K(+) during apoptosis that was concomitant with, but did not precede, other apoptotic changes, including phosphatidylserine externalization, mitochondrial depolarization and cell shrinkage. To further clarify the role of K(+) ions in apoptosis, cytoprotection by elevated extracellular [K(+)] was studied. Induction of apoptosis by diverse death-receptor and chemical stimuli in two cell lines was inhibited prior to phosphatidylserine externalization, mitochondrial depolarization, cytochrome c release and caspase activation. Using a cell-free system, we have demonstrated a novel mechanism by which increasing [K(+)] inhibited caspase activation. In control dATP-activated lysates, Apaf-1 oligomerized to a biologically active caspase processing approximately 700 kDa complex and an inactive approximately 1.4 MDa complex. Increasing [K(+)] inhibited caspase activation by preventing formation of the approximately 700 kDa complex, but not of the inactive complex. Thus intracellular and extracellular [K(+)] markedly affect caspase activation and the initiation of apoptosis induced by both death-receptor ligation and chemical stress. PMID:11415444

Protein interactions and complexes in human microRNA biogenesis and function

PubMed Central

Perron, Marjorie P.; Provost, Patrick

2010-01-01

Encoded in the genome of most eukaryotes, microRNAs (miRNAs) have been proposed to regulate specifically up to 90% of human genes through a process known as miRNA-guided RNA silencing. The aim of this review is to present this process as the integration of a succession of specialized molecular machines exerting well defined functions. The nuclear microprocessor complex initially recognizes and processes its primary miRNA substrate into a miRNA precursor (pre-miRNA). This structure is then exported to the cytoplasm by the Exportin-5 complex where it is presented to the pre-miRNA processing complex. Following pre-miRNA conversion into a miRNA:miRNA* duplex, this complex is assembled into a miRNA-containing ribonucleoprotein (miRNP) complex, after which the miRNA strand is selected. The degree of complementarity of the miRNA for its messenger RNA (mRNA) target guides the recruitment of the miRNP complex. Initially repressing its translation, the miRNP-silenced mRNA is directed to the P-bodies, where the mRNA is either released from its inhibition upon a cellular signal and/or actively degraded. The potency and specificity of miRNA biogenesis and function rely on the distinct protein·protein, protein·RNA and RNA:RNA interactions found in different complexes, each of which fulfill a specific function in a well orchestrated process. PMID:17981733

New Universal Rules of Eukaryotic Translation Initiation Fidelity

PubMed Central

Zur, Hadas; Tuller, Tamir

2013-01-01

The accepted model of eukaryotic translation initiation begins with the scanning of the transcript by the pre-initiation complex from the 5′end until an ATG codon with a specific nucleotide (nt) context surrounding it is recognized (Kozak rule). According to this model, ATG codons upstream to the beginning of the ORF should affect translation. We perform for the first time, a genome-wide statistical analysis, uncovering a new, more comprehensive and quantitative, set of initiation rules for improving the cost of translation and its efficiency. Analyzing dozens of eukaryotic genomes, we find that in all frames there is a universal trend of selection for low numbers of ATG codons; specifically, 16–27 codons upstream, but also 5–11 codons downstream of the START ATG, include less ATG codons than expected. We further suggest that there is selection for anti optimal ATG contexts in the vicinity of the START ATG. Thus, the efficiency and fidelity of translation initiation is encoded in the 5′UTR as required by the scanning model, but also at the beginning of the ORF. The observed nt patterns suggest that in all the analyzed organisms the pre-initiation complex often misses the START ATG of the ORF, and may start translation from an alternative initiation start-site. Thus, to prevent the translation of undesired proteins, there is selection for nucleotide sequences with low affinity to the pre-initiation complex near the beginning of the ORF. With the new suggested rules we were able to obtain a twice higher correlation with ribosomal density and protein levels in comparison to the Kozak rule alone (e.g. for protein levels r = 0.7 vs. r = 0.31; p<10−12). PMID:23874179

Renal cyst formation in patients treated with crizotinib for non-small cell lung cancer-Incidence, radiological features and clinical characteristics.

PubMed

Halpenny, Darragh F; McEvoy, Sinead; Li, Angela; Hayan, Sumar; Capanu, Marinela; Zheng, Junting; Riely, Gregory; Ginsberg, Michelle S

2017-04-01

Treatment with the ALK inhibitor crizotinib has been associated with complex renal cyst formation in patients with non-small cell lung cancer (NSCLC). Using patients treated with crizotinib, we aimed to evaluate the incidence of renal cyst formation, to identify risk factors for cyst formation and to provide a radiological description of cyst characteristics. Patients with ALK-positive NSCLC treated with crizotinib were retrospectively identified from an institutional database. Computed tomography (CT) imaging performed prior to and during crizotinib treatment was retrospectively reviewed to assess the size and complexity of pre-existing cysts, new cysts, and enlarging cysts. Demographic data including age, sex, ethnicity, smoking history and length of treatment were also recorded. Data from 60 patients with NSCLC treated with crizotinib at our institution between 6/5/2009 and 7/1/2015 were collected. 57 had CT imaging before and during treatment. Mean length of imaging follow-up was 18 months. 9 (16%) patients had cysts which enlarged or developed de novo during treatment. 2 (4%) patients developed complex renal cysts (1 of these patients also developed complex hepatic cysts). Female gender (p=0.008) and the presence of renal cysts on baseline scans (p=0.044) were significantly associated with cyst formation or growth. Renal cyst formation or growth occurred in 16% of crizotinib-treated patients. Women and those with pre-existing cysts were at greatest risk. Although the potential causal relationship between crizotinib use and renal cyst formation has yet to be fully defined, it is important for radiologists and clinicians to be aware of this finding. Copyright © 2017. Published by Elsevier B.V.

Geometrical and mechanical constraints on the formation of ring-fault calderas

NASA Astrophysics Data System (ADS)

Folch, A.; Martí, J.

2004-04-01

Ash-flow, plate-subsidence (piston-like) calderas are bounded by a set of arcuated sub-vertical collapse faults named ring-faults. Experimental studies on caldera formation, performed mostly using spherical or cylindrical magma chamber geometries, find that the resulting ring-faults correspond to steeply outward dipping reverse faults, and show that pre-existing fractures developed during pre-eruptive phases of pressure increase may play a major role in controlling the final collapse mechanism, a situation that should be expected in small to medium sized ring-fault calderas developed on top of composite volcanoes or volcanic clusters. On the other hand, some numerical experiments indicate that large sill-like, elongated magma chambers may induce collapse due to roof bending without fault reactivation, as seems to occur in large plate-subsidence calderas formed independently of pre-existing volcanoes. Also, numerical experiments allow the formation of nearly vertical or steeply inward dipping normal ring-faults, in contrast with most of the analogue models. Using a thermoelastic model, we investigate the geometrical and mechanical conditions to form ring-fault calderas, in particular the largest ones, without needing a previous crust fracturing. Results are given in terms of two dimensionless geometrical parameters, namely λ and e. The former is the chamber extension to chamber depth ratio, whereas the latter stands for the chamber eccentricity. We propose that the ( λ, e) pair determinates two different types of ring-fault calderas with different associated collapse regimes. Ring-fault region A is related to large plate-subsidence calderas (i.e. Andean calderas or Western US calderas), for which few depressurisation is needed to set up a collapse initially governed by flexural bending of the chamber roof. In contrast, ring-fault region B is related to small to moderate sized calderas (i.e. composite volcano calderas), for which much depressurisation is needed. Our opinion is that collapse requires, in the latter case, reactivation of pre-existing fractures and it is therefore more complex and history dependent.

Structures of transcription pre-initiation complex with TFIIH and Mediator.

PubMed

Schilbach, S; Hantsche, M; Tegunov, D; Dienemann, C; Wigge, C; Urlaub, H; Cramer, P

2017-11-09

For the initiation of transcription, RNA polymerase II (Pol II) assembles with general transcription factors on promoter DNA to form the pre-initiation complex (PIC). Here we report cryo-electron microscopy structures of the Saccharomyces cerevisiae PIC and PIC-core Mediator complex at nominal resolutions of 4.7 Å and 5.8 Å, respectively. The structures reveal transcription factor IIH (TFIIH), and suggest how the core and kinase TFIIH modules function in the opening of promoter DNA and the phosphorylation of Pol II, respectively. The TFIIH core subunit Ssl2 (a homologue of human XPB) is positioned on downstream DNA by the 'E-bridge' helix in TFIIE, consistent with TFIIE-stimulated DNA opening. The TFIIH kinase module subunit Tfb3 (MAT1 in human) anchors the kinase Kin28 (CDK7), which is mobile in the PIC but preferentially located between the Mediator hook and shoulder in the PIC-core Mediator complex. Open spaces between the Mediator head and middle modules may allow access of the kinase to its substrate, the C-terminal domain of Pol II.

Integration of mRNP formation and export.

PubMed

Björk, Petra; Wieslander, Lars

2017-08-01

Expression of protein-coding genes in eukaryotes relies on the coordinated action of many sophisticated molecular machineries. Transcription produces precursor mRNAs (pre-mRNAs) and the active gene provides an environment in which the pre-mRNAs are processed, folded, and assembled into RNA-protein (RNP) complexes. The dynamic pre-mRNPs incorporate the growing transcript, proteins, and the processing machineries, as well as the specific protein marks left after processing that are essential for export and the cytoplasmic fate of the mRNPs. After release from the gene, the mRNPs move by diffusion within the interchromatin compartment, making up pools of mRNPs. Here, splicing and polyadenylation can be completed and the mRNPs recruit the major export receptor NXF1. Export competent mRNPs interact with the nuclear pore complex, leading to export, concomitant with compositional and conformational changes of the mRNPs. We summarize the integrated nuclear processes involved in the formation and export of mRNPs.

"Because Teaching Is Like a Plantation of 'Dakwah'": Understanding Complexities in Choosing to Be a Teacher in Indonesia

ERIC Educational Resources Information Center

Afrianto

2014-01-01

This paper reports on findings from an ongoing research project involving pre-service English teachers' identity formation during teaching practicum at Riau University, Indonesia. It explores the motivations behind participants' decisions to become English teachers. Qualitative data were gathered during pre- and post-teaching practicum periods…

Numerical Modelling of Extended Leak-Off Test with a Pre-Existing Fracture

NASA Astrophysics Data System (ADS)

Lavrov, A.; Larsen, I.; Bauer, A.

2016-04-01

Extended leak-off test (XLOT) is one of the few techniques available for stress measurements in oil and gas wells. Interpretation of the test is often difficult since the results depend on a multitude of factors, including the presence of natural or drilling-induced fractures in the near-well area. Coupled numerical modelling of XLOT has been performed to investigate the pressure behaviour during the flowback phase as well as the effect of a pre-existing fracture on the test results in a low-permeability formation. Essential features of XLOT known from field measurements are captured by the model, including the saw-tooth shape of the pressure vs injected volume curve, and the change of slope in the pressure vs time curve during flowback used by operators as an indicator of the bottomhole pressure reaching the minimum in situ stress. Simulations with a pre-existing fracture running from the borehole wall in the radial direction have revealed that the results of XLOT are quite sensitive to the orientation of the pre-existing fracture. In particular, the fracture initiation pressure and the formation breakdown pressure increase steadily with decreasing angle between the fracture and the minimum in situ stress. Our findings seem to invalidate the use of the fracture initiation pressure and the formation breakdown pressure for stress measurements or rock strength evaluation purposes.

Astrochemical evolution along star formation: overview of the IRAM Large Program ASAI

NASA Astrophysics Data System (ADS)

Lefloch, Bertrand; Bachiller, R.; Ceccarelli, C.; Cernicharo, J.; Codella, C.; Fuente, A.; Kahane, C.; López-Sepulcre, A.; Tafalla, M.; Vastel, C.; Caux, E.; González-García, M.; Bianchi, E.; Gómez-Ruiz, A.; Holdship, J.; Mendoza, E.; Ospina-Zamudio, J.; Podio, L.; Quénard, D.; Roueff, E.; Sakai, N.; Viti, S.; Yamamoto, S.; Yoshida, K.; Favre, C.; Monfredini, T.; Quitián-Lara, H. M.; Marcelino, N.; Boechat-Roberty, H. M.; Cabrit, S.

2018-07-01

Evidence is mounting that the small bodies of our Solar system, such as comets and asteroids, have at least partially inherited their chemical composition from the first phases of the Solar system formation. It then appears that the molecular complexity of these small bodies is most likely related to the earliest stages of star formation. It is therefore important to characterize and to understand how the chemical evolution changes with solar-type protostellar evolution. We present here the Large Program `Astrochemical Surveys At IRAM' (ASAI). Its goal is to carry out unbiased millimetre line surveys between 80 and 272 GHz of a sample of 10 template sources, which fully cover the first stages of the formation process of solar-type stars, from pre-stellar cores to the late protostellar phase. In this paper, we present an overview of the surveys and results obtained from the analysis of the 3 mm band observations. The number of detected main isotopic species barely varies with the evolutionary stage and is found to be very similar to that of massive star-forming regions. The molecular content in O- and C-bearing species allows us to define two chemical classes of envelopes, whose composition is dominated by either (a) a rich content in O-rich complex organic molecules, associated with hot corino sources, or (b) a rich content in hydrocarbons, typical of warm carbon-chain chemistry sources. Overall, a high chemical richness is found to be present already in the initial phases of solar-type star formation.

Formation of a Criegee intermediate in the low-temperature oxidation of dimethyl sulfoxide.

PubMed

Asatryan, Rubik; Bozzelli, Joseph W

2008-04-07

Dimethyl sulfoxide (DMSO) is the major sulfur-containing constituent of the Marine Boundary Layer. It is a significant source of H2SO4 aerosol/particles and methane sulfonic acid via atmospheric oxidation processes, where the mechanism is not established. In this study, several new, low-temperature pathways are revealed in the oxidation of DMSO using CBS-QB3 and G3MP2 multilevel and B3LYP hybrid density functional quantum chemical methods. Unlike analogous hydrocarbon peroxy radicals the chemically activated DMSO peroxy radical, [CH3S(=O)CH2OO*]*, predominantly undergoes simple dissociation to a methylsulfinyl radical CH3S*(=O) and a Criegee intermediate, CH2OO, with the barrier to dissociation 11.3 kcal mol(-1) below the energy of the CH3S(=O)CH2* + O2 reactants. The well depth for addition of O2 to the CH3S(=O)CH2 precursor radical is 29.6 kcal mol(-1) at the CBS-QB3 level of theory. We believe that this reaction may serve an important role in atmospheric photochemical and irradiated biological (oxygen-rich) media where formation of initial radicals is facilitated even at lower temperatures. The Criegee intermediate (carbonyl oxide, peroxymethylene) and sulfinyl radical can further decompose, resulting in additional chain branching. A second reaction channel important for oxidation processes includes formation (via intramolecular H atom transfer) and further decomposition of hydroperoxide methylsulfoxide radical, *CH2S(=O)CH2OOH over a low barrier of activation. The initial H-transfer reaction is similar and common in analogous hydrocarbon radical + O2 reactions; but the subsequent very low (3-6 kcal mol(-1)) barrier (14 kcal mol(-1) below the initial reagents) to beta-scission products is not common in HC systems. The low energy reaction of the hydroperoxide radical is a beta-scission elimination of *CH2S(=O)CH2OOH into the CH2=S=O + CH2O + *OH product set. This beta-scission barrier is low, because of the delocalization of the *CH2 radical center through the -S(=O) group, to the -CH2OOH fragment in the transition state structure. The hydroperoxide methylsulfoxide radical can also decompose via a second reaction channel of intramolecular OH migration, yielding formaldehyde and a sulfur-centered hydroxymethylsulfinyl radical HOCH2S*(=O). The barrier of activation relative to initial reagents is 4.2 kcal mol(-1). Heats of formation for DMSO, DMSO carbon-centered radical and Criegee intermediate are evaluated at 298 K as -35.97 +/- 0.05, 13.0 +/- 0.2 and 25.3 +/- 0.7 kcal mol(-1) respectively using isodesmic reaction analysis. The [CH3S*(=O) + CH2OO] product set is shown to form a van der Waals complex that results in O-atom transfer reaction and the formation of new products CH3SO2* radical and CH2O. Proper orientation of the Criegee intermediate and methylsulfinyl radical, as a pre-stabilized pre-reaction complex, assist the process. The DMSO radical reaction is also compared to that of acetonyl radical.

Intrinsic Membrane Properties of Pre-oromotor Neurons in the Intermediate Zone of the Medullary Reticular Formation

PubMed Central

Venugopal, Sharmila; Boulant, Jack A.; Chen, Zhixiong; Travers, Joseph B.

2010-01-01

Neurons in the lower brainstem that control consummatory behavior are widely distributed in the reticular formation (RF) of the pons and medulla. The intrinsic membrane properties of neurons within this distributed system shape complex excitatory and inhibitory inputs from both orosensory and central structures implicated in homeostatic control to produce coordinated oromotor patterns. The current study explored the intrinsic membrane properties of neurons in the intermediate subdivision of the medullary reticular formation (IRt). Neurons in the IRt receive input from the overlying (gustatory) nucleus of the solitary tract and project to the oromotor nuclei. Recent behavioral pharmacology studies as well as computational modeling suggest that inhibition in the IRt plays an important role in the transition from a taste-initiated oromotor pattern of ingestion to one of rejection. The present study explored the impact of hyperpolarization on membrane properties. In response to depolarization, neurons responded with either a tonic discharge, an irregular/burst pattern or were spike-adaptive. A hyperpolarizing pre-pulse modulated the excitability of most (82%) IRt neurons to subsequent depolarization. Instances of both increased (30%) and decreased (52%) excitability were observed. Currents induced by the hyperpolarization included an outward 4-AP sensitive K+ current that suppressed excitability and an inward cation current that increased excitability. These currents are also present in other subpopulations of RF neurons that influence the oromotor nuclei and we discuss how these currents could alter ring characteristics to impact pattern generation. PMID:20338224

A non-canonical mechanism for Crm1-export cargo complex assembly.

PubMed

Fischer, Ute; Schäuble, Nico; Schütz, Sabina; Altvater, Martin; Chang, Yiming; Faza, Marius Boulos; Panse, Vikram Govind

2015-04-21

The transport receptor Crm1 mediates the export of diverse cargos containing leucine-rich nuclear export signals (NESs) through complex formation with RanGTP. To ensure efficient cargo release in the cytoplasm, NESs have evolved to display low affinity for Crm1. However, mechanisms that overcome low affinity to assemble Crm1-export complexes in the nucleus remain poorly understood. In this study, we reveal a new type of RanGTP-binding protein, Slx9, which facilitates Crm1 recruitment to the 40S pre-ribosome-associated NES-containing adaptor Rio2. In vitro, Slx9 binds Rio2 and RanGTP, forming a complex. This complex directly loads Crm1, unveiling a non-canonical stepwise mechanism to assemble a Crm1-export complex. A mutation in Slx9 that impairs Crm1-export complex assembly inhibits 40S pre-ribosome export. Thus, Slx9 functions as a scaffold to optimally present RanGTP and the NES to Crm1, therefore, triggering 40S pre-ribosome export. This mechanism could represent one solution to the paradox of weak binding events underlying rapid Crm1-mediated export.

Distinguishing Grenvillian basement from pre-Taconian cover rocks in the Northern Appalachians

USGS Publications Warehouse

Karabinos, P.; Aleinikoff, J.N.; Fanning, C.M.

1999-01-01

Distinguishing Grenvillian basement rocks from pre-Taconian cover sequences in the Appalachians is a first-order problem essential for accurate structural interpretations. The Cavendish Formation in southeastern Vermont presents a classic example of this problem. Doll and others (1961) showed the Cavendish Formation as younger than the Middle Proterozoic Mount Holly Complex but older than the lithologically similar Cambrian Tyson and Hoosac Formations. More recently, the name Cavendish Formation has been informally abandoned, and its metasedimentary units have been mapped as the Tyson and Hoosac Formations of Late Proterozoic to Cambrian age. In a radical departure from these interpretations, Ratcliffe and others (1997) reassigned metasedimentary rocks of the Cavendish Formation to the Mount Holly Complex based on an inferred intrusive relationship between them and a 1.42 Ga tonalite. This new age assignment, if correct, requires a completely new structural interpretation of the region. SHRIMP and Pb evaporation ages of detrital zircons extracted from a quartzite layer from Cavendish Gorge near the proposed intrusive contact with the tonalite constrain the time of deposition of the Cavendish Formation. Grain shapes of the zircons vary from euhedral to nearly spherical. Virtually all the grains have pitted surfaces and show at least some rounding of edges and terminations; grains exhibit oscillatory zoning typical of zircons that crystallized from a magma. Single-grain Pb evaporation analyses of ten zircons and SHRIMP analyses of 15 zircons all yield ages less than 1.42 Ga. Seven of the grains are consistent with derivation from the Bull Hill Gneiss that postdates the Grenville orogenic cycle and predates deposition of the Cavendish Formation. Thus, the metasedimentary units of the Cavendish Formation should not be assigned to the Mount Holly Complex.

Influence of Arrestin on the Photodecay of Bovine Rhodopsin.

PubMed

Chatterjee, Deep; Eckert, Carl Elias; Slavov, Chavdar; Saxena, Krishna; Fürtig, Boris; Sanders, Charles R; Gurevich, Vsevolod V; Wachtveitl, Josef; Schwalbe, Harald

2015-11-09

Continued activation of the photocycle of the dim-light receptor rhodopsin leads to the accumulation of all-trans-retinal in the rod outer segments (ROS). This accumulation can damage the photoreceptor cell. For retinal homeostasis, deactivation processes are initiated in which the release of retinal is delayed. One of these processes involves the binding of arrestin to rhodopsin. Here, the interaction of pre-activated truncated bovine visual arrestin (Arr(Tr)) with rhodopsin in 1,2-diheptanoyl-sn-glycero-3-phosphocholine (DHPC) micelles is investigated by solution NMR techniques and flash photolysis spectroscopy. Our results show that formation of the rhodopsin-arrestin complex markedly influences partitioning in the decay kinetics of rhodopsin, which involves the simultaneous formation of a meta II and a meta III state from the meta I state. Binding of Arr(Tr) leads to an increase in the population of the meta III state and consequently to an approximately twofold slower release of all-trans-retinal from rhodopsin. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

ATP can be dispensable for prespliceosome formation in yeast

PubMed Central

Perriman, Rhonda; Ares, Manuel

2000-01-01

The first ATP-dependent step in pre-mRNA splicing involves the stable binding of U2 snRNP to form the prespliceosome. We show that a prespliceosome-like complex forms in the absence of ATP in yeast extracts lacking the U2 suppressor protein CUS2. These complexes display the same pre-mRNA and U snRNA requirements as authentic prespliceosomes and can be chased through the splicing pathway, indicating that they are a functional intermediate in the spliceosome assembly pathway. ATP-independent prespliceosome-like complexes are also observed in extracts containing a mutant U2 snRNA. Loss of CUS2 does not bypass the role of PRP5, an RNA helicase family member required for ATP-dependent prespliceosome formation. Genetic interactions between CUS2 and a heat-sensitive prp5 allele parallel those observed between CUS2 and U2, and suggest that CUS2 mediates functional interactions between U2 RNA and PRP5. We propose that CUS2 enforces ATP dependence during formation of the prespliceosome by brokering an interaction between PRP5 and the U2 snRNP that depends on correct U2 RNA structure. PMID:10640279

Quantification of trace metals in water using complexation and filter concentration.

PubMed

Dolgin, Bella; Bulatov, Valery; Japarov, Julia; Elish, Eyal; Edri, Elad; Schechter, Israel

2010-06-15

Various metals undergo complexation with organic reagents, resulting in colored products. In practice, their molar absorptivities allow for quantification in the ppm range. However, a proper pre-concentration of the colored complex on paper filter lowers the quantification limit to the low ppb range. In this study, several pre-concentration techniques have been examined and compared: filtering the already complexed mixture, complexation on filter, and dipping of dye-covered filter in solution. The best quantification has been based on the ratio of filter reflectance at a certain wavelength to that at zero metal concentration. The studied complex formations (Ni ions with TAN and Cd ions with PAN) involve production of nanoparticle suspensions, which are associated with complicated kinetics. The kinetics of the complexation of Ni ions with TAN has been investigated and optimum timing could be found. Kinetic optimization in regard to some interferences has also been suggested.

Understanding the operational parameters affecting NDMA formation at Advanced Water Treatment Plants.

PubMed

Farré, Maria José; Döderer, Katrin; Hearn, Laurence; Poussade, Yvan; Keller, Jurg; Gernjak, Wolfgang

2011-01-30

N-nitrosodimethylamine (NDMA) can be formed when secondary effluents are disinfected by chloramines. By means of bench scale experiments this paper investigates operational parameters than can help Advanced Water Treatment Plants (AWTPs) to reduce the formation of NDMA during the production of high quality recycled water. The formation of NDMA was monitored during a contact time of 24h using dimethylamine as NDMA model precursor and secondary effluent from wastewater treatment plants. The three chloramine disinfection strategies tested were pre-formed and in-line formed monochloramine, and pre-formed dichloramine. Although the latter is not employed on purpose in full-scale applications, it has been suggested as the main contributing chemical generating NDMA during chloramination. After 24h, the NDMA formation decreased in both matrices tested in the order: pre-formed dichloramine>in-line formed monochloramine≫pre-formed monochloramine. The most important parameter to consider for the inhibition of NDMA formation was the length of contact time between disinfectant and wastewater. Formation of NDMA was initially inhibited for up to 6h with concentrations consistently <10 ng/L during these early stages of disinfection, regardless of the disinfection strategy. The reduction of the contact time was implemented in Bundamba AWTP (Queensland, Australia), where NDMA concentrations were reduced by a factor of 20 by optimizing the disinfection strategy. Copyright © 2010 Elsevier B.V. All rights reserved.

Patterns of pair formation and mating in an ectoparasitic caligid copepod Lepeophtheirus salmonis (Krøyer 1837): implications for its sensory and mating biology

PubMed Central

Hull, M. Q.

1998-01-01

Non-invasive observations of single cohort and manipulated populations of the sealouse on laboratory-maintained salmon established the sequence of reproductive events and mating. Protandry occurs with adult male emergence synchronized with pre-adult II female emergence, the stage at which most pair formation and pre-copular guarding takes place. Male competence for pair formation and mating was achieved within 24 h of the final moult and pairing occurred according to the preference hierarchy, virgin adult females greater than pre-adult II females much greater than pre-adult I females. This hierarchy broke down when the adult male to unmated female ratio increased rapidly. Males mated successfully not only with newly moulted adult females, but also with older virgin females in which enlargement of the genital complex and premature extrusion of egg strings had occurred. Multiple mating by adult males was demonstrated and may be widespread. Significant inter-host transfer was also demonstrated. Adult males were more mobile than adult females and showed significantly more inter-host transfer. Ablation of the distal tip of the antennules significantly reduced the success of host-finding, pair formation and males' mating.

Shock-induced kelyphite formation in the core of a complex impact crater

NASA Astrophysics Data System (ADS)

Deseta, Natalie; Boonsue, Suporn; Gibson, Roger L.; Spray, John G.

2017-10-01

We present a compositional and textural analysis of shock-induced microtextures in garnet porphyroblasts in migmatitic garnet-cordierite-biotite paragneisses from the centre of the Vredefort impact structure, South Africa. Detailed imaging and major element analysis of deformation features in, and adjacent to, the garnet porphyroblasts record a complex, heterogeneous distribution of shock effects at the microscale. As the most competent silicate mineral in the assemblage, with the highest Hugoniot Elastic Limit and a wide pressure-temperature stability field, the porphyroblastic garnet preserves a more diverse shock deformation response compared to minerals such as quartz and feldspar, which underwent more comprehensive shock metamorphism and subsequent annealing. The garnet porphyroblasts display pre-impact fractures that are overprinted by later intra-granular Hertzian and distinctive planar fractures associated with the impact event. Shock-induced strain localization occurred along internal slip planes and defects, including pre-existing fractures and inclusion boundaries in the garnet. Symplectitic (kelyphitic) coronas commonly enclose the garnet porphyroblasts, and inhabit intra-granular fractures. The kelyphite assemblage in fractures with open communication beyond garnet grain boundaries is characterized by orthopyroxene—cordierite—sapphirine. Conversely, the kelyphite assemblage in closed-off intra-granular fractures is highly variable, comprising spatially restricted combinations of a secondary garnet phase with a majoritic component, Al-rich orthopyroxene, sapphirine and cordierite. The impedance contrast between garnet porphyroblasts and their inclusions further facilitated the formation of shock-induced features (Al-rich orthopyroxene coronas). Together, the textural and mineralogical data suggest that these features provide a record of oscillatory shock perturbations initiated under confining pressure beneath the transient crater floor. This occurred as the shocked rock volume underwent post-shock expansion, forming the core of the central uplift, and was followed by variable textural re-equilibration. This study thus provides a microtextural and mineralogical perspective of the shock regime within confined crust immediately prior to and during central uplift formation.

Evolution of Pre-Main Sequence Accretion Disks

NASA Technical Reports Server (NTRS)

Hartmann, Lee W.

2002-01-01

The aim of this project is to develop a comprehensive global picture of the physical conditions in, and evolutionary timescales of, pre-main sequence accretion disks. The results of this work will help constrain the initial conditions for planet formation. To this end we plan to: (1) Develop much larger samples of 3-10 Myr-old stars to provide better empirical constraints on protoplanetary disk evolution; (2) Study the dusty emission and accretion rates in these systems, with ages closer to the expected epoch of (giant) planet formation at 3-10 Myr; and (3) Develop detailed model disk structures consistent with observations to infer physical conditions in protoplanetary disks and to constrain possible grain growth as the first stage of planetesimal formation.

Endochondral bone formation in embryonic mouse pre-metatarsals

NASA Technical Reports Server (NTRS)

Klement, B. J.; Spooner, B. S.

1992-01-01

Long term exposure to a reduced gravitational environment has a deleterious effect on bone. The developmental events which occur prior to initial bone deposition will provide insight into the regulation of mature bone physiology. We have characterized a system in which the events preceding bone formation take place in an isolated in vitro organ culture environment. We show that cultured pre-metatarsal tissue parallels development of pre-metatarsal tissue in the embryo. Both undergo mesenchyme differentiation and morphogenesis to form a cartilage rod, which resembles the future bone, followed by terminal chondrocyte differentiation in a definite morphogenetic pattern. These sequential steps occur prior to osteoblast maturation and bone matrix deposition in the developing organism. Alkaline phosphatase (ALP) activity is a distinctive enzymatic marker for mineralizing tissues. We have measured this activity throughout pre-metatarsal development and show (a) where in the tissue it is predominantly found, and (b) that this is indeed the mineralizing isoform of the enzyme.

Photo-induced living radical polymerization of acrylates utilizing a discrete copper(II)-formate complex.

PubMed

Anastasaki, Athina; Nikolaou, Vasiliki; Brandford-Adams, Francesca; Nurumbetov, Gabit; Zhang, Qiang; Clarkson, Guy J; Fox, David J; Wilson, Paul; Kempe, Kristian; Haddleton, David M

2015-04-04

A photo-polymerization protocol, utilizing a pre-formed and well-characterized Cu(II) formate complex, [Cu(Me6-Tren)(O2CH)](ClO4), mediated by UV light is described. In the absence of additional reducing agents and/or photosensitizers, ppm concentrations of the oxidatively stable [Cu(Me6-Tren)(O2CH)](ClO4), furnish near-quantitative conversions within 2 h, yielding poly(acrylates) with low dispersities (∼1.10) and exceptional end-group fidelity, capable of undergoing in situ chain extension and block copolymerization.

Complexation-assisted reduction: complexes of glutaroimide-dioxime with tetravalent actinides (Np( iv ) and Th( iv ))

DOE PAGES

Zhang, Zhicheng; Parker, Bernard F.; Lohrey, Trevor D.; ...

2018-01-01

Glutaroimide-dioxime forms strong complexes with Np( iv ) and Th( iv ) in aqueous solution and in crystals. The formation of Np( iv ) complexes from initial Np( v ) is interpreted by a complexation-assisted reduction mechanism.

Complexation-assisted reduction: complexes of glutaroimide-dioxime with tetravalent actinides (Np( iv ) and Th( iv ))

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Zhicheng; Parker, Bernard F.; Lohrey, Trevor D.

Glutaroimide-dioxime forms strong complexes with Np( iv ) and Th( iv ) in aqueous solution and in crystals. The formation of Np( iv ) complexes from initial Np( v ) is interpreted by a complexation-assisted reduction mechanism.

HIV-1 Nef limits communication between linker of activated T cells and SLP-76 to reduce formation of SLP-76-signaling microclusters following TCR stimulation.

PubMed

Abraham, Libin; Bankhead, Peter; Pan, Xiaoyu; Engel, Ulrike; Fackler, Oliver T

2012-08-15

Signal initiation by engagement of the TCR triggers actin rearrangements, receptor clustering, and dynamic organization of signaling complexes to elicit and sustain downstream signaling. Nef, a pathogenicity factor of HIV, disrupts early TCR signaling in target T cells. To define the mechanism underlying this Nef-mediated signal disruption, we employed quantitative single-cell microscopy following surface-mediated TCR stimulation that allows for dynamic visualization of distinct signaling complexes as microclusters (MCs). Despite marked inhibition of actin remodeling and cell spreading, the induction of MCs containing TCR-CD3 or ZAP70 was not affected significantly by Nef. However, Nef potently inhibited the subsequent formation of MCs positive for the signaling adaptor Src homology-2 domain-containing leukocyte protein of 76 kDa (SLP-76) to reduce MC density in Nef-expressing and HIV-1-infected T cells. Further analyses suggested that Nef prevents formation of SLP-76 MCs at the level of the upstream adaptor protein, linker of activated T cells (LAT), that couples ZAP70 to SLP-76. Nef did not disrupt pre-existing MCs positive for LAT. However, the presence of the viral protein prevented de novo recruitment of active LAT into MCs due to retargeting of LAT to an intracellular compartment. These modulations in MC formation and composition depended on Nef's ability to simultaneously disrupt both actin remodeling and subcellular localization of TCR-proximal machinery. Nef thus employs a dual mechanism to disturb early TCR signaling by limiting the communication between LAT and SLP-76 and preventing the dynamic formation of SLP-76-signaling MCs.

Structure of a bacterial RNA polymerase holoenzyme open promoter complex

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bae, Brian; Feklistov, Andrey; Lass-Napiorkowska, Agnieszka

2015-09-08

Initiation of transcription is a primary means for controlling gene expression. In bacteria, the RNA polymerase (RNAP) holoenzyme binds and unwinds promoter DNA, forming the transcription bubble of the open promoter complex (RPo). We have determined crystal structures, refined to 4.14 Å-resolution, of RPo containing Thermus aquaticus RNAP holoenzyme and promoter DNA that includes the full transcription bubble. The structures, combined with biochemical analyses, reveal key features supporting the formation and maintenance of the double-strand/single-strand DNA junction at the upstream edge of the -10 element where bubble formation initiates. The results also reveal RNAP interactions with duplex DNA just upstreammore » of the -10 element and potential protein/DNA interactions that direct the DNA template strand into the RNAP active site. Addition of an RNA primer to yield a 4 base-pair post-translocated RNA:DNA hybrid mimics an initially transcribing complex at the point where steric clash initiates abortive initiation and σA dissociation.« less

Structure of a bacterial RNA polymerase holoenzyme open promoter complex

DOE PAGES

Bae, Brian; Feklistov, Andrey; Lass-Napiorkowska, Agnieszka; ...

2015-09-08

Initiation of transcription is a primary means for controlling gene expression. In bacteria, the RNA polymerase (RNAP) holoenzyme binds and unwinds promoter DNA, forming the transcription bubble of the open promoter complex (RPo). We have determined crystal structures, refined to 4.14 Å-resolution, of RPo containing Thermus aquaticus RNAP holoenzyme and promoter DNA that includes the full transcription bubble. The structures, combined with biochemical analyses, reveal key features supporting the formation and maintenance of the double-strand/single-strand DNA junction at the upstream edge of the -10 element where bubble formation initiates. The results also reveal RNAP interactions with duplex DNA just upstreammore » of the -10 element and potential protein/DNA interactions that direct the DNA template strand into the RNAP active site. Additionally a RNA primer to yield a 4 base-pair post-translocated RNA:DNA hybrid mimics an initially transcribing complex at the point where steric clash initiates abortive initiation and σ A dissociation.« less

A non-canonical mechanism for Crm1-export cargo complex assembly

PubMed Central

Fischer, Ute; Schäuble, Nico; Schütz, Sabina; Altvater, Martin; Chang, Yiming; Boulos Faza, Marius; Panse, Vikram Govind

2015-01-01

The transport receptor Crm1 mediates the export of diverse cargos containing leucine-rich nuclear export signals (NESs) through complex formation with RanGTP. To ensure efficient cargo release in the cytoplasm, NESs have evolved to display low affinity for Crm1. However, mechanisms that overcome low affinity to assemble Crm1-export complexes in the nucleus remain poorly understood. In this study, we reveal a new type of RanGTP-binding protein, Slx9, which facilitates Crm1 recruitment to the 40S pre-ribosome-associated NES-containing adaptor Rio2. In vitro, Slx9 binds Rio2 and RanGTP, forming a complex. This complex directly loads Crm1, unveiling a non-canonical stepwise mechanism to assemble a Crm1-export complex. A mutation in Slx9 that impairs Crm1-export complex assembly inhibits 40S pre-ribosome export. Thus, Slx9 functions as a scaffold to optimally present RanGTP and the NES to Crm1, therefore, triggering 40S pre-ribosome export. This mechanism could represent one solution to the paradox of weak binding events underlying rapid Crm1-mediated export. DOI: http://dx.doi.org/10.7554/eLife.05745.001 PMID:25895666

Anaerobic digestion and co-digestion of slaughterhouse waste (SHW): influence of heat and pressure pre-treatment in biogas yield.

PubMed

Cuetos, M J; Gómez, X; Otero, M; Morán, A

2010-10-01

Mesophilic anaerobic digestion (34+/-1 degrees C) of pre-treated (for 20 min at 133 degrees C, >3 bar) slaughterhouse waste and its co-digestion with the organic fraction of municipal solid waste (OFMSW) have been assessed. Semi-continuously-fed digesters worked with a hydraulic retention time (HRT) of 36 d and organic loading rates (OLR) of 1.2 and 2.6 kg VS(feed)/m(3)d for digestion and co-digestion, respectively, with a previous acclimatization period in all cases. It was not possible to carry out an efficient treatment of hygienized waste, even less so when OFMSW was added as co-substrate. These digesters presented volatile fatty acids (VFA), long chain fatty acids (LCFA) and fats accumulation, leading to instability and inhibition of the degradation process. The aim of applying a heat and pressure pre-treatment to promote splitting of complex lipids and nitrogen-rich waste into simpler and more biodegradable constituents and to enhance biogas production was not successful. These results indicate that the temperature and the high pressure of the pre-treatment applied favoured the formation of compounds that are refractory to anaerobic digestion. The pre-treated slaughterhouse wastes and the final products of these systems were analyzed by FTIR and TGA. These tools verified the existence of complex nitrogen-containing polymers in the final effluents, confirming the formation of refractory compounds during pre-treatment. (c) 2010 Elsevier Ltd. All rights reserved.

Morphometric analysis of astrocytes in brainstem respiratory regions.

PubMed

Sheikhbahaei, Shahriar; Morris, Brian; Collina, Jared; Anjum, Sommer; Znati, Sami; Gamarra, Julio; Zhang, Ruli; Gourine, Alexander V; Smith, Jeffrey C

2018-06-11

Astrocytes, the most abundant and structurally complex glial cells of the central nervous system, are proposed to play an important role in modulating the activities of neuronal networks, including respiratory rhythm-generating circuits of the preBötzinger complex (preBötC) located in the ventrolateral medulla of the brainstem. However, structural properties of astrocytes residing within different brainstem regions are unknown. In this study astrocytes in the preBötC, an intermediate reticular formation (IRF) region with respiratory-related function, and a region of the nucleus tractus solitarius (NTS) in adult rats were reconstructed and their morphological features were compared. Detailed morphological analysis revealed that preBötC astrocytes are structurally more complex than those residing within the functionally distinct neighboring IRF region, or the NTS, located at the dorsal aspect of the medulla oblongata. Structural analyses of the brainstem microvasculature indicated no significant regional differences in vascular properties. We hypothesize that high morphological complexity of preBötC astrocytes reflects their functional role in providing structural/metabolic support and modulation of the key neuronal circuits essential for breathing, as well as constraints imposed by arrangements of associated neurons and/or other local structural features of the brainstem parenchyma. This article is protected by copyright. All rights reserved. © 2018 Wiley Periodicals, Inc.

The path from nucleolar 90S to cytoplasmic 40S pre-ribosomes.

PubMed

Schäfer, Thorsten; Strauss, Daniela; Petfalski, Elisabeth; Tollervey, David; Hurt, Ed

2003-03-17

Recent reports have increased our knowledge of the consecutive steps during 60S ribosome biogenesis substantially, but 40S subunit formation is less well understood. Here, we investigate the maturation of nucleolar 90S pre-ribosomes into cytoplasmic 40S pre-ribosomes. During the transition from 90S to 40S particles, the majority of non-ribosomal proteins (approximately 30 species) dissociate, and significantly fewer factors associate with 40S pre-ribosomes. Notably, some of these components are part of both early 90S and intermediate 40S pre-particles in the nucleolus (e.g. Enp1p, Dim1p and Rrp12p), whereas others (e.g. Rio2p and Nob1p) are found mainly on late cytoplasmic pre-40S subunits. Finally, temperature-sensitive mutants mapping either in earlier (enp1-1) or later (rio2-1) components exhibit defects in the formation and nuclear export of pre-40S subunits. Our data provide an initial biochemical map of the pre-40S ribosomal subunit on its path from the nucleolus to the cytoplasm. This pathway involves fewer changes in composition than seen during 60S biogenesis.

STATIC AND KINETIC SITE-SPECIFIC PROTEIN-DNA PHOTOCROSSLINKING: ANALYSIS OF BACTERIAL TRANSCRIPTION INITIATION COMPLEXES

PubMed Central

Naryshkin, Nikolai; Druzhinin, Sergei; Revyakin, Andrei; Kim, Younggyu; Mekler, Vladimir; Ebright, Richard H.

2009-01-01

Static site-specific protein-DNA photocrosslinking permits identification of protein-DNA interactions within multiprotein-DNA complexes. Kinetic site-specific protein-DNA photocrosslinking--involving rapid-quench-flow mixing and pulsed-laser irradiation--permits elucidation of pathways and kinetics of formation of protein-DNA interactions within multiprotein-DNA complexes. We present detailed protocols for application of static and kinetic site-specific protein-DNA photocrosslinking to bacterial transcription initiation complexes. PMID:19378179

Origination of asexual plantlets in three species of Crassulaceae.

PubMed

Guo, Jiansheng; Liu, Hailiang; He, Yangyang; Cui, Xianghuan; Du, Xiling; Zhu, Jian

2015-03-01

During asexual plant reproduction, cells from different organs can be reprogrammed to produce new individuals, a process that requires the coordination of cell cycle reactivation with the acquisition of other cellular morphological characteristics. However, the factors that influence the variety of asexual reproduction have not yet been determined. Here, we report on plantlet formation in Kalanchoe daigremontiana, Graptopetalum paraguayense, and Crassula portulacea (Crassulaceae) and analyse the effect of initiating cells on asexual reproduction in these three species. Additionally, the roles of WUSCHEL (WUS) and CUP-SHAPED COTYLEDON 1 (CUC1) in the asexual reproduction of these species were analysed through qRT-PCR. Our results indicated that pre-existing stem cell-like cells at the sites of asexual reproduction were responsible for the formation of plantlets. These cells were arrested in different phases of the cell cycle and showed different cell morphological characteristics and cell counts. The accumulation of auxin and cytokinin at the sites of asexual plantlet formation indicated their important functions, particularly for cell cycle reactivation. These differences may influence the pattern and complexity of asexual reproduction in these Crassulaceae species. Additionally, the dynamic expression levels of CUC1 and WUS may indicate that CUC1 functions in the formation of callus and shoot meristems; whereas, WUS was only associated with shoot induction.

Intrinsic membrane properties of pre-oromotor neurons in the intermediate zone of the medullary reticular formation.

PubMed

Venugopal, S; Boulant, J A; Chen, Z; Travers, J B

2010-06-16

Neurons in the lower brainstem that control consummatory behavior are widely distributed in the reticular formation (RF) of the pons and medulla. The intrinsic membrane properties of neurons within this distributed system shape complex excitatory and inhibitory inputs from both orosensory and central structures implicated in homeostatic control to produce coordinated oromotor patterns. The current study explored the intrinsic membrane properties of neurons in the intermediate subdivision of the medullary reticular formation (IRt). Neurons in the IRt receive input from the overlying (gustatory) nucleus of the solitary tract and project to the oromotor nuclei. Recent behavioral pharmacology studies as well as computational modeling suggest that inhibition in the IRt plays an important role in the transition from a taste-initiated oromotor pattern of ingestion to one of rejection. The present study explored the impact of hyperpolarization on membrane properties. In response to depolarization, neurons responded with either a tonic discharge, an irregular/burst pattern or were spike-adaptive. A hyperpolarizing pre-pulse modulated the excitability of most (82%) IRt neurons to subsequent depolarization. Instances of both increased (30%) and decreased (52%) excitability were observed. Currents induced by the hyperpolarization included an outward 4-aminopyridine (4-AP) sensitive K+ current that suppressed excitability and an inward cation current that increased excitability. These currents are also present in other subpopulations of RF neurons that influence the oromotor nuclei and we discuss how these currents could alter firing characteristics to impact pattern generation. 2010 IBRO. Published by Elsevier Ltd. All rights reserved.

Dynamic interaction of Y RNAs with chromatin and initiation proteins during human DNA replication

PubMed Central

Zhang, Alice Tianbu; Langley, Alexander R.; Christov, Christo P.; Kheir, Eyemen; Shafee, Thomas; Gardiner, Timothy J.; Krude, Torsten

2011-01-01

Non-coding Y RNAs are required for the initiation of chromosomal DNA replication in mammalian cells. It is unknown how they perform this function or if they associate with a nuclear structure during DNA replication. Here, we investigate the association of Y RNAs with chromatin and their interaction with replication proteins during DNA replication in a human cell-free system. Our results show that fluorescently labelled Y RNAs associate with unreplicated euchromatin in late G1 phase cell nuclei before the initiation of DNA replication. Following initiation, Y RNAs are displaced locally from nascent and replicated DNA present in replication foci. In intact human cells, a substantial fraction of endogenous Y RNAs are associated with G1 phase nuclei, but not with G2 phase nuclei. Y RNAs interact and colocalise with the origin recognition complex (ORC), the pre-replication complex (pre-RC) protein Cdt1, and other proteins implicated in the initiation of DNA replication. These data support a molecular ‘catch and release’ mechanism for Y RNA function during the initiation of chromosomal DNA replication, which is consistent with Y RNAs acting as replication licensing factors. PMID:21610089

The RNA-induced transcriptional silencing complex targets chromatin exclusively via interacting with nascent transcripts.

PubMed

Shimada, Yukiko; Mohn, Fabio; Bühler, Marc

2016-12-01

Small RNAs regulate chromatin modification and transcriptional gene silencing across the eukaryotic kingdom. Although these processes have been well studied, fundamental mechanistic aspects remain obscure. Specifically, it is unclear exactly how small RNA-loaded Argonaute protein complexes target chromatin to mediate silencing. Here, using fission yeast, we demonstrate that transcription of the target locus is essential for RNA-directed formation of heterochromatin. However, high transcriptional activity is inhibitory; thus, a transcriptional window exists that is optimal for silencing. We further found that pre-mRNA splicing is compatible with RNA-directed heterochromatin formation. However, the kinetics of pre-mRNA processing is critical. Introns close to the 5' end of a transcript that are rapidly spliced result in a bistable response whereby the target either remains euchromatic or becomes fully silenced. Together, our results discount siRNA-DNA base pairing in RNA-mediated heterochromatin formation, and the mechanistic insights further reveal guiding paradigms for the design of small RNA-directed chromatin silencing studies in multicellular organisms. © 2016 Shimada et al.; Published by Cold Spring Harbor Laboratory Press.

A depth versus diameter scaling relationship for the best-preserved melt-bearing complex craters on Mars

NASA Astrophysics Data System (ADS)

Tornabene, Livio L.; Watters, Wesley A.; Osinski, Gordon R.; Boyce, Joseph M.; Harrison, Tanya N.; Ling, Victor; McEwen, Alfred S.

2018-01-01

We use topographic data to show that impact craters with pitted floor deposits are among the deepest on Mars. This is consistent with the interpretation of pitted materials as primary crater-fill impactite deposits emplaced during crater formation. Our database consists of 224 pitted material craters ranging in size from ∼1 to 150 km in diameter. Our measurements are based on topographic data from the Mars Orbiter Laser Altimeter (MOLA) and the High-Resolution Stereo Camera (HRSC). We have used these craters to measure the relationship between crater diameter and the initial post-formation depth. Depth was measured as maximum rim-to-floor depth, (dr), but we also report the depth measured using other definitions. The database was down-selected by refining or removing elevation measurements from ;problematic; craters affected by processes and conditions that influenced their dr/D, such as pre-impact slopes/topography and later overprinting craters. We report a maximum (deepest) and mean scaling relationship of dr = (0.347 ± 0.021)D0.537 ± 0.017 and dr = (0.323 ± 0.017)D0.538 ± 0.016, respectively. Our results suggest that significant variations between previously-reported MOLA-based dr vs. D relationships may result from the inclusion of craters that: 1) are influenced by atypical processes (e.g., highly oblique impact), 2) are significantly degraded, 3) reside within high-strength regions, and 4) are transitional (partially collapsed). By taking such issues into consideration and only measuring craters with primary floor materials, we present the best estimate to date of a MOLA-based relationship of dr vs. D for the least-degraded complex craters on Mars. This can be applied to crater degradation studies and provides a useful constraint for models of complex crater formation.

Infrared spectroscopy and density functional calculations on titanium-dinitrogen complexes

NASA Astrophysics Data System (ADS)

Yoo, Hae-Wook; Choi, Changhyeok; Cho, Soo Gyeong; Jung, Yousung; Choi, Myong Yong

2018-04-01

Titanium-nitrogen complexes were generated by laser ablated titanium (Ti) atoms and N2 gas molecules in this study. These complexes were isolated on the pre-deposited solid Ar matrix on the pre-cooled KBr window (T ∼ 5.4 K), allowing infrared spectra to be measured. Laser ablation experiments with 15N2 isotope provided distinct isotopic shifts in the infrared spectra that strongly implicated the formation of titanium-nitrogen complexes, Ti(NN)x. Density functional theory (DFT) calculations were employed to investigate the molecular structures, electronic ground state, relative energies, and IR frequencies of the anticipated Ti(NN)x complexes. Based on laser ablation experiments and DFT calculations, we were able to assign multiple Ti(NN)x (x = 1-6) species. Particularly, Ti(NN)5 and Ti(NN)6, which have high nitrogen content, may serve as good precursors in preparing polynitrogens.

Fully Coupled 3D Finite Element Model of Hydraulic Fracturing in a Permeable Rock Formation

NASA Astrophysics Data System (ADS)

Salimzadeh, S.; Paluszny, A.; Zimmerman, R. W.

2015-12-01

Hydraulic fracturing in permeable rock formations is a complex three-dimensional multi-physics phenomenon. Numerous analytical models of hydraulic fracturing processes have been proposed that typically simplify the physical processes, or somehow reduce the problem from three dimensions to two dimensions. Moreover, although such simplified models are able to model the growth of a single hydraulic fracture into an initially intact, homogeneous rock mass, they are generally not able to model fracturing of heterogeneous rock formations, or to account for interactions between multiple induced fractures, or between an induced fracture and pre-existing natural fractures. We have developed a numerical finite-element model for hydraulic fracturing that does not suffer from any of the limitations mentioned above. The model accounts for fluid flow within a fracture, the propagation of the fracture, and the leak-off of fluid from the fracture into the host rock. Fluid flow through the permeable rock matrix is modelled using Darcy's law, and is coupled with the laminar flow within the fracture. Fractures are discretely modelled in the three-dimensional mesh. Growth of a fracture is modelled using the concepts of linear elastic fracture mechanics (LEFM), with the onset and direction of growth based on stress intensity factors that are computed for arbitrary tetrahedral meshes. The model has been verified against several analytical solutions available in the literature for plane-strain (2D) and penny-shaped (3D) fractures, for various regimes of domination: viscosity, toughness, storage and leak-off. The interaction of the hydraulically driven fracture with pre-existing fractures and other fluid-driven fractures in terms of fluid leak-off, stress interaction and fracture arrest is investigated and the results are presented. Finally, some preliminary results are presented regarding the interaction of a hydraulically-induced fracture with a set of pre-existing natural fractures.

The Mediator complex: a central integrator of transcription

PubMed Central

Allen, Benjamin L.; Taatjes, Dylan J.

2016-01-01

The RNA polymerase II (pol II) enzyme transcribes all protein-coding and most non-coding RNA genes and is globally regulated by Mediator, a large, conformationally flexible protein complex with variable subunit composition (for example, a four-subunit CDK8 module can reversibly associate). These biochemical characteristics are fundamentally important for Mediator's ability to control various processes important for transcription, including organization of chromatin architecture and regulation of pol II pre-initiation, initiation, re-initiation, pausing, and elongation. Although Mediator exists in all eukaryotes, a variety of Mediator functions appear to be specific to metazoans, indicative of more diverse regulatory requirements. PMID:25693131

Hydride-Meisenheimer Complex Formation and Protonation as Key Reactions of 2,4,6-Trinitrophenol Biodegradation by Rhodococcus erythropolis

PubMed Central

Rieger, Paul-Gerhard; Sinnwell, Volker; Preuß, Andrea; Francke, Wittko; Knackmuss, Hans-Joachim

1999-01-01

Biodegradation of 2,4,6-trinitrophenol (picric acid) by Rhodococcus erythropolis HLPM-1 proceeds via initial hydrogenation of the aromatic ring system. Here we present evidence for the formation of a hydride-Meisenheimer complex (anionic ς-complex) of picric acid and its protonated form under physiological conditions. These complexes are key intermediates of denitration and productive microbial degradation of picric acid. For comparative spectroscopic identification of the hydride complex, it was necessary to synthesize this complex for the first time. Spectroscopic data revealed the initial addition of a hydride ion at position 3 of picric acid. This hydride complex readily picks up a proton at position 2, thus forming a reactive species for the elimination of nitrite. Cell extracts of R. erythropolis HLPM-1 transform the chemically synthesized hydride complex into 2,4-dinitrophenol. Picric acid is used as the sole carbon, nitrogen, and energy source by R. erythropolis HLPM-1. PMID:9973345

DNA Polymerase α Subunit Residues and Interactions Required for Efficient Initiation Complex Formation Identified by a Genetic Selection.

PubMed

Lindow, Janet C; Dohrmann, Paul R; McHenry, Charles S

2015-07-03

Biophysical and structural studies have defined many of the interactions that occur between individual components or subassemblies of the bacterial replicase, DNA polymerase III holoenzyme (Pol III HE). Here, we extended our knowledge of residues and interactions that are important for the first step of the replicase reaction: the ATP-dependent formation of an initiation complex between the Pol III HE and primed DNA. We exploited a genetic selection using a dominant negative variant of the polymerase catalytic subunit that can effectively compete with wild-type Pol III α and form initiation complexes, but cannot elongate. Suppression of the dominant negative phenotype was achieved by secondary mutations that were ineffective in initiation complex formation. The corresponding proteins were purified and characterized. One class of mutant mapped to the PHP domain of Pol III α, ablating interaction with the ϵ proofreading subunit and distorting the polymerase active site in the adjacent polymerase domain. Another class of mutation, found near the C terminus, interfered with τ binding. A third class mapped within the known β-binding domain, decreasing interaction with the β2 processivity factor. Surprisingly, mutations within the β binding domain also ablated interaction with τ, suggesting a larger τ binding site than previously recognized. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

The interaction of DiaA and DnaA regulates the replication cycle in E. coli by directly promoting ATP–DnaA-specific initiation complexes

PubMed Central

Keyamura, Kenji; Fujikawa, Norie; Ishida, Takuma; Ozaki, Shogo; Su’etsugu, Masayuki; Fujimitsu, Kazuyuki; Kagawa, Wataru; Yokoyama, Shigeyuki; Kurumizaka, Hitoshi; Katayama, Tsutomu

2007-01-01

Escherichia coli DiaA is a DnaA-binding protein that is required for the timely initiation of chromosomal replication during the cell cycle. In this study, we determined the crystal structure of DiaA at 1.8 Å resolution. DiaA forms a homotetramer consisting of a symmetrical pair of homodimers. Mutational analysis revealed that the DnaA-binding activity and formation of homotetramers are required for the stimulation of initiation by DiaA. DiaA tetramers can bind multiple DnaA molecules simultaneously. DiaA stimulated the assembly of multiple DnaA molecules on oriC, conformational changes in ATP–DnaA-specific initiation complexes, and unwinding of oriC duplex DNA. The mutant DiaA proteins are defective in these stimulations. DiaA associated also with ADP–DnaA, and stimulated the assembly of inactive ADP–DnaA–oriC complexes. Specific residues in the putative phosphosugar-binding motif of DiaA were required for the stimulation of initiation and formation of ATP–DnaA-specific–oriC complexes. Our data indicate that DiaA regulates initiation by a novel mechanism, in which DiaA tetramers most likely bind to multiple DnaA molecules and stimulate the assembly of specific ATP–DnaA–oriC complexes. These results suggest an essential role for DiaA in the promotion of replication initiation in a cell cycle coordinated manner. PMID:17699754

Star formation in a hierarchical model for Cloud Complexes

NASA Astrophysics Data System (ADS)

Sanchez, N.; Parravano, A.

The effects of the external and initial conditions on the star formation processes in Molecular Cloud Complexes are examined in the context of a schematic model. The model considers a hierarchical system with five predefined phases: warm gas, neutral gas, low density molecular gas, high density molecular gas and protostars. The model follows the mass evolution of each substructure by computing its mass exchange with their parent and children. The parent-child mass exchange depends on the radiation density at the interphase, which is produced by the radiation coming from the stars that form at the end of the hierarchical structure, and by the external radiation field. The system is chaotic in the sense that its temporal evolution is very sensitive to small changes in the initial or external conditions. However, global features such as the star formation efficience and the Initial Mass Function are less affected by those variations.

RecQL4 is required for the association of Mcm10 and Ctf4 with replication origins in human cells

PubMed Central

Im, Jun-Sub; Park, Soon-Young; Cho, Won-Ho; Bae, Sung-Ho; Hurwitz, Jerard; Lee, Joon-Kyu

2015-01-01

Though RecQL4 was shown to be essential for the initiation of DNA replication in mammalian cells, its role in initiation is poorly understood. Here, we show that RecQL4 is required for the origin binding of Mcm10 and Ctf4, and their physical interactions and association with replication origins are controlled by the concerted action of both CDK and DDK activities. Although RecQL4-dependent binding of Mcm10 and Ctf4 to chromatin can occur in the absence of pre-replicative complex, their association with replication origins requires the presence of the pre-replicative complex and CDK and DDK activities. Their association with replication origins and physical interactions are also targets of the DNA damage checkpoint pathways which prevent initiation of DNA replication at replication origins. Taken together, the RecQL4-dependent association of Mcm10 and Ctf4 with replication origins appears to be the first important step controlled by S phase promoting kinases and checkpoint pathways for the initiation of DNA replication in human cells. PMID:25602958

The roles of SSU processome components and surveillance factors in the initial processing of human ribosomal RNA

PubMed Central

Sloan, Katherine E.; Bohnsack, Markus T.; Schneider, Claudia; Watkins, Nicholas J.

2014-01-01

During eukaryotic ribosome biogenesis, three of the mature ribosomal (r)RNAs are released from a single precursor transcript (pre-rRNA) by an ordered series of endonucleolytic cleavages and exonucleolytic processing steps. Production of the 18S rRNA requires the removal of the 5′ external transcribed spacer (5′ETS) by endonucleolytic cleavages at sites A0 and A1/site 1. In metazoans, an additional cleavage in the 5′ETS, at site A′, upstream of A0, has also been reported. Here, we have investigated how A′ processing is coordinated with assembly of the early preribosomal complex. We find that only the tUTP (UTP-A) complex is critical for A′ cleavage, while components of the bUTP (UTP-B) and U3 snoRNP are important, but not essential, for efficient processing at this site. All other factors involved in the early stages of 18S rRNA processing that were tested here function downstream from this processing step. Interestingly, we show that the RNA surveillance factors XRN2 and MTR4 are also involved in A′ cleavage in humans. A′ cleavage is largely bypassed when XRN2 is depleted, and we also discover that A′ cleavage is not always the initial processing event in all cell types. Together, our data suggest that A′ cleavage is not a prerequisite for downstream pre-rRNA processing steps and may, in fact, represent a quality control step for initial pre-rRNA transcripts. Furthermore, we show that components of the RNA surveillance machinery, including the exosome and TRAMP complexes, also play key roles in the recycling of excised spacer fragments and degradation of aberrant pre-rRNAs in human cells. PMID:24550520

The Aegean/Cycladic and the Basin and Range Extensional Provinces - A Tectonic and Geochronologic Perspective

NASA Astrophysics Data System (ADS)

Stockli, D. F.

2017-12-01

The Aegean/Cycladic region (AC) and the Basin and Range Province (B&R) are two of the most famous Cenozoic extensional provinces and have greatly influenced our thinking about syn-convergent back-arc extension, core complex formation, syn-extensional magmatism, and kinematic transitions. They share numerous tectonic and structural similarities, such as a syn-convergent setting, previous contractional deformation, and core complex formation, but fundamental geological ambiguities remain, mainly centering around timing. The B&R affected a previously contractional belt (Sevier) and voluminous continental magmatic arc that created a pre-extensional orogenic highland. Extension was long-lived and complex, driven by both gravitational collapse and temporally distinct kinematic boundary condition changes. The B&R was also affected by massive, largely pre-extensional regional magmatic flare-ups that modified both the thermal and crustal composition. As the B&R occupies an elevated interior plateau, syn-extensional basin deposits are exclusively continental in character. In contrast, the AC is a classic marine back-arc extensional province that affected an active subduction margin with numerous accreted oceanic and continental ribbons, exhuming an early Cenozoic HP-LT subduction complex. Exhumation of the HP-LT complex, however, was accommodated both by vertical extrusion and crustal extension. Late Cenozoic extensional faulting was contemporaneous with S-ward sweeping arc magmatism and affected by little to no kinematic changes. As both the AC and B&R experienced contractional deformation during K-Cz subduction and J-K shortening, respectively, it is critical to differentiate between contractional and extensional structures and fabrics. The lack of temporal constraints hampers the reconstructions of pre-extensional structural anatomies and extensional strain magnitudes or even the attribution of structures to specific geodynamic settings. Novel methodologies in petrochronology, detrital geochronology, and high- and low-T thermochronometry allow us to elucidate pre-extensional crustal geometries, differentiate contractional from extensional fabrics, and understand the thermal and rheological evolution of these extensional provinces in a more holistic fashion.

Zinc oxide nanoflowers make new blood vessels

NASA Astrophysics Data System (ADS)

Barui, Ayan Kumar; Veeriah, Vimal; Mukherjee, Sudip; Manna, Joydeb; Patel, Ajay Kumar; Patra, Sujata; Pal, Krishnendu; Murali, Shruthi; Rana, Rohit K.; Chatterjee, Suvro; Patra, Chitta Ranjan

2012-11-01

It is well established that angiogenesis is the process of formation of new capillaries from pre-existing blood vessels. It is a complex process, involving both pro- and anti-angiogenic factors, and plays a significant role in physiological and pathophysiological processes such as embryonic development, atherosclerosis, post-ischemic vascularization of the myocardium, tumor growth and metastasis, rheumatoid arthritis etc. This is the first report of zinc oxide (ZnO) nanoflowers that show significant pro-angiogenic properties (formation of new capillaries from pre-existing blood vessels), observed by in vitro and in vivo angiogenesis assays. The egg yolk angiogenesis assay using ZnO nanoflowers indicates the presence of matured blood vessels formation. Additionally, it helps to promote endothelial cell (EA.hy926 cells) migration in wound healing assays. Formation of reactive oxygen species (ROS), especially hydrogen peroxide (H2O2)--a redox signaling molecule, might be the plausible mechanism for nanoflower-based angiogenesis. Angiogenesis by nanoflowers may provide the basis for the future development of new alternative therapeutic treatment strategies for cardiovascular and ischemic diseases, where angiogenesis plays a significant role.It is well established that angiogenesis is the process of formation of new capillaries from pre-existing blood vessels. It is a complex process, involving both pro- and anti-angiogenic factors, and plays a significant role in physiological and pathophysiological processes such as embryonic development, atherosclerosis, post-ischemic vascularization of the myocardium, tumor growth and metastasis, rheumatoid arthritis etc. This is the first report of zinc oxide (ZnO) nanoflowers that show significant pro-angiogenic properties (formation of new capillaries from pre-existing blood vessels), observed by in vitro and in vivo angiogenesis assays. The egg yolk angiogenesis assay using ZnO nanoflowers indicates the presence of matured blood vessels formation. Additionally, it helps to promote endothelial cell (EA.hy926 cells) migration in wound healing assays. Formation of reactive oxygen species (ROS), especially hydrogen peroxide (H2O2)--a redox signaling molecule, might be the plausible mechanism for nanoflower-based angiogenesis. Angiogenesis by nanoflowers may provide the basis for the future development of new alternative therapeutic treatment strategies for cardiovascular and ischemic diseases, where angiogenesis plays a significant role. Electronic supplementary information (ESI) available: See DOI: 10.1039/c2nr32369a

A complete backbone spectral assignment of human apolipoprotein AI on a 38 kDa preβHDL (Lp1-AI) particle

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ren, Xuefeng; Yang, Yunhuang; Neville, T.

2007-06-12

Apolipoprotein A-I (apoAI, 243-residues) is the major protein component of the high-density lipoprotein (HDL) that has been a hot subject of interests because of its anti-atherogenic properties. This important property of apoAI is related to its roles in reverse cholesterol transport pathway. Upon lipid-binding, apoAI undergoes conformational changes from lipid-free to several different HDL-associated states (1). These different conformational states regulate HDL formation, maturation and transportation. Two initial conformational states of apoAI are lipid-free apoAI and apoAI/preβHDL that recruit phospholipids and cholesterol to form HDL particles. In particular, lipid-free apoAI specifically binds to phospholipids to form lipid-poor apoAI, including apoAI/preβ-HDLmore » (~37 kDa). As a unique class of lipid poor HDL, both in vitro and in vivo evidence demonstrates that apoAI/preβ-HDLs are the most effective acceptors specifically for free cholesterol in human plasma and serves as the precursor of HDL particles (2). Here we report a complete backbone spectral assignment of human apoAI/preβHDL. Secondary structure prediction using backbone NMR parameters indicates that apoAI/preβHDL displays a two-domain structure: the N-terminal four helix-bundle domain (residues 1-186) and the C-terminal flexible domain (residues 187-243). A structure of apoAI/preβ-HDL is the first lipid-associated structure of apoAI and is critical for us to understand how apoAI recruits cholesterol to initialize HDL formation. BMRB deposit with accession number: 15093.« less

In vivo characterization of the Drosophila mRNA 3′ end processing core cleavage complex

PubMed Central

Michalski, Daniel; Steiniger, Mindy

2015-01-01

A core cleavage complex (CCC) consisting of CPSF73, CPSF100, and Symplekin is required for cotranscriptional 3′ end processing of all metazoan pre-mRNAs, yet little is known about the in vivo molecular interactions within this complex. The CCC is a component of two distinct complexes, the cleavage/polyadenylation complex and the complex that processes nonpolyadenylated histone pre-mRNAs. RNAi-depletion of CCC factors in Drosophila culture cells causes reduction of CCC processing activity on histone mRNAs, resulting in read through transcription. In contrast, RNAi-depletion of factors only required for histone mRNA processing allows use of downstream cryptic polyadenylation signals to produce polyadenylated histone mRNAs. We used Dmel-2 tissue culture cells stably expressing tagged CCC components to determine that amino acids 272–1080 of Symplekin and the C-terminal approximately 200 amino acids of both CPSF73 and CPSF100 are required for efficient CCC formation in vivo. Additional experiments reveal that the C-terminal 241 amino acids of CPSF100 are sufficient for histone mRNA processing indicating that the first 524 amino acids of CPSF100 are dispensable for both CCC formation and histone mRNA 3′ end processing. CCCs containing deletions of Symplekin lacking the first 271 amino acids resulted in dramatic increased use of downstream polyadenylation sites for histone mRNA 3′ end processing similar to RNAi-depletion of histone-specific 3′ end processing factors FLASH, SLBP, and U7 snRNA. We propose a model in which CCC formation is mediated by CPSF73, CPSF100, and Symplekin C-termini, and the N-terminal region of Symplekin facilitates cotranscriptional 3′ end processing of histone mRNAs. PMID:26081560

Globular cluster formation with multiple stellar populations from hierarchical star cluster complexes

NASA Astrophysics Data System (ADS)

Bekki, Kenji

2017-05-01

Most old globular clusters (GCs) in the Galaxy are observed to have internal chemical abundance spreads in light elements. We discuss a new GC formation scenario based on hierarchical star formation within fractal molecular clouds. In the new scenario, a cluster of bound and unbound star clusters ('star cluster complex', SCC) that have a power-law cluster mass function with a slope (β) of 2 is first formed from a massive gas clump developed in a dwarf galaxy. Such cluster complexes and β = 2 are observed and expected from hierarchical star formation. The most massive star cluster ('main cluster'), which is the progenitor of a GC, can accrete gas ejected from asymptotic giant branch (AGB) stars initially in the cluster and other low-mass clusters before the clusters are tidally stripped or destroyed to become field stars in the dwarf. The SCC is initially embedded in a giant gas hole created by numerous supernovae of the SCC so that cold gas outside the hole can be accreted on to the main cluster later. New stars formed from the accreted gas have chemical abundances that are different from those of the original SCC. Using hydrodynamical simulations of GC formation based on this scenario, we show that the main cluster with the initial mass as large as [2-5] × 105 M⊙ can accrete more than 105 M⊙ gas from AGB stars of the SCC. We suggest that merging of hierarchical SSCs can play key roles in stellar halo formation around GCs and self-enrichment processes in the early phase of GC formation.

Pre-attentive processing of spectrally complex sounds with asynchronous onsets: an event-related potential study with human subjects.

PubMed

Tervaniemi, M; Schröger, E; Näätänen, R

1997-05-23

Neuronal mechanisms involved in the processing of complex sounds with asynchronous onsets were studied in reading subjects. The sound onset asynchrony (SOA) between the leading partial and the remaining complex tone was varied between 0 and 360 ms. Infrequently occurring deviant sounds (in which one out of 10 harmonics was different in pitch relative to the frequently occurring standard sound) elicited the mismatch negativity (MMN), a change-specific cortical event-related potential (ERP) component. This indicates that the pitch of standard stimuli had been pre-attentively coded by sensory-memory traces. Moreover, when the complex-tone onset fell within temporal integration window initiated by the leading-partial onset, the deviants elicited the N2b component. This indexes that involuntary attention switch towards the sound change occurred. In summary, the present results support the existence of pre-perceptual integration mechanism of 100-200 ms duration and emphasize its importance in switching attention towards the stimulus change.

Application of ion exchange resin in floating drug delivery system.

PubMed

Upadhye, Abhijeet A; Ambike, Anshuman A; Mahadik, Kakasaheb R; Paradkar, Anant

2008-10-01

The purpose of this study was to explore the application of low-density ion exchange resin (IER) Tulsion(R) 344, for floating drug delivery system (FDDS), and study the effect of its particle size on rate of complexation, water uptake, drug release, and in situ complex formation. Batch method was used for the preparation of complexes, which were characterized by physical methods. Tablet containing resin with high degree of crosslinking showed buoyancy lag time (BLT) of 5-8 min. Decreasing the particle size of resin showed decrease in water uptake and drug release, with no significant effect on the rate of complexation and in situ complex formation for both preformed complexes (PCs) and physical mixtures (PMs). Thus, low-density and high degree of crosslinking of resin and water uptake may be the governing factor for controlling the initial release of tablet containing PMs but not in situ complex formation. However, further sustained release may be due to in situ complex formation.

Evolution of Pre-Main Sequence Accretion Disks

NASA Technical Reports Server (NTRS)

Hartmann, Lee W.

2000-01-01

The aim of this project was to develop a comprehensive global picture of the physical conditions in, and evolutionary timescales of, pre-main sequence accretion disks. The results of this work will help constrain the initial conditions for planet formation. To this end we: (1) Developed detailed calculations of disk structure to study physical conditions and investigate the observational effects of grain growth in T Tauri disks; (2) Studied the dusty emission and accretion rates in older disk systems, with ages closer to the expected epoch of (giant) planet formation at 3-10 Myr, and (3) Began a project to develop much larger samples of 3-10 Myr-old stars to provide better empirical constraints on protoplanetary disk evolution.

Pre-Hawking radiation cannot prevent the formation of apparent horizon

NASA Astrophysics Data System (ADS)

Chen, Pisin; Unruh, William G.; Wu, Chih-Hung; Yeom, Dong-Han

2018-03-01

As an attempt to solve the black hole information loss paradox, recently there has been the suggestion that, due to semiclassical effects, a pre-Hawking radiation must exist during the gravitational collapse of matter, which in turn prevents the apparent horizon from forming. Assuming the pre-Hawking radiation does exist, here we argue the opposite. First we note that the stress energy tensor near the horizon for the pre-Hawking radiation is far too small to do anything to the motion of a collapsing shell. Thus the shell will always cross the apparent horizon within a finite proper time. Moreover, the amount of energy that can be radiated must be less than half of the total initial energy (if the particle starts at rest at infinity) before the shell becomes a null shell and cannot radiate any more without becoming tachyonic. We conclude that for any gravitational collapsing process within Einstein gravity and semiclassical quantum field theory, the formation of the apparent horizon is inevitable. Pre-Hawking radiation is therefore not a valid solution to the information paradox.

Pre-Hawking radiation cannot prevent the formation of apparent horizon

DOE PAGES

Chen, Pisin; Unruh, William G.; Wu, Chih-Hung; ...

2018-03-30

As an attempt to solve the black hole information loss paradox, recently there has been the suggestion that, due to semiclassical effects, a pre-Hawking radiation must exist during the gravitational collapse of matter, which in turn prevents the apparent horizon from forming. Assuming the pre-Hawking radiation does exist, here we argue the opposite. First we note that the stress energy tensor near the horizon for the pre-Hawking radiation is far too small to do anything to the motion of a collapsing shell. Thus the shell will always cross the apparent horizon within a finite proper time. Moreover, the amount ofmore » energy that can be radiated must be less than half of the total initial energy (if the particle starts at rest at infinity) before the shell becomes a null shell and cannot radiate any more without becoming tachyonic. Here, we conclude that for any gravitational collapsing process within Einstein gravity and semiclassical quantum field theory, the formation of the apparent horizon is inevitable. Pre-Hawking radiation is therefore not a valid solution to the information paradox.« less

Pre-Hawking radiation cannot prevent the formation of apparent horizon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Pisin; Unruh, William G.; Wu, Chih-Hung

As an attempt to solve the black hole information loss paradox, recently there has been the suggestion that, due to semiclassical effects, a pre-Hawking radiation must exist during the gravitational collapse of matter, which in turn prevents the apparent horizon from forming. Assuming the pre-Hawking radiation does exist, here we argue the opposite. First we note that the stress energy tensor near the horizon for the pre-Hawking radiation is far too small to do anything to the motion of a collapsing shell. Thus the shell will always cross the apparent horizon within a finite proper time. Moreover, the amount ofmore » energy that can be radiated must be less than half of the total initial energy (if the particle starts at rest at infinity) before the shell becomes a null shell and cannot radiate any more without becoming tachyonic. Here, we conclude that for any gravitational collapsing process within Einstein gravity and semiclassical quantum field theory, the formation of the apparent horizon is inevitable. Pre-Hawking radiation is therefore not a valid solution to the information paradox.« less

Mammalian poly(A)-binding protein is a eukaryotic translation initiation factor, which acts via multiple mechanisms.

PubMed

Kahvejian, Avak; Svitkin, Yuri V; Sukarieh, Rami; M'Boutchou, Marie-Noël; Sonenberg, Nahum

2005-01-01

Translation initiation is a multistep process involving several canonical translation factors, which assemble at the 5'-end of the mRNA to promote the recruitment of the ribosome. Although the 3' poly(A) tail of eukaryotic mRNAs and its major bound protein, the poly(A)-binding protein (PABP), have been studied extensively, their mechanism of action in translation is not well understood and is confounded by differences between in vivo and in vitro systems. Here, we provide direct evidence for the involvement of PABP in key steps of the translation initiation pathway. Using a new technique to deplete PABP from mammalian cell extracts, we show that extracts lacking PABP exhibit dramatically reduced rates of translation, reduced efficiency of 48S and 80S ribosome initiation complex formation, and impaired interaction of eIF4E with the mRNA cap structure. Supplementing PABP-depleted extracts with wild-type PABP completely rectified these deficiencies, whereas a mutant of PABP, M161A, which is incapable of interacting with eIF4G, failed to restore translation. In addition, a stronger inhibition (approximately twofold) of 80S as compared to 48S ribosome complex formation (approximately 65% vs. approximately 35%, respectively) by PABP depletion suggests that PABP plays a direct role in 60S subunit joining. PABP can thus be considered a canonical translation initiation factor, integral to initiation complex formation at the 5'-end of mRNA.

Mammalian poly(A)-binding protein is a eukaryotic translation initiation factor, which acts via multiple mechanisms

PubMed Central

Kahvejian, Avak; Svitkin, Yuri V.; Sukarieh, Rami; M'Boutchou, Marie-Noël; Sonenberg, Nahum

2005-01-01

Translation initiation is a multistep process involving several canonical translation factors, which assemble at the 5′-end of the mRNA to promote the recruitment of the ribosome. Although the 3′ poly(A) tail of eukaryotic mRNAs and its major bound protein, the poly(A)-binding protein (PABP), have been studied extensively, their mechanism of action in translation is not well understood and is confounded by differences between in vivo and in vitro systems. Here, we provide direct evidence for the involvement of PABP in key steps of the translation initiation pathway. Using a new technique to deplete PABP from mammalian cell extracts, we show that extracts lacking PABP exhibit dramatically reduced rates of translation, reduced efficiency of 48S and 80S ribosome initiation complex formation, and impaired interaction of eIF4E with the mRNA cap structure. Supplementing PABP-depleted extracts with wild-type PABP completely rectified these deficiencies, whereas a mutant of PABP, M161A, which is incapable of interacting with eIF4G, failed to restore translation. In addition, a stronger inhibition (approximately twofold) of 80S as compared to 48S ribosome complex formation (∼65% vs. ∼35%, respectively) by PABP depletion suggests that PABP plays a direct role in 60S subunit joining. PABP can thus be considered a canonical translation initiation factor, integral to initiation complex formation at the 5′-end of mRNA. PMID:15630022

Enhanced chlorine dioxide decay in the presence of metal oxides: relevance to drinking water distribution systems.

PubMed

Liu, Chao; von Gunten, Urs; Croué, Jean-Philippe

2013-08-06

Chlorine dioxide (ClO2) decay in the presence of typical metal oxides occurring in distribution systems was investigated. Metal oxides generally enhanced ClO2 decay in a second-order process via three pathways: (1) catalytic disproportionation with equimolar formation of chlorite and chlorate, (2) reaction to chlorite and oxygen, and (3) oxidation of a metal in a reduced form (e.g., cuprous oxide) to a higher oxidation state. Cupric oxide (CuO) and nickel oxide (NiO) showed significantly stronger abilities than goethite (α-FeOOH) to catalyze the ClO2 disproportionation (pathway 1), which predominated at higher initial ClO2 concentrations (56-81 μM). At lower initial ClO2 concentrations (13-31 μM), pathway 2 also contributed. The CuO-enhanced ClO2 decay is a base-assisted reaction with a third-order rate constant of 1.5 × 10(6) M(-2) s(-1) in the presence of 0.1 g L(-1) CuO at 21 ± 1 °C, which is 4-5 orders of magnitude higher than in the absence of CuO. The presence of natural organic matter (NOM) significantly enhanced the formation of chlorite and decreased the ClO2 disproportionation in the CuO-ClO2 system, probably because of a higher reactivity of CuO-activated ClO2 with NOM. Furthermore, a kinetic model was developed to simulate CuO-enhanced ClO2 decay at various pH values. Model simulations that agree well with the experimental data include a pre-equilibrium step with the rapid formation of a complex, namely, CuO-activated Cl2O4. The reaction of this complex with OH(-) is the rate-limiting and pH-dependent step for the overall reaction, producing chlorite and an intermediate that further forms chlorate and oxygen in parallel. These novel findings suggest that the possible ClO2 loss and the formation of chlorite/chlorate should be carefully considered in drinking water distribution systems containing copper pipes.

Elongation factor Ts directly facilitates the formation and disassembly of the Escherichia coli elongation factor Tu·GTP·aminoacyl-tRNA ternary complex.

PubMed

Burnett, Benjamin J; Altman, Roger B; Ferrao, Ryan; Alejo, Jose L; Kaur, Navdep; Kanji, Joshua; Blanchard, Scott C

2013-05-10

Aminoacyl-tRNA (aa-tRNA) enters the ribosome in a ternary complex with the G-protein elongation factor Tu (EF-Tu) and GTP. EF-Tu·GTP·aa-tRNA ternary complex formation and decay rates are accelerated in the presence of the nucleotide exchange factor elongation factor Ts (EF-Ts). EF-Ts directly facilitates the formation and disassociation of ternary complex. This system demonstrates a novel function of EF-Ts. Aminoacyl-tRNA enters the translating ribosome in a ternary complex with elongation factor Tu (EF-Tu) and GTP. Here, we describe bulk steady state and pre-steady state fluorescence methods that enabled us to quantitatively explore the kinetic features of Escherichia coli ternary complex formation and decay. The data obtained suggest that both processes are controlled by a nucleotide-dependent, rate-determining conformational change in EF-Tu. Unexpectedly, we found that this conformational change is accelerated by elongation factor Ts (EF-Ts), the guanosine nucleotide exchange factor for EF-Tu. Notably, EF-Ts attenuates the affinity of EF-Tu for GTP and destabilizes ternary complex in the presence of non-hydrolyzable GTP analogs. These results suggest that EF-Ts serves an unanticipated role in the cell of actively regulating the abundance and stability of ternary complex in a manner that contributes to rapid and faithful protein synthesis.

Complex Organic Parents during Star-Forming Infall

NASA Astrophysics Data System (ADS)

Drozdovskaya, Maria; Walsh, Catherine; Visser, Ruud; Harsono, Daniel; van Dishoeck, Ewine

2013-07-01

Stars are born upon the gravitation infall of clumps in molecular clouds. Complex organic compounds have been observed to accompany star formation and are also believed to be the simplest ingredients to life. Therefore understanding complex organics under star forming conditions is fundamentally interesting. This work models the formation and distribution of several potential parent species for complex organic compounds, such as formaldehyde (H2CO) and methanol (CH3OH), along trajectories of matter parcels, as they undergo infall from the cold outer envelope towards the hot core region and eventually onto the disk. The code from Visser et al. (2009, 2011) serves as the basis for this research. The gas-phase chemistry network has now been expanded with grain-surface reactions to form CH3OH and, ultimately, larger organics such as methyl formate (HCOOCH3) and dimethyl ether (CH3OCH3). The intention behind this work is to obtain information on complex organic parents in the star formation scenario by means of a physically and chemically robust model. The availability of complex organic compounds will vary depending on where the parent species are abundant, such as in the pre-stellar stage, hot-core, or only in the disk; and where they are available for a sufficient amount of time for the complexity enhancement. Such model-based conclusions can then be used in order to explain the observational data on complex organic compounds.

Xenopus origin recognition complex (ORC) initiates DNA replication preferentially at sequences targeted by Schizosaccharomyces pombe ORC

PubMed Central

Kong, Daochun; Coleman, Thomas R.; DePamphilis, Melvin L.

2003-01-01

Budding yeast (Saccharomyces cerevisiae) origin recognition complex (ORC) requires ATP to bind specific DNA sequences, whereas fission yeast (Schizosaccharomyces pombe) ORC binds to specific, asymmetric A:T-rich sites within replication origins, independently of ATP, and frog (Xenopus laevis) ORC seems to bind DNA non-specifically. Here we show that despite these differences, ORCs are functionally conserved. Firstly, SpOrc1, SpOrc4 and SpOrc5, like those from other eukaryotes, bound ATP and exhibited ATPase activity, suggesting that ATP is required for pre-replication complex (pre-RC) assembly rather than origin specificity. Secondly, SpOrc4, which is solely responsible for binding SpORC to DNA, inhibited up to 70% of XlORC-dependent DNA replication in Xenopus egg extract by preventing XlORC from binding to chromatin and assembling pre-RCs. Chromatin-bound SpOrc4 was located at AT-rich sequences. XlORC in egg extract bound preferentially to asymmetric A:T-sequences in either bare DNA or in sperm chromatin, and it recruited XlCdc6 and XlMcm proteins to these sequences. These results reveal that XlORC initiates DNA replication preferentially at the same or similar sites to those targeted in S.pombe. PMID:12840006

Precursor microRNA Programmed Silencing Complex Assembly Pathways in Mammals

PubMed Central

Liu, Xuhang; Jin, Dong-Yan; McManus, Michael T.; Mourelatos, Zissimos

2012-01-01

Summary Assembly of microRNA Ribonucleoproteins (miRNPs) or RNA-Induced Silencing Complexes (RISCs) is essential for the function of miRNAs and initiates from processing of precursor miRNAs (pre-miRNAs) by Dicer or by Ago2. Here, we report an in-vitro miRNP/RISC assembly assay programmed by pre-miRNAs from mammalian cell lysates. Combining in-vivo studies in Dicer Knock-Out cells reconstituted with wild type or catalytically inactive Dicer, we find that the miRNA Loading Complex (miRLC) is the primary machinery linking pre-miRNA processing to miRNA loading. We show that a miRNA Precursor Deposit Complex (miPDC) plays a crucial role in Dicer-independent miRNA biogenesis and promotes miRNP assembly of certain Dicer-dependent miRNAs. Furthermore, we find that 5′-uridine, 3′-mid base pairing and 5′-mid mismatches within pre-miRNAs promote their assembly into miPDC. Our studies provide a comprehensive view of miRNP/RISC assembly pathways in mammals and our assay provides a versatile platform for further mechanistic dissection of such pathways in mammals. PMID:22503104

Precursor microRNA-programmed silencing complex assembly pathways in mammals.

PubMed

Liu, Xuhang; Jin, Dong-Yan; McManus, Michael T; Mourelatos, Zissimos

2012-05-25

Assembly of microRNA ribonucleoproteins (miRNPs) or RNA-induced silencing complexes (RISCs) is essential for the function of miRNAs and initiates from processing of precursor miRNAs (pre-miRNAs) by Dicer or by Ago2. Here, we report an in vitro miRNP/RISC assembly assay programmed by pre-miRNAs from mammalian cell lysates. Combining in vivo studies in Dicer Knockout cells reconstituted with wild-type or catalytically inactive Dicer, we find that the miRNA loading complex (miRLC) is the primary machinery linking pre-miRNA processing to miRNA loading. We show that a miRNA precursor deposit complex (miPDC) plays a crucial role in Dicer-independent miRNA biogenesis and promotes miRNP assembly of certain Dicer-dependent miRNAs. Furthermore, we find that 5'-uridine, 3'-mid base pairing, and 5'-mid mismatches within pre-miRNAs promote their assembly into miPDC. Our studies provide a comprehensive view of miRNP/RISC assembly pathways in mammals, and our assay provides a versatile platform for further mechanistic dissection of such pathways in mammals. Copyright © 2012 Elsevier Inc. All rights reserved.

Life without water: cross-resistance of anhydrobiotic cell line to abiotic stresses

NASA Astrophysics Data System (ADS)

Gusev, Oleg

2016-07-01

Anhydrobiosis is an intriguing phenomenon of natural ability of some organisms to resist water loss. The larvae of Polypedilum vanderplanki, the sleeping chironomid is the largest and most complex anhydrobionts known to date. The larvae showed ability to survive variety of abiotic stresses, including outer space environment. Recently cell line (Pv11) derived from the embryonic mass of the chironomid was established. Initially sensitive to desiccation cells, are capable to "induced" anhydrobiosis, when the resistance to desiccation can be developed by pre-treatment of the cells with trehalose followed by quick desiccation. We have further conducted complex analysis of the whole genome transcription response of Pv11 cells to different abiotic stresses, including oxidative stress and irradiation. Comparative analysis showed that the gene set, responsible for formation of desiccation resistance (ARID regions in the genome) is also activated in response to other types of stresses and likely to contribute to general enhancing of the resistance of the cells to harsh environment. We have further demonstrated that the cells are able to protect recombinant proteins from harmful effect of desiccation

Application of gamma spectrometry in the Kola peninsula (in Russian)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Golovin, I.V.; Kolesnik, N.I.; Antipov, V.S.

1973-01-01

The methodology used and results obtained in gamma spectrometric studies of pre-Cambrian formations of some nickel-bearing regions of the Kola Penlnsula are described. The radioactive element contents of typical metamorphic and magmatic complexes and sulfide ores are presented. (au-trans)

The Destructive Birth of Massive Stars and Massive Star Clusters

NASA Astrophysics Data System (ADS)

Rosen, Anna; Krumholz, Mark; McKee, Christopher F.; Klein, Richard I.; Ramirez-Ruiz, Enrico

2017-01-01

Massive stars play an essential role in the Universe. They are rare, yet the energy and momentum they inject into the interstellar medium with their intense radiation fields dwarfs the contribution by their vastly more numerous low-mass cousins. Previous theoretical and observational studies have concluded that the feedback associated with massive stars' radiation fields is the dominant mechanism regulating massive star and massive star cluster (MSC) formation. Therefore detailed simulation of the formation of massive stars and MSCs, which host hundreds to thousands of massive stars, requires an accurate treatment of radiation. For this purpose, we have developed a new, highly accurate hybrid radiation algorithm that properly treats the absorption of the direct radiation field from stars and the re-emission and processing by interstellar dust. We use our new tool to perform a suite of three-dimensional radiation-hydrodynamic simulations of the formation of massive stars and MSCs. For individual massive stellar systems, we simulate the collapse of massive pre-stellar cores with laminar and turbulent initial conditions and properly resolve regions where we expect instabilities to grow. We find that mass is channeled to the massive stellar system via gravitational and Rayleigh-Taylor (RT) instabilities. For laminar initial conditions, proper treatment of the direct radiation field produces later onset of RT instability, but does not suppress it entirely provided the edges of the radiation-dominated bubbles are adequately resolved. RT instabilities arise immediately for turbulent pre-stellar cores because the initial turbulence seeds the instabilities. To model MSC formation, we simulate the collapse of a dense, turbulent, magnetized Mcl = 106 M⊙ molecular cloud. We find that the influence of the magnetic pressure and radiative feedback slows down star formation. Furthermore, we find that star formation is suppressed along dense filaments where the magnetic field is amplified. Our results suggest that the combined effect of turbulence, magnetic pressure, and radiative feedback from massive stars is responsible for the low star formation efficiencies observed in molecular clouds.

Stellar Clusters in the NGC 6334 Star-Forming Complex

NASA Astrophysics Data System (ADS)

Feigelson, Eric D.; Martin, Amanda L.; McNeill, Collin J.; Broos, Patrick S.; Garmire, Gordon P.

2009-07-01

The full stellar population of NGC 6334, one of the most spectacular regions of massive star formation in the nearby Galaxy, has not been well sampled in past studies. We analyze here a mosaic of two Chandra X-ray Observatory images of the region using sensitive data analysis methods, giving a list of 1607 faint X-ray sources with arcsecond positions and approximate line-of-sight absorption. About 95% of these are expected to be cluster members, most lower mass pre-main-sequence stars. Extrapolating to low X-ray levels, the total stellar population is estimated to be 20,000-30,000 pre-main-sequence stars. The X-ray sources show a complicated spatial pattern with ~10 distinct star clusters. The heavily obscured clusters are mostly associated with previously known far-infrared sources and radio H II regions. The lightly obscured clusters are mostly newly identified in the X-ray images. Dozens of likely OB stars are found, both in clusters and dispersed throughout the region, suggesting that star formation in the complex has proceeded over millions of years. A number of extraordinarily heavily absorbed X-ray sources are associated with the active regions of star formation.

Characterization of Unconventional Reservoirs: CO2 Induced Petrophysics

NASA Astrophysics Data System (ADS)

Verba, C.; Goral, J.; Washburn, A.; Crandall, D.; Moore, J.

2017-12-01

As concerns about human-driven CO2 emissions grow, it is critical to develop economically and environmentally effective strategies to mitigate impacts associated with fossil energy. Geologic carbon storage (GCS) is a potentially promising technique which involves the injection of captured CO2 into subsurface formations. Unconventional shale formations are attractive targets for GCS while concurrently improving gas recovery. However, shales are inherently heterogeneous, and minor differences can impact the ability of the shale to effectively adsorb and store CO2. Understanding GCS capacity from such endemic heterogeneities is further complicated by the complex geochemical processes which can dynamically alter shale petrophysics. We investigated the size distribution, connectivity, and type (intraparticle, interparticle, and organic) of pores in shale; the mineralogy of cores from unconventional shale (e.g. Bakken); and the changes to these properties under simulated GCS conditions. Electron microscopy and dual beam focused ion beam scanning electron microscopy were used to reconstruct 2D/3D digital matrix and pore structures. Comparison of pre and post-reacted samples gives insights into CO2-shale interactions - such as the mechanism of CO2 sorption in shales- intended for enhanced oil recovery and GCS initiatives. These comparisons also show how geochemical processes proceed differently across shales based on their initial diagenesis. Results show that most shale pore sizes fall within meso-macro pore classification (> 2 nm), but have variable porosity and organic content. The formation of secondary minerals (calcite, gypsum, and halite) may play a role in the infilling of fractures and pore spaces in the shale, which may reduce permeability and inhibit the flow of fluids.

Characteristics of pattern formation and evolution in approximations of Physarum transport networks.

PubMed

Jones, Jeff

2010-01-01

Most studies of pattern formation place particular emphasis on its role in the development of complex multicellular body plans. In simpler organisms, however, pattern formation is intrinsic to growth and behavior. Inspired by one such organism, the true slime mold Physarum polycephalum, we present examples of complex emergent pattern formation and evolution formed by a population of simple particle-like agents. Using simple local behaviors based on chemotaxis, the mobile agent population spontaneously forms complex and dynamic transport networks. By adjusting simple model parameters, maps of characteristic patterning are obtained. Certain areas of the parameter mapping yield particularly complex long term behaviors, including the circular contraction of network lacunae and bifurcation of network paths to maintain network connectivity. We demonstrate the formation of irregular spots and labyrinthine and reticulated patterns by chemoattraction. Other Turing-like patterning schemes were obtained by using chemorepulsion behaviors, including the self-organization of regular periodic arrays of spots, and striped patterns. We show that complex pattern types can be produced without resorting to the hierarchical coupling of reaction-diffusion mechanisms. We also present network behaviors arising from simple pre-patterning cues, giving simple examples of how the emergent pattern formation processes evolve into networks with functional and quasi-physical properties including tensionlike effects, network minimization behavior, and repair to network damage. The results are interpreted in relation to classical theories of biological pattern formation in natural systems, and we suggest mechanisms by which emergent pattern formation processes may be used as a method for spatially represented unconventional computation.

Effect of intravenous administration of D-lysergic acid diethylamide on initiation of protein synthesis in a cell-free system derived from brain.

PubMed

Cosgrove, J W; Brown, I R

1984-05-01

An initiating cell-free protein synthesis system derived from brain was utilized to demonstrate that the intravenous injection of D-lysergic acid diethylamide (LSD) to rabbits resulted in a lesion at the initiation stage of brain protein synthesis. Three inhibitors of initiation, edeine, poly(I), and aurintricarboxylic acid were used to demonstrate a reduction in initiation-dependent amino acid incorporation in the brain cell-free system. One hour after LSD injection, there was also a measurable decrease in the formation of 40S and 80S initiation complexes in vitro, using either [35S]methionine or [35S]Met-tRNAf. Analysis of the methionine pool size after LSD administration indicated there was no change in methionine levels. Analysis of the formation of initiation complexes in the brain cell-free protein synthesis system prepared 6 h after LSD administration indicated that there was a return to control levels at this time. The effects of LSD on steps in the initiation process are thus reversible.

On the coupling of convective updrafts prior to secondary eyewall formation in Hurricane Katrina (2005)

NASA Astrophysics Data System (ADS)

Garcia-Rivera, Jose M.; Lin, Yuh-Lang

2017-09-01

Hurricane Katrina (2005) was simulated by the Advanced Research Weather Research and Forecasting model to understand the mechanism of a secondary eyewall formation (SEF) prior to its last landfall. The storm underwent a series of structural changes that were deemed necessary for the concentric cycle to begin, which included (1) increased rainband activity outside the primary eyewall in the hours before, mostly related to an intensifying main feeder band, (2) close to initiation of the SEF, an updraft (explained by a pre-existing hypothesis) emerged outside the primary eyewall near the top of the boundary layer (BL), (3) this updraft then intensified and extended both upward and outward, while the storm intensified and approached SEF, (4) eventually, the updraft coupled with the upward motion associated with rainband-related convection near the SEF radius, and (5) once the alignment occurred, the deep updraft quickly organized to support deep convection that led to SEF within hours of initiation. The coupling of updrafts emanating from the BL with the environmental upward motion associated with the pre-existing rainband activity is proposed to be the key mechanism for the SEF initiation in this case.

TGF-{beta} signals the formation of a unique NF1/Smad4-dependent transcription repressor-complex in human diploid fibroblasts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luciakova, Katarina, E-mail: katarina.luciakova@savba.sk; Kollarovic, Gabriel; Kretova, Miroslava

2011-08-05

Highlights: {yields} TGF-{beta} induces the formation of unique nuclear NF1/Smad4 complexes that repress expression of the ANT-2 gene. {yields} Repression is mediated through an NF1-dependent repressor element in the promoter. {yields} The formation of NF1/Smad4 complexes and the repression of ANT2 are prevented by inhibitors of p38 kinase and TGF-{beta} RI. {yields} NF1/Smad complexes implicate novel role for NF1 and Smad proteins in the regulation of growth. -- Abstract: We earlier reported the formation of a unique nuclear NF1/Smad complex in serum-restricted fibroblasts that acts as an NF1-dependent repressor of the human adenine nucleotide translocase-2 gene (ANT2) [K. Luciakova, G.more » Kollarovic, P. Barath, B.D. Nelson, Growth-dependent repression of human adenine nucleotide translocator-2 (ANT2) transcription: evidence for the participation of Smad and Sp family proteins in the NF1-dependent repressor complex, Biochem. J. 412 (2008) 123-130]. In the present study, we show that TGF-{beta}, like serum-restriction: (a) induces the formation of NF1/Smad repressor complexes, (b) increases binding of the complexes to the repressor elements (Go elements) in the ANT2 promoter, and (c) inhibits ANT2 expression. Repression of ANT2 by TGF-{beta} is eliminated by mutating the NF1 binding sites in the Go repressor elements. All of the above responses to TGF-{beta} are prevented by inhibitors of TGF-{beta} RI and MAPK p38. These inhibitors also prevent NF1/Smad4 repressor complex formation and repression of ANT2 expression in serum-restricted cells, suggesting that similar signaling pathways are initiated by TGF-{beta} and serum-restriction. The present finding that NF1/Smad4 repressor complexes are formed through TGF-{beta} signaling pathways suggests a new, but much broader, role for these complexes in the initiation or maintenance of the growth-inhibited state.« less

Efficient Isoprene Secondary Organic Aerosol Formation from a Non-IEPOX Pathway

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Jiumeng; D’Ambro, Emma L.; Lee, Ben H.

2016-09-20

With a large global emission rate and high reactivity, isoprene has a profound effect upon atmospheric chemistry and composition. The atmospheric pathways by which isoprene converts to secondary organic aerosol (SOA) and how anthropogenic pollutants such as nitrogen oxides and sulfur affect this process are a subject of intense research because particles affect Earth’s climate and local air quality. In the absence of both nitrogen oxides and reactive aqueous seed particles, we measure SOA mass yields from isoprene photochemical oxidation of up to 15%, which are factors of 2, or more, higher than those typically used in coupled chemistry-climate models.more » SOA yield is initially constant with the addition of increasing amounts of nitric oxide (NO) but then sharply decreases for input concentrations above 10 ppbv. Online measurements of aerosol molecular composition show that the fate of second-generation RO2 radicals is key to understanding the efficient SOA formation and the NOx dependent yields described here and in the literature. These insights allow for improved quantitative estimates of SOA formation in the pre-industrial atmosphere and in biogenic-rich regions with limited anthropogenic impacts and suggest a more complex representation of NOx dependent SOA yields may be important in models.« less

The Fission Yeast Minichromosome Maintenance (MCM)-binding Protein (MCM-BP), Mcb1, Regulates MCM Function during Prereplicative Complex Formation in DNA Replication*

PubMed Central

Santosa, Venny; Martha, Sabrina; Hirose, Noriaki; Tanaka, Katsunori

2013-01-01

The minichromosome maintenance (MCM) complex is a replicative helicase, which is essential for chromosome DNA replication. In recent years, the identification of a novel MCM-binding protein (MCM-BP) in most eukaryotes has led to numerous studies investigating its function and its relationship to the MCM complex. However, the mechanisms by which MCM-BP functions and associates with MCM complexes are not well understood; in addition, the functional role of MCM-BP remains controversial and may vary between model organisms. The present study aims to elucidate the nature and biological function of the MCM-BP ortholog, Mcb1, in fission yeast. The Mcb1 protein continuously interacts with MCM proteins during the cell cycle in vivo and can interact with any individual MCM subunit in vitro. To understand the detailed characteristics of mcb1+, two temperature-sensitive mcb1 gene mutants (mcb1ts) were isolated. Extensive genetic analysis showed that the mcb1ts mutants were suppressed by a mcm5+ multicopy plasmid and displayed synthetic defects with many S-phase-related gene mutants. Moreover, cyclin-dependent kinase modulation by Cig2 repression or Rum1 overproduction suppressed the mcb1ts mutants, suggesting the involvement of Mcb1 in pre-RC formation during DNA replication. These data are consistent with the observation that Mcm7 loading onto replication origins is reduced and S-phase progression is delayed in mcb1ts mutants. Furthermore, the mcb1ts mutation led to the redistribution of MCM subunits to the cytoplasm, and this redistribution was dependent on an active nuclear export system. These results strongly suggest that Mcb1 promotes efficient pre-RC formation during DNA replication by regulating the MCM complex. PMID:23322785

The fission yeast minichromosome maintenance (MCM)-binding protein (MCM-BP), Mcb1, regulates MCM function during prereplicative complex formation in DNA replication.

PubMed

Santosa, Venny; Martha, Sabrina; Hirose, Noriaki; Tanaka, Katsunori

2013-03-08

The minichromosome maintenance (MCM) complex is a replicative helicase, which is essential for chromosome DNA replication. In recent years, the identification of a novel MCM-binding protein (MCM-BP) in most eukaryotes has led to numerous studies investigating its function and its relationship to the MCM complex. However, the mechanisms by which MCM-BP functions and associates with MCM complexes are not well understood; in addition, the functional role of MCM-BP remains controversial and may vary between model organisms. The present study aims to elucidate the nature and biological function of the MCM-BP ortholog, Mcb1, in fission yeast. The Mcb1 protein continuously interacts with MCM proteins during the cell cycle in vivo and can interact with any individual MCM subunit in vitro. To understand the detailed characteristics of mcb1(+), two temperature-sensitive mcb1 gene mutants (mcb1(ts)) were isolated. Extensive genetic analysis showed that the mcb1(ts) mutants were suppressed by a mcm5(+) multicopy plasmid and displayed synthetic defects with many S-phase-related gene mutants. Moreover, cyclin-dependent kinase modulation by Cig2 repression or Rum1 overproduction suppressed the mcb1(ts) mutants, suggesting the involvement of Mcb1 in pre-RC formation during DNA replication. These data are consistent with the observation that Mcm7 loading onto replication origins is reduced and S-phase progression is delayed in mcb1(ts) mutants. Furthermore, the mcb1(ts) mutation led to the redistribution of MCM subunits to the cytoplasm, and this redistribution was dependent on an active nuclear export system. These results strongly suggest that Mcb1 promotes efficient pre-RC formation during DNA replication by regulating the MCM complex.

Elucidation of metal-ion accumulation induced by hydrogen bonds on protein surfaces by using porous lysozyme crystals containing Rh(III) ions as the model surfaces.

PubMed

Ueno, Takafumi; Abe, Satoshi; Koshiyama, Tomomi; Ohki, Takahiro; Hikage, Tatsuo; Watanabe, Yoshihito

2010-03-01

Metal-ion accumulation on protein surfaces is a crucial step in the initiation of small-metal clusters and the formation of inorganic materials in nature. This event is expected to control the nucleation, growth, and position of the materials. There remain many unknowns, as to how proteins affect the initial process at the atomic level, although multistep assembly processes of the materials formation by both native and model systems have been clarified at the macroscopic level. Herein the cooperative effects of amino acids and hydrogen bonds promoting metal accumulation reactions are clarified by using porous hen egg white lysozyme (HEWL) crystals containing Rh(III) ions, as model protein surfaces for the reactions. The experimental results reveal noteworthy implications for initiation of metal accumulation, which involve highly cooperative dynamics of amino acids and hydrogen bonds: i) Disruption of hydrogen bonds can induce conformational changes of amino-acid residues to capture Rh(III) ions. ii) Water molecules pre-organized by hydrogen bonds can stabilize Rh(III) coordination as aqua ligands. iii) Water molecules participating in hydrogen bonds with amino-acid residues can be replaced by Rh(III) ions to form polynuclear structures with the residues. iv) Rh(III) aqua complexes are retained on amino-acid residues through stabilizing hydrogen bonds even at low pH (approximately 2). These metal-protein interactions including hydrogen bonds may promote native metal accumulation reactions and also may be useful in the preparation of new inorganic materials that incorporate proteins.

Effects of operational parameters on dark fermentative hydrogen production from biodegradable complex waste biomass.

PubMed

Ghimire, Anish; Sposito, Fabio; Frunzo, Luigi; Trably, Eric; Escudié, Renaud; Pirozzi, Francesco; Lens, Piet N L; Esposito, Giovanni

2016-04-01

This work aimed to investigate the effect of the initial pH, combination of food to microorganism ratio (F/M) and initial pH, substrate pre-treatment and different inoculum sources on the dark fermentative biohydrogen (H2) yields. Three model complex waste biomasses (food waste, olive mill wastewater (OMWW) and rice straw) were used to assess the effect of the aforementioned parameters. The effect of the initial pH between 4.5 and 7.0 was investigated in batch tests carried out with food waste. The highest H2 yields were shown at initial pH 4.5 (60.6 ± 9.0 mL H2/g VS) and pH 5.0 (50.7 ± 0.8 mL H2/g VS). Furthermore, tests carried out with F/M ratios of 0.5, 1.0 and 1.5 at initial pH 5.0 and 6.5 revealed that a lower F/M ratio (0.5 and 1.0) favored the H2 production at an initial pH 5.0 compared to pH 6.5. Alkaline pre-treatment of raw rice straw using 4% and 8% NaOH at 55°C for 24h, increased the H2 yield by 26 and 57-fold, respectively. In the dark fermentation of OMWW, the H2 yield was doubled when heat-shock pre-treated activated sludge was used as inoculum in comparison to anaerobic sludge. Overall, this study shows that the application of different operating parameters to maximize the H2 yields strongly depends on the biodegradability of the substrate. Copyright © 2016 Elsevier Ltd. All rights reserved.

Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation.

PubMed

Glyde, Robert; Ye, Fuzhou; Darbari, Vidya Chandran; Zhang, Nan; Buck, Martin; Zhang, Xiaodong

2017-07-06

Gene transcription is carried out by RNA polymerases (RNAPs). For transcription to occur, the closed promoter complex (RPc), where DNA is double stranded, must isomerize into an open promoter complex (RPo), where the DNA is melted out into a transcription bubble and the single-stranded template DNA is delivered to the RNAP active site. Using a bacterial RNAP containing the alternative σ 54 factor and cryoelectron microscopy, we determined structures of RPc and the activator-bound intermediate complex en route to RPo at 3.8 and 5.8 Å. Our structures show how RNAP-σ 54 interacts with promoter DNA to initiate the DNA distortions required for transcription bubble formation, and how the activator interacts with RPc, leading to significant conformational changes in RNAP and σ 54 that promote RPo formation. We propose that DNA melting is an active process initiated in RPc and that the RNAP conformations of intermediates are significantly different from that of RPc and RPo. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Memory circuits: CA2.

PubMed

Piskorowski, Rebecca A; Chevaleyre, Vivien

2018-04-26

The hippocampus is a central region in the coding of spatial, temporal and episodic memory. Recent discoveries have revealed surprising and complex roles of the small area CA2 in hippocampal function. Lesion studies have revealed that this region is required for social memory formation. Area CA2 is targeted by extra-hippocampal paraventricular inputs that release vasopressin and can act to enhance social memory performance. In vivo recordings have revealed nonconventional activity by neurons in this region that act to both initiate hippocampal sharp-wave ripple events as well as encode spatial information during immobility. Silencing of CA2 pyramidal neurons has revealed that this area also acts to control hippocampal network excitability during encoding, and this balance of excitation and inhibition is disrupted in disease. This review summarizes recent findings and attempts to integrate these results into pre-existing models. Copyright © 2018 Elsevier Ltd. All rights reserved.

Interfacial behaviour of biopolymer multilayers: Influence of in vitro digestive conditions.

PubMed

Corstens, Meinou N; Osorio Caltenco, Lilia A; de Vries, Renko; Schroën, Karin; Berton-Carabin, Claire C

2017-05-01

Although multilayered emulsions have been related to reduced lipolysis, the involved interfacial phenomena have never been studied directly. In this work, we systematically built multilayers of whey protein and pectin, which we further subjected to digestive conditions, using two different techniques: droplet volume tensiometry to investigate interfacial rheology, and reflectometry to determine the amount of adsorbed material. Interfacial tension and dilatational rheology were linked to adsorption/desorption kinetics measured under static in vitro conditions. The interfacial tension and rheology of the multilayers was rather similar to those found for single whey protein layers, as well as their resistance to duodenal conditions and lipolytic components, which is explained by the rapid destabilisation of multilayers at neutral pH. Sequential adsorption of bile extract or lipase to pre-adsorbed films rapidly lowered the interfacial tension via co-adsorption and displacement, forming a viscoelastic film with low mechanical strength, and highly dynamic adsorption/desorption. When both were present, bile salts dominated the initial adsorption, followed by lipase co-adsorption and formation of lipolysis products that further lowered the interfacial tension, forming a complex interface (including biopolymers, bile salts, lipase, and lipolysis products), independent of pre-adsorbed biopolymer layers. Our study shows that the combination of drop volume tensiometry and reflectometry can be used to study complex interfacial behaviours under digestive conditions, which can lead to smart design of interfacial structures for controlled lipolysis in food emulsions. Copyright © 2017 Elsevier B.V. All rights reserved.

Authoring a CAI Lesson in Nutrition Education.

ERIC Educational Resources Information Center

Ries, Carol P.; And Others

1984-01-01

A nutrition lesson on vegetarianism (focusing on vegetarian types, complementary protein, special-care nutrients, and diet planning) that uses a pre-developed plan which concentrates on lesson content and design has been developed. Initial planning and procedures involved in developing the unit (selecting teaching modes, text writing, formatting,…

The paredon, Mexico, obsidian source and early formative exchange.

PubMed

Charlton, T H; Grove, D C; Hopke, P K

1978-09-01

In 1975, archeological surface surveys of trade routes located again a pre-Hispanic obsidian source in central Mexico first reported in 1902. Initial trace element studies of the Paredón source through an analysis by neutron activation have been compared with similar studies of the obsidian found at Chalcatzingo 150 kilometers from the source. These comparisons indicate that obsidian from Paredón, rather than Otumba, was of primary importance during the Early Formative in central Mexico.

The Uttar Pradesh State Observatory --- some recollections and some history (1954-1982)

NASA Astrophysics Data System (ADS)

Sinvhal, S. D.

2006-03-01

An attempt is made to present a picture of pre-historic and initial formative years of the well known Uttar Pradesh State Observatory, Nainital. The development of academic activities along with infrastructure are described. The emphasis on the frontline research work, self-reliance and international interaction was given during the formative years of the observatory. The largest telescope 104-cm of the observatory was installed in 1972 and has produced good scientific results.

Cas5d Protein Processes Pre-crRNA and Assembles into a Cascade-like Interference Complex in Subtype I-C/Dvulg CRISPR-Cas System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nam, Ki Hyun; Haitjema, Charles; Liu, Xueqi

Clustered regularly interspaced short palindromic repeats (CRISPRs), together with an operon of CRISPR-associated (Cas) proteins, form an RNA-based prokaryotic immune system against exogenous genetic elements. Cas5 family proteins are found in several type I CRISPR-Cas systems. Here, we report the molecular function of subtype I-C/Dvulg Cas5d from Bacillus halodurans. We show that Cas5d cleaves pre-crRNA into unit length by recognizing both the hairpin structure and the 3 single stranded sequence in the CRISPR repeat region. Cas5d structure reveals a ferredoxin domain-based architecture and a catalytic triad formed by Y46, K116, and H117 residues. We further show that after pre-crRNA processing,more » Cas5d assembles with crRNA, Csd1, and Csd2 proteins to form a multi-sub-unit interference complex similar to Escherichia coli Cascade (CRISPR-associated complex for antiviral defense) in architecture. Our results suggest that formation of a crRNA-presenting Cascade-like complex is likely a common theme among type I CRISPR subtypes.« less

Kinetic Evidence of an Apparent Negative Activation Enthalpy in an Organocatalytic Process

PubMed Central

Han, Xiao; Lee, Richmond; Chen, Tao; Luo, Jie; Lu, Yixin; Huang, Kuo-Wei

2013-01-01

A combined kinetic and computational study on our tryptophan-based bifunctional thiourea catalyzed asymmetric Mannich reactions reveals an apparent negative activation enthalpy. The formation of the pre-transition state complex has been unambiguously confirmed and these observations provide an experimental support for the formation of multiple hydrogen bonding network between the substrates and the catalyst. Such interactions allow the creation of a binding cavity, a key factor to install high enantioselectivity. PMID:23990028

Genome-wide uniformity of human ‘open’ pre-initiation complexes

PubMed Central

Lai, William K.M.; Pugh, B. Franklin

2017-01-01

Transcription of protein-coding and noncoding DNA occurs pervasively throughout the mammalian genome. Their sites of initiation are generally inferred from transcript 5′ ends and are thought to be either locally dispersed or focused. How these two modes of initiation relate is unclear. Here, we apply permanganate treatment and chromatin immunoprecipitation (PIP-seq) of initiation factors to identify the precise location of melted DNA separately associated with the preinitiation complex (PIC) and the adjacent paused complex (PC). This approach revealed the two known modes of transcription initiation. However, in contrast to prevailing views, they co-occurred within the same promoter region: initiation originating from a focused PIC, and broad nucleosome-linked initiation. PIP-seq allowed transcriptional orientation of Pol II to be determined, which may be useful near promoters where sufficient sense/anti-sense transcript mapping information is lacking. PIP-seq detected divergently oriented Pol II at both coding and noncoding promoters, as well as at enhancers. Their occupancy levels were not necessarily coupled in the two orientations. DNA sequence and shape analysis of initiation complex sites suggest that both sequence and shape contribute to specificity, but in a context-restricted manner. That is, initiation sites have the locally “best” initiator (INR) sequence and/or shape. These findings reveal a common core to pervasive Pol II initiation throughout the human genome. PMID:27927716

An inhibitor of eIF2 activity in the sRNA pool of eukaryotic cells.

PubMed

Centrella, Michael; Porter, David L; McCarthy, Thomas L

2011-08-15

Eukaryotic protein synthesis is a multi-step and highly controlled process that includes an early initiation complex containing eukaryotic initiation factor 2 (eIF2), GTP, and methionine-charged initiator methionyl-tRNA (met-tRNAi). During studies to reconstruct formation of the ternary complex containing these molecules, we detected a potent inhibitor in low molecular mass RNA (sRNA) preparations of eukaryotic tRNA. The ternary complex inhibitor (TCI) was retained in the total sRNA pool after met-tRNAi was charged by aminoacyl tRNA synthetase, co-eluted with sRNA by size exclusion chromatography, but resolved from met-tRNAi by ion exchange chromatography. The adverse effect of TCI was not overcome by high GTP or magnesium omission and was independent of GTP regeneration. Rather, TCI suppressed the rate of ternary complex formation, and disrupted protein synthesis and the accumulation of heavy polymeric ribosomes in reticulocyte lysates in vitro. Lastly, a component or components in ribosome depleted cell lysate significantly reversed TCI activity. Since assembly of the met-tRNAi/eIF2/GTP ternary complex is integral to protein synthesis, awareness of TCI is important to avoid confusion in studies of translation initiation. A clear definition of TCI may also allow a better appreciation of physiologic or pathologic situations, factors, and events that control protein synthesis in vivo. Copyright © 2011 Elsevier B.V. All rights reserved.

The Origin of Life from the Astrophysical Point of View

NASA Astrophysics Data System (ADS)

Yeghikyan, Ararat

2017-11-01

Тhe problem of the origin of life is discussed from the astrophysical point of view. Most biologists and geologists up to the present time believe that Life was originated on the Earth in some initial natural chemical pre-reactors, where a mixture of water, ammonia, methane containing species and some other substances, under the influence of an energy source like, e.g. lightning, turned into quite complex compounds such as amino acids and complex hydrocarbons. In fact, under conditions of the primordial Earth, it is not possible to obtain such pre-biological molecules by a-bio-chemical methods, as discussed in this lecture. Instead, an astrophysical view of the problem of the origin of life on the Earth is proposed and it is recalled that the biological evolution on the Earth was preceded by the chemical evolution of complex chemical compounds, mostly under extraterrestrial conditions, where it is only possible to form optically active amino acids, sugars and hydrocarbon is necessary for constructing the first pre-biomolecules .

The MARVEL domain protein, Singles Bar, is required for progression past the pre-fusion complex stage of myoblast fusion.

PubMed

Estrada, Beatriz; Maeland, Anne D; Gisselbrecht, Stephen S; Bloor, James W; Brown, Nicholas H; Michelson, Alan M

2007-07-15

Multinucleated myotubes develop by the sequential fusion of individual myoblasts. Using a convergence of genomic and classical genetic approaches, we have discovered a novel gene, singles bar (sing), that is essential for myoblast fusion. sing encodes a small multipass transmembrane protein containing a MARVEL domain, which is found in vertebrate proteins involved in processes such as tight junction formation and vesicle trafficking where--as in myoblast fusion--membrane apposition occurs. sing is expressed in both founder cells and fusion competent myoblasts preceding and during myoblast fusion. Examination of embryos injected with double-stranded sing RNA or embryos homozygous for ethane methyl sulfonate-induced sing alleles revealed an identical phenotype: replacement of multinucleated myofibers by groups of single, myosin-expressing myoblasts at a stage when formation of the mature muscle pattern is complete in wild-type embryos. Unfused sing mutant myoblasts form clusters, suggesting that early recognition and adhesion of these cells are unimpaired. To further investigate this phenotype, we undertook electron microscopic ultrastructural studies of fusing myoblasts in both sing and wild-type embryos. These experiments revealed that more sing mutant myoblasts than wild-type contain pre-fusion complexes, which are characterized by electron-dense vesicles paired on either side of the fusing plasma membranes. In contrast, embryos mutant for another muscle fusion gene, blown fuse (blow), have a normal number of such complexes. Together, these results lead to the hypothesis that sing acts at a step distinct from that of blow, and that sing is required on both founder cell and fusion-competent myoblast membranes to allow progression past the pre-fusion complex stage of myoblast fusion, possibly by mediating fusion of the electron-dense vesicles to the plasma membrane.

The Mediator Complex and Transcription Elongation

PubMed Central

Conaway, Ronald C.; Conaway, Joan Weliky

2013-01-01

Background Mediator is an evolutionarily conserved multisubunit RNA polymerase II (Pol II) coregulatory complex. Although Mediator was initially found to play a critical role in regulation of the initiation of Pol II transcription, recent studies have brought to light an expanded role for Mediator at post-initiation stages of transcription. Scope of review We provide a brief description of the structure of Mediator and its function in the regulation of Pol II transcription initiation, and we summarize recent findings implicating Mediator in the regulation of various stages of Pol II transcription elongation. Major conclusions Emerging evidence is revealing new roles for Mediator in nearly all stages of Pol II transcription, including initiation, promoter escape, elongation, pre-mRNA processing, and termination. General significance Mediator plays a central role in the regulation of gene expression by impacting nearly all stages of mRNA synthesis. PMID:22983086

Aerobic oxidations catalyzed by chromium corroles.

PubMed

Mahammed, Atif; Gray, Harry B; Meier-Callahan, Alexandre E; Gross, Zeev

2003-02-05

Oxochromium(V) complexes of 5,10,15-tris(pentafluorophenyl)corrole and brominated derivatives oxygenate substrates (triphenylphosphine and norbornene) with concomitant production of chromium(III). Regeneration of CrVO by reaction of dioxygen with CrIII completes an aerobic catalytic cycle, with very large solvent effects; in acetonitrile, rapid initial turnovers observed initially are shut down by formation of CrIVO, while in toluene, THF, and methanol, relatively slow reactions are further inhibited by product formation.

Degradation of Endeavour Crater, Mars

NASA Technical Reports Server (NTRS)

Grant, J. A.; Crumpler, L. S.; Parker, T. J.; Golombek, M. P.; Wilson, S. A.; Mittlefehldt, D. W.

2015-01-01

The Opportunity rover has traversed portions of two western rim segments of Endeavour, a 22 km-diameter crater in Meridiani Planum, for the past three years. The resultant data enables the evaluation of the geologic expression and degradation state of the crater. Endeavour is Noa-chian-aged, complex in morphology, and originally may have appeared broadly similar to the more pristine 20.5 km-diameter Santa Fe complex crater in Lunae Palus (19.5degN, 312.0degE). By contrast, Endeavour is considerably subdued and largely buried by younger sulfate-rich plains. Exposed rim segments dubbed Cape York (CY) and Solander Point/Murray Ridge/Pillinger Point (MR) located approximately1500 m to the south reveal breccias interpreted as remnants of the ejecta deposit, dubbed the Shoemaker Formation. At CY, the Shoemaker Formation overlies the pre-impact rocks, dubbed the Matijevic Formation.

Nanoparticle-protein complexes mimicking corona formation in ocular environment.

PubMed

Jo, Dong Hyun; Kim, Jin Hyoung; Son, Jin Gyeong; Dan, Ki Soon; Song, Sang Hoon; Lee, Tae Geol; Kim, Jeong Hun

2016-12-01

Nanoparticles adsorb biomolecules to form corona upon entering the biological environment. In this study, tissue-specific corona formation is provided as a way of controlling protein interaction with nanoparticles in vivo. In the vitreous, the composition of the corona was determined by the electrostatic and hydrophobic properties of the associated proteins, regardless of the material (gold and silica) or size (20- and 100-nm diameter) of the nanoparticles. To control protein adsorption, we pre-incubate 20-nm gold nanoparticles with 5 selectively enriched proteins from the corona, formed in the vitreous, to produce nanoparticle-protein complexes. Compared to bare nanoparticles, nanoparticle-protein complexes demonstrate improved binding to vascular endothelial growth factor (VEGF) in the vitreous. Furthermore, nanoparticle-protein complexes retain in vitro anti-angiogenic properties of bare nanoparticles. In particular, priming the nanoparticles (gold and silica) with tissue-specific corona proteins allows nanoparticle-protein complexes to exert better in vivo therapeutic effects by higher binding to VEGF than bare nanoparticles. These results suggest that controlled corona formation that mimics in vivo processes may be useful in the therapeutic use of nanomaterials in local environment. Copyright © 2016 Elsevier Ltd. All rights reserved.

Purification of ribonucleoproteins by a novel approach: isolation of the SSB1 ribonucleoprotein from yeast and demonstration that it has no role in mRNA splicing.

PubMed

Cusick, M E

1992-12-29

A novel approach is described to purify potential ribonucleoproteins (RNP) of yeast. The method assays a yeast RNP complex, assembled in vitro on actin pre-mRNA, by low-ionic strength acrylamide gel electrophoresis. The minimal protein components of this RNP complex were three proteins, one of 30 kDa and two at 42-44 kDa, defined by formation of the complex on biotinylated-RNA, binding of this complex to avidin-agarose, and salt elution of the protein in the biotinylated-RNP complex. Using the assay for RNP complex formation, an RNP protein was purified to homogeneity on the basis of its affinity towards single-stranded DNA and RNA. This RNP protein turned out to be identical to a known RNP protein, the single-stranded binding protein 1 (ssb1) of yeast, on the basis of identical gel electrophoretic migration, antibody cross-reactivity, and identical properties on the gel complex formation assay. In vitro mRNA splicing was normal in extracts made from a yeast strain missing ssb1 (ssb1- strain). Addition of anti-ssb1 antibody to splicing extracts made from a wild type strain did not inhibit or diminish splicing. Instead, mRNA splicing was reproducibly stimulated several fold, indicating competition between ssb1 and splicing factors for binding to single-stranded RNA in the extracts. RNP complexes still formed in the ssb1- strain, demonstrating that it would be possible to purify other RNP proteins from this strain using the gel complex formation assay.

Amyloidogenic Regions and Interaction Surfaces Overlap in Globular Proteins Related to Conformational Diseases

PubMed Central

Castillo, Virginia; Ventura, Salvador

2009-01-01

Protein aggregation underlies a wide range of human disorders. The polypeptides involved in these pathologies might be intrinsically unstructured or display a defined 3D-structure. Little is known about how globular proteins aggregate into toxic assemblies under physiological conditions, where they display an initially folded conformation. Protein aggregation is, however, always initiated by the establishment of anomalous protein-protein interactions. Therefore, in the present work, we have explored the extent to which protein interaction surfaces and aggregation-prone regions overlap in globular proteins associated with conformational diseases. Computational analysis of the native complexes formed by these proteins shows that aggregation-prone regions do frequently overlap with protein interfaces. The spatial coincidence of interaction sites and aggregating regions suggests that the formation of functional complexes and the aggregation of their individual subunits might compete in the cell. Accordingly, single mutations affecting complex interface or stability usually result in the formation of toxic aggregates. It is suggested that the stabilization of existing interfaces in multimeric proteins or the formation of new complexes in monomeric polypeptides might become effective strategies to prevent disease-linked aggregation of globular proteins. PMID:19696882

Elongation Factor Ts Directly Facilitates the Formation and Disassembly of the Escherichia coli Elongation Factor Tu·GTP·Aminoacyl-tRNA Ternary Complex*

PubMed Central

Burnett, Benjamin J.; Altman, Roger B.; Ferrao, Ryan; Alejo, Jose L.; Kaur, Navdep; Kanji, Joshua; Blanchard, Scott C.

2013-01-01

Aminoacyl-tRNA enters the translating ribosome in a ternary complex with elongation factor Tu (EF-Tu) and GTP. Here, we describe bulk steady state and pre-steady state fluorescence methods that enabled us to quantitatively explore the kinetic features of Escherichia coli ternary complex formation and decay. The data obtained suggest that both processes are controlled by a nucleotide-dependent, rate-determining conformational change in EF-Tu. Unexpectedly, we found that this conformational change is accelerated by elongation factor Ts (EF-Ts), the guanosine nucleotide exchange factor for EF-Tu. Notably, EF-Ts attenuates the affinity of EF-Tu for GTP and destabilizes ternary complex in the presence of non-hydrolyzable GTP analogs. These results suggest that EF-Ts serves an unanticipated role in the cell of actively regulating the abundance and stability of ternary complex in a manner that contributes to rapid and faithful protein synthesis. PMID:23539628

Meaningful Learning and Summative Assessment in Geography Education: An Analysis in Secondary Education in the Netherlands

ERIC Educational Resources Information Center

Bijsterbosch, Erik; van der Schee, Joop; Kuiper, Wilmad

2017-01-01

Enhancing meaningful learning is an important aim in geography education. Also, assessment should reflect this aim. Both formative and summative assessments contribute to meaningful learning when more complex knowledge and cognitive processes are assessed. The internal school-based geography examinations of the final exam in pre-vocational…

A Story of Culture and Teaching: The Complexity of Teacher Identity Formation

ERIC Educational Resources Information Center

Edwards, F. C. E.; Edwards, R. J.

2017-01-01

Research in teacher education repeatedly suggests that the background and underlying beliefs held by pre-service teachers about teaching and assessment act to shape their interpretations of ideas, powerfully influencing their praxis and their developing teacher identity. This paper explores how a young New Zealand secondary science teacher, raised…

Evolution of Pre-Main Sequence Accretion Disks

NASA Technical Reports Server (NTRS)

Hartmann, Lee W.

2004-01-01

The aim of this project is to develop a comprehensive global picture of the physical conditions in, and evolutionary timescales of, pre-main sequence accretion disks. The results of this work will help constrain the initial conditions for planet formation. To this end we are developing much larger samples of 3-10 Myr-old stars to provide better empirical constraints on protoplanetary disk evolution; measuring disk accretion rates in these systems; and constructing detailed model disk structures consistent with observations to infer physical conditions such as grain growth in protoplanetary disks.

Evolution of Pre-Main Sequence Accretion Disks

NASA Technical Reports Server (NTRS)

Hartmann, Lee W.

2003-01-01

The aim of this project is to develop a comprehensive global picture of the physical conditions in, and evolutionary timescales of, pre-main sequence accretion disks. The results of this work will help constrain the initial conditions for planet formation. To this end we are developing much larger samples of 3-10 Myr-old stars to provide better empirical constraints on protoplanetary disk evolution; measuring disk accretion rates in these systems; and constructing detailed model disk structures consistent with observations to infer physical conditions such as grain growth in protoplanetary disks.

Sesquinary reimpacts dominate surface characteristics on Phobos

NASA Astrophysics Data System (ADS)

Nayak, Michael

2018-01-01

We use topographic data to show that impact craters with pitted floor deposits are among the deepest on Mars. This is consistent with the interpretation of pitted materials as primary crater-fill impactite deposits emplaced during crater formation. Our database consists of 224 pitted material craters ranging in size from ˜1 to 150 km in diameter. Our measurements are based on topographic data from the Mars Orbiter Laser Altimeter (MOLA) and the High-Resolution Stereo Camera (HRSC). We have used these craters to measure the relationship between crater diameter and the initial post-formation depth. Depth was measured as maximum rim-to-floor depth, (dr), but we also report the depth measured using other definitions. The database was down-selected by refining or removing elevation measurements from "problematic" craters affected by processes and conditions that influenced their dr/D, such as pre-impact slopes/topography and later overprinting craters. We report a maximum (deepest) and mean scaling relationship of dr = (0.347±0.021)D0.537±0.017 and dr = (0.323±0.017)D0.538±0.016, respectively. Our results suggest that significant variations between previously-reported MOLA-based dr vs. D relationships may result from the inclusion of craters that: 1) are influenced by atypical processes (e.g., highly oblique impact), 2) are significantly degraded, 3) reside within high-strength regions, and 4) are transitional (partially collapsed). By taking such issues into consideration and only measuring craters with primary floor materials, we present the best estimate to date of a MOLA-based relationship of dr vs. D for the least-degraded complex craters on Mars. This can be applied to crater degradation studies and provides a useful constraint for models of complex crater formation.

Genetic and epigenetic mechanisms of gene regulation during lens development

PubMed Central

Cvekl, Ales; Duncan, Melinda K.

2007-01-01

Recent studies demonstrated a number of links between chromatin structure, gene expression, extracellular signaling and cellular differentiation during lens development. Lens progenitor cells originate from a pool of common progenitor cells, the pre-placodal region (PPR) which is formed due to a complex exchange of extracellular signals between the neural plate, naïve ectoderm and mesendoderm. A specific commitment to the lens program over alternate choices such as the formation of olfactory epithelium or the anterior pituitary is manifested by the formation of a thickened surface ectoderm, the lens placode. Mouse lens progenitor cells are characterized by the expression of a complement of lens lineage-specific transcription factors including Pax6, Six3 and Sox2, controlled by FGF and BMP signaling, followed later by c-Maf, Mab21like1, Prox1 and FoxE3. Proliferation of lens progenitors together with their morphogenetic movements results in the formation of the lens vesicle. This transient structure, comprised of lens precursor cells, is polarized with its anterior cells retaining their epithelial morphology and proliferative capacity, whereas the posterior lens precursor cells initiate terminal differentiation forming the primary lens fibers. Lens differentiation is marked by expression and accumulation of crystallins and other structural proteins. The transcriptional control of crystallin genes is characterized by the reiterative use of transcription factors required for the establishment of lens precursors in combination with more ubiquitously expressed factors (e.g. AP-1, AP-2α, CREB and USF) and recruitment of histone acetyltransferases (HATs) CBP and p300, and chromatin remodeling complexes SWI/SNF and ISWI. These studies have poised the study of lens development at the forefront of efforts to understand the connections between development, cell signaling, gene transcription and chromatin remodeling. PMID:17905638

Changes in bone turnover markers with HIV seroconversion and ART initiation

PubMed Central

Slama, Laurence; Reddy, Susheel; Phair, John; Palella, Frank J.; Brown, Todd T.

2017-01-01

Background: Osteoporosis is common among HIV-infected persons and contributes to risk of fragility fracture. While ART initiation is associated with decreases in bone mineral density and increases in bone turnover, the impact of HIV on bone metabolism is unclear. Methods: We identified men at the Chicago site of the Multicenter AIDS Cohort Study who HIV seroconverted while under observation. Concentrations of 25-OH vitamin D, bone turnover markers [procollagen type 1 N terminal propeptide (P1NP), osteocalcin (OC), C-telopeptide (CTX)] and sclerostin were measured from stored serum obtained at pre-HIV infection, pre-ART and post-ART initiation timepoints. Mixed models, with each biomarker as an outcome, were fitted. Timepoint, age, CD4 count (cells/mm3), HIV-viral suppression, season and an age by timepoint interaction term were considered as fixed effects. Results: Data from 52 participants revealed that median duration between HIV seroconversion and ART initiation was 8.7 years (IQR 3.7–11.6). Median CD4 and plasma HIV-RNA concentrations were 445 (IQR 298.5–689) and 20 184 copies/mL (IQR 6237–64 340), respectively, at the pre-ART timepoint. Multivariate analyses demonstrated pre-HIV infection levels of OC that were higher than pre-ART levels (6.8 versus 5.7 ng/mL, P = 0.04); and pre-ART levels of sclerostin that were higher than post-ART levels (0.033 versus 0.02 ng/mL, P <0.001). No changes in P1NP, CTX and 25-OH vitamin D levels were detected. Conclusions: HIV seroconversion was associated with decreased OC levels while ART initiation was associated with decreases in sclerostin, a negative regulator of bone formation. Our results suggest that both HIV infection and ART have an impact on bone metabolism in white men. PMID:28175307

Changes in bone turnover markers with HIV seroconversion and ART initiation.

PubMed

Slama, Laurence; Reddy, Susheel; Phair, John; Palella, Frank J; Brown, Todd T

2017-05-01

Osteoporosis is common among HIV-infected persons and contributes to risk of fragility fracture. While ART initiation is associated with decreases in bone mineral density and increases in bone turnover, the impact of HIV on bone metabolism is unclear. We identified men at the Chicago site of the Multicenter AIDS Cohort Study who HIV seroconverted while under observation. Concentrations of 25-OH vitamin D, bone turnover markers [procollagen type 1 N terminal propeptide (P1NP), osteocalcin (OC), C-telopeptide (CTX)] and sclerostin were measured from stored serum obtained at pre-HIV infection, pre-ART and post-ART initiation timepoints. Mixed models, with each biomarker as an outcome, were fitted. Timepoint, age, CD4 count (cells/mm 3 ), HIV-viral suppression, season and an age by timepoint interaction term were considered as fixed effects. Data from 52 participants revealed that median duration between HIV seroconversion and ART initiation was 8.7 years (IQR 3.7-11.6). Median CD4 and plasma HIV-RNA concentrations were 445 (IQR 298.5-689) and 20 184 copies/mL (IQR 6237-64 340), respectively, at the pre-ART timepoint. Multivariate analyses demonstrated pre-HIV infection levels of OC that were higher than pre-ART levels (6.8 versus 5.7 ng/mL, P  =   0.04); and pre-ART levels of sclerostin that were higher than post-ART levels (0.033 versus 0.02 ng/mL, P  <0.001). No changes in P1NP, CTX and 25-OH vitamin D levels were detected. HIV seroconversion was associated with decreased OC levels while ART initiation was associated with decreases in sclerostin, a negative regulator of bone formation. Our results suggest that both HIV infection and ART have an impact on bone metabolism in white men. © The Author 2017. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Cognitive and neural foundations of discrete sequence skill: a TMS study.

PubMed

Ruitenberg, Marit F L; Verwey, Willem B; Schutter, Dennis J L G; Abrahamse, Elger L

2014-04-01

Executing discrete movement sequences typically involves a shift with practice from a relatively slow, stimulus-based mode to a fast mode in which performance is based on retrieving and executing entire motor chunks. The dual processor model explains the performance of (skilled) discrete key-press sequences in terms of an interplay between a cognitive processor and a motor system. In the present study, we tested and confirmed the core assumptions of this model at the behavioral level. In addition, we explored the involvement of the pre-supplementary motor area (pre-SMA) in discrete sequence skill by applying inhibitory 20 min 1-Hz off-line repetitive transcranial magnetic stimulation (rTMS). Based on previous work, we predicted pre-SMA involvement in the selection/initiation of motor chunks, and this was confirmed by our results. The pre-SMA was further observed to be more involved in more complex than in simpler sequences, while no evidence was found for pre-SMA involvement in direct stimulus-response translations or associative learning processes. In conclusion, support is provided for the dual processor model, and for pre-SMA involvement in the initiation of motor chunks. Copyright © 2014 Elsevier Ltd. All rights reserved.

Impact of fermentation rate changes on potential hydrogen sulfide concentrations in wine.

PubMed

Butzke, Christian E; Park, Seung Kook

2011-05-01

The correlation between alcoholic fermentation rate, measured as carbon dioxide (CO2) evolution, and the rate of hydrogen sulfide (H2S) formation during wine production was investigated. Both rates and the resulting concentration peaks in fermentor headspace H2S were directly impacted by yeast assimilable nitrogenous compounds in the grape juice. A series of model fermentations was conducted in temperature-controlled and stirred fermentors using a complex model juice with defined concentrations of ammonium ions and/or amino acids. The fermentation rate was measured indirectly by noting the weight loss of the fermentor; H2S was quantitatively trapped in realtime using a pre-calibrated H2S detection tube which was inserted into a fermentor gas relief port. Evolution rates for CO2 and H2S as well as the relative ratios between them were calculated. These fermentations confirmed that total sulfide formation was strongly yeast strain-dependent, and high concentrations of yeast assimilable nitrogen did not necessarily protect against elevated H2S formation. High initial concentrations of ammonium ions via addition of diammonium phosphate (DAP) caused a higher evolution of H2S when compared with a non-supplemented but nondeficient juice. It was observed that the excess availability of a certain yeast assimilable amino acid, arginine, could result in a more sustained CO2 production rate throughout the wine fermentation. The contribution of yeast assimilable amino acids from conventional commercial yeast foods to lowering of the H2S formation was marginal.

Detailed Numerical Simulations on the Formation of Pillars Around H II Regions

NASA Astrophysics Data System (ADS)

Gritschneder, Matthias; Burkert, Andreas; Naab, Thorsten; Walch, Stefanie

2010-11-01

We study the structural evolution of turbulent molecular clouds under the influence of ionizing radiation emitted from a nearby massive star by performing a high-resolution parameter study with the iVINE code. The temperature is taken to be 10 K or 100 K, the mean number density is either 100 cm-3 or 300 cm-3. Furthermore, the turbulence is varied between Mach 1.5 and Mach 12.5, the main driving scale of the turbulence is varied between 1 pc and 8 pc. We vary the ionizing flux by an order of magnitude, corresponding to allowing between 0.5% and 5% of the mass in the domain to be ionized immediately. In our simulations, the ionizing radiation enhances the initial turbulent density distribution and thus leads to the formation of pillar-like structures observed adjacent to H II regions in a natural way. Gravitational collapse occurs regularly at the tips of the structures. We find a clear correlation between the initial state of the turbulent cold cloud and the final morphology and physical properties of the structures formed. The most favorable regime for the formation of pillars is Mach 4-10. Structures and therefore stars only form if the initial density contrast between the high-density unionized gas and the gas that is going to be ionized is lower than the temperature contrast between the hot and the cold gas. The density of the resulting pillars is determined by a pressure equilibrium between the hot and the cold gas. A thorough analysis of the simulations shows that the complex kinematical and geometrical structure of the formed elongated filaments reflects that of observed pillars to an impressive level of detail. In addition, we find that the observed line-of-sight velocities allow for a distinct determination of different formation mechanisms. Comparing the current simulations to previous results and recent observations, we conclude that, e.g., the pillars of creation in M16 formed by the mechanism proposed here and not by the radiation driven implosion of pre-existing clumps.

DETAILED NUMERICAL SIMULATIONS ON THE FORMATION OF PILLARS AROUND H II REGIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gritschneder, Matthias; Burkert, Andreas; Naab, Thorsten

2010-11-10

We study the structural evolution of turbulent molecular clouds under the influence of ionizing radiation emitted from a nearby massive star by performing a high-resolution parameter study with the iVINE code. The temperature is taken to be 10 K or 100 K, the mean number density is either 100 cm{sup -3} or 300 cm{sup -3}. Furthermore, the turbulence is varied between Mach 1.5 and Mach 12.5, the main driving scale of the turbulence is varied between 1 pc and 8 pc. We vary the ionizing flux by an order of magnitude, corresponding to allowing between 0.5% and 5% of themore » mass in the domain to be ionized immediately. In our simulations, the ionizing radiation enhances the initial turbulent density distribution and thus leads to the formation of pillar-like structures observed adjacent to H II regions in a natural way. Gravitational collapse occurs regularly at the tips of the structures. We find a clear correlation between the initial state of the turbulent cold cloud and the final morphology and physical properties of the structures formed. The most favorable regime for the formation of pillars is Mach 4-10. Structures and therefore stars only form if the initial density contrast between the high-density unionized gas and the gas that is going to be ionized is lower than the temperature contrast between the hot and the cold gas. The density of the resulting pillars is determined by a pressure equilibrium between the hot and the cold gas. A thorough analysis of the simulations shows that the complex kinematical and geometrical structure of the formed elongated filaments reflects that of observed pillars to an impressive level of detail. In addition, we find that the observed line-of-sight velocities allow for a distinct determination of different formation mechanisms. Comparing the current simulations to previous results and recent observations, we conclude that, e.g., the pillars of creation in M16 formed by the mechanism proposed here and not by the radiation driven implosion of pre-existing clumps.« less

Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hubin, Elizabeth A.; Fay, Allison; Xu, Catherine

RbpA and CarD are essential transcription regulators in mycobacteria. Mechanistic analyses of promoter open complex (RPo) formation establish that RbpA and CarD cooperatively stimulate formation of an intermediate (RP2) leading to RPo; formation of RP2 is likely a bottleneck step at the majority of mycobacterial promoters. Once RPo forms, CarD also disfavors its isomerization back to RP2. We determined a 2.76 Å-resolution crystal structure of a mycobacterial transcription initiation complex (TIC) with RbpA as well as a CarD/RbpA/TIC model. Both CarD and RbpA bind near the upstream edge of the -10 element where they likely facilitate DNA bending and impedemore » transcription bubble collapse. In vivo studies demonstrate the essential role of RbpA, show the effects of RbpA truncations on transcription and cell physiology, and indicate additional functions for RbpA not evident in vitro. This work provides a framework to understand the control of mycobacterial transcription by RbpA and CarD.« less

Structural insights into the light-driven auto-assembly process of the water-oxidizing Mn 4CaO 5-cluster in photosystem II

DOE PAGES

Zhang, Miao; Bommer, Martin; Chatterjee, Ruchira; ...

2017-07-18

In plants, algae and cyanobacteria, Photosystem II (PSII) catalyzes the light-driven splitting of water at a protein-bound Mn 4CaO 5-cluster, the water-oxidizing complex (WOC). In the photosynthetic organisms, the light-driven formation of the WOC from dissolved metal ions is a key process because it is essential in both initial activation and continuous repair of PSII. Structural information is required for understanding of this chaperone-free metal-cluster assembly. For the first time, we obtained a structure of PSII from Thermosynechococcus elongatus without the Mn 4CaO 5-cluster. Surprisingly, cluster-removal leaves the positions of all coordinating amino acid residues and most nearby water moleculesmore » largely unaffected, resulting in a pre-organized ligand shell for kinetically competent and error-free photo-assembly of the Mn 4CaO 5-cluster. First experiments initiating (i) partial disassembly and (ii) partial re-assembly after complete depletion of the Mn4CaO5-cluster agree with a specific bi-manganese cluster, likely a di-µ-oxo bridged pair of Mn(III) ions, as an assembly intermediate.« less

Structural insights into the light-driven auto-assembly process of the water-oxidizing Mn4CaO5-cluster in photosystem II.

PubMed

Zhang, Miao; Bommer, Martin; Chatterjee, Ruchira; Hussein, Rana; Yano, Junko; Dau, Holger; Kern, Jan; Dobbek, Holger; Zouni, Athina

2017-07-18

In plants, algae and cyanobacteria, Photosystem II (PSII) catalyzes the light-driven splitting of water at a protein-bound Mn 4 CaO 5 -cluster, the water-oxidizing complex (WOC). In the photosynthetic organisms, the light-driven formation of the WOC from dissolved metal ions is a key process because it is essential in both initial activation and continuous repair of PSII. Structural information is required for understanding of this chaperone-free metal-cluster assembly. For the first time, we obtained a structure of PSII from Thermosynechococcus elongatus without the Mn 4 CaO 5 -cluster. Surprisingly, cluster-removal leaves the positions of all coordinating amino acid residues and most nearby water molecules largely unaffected, resulting in a pre-organized ligand shell for kinetically competent and error-free photo-assembly of the Mn 4 CaO 5 -cluster. First experiments initiating (i) partial disassembly and (ii) partial re-assembly after complete depletion of the Mn 4 CaO 5 -cluster agree with a specific bi-manganese cluster, likely a di-µ-oxo bridged pair of Mn(III) ions, as an assembly intermediate.

Schizosaccharomyces pombe Noc3 Is Essential for Ribosome Biogenesis and Cell Division but Not DNA Replication▿

PubMed Central

Houchens, Christopher R.; Perreault, Audrey; Bachand, François; Kelly, Thomas J.

2008-01-01

The initiation of eukaryotic DNA replication is preceded by the assembly of prereplication complexes (pre-RCs) at chromosomal origins of DNA replication. Pre-RC assembly requires the essential DNA replication proteins ORC, Cdc6, and Cdt1 to load the MCM DNA helicase onto chromatin. Saccharomyces cerevisiae Noc3 (ScNoc3), an evolutionarily conserved protein originally implicated in 60S ribosomal subunit trafficking, has been proposed to be an essential regulator of DNA replication that plays a direct role during pre-RC formation in budding yeast. We have cloned Schizosaccharomyces pombe noc3+ (Spnoc3+), the S. pombe homolog of the budding yeast ScNOC3 gene, and functionally characterized the requirement for the SpNoc3 protein during ribosome biogenesis, cell cycle progression, and DNA replication in fission yeast. We showed that fission yeast SpNoc3 is a functional homolog of budding yeast ScNoc3 that is essential for cell viability and ribosome biogenesis. We also showed that SpNoc3 is required for the normal completion of cell division in fission yeast. However, in contrast to the proposal that ScNoc3 plays an essential role during DNA replication in budding yeast, we demonstrated that fission yeast cells do enter and complete S phase in the absence of SpNoc3, suggesting that SpNoc3 is not essential for DNA replication in fission yeast. PMID:18606828

Dual role of the integrated stress response in medulloblastoma tumorigenesis

PubMed Central

Li, Xiting; Jamison, Stephanie; Harding, Heather P.; Ron, David; Lin, Wensheng

2016-01-01

In response to endoplasmic reticulum (ER) stress, activation of pancreatic ER kinase (PERK) coordinates an adaptive program known as the integrated stress response (ISR) by phosphorylating translation initiation factor 2α (eIF2α). Phosphorylated eIF2α is quickly dephosphorylated by the protein phosphatase 1 and growth arrest and DNA damage 34 (GADD34) complex. Data indicate that the ISR can either promote or suppress tumor development. Our previous studies showed that the ISR is activated in medulloblastoma in both human patients and animal models, and that the decreased ISR via PERK heterozygous deficiency attenuates medulloblastoma formation in Patched1 heterozygous deficient (Ptch1+/−) mice by enhancing apoptosis of pre-malignant granule cell precursors (GCPs) during cell transformation. We showed here that GADD34 heterozygous mutation moderately enhanced the ISR and noticeably increased the incidence of medulloblastoma in adult Ptch1+/− mice. Surprisingly, GADD34 homozygous mutation strongly enhanced the ISR, but significantly decreased the incidence of medulloblastoma in adult Ptch1+/− mice. Intriguingly, GADD34 homozygous mutation significantly enhanced pre-malignant GCP apoptosis in cerebellar hyperplastic lesions and reduced the lesion numbers in young Ptch1+/− mice. Nevertheless, neither GADD34 heterozygous mutation nor GADD34 homozygous mutation had a significant effect on medulloblastoma cells in adult Ptch1+/− mice. Collectively, these data imply the dual role of the ISR, promoting and inhibiting, in medulloblastoma tumorigenesis by regulating apoptosis of pre-malignant GCPs during the course of malignant transformation. PMID:27802424

Dual role of the integrated stress response in medulloblastoma tumorigenesis.

PubMed

Stone, Sarrabeth; Ho, Yeung; Li, Xiting; Jamison, Stephanie; Harding, Heather P; Ron, David; Lin, Wensheng

2016-09-27

In response to endoplasmic reticulum (ER) stress, activation of pancreatic ER kinase (PERK) coordinates an adaptive program known as the integrated stress response (ISR) by phosphorylating translation initiation factor 2α (eIF2α). Phosphorylated eIF2α is quickly dephosphorylated by the protein phosphatase 1 and growth arrest and DNA damage 34 (GADD34) complex. Data indicate that the ISR can either promote or suppress tumor development. Our previous studies showed that the ISR is activated in medulloblastoma in both human patients and animal models, and that the decreased ISR via PERK heterozygous deficiency attenuates medulloblastoma formation in Patched1 heterozygous deficient (Ptch1+/-) mice by enhancing apoptosis of pre-malignant granule cell precursors (GCPs) during cell transformation. We showed here that GADD34 heterozygous mutation moderately enhanced the ISR and noticeably increased the incidence of medulloblastoma in adult Ptch1+/- mice. Surprisingly, GADD34 homozygous mutation strongly enhanced the ISR, but significantly decreased the incidence of medulloblastoma in adult Ptch1+/- mice. Intriguingly, GADD34 homozygous mutation significantly enhanced pre-malignant GCP apoptosis in cerebellar hyperplastic lesions and reduced the lesion numbers in young Ptch1+/- mice. Nevertheless, neither GADD34 heterozygous mutation nor GADD34 homozygous mutation had a significant effect on medulloblastoma cells in adult Ptch1+/- mice. Collectively, these data imply the dual role of the ISR, promoting and inhibiting, in medulloblastoma tumorigenesis by regulating apoptosis of pre-malignant GCPs during the course of malignant transformation.

Reflections on the history of pre-mRNA processing and highlights of current knowledge: A unified picture

PubMed Central

Darnell, James E.

2013-01-01

Several strong conclusions emerge concerning pre-mRNA processing from both old and newer experiments. The RNAPII complex is involved with pre-mRNA processing through binding of processing proteins to the CTD (carboxyl terminal domain) of the largest RNAPII subunit. These interactions are necessary for efficient processing, but whether factor binding to the CTD and delivery to splicing sites is obligatory or facilitatory is unsettled. Capping, addition of an m7Gppp residue (cap) to the initial transcribed residue of a pre-mRNA, occurs within seconds. Splicing of pre-mRNA by spliceosomes at particular sites is most likely committed during transcription by the binding of initiating processing factors and ∼50% of the time is completed in mammalian cells before completion of the primary transcript. This fact has led to an outpouring in the literature about “cotranscriptional splicing.” However splicing requires several minutes for completion and can take longer. The RNAPII complex moves through very long introns and also through regions dense with alternating exons and introns at an average rate of ∼3 kb per min and is, therefore, not likely detained at each splice site for more than a few seconds, if at all. Cleavage of the primary transcript at the 3′ end and polyadenylation occurs within 30 sec or less at recognized polyA sites, and the majority of newly polyadenylated pre-mRNA molecules are much larger than the average mRNA. Finally, it seems quite likely that the nascent RNA most often remains associated with the chromosomal locus being transcribed until processing is complete, possibly acquiring factors related to the transport of the new mRNA to the cytoplasm. PMID:23440351

MCM-BP regulates unloading of the MCM2–7 helicase in late S phase

PubMed Central

Nishiyama, Atsuya; Frappier, Lori; Méchali, Marcel

2011-01-01

Origins of DNA replication are licensed by recruiting MCM2–7 to assemble the prereplicative complex (pre-RC). How MCM2–7 is inactivated or removed from chromatin at the end of S phase is still unclear. Here, we show that MCM-BP can disassemble the MCM2–7 complex and might function as an unloader of MCM2–7 from chromatin. In Xenopus egg extracts, MCM-BP exists in a stable complex with MCM7, but is not associated with the MCM2–7 hexameric complex. MCM-BP accumulates in nuclei in late S phase, well after the loading of MCM2–7 onto chromatin. MCM-BP immunodepletion in Xenopus egg extracts inhibits replication-dependent MCM dissociation without affecting pre-RC formation and DNA replication. When excess MCM-BP is incubated with Xenopus egg extracts or immunopurified MCM2–7, it binds to MCM proteins and promotes disassembly of the MCM2–7 complex. Recombinant MCM-BP also releases MCM2–7 from isolated late-S-phase chromatin, but this activity is abolished when DNA replication is blocked. MCM-BP silencing in human cells also delays MCM dissociation in late S phase. We propose that MCM-BP plays a key role in the mechanism by which pre-RC is cleared from replicated DNA in vertebrate cells. PMID:21196493

IRON AND FREE RADICAL OXIDATIONS IN CELL MEMBRANES

PubMed Central

Schafer, Freya Q.; Yue Qian, Steven; Buettner, Garry R.

2013-01-01

Brain tissue being rich in polyunsaturated fatty acids, is very susceptible to lipid peroxidation. Iron is well known to be an important initiator of free radical oxidations. We propose that the principal route to iron-mediated lipid peroxidations is via iron-oxygen complexes rather than the reaction of iron with hydrogen peroxide, the Fenton reaction. To test this hypothesis, we enriched leukemia cells (K-562 and L1210 cells) with docosahexaenoic acid (DHA) as a model for brain tissue, increasing the amount of DHA from approximately 3 mole % to 32 mole %. These cells were then subjected to ferrous iron and dioxygen to initiate lipid peroxidation in the presence or absence of hydrogen peroxide. Lipid-derived radicals were detected using EPR spin trapping with α-(4-pyridyl-1-oxide)-N-t-butylnitrone (POBN). As expected, lipid-derived radical formation increases with increasing cellular lipid unsaturation. Experiments with Desferal demonstrate that iron is required for the formation of lipid radicals from these cells. Addition of iron to DHA-enriched L1210 cells resulted in significant amounts of radical formation; radical formation increased with increasing amount of iron. However, the exposure of cells to hydrogen peroxide before the addition of ferrous iron did not increase cellular radical formation, but actually decreased spin adduct formation. These data suggest that iron-oxygen complexes are the primary route to the initiation of biological free radical oxidations. This model proposes a mechanism to explain how catalytic iron in brain tissue can be so destructive. PMID:10872752

Origin Licensing Requires ATP Binding and Hydrolysis by the MCM Replicative Helicase

PubMed Central

Coster, Gideon; Frigola, Jordi; Beuron, Fabienne; Morris, Edward P.; Diffley, John F.X.

2014-01-01

Summary Loading of the six related Minichromosome Maintenance (MCM) proteins as head-to-head double hexamers during DNA replication origin licensing is crucial for ensuring once-per-cell-cycle DNA replication in eukaryotic cells. Assembly of these prereplicative complexes (pre-RCs) requires the Origin Recognition Complex (ORC), Cdc6, and Cdt1. ORC, Cdc6, and MCM are members of the AAA+ family of ATPases, and pre-RC assembly requires ATP hydrolysis. Here we show that ORC and Cdc6 mutants defective in ATP hydrolysis are competent for origin licensing. However, ATP hydrolysis by Cdc6 is required to release nonproductive licensing intermediates. We show that ATP binding stabilizes the wild-type MCM hexamer. Moreover, by analyzing MCM containing mutant subunits, we show that ATP binding and hydrolysis by MCM are required for Cdt1 release and double hexamer formation. This work alters our view of how ATP is used by licensing factors to assemble pre-RCs. PMID:25087873

Dynamic pre-BCR homodimers fine-tune autonomous survival signals in B cell precursor acute lymphoblastic leukemia

PubMed Central

Erasmus, M. Frank; Matlawska-Wasowska, Ksenia; Kinjyo, Ichiko; Mahajan, Avanika; Winter, Stuart S.; Xu, Li; Horowitz, Michael; Lidke, Diane S.; Wilson, Bridget S.

2017-01-01

The pre-B cell receptor (pre-BCR) is an immature form of the BCR critical for early B lymphocyte development. It is composed of the membrane-bound immunoglobulin (Ig) heavy chain, surrogate light chain components, and the signaling subunits Igα and Igβ. We developed monovalent Quantum Dot (QD)-labeled probes specific for Igβ to study the behavior of pre-BCRs engaged in autonomous, ligand-independent signaling in live B cells. Single-particle tracking revealed that QD-labeled pre-BCRs engaged in transient, but frequent, homotypic interactions. Receptor motion was correlated at short separation distances, consistent with the formation of dimers and higher-order oligomers. Repeated encounters between diffusing pre-BCRs appeared to reflect transient co-confinement in plasma membrane domains. In human B cell precursor acute lymphoblastic leukemia (BCP-ALL) cells, we showed that frequent, short-lived, homotypic pre-BCR interactions stimulated survival signals, including expression of BCL6, which encodes a transcriptional repressor. These survival signals were blocked by inhibitory monovalent antigen-binding antibody fragments (Fabs) specific for the surrogate light chain components of the pre-BCR or by inhibitors of the tyrosine kinases Lyn and Syk. For comparison, we evaluated pre-BCR aggregation mediated by dimeric galectin-1, which has binding sites for carbohydrate and for the λ5 component of the surrogate light chain. Galectin-1 binding resulted in the formation of large, highly immobile pre-BCR aggregates, which was partially relieved by the addition of lactose to prevent the crosslinking of galectin-BCR complexes to other glycosylated membrane components. Analysis of the pre-BCR and its signaling partners suggested that they could be potential targets for combination therapy in BCP-ALL. PMID:27899526

Biofilm formation, communication and interactions of leaching bacteria during colonization of pyrite and sulfur surfaces.

PubMed

Bellenberg, Sören; Díaz, Mauricio; Noël, Nanni; Sand, Wolfgang; Poetsch, Ansgar; Guiliani, Nicolas; Vera, Mario

2014-11-01

Bioleaching of metal sulfides is an interfacial process where biofilm formation is considered to be important in the initial steps of this process. Among the factors regulating biofilm formation, molecular cell-to-cell communication such as quorum sensing is involved. A functional LuxIR-type I quorum sensing system is present in Acidithiobacillus ferrooxidans. However, cell-to-cell communication among different species of acidophilic mineral-oxidizing bacteria has not been studied in detail. These aspects were the scope of this study with emphasis on the effects exerted by the external addition of mixtures of synthetic N-acyl-homoserine-lactones on pure and binary cultures. Results revealed that some mixtures had inhibitory effects on pyrite leaching. Some of them correlated with changes in biofilm formation patterns on pyrite coupons. We also provide evidence that A. thiooxidans and Acidiferrobacter spp. produce N-acyl-homoserine-lactones. In addition, the observation that A. thiooxidans cells attached more readily to pyrite pre-colonized by living iron-oxidizing acidophiles than to heat-inactivated or biofilm-free pyrite grains suggests that other interactions also occur. Our experiments show that pre-cultivation conditions influence A. ferrooxidans attachment to pre-colonized pyrite surfaces. The understanding of cell-to-cell communication may consequently be used to develop attempts to influence biomining/bioremediation processes. Copyright © 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Prereplicative complexes assembled in vitro support origin-dependent and independent DNA replication

PubMed Central

On, Kin Fan; Beuron, Fabienne; Frith, David; Snijders, Ambrosius P; Morris, Edward P; Diffley, John F X

2014-01-01

Eukaryotic DNA replication initiates from multiple replication origins. To ensure each origin fires just once per cell cycle, initiation is divided into two biochemically discrete steps: the Mcm2-7 helicase is first loaded into prereplicative complexes (pre-RCs) as an inactive double hexamer by the origin recognition complex (ORC), Cdt1 and Cdc6; the helicase is then activated by a set of “firing factors.” Here, we show that plasmids containing pre-RCs assembled with purified proteins support complete and semi-conservative replication in extracts from budding yeast cells overexpressing firing factors. Replication requires cyclin-dependent kinase (CDK) and Dbf4-dependent kinase (DDK). DDK phosphorylation of Mcm2-7 does not by itself promote separation of the double hexamer, but is required for the recruitment of firing factors and replisome components in the extract. Plasmid replication does not require a functional replication origin; however, in the presence of competitor DNA and limiting ORC concentrations, replication becomes origin-dependent in this system. These experiments indicate that Mcm2-7 double hexamers can be precursors of replication and provide insight into the nature of eukaryotic DNA replication origins. PMID:24566989

Using auditory pre-information to solve the cocktail-party problem: electrophysiological evidence for age-specific differences.

PubMed

Getzmann, Stephan; Lewald, Jörg; Falkenstein, Michael

2014-01-01

Speech understanding in complex and dynamic listening environments requires (a) auditory scene analysis, namely auditory object formation and segregation, and (b) allocation of the attentional focus to the talker of interest. There is evidence that pre-information is actively used to facilitate these two aspects of the so-called "cocktail-party" problem. Here, a simulated multi-talker scenario was combined with electroencephalography to study scene analysis and allocation of attention in young and middle-aged adults. Sequences of short words (combinations of brief company names and stock-price values) from four talkers at different locations were simultaneously presented, and the detection of target names and the discrimination between critical target values were assessed. Immediately prior to speech sequences, auditory pre-information was provided via cues that either prepared auditory scene analysis or attentional focusing, or non-specific pre-information was given. While performance was generally better in younger than older participants, both age groups benefited from auditory pre-information. The analysis of the cue-related event-related potentials revealed age-specific differences in the use of pre-cues: Younger adults showed a pronounced N2 component, suggesting early inhibition of concurrent speech stimuli; older adults exhibited a stronger late P3 component, suggesting increased resource allocation to process the pre-information. In sum, the results argue for an age-specific utilization of auditory pre-information to improve listening in complex dynamic auditory environments.

Using auditory pre-information to solve the cocktail-party problem: electrophysiological evidence for age-specific differences

PubMed Central

Getzmann, Stephan; Lewald, Jörg; Falkenstein, Michael

2014-01-01

Speech understanding in complex and dynamic listening environments requires (a) auditory scene analysis, namely auditory object formation and segregation, and (b) allocation of the attentional focus to the talker of interest. There is evidence that pre-information is actively used to facilitate these two aspects of the so-called “cocktail-party” problem. Here, a simulated multi-talker scenario was combined with electroencephalography to study scene analysis and allocation of attention in young and middle-aged adults. Sequences of short words (combinations of brief company names and stock-price values) from four talkers at different locations were simultaneously presented, and the detection of target names and the discrimination between critical target values were assessed. Immediately prior to speech sequences, auditory pre-information was provided via cues that either prepared auditory scene analysis or attentional focusing, or non-specific pre-information was given. While performance was generally better in younger than older participants, both age groups benefited from auditory pre-information. The analysis of the cue-related event-related potentials revealed age-specific differences in the use of pre-cues: Younger adults showed a pronounced N2 component, suggesting early inhibition of concurrent speech stimuli; older adults exhibited a stronger late P3 component, suggesting increased resource allocation to process the pre-information. In sum, the results argue for an age-specific utilization of auditory pre-information to improve listening in complex dynamic auditory environments. PMID:25540608

The Biophysics Microgravity Initiative

NASA Technical Reports Server (NTRS)

Gorti, S.

2016-01-01

Biophysical microgravity research on the International Space Station using biological materials has been ongoing for several decades. The well-documented substantive effects of long duration microgravity include the facilitation of the assembly of biological macromolecules into large structures, e.g., formation of large protein crystals under micro-gravity. NASA is invested not only in understanding the possible physical mechanisms of crystal growth, but also promoting two flight investigations to determine the influence of µ-gravity on protein crystal quality. In addition to crystal growth, flight investigations to determine the effects of shear on nucleation and subsequent formation of complex structures (e.g., crystals, fibrils, etc.) are also supported. It is now considered that long duration microgravity research aboard the ISS could also make possible the formation of large complex biological and biomimetic materials. Investigations of various materials undergoing complex structure formation in microgravity will not only strengthen NASA science programs, but may also provide invaluable insight towards the construction of large complex tissues, organs, or biomimetic materials on Earth.

A combination SMS and transportation reimbursement intervention to improve HIV care following abnormal CD4 test results in rural Uganda: a prospective observational cohort study.

PubMed

Siedner, Mark J; Santorino, Data; Lankowski, Alexander J; Kanyesigye, Michael; Bwana, Mwebesa B; Haberer, Jessica E; Bangsberg, David R

2015-07-06

Up to 50 % of HIV-infected persons in sub-Saharan Africa are lost from care between HIV diagnosis and antiretroviral therapy (ART) initiation. Structural barriers, including cost of transportation to clinic and poor communication systems, are major contributors. We conducted a prospective, pragmatic, before-and-after clinical trial to evaluate a combination mobile health and transportation reimbursement intervention to improve care at a publicly operated HIV clinic in Uganda. Patients undergoing CD4 count testing were enrolled, and clinicians selected a result threshold that would prompt early return for ART initiation or further care. Participants enrolled in the pre-intervention period (January - August 2012) served as a control group. Participants in the intervention period (September 2012 - November 2013) were randomized to receive daily short message service (SMS) messages for up to seven days in one of three formats: 1) messages reporting an abnormal result directly, 2) personal identification number-protected messages reporting an abnormal result, or 3) messages reading "ABCDEFG" to confidentially convey an abnormal result. Participants returning within seven days of their first message received transportation reimbursements (about $6USD). Our primary outcomes of interest were time to return to clinic and time to ART initiation. There were 45 participants in the pre-intervention period and 138 participants in the intervention period (46, 49, and 43 in the direct, PIN, and coded groups, respectively) with low CD4 count results. Median time to clinic return was 33 days (IQR 11-49) in the pre-intervention period and 6 days (IQR 3-16) in the intervention period (P < 0.001); and median time to ART initiation was 47 days (IQR 11-75) versus 12 days (IQR 5-19), (P < 0.001). In multivariable models, participants in the intervention period had earlier return to clinic (AHR 2.32, 95 %CI 1.53 to 3.51) and earlier time to ART initiation (AHR 2.27, 95 %CI 1.38 to 3.72). All three randomized message formats improved time to return to clinic and time to ART initiation (P < 0.01 for all comparisons versus the pre-intervention period). A combination of an SMS laboratory result communication system and transportation reimbursements significantly decreased time to clinic return and time to ART initiation after abnormal CD4 test results. Clinicaltrials.gov NCT01579214 , approved 13 April 2012.

Initiation of and distributed deformation at and around stylolite interfaces: Insights from detailed microstructural analysis

NASA Astrophysics Data System (ADS)

Ebner, M.; Piazolo, S.; Koehn, D.

2009-04-01

In the present contribution we investigate the microstructure of bedding parallel and bedding normal stylolites in carbonate rocks. We focused our study on micro-stylolites which represent an initial stage of this localised pressure solution process as stylolite roughness amplitude is a function of strain. We use electron backscatter diffraction analysis (EBSD) and orientation contrast imaging to address the following issues: (i) What causes the initiation of stylolite interfaces at a submicroscopic scale, (ii) is there distributed deformation around the stylolite interface and (iii) what is the role of the interface (residuum)? Our findings demonstrate that the characteristic stylolite teeth are initiated at a pre-existing heterogeneity in the host-rock. This quenched noise in carbonate rocks is typically composed of clay particles in the submicron scale. In addition, qtz-grains are present along especially pronounced stylolite peaks. The stylolite interface evolves with increasing strain from individual clay particles separated by grain-grain contacts of calcite along the interface to a continuous layer of clay and oxides. Thickness variation of the residuum along the interface is inferred to be strongly influenced by the pre-existing distribution of pinning particles that are more resistant to dissolution. Another important observation is that a shaped preferred orientation (SPO) exists in a halo around the stylolite. This SPO increases with proximity to the stylolite interface. Within this halo, crystal plastic deformation is expressed by subgrain formation with subgrain boundaries usually aligned parallel to shortening direction. Bedding normal (tectonic) stylolites which overprint already compacted beds i.e. with a pre-existing sedimentary SPO parallel to the bedding plane exhibit a SPO at a high angle to the sedimentary SPO. We conclude that stylolite roughness is primarily caused by pre-existing heterogeneities in the host-rock which are more resistant to dissolution e.g. clay particles and/or qtz grains. Secondly, we demonstrate that stylolite formation is not a process that is restricted to the stylolite interface itself but a process that is active in a broader zone around the actual interface.

Conformational heterogeneity and bubble dynamics in single bacterial transcription initiation complexes

PubMed Central

Duchi, Diego; Gryte, Kristofer; Robb, Nicole C; Morichaud, Zakia; Sheppard, Carol; Wigneshweraraj, Sivaramesh

2018-01-01

Abstract Transcription initiation is a major step in gene regulation for all organisms. In bacteria, the promoter DNA is first recognized by RNA polymerase (RNAP) to yield an initial closed complex. This complex subsequently undergoes conformational changes resulting in DNA strand separation to form a transcription bubble and an RNAP-promoter open complex; however, the series and sequence of conformational changes, and the factors that influence them are unclear. To address the conformational landscape and transitions in transcription initiation, we applied single-molecule Förster resonance energy transfer (smFRET) on immobilized Escherichia coli transcription open complexes. Our results revealed the existence of two stable states within RNAP–DNA complexes in which the promoter DNA appears to adopt closed and partially open conformations, and we observed large-scale transitions in which the transcription bubble fluctuated between open and closed states; these transitions, which occur roughly on the 0.1 s timescale, are distinct from the millisecond-timescale dynamics previously observed within diffusing open complexes. Mutational studies indicated that the σ70 region 3.2 of the RNAP significantly affected the bubble dynamics. Our results have implications for many steps of transcription initiation, and support a bend-load-open model for the sequence of transitions leading to bubble opening during open complex formation. PMID:29177430

The Impact of Adaptive Complex Assessment on the HOT Skill Development of Students

ERIC Educational Resources Information Center

Raiyn, Jamal; Tilchin, Oleg

2016-01-01

In this paper we propose a method for the adaptive complex assessment (ACA) of the higher-order thinking (HOT) skills needed by students for problem solving, and we examine the impact of the method on the development of HOT skills in a problem-based learning (PBL) environment. Complexity in the assessment is provided by initial, formative, and…

Multifaceted regulation of V(D)J recombination

NASA Astrophysics Data System (ADS)

Wang, Guannan

V(D)J recombination is responsible for generating an enormous repertoire of immunoglobulins and T cell receptors, therefore it is a centerpiece to the formation of the adaptive immune system. The V(D)J recombination process proceeds through two steps, site-specific cleavage at RSS (Recombination Signal Sequence) site mediated by the RAG recombinase (RAG1/2) and the subsequent imprecise resolution of the DNA ends, which is carried out by the ubiquitous non-homologous end joining pathway (NHEJ). The V(D)J recombination reaction is obliged to be tightly controlled under all circumstances, as it involves generations of DNA double strand breaks, which are considered the most dangerous lesion to a cell. Multifaceted regulatory mechanisms have been evolved to create great diversity of the antigen receptor repertoire while ensuring genome stability. The RAG-mediated cleavage reaction is stringently regulated at both the pre-cleavage stage and the post-cleavage stage. Specifically, RAG1/2 first forms a pre-cleavage complex assembled at the boarder of RSS and coding flank, which ensures the appropriate DNA targeting. Subsequently, this complex initiates site-specific cleavage, generating two types of double stranded DNA breaks, hairpin-ended coding ends (HP-CEs) and blunt signal ends (SEs). After the cleavage, RAG1/2 proteins bind and retain the recombination ends to form post-cleavage complexes (PCC), which collaborates with the NHEJ machinery for appropriate transfer of recombination ends to NHEJ for proper end resolution. However, little is known about the molecular basis of this collaboration, partly attributed to the lack of sensitive assays to reveal the interaction of PCC with HP-CEs. Here, for the first time, by using two complementary fluorescence-based techniques, fluorescence anisotropy and fluorescence resonance energy transfer (FRET), I managed to monitor the RAG1/2-catalyzed cleavage reaction in real time, from the pre-cleavage to the post-cleavage stages. By examining the dynamic fluorescence changes during the RAG-mediated cleavage reactions, and by manipulating the reaction conditions, I was able to characterize some fundamental properties of RAG-DNA interactions before and after cleavage. Firstly, Mg 2+, known as a physiological cofactor at the excision step, also promotes the HP-CEs retention in the RAG complex after cleavage. Secondly, the structure of pre-cleavage complex may affect the subsequent collaborations with NHEJ for end resolution. Thirdly, the non-core region of RAG2 may have differential influences on the PCC retention of HP-CEs and SEs. Furthermore, I also provide the first evidence of RAG1-mediated regulation of RAG2. Our study provides important insights into the multilayered regulatory mechanisms, in modulating recombination events in developing lymphocytes and paves the way for possible development of detection and diagnotic markers for defective recombination events that are often associated immunodeficiency and/or lymphoid malignancy.

Reconstructing the eruption magnitude and energy budgets for the pre-historic eruption of the monogenetic ˜5 ka Mt. Gambier Volcanic Complex, south-eastern Australia

NASA Astrophysics Data System (ADS)

van Otterloo, Jozua; Cas, Raymond A. F.

2013-12-01

Understanding explosive volcanic eruptions, especially phreatomagmatic eruptions, their intensities and energy budgets is of major importance when it comes to risk and hazard studies. With only a few historic occurrences of phreatomagmatic activity, a large amount of our understanding comes from the study of pre-historic volcanic centres, which causes issues when it comes to preservation and vegetation. In this research, we show that using 3D geometrical modelling it is possible to obtain volume estimates for different deposits of a pre-historic, complex, monogenetic centre, the Mt. Gambier Volcanic Complex, south-eastern Australia. Using these volumes, we further explore the energy budgets and the magnitude of this eruption (VEI 4), including dispersal patterns (eruption columns varying between 5 and 10 km, dispersed towards north-east to south), to further our understanding of intraplate, monogenetic eruptions involving phreatomagmatic activity. We also compare which thermodynamic model fits best in the creation of the maar crater of Mt. Gambier: the major-explosion-dominated model or the incremental growth model. In this case, the formation of most of the craters can best be explained by the latter model.

Symportin 1 chaperones 5S RNP assembly during ribosome biogenesis by occupying an essential rRNA-binding site

PubMed Central

Calviño, Fabiola R.; Kharde, Satyavati; Ori, Alessandro; Hendricks, Astrid; Wild, Klemens; Kressler, Dieter; Bange, Gert; Hurt, Ed; Beck, Martin; Sinning, Irmgard

2015-01-01

During 60S biogenesis, mature 5S RNP consisting of 5S RNA, RpL5 and RpL11, assembles into a pre-60S particle, where docking relies on RpL11 interacting with helix 84 (H84) of the 25S RNA. How 5S RNP is assembled for recruitment into the pre-60S is not known. Here we report the crystal structure of a ternary symportin Syo1–RpL5-N–RpL11 complex and provide biochemical and structural insights into 5S RNP assembly. Syo1 guards the 25S RNA-binding surface on RpL11 and competes with H84 for binding. Pull-down experiments show that H84 releases RpL11 from the ternary complex, but not in the presence of 5S RNA. Crosslinking mass spectrometry visualizes structural rearrangements on incorporation of 5S RNA into the Syo1–RpL5–RpL11 complex supporting the formation of a pre-5S RNP. Our data underline the dual role of Syo1 in ribosomal protein transport and as an assembly platform for 5S RNP. PMID:25849277

Symportin 1 chaperones 5S RNP assembly during ribosome biogenesis by occupying an essential rRNA-binding site.

PubMed

Calviño, Fabiola R; Kharde, Satyavati; Ori, Alessandro; Hendricks, Astrid; Wild, Klemens; Kressler, Dieter; Bange, Gert; Hurt, Ed; Beck, Martin; Sinning, Irmgard

2015-04-07

During 60S biogenesis, mature 5S RNP consisting of 5S RNA, RpL5 and RpL11, assembles into a pre-60S particle, where docking relies on RpL11 interacting with helix 84 (H84) of the 25S RNA. How 5S RNP is assembled for recruitment into the pre-60S is not known. Here we report the crystal structure of a ternary symportin Syo1-RpL5-N-RpL11 complex and provide biochemical and structural insights into 5S RNP assembly. Syo1 guards the 25S RNA-binding surface on RpL11 and competes with H84 for binding. Pull-down experiments show that H84 releases RpL11 from the ternary complex, but not in the presence of 5S RNA. Crosslinking mass spectrometry visualizes structural rearrangements on incorporation of 5S RNA into the Syo1-RpL5-RpL11 complex supporting the formation of a pre-5S RNP. Our data underline the dual role of Syo1 in ribosomal protein transport and as an assembly platform for 5S RNP.

Terabit bandwidth-adaptive transmission using low-complexity format-transparent digital signal processing.

PubMed

Zhuge, Qunbi; Morsy-Osman, Mohamed; Chagnon, Mathieu; Xu, Xian; Qiu, Meng; Plant, David V

2014-02-10

In this paper, we propose a low-complexity format-transparent digital signal processing (DSP) scheme for next generation flexible and energy-efficient transceiver. It employs QPSK symbols as the training and pilot symbols for the initialization and tracking stage of the receiver-side DSP, respectively, for various modulation formats. The performance is numerically and experimentally evaluated in a dual polarization (DP) 11 Gbaud 64QAM system. Employing the proposed DSP scheme, we conduct a system-level study of Tb/s bandwidth-adaptive superchannel transmissions with flexible modulation formats including QPSK, 8QAM and 16QAM. The spectrum bandwidth allocation is realized in the digital domain instead of turning on/off sub-channels, which improves the performance of higher order QAM. Various transmission distances ranging from 240 km to 6240 km are demonstrated with a colorless detection for hardware complexity reduction.

The role of a combined coagulation and disk filtration process as a pre-treatment to microfiltration and reverse osmosis membranes in a municipal wastewater pilot plant.

PubMed

Chon, Kangmin; Cho, Jaeweon; Kim, Seung Joon; Jang, Am

2014-12-01

A pilot study was conducted to assess the performance of a municipal wastewater reclamation plant consisting of a combined coagulation-disk filtration (CC-DF) process, microfiltration (MF) and reverse osmosis (RO) membranes, in terms of the removal of water contaminants and changes in characteristics of effluent organic matter (EfOM). The CC-DF and MF membranes were not effective for the removal of dissolved water contaminants. However, they could partially reduce the turbidity associated with the cake layer formation by particulate materials on the membrane surfaces. Furthermore, most of water contaminants were completely removed by the RO membranes. Although the CC-DF process could remove approximately 20% of turbidity, the aluminium concentrations considerably increased after the CC-DF process due to the residual coagulants complexed with both carboxylic acid and alcohol functional groups of EfOM. Those aluminium-EfOM complexes had a lower negative charge and higher molecular weight (>0.1 μm pore size of the MF membranes) compared to non-complexed EfOM. These results indicate that the control of the formation of the aluminium-EfOM complexes should be considered as a key step to use the CC-DF process as a pre-treatment of the MF and RO membranes for mitigation of membrane fouling in the tested pilot plant. Copyright © 2014 Elsevier Ltd. All rights reserved.

Ab initio calculations of supramolecular complexes of fullerene C60 with CdTe and CdS

NASA Astrophysics Data System (ADS)

Kvyatkovskii, O. E.; Zakharova, I. B.; Ziminov, V. M.

2014-06-01

This paper presents the results of ab initio quantum-chemical calculations of supramolecular complexes C60CdHal, [C60]4CdHal, and [C60]6CdHal (Hal = S, Te), which simulate the defects forming in fullerite during the absorption or adsorption of cadmium telluride (sulfide). Calculations of the electronic structure of complexes with inclusion of their relaxation to the equilibrium state have been performed in terms of the density functional theory with the B3LYP hybrid functional. The obtained enthalpies of formation of complexes show that their formation leads to the energy gain of the order of 0.5-1.5 eV depending on the complex type. It has been shown that the formation of tetrahedral complexes [C60]4CdTe with the intercalated CdTe molecule is possible only with a considerable distortion of the tetrahedral void. The energy spectrum of low-lying excited electron states for the linear and octahedral complexes has been calculated. It has been found that a decrease in symmetry with the formation of complexes leads to the appearance of excited states of allowed singlet transitions in the electron spectrum, which are forbidden in optical spectra of initial components.

NMR spectroscopy and X-ray characterisation of cationic N-heteroaryl-pyridylamido Zr(IV) complexes: a further level of complexity for the elusive active species of pyridylamido olefin polymerisation catalysts.

PubMed

Li, Gang; Zuccaccia, Cristiano; Tedesco, Consiglia; D'Auria, Ilaria; Macchioni, Alceo; Pellecchia, Claudio

2014-01-03

New [(N(-),N,N(-))ZrR2] dialkyl complexes (N(-),N,N(-)=pyrrolyl-pyridyl-amido or indolyl-pyridyl-amido; R=Me or CH2Ph) have been synthesised and tested as pre-catalysts for ethene and propene polymerisation in combination with different activators, such as B(C6F5)3, [Ph3C][B(C6F5)4], [HNMe2Ph][B(C6F5)4] or solid AlMe3-depleted methylaluminoxane (DMAO). Polyethylene (M(w)>2 MDa and M(w)/M(n)= 1.3-1.6) has been produced if pre-catalysts were activated with 1000 equivalents of DMAO (based on Al) [activity >1000 kg(PE)(mol([Zr]) h mol atm)(-1)] or by using a higher pre-catalyst concentration and a mixture of [HNPhMe2][B(C6F5)4] (1 equiv) and AliBu2H (60 equiv). In the case of propene polymerisation, activity has been observed only if pre-catalysts were treated with an excess of AliBu2H prior to addition of DMAO, which led to highly isotactic polypropylene ([mmmm]>95%). Neutral pre-catalysts and ion pairs derived from their activation have been characterised in solution by using advanced 1D and 2D NMR spectroscopy experiments. The detection and rationalisation of intercationic NOEs clearly showed the formation of dimeric species in which some pyrrolyl or indolyl π-electron density of one unit is engaged in stabilising the metal centre of the other unit, which relegates the counterions in the second coordination sphere. The solid-state structure of the dimeric indolyl-pyridyl-amidomethylzirconium derivative, determined by X-ray diffraction studies, points toward a weak Zr···η(3)-indolyl interaction. It can be hypothesised that the formation of dimeric cationic species hampers monomer coordination (especially of less reactive α-olefins) and that addition of AliBu2H is crucial to split the homodimers. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Investigation of IGES for CAD/CAE data transfer

NASA Technical Reports Server (NTRS)

Zobrist, George W.

1989-01-01

In a CAD/CAE facility there is always the possibility that one may want to transfer the design graphics database from the native system to a non-native system. This may occur because of dissimilar systems within an organization or a new CAD/CAE system is to be purchased. The Initial Graphics Exchange Specification (IGES) was developed in an attempt to solve this scenario. IGES is a neutral database format into which the CAD/CAE native database format can be translated to and from. Translating the native design database format to IGES requires a pre-processor and transling from IGES to the native database format requires a post-processor. IGES is an artifice to represent CAD/CAE product data in a neutral environment to allow interfacing applications, archive the database, interchange of product data between dissimilar CAD/CAE systems, and other applications. The intent here is to present test data on translating design product data from a CAD/CAE system to itself and to translate data initially prepared in IGES format to various native design formats. This information can be utilized in planning potential procurement and developing a design discipline within the CAD/CAE community.

Role of IκB kinase β in regulating the remodeling of the CARMA1-Bcl10-MALT1 complex.

PubMed

Karim, Zubair A; Hensch, Nicole R; Qasim, Hanan; Alshbool, Fatima Z; Khasawneh, Fadi T

2018-06-02

The current work investigates the notion that inducible clustering of signaling mediators of the IKK pathway is important for platelet activation. Thus, while the CARMA1, Bcl10, and MALT1 (CBM) complex is essential for triggering IKK/NF-κB activation upon platelet stimulation, the signals that elicit its formation and downstream effector activation remain elusive. We demonstrate herein that IKKβ is involved in membrane fusion, and serves as a critical protein kinase required for initial formation and the regulation of the CARMA1/MALT1/Bcl10/CBM complex in platelets. We also show that IKKβ regulates these processes via modulation of phosphorylation of Bcl10 and IKKγ polyubiquitination. Collectively, our data demonstrate that IKKβ regulates membrane fusion and the remodeling of the CBM complex formation. Copyright © 2018 Elsevier Inc. All rights reserved.

Viewing pre-60S maturation at a minute’s timescale

PubMed Central

Zisser, Gertrude; Ohmayer, Uli; Mauerhofer, Christina; Mitterer, Valentin; Klein, Isabella; Rechberger, Gerald N; Wolinski, Heimo; Prattes, Michael; Pertschy, Brigitte; Milkereit, Philipp

2018-01-01

Abstract The formation of ribosomal subunits is a highly dynamic process that is initiated in the nucleus and involves more than 200 trans-acting factors, some of which accompany the pre-ribosomes into the cytoplasm and have to be recycled into the nucleus. The inhibitor diazaborine prevents cytoplasmic release and recycling of shuttling pre-60S maturation factors by inhibiting the AAA-ATPase Drg1. The failure to recycle these proteins results in their depletion in the nucleolus and halts the pathway at an early maturation step. Here, we made use of the fast onset of inhibition by diazaborine to chase the maturation path in real-time from 27SA2 pre-rRNA containing pre-ribosomes localized in the nucleolus up to nearly mature 60S subunits shortly after their export into the cytoplasm. This allows for the first time to put protein assembly and disassembly reactions as well as pre-rRNA processing into a chronological context unraveling temporal and functional linkages during ribosome maturation. PMID:29294095

Formation, Detection and the Distribution of Complex Organic Molecules with the Atacama Large Millimeter/submillimeter Array (ALMA)

NASA Astrophysics Data System (ADS)

Remijan, Anthony John

2015-08-01

The formation and distribution of complex organic material in astronomical environments continues to be a focused research area in astrochemistry. For several decades now, emphasis has been placed on the millimeter/submillimeter regime of the radio spectrum for trying to detect new molecular species and to constrain the chemical formation route of complex molecules by comparing and contrasting their relative distributions towards varying astronomical environments. This effort has been extremely laborious as millimeter/submillimeter facilities have been only able to detect and map the distribution of the strongest transition(s) of the simplest organic molecules. Even then, these single transition "chemical maps" have been very low spatial resolution because early millimeter/submillimeter facilities did not have access to broadband spectral coverage or the imaging capabilities to truly ascertain the morphology of the molecular emission. In the era of ALMA, these limitations have been greatly lifted. Broadband spectral line surveys now hold the key to uncovering the full molecular complexity in astronomical environments. In addition, searches for complex organic material is no longer limited to investigating the strongest lines of the simplest molecules toward the strongest sources of emission in the Galaxy. ALMA is issuing a new era of exploration as the search for complex molecules will now be available to an increased suite of sources in the Galaxy and our understanding of the formation of this complex material will be greatly increased as a result. This presentation will highlight the current and future ALMA capabilities in the search for complex molecules towards astronomical environments, highlight the recent searches that ALMA scientists have conducted from the start of ALMA Early Science and provide the motivation for the next suite of astronomical searches to investigate our pre-biotic origins in the universe.

Joint explorative analysis of neuroreceptor subsystems in the human brain: application to receptor-transporter correlation using PET data.

PubMed

Cselényi, Zsolt; Lundberg, Johan; Halldin, Christer; Farde, Lars; Gulyás, Balázs

2004-10-01

Positron emission tomography (PET) has proved to be a highly successful technique in the qualitative and quantitative exploration of the human brain's neurotransmitter-receptor systems. In recent years, the number of PET radioligands, targeted to different neuroreceptor systems of the human brain, has increased considerably. This development paves the way for a simultaneous analysis of different receptor systems and subsystems in the same individual. The detailed exploration of the versatility of neuroreceptor systems requires novel technical approaches, capable of operating on huge parametric image datasets. An initial step of such explorative data processing and analysis should be the development of novel exploratory data-mining tools to gain insight into the "structure" of complex multi-individual, multi-receptor data sets. For practical reasons, a possible and feasible starting point of multi-receptor research can be the analysis of the pre- and post-synaptic binding sites of the same neurotransmitter. In the present study, we propose an unsupervised, unbiased data-mining tool for this task and demonstrate its usefulness by using quantitative receptor maps, obtained with positron emission tomography, from five healthy subjects on (pre-synaptic) serotonin transporters (5-HTT or SERT) and (post-synaptic) 5-HT(1A) receptors. Major components of the proposed technique include the projection of the input receptor maps to a feature space, the quasi-clustering and classification of projected data (neighbourhood formation), trans-individual analysis of neighbourhood properties (trajectory analysis), and the back-projection of the results of trajectory analysis to normal space (creation of multi-receptor maps). The resulting multi-receptor maps suggest that complex relationships and tendencies in the relationship between pre- and post-synaptic transporter-receptor systems can be revealed and classified by using this method. As an example, we demonstrate the regional correlation of the serotonin transporter-receptor systems. These parameter-specific multi-receptor maps can usefully guide the researchers in their endeavour to formulate models of multi-receptor interactions and changes in the human brain.

General Relativistic MHD Simulations of Jet Formation

NASA Technical Reports Server (NTRS)

Mizuno, Y.; Nishikawa, K.-I.; Hardee, P.; Koide, S.; Fishman, G. J.

2005-01-01

We have performed 3-dimensional general relativistic magnetohydrodynamic (GRMHD) simulations of jet formation from an accretion disk with/without initial perturbation around a rotating black hole. We input a sinusoidal perturbation (m = 5 mode) in the rotation velocity of the accretion disk. The simulation results show the formation of a relativistic jet from the accretion disk. Although the initial perturbation becomes weakened by the coupling among different modes, it survives and triggers lower modes. As a result, complex non-axisymmetric density structure develops in the disk and the jet. Newtonian MHD simulations of jet formation with a non-axisymmetric mode show the growth of the m = 2 mode but GRMHD simulations cannot see the clear growth of the m = 2 mode.

The mediator complex in genomic and non-genomic signaling in cancer.

PubMed

Weber, Hannah; Garabedian, Michael J

2018-05-01

Mediator is a conserved, multi-subunit macromolecular machine divided structurally into head, middle, and tail modules, along with a transiently associating kinase module. Mediator functions as an integrator of transcriptional regulatory activity by interacting with DNA-bound transcription factors and with RNA polymerase II (Pol II) to both activate and repress gene expression. Mediator has been shown to affect multiple steps in transcription, including chromatin looping between enhancers and promoters, pre-initiation complex formation, transcriptional elongation, and mRNA splicing. Individual Mediator subunits participate in regulation of gene expression by the estrogen and androgen receptors and are altered in a number of endocrine cancers, including breast and prostate cancer. In addition to its role in genomic signaling, MED12 has been implicated in non-genomic signaling by interacting with and activating TGF-beta receptor 2 in the cytoplasm. Recent structural studies have revealed extensive inter-domain interactions and complex architecture of the Mediator-Pol II complex, suggesting that Mediator is capable of reorganizing its conformation and composition to fit cellular needs. We propose that alterations in Mediator subunit expression that occur in various cancers could impact the organization and function of Mediator, resulting in changes in gene expression that promote malignancy. A better understanding of the role of Mediator in cancer could reveal new approaches to the diagnosis and treatment of Mediator-dependent endocrine cancers, especially in settings of therapy resistance. Copyright © 2017 Elsevier Inc. All rights reserved.

IODP Expedition 351 Izu-Bonin-Mariana Arc Origins: Preliminary Results

NASA Astrophysics Data System (ADS)

Ishizuka, O.; Arculus, R. J.; Bogus, K.

2014-12-01

Understanding how subduction zones initiate and continental crust forms in intraoceanic arcs requires knowledge of the inception and evolution of a representative intraoceanic arc, such as the Izu-Bonin-Mariana (IBM) Arc system. This can be obtained by exploring regions adjacent to an arc, where unequivocal pre-arc crust overlain by undisturbed arc-derived materials exists. IODP Exp. 351 (June-July 2014) specifically targeted evidence for the earliest evolution of the IBM system following inception. Site U1438 (4711 m water depth) is located in the Amami Sankaku Basin (ASB), west of the Kyushu-Palau Ridge (KPR), a paleo-IBM arc. Primary objectives of Exp. 351 were: 1) determine the nature of the crust and mantle pre-existing the IBM arc; 2) identify and model the process of subduction initiation and initial arc crust formation; 3) determine the compositional evolution of the IBM arc during the Paleogene; 4) establish geophysical properties of the ASB. Seismic reflection profiles indicate a ~1.3 km thick sediment layer overlying ~5.5 km thick igneous crust, presumed to be oceanic. This igneous crust seemed likely to be the basement of the IBM arc. Four holes were cored at Site U1438 spanning the entire sediment section and into basement. The cored interval comprises 5 units: uppermost Unit I is hemipelagic sediment with intercalated ash layers, presumably recording explosive volcanism mainly from the Ryukyu and Kyushu arcs; Units II and III host a series of volcaniclastic gravity-flow deposits, likely recording the magmatic history of the IBM Arc from arc initiation until 25 Ma; Siliceous pelagic sediment (Unit IV) underlies these deposits with minimal coarse-grained sediment input and may pre-date arc initiation. Sediment-basement contact occurs at 1461 mbsf. A basaltic lava flow section dominantly composed of plagioclase and clinopyroxene with rare chilled margins continues to the bottom of the Site (1611 mbsf). The expedition successfully recovered pre-IBM Arc basement, a volcanic and geologic record spanning pre-Arc, Arc initiation to remnant Arc stages, which permits testing for subduction initiation and subsequent Arc evolution.

Molecular requirements for RNA-induced silencing complex assembly in the Drosophila RNA interference pathway.

PubMed

Pham, John W; Sontheimer, Erik J

2005-11-25

Complexes in the Drosophila RNA-induced silencing complex (RISC) assembly pathway can be resolved using native gel electrophoresis, revealing an initiator called R1, an intermediate called R2, and an effector called R3 (now referred to as holo-RISC). Here we show that R1 forms when the Dicer-2/R2D2 heterodimer binds short interfering RNA (siRNA) duplexes. The heterodimer alone can initiate RISC assembly, indicating that other factors are dispensable for initiation. During assembly, R2 requires Argonaute 2 to convert into holo-RISC. This requirement is reminiscent of the RISC-loading complex, which also requires Argonaute 2 for assembly into RISC. We have compared R2 to the RISC-loading complex and show that the two complexes are similar in their sensitivities to ATP and to chemical modifications on siRNA duplexes, indicating that they are likely to be identical. We have examined the requirements for RISC formation and show that the siRNA 5'-termini are repeatedly monitored during RISC assembly, first by the Dcr-2/R2D2 heterodimer and again after R2 formation, before siRNA unwinding. The 2'-position of the 5'-terminal nucleotide also affects RISC assembly, because an siRNA strand bearing a 2'-deoxyribose at this position can inhibit the cognate strand from entering holo-RISC; in contrast, the 2'-deoxyribose-modified strand has enhanced activity in the RNA interference pathway.

Stability, chromatin association and functional activity of mammalian pre-replication complex proteins during the cell cycle

PubMed Central

Okuno, Yukiko; McNairn, Adrian J.; den Elzen, Nicole; Pines, Jonathon; Gilbert, David M.

2001-01-01

We have examined the behavior of pre-replication complex (pre-RC) proteins in relation to key cell cycle transitions in Chinese Hamster Ovary (CHO) cells. ORC1, ORC4 and Cdc6 were stable (T1/2 >2 h) and associated with a chromatin-containing fraction throughout the cell cycle. Green fluorescent protein-tagged ORC1 associated with chromatin throughout mitosis in living cells and co-localized with ORC4 in metaphase spreads. Association of Mcm proteins with chromatin took place during telophase, ∼30 min after the destruction of geminin and cyclins A and B, and was coincident with the licensing of chromatin to replicate in geminin-supplemented Xenopus egg extracts. Neither Mcm recruitment nor licensing required protein synthesis throughout mitosis. Moreover, licensing could be uncoupled from origin specification in geminin-supplemented extracts; site-specific initiation within the dihydrofolate reductase locus required nuclei from cells that had passed through the origin decision point (ODP). These results demonstrate that mammalian pre-RC assembly takes place during telophase, mediated by post-translational modifications of pre-existing proteins, and is not sufficient to select specific origin sites. A subsequent, as yet undefined, step selects which pre-RCs will function as replication origins. PMID:11483529

Introducing and Integrating Gifted Education into an Existing Independent School: An Analysis of Practice

ERIC Educational Resources Information Center

McKibben, Stephen

2013-01-01

In this analysis of practice, I conduct a combination formative and summative program evaluation of an initiative introduced to serve gifted learners at The Ocean School (TOS), an independent, Pre-K-grade 8 day school located in a rural area of the West Coast. Using the best practices as articulated by the National Association of Gifted Children…

Deformation-Induced Microstructural Banding in TRIP Steels

NASA Astrophysics Data System (ADS)

Celotto, S.; Ghadbeigi, H.; Pinna, C.; Shollock, B. A.; Efthymiadis, P.

2018-05-01

Microstructure inhomogeneities can strongly influence the mechanical properties of advanced high-strength steels in a detrimental manner. This study of a transformation-induced plasticity (TRIP) steel investigates the effect of pre-existing contiguous grain boundary networks (CGBNs) of hard second-phases and shows how these develop into bands during tensile testing using in situ observations in conjunction with digital image correlation (DIC). The bands form by the lateral contraction of the soft ferrite matrix, which rotates and displaces the CGBNs of second-phases and the individual features within them to become aligned with the loading direction. The more extensive pre-existing CGBNs that were before the deformation already aligned with the loading direction are the most critical microstructural feature for damage initiation and propagation. They induce micro-void formation between the hard second-phases along them, which coalesce and develop into long macroscopic fissures. The hard phases, retained austenite and martensite, were not differentiated as it was found that the individual phases do not play a role in the formation of these bands. It is suggested that minimizing the presence of CGBNs of hard second-phases in the initial microstructure will increase the formability.

Deformation-Induced Microstructural Banding in TRIP Steels

NASA Astrophysics Data System (ADS)

Celotto, S.; Ghadbeigi, H.; Pinna, C.; Shollock, B. A.; Efthymiadis, P.

2018-07-01

Microstructure inhomogeneities can strongly influence the mechanical properties of advanced high-strength steels in a detrimental manner. This study of a transformation-induced plasticity (TRIP) steel investigates the effect of pre-existing contiguous grain boundary networks (CGBNs) of hard second-phases and shows how these develop into bands during tensile testing using in situ observations in conjunction with digital image correlation (DIC). The bands form by the lateral contraction of the soft ferrite matrix, which rotates and displaces the CGBNs of second-phases and the individual features within them to become aligned with the loading direction. The more extensive pre-existing CGBNs that were before the deformation already aligned with the loading direction are the most critical microstructural feature for damage initiation and propagation. They induce micro-void formation between the hard second-phases along them, which coalesce and develop into long macroscopic fissures. The hard phases, retained austenite and martensite, were not differentiated as it was found that the individual phases do not play a role in the formation of these bands. It is suggested that minimizing the presence of CGBNs of hard second-phases in the initial microstructure will increase the formability.

Formation of methyl formate in comets by irradiation of methanol-bearing ices

NASA Astrophysics Data System (ADS)

Modica, P.; Palumbo, M. E.; Strazzulla, G.

2012-12-01

Methyl formate is a complex organic molecule considered potentially relevant as precursor of biologically active molecules. It has been observed in several astrophysical environments, such as hot cores, hot corinos, and comets. The processes that drive the formation of molecules in cometary ices are poorly understood. In particular it is not yet clear if molecules are directly accreted from the pre-solar nebula to form comets or are formed after accretion. The present work analyzes the possible role of cosmic ion irradiation and radioactive decay in methyl formate formation in methanol-bearing ices. The results indicate that cosmic ion irradiation can account for about 12% of the methyl formate observed in comet Hale-Bopp, while radioactive decay can account for about 6% of this amount. The need of new data coming from earth based and space observational projects as well as from laboratory experiments is outlined.

The South China sea margins: Implications for rifting contrasts

USGS Publications Warehouse

Hayes, D.E.; Nissen, S.S.

2005-01-01

Implications regarding spatially complex continental rifting, crustal extension, and the subsequent evolution to seafloor spreading are re-examined for the northern and southern-rifted margins of the South China Sea. Previous seismic studies have shown dramatic differences in the present-day crustal thicknesses as the manifestations of the strain experienced during the rifting of the margin of south China. Although the total crustal extension is presumed to be the same along the margin and adjacent ocean basin, the amount of continental crustal extension that occurred is much less along the east and central segments of the margin than along the western segment. This difference was accommodated by the early formation of oceanic crust (creating the present-day South China Sea basin) adjacent to the eastern margin segment while continued extension of continental crust was sustained to the west. Using the observed cross-sectional areas of extended continental crust derived from deep penetration seismics, two end-member models of varying rift zone widths and varying initial crustal thicknesses are qualitatively examined for three transects. Each model implies a time difference in the initiation of seafloor spreading inferred for different segments along the margin. The two models examined predict that the oceanic crust of the South China Sea basin toward the west did not begin forming until sometime between 6-12 my after its initial formation (???32 Ma) toward the east. These results are compatible with crustal age interpretations of marine magnetic anomalies. Assuming rifting symmetry with conjugate margin segments now residing along the southern portions of the South China Sea basin implies that the total width of the zone of rifting in the west was greater than in the east by about a factor of two. We suggest the most likely causes of the rifting differences were east-west variations in the rheology of the pre-rift crust and associated east-west variations in the thermal structure of the pre-rift lithosphere. The calculated widths of rifted continental crust for the northern and southern margins, when combined with the differential widths of seafloor generated during the seafloor spreading phase, indicate the total crustal extension that occurred is about 1100 km and is remarkably consistent to within ???10% for all three (eastern, central, western) segments examined. ?? 2005 Elsevier B.V. All rights reserved.

Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA

PubMed Central

Hubin, Elizabeth A; Fay, Allison; Xu, Catherine; Bean, James M; Saecker, Ruth M; Glickman, Michael S; Darst, Seth A; Campbell, Elizabeth A

2017-01-01

RbpA and CarD are essential transcription regulators in mycobacteria. Mechanistic analyses of promoter open complex (RPo) formation establish that RbpA and CarD cooperatively stimulate formation of an intermediate (RP2) leading to RPo; formation of RP2 is likely a bottleneck step at the majority of mycobacterial promoters. Once RPo forms, CarD also disfavors its isomerization back to RP2. We determined a 2.76 Å-resolution crystal structure of a mycobacterial transcription initiation complex (TIC) with RbpA as well as a CarD/RbpA/TIC model. Both CarD and RbpA bind near the upstream edge of the −10 element where they likely facilitate DNA bending and impede transcription bubble collapse. In vivo studies demonstrate the essential role of RbpA, show the effects of RbpA truncations on transcription and cell physiology, and indicate additional functions for RbpA not evident in vitro. This work provides a framework to understand the control of mycobacterial transcription by RbpA and CarD. DOI: http://dx.doi.org/10.7554/eLife.22520.001 PMID:28067618

Conjugated linoleic acid prevents age-induced bone loss in mice by regulating both osteoblastogenesis and adipogenesis.

PubMed

Lin, Guanlin; Wang, Huan; Dai, Jun; Li, Xiao; Guan, Ming; Gao, Shutao; Ding, Qing; Wang, Huaixi; Fang, Huang

2017-08-26

Osteoporosis (OP) can increase the risk of bone fracture and other complications, which is a major clinical problem. Previous researches have revealed that conjugated linoleic acid (CLA) can promote the bone formation. But the mechanisms are not clear. Thus, we tested the hypothesis that CLA acts on bone formation might be via mTOR Complex1 (mTORC 1) pathway by in vitro and vivo assays. We studied the effect of CLA mix on MC3T3-E1 pre-osteoblasts differentiation into osteoblasts, and bone formation under osteoporotic conditions. At the same time, 3T3-L1 pre-adipocyte with the same CLA mix concentration gradient for 8 days with adipogenic differentiation medium. We found that Alkaline phosphatase (ALP), runt-related transcription factor 2 (RUNX2) and osteocalcin (OCN) expressions of pre-osteoblasts were up-regulated. Moreover in presence of CLA, peroxisome proliferators-activated receptor γ(PPARγ) and CCAAT/enhancer-binding protein (C/EBPα) were down-regulated. Osteoporosis mice bone parameters in the distal femoral meraphysis were significantly increased compared with placebo mice. Furthermore, the phosphor-S6 (P-S6) was suppressed and phosphor-AKT (P-AKT) was up-regulated. Consistently, CLA can stimulate differentiation of osteoblasts and inhibited pre-adipocytes differentiated into adipocytes via AKT/mTORC1 signal pathway. Overall CLA thus be a suitable candidate for the treatment of patients with postmenopausal osteoporosis and obesity. Copyright © 2017 Elsevier Inc. All rights reserved.

Prehistoric cooking versus accurate palaeotemperature records in shell midden constituents.

PubMed

Müller, Peter; Staudigel, Philip T; Murray, Sean T; Vernet, Robert; Barusseau, Jean-Paul; Westphal, Hildegard; Swart, Peter K

2017-06-15

The reconstruction of pre-depositional cooking treatments used by prehistoric coastal populations for processing aquatic faunal resources is often difficult in archaeological shell midden assemblages. Besides limiting our knowledge of various social, cultural, economic and technological aspects of shell midden formation, unknown pre-depositional cooking techniques can also introduce large errors in palaeoclimate reconstructions as they can considerably alter the geochemical proxy signatures in calcareous skeletal structures such as bivalve shells or fish otoliths. Based on experimental and archaeological data, we show that carbonate clumped-isotope thermometry can be used to detect and reconstruct prehistoric processing methods in skeletal aragonite from archaeological shell midden assemblages. Given the temperature-dependent re-equilibration of clumped isotopes in aragonitic carbonates, this allows specific processing, cooking or trash dispersal strategies such as boiling, roasting, or burning to be differentiated. Besides permitting the detailed reconstruction of cultural or technological aspects of shell midden formation, this also allows erroneous palaeoclimate reconstructions to be avoided as all aragonitic shells subjected to pre-historic cooking methods show a clear alteration of their initial oxygen isotopic composition.

Transmetallation from CCC-NHC pincer Zr complexes in the synthesis of air-stable CCC-NHC pincer Co(iii) complexes and initial hydroboration trials.

PubMed

Reilly, Sean W; Webster, Charles Edwin; Hollis, T Keith; Valle, Henry U

2016-02-21

Development of CCC-NHC pincer Co complexes via transmetalation from Zr is reported. Formation of these air-stable Co(iii) complexes was achieved through use of a CoCl2 or Co(acac)3in situ or with a discrete CCC-NHC pincer Zr transmetallating agent. Preliminary activity in the hydroboration of styrene is reported. This facile methodology will further the development of CCC-NHC pincer first-row transition metal complexes.

The power of fission: yeast as a tool for understanding complex splicing.

PubMed

Fair, Benjamin Jung; Pleiss, Jeffrey A

2017-06-01

Pre-mRNA splicing is an essential component of eukaryotic gene expression. Many metazoans, including humans, regulate alternative splicing patterns to generate expansions of their proteome from a limited number of genes. Importantly, a considerable fraction of human disease causing mutations manifest themselves through altering the sequences that shape the splicing patterns of genes. Thus, understanding the mechanistic bases of this complex pathway will be an essential component of combating these diseases. Dating almost to the initial discovery of splicing, researchers have taken advantage of the genetic tractability of budding yeast to identify the components and decipher the mechanisms of splicing. However, budding yeast lacks the complex splicing machinery and alternative splicing patterns most relevant to humans. More recently, many researchers have turned their efforts to study the fission yeast, Schizosaccharomyces pombe, which has retained many features of complex splicing, including degenerate splice site sequences, the usage of exonic splicing enhancers, and SR proteins. Here, we review recent work using fission yeast genetics to examine pre-mRNA splicing, highlighting its promise for modeling the complex splicing seen in higher eukaryotes.

Amorphization due to electronic energy deposition in defective strontium titanate

DOE PAGES

Xue, Haizhou; Zarkadoula, Eva; Liu, Peng; ...

2017-01-27

The synergistic interaction of electronic energy loss by ions with ion-induced defects created by elastic nuclear scattering processes has been investigated for single crystal SrTiO 3. An initial pre-damaged defect state corresponding to a relative disorder level of 0.10–0.15 sensitizes the SrTiO 3 to amorphous track formation along the ion path of 12 and 20 MeV Ti, 21 MeV Cl and 21 MeV Ni ions, where Ti, Cl and Ni ions otherwise do not produce amorphous or damage tracks in pristine SrTiO 3. The electronic stopping power threshold for amorphous ion track formation is found to be 6.7 keV/nm formore » the pre-damaged defect state studied in this work. Lastly, these results suggest the possibility of selectively producing nanometer scale, amorphous ion tracks in thin films of epitaxial SrTiO 3.« less

Simulations of Emerging Magnetic Flux. II. The Formation of Unstable Coronal Flux Ropes and the Initiation of Coronal Mass Ejections

NASA Technical Reports Server (NTRS)

Leake, James E.; Linton, Mark G.; Antiochos, Spiro K.

2014-01-01

We present results from three-dimensional magnetohydrodynamic simulations of the emergence of a twisted convection zone flux tube into a pre-existing coronal dipole field. As in previous simulations, following the partial emergence of the sub-surface flux into the corona, a combination of vortical motions and internal magnetic reconnection forms a coronal flux rope. Then, in the simulations presented here, external reconnection between the emerging field and the pre-existing dipole coronal field allows further expansion of the coronal flux rope into the corona. After sufficient expansion, internal reconnection occurs beneath the coronal flux rope axis, and the flux rope erupts up to the top boundary of the simulation domain (approximately 36 Mm above the surface).We find that the presence of a pre-existing field, orientated in a direction to facilitate reconnection with the emerging field, is vital to the fast rise of the coronal flux rope. The simulations shown in this paper are able to self-consistently create many of the surface and coronal signatures used by coronal mass ejection (CME) models. These signatures include surface shearing and rotational motions, quadrupolar geometry above the surface, central sheared arcades reconnecting with oppositely orientated overlying dipole fields, the formation of coronal flux ropes underlying potential coronal field, and internal reconnection which resembles the classical flare reconnection scenario. This suggests that proposed mechanisms for the initiation of a CME, such as "magnetic breakout," are operating during the emergence of new active regions.

The Spatial Distribution of Complex Organic Molecules in the L1544 Pre-stellar Core.

PubMed

Jiménez-Serra, Izaskun; Vasyunin, Anton I; Caselli, Paola; Marcelino, Nuria; Billot, Nicolas; Viti, Serena; Testi, Leonardo; Vastel, Charlotte; Lefloch, Bertrand; Bachiller, Rafael

2016-10-10

The detection of complex organic molecules (COMs) toward cold sources such as pre-stellar cores (with T<10 K), has challenged our understanding of the formation processes of COMs in the interstellar medium. Recent modelling on COM chemistry at low temperatures has provided new insight into these processes predicting that COM formation depends strongly on parameters such as visual extinction and the level of CO freeze out. We report deep observations of COMs toward two positions in the L1544 pre-stellar core: the dense, highly-extinguished continuum peak with A V ≥30 mag within the inner 2700 au; and a low-density shell with average A V ~7.5-8 mag located at 4000 au from the core's center and bright in CH 3 OH. Our observations show that CH 3 O, CH 3 OCH 3 and CH 3 CHO are more abundant (by factors ~2-10) toward the low-density shell than toward the continuum peak. Other COMs such as CH 3 OCHO, c-C 3 H 2 O, HCCCHO, CH 2 CHCN and HCCNC show slight enhancements (by factors ≤3) but the associated uncertainties are large. This suggests that COMs are actively formed and already present in the low-density shells of pre-stellar cores. The modelling of the chemistry of O-bearing COMs in L1544 indicates that these species are enhanced in this shell because i) CO starts freezing out onto dust grains driving an active surface chemistry; ii) the visual extinction is sufficiently high to prevent the UV photo-dissociation of COMs by the external interstellar radiation field; and iii) the density is still moderate to prevent severe depletion of COMs onto grains.

The Spatial Distribution of Complex Organic Molecules in the L1544 Pre-stellar Core

PubMed Central

Jiménez-Serra, Izaskun; Vasyunin, Anton I.; Caselli, Paola; Marcelino, Nuria; Billot, Nicolas; Viti, Serena; Testi, Leonardo; Vastel, Charlotte; Lefloch, Bertrand; Bachiller, Rafael

2016-01-01

The detection of complex organic molecules (COMs) toward cold sources such as pre-stellar cores (with T<10 K), has challenged our understanding of the formation processes of COMs in the interstellar medium. Recent modelling on COM chemistry at low temperatures has provided new insight into these processes predicting that COM formation depends strongly on parameters such as visual extinction and the level of CO freeze out. We report deep observations of COMs toward two positions in the L1544 pre-stellar core: the dense, highly-extinguished continuum peak with AV ≥30 mag within the inner 2700 au; and a low-density shell with average AV ~7.5-8 mag located at 4000 au from the core’s center and bright in CH3OH. Our observations show that CH3O, CH3OCH3 and CH3CHO are more abundant (by factors ~2-10) toward the low-density shell than toward the continuum peak. Other COMs such as CH3OCHO, c-C3H2O, HCCCHO, CH2CHCN and HCCNC show slight enhancements (by factors ≤3) but the associated uncertainties are large. This suggests that COMs are actively formed and already present in the low-density shells of pre-stellar cores. The modelling of the chemistry of O-bearing COMs in L1544 indicates that these species are enhanced in this shell because i) CO starts freezing out onto dust grains driving an active surface chemistry; ii) the visual extinction is sufficiently high to prevent the UV photo-dissociation of COMs by the external interstellar radiation field; and iii) the density is still moderate to prevent severe depletion of COMs onto grains. PMID:27733899

Poly(allyl methacrylate) functionalized hydroxyapatite nanocrystals via the combination of surface-initiated RAFT polymerization and thiol-ene protocol: a potential anticancer drug nanocarrier.

PubMed

Bach, Long Giang; Islam, Md Rafiqul; Vo, Thanh-Sang; Kim, Se-Kwon; Lim, Kwon Taek

2013-03-15

Hydroxyapatite nanocrystals (HAP NCs) were encapsulated by poly(allyl methacrylate) (PolyAMA) employing controlled surface-initiated reversible addition-fragmentation chain transfer (SI-RAFT) polymerization of allyl methacrylate to afford HAP-PolyAMA nanohybrids. The subsequent thiol-ene coupling of nanohybrids with 2-mercaptosuccinic acid resulted HAP-Poly(AMA-COOH) possessing multicarboxyl group. The formation of the nanohybrids was confirmed by FT-IR and EDS analyses. The TGA and FE-SEM investigation were further suggested the grafting of PolyAMA onto HAP NCs. The utility of the HAP-PolyAMA nanohybrid as drug carrier was also explored. The pendant carboxyl groups on the external layers of nanohybrids were conjugated with anticancer drug cisplatin to afford HAP-Poly(AMA-COOH)/Pt complex. The formation of the complex was confirmed by FT-IR, XPS, and FE-SEM. In vitro evaluation of the synthesized complex as nanomedicine revealed its potential chemotherapeutic efficacy against cancer cell lines. Copyright © 2012 Elsevier Inc. All rights reserved.

Efficient surface formation route of interstellar hydroxylamine through NO hydrogenation. II. The multilayer regime in interstellar relevant ices

NASA Astrophysics Data System (ADS)

Fedoseev, G.; Ioppolo, S.; Lamberts, T.; Zhen, J. F.; Cuppen, H. M.; Linnartz, H.

2012-08-01

Hydroxylamine (NH2OH) is one of the potential precursors of complex pre-biotic species in space. Here, we present a detailed experimental study of hydroxylamine formation through nitric oxide (NO) surface hydrogenation for astronomically relevant conditions. The aim of this work is to investigate hydroxylamine formation efficiencies in polar (water-rich) and non-polar (carbon monoxide-rich) interstellar ice analogues. A complex reaction network involving both final (N2O, NH2OH) and intermediate (HNO, NH2O., etc.) products is discussed. The main conclusion is that hydroxyl-amine formation takes place via a fast and barrierless mechanism and it is found to be even more abundantly formed in a water-rich environment at lower temperatures. In parallel, we experimentally verify the non-formation of hydroxylamine upon UV photolysis of NO ice at cryogenic temperatures as well as the non-detection of NC- and NCO-bond bearing species after UV processing of NO in carbon monoxide-rich ices. Our results are implemented into an astrochemical reaction model, which shows that NH2OH is abundant in the solid phase under dark molecular cloud conditions. Once NH2OH desorbs from the ice grains, it becomes available to form more complex species (e.g., glycine and β-alanine) in gas phase reaction schemes.

21st Century Teachers: How Non-Traditional Pre-Service Teachers Navigate Their Initial Experiences of Contemporary Classrooms

ERIC Educational Resources Information Center

Crosswell, Leanne; Beutel, Denise

2017-01-01

In the twenty-first century, teachers' work has become more complex with high levels of accountability, increased bureaucratic responsibilities and unprecedented levels of public scrutiny. However, teaching fundamentally remains a caring profession, requiring well-developed social skills and emotional labour to successfully engage and motivate…

PAM-Dependent Target DNA Recognition and Cleavage by C2c1 CRISPR-Cas Endonuclease

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Hui; Gao, Pu; Rajashankar, Kanagalaghatta R.

C2c1 is a newly identified guide RNA-mediated type V-B CRISPR-Cas endonuclease that site-specifically targets and cleaves both strands of target DNA. We have determined crystal structures of Alicyclobacillus acidoterrestris C2c1 (AacC2c1) bound to sgRNA as a binary complex and to target DNAs as ternary complexes, thereby capturing catalytically competent conformations of AacC2c1 with both target and non-target DNA strands independently positioned within a single RuvC catalytic pocket. Moreover, C2c1-mediated cleavage results in a staggered seven-nucleotide break of target DNA. crRNA adopts a pre-ordered five-nucleotide A-form seed sequence in the binary complex, with release of an inserted tryptophan, facilitating zippering upmore » of 20-bp guide RNA:target DNA heteroduplex on ternary complex formation. Notably, the PAM-interacting cleft adopts a “locked” conformation on ternary complex formation. Structural comparison of C2c1 ternary complexes with their Cas9 and Cpf1 counterparts highlights the diverse mechanisms adopted by these distinct CRISPR-Cas systems, thereby broadening and enhancing their applicability as genome editing tools.« less

High-frequency promoter firing links THO complex function to heavy chromatin formation.

PubMed

Mouaikel, John; Causse, Sébastien Z; Rougemaille, Mathieu; Daubenton-Carafa, Yves; Blugeon, Corinne; Lemoine, Sophie; Devaux, Frédéric; Darzacq, Xavier; Libri, Domenico

2013-11-27

The THO complex is involved in transcription, genome stability, and messenger ribonucleoprotein (mRNP) formation, but its precise molecular function remains enigmatic. Under heat shock conditions, THO mutants accumulate large protein-DNA complexes that alter the chromatin density of target genes (heavy chromatin), defining a specific biochemical facet of THO function and a powerful tool of analysis. Here, we show that heavy chromatin distribution is dictated by gene boundaries and that the gene promoter is necessary and sufficient to convey THO sensitivity in these conditions. Single-molecule fluorescence in situ hybridization measurements show that heavy chromatin formation correlates with an unusually high firing pace of the promoter with more than 20 transcription events per minute. Heavy chromatin formation closely follows the modulation of promoter firing and strongly correlates with polymerase occupancy genome wide. We propose that the THO complex is required for tuning the dynamic of gene-nuclear pore association and mRNP release to the same high pace of transcription initiation. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

Single-stranded nucleic acids promote SAMHD1 complex formation.

PubMed

Tüngler, Victoria; Staroske, Wolfgang; Kind, Barbara; Dobrick, Manuela; Kretschmer, Stefanie; Schmidt, Franziska; Krug, Claudia; Lorenz, Mike; Chara, Osvaldo; Schwille, Petra; Lee-Kirsch, Min Ae

2013-06-01

SAM domain and HD domain-containing protein 1 (SAMHD1) is a dGTP-dependent triphosphohydrolase that degrades deoxyribonucleoside triphosphates (dNTPs) thereby limiting the intracellular dNTP pool. Mutations in SAMHD1 cause Aicardi-Goutières syndrome (AGS), an inflammatory encephalopathy that mimics congenital viral infection and that phenotypically overlaps with the autoimmune disease systemic lupus erythematosus. Both disorders are characterized by activation of the antiviral cytokine interferon-α initiated by immune recognition of self nucleic acids. Here we provide first direct evidence that SAMHD1 associates with endogenous nucleic acids in situ. Using fluorescence cross-correlation spectroscopy, we demonstrate that SAMHD1 specifically interacts with ssRNA and ssDNA and establish that nucleic acid-binding and formation of SAMHD1 complexes are mutually dependent. Interaction with nucleic acids and complex formation do not require the SAM domain, but are dependent on the HD domain and the C-terminal region of SAMHD1. We finally demonstrate that mutations associated with AGS exhibit both impaired nucleic acid-binding and complex formation implicating that interaction with nucleic acids is an integral aspect of SAMHD1 function.

Hmo1 directs pre-initiation complex assembly to an appropriate site on its target gene promoters by masking a nucleosome-free region

PubMed Central

Kasahara, Koji; Ohyama, Yoshifumi; Kokubo, Tetsuro

2011-01-01

Saccharomyces cerevisiae Hmo1 binds to the promoters of ∼70% of ribosomal protein genes (RPGs) at high occupancy, but is observed at lower occupancy on the remaining RPG promoters. In Δhmo1 cells, the transcription start site (TSS) of the Hmo1-enriched RPS5 promoter shifted upstream, while the TSS of the Hmo1-limited RPL10 promoter did not shift. Analyses of chimeric RPS5/RPL10 promoters revealed a region between the RPS5 upstream activating sequence (UAS) and core promoter, termed the intervening region (IVR), responsible for strong Hmo1 binding and an upstream TSS shift in Δhmo1 cells. Chromatin immunoprecipitation analyses showed that the RPS5-IVR resides within a nucleosome-free region and that pre-initiation complex (PIC) assembly occurs at a site between the IVR and a nucleosome overlapping the TSS (+1 nucleosome). The PIC assembly site was shifted upstream in Δhmo1 cells on this promoter, indicating that Hmo1 normally masks the RPS5-IVR to prevent PIC assembly at inappropriate site(s). This novel mechanism ensures accurate transcriptional initiation by delineating the 5′- and 3′-boundaries of the PIC assembly zone. PMID:21288884

Development of Field-Reversed Configuration Plasma Gun Formation Techniques for Magnetized Target Fusion

NASA Astrophysics Data System (ADS)

Lynn, Alan; Gilmore, Mark; Wynkoop, Tyler; Intrator, Thomas; Weber, Thomas

2012-10-01

Magnetized Target Fusion (MTF) is an innovative approach for a relatively fast and cheap path to the production of fusion energy that utilizes magnetic confinement to assist in the compression of a hot plasma to thermonuclear conditions by an external driver. Los Alamos National Laboratory (LANL) is currently pursing demonstration of the MTF concept via compression of an FRC (field-reversed configuration) plasma by a metal liner z-pinch in conjunction with the Air Force Research Laboratory in Albuquerque, NM. A key physics issue for the FRC as an MTF target lies in the initial pre-ionization (PI) stage. The PI formation process determines the amount of magnetic flux that can be trapped to form the FRC. This trapped flux plays an important role in the FRC's final equilibrium, transport, and stability properties. It also provides the route to greatest potential gains in FRC lifetime, which is essential to provide enough time to translate and compress the FRC effectively. In conjunction with LANL we plan to test and characterize a new system to improve the initial PI plasma formation. This system will use an array of plasma guns to form the initial plasma. Initial characterization of the plasma gun behavior will be presented.

Improvements in the Formation of Boron-Doped Diamond Coatings on Platinum Wires Using the Novel Nucleation Process (NNP)

PubMed Central

Fhaner, Mathew; Zhao, Hong; Bian, Xiaochun; Galligan, James J.; Swain, Greg M.

2010-01-01

In order to increase the initial nucleation density for the growth of boron-doped diamond on platinum wires, we employed the novel nucleation process (NNP) originally developed by Rotter et al. and discussed by others [1–3]. This pretreatment method involves (i) the initial formation of a thin carbon layer over the substrate followed by (ii) ultrasonic seeding of this “soft” carbon layer with nanoscale particles of diamond. This two-step pretreatment is followed by the deposition of boron-doped diamond by microwave plasma-assisted CVD. Both the diamond seed particles and sites on the carbon layer itself function as the initial nucleation zones for diamond growth from an H2-rich source gas mixture. We report herein on the characterization of the pre-growth carbon layer formed on Pt as well as boron-doped films grown for 2, 4 and 6 h post NNP pretreatment. Results from scanning electron microscopy, Raman spectroscopy and electrochemical studies are reported. The NNP method increases the initial nucleation density on Pt and leads to the formation of a continuous diamond film in a shorter deposition time than is typical for wires pretreated by conventional ultrasonic seeding. The results indicate that the pregrowth layer itself consists of nanoscopic domains of diamond and functions well to enhance the initial nucleation of diamond without any diamond powder seeding. PMID:21617759

Analysis of Europan Cycloid Morphology and Implications for Formation Mechanisms

NASA Technical Reports Server (NTRS)

Marshall, S. T.; Kattenhorn, S. A.

2004-01-01

Europa's highly fractured crust has been shown to contain features with a range of differing morphologies. Most lineaments on Europa are believed to have initiated as cracks, although the type of cracking (e.g. tensile vs. shear) remains unclear and may vary for different morphologies. Arcuate lineaments, called cycloids or flexi, have been observed in nearly all imaged regions of Europa and have been modeled as tensile fractures that were initiated in response to diurnal variations in tides. Despite this hypothesis about the formation mechanism, there have been no detailed analyses of the variable morphologies of cycloids. We have examined Galileo images of numerous locations on Europa to develop a catalog of the different morphologies of cycloids. This study focuses on variations in morphology along individual cycloid segments and differences in cusp styles between segments, while illustrating how morphologic evidence can help unravel formation mechanisms. In so doing, we present evidence for cycloid cusps forming due to secondary fracturing during strike-slip sliding on pre-existing cycloid segments.

Are pre-crater mounds gas-inflated?

NASA Astrophysics Data System (ADS)

Leibman, Marina; Kizyakov, Alexandr; Khomutov, Artem; Dvornikov, Yury; Babkina, Elena; Arefiev, Stanislav; Khairullin, Rustam

2017-04-01

Gas-emission craters (GEC) on Yamal peninsula, which occupied minds of researches for the last couple of years since first discovered in 2014, appeared to form on the place of specifically shaped mounds. There was a number of hypotheses involving pingo as an origin of these mounds. This arouse an interest in mapping pingo thus marking the areas of GEC formation risk. Our field research allows us to suggest that remote-sensing-based mapping of pingo may result in mix up of mounds of various origin. Thus, we started with classification of the mounds based on remote-sensing, field observations and survey from helicopter. Then we compared indicators of mounds of various classes to the properties of pre-crater mounds to conclude on their origin. Summarizing field experience, there are three main mound types on Yamal. (1) Outliers (remnant hills), separated from the main geomorphic landform by erosion. Often these mounds comprise polygonal blocks, kind of "baydzherakh". Their indicators are asymmetry (short gentle slope towards the main landform, and steep slope often descending into a small pond of thermokarst-nivation origin), often quadrangle or conic shape, and large size. (2) Pingo, appear within the khasyrei (drain lake basin); often are characterized by open cracks resulting from expansion of polygonal network formed when re-freezing of lake talik prior to pingo formation; old pingo may bear traces of collapse on the top, with depression which differs from the GEC by absence of parapet. (3) Frost-heave mounds (excluding pingo) may form on deep active layer, reducing due to moss-peat formation and forming ice lenses from an active layer water, usually they appear in the drainage hollows, valley bottoms, drain-lake basins periphery. These features are smaller than the first two types of mounds. Their tops as a rule are well vegetated. We were unable to find a single or a set of indicators unequivocally defining any specific mound type, thus indicators of pre-crater mounds are still debatable. Our hypothesis initially does not involve pingo origin of pre-crater mounds for several reasons, among which were the initial depth (70 m) and width (18 m) of the crater void, frozen walls and bottom, no traces of sub-lake talik, an important control for pingo formation, and more. Pre-crater mounds are closer to frost-heave mounds in size (4-7 m high and 30-60 m in diameter). Yet frost-heave mounds like palsa or lithalsa have segregated ice lenses closer to the surface, total thickness of these lenses is equal to the height of the mound. Pre-crater mounds have at least 20 m of tabular ground ice in the section that has no manifestation in the mound height or diameter. All above-mentioned leads to the conclusion that pre-crater mounds form because of gas inflation rather than regular frost heave process involving moisture migration towards the freezing front. This research is supported by Russian Science Foundation Grant 16-17-10203.

Stereocontrolled intramolecular iron-mediated diene/olefin cyclocoupling

NASA Astrophysics Data System (ADS)

Dorange, Ismet B.

A methodology for stereocontrol during the intramolecular coupling between cyclohexadiene-Fe(CO)3 complexes and pendant alkenes is presented. Introduction of a methoxy group at the C(3) position of the diene moiety controls pre- and post-cyclization rearrangements of the diene Fe(CO)3 unit, allowing the preparation of spirolactams with defined relative stereochemistry and with a cyclohexenone framework, thus making this reaction a potentially valuable tool for the construction of quaternary carbon centers.* A new methodology for the formation of tricarbonyl(cyclohexadienyl)ketone iron complexes was also developed. This method involves the coupling of a Grignard reagent with an acyl mesylate iron complex, giving rise to ketone derivatives in excellent yields. The possibility of intramolecular coupling between diene-Fe(CO)3 complexes and homoallylic olefin was demonstrated. The stereospecific formation of spiroketones occurred in excellent yields under thermal conditions, but appeared to be limited to the simpler, less substituted pendant alkenes. The control of the stereochemical outcome of these spirocyclization was achieved using the "C(3) substitution method" previously described. The same trends were observed in these series. Also illustrated in these studies is the extension of this spirocoupling to the formation of a spiro[5.5]undecane framework. It is the first time that this framework has been accessed using this intramolecular coupling.* *Please refer to dissertation for diagram.

Single Molecule Force Measurement for Protein Synthesis on the Ribosome

NASA Astrophysics Data System (ADS)

Uemura, Sotaro

2008-04-01

The ribosome is a molecular machine that translates the genetic code described on the messenger RNA (mRNA) into an amino acid sequence through repetitive cycles of transfer RNA (tRNA) selection, peptide bond formation and translocation. Although the detailed interactions between the translation components have been revealed by extensive structural and biochemical studies, it is not known how the precise regulation of macromolecular movements required at each stage of translation is achieved. Here we demonstrate an optical tweezer assay to measure the rupture force between a single ribosome complex and mRNA. The rupture force was compared between ribosome complexes assembled on an mRNA with and without a strong Shine-Dalgarno (SD) sequence. The removal of the SD sequence significantly reduced the rupture force, indicating that the SD interactions contribute significantly to the stability of the ribosomal complex on the mRNA in a pre-peptidyl transfer state. In contrast, the post-peptidyl transfer state weakened the rupture force as compared to the complex in a pre-peptidyl transfer state and it was the same for both the SD-containing and SD-deficient mRNAs. The results suggest that formation of the first peptide bond destabilizes the SD interaction, resulting in the weakening of the force with which the ribosome grips an mRNA. This might be an important requirement to facilitate movement of the ribosome along mRNA during the first translocation step. In this article, we discuss about the above new results including the introduction of the ribosome translation mechanism and the optical tweezer method.

Measuring kinetic drivers of pneumolysin pore structure.

PubMed

Gilbert, Robert J C; Sonnen, Andreas F-P

2016-05-01

Most membrane attack complex-perforin/cholesterol-dependent cytolysin (MACPF/CDC) proteins are thought to form pores in target membranes by assembling into pre-pore oligomers before undergoing a pre-pore to pore transition. Assembly during pore formation is into both full rings of subunits and incomplete rings (arcs). The balance between arcs and full rings is determined by a mechanism dependent on protein concentration in which arc pores arise due to kinetic trapping of the pre-pore forms by the depletion of free protein subunits during oligomerization. Here we describe the use of a kinetic assay to study pore formation in red blood cells by the MACPF/CDC pneumolysin from Streptococcus pneumoniae. We show that cell lysis displays two kinds of dependence on protein concentration. At lower concentrations, it is dependent on the pre-pore to pore transition of arc oligomers, which we show to be a cooperative process. At higher concentrations, it is dependent on the amount of pneumolysin bound to the membrane and reflects the affinity of the protein for its receptor, cholesterol. A lag occurs before cell lysis begins; this is dependent on oligomerization of pneumolysin. Kinetic dissection of cell lysis by pneumolysin demonstrates the capacity of MACPF/CDCs to generate pore-forming oligomeric structures of variable size with, most likely, different functional roles in biology.

Spectroscopic Studies of Pre-Biotic Carbon Chemistry

NASA Technical Reports Server (NTRS)

Blake, Geoffrey A.

2003-01-01

As described in the original proposal and in our progress reports, research in the Blake group supported by the Exobiology program seeks to understand the pre-biotic chemistry of carbon along with that of other first- and second-row elements from the earliest stages of star formation through the development of planetary systems. The major tool used is spectroscopy, and the program has observational, laboratory, and theoretical components. The observational and theoretical programs are concerned primarily with a quantitative assessment of the chemical budgets of the biogenic elements in the circumstellar environment of forming stars and planetary systems, while the laboratory work is focused on the complex species that characterize the pre-biotic chemistry of carbon. We outline below our results over the past year acquired, in part, with Exobiology support.

Structural insights into the light-driven auto-assembly process of the water-oxidizing Mn4CaO5-cluster in photosystem II

PubMed Central

Zhang, Miao; Bommer, Martin; Chatterjee, Ruchira; Hussein, Rana; Yano, Junko; Dau, Holger; Kern, Jan; Dobbek, Holger; Zouni, Athina

2017-01-01

In plants, algae and cyanobacteria, Photosystem II (PSII) catalyzes the light-driven splitting of water at a protein-bound Mn4CaO5-cluster, the water-oxidizing complex (WOC). In the photosynthetic organisms, the light-driven formation of the WOC from dissolved metal ions is a key process because it is essential in both initial activation and continuous repair of PSII. Structural information is required for understanding of this chaperone-free metal-cluster assembly. For the first time, we obtained a structure of PSII from Thermosynechococcus elongatus without the Mn4CaO5-cluster. Surprisingly, cluster-removal leaves the positions of all coordinating amino acid residues and most nearby water molecules largely unaffected, resulting in a pre-organized ligand shell for kinetically competent and error-free photo-assembly of the Mn4CaO5-cluster. First experiments initiating (i) partial disassembly and (ii) partial re-assembly after complete depletion of the Mn4CaO5-cluster agree with a specific bi-manganese cluster, likely a di-µ-oxo bridged pair of Mn(III) ions, as an assembly intermediate. DOI: http://dx.doi.org/10.7554/eLife.26933.001 PMID:28718766

Function of the growth-regulated transcription initiation factor TIF-IA in initiation complex formation at the murine ribosomal gene promoter.

PubMed

Schnapp, A; Schnapp, G; Erny, B; Grummt, I

1993-11-01

Alterations in the rate of cell proliferation are accompanied by changes in the transcription of rRNA genes. In mammals, this growth-dependent regulation of transcription of genes coding for rRNA (rDNA) is due to reduction of the amount or activity of an essential transcription factor, called TIF-IA. Extracts prepared from quiescent cells lack this factor activity and, therefore, are transcriptionally inactive. We have purified TIF-IA from exponentially growing cells and have shown that it is a polypeptide with a molecular mass of 75 kDa which exists as a monomer in solution. Using a reconstituted transcription system consisting of purified transcription factors, we demonstrate that TIF-IA is a bona fide transcription initiation factor which interacts with RNA polymerase I. Preinitiation complexes can be assembled in the absence of TIF-IA, but formation of the first phosphodiester bonds of nascent rRNA is precluded. After initiation, TIF-IA is liberated from the initiation complex and facilitates transcription from templates bearing preinitiation complexes which lack TIF-IA. Despite the pronounced species specificity of class I gene transcription, this growth-dependent factor has been identified not only in mouse but also in human cells. Murine TIF-IA complements extracts from both growth-inhibited mouse and human cells. The analogous human activity appears to be similar or identical to that of TIF-IA. Therefore, despite the fact that the RNA polymerase transcription system has evolved sufficiently rapidly that an rDNA promoter from one species will not function in another species, the basic mechanisms that adapt ribosome synthesis to cell proliferation have been conserved.

Roles of URLs in Probing Controls on Induced Seismicity and Permeability Evolution

NASA Astrophysics Data System (ADS)

Elsworth, D.

2014-12-01

The generation and extension of new fractures and the development of controlled slip and opening are an implicit component in both forming and in enhancing flow pathways to unlock hydrocarbons and geothermal energy in otherwise very low permeability formations. The opposite is true for containment structures and caprocks. The complex stress state coupled with pre-existing fracture networks means that new flow pathways may develop in complex ways including varied modes of dilatation and slip, deformation that may be seismic or aseismic and permeability that may net increase of decrease. Where this deformation relies on either the reactivation, extension or development of fractures, this evolution is intrinsically scale dependent requiring that an improved understanding of this dynamic response must interrogate its evolution at representative scales - scales of decimeters to a few meters. We explore the controls on instability through frictional slip and instability including changes related to environmental conditions and physical properties. The former relate to changes in effective stress driven by fluid pressures, thermal and chemical stresses and the latter to changes in strength and stability conditioned on initial or evolving mineralogy. We identify important contemporary questions that are intrinsically scale dependent and may be effectively probed by field experimentation linking deformation and permeability.

Wounding induces changes in tuber polyamine content, polyamine metabolic gene expression, and enzyme activity during closing layer formation and initiation of wound periderm formation

USDA-ARS?s Scientific Manuscript database

Tuber wound-healing processes are complex, and the associated regulation and modulation of these processes are poorly understood. Polyamines (PA) have been shown to be involved in modulating a variety of responses to biotic and abiotic plant stresses and have been suggested to be involved in tuber ...

Mechanisms of Translation Control Underlying Long-lasting Synaptic Plasticity and the Consolidation of Long-term Memory

PubMed Central

Santini, Emanuela; Huynh, Thu N.; Klann, Eric

2018-01-01

The complexity of memory formation and its persistence is a phenomenon that has been studied intensely for centuries. Memory exists in many forms and is stored in various brain regions. Generally speaking, memories are reorganized into broadly distributed cortical networks over time through systems level consolidation. At the cellular level, storage of information is believed to initially occur via altered synaptic strength by processes such as long-term potentiation (LTP). New protein synthesis is required for long-lasting synaptic plasticity as well as for the formation of long-term memory. The mammalian target of rapamycin complex 1 (mTORC1) is a critical regulator of cap-dependent protein synthesis and is required for numerous forms of long-lasting synaptic plasticity and long-term memory. As such, the study of mTORC1 and protein factors that control translation initiation and elongation have enhanced our understanding of how the process of protein synthesis is regulated during memory formation. Herein we will discuss the molecular mechanisms that regulate protein synthesis as well as pharmacological and genetic manipulations that demonstrate the requirement for proper translational control in long-lasting synaptic plasticity and long-term memory formation. PMID:24484700

Concerted removal of the Erb1–Ytm1 complex in ribosome biogenesis relies on an elaborate interface

PubMed Central

Thoms, Matthias; Ahmed, Yasar Luqman; Maddi, Karthik; Hurt, Ed; Sinning, Irmgard

2016-01-01

The complicated process of eukaryotic ribosome biogenesis involves about 200 assembly factors that transiently associate with the nascent pre-ribosome in a spatiotemporally ordered way. During the early steps of 60S subunit formation, several proteins, collectively called A3 cluster factors, participate in the removal of the internal transcribed spacer 1 (ITS1) from 27SA3 pre-rRNA. Among these factors is the conserved hetero-trimeric Nop7–Erb1–Ytm1 complex (or human Pes1–Bop1–Wdr12), which is removed from the evolving pre-60S particle by the AAA ATPase Rea1 to allow progression in the pathway. Here, we clarify how Ytm1 and Erb1 interact, which has implications for the release mechanism of both factors from the pre-ribosome. Biochemical studies show that Ytm1 and Erb1 bind each other via their ß-propeller domains. The crystal structure of the Erb1–Ytm1 heterodimer determined at 2.67Å resolution reveals an extended interaction surface between the propellers in a rarely observed binding mode. Structure-based mutations in the interface that impair the Erb1–Ytm1 interaction do not support growth, with specific defects in 60S subunit synthesis. Under these mutant conditions, it becomes clear that an intact Erb1–Ytm1 complex is required for 60S maturation and that loss of this stable interaction prevents ribosome production. PMID:26657628

Dynamical singularities for complex initial conditions and the motion at a real separatrix.

PubMed

Shnerb, Tamar; Kay, K G

2006-04-01

This work investigates singularities occurring at finite real times in the classical dynamics of one-dimensional double-well systems with complex initial conditions. The objective is to understand the relationship between these singularities and the behavior of the systems for real initial conditions. An analytical treatment establishes that the dynamics of a quartic double well system possesses a doubly infinite sequence of singularities. These are associated with initial conditions that converge to those for the real separatrix as the singularity time becomes infinite. This confluence of singularities is shown to lead to the unstable behavior that characterizes the real motion at the separatrix. Numerical calculations confirm the existence of a large number of singularities converging to the separatrix for this and two additional double-well systems. The approach of singularities to the real axis is of particular interest since such behavior has been related to the formation of chaos in nonintegrable systems. The properties of the singular trajectories which cause this convergence to the separatrix are identified. The hyperbolic fixed point corresponding to the potential energy maximum, responsible for the characteristic motion at a separatrix, also plays a critical role in the formation of the complex singularities by delaying trajectories and then deflecting them into asymptotic regions of space from where they are directly repelled to infinity in a finite time.

The Birth of a Cratonic Core: Petrologic Evolution of the Hadean-Eoarchean Acasta Gneiss Complex

NASA Astrophysics Data System (ADS)

Reimink, J. R.; Chacko, T.; Davies, J.; Pearson, D. G.; Stern, R. A.; Heaman, L. M.; Carlson, R.; Shirey, S. B.

2016-12-01

Granitoid magmatism within the 4.02-3.6 Ga Acasta Gneiss Complex records distinct whole-rock compositional changes during the building the Slave Craton. Previously1,2 we suggested that these signatures implied petrologic changes from initiation of evolved crust formation in an Iceland-like setting to partial melting of hydrated mafic crust at increasing depth through time, culminating in relatively voluminous magmatism at 3.6 Ga. Increasing La/Yb in these rocks suggest increasing depth of melting (and increasing residual garnet content) with time, ending in emplacement of rocks comparable to other Archean TTG suites3, with both high pressure (high La/Yb) and low pressure (low La/Yb) rocks represented at 3.6 Ga. Data from rocks with variable La/Yb that crystallized 3.6 Ga allow us to evaluate potential mechanisms for formation of rocks of this age such as subduction/accretion or intracrustal melting/delamination. Despite major and trace element compositional and age variability, zircon oxygen isotope compositions from a wide variety of rocks are extremely consistent (+6.0-6.5 ‰ from 3.9-2.9 Ga), implying a similar source, one that had been altered by surface waters1. Potential source rocks include the upper portion of oceanic crust, which contains a large portion of mafic crust that had been altered at low temperatures (e.g., 4). Paired whole rock and zircon radiogenic isotopic data are especially sensitive to the extent of pre-existing felsic material in the region, as well as the longevity of primary, basaltic rocks prior to their reworking into more evolved crust. New paired zircon Hf and whole rock Nd isotope data collected from these samples show variably unradiogenic signatures and allow an exploration of similarities and disparities between crust formation in the Acasta Gneiss Complex and other Paleoarchean-Mesoarchean crustal blocks. [1] Reimink et al., 2016. Precambrian Research 281, 453-472. [2] Reimink et al., 2014 Nature Geoscience 7, 529-533. [3] Moyen and Martin, 2012 Lithos 148, 312-348. [4] Eiler, J.M., 2001 Reviews in Mineralogy and Geochemistry 43, 319-364.

DNA Replication and Cell Cycle Progression Regulatedby Long Range Interaction between Protein Complexes bound to DNA.

PubMed

Matsson, L

2001-12-01

A nonstationary interaction that controlsDNA replication and the cell cycle isderived from many-body physics in achemically open T cell. The model predictsa long range force F'(ξ) =- (κ/2) ξ(1 - ξ)(2 - ξ)between thepre-replication complexes (pre-RCs) boundby the origins in DNA, ξ = ϕ/N being the relativedisplacement of pre-RCs, ϕ the number of pre-RCs, N the number of replicons to be replicated,and κ the compressibilitymodulus in the lattice of pre-RCs whichbehaves dynamically like an elasticallybraced string. Initiation of DNAreplication is induced at the thresholdϕ = N by a switch ofsign of F''(ξ), fromattraction (-) and assembly in the G(1) phase (0<ϕ

Voltammetric study of the boric acid-salicylaldehyde-H-acid ternary system and its application to the voltammetric determination of boron.

PubMed

Kajiwara, Mari; Ito, Yoshio N; Miyazaki, Yoshinobu; Fujimori, Takao; Takehara, Kô; Yoshimura, Kazuhisa

2015-02-14

The ternary system of boric acid, salicylaldehyde (SA) and H-acid (HA) was voltammetrically studied from kinetic and equilibrium points of view. The effect of the SA substituents was also studied by using two analogs, 5-fluorosalicylaldehyde (F-SA) and 5-methylsalicylaldehyde (Me-SA). The three cathodic peaks of Azomethine H (AzH), Azomethine H-boric acid complex (AzB), and free SA were observed in the solution containing boric acid, SA and HA. The peak potentials of AzH and SA were shifted to negative potentials with increasing pH, while the peak potential of AzB was pH-independent. This difference indicates that a proton participates in the charge-transfer steps of the AzH and SA reductions, but not in that of the AzB reduction. The formation constants for the AzB complexation were similar among all the examined analogs. In the kinetic study, the reaction rate was higher in an acidic condition for the AzH formation, but in a neutral condition for the AzB formation. The rate constants for the AzB complexes were in the order of F-SA > SA ≈ Me-SA, indicating that the fluoro group accelerates the F-AzB complexation. The AzB complexation mechanism is considered to consist of more than three steps, i.e., the pre-equilibrium of the salicylaldehyde-boric acid complex (SA-B) formation, the nucleophilic attack of HA on SA-B, and the remaining some steps to form AzB. Based on these results, the voltammetric determination method of boron using F-SA was optimized, which allowed the boron concentration to be determined within only 5 min with a 0.03 mg B dm(-3) detection limit.

Modelling NOx emissions of single droplet combustion

NASA Astrophysics Data System (ADS)

Moesl, Klaus G.; Schwing, Joachim E.; Sattelmayer, Thomas

2012-02-01

An approach for modelling and simulation of the generation of nitrogen oxide (NOx) in the gas phase surrounding single burning droplets is presented. Assuming spherical symmetry (no gravity, no forced convection), the governing equations are derived first. Then simplifications are introduced and it is proven that they are appropriate. The influences of the initial droplet diameter, the ambient conditions, and the droplet pre-vapourisation on NOx are investigated. The fuel of choice is n-decane (C10H22) as it resembles kerosene and diesel fuel best, and the complexity of the reaction mechanism is manageable. Combinations of C10H22 mechanisms and well-established NOx kinetics are evaluated in detail and validated for their applicability in the context of this work. The conducted simulations of droplet combustion in an atmosphere of hot exhaust gas show that NOx formation (by mass of fuel) increases linearly with the droplet diameter. There is a trade-off between available oxygen and ambient temperature. Increasing the equivalence ratio of the exhaust gas leads to higher NOx emissions in the very lean regime, but to lower emissions if the equivalence ratio exceeds 0.85. Pre-vapourisation of fuel at ambient conditions becomes beneficial with respect to NOx emissions only if the degree of vapourisation is above a minimum limit. If less fuel is vapourised before ignition, the NOx emissions remain almost unaffected.

Upper Triassic mafic dykes of Lake Nyos, Cameroon (West Africa) I: K-Ar age evidence within the context of Cameroon Line magmatism, and the tectonic significance

NASA Astrophysics Data System (ADS)

Aka, Festus Tongwa; Hasegawa, Takeshi; Nche, Linus Anye; Asaah, Asobo Nkengmatia Elvis; Mimba, Mumbfu Ernestine; Teitchou, Isidore; Ngwa, Caroline; Miyabuchi, Yasuo; Kobayashi, Tetsuo; Kankeu, Boniface; Yokoyama, Tetsuya; Tanyileke, Gregory; Ohba, Takeshi; Hell, Joseph Victor; Kusakabe, Minoru

2018-05-01

The hydrodynamic fragmentation that formed Lake Nyos in northwest Cameroon did not only make it the most unpopular lake in the world from a gas disaster perspective, it also opened a rare and formidable window through which much of the geology of Cameroon can be studied in a single locality. The Cambrian quartz monzonite cliff excavated by the maar-forming explosion and exposed in its northeastern shore is intruded by mafic dykes, two of which we dated. Even though close to one another, the dykes are different in composition. The alkaline dyke yields a slightly older (Carnian) K-Ar fedspar age of 231.1 ± 4.8 Ma, while the sub alkaline dyke yields an age of 224.8 ± 4.7 Ma (Norian). Based on radioisotopic age data available over the last 48 years (347 data) for the Cameroon Line magmatism comprising eruptives and volcano-plutonic complexes, the Nyos dykes are way older than the Cameroon Line, and even pre-date the Lower Cretaceous initiation of west Gondwana fragmentation in Equatorial Atlantic domain. They would therefore not have been directly linked to the formation of the Cameroon Line. Alternatively, they might be associated with the development of intra-continental rift systems in West Central Africa that pre-dated west Gondwana breakup to form the Atlantic Ocean.

A pre-steady state and steady state kinetic analysis of the N-ribosyl hydrolase activity of hCD157.

PubMed

Preugschat, Frank; Carter, Luke H; Boros, Eric E; Porter, David J T; Stewart, Eugene L; Shewchuk, Lisa M

2014-12-15

hCD157 catalyzes the hydrolysis of nicotinamide riboside (NR) and nicotinic acid riboside (NAR). The release of nicotinamide or nicotinic acid from NR or NAR was confirmed by spectrophotometric, HPLC and NMR analyses. hCD157 is inactivated by a mechanism-based inhibitor, 2'-deoxy-2'-fluoro-nicotinamide arabinoside (fNR). Modification of the enzyme during the catalytic cycle by NR, NAR, or fNR increased the intrinsic protein fluorescence by approximately 50%. Pre-steady state and steady state data were used to derive a minimal kinetic scheme for the hydrolysis of NR. After initial complex formation a reversible step (360 and 30s(-1)) is followed by a slow irreversible step (0.1s(-1)) that defined the rate limiting step, or kcat. The calculated KMapp value for NR in the hydrolytic reaction is 6nM. The values of the kinetic constants suggest that one biological function of cell-surface hCD157 is to bind and slowly hydrolyze NR, possibly converting it to a ligand-activated receptor. Differences in substrate preference between hCD157 and hCD38 were rationalized through a comparison of the crystal structures of the two proteins. This comparison identified several residues in hCD157 (F108 and F173) that can potentially hinder the binding of dinucleotide substrates (NAD+). Copyright © 2014 Elsevier Inc. All rights reserved.

Ku Protein Levels, Localization and Association to Replication Origins in Different Stages of Breast Tumor Progression

PubMed Central

Abdelbaqi, Khalil; Di Paola, Domenic; Rampakakis, Emmanouil; Zannis-Hadjopoulos, Maria

2013-01-01

Human origins of DNA replication are specific sequences within the genome whereby DNA replication is initiated. A select group of proteins, known as the pre-replication (pre-RC) complex, in whose formation the Ku protein (Ku70/Ku86) was shown to play a role, bind to replication origins to initiate DNA replication. In this study, we have examined the involvement of Ku in breast tumorigenesis and tumor progression and found that the Ku protein expression levels in human breast metastatic (MCF10AC1a) cells were higher in the chromatin fraction compared to hyperplastic (MCF10AT) and normal (MCF10A) human breast cells, but remained constant in both the nuclear and cytoplasmic fractions. In contrast, in human intestinal cells, the Ku expression level was relatively constant for all cell fractions. Nascent DNA abundance and chromatin association of Ku70/86 revealed that the c-myc origin activity in MCF10AC1a is 2.5 to 5-fold higher than in MCF10AT and MCF10A, respectively, and Ku was bound to the c-myc origin more abundantly in MCF10AC1a, by approximately 1.5 to 4.2-fold higher than in MCF10AT and MCF10A, respectively. In contrast, similar nascent DNA abundance and chromatin association was found for all cell lines for the lamin B2 origin, associated with the constitutively active housekeeping lamin B2 gene. Electrophoretic mobility shift assays (EMSAs) performed on the nuclear extracts (NEs) of the three cell types revealed the presence of protein-DNA replication complexes on both the c-myc and lamin B2 origins, but an increase in binding activity was observed from normal, to transformed, to cancer cells for the c-myc origin, whereas no such difference was seen for the lamin B2 origin. Overall, the results suggest that increased Ku chromatin association, beyond wild type levels, alters cellular processes, which have been implicated in tumorigenesis. PMID:23781282

Pentachlorophenol radical cations generated on Fe(III)-montmorillonite initiate octachlorodibenzo-p-dioxin formation in clays: DFT and FTIR studies

PubMed Central

Gu, Cheng; Liu, Cun; Johnston, Cliff T.; Teppen, Brian J.; Li, Hui; Boyd, Stephen A.

2011-01-01

Octachlorodibenzodioxin (OCDD) forms spontaneously from pentachlorophenol (PCP) on the surfaces of Fe(III)-saturated smectite clay (1). Here, we used in situ FTIR methods and quantum mechanical calculations to determine the mechanism by which this reaction is initiated. As the clay was dehydrated, vibrational spectra showed new peaks that grew and then reversibly disappeared as the clay rehydrated. First principle DFT calculations of hydrated Fe-PCP clusters reproduced these transient FTIR peaks when inner-sphere complexation and concomitant electron transfer produced Fe(II) and PCP radical cations. Thus, our experimental (FTIR) and theoretical (quantum mechanical) results mutually support the hypothesis that OCDD formation on Fe-smectite surfaces is initiated by the reversible formation of metastable PCP radical cations via single electron transfer from PCP to Fe(III). The negatively charged clay surface apparently selects for this reaction mechanism by stabilizing PCP radical cations. PMID:21254769

Formation of costs of high-rise objects of housing and civil purpose based on enlarged norms

NASA Astrophysics Data System (ADS)

Vorotyntseva, Anna; Ovsiannikov, Andrei; Bolgov, Vladimir

2018-03-01

When determining the cost of capital construction objects, for purposes of pre-design workings out and purposes of initial maximum initial price determination on tenders, construction price norms are used (CPNs). Modern CPNs are not designed to determine the value of high-rise buildings. It is necessary to adapt modern CPNs to get opportunity for the possibility to take into account special cost factors in determining the cost of high-rise buildings. The main ways can be: selection of new representative objects or application of additional correction factors.

Inhibition of ribosome recruitment induces stress granule formation independently of eukaryotic initiation factor 2alpha phosphorylation.

PubMed

Mazroui, Rachid; Sukarieh, Rami; Bordeleau, Marie-Eve; Kaufman, Randal J; Northcote, Peter; Tanaka, Junichi; Gallouzi, Imed; Pelletier, Jerry

2006-10-01

Cytoplasmic aggregates known as stress granules (SGs) arise as a consequence of cellular stress and contain stalled translation preinitiation complexes. These foci are thought to serve as sites of mRNA storage or triage during the cell stress response. SG formation has been shown to require induction of eukaryotic initiation factor (eIF)2alpha phosphorylation. Herein, we investigate the potential role of other initiation factors in this process and demonstrate that interfering with eIF4A activity, an RNA helicase required for the ribosome recruitment phase of translation initiation, induces SG formation and that this event is not dependent on eIF2alpha phosphorylation. We also show that inhibition of eIF4A activity does not impair the ability of eIF2alpha to be phosphorylated under stress conditions. Furthermore, we observed SG assembly upon inhibition of cap-dependent translation after poliovirus infection. We propose that SG modeling can occur via both eIF2alpha phosphorylation-dependent and -independent pathways that target translation initiation.

Inhibition of Ribosome Recruitment Induces Stress Granule Formation Independently of Eukaryotic Initiation Factor 2α Phosphorylation

PubMed Central

Mazroui, Rachid; Sukarieh, Rami; Bordeleau, Marie-Eve; Kaufman, Randal J.; Northcote, Peter; Tanaka, Junichi; Gallouzi, Imed

2006-01-01

Cytoplasmic aggregates known as stress granules (SGs) arise as a consequence of cellular stress and contain stalled translation preinitiation complexes. These foci are thought to serve as sites of mRNA storage or triage during the cell stress response. SG formation has been shown to require induction of eukaryotic initiation factor (eIF)2α phosphorylation. Herein, we investigate the potential role of other initiation factors in this process and demonstrate that interfering with eIF4A activity, an RNA helicase required for the ribosome recruitment phase of translation initiation, induces SG formation and that this event is not dependent on eIF2α phosphorylation. We also show that inhibition of eIF4A activity does not impair the ability of eIF2α to be phosphorylated under stress conditions. Furthermore, we observed SG assembly upon inhibition of cap-dependent translation after poliovirus infection. We propose that SG modeling can occur via both eIF2α phosphorylation-dependent and -independent pathways that target translation initiation. PMID:16870703

Empowerment through Risk: Unpacking an Approach to Working in Dance with Pre-Service Primary Teachers in New Zealand

ERIC Educational Resources Information Center

Cheesman, Sue

2016-01-01

This article, through interrogating, exploring, and probing my pedagogical practice, aims to probe the issues and complexities involved in teaching dance education with university students studying to be primary classroom teachers in New Zealand. Drawing on two decades of experience, working with students in initial teacher education programs,…

Cwf16p Associating with the Nineteen Complex Ensures Ordered Exon Joining in Constitutive Pre-mRNA Splicing in Fission Yeast

PubMed Central

Sasaki-Haraguchi, Noriko; Ikuyama, Takeshi; Yoshii, Shogo; Takeuchi-Andoh, Tomoko; Frendewey, David; Tani, Tokio

2015-01-01

Exons are ligated in an ordered manner without the skipping of exons in the constitutive splicing of pre-mRNAs with multiple introns. To identify factors ensuring ordered exon joining in constitutive pre-mRNA splicing, we previously screened for exon skipping mutants in Schizosaccharomyces pombe using a reporter plasmid, and characterized three exon skipping mutants named ods1 (ordered splicing 1), ods2, and ods3, the responsible genes of which encode Prp2/U2AF59, U2AF23, and SF1, respectively. They form an SF1-U2AF59-U2AF23 complex involved in recognition of the branch and 3′ splice sites in pre-mRNA. In the present study, we identified a fourth ods mutant, ods4, which was isolated in an exon-skipping screen. The ods4 + gene encodes Cwf16p, which interacts with the NineTeen Complex (NTC), a complex thought to be involved in the first catalytic step of the splicing reaction. We isolated two multi-copy suppressors for the ods4-1 mutation, Srp2p, an SR protein essential for pre-mRNA splicing, and Tif213p, a translation initiation factor, in S. pombe. The overexpression of Srp2p suppressed the exon-skipping phenotype of all ods mutants, whereas Tif213p suppressed only ods4-1, which has a mutation in the translational start codon of the cwf16 gene. We also showed that the decrease in the transcriptional elongation rate induced by drug treatment suppressed exon skipping in ods4-1. We propose that Cwf16p/NTC participates in the early recognition of the branch and 3′ splice sites and cooperates with the SF1-U2AF59-U2AF23 complex to maintain ordered exon joining. PMID:26302002

Novel One-Tube-One-Step Real-Time Methodology for Rapid Transcriptomic Biomarker Detection: Signal Amplification by Ternary Initiation Complexes.

PubMed

Fujita, Hiroto; Kataoka, Yuka; Tobita, Seiji; Kuwahara, Masayasu; Sugimoto, Naoki

2016-07-19

We have developed a novel RNA detection method, termed signal amplification by ternary initiation complexes (SATIC), in which an analyte sample is simply mixed with the relevant reagents and allowed to stand for a short time under isothermal conditions (37 °C). The advantage of the technique is that there is no requirement for (i) heat annealing, (ii) thermal cycling during the reaction, (iii) a reverse transcription step, or (iv) enzymatic or mechanical fragmentation of the target RNA. SATIC involves the formation of a ternary initiation complex between the target RNA, a circular DNA template, and a DNA primer, followed by rolling circle amplification (RCA) to generate multiple copies of G-quadruplex (G4) on a long DNA strand like beads on a string. The G4s can be specifically fluorescence-stained with N(3)-hydroxyethyl thioflavin T (ThT-HE), which emits weakly with single- and double-stranded RNA/DNA but strongly with parallel G4s. An improved dual SATIC system, which involves the formation of two different ternary initiation complexes in the RCA process, exhibited a wide quantitative detection range of 1-5000 pM. Furthermore, this enabled visual observation-based RNA detection, which is more rapid and convenient than conventional isothermal methods, such as reverse transcription-loop-mediated isothermal amplification, signal mediated amplification of RNA technology, and RNA-primed rolling circle amplification. Thus, SATIC methodology may serve as an on-site and real-time measurement technique for transcriptomic biomarkers for various diseases.

Electrocatalytic Oxidation of Formate by [Ni(P R 2 N R' 2 ) 2 (CH 3 CN)] 2+ Complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Galan, Brandon R.; Schöffel, Julia; Linehan, John C.

2011-08-17

New [Ni(P R 2N R` 2) 2+(CH 3CN)] 2+ complexes with R = Ph, R` = 4-MeOPh; R = Cy, R` = Ph and a mixed ligand [Ni(P R 2N R` 2)(P R`` 2N R` 2)] 2+ with R = Cy, R` = Ph, R`` = Ph have been synthesized and characterized by single crystal X-ray crystallography. These complexes are shown to be electrocatalysts for the oxidation of formate in solution to produce CO 2, protons, and electrons with rates which are first order in catalyst and in formate at formate concentrations below approximately 0.05 M. For the catalysts studied,more » maximum observed turnover frequencies vary from <1.1 s -1 to 12.5 s -1 at room temperature, which are the highest rates yet reported for formate oxidation by homogeneous catalysts. A mechanistic scheme is proposed which involves an initial nickel complex bound <1-OC(O)H followed by a rate limiting hydride transfer step. An acetate complex demonstrating the η 1-OC(O)CH 3 binding mode to nickel has also been synthesized and characterized by single crystal X-ray crystallography. The pendant amines have been demonstrated to be essential for this electrocatalytic activity as no activity toward formate was found for the similar [Ni(depe) 2][BF 4] 2+ (depe = diethylphosphinoethane) complex. This work was supported by the US Department of Energy Basic Energy Sciences' Chemical Sciences, Geosciences & Biosciences Division. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.« less

Splicing of goose parvovirus pre-mRNA influences cytoplasmic translation of the processed mRNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Long; Pintel, David J., E-mail: pinteld@missouri.edu

2012-04-25

Translation of goose parvovirus (GPV) 72 kDa Rep 1 is initiated from unspliced P9-generated mRNAs in ORF1 from the first in-frame AUG (537 AUG); however, this AUG is bypassed in spliced P9-generated RNA: translation of the 52 kDa Rep 2 protein from spliced RNA is initiated in ORF2 at the next AUG downstream (650 AUG). Usage of the 537 AUG was restored in spliced RNA when the GPV intron was replaced with a chimeric SV40 intron, or following specific mutations of the GPV intron which did not appear in the final spliced mRNA. Additionally, 650 AUG usage was gained inmore » unspliced RNA when the GPV intron splice sites were debilitated. Splicing-dependent regulation of translation initiation was mediated in cis by GPV RNA surrounding the target AUGs. Thus, nuclear RNA processing of GPV P9-generated pre-mRNAs has a complex, but significant, effect on alternative translation initiation of the GPV Rep proteins.« less

Quantitative assessment of Hox complex expression in the indirect development of the polychaete annelid Chaetopterus sp

NASA Technical Reports Server (NTRS)

Peterson, K. J.; Irvine, S. Q.; Cameron, R. A.; Davidson, E. H.

2000-01-01

A prediction from the set-aside theory of bilaterian origins is that pattern formation processes such as those controlled by the Hox cluster genes are required specifically for adult body plan formation. This prediction can be tested in animals that use maximal indirect development, in which the embryonic formation of the larva and the postembryonic formation of the adult body plan are temporally and spatially distinct. To this end, we quantitatively measured the amount of transcripts for five Hox genes in embryos of a lophotrochozoan, the polychaete annelid Chaetopterus sp. The polychaete Hox complex is shown not to be expressed during embryogenesis, but transcripts of all measured Hox complex genes are detected at significant levels during the initial stages of adult body plan formation. Temporal colinearity in the sequence of their activation is observed, so that activation follows the 3'-5' arrangement of the genes. Moreover, Hox gene expression is spatially localized to the region of teloblastic set-aside cells of the later-stage embryos. This study shows that an indirectly developing lophotrochozoan shares with an indirectly developing deuterostome, the sea urchin, a common mode of Hox complex utilization: construction of the larva, whether a trochophore or dipleurula, does not involve Hox cluster expression, but in both forms the complex is expressed in the set-aside cells from which the adult body plan derives.

Crystal structure and solution species of Ce(III) and Ce(IV) formates: from mononuclear to hexanuclear complexes.

PubMed

Hennig, Christoph; Ikeda-Ohno, Atsushi; Kraus, Werner; Weiss, Stephan; Pattison, Philip; Emerich, Hermann; Abdala, Paula M; Scheinost, Andreas C

2013-10-21

Cerium(III) and cerium(IV) both form formate complexes. However, their species in aqueous solution and the solid-state structures are surprisingly different. The species in aqueous solutions were investigated with Ce K-edge EXAFS spectroscopy. Ce(III) formate shows only mononuclear complexes, which is in agreement with the predicted mononuclear species of Ce(HCOO)(2+) and Ce(HCOO)2(+). In contrast, Ce(IV) formate forms in aqueous solution a stable hexanuclear complex of [Ce6(μ3-O)4(μ3-OH)4(HCOO)x(NO3)y](12-x-y). The structural differences reflect the different influence of hydrolysis, which is weak for Ce(III) and strong for Ce(IV). Hydrolysis of Ce(IV) ions causes initial polymerization while complexation through HCOO(-) results in 12 chelate rings stabilizing the hexanuclear Ce(IV) complex. Crystals were grown from the above-mentioned solutions. Two crystal structures of Ce(IV) formate were determined. Both form a hexanuclear complex with a [Ce6(μ3-O)4(μ3-OH)4](12+) core in aqueous HNO3/HCOOH solution. The pH titration with NaOH resulted in a structure with the composition [Ce6(μ3-O)4(μ3-OH)4(HCOO)10(NO3)2(H2O)3]·(H2O)9.5, while the pH adjustment with NH3 resulted in [Ce6(μ3-O)4(μ3-OH)4(HCOO)10(NO3)4]·(NO3)3(NH4)5(H2O)5. Furthermore, the crystal structure of Ce(III) formate, Ce(HCOO)3, was determined. The coordination polyhedron is a tricapped trigonal prism which is formed exclusively by nine HCOO(-) ligands. The hexanuclear Ce(IV) formate species from aqueous solution is widely preserved in the crystal structure, whereas the mononuclear solution species of Ce(III) formate undergoes a polymerization during the crystallization process.

Evidence for top-heavy stellar initial mass functions with increasing density and decreasing metallicity

NASA Astrophysics Data System (ADS)

Marks, Michael; Kroupa, Pavel; Dabringhausen, Jörg; Pawlowski, Marcel S.

2012-05-01

Residual-gas expulsion after cluster formation has recently been shown to leave an imprint in the low-mass present-day stellar mass function (PDMF) which allowed the estimation of birth conditions of some Galactic globular clusters (GCs) such as mass, radius and star formation efficiency. We show that in order to explain their characteristics (masses, radii, metallicity and PDMF) their stellar initial mass function (IMF) must have been top heavy. It is found that the IMF is required to become more top heavy the lower the cluster metallicity and the larger the pre-GC cloud-core density are. The deduced trends are in qualitative agreement with theoretical expectation. The results are consistent with estimates of the shape of the high-mass end of the IMF in the Arches cluster, Westerlund 1, R136 and NGC 3603, as well as with the IMF independently constrained for ultra-compact dwarf galaxies (UCDs). The latter suggests that GCs and UCDs might have formed along the same channel or that UCDs formed via mergers of GCs. A Fundamental Plane is found which describes the variation of the IMF with density and metallicity of the pre-GC cloud cores. The implications for the evolution of galaxies and chemical enrichment over cosmological times are expected to be major.

Near-atomic resolution visualization of human transcription promoter opening

PubMed Central

He, Yuan; Yan, Chunli; Fang, Jie; Inouye, Carla; Tjian, Robert; Ivanov, Ivaylo; Nogales, Eva

2016-01-01

In eukaryotic transcription initiation, a large multi-subunit pre-initiation complex (PIC) that assembles at the core promoter is required for the opening of the duplex DNA and identification of the start site for transcription by RNA polymerase II. Here we use cryo-electron microscropy (cryo-EM) to determine near-atomic resolution structures of the human PIC in a closed state (engaged with duplex DNA), an open state (engaged with a transcription bubble), and an initially transcribing complex (containing six base pairs of DNA–RNA hybrid). Our studies provide structures for previously uncharacterized components of the PIC, such as TFIIE and TFIIH, and segments of TFIIA, TFIIB and TFIIF. Comparison of the different structures reveals the sequential conformational changes that accompany the transition from each state to the next throughout the transcription initiation process. This analysis illustrates the key role of TFIIB in transcription bubble stabilization and provides strong structural support for a translocase activity of XPB. PMID:27193682

The excavation stage of basin formation - A qualitative model

NASA Technical Reports Server (NTRS)

Croft, S. K.

1981-01-01

One of the most complex problems in planetary geology and geophysics is the determination of the nature of the impact cratering processes at scales of tens to thousands of kilometers that produce the complex morphological structures of multiring basins. The cratering process is frequently considered to be divided into three stages, including a short high-pressure stage of initial contact between the projectile and the planetary crust, a longer excavation or cratering flow stage culminating in the formation of a transient crater, and a still longer modification stage during which the transient crater is modified into the observed final geologic form. The transient crater may be considered as the initial boundary condition of the modification stage. In the present investigation, the nature of the transient crater is indicated by the cratering flow field determined from numerical simulations of the excavation stage. Attention is given to empirical and theoretical scaling.

Density functional theory study of HfCl4, ZrCl4, and Al(CH3)3 decomposition on hydroxylated SiO2: Initial stage of high-k atomic layer deposition

NASA Astrophysics Data System (ADS)

Jeloaica, L.; Estève, A.; Djafari Rouhani, M.; Estève, D.

2003-07-01

The initial stage of atomic layer deposition of HfO2, ZrO2, and Al2O3 high-k films, i.e., the decomposition of HfCl4, ZrCl4, and Al(CH3)3 precursor molecules on an OH-terminated SiO2 surface, is investigated within density functional theory. The energy barriers are determined using artificial activation of vibrational normal modes. For all precursors, reaction proceeds through the formation of intermediate complexes that have equivalent formation energies (˜-0.45 eV), and results in HCl and CH4 formation with activation energies of 0.88, 0.91, and 1.04 eV for Hf, Zr, and Al based precursors, respectively. The reaction product of Al(CH3)3 decomposition is found to be more stable (by -1.45 eV) than the chemisorbed intermediate complex compared to the endothermic decomposition of HfCl4 and ZrCl4 chemisorbed precursors (0.26 and 0.29 eV, respectively).

Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis

PubMed Central

El Hage, Aziz; French, Sarah L.; Beyer, Ann L.; Tollervey, David

2010-01-01

Pre-rRNA transcription by RNA Polymerase I (Pol I) is very robust on active rDNA repeats. Loss of yeast Topoisomerase I (Top1) generated truncated pre-rRNA fragments, which were stabilized in strains lacking TRAMP (Trf4/Trf5–Air1/Air2–Mtr4 polyadenylation complexes) or exosome degradation activities. Loss of both Top1 and Top2 blocked pre-rRNA synthesis, with pre-rRNAs truncated predominately in the 18S 5′ region. Positive supercoils in front of Pol I are predicted to slow elongation, while rDNA opening in its wake might cause R-loop formation. Chromatin immunoprecipitation analysis showed substantial levels of RNA/DNA hybrids in the wild type, particularly over the 18S 5′ region. The absence of RNase H1 and H2 in cells depleted of Top1 increased the accumulation of RNA/DNA hybrids and reduced pre-rRNA truncation and pre-rRNA synthesis. Hybrid accumulation over the rDNA was greatly exacerbated when Top1, Top2, and RNase H were all absent. Electron microscopy (EM) analysis revealed Pol I pileups in the wild type, particularly over the 18S. Pileups were longer and more frequent in the absence of Top1, and their frequency was exacerbated when RNase H activity was also lacking. We conclude that the loss of Top1 enhances inherent R-loop formation, particularly over the 5′ region of the rDNA, imposing persistent transcription blocks when RNase H is limiting. PMID:20634320

Transcription closed and open complex dynamics studies reveal balance between genetic determinants and co-factors

NASA Astrophysics Data System (ADS)

Sala, Adrien; Shoaib, Muhammad; Anufrieva, Olga; Mutharasu, Gnanavel; Jahan Hoque, Rawnak; Yli-Harja, Olli; Kandhavelu, Meenakshisundaram

2015-05-01

In E. coli, promoter closed and open complexes are key steps in transcription initiation, where magnesium-dependent RNA polymerase catalyzes RNA synthesis. However, the exact mechanism of initiation remains to be fully elucidated. Here, using single mRNA detection and dual reporter studies, we show that increased intracellular magnesium concentration affects Plac initiation complex formation resulting in a highly dynamic process over the cell growth phases. Mg2+ regulates transcription transition, which modulates bimodality of mRNA distribution in the exponential phase. We reveal that Mg2+ regulates the size and frequency of the mRNA burst by changing the open complex duration. Moreover, increasing magnesium concentration leads to higher intrinsic and extrinsic noise in the exponential phase. RNAP-Mg2+ interaction simulation reveals critical movements creating a shorter contact distance between aspartic acid residues and Nucleotide Triphosphate residues and increasing electrostatic charges in the active site. Our findings provide unique biophysical insights into the balanced mechanism of genetic determinants and magnesium ion in transcription initiation regulation during cell growth.

Effect of sulfide on As(III) and As(V) sequestration by ferrihydrite.

PubMed

Zhao, Zhixi; Wang, Shaofeng; Jia, Yongfeng

2017-10-01

The sulfide-induced change in arsenic speciation is often coupled to iron geochemical processes, including redox reaction, adsorption/desorption and precipitation/dissolution. Knowledge about how sulfide influenced the coupled geochemistry of iron and arsenic was not explored well up to now. In this work, retention and mobilization of As(III) and As(V) on ferrihydrite in sulfide-rich environment was studied. The initial oxidation states of arsenic and the contact order of sulfide notably influenced arsenic sequestration on ferrihydrite. For As(III) systems, pre-sulfidation of As(III) decreased arsenic sequestration mostly. The arsenic adsorption capacity decreased about 50% in comparison with the system without sulfide addition. For As(V) systems, pre-sulfidation of ferrihydrite decreased 30% sequestration of arsenic on ferrihydrite. Reduction of ferrihydrite by sulfide in As(V) system was higher than that in As(III) system. Geochemical modeling calculations identified formation of thioarsenite in the pre-sulfidation of As(III) system. Formation of arsenic thioanions enhanced As solubility in the pre-sulfidation of As(III) system. The high concentration of sulfide and Fe(II) in pre-sulfidation of ferrihydrite system contributed to saturation of FeS. This supplied new solid phase to immobilize soluble arsenic in aqueous phase. X-ray absorption near edge spectroscopy (XANES) of sulfur K-edge, arsenic K-edge and iron L-edge analysis gave the consistent evidence for the sulfidation reaction of arsenic and ferrihydrite under specific geochemical settings. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Developmental Framework for Complex Plasmodesmata Formation Revealed by Large-Scale Imaging of the Arabidopsis Leaf Epidermis[W

PubMed Central

Fitzgibbon, Jessica; Beck, Martina; Zhou, Ji; Faulkner, Christine; Robatzek, Silke; Oparka, Karl

2013-01-01

Plasmodesmata (PD) form tubular connections that function as intercellular communication channels. They are essential for transporting nutrients and for coordinating development. During cytokinesis, simple PDs are inserted into the developing cell plate, while during wall extension, more complex (branched) forms of PD are laid down. We show that complex PDs are derived from existing simple PDs in a pattern that is accelerated when leaves undergo the sink–source transition. Complex PDs are inserted initially at the three-way junctions between epidermal cells but develop most rapidly in the anisocytic complexes around stomata. For a quantitative analysis of complex PD formation, we established a high-throughput imaging platform and constructed PDQUANT, a custom algorithm that detected cell boundaries and PD numbers in different wall faces. For anticlinal walls, the number of complex PDs increased with increasing cell size, while for periclinal walls, the number of PDs decreased. Complex PD insertion was accelerated by up to threefold in response to salicylic acid treatment and challenges with mannitol. In a single 30-min run, we could derive data for up to 11k PDs from 3k epidermal cells. This facile approach opens the door to a large-scale analysis of the endogenous and exogenous factors that influence PD formation. PMID:23371949

Location of RAD51-like protein during meiotic prophase in Eimeria tenella.

PubMed

Del Cacho, Emilio; Gallego, Margarita; Pagés, Marc; Barbero, José Luís; Monteagudo, Luís; Sánchez-Acedo, Caridad

2011-05-31

This study focuses on reporting events in Eimeria tenella oocysts from early to late prophase I in terms of RAD51 protein in association with the synaptonemal complex formed between homologous chromosomes. The aim of the study was the sequential localization of RAD51 protein, which is involved in the repair of double-strand breaks (DSBs) on the eimerian chromosomes as they synapse and desynapse. Structural Maintenance of Chromosome protein SMC3, which plays a role in synaptonemal complex formation, was labeled to identify initiation and progress of chromosome synapsis and desynapsis in parallel with the appearance and disappearance of RAD51 foci. Antibodies directed against RAD51 and cohesin subunit SMC3 proteins were labeled with either fluorescence or colloidal gold to visualize RAD51 protein foci and synaptonemal complexes. RAD51 protein localization during prophase I was studied on meiotic chromosomes spreads obtained from oocysts at different points in time after the start of sporulation. The present findings showed that foci detected with the antibody directed against RAD51 protein first appeared at the pre-leptotene stage before homologous chromosomes began pairing. Subsequently, the foci were detected in association with the lateral elements at the precise sites where synapsis were in progress. These findings lead us to suggest that in E. tenella, homologous chromosome pairing was a DSB-dependent mechanism and reinforced the participation of RAD51 protein in meiotic homology search, alignment and pairing of chromosomes. Copyright © 2010 Elsevier B.V. All rights reserved.

LDB1-mediated enhancer looping can be established independent of mediator and cohesin.

PubMed

Krivega, Ivan; Dean, Ann

2017-08-21

Mechanistic studies in erythroid cells indicate that LDB1, as part of a GATA1/TAL1/LMO2 complex, brings erythroid-expressed genes into proximity with enhancers for transcription activation. The role of co-activators in establishing this long-range interaction is poorly understood. Here we tested the contributions of the RNA Pol II pre-initiation complex (PIC), mediator and cohesin to establishment of locus control region (LCR)/β-globin proximity. CRISPR/Cas9 editing of the β-globin promoter to eliminate the RNA Pol II PIC by deleting the TATA-box resulted in loss of transcription, but enhancer-promoter interaction was unaffected. Additional deletion of the promoter GATA1 site eliminated LDB1 complex and mediator occupancy and resulted in loss of LCR/β-globin proximity. To separate the roles of LDB1 and mediator in LCR looping, we expressed a looping-competent but transcription-activation deficient form of LDB1 in LDB1 knock down cells: LCR/β-globin proximity was restored without mediator core occupancy. Further, Cas9-directed tethering of mutant LDB1 to the β-globin promoter forced LCR loop formation in the absence of mediator or cohesin occupancy. Moreover, ENCODE data and our chromatin immunoprecipitation results indicate that cohesin is almost completely absent from validated and predicted LDB1-regulated erythroid enhancer-gene pairs. Thus, lineage specific factors largely mediate enhancer-promoter looping in erythroid cells independent of mediator and cohesin. Published by Oxford University Press on behalf of Nucleic Acids Research 2017.

Livestock-Associated Methicillin-Resistant Staphylococcus aureus (LA-MRSA) Isolates of Swine Origin Form Robust Biofilms

PubMed Central

Nicholson, Tracy L.; Shore, Sarah M.; Smith, Tara C.; Fraena, Timothy S.

2013-01-01

Methicillin-resistant Staphylococcus aureus (MRSA) colonization of livestock animals is common and prevalence rates for pigs have been reported to be as high as 49%. Mechanisms contributing to the persistent carriage and high prevalence rates of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) strains in swine herds and production facilities have not been investigated. One explanation for the high prevalence of MRSA in swine herds is the ability of these organisms to exist as biofilms. In this report, the ability of swine LA-MRSA strains, including ST398, ST9, and ST5, to form biofilms was quantified and compared to several swine and human isolates. The contribution of known biofilm matrix components, polysaccharides, proteins and extracellular DNA (eDNA), was tested in all strains as well. All MRSA swine isolates formed robust biofilms similar to human clinical isolates. The addition of Dispersin B had no inhibitory effect on swine MRSA isolates when added at the initiation of biofilm growth or after pre-established mature biofilms formed. In contrast, the addition of proteinase K inhibited biofilm formation in all strains when added at the initiation of biofilm growth and was able to disperse pre-established mature biofilms. Of the LA-MRSA strains tested, we found ST398 strains to be the most sensitive to both inhibition of biofilm formation and dispersal of pre-formed biofilms by DNaseI. Collectively, these findings provide a critical first step in designing strategies to control or eliminate MRSA in swine herds. PMID:23951352

Sequential Metabolism of Secondary Alkyl Amines to Metabolic-Intermediate Complexes: Opposing Roles for the Secondary Hydroxylamine and Primary Amine Metabolites of Desipramine, (S)-Fluoxetine, and N-Desmethyldiltiazem

PubMed Central

Hanson, Kelsey L.; VandenBrink, Brooke M.; Babu, Kantipudi N.; Allen, Kyle E.; Nelson, Wendel L.

2010-01-01

Three secondary amines desipramine (DES), (S)-fluoxetine [(S)-FLX], and N-desmethyldiltiazem (MA) undergo N-hydroxylation to the corresponding secondary hydroxylamines [N-hydroxydesipramine, (S)-N-hydroxyfluoxetine, and N-hydroxy-N-desmethyldiltiazem] by cytochromes P450 2C11, 2C19, and 3A4, respectively. The expected primary amine products, N-desmethyldesipramine, (S)-norfluoxetine, and N,N-didesmethyldiltiazem, are also observed. The formation of metabolic-intermediate (MI) complexes from these substrates and metabolites was examined. In each example, the initial rates of MI complex accumulation followed the order secondary hydroxylamine > secondary amine ≫ primary amine, suggesting that the primary amine metabolites do not contribute to formation of MI complexes from these secondary amines. Furthermore, the primary amine metabolites, which accumulate in incubations of the secondary amines, inhibit MI complex formation. Mass balance studies provided estimates of the product ratios of N-dealkylation to N-hydroxylation. The ratios were 2.9 (DES-CYP2C11), 3.6 [(S)-FLX-CYP2C19], and 0.8 (MA-CYP3A4), indicating that secondary hydroxylamines are significant metabolites of the P450-mediated metabolism of secondary alkyl amines. Parallel studies with N-methyl-d3-desipramine and CYP2C11 demonstrated significant isotopically sensitive switching from N-demethylation to N-hydroxylation. These findings demonstrate that the major pathway to MI complex formation from these secondary amines arises from N-hydroxylation rather than N-dealkylation and that the primary amines are significant competitive inhibitors of MI complex formation. PMID:20200233

Sequential metabolism of secondary alkyl amines to metabolic-intermediate complexes: opposing roles for the secondary hydroxylamine and primary amine metabolites of desipramine, (s)-fluoxetine, and N-desmethyldiltiazem.

PubMed

Hanson, Kelsey L; VandenBrink, Brooke M; Babu, Kantipudi N; Allen, Kyle E; Nelson, Wendel L; Kunze, Kent L

2010-06-01

Three secondary amines desipramine (DES), (S)-fluoxetine [(S)-FLX], and N-desmethyldiltiazem (MA) undergo N-hydroxylation to the corresponding secondary hydroxylamines [N-hydroxydesipramine, (S)-N-hydroxyfluoxetine, and N-hydroxy-N-desmethyldiltiazem] by cytochromes P450 2C11, 2C19, and 3A4, respectively. The expected primary amine products, N-desmethyldesipramine, (S)-norfluoxetine, and N,N-didesmethyldiltiazem, are also observed. The formation of metabolic-intermediate (MI) complexes from these substrates and metabolites was examined. In each example, the initial rates of MI complex accumulation followed the order secondary hydroxylamine > secondary amine > primary amine, suggesting that the primary amine metabolites do not contribute to formation of MI complexes from these secondary amines. Furthermore, the primary amine metabolites, which accumulate in incubations of the secondary amines, inhibit MI complex formation. Mass balance studies provided estimates of the product ratios of N-dealkylation to N-hydroxylation. The ratios were 2.9 (DES-CYP2C11), 3.6 [(S)-FLX-CYP2C19], and 0.8 (MA-CYP3A4), indicating that secondary hydroxylamines are significant metabolites of the P450-mediated metabolism of secondary alkyl amines. Parallel studies with N-methyl-d(3)-desipramine and CYP2C11 demonstrated significant isotopically sensitive switching from N-demethylation to N-hydroxylation. These findings demonstrate that the major pathway to MI complex formation from these secondary amines arises from N-hydroxylation rather than N-dealkylation and that the primary amines are significant competitive inhibitors of MI complex formation.

Functional Architecture of T7 RNA Polymerase Transcription Complexes

PubMed Central

Nayak, Dhananjaya; Guo, Qing; Sousa, Rui

2007-01-01

Summary T7 RNA polymerase is the best-characterized member of a widespread family of single-subunit RNA polymerases. Crystal structures of T7 RNA polymerase initiation and elongation complexes have provided a wealth of detailed information on RNA polymerase interactions with the promoter and transcription bubble, but the absence of DNA downstream of the melted region of the template in the initiation complex structure, and the absence of DNA upstream of the transcription bubble in the elongation complex structure means that our picture of the functional architecture of T7 RNA polymerase transcription complexes remains incomplete. Here we use the site-specifically tethered chemical nucleases and functional characterization of directed T7 RNAP mutants to both reveal the architecture of the duplex DNA that flanks the transcription bubble in the T7 RNAP initiation and elongation complexes, and to define the function of the interactions made by these duplex elements. We find that downstream duplex interactions made with a cluster of lysines (K711/K713/K714) are present during both elongation and initiation where they contribute to stabilizing a bend in the downstream DNA that is important for promoter opening. The upstream DNA in the elongation complex is also found to be sharply bent at the upstream edge of the transcription bubble, thereby allowing formation of upstream duplex:polymerase interactions that contribute to elongation complex stability. PMID:17580086

N-terminal lysines are essential for protein translocation via a modified ERAD system in complex plastids.

PubMed

Lau, Julia B; Stork, Simone; Moog, Daniel; Sommer, Maik S; Maier, Uwe G

2015-05-01

Nuclear-encoded pre-proteins being imported into complex plastids of red algal origin have to cross up to five membranes. Thereby, transport across the second outermost or periplastidal membrane (PPM) is facilitated by SELMA (symbiont-specific ERAD-like machinery), an endoplasmic reticulum-associated degradation (ERAD)-derived machinery. Core components of SELMA are enzymes involved in ubiquitination (E1-E3), a Cdc48 ATPase complex and Derlin proteins. These components are present in all investigated organisms with four membrane-bound complex plastids of red algal origin, suggesting a ubiquitin-dependent translocation process of substrates mechanistically similar to the process of retro-translocation in ERAD. Even if, according to the current model, translocation via SELMA does not end up in the classical poly-ubiquitination, transient mono-/oligo-ubiquitination of pre-proteins might be required for the mechanism of translocation. We investigated the import mechanism of SELMA and were able to show that protein transport across the PPM depends on lysines in the N-terminal but not in the C-terminal part of pre-proteins. These lysines are predicted to be targets of ubiquitination during the translocation process. As proteins lacking the N-terminal lysines get stuck in the PPM, a 'frozen intermediate' of the translocation process could be envisioned and initially characterized. © 2015 John Wiley & Sons Ltd.

Quantitative imaging reveals real-time Pou5f3–Nanog complexes driving dorsoventral mesendoderm patterning in zebrafish

PubMed Central

Perez-Camps, Mireia; Tian, Jing; Chng, Serene C; Sem, Kai Pin; Sudhaharan, Thankiah; Teh, Cathleen; Wachsmuth, Malte; Korzh, Vladimir; Ahmed, Sohail; Reversade, Bruno

2016-01-01

Formation of the three embryonic germ layers is a fundamental developmental process that initiates differentiation. How the zebrafish pluripotency factor Pou5f3 (homologous to mammalian Oct4) drives lineage commitment is unclear. Here, we introduce fluorescence lifetime imaging microscopy and fluorescence correlation spectroscopy to assess the formation of Pou5f3 complexes with other transcription factors in real-time in gastrulating zebrafish embryos. We show, at single-cell resolution in vivo, that Pou5f3 complexes with Nanog to pattern mesendoderm differentiation at the blastula stage. Later, during gastrulation, Sox32 restricts Pou5f3–Nanog complexes to the ventrolateral mesendoderm by binding Pou5f3 or Nanog in prospective dorsal endoderm. In the ventrolateral endoderm, the Elabela / Aplnr pathway limits Sox32 levels, allowing the formation of Pou5f3–Nanog complexes and the activation of downstream BMP signaling. This quantitative model shows that a balance in the spatiotemporal distribution of Pou5f3–Nanog complexes, modulated by Sox32, regulates mesendoderm specification along the dorsoventral axis. DOI: http://dx.doi.org/10.7554/eLife.11475.001 PMID:27684073

Pre-injection brine production for managing pressure in compartmentalized CO₂ storage reservoirs

DOE PAGES

Buscheck, Thomas A.; White, Joshua A.; Chen, Mingjie; ...

2014-12-31

We present a reservoir management approach for geologic CO₂ storage that combines CO₂ injection with brine extraction. In our approach, dual-mode wells are initially used to extract formation brine and subsequently used to inject CO₂. These wells can also be used to monitor the subsurface during pre-injection brine extraction so that key data is acquired and analyzed prior to CO₂ injection. The relationship between pressure drawdown during pre-injection brine extraction and pressure buildup during CO₂ injection directly informs reservoir managers about CO₂ storage capacity. These data facilitate proactive reservoir management, and thus reduce costs and risks. The brine may bemore » used directly as make-up brine for nearby reservoir operations; it can also be desalinated and/or treated for a variety of beneficial uses.« less

Antibiofilm Activity of an Exopolysaccharide from Marine Bacterium Vibrio sp. QY101

PubMed Central

Han, Feng; Duan, Gaofei; Lu, Xinzhi; Gu, Yuchao; Yu, Wengong

2011-01-01

Bacterial exopolysaccharides have always been suggested to play crucial roles in the bacterial initial adhesion and the development of complex architecture in the later stages of bacterial biofilm formation. However, Escherichia coli group II capsular polysaccharide was characterized to exert broad-spectrum biofilm inhibition activity. In this study, we firstly reported that a bacterial exopolysaccharide (A101) not only inhibits biofilm formation of many bacteria but also disrupts established biofilm of some strains. A101 with an average molecular weight of up to 546 KDa, was isolated and purified from the culture supernatant of the marine bacterium Vibrio sp. QY101 by ethanol precipitation, iron-exchange chromatography and gel filtration chromatography. High performance liquid chromatography traces of the hydrolyzed polysaccharides showed that A101 is primarily consisted of galacturonic acid, glucuronic acid, rhamnose and glucosamine. A101 was demonstrated to inhibit biofilm formation by a wide range of Gram-negative and Gram-positive bacteria without antibacterial activity. Furthermore, A101 displayed a significant disruption on the established biofilm produced by Pseudomonas aeruginosa, but not by Staphylococcus aureus. Importantly, A101 increased the aminoglycosides antibiotics' capability of killing P. aeruginosa biofilm. Cell primary attachment to surfaces and intercellular aggregates assays suggested that A101 inhibited cell aggregates of both P. aeruginosa and S. aureus, while the cell-surface interactions inhibition only occurred in S. aureus, and the pre-formed cell aggregates dispersion induced by A101 only occurred in P. aeruginosa. Taken together, these data identify the antibiofilm activity of A101, which may make it potential in the design of new therapeutic strategies for bacterial biofilm-associated infections and limiting biofilm formation on medical indwelling devices. The found of A101 antibiofilm activity may also promote a new recognition about the functions of bacterial exopolysaccharides. PMID:21490923

Structural basis of agrin-LRP4-MuSK signaling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zong, Yinong; Zhang, Bin; Gu, Shenyan

Synapses are the fundamental units of neural circuits that enable complex behaviors. The neuromuscular junction (NMJ), a synapse formed between a motoneuron and a muscle fiber, has contributed greatly to understanding of the general principles of synaptogenesis as well as of neuromuscular disorders. NMJ formation requires neural agrin, a motoneuron-derived protein, which interacts with LRP4 (low-density lipoprotein receptor-related protein 4) to activate the receptor tyrosine kinase MuSK (muscle-specific kinase). However, little is known of how signals are transduced from agrin to MuSK. Here, we present the first crystal structure of an agrin-LRP4 complex, consisting of two agrin-LRP4 heterodimers. Formation ofmore » the initial binary complex requires the z8 loop that is specifically present in neuronal, but not muscle, agrin and that promotes the synergistic formation of the tetramer through two additional interfaces. We show that the tetrameric complex is essential for neuronal agrin-induced acetylcholine receptor (AChR) clustering. Collectively, these results provide new insight into the agrin-LRP4-MuSK signaling cascade and NMJ formation and represent a novel mechanism for activation of receptor tyrosine kinases.« less

Chabazite and dolomite formation in a dolocrete profile: An example of a complex alkaline paragenesis in Lanzarote, Canary Islands

NASA Astrophysics Data System (ADS)

Alonso-Zarza, Ana M.; Bustamante, Leticia; Huerta, Pedro; Rodríguez-Berriguete, Álvaro; Huertas, María José

2016-05-01

This paper studies the weathering and soil formation processes operating on detrital sediments containing alkaline volcanic rock fragments of the Mirador del Río dolocrete profile. The profile consists of a lower horizon of removilised weathered basalts, an intermediate red sandy mudstones horizon with irregular carbonate layers and a topmost horizon of amalgamated carbonate layers with root traces. Formation occurred in arid to semiarid climates, giving place to a complex mineralogical association, including Mg-carbonates and chabazite, rarely described in cal/dolocretes profiles. Initial vadose weathering processes occurred in the basalts and in directly overlying detrital sediments, producing (Stage 1) red-smectites and dolomicrite. Dominant phreatic (Stage 2) conditions allowed precipitation of coarse-zoned dolomite and chabazite filling porosities. In Stages 3 and 4, mostly pedogenic, biogenic processes played an important role in dolomite and calcite accumulation in the profile. Overall evolution of the profile and its mineralogical association involved initial processes dominated by alteration of host rock, to provide silica and Mg-rich alkaline waters, suitable for chabazite and dolomite formation, without a previous carbonate phase. Dolomite formed both abiogenically and biogenically, but without a previous carbonate precursor and in the absence of evaporites. Dominance of calcite towards the profile top is the result of Mg/Ca decrease in the interstitial meteoric waters due to decreased supply of Mg from weathering, and increased supply of Ca in aeolian dust. Meteoric origin of the water is confirmed by C and O isotope values, which also indicate lack of deep sourced CO2. The dolocrete studied and its complex mineral association reveal the complex interactions that occur at surface during weathering and pedogenesis of basalt-sourced rocks.

Ultrastructural analyses of somatic embryo initiation, development and polarity establishment from mesophyll cells of Dactylis glomerata

NASA Technical Reports Server (NTRS)

Vasilenko, A.; McDaniel, J. K.; Conger, B. V.

2000-01-01

Somatic embryos initiate and develop directly from single mesophyll cells in in vitro-cultured leaf segments of orchardgrass (Dactylis glomerata L.). Embryogenic cells establish themselves in the predivision stage by formation of thicker cell walls and dense cytoplasm. Electron microscopy observations for embryos ranging from the pre-cell-division stage to 20-cell proembryos confirm previous light microscopy studies showing a single cell origin. They also confirm that the first division is predominantly periclinal and that this division plane is important in establishing embryo polarity and in determining the embryo axis. If the first division is anticlinal or if divisions are in random planes after the first division, divisions may not continue to produce an embryo. This result may produce an embryogenic cell mass, callus formation, or no structure at all. Grant numbers: NAGW-3141, NAG10-0221.

Hemolymph Melanization in the Silkmoth Bombyx mori Involves Formation of a High Molecular Mass Complex That Metabolizes Tyrosine*

PubMed Central

Clark, Kevin D.; Strand, Michael R.

2013-01-01

The phenoloxidase (PO) cascade regulates the melanization of blood (hemolymph) in insects and other arthropods. Most studies indicate that microbial elicitors activate the PO cascade, which results in processing of the zymogen PPO to PO. PO is then thought to oxidize tyrosine and o-diphenols to quinones, which leads to melanin. However, different lines of investigation raise questions as to whether these views are fully correct. Here we report that hemolymph from the silkmoth, Bombyx mori, rapidly melanizes after collection from a wound site. Prior studies indicated that in vitro activated PPO hydroxylates Tyr inefficiently. Measurement of in vivo substrate titers, however, suggested that Tyr was the only PO substrate initially present in B. mori plasma and that it is rapidly metabolized by PO. Fractionation of plasma by gel filtration chromatography followed by bioassays indicated that melanization activity was primarily associated with a high mass complex (∼670 kDa) that contained PO. The prophenoloxidase-activating protease inhibitor Egf1.0 blocked formation of this complex and Tyr metabolism, but the addition of phenylthiourea to plasma before fractionation enhanced complex formation and Tyr metabolism. Mass spectrometry analysis indicated that the complex contained PO plus other proteins. Taken together, our results indicate that wounding alone activates the PO cascade in B. mori. They also suggest that complex formation is required for efficient use of Tyr as a substrate. PMID:23553628

Effect of milling time and annealing temperature on nanoparticles evolution for 13.5% Cr ODS ferritic steel powders by joint application of XAFS and TEM

NASA Astrophysics Data System (ADS)

He, P.; Hoffmann, J.; Möslang, A.

2018-04-01

The characteristics of strengthening nanoparticles have a major influence on the mechanical property and irradiation resistance of oxide dispersion strengthened (ODS) steels. To determine how to control nanoparticles evolution, 0.3% Ti with 0.3% Y2O3 were added in 13.5%Cr pre-alloyed steel powders via different milling and consolidation conditions, then characterized by transmission electron microscopy (TEM) and X-ray absorption fine structure (XAFS) at synchrotron irradiation facility. The dissolution of Y2O3 is greatly dependent on the milling time at fixed milling speeds. After 24 h of milling, only minor amounts of the initially added Y2O3 dissolve into the steel matrix whereas TEM results reveal nearly complete dissolution of Y2O3 in 80-h-milled powder. The annealed powder FT-A800 (at 800 °C for 1 h) exhibits a structure near to the initially added Y2O3. The slightly deviation may be accounted for considerable lattice distortion related to the presence of atomic vacancies or formation of Y-Ti-O nucleus. The annealed powders FT-A1000 and FT-A1100 contain complex mixtures of Y-O/Y-Ti-O oxides, which cannot be fitted by any single thermally stable compounds. The coordination numbers of these first two shells in the annealed powders significantly raise as a function of the annealing temperature, indicating the formation of more ordered Y-O or Y-Ti-O particles. The extended X-ray absorption fine structure (EXAFS) spectrum could not necessarily distinguish the dominant oxide species.

MYSST: Mapping Young Stars in Space and Time - The HII Complex N44 in the LMC

NASA Astrophysics Data System (ADS)

Gouliermis, Dimitrios

2016-10-01

The stellar initial mass function (IMF), and the timescale and lengthscale of star formation (SF) are critical issues for our understanding of how stars form. Low-mass pre-main-sequence (PMS) stars, having typical contraction times on the order of a few 10 Myr, are the live chronometers of the SF process and primary informants on the low-mass IMF of their host clusters. Our studies show that young star clusters, embedded in star-forming regions of the Large Magellanic Cloud (LMC), encompass rich samples of PMS stars, sufficient to study clustered SF in low-metallicities with optical HST photometry. Yet, the lack of a complete comprehensive stellar sample retains important questions about the universality of the IMF, and the time- and length-scale of SF across a typical molecular cloud unanswered. We propose to address these issues by employing both ACS and WFC3 with their high sensitivity and spatial resolving power to obtain deep photometry (m_555 29 mag) of the LMC star-forming complex N44. We will accomplish a detailed mapping of PMS stars that will trace the whole hierarchy of star formation springing from one giant molecular cloud. Our analysis will provide an unbiased determination of the timescale for SF and the sub-solar IMF down to the hydrogen burning limit in a variety of clustering scales for the first time. Our findings will have a significant impact on our comprehensive understanding of SF in the low-metallicity environment of the LMC. We maximize the HST observing efficiency using both ACS/WFC and WFC3/UVIS in parallel for the simultaneous observations of N44, its ensemble of HII regions and their young stellar clusters in the same F555W and F814W filters.

Carbonate-coordinated metal complexes precede the formation of liquid amorphous mineral emulsions of divalent metal carbonates†

PubMed Central

Wolf, Stephan E.; Müller, Lars; Barrea, Raul; Kampf, Christopher J.; Leiterer, Jork; Panne, Ulrich; Hoffmann, Thorsten

2011-01-01

During the mineralisation of metal carbonates MCO3 (M = Ca, Sr, Ba, Mn, Cd, Pb) liquid-like amorphous intermediates emerge. These intermediates that form via a liquid/liquid phase separation behave like a classical emulsion and are stabilized electrostatically. The occurrence of these intermediates is attributed to the formation of highly hydrated networks whose stability is mainly based on weak interactions and the variability of the metal-containing pre-critical clusters. Their existence and compositional freedom are evidenced by electrospray ionization mass spectrometry (ESI-MS). Liquid intermediates in non-classical crystallisation pathways seem to be more common than assumed. PMID:21218241

A Preliminary Analysis of the Linguistic Complexity of Numeracy Skills Test Items for Pre Service Teachers

ERIC Educational Resources Information Center

O'Keeffe, Lisa

2016-01-01

Language is frequently discussed as barrier to mathematics word problems. Hence this paper presents the initial findings of a linguistic analysis of numeracy skills test sample items. The theoretical perspective of multi-modal text analysis underpinned this study, in which data was extracted from the ten sample numeracy test items released by the…

Star Formation in the Orion Nebula Cluster

NASA Astrophysics Data System (ADS)

Palla, Francesco; Stahler, Steven W.

1999-11-01

We study the record of star formation activity within the dense cluster associated with the Orion Nebula. The bolometric luminosity function of 900 visible members is well matched by a simplified theoretical model for cluster formation. This model assumes that stars are produced at a constant rate and distributed according to the field-star initial mass function. Our best-fit age for the system, within this framework, is 2×106 yr. To undertake a more detailed analysis, we present a new set of theoretical pre-main-sequence tracks. These cover all masses from 0.1 to 6.0 Msolar, and start from a realistic stellar birthline. The tracks end along a zero-age main-sequence that is in excellent agreement with the empirical one. As a further aid to cluster studies, we offer an heuristic procedure for the correction of pre-main-sequence luminosities and ages to account for the effects of unresolved binary companions. The Orion Nebula stars fall neatly between our birthline and zero-age main-sequence in the H-R diagram. All those more massive than about 8 Msolar lie close to the main sequence, as also predicted by theory. After accounting for the finite sensitivity of the underlying observations, we confirm that the population between 0.4 and 6.0 Msolar roughly follows a standard initial mass function. We see no evidence for a turnover at lower masses. We next use our tracks to compile stellar ages, also between 0.4 and 6.0 Msolar. Our age histogram reveals that star formation began at a low level some 107 yr ago and has gradually accelerated to the present epoch. The period of most active formation is indeed confined to a few×106 yr, and has recently ended with gas dispersal from the Trapezium. We argue that the acceleration in stellar births, which extends over a wide range in mass, reflects the gravitational contraction of the parent cloud spawning this cluster.

Viability of a Web-Based Module for Teaching Electrocardiogram Reading Skills to Psychiatry Residents: Learning Outcomes and Trainee Interest.

PubMed

DeBonis, Katrina; Blair, Thomas R; Payne, Samuel T; Wigan, Katherine; Kim, Sara

2015-12-01

Web-based instruction in post-graduate psychiatry training has shown comparable effectiveness to in-person instruction, but few topics have been addressed in this format. This study sought to evaluate the viability of a web-based curriculum in teaching electrocardiogram (EKG) reading skills to psychiatry residents. Interest in receiving educational materials in this format was also assessed. A web-based curriculum of 41 slides, including eight pre-test and eight post-test questions with emphasis on cardiac complications of psychotropic medications, was made available to all psychiatry residents via email. Out of 57 residents, 30 initiated and 22 completed the module. Mean improvement from pre-test to post-test was 25 %, and all 22 completing participants indicated interest in future web-based instruction. This pilot study suggests that web-based instruction is feasible and under-utilized as a means of teaching psychiatry residents. Potential uses of web-based instruction, such as tracking learning outcomes or patient care longitudinally, are also discussed.

Transequatorial Propagation and Depletion Precursors

NASA Astrophysics Data System (ADS)

Miller, E. S.; Bust, G. S.; Kaeppler, S. R.; Frissell, N. A.; Paxton, L. J.

2014-12-01

The bottomside equatorial ionosphere in the afternoon and evening sector frequently evolves rapidly from smoothly stratified to violently unstable with large wedges of depleted plasma growing through to the topside on timescales of a few tens of minutes. These depletions have numerous practical impacts on radio propagation, including amplitude scintillation, field-aligned irregularity scatter, HF blackouts, and long-distance transequatorial propagation at frequencies above the MUF. Practical impacts notwithstanding, the pathways and conditions under which depletions form remain a topic of vigorous inquiry some 80 years after their first report. Structuring of the pre-sunset ionosphere---morphology of the equatorial anomalies and long-wavelength undulations of the isodensity contours on the bottomside---are likely to hold some clues to conditions that are conducive to depletion formation. The Conjugate Depletion Experiment is an upcoming transequatorial forward-scatter HF/VHF experiment to investigate pre-sunset undulations and their connection with depletion formation. We will present initial results from the Conjugate Depletion Experiment, as well as a companion analysis of a massive HF propagation data set.

Efficient ECH-assisted plasma start-up using trapped particle configuration in the versatile experiment spherical torus

NASA Astrophysics Data System (ADS)

An, YoungHwa; Lee, Jeongwon; Jo, JongGab; Jung, Bong-Ki; Lee, HyunYeong; Chung, Kyoung-Jae; Na, Yong-Su; Hahm, T. S.; Hwang, Y. S.

2017-01-01

An efficient and robust ECH (electron cyclotron heating)-assisted plasma start-up scheme with a low loop voltage and low volt-second consumption utilizing the trapped particle configuration (TPC) has been developed in the versatile experiment spherical torus (VEST). The TPC is a mirror-like magnetic field configuration providing a vertical magnetic field in the same direction as the equilibrium field. It significantly enhances ECH pre-ionization with enhanced particle confinement due to its mirror effect, and intrinsically provides an equilibrium field with a stable decay index enabling prompt plasma current initiation. Consequently, the formation of TPC before the onset of the loop voltage allows the plasma to start up with a lower loop voltage and lower volt-second consumption as well as a wider operation range in terms of ECH pre-ionization power and H2 filling pressure. The TPC can improve the widely-used field null configuration significantly for more efficient start-up when ECH pre-ionization is used. This can then be utilized in superconducting tokamaks requiring a low loop voltage start-up, such as ITER, or in spherical tori with limited volt-seconds. The TPC can be particularly useful in superconducting tokamaks with a limited current slew-rate of superconducting PF coils, as it can save volt-second consumption before plasma current initiation by providing prompt initiation with an intrinsic stable equilibrium field.

Mechanism of Promoter Melting by the Xeroderma Pigmentosum Complementation Group B Helicase of Transcription Factor IIH Revealed by Protein-DNA Photo-Cross-Linking

PubMed Central

Douziech, Maxime; Coin, Frédéric; Chipoulet, Jean-Marc; Arai, Yoko; Ohkuma, Yoshiaki; Egly, Jean-Marc; Coulombe, Benoit

2000-01-01

The p89/xeroderma pigmentosum complementation group B (XPB) ATPase-helicase of transcription factor IIH (TFIIH) is essential for promoter melting prior to transcription initiation by RNA polymerase II (RNAPII). By studying the topological organization of the initiation complex using site-specific protein-DNA photo-cross-linking, we have shown that p89/XPB makes promoter contacts both upstream and downstream of the initiation site. The upstream contact, which is in the region where promoter melting occurs (positions −9 to +2), requires tight DNA wrapping around RNAPII. The addition of hydrolyzable ATP tethers the template strand at positions −5 and +1 to RNAPII subunits. A mutation in p89/XPB found in a xeroderma pigmentosum patient impairs the ability of TFIIH to associate correctly with the complex and thereby melt promoter DNA. A model for open complex formation is proposed. PMID:11027286

Poly-MVA attenuates 7,12- dimethylbenz[a]anthracene initiated and croton oil promoted skin papilloma formation on mice skin.

PubMed

Veena, Ravindran K; Ajith, Thekkuttuparambil A; Janardhanan, Kainoor K; Antonawich, Francis

2017-09-01

Chemopreventive agents which exhibit activities such as anti-inflammation, inhibition of carcinogen induced mutagenesis and scavenging of free radical might play a decisive role in the inhibition of chemical carcinogenesis either at the initiation or promotion stage. Many synthesized palladium (Pd) complexes tested experimentally for antitumor activity are found effective. Poly-MVA is a liquid blend preparation containing B complex vitamins, ruthenium with Pd complexed with alpha lipoic acid as the major ingredients. The antitumor effect of Poly-MVA was evaluated against 7,12-dimethylbenz[a] anthracene-initiated croton oil-promoted papilloma formation on mice skin. Skin tumor was initiated with a single application of 390 nmol of DMBA in 20 µl acetone. The effect of Poly-MVA against croton oil- induced inflammation and lipid peroxidation on the mice skin was also evaluated. Topical application of Poly-MVA (100 µl, twice weekly for 18 weeks) 30 minutes prior to each croton oil application, significantly decreased the tumor incidence (11%) and the average number of tumor per animals. Application of Poly-MVA (100 µl) before croton oil significantly (p &#60; 0.05) protected the mouse skin from inflammation (36%) and lipid peroxidation (14%) when compared to the croton oil alone treated group. Experimental results indicate that Poly-MVA attenuate the tumor promoting effects of croton oil and the effect may probably be due to its anti-inflammatory and antioxidant activity.

A Role of hIPI3 in DNA Replication Licensing in Human Cells.

PubMed

Huang, Yining; Amin, Aftab; Qin, Yan; Wang, Ziyi; Jiang, Huadong; Liang, Lu; Shi, Linjing; Liang, Chun

2016-01-01

The yeast Ipi3p is required for DNA replication and cell viability in Sacharomyces cerevisiae. It is an essential component of the Rix1 complex (Rix1p/Ipi2p-Ipi1p-Ipi3p) that is required for the processing of 35S pre-rRNA in pre-60S ribosomal particles and for the initiation of DNA replication. The human IPI3 homolog is WDR18 (WD repeat domain 18), which shares significant homology with yIpi3p. Here we report that knockdown of hIPI3 resulted in substantial defects in the chromatin association of the MCM complex, DNA replication, cell cycle progression and cell proliferation. Importantly, hIPI3 silencing did not result in a reduction of the protein level of hCDC6, hMCM7, or the ectopically expressed GFP protein, indicating that protein synthesis was not defective in the same time frame of the DNA replication and cell cycle defects. Furthermore, the mRNA and protein levels of hIPI3 fluctuate in the cell cycle, with the highest levels from M phase to early G1 phase, similar to other pre-replicative (pre-RC) proteins. Moreover, hIPI3 interacts with other replication-initiation proteins, co-localizes with hMCM7 in the nucleus, and is important for the nuclear localization of hMCM7. We also found that hIPI3 preferentially binds to the origins of DNA replication including those at the c-Myc, Lamin-B2 and β-Globin loci. These results indicate that hIPI3 is involved in human DNA replication licensing independent of its role in ribosome biogenesis.

Effect of a pre-brush mounthrinse containing triclosan and a copolymer on calculus formation: a three-month clinical study in Thailand.

PubMed

Triratana, T; Kraivaphan, P; Tandhachoon, K; Rustogi, K; Volpe, A R; Petrone, M

1995-01-01

A three-month, double-blind, parallel clinical study was conducted on a population of Thai adults to evaluate the effect of the twice daily use of a commercially available pre-brush mouthrinse on supragingival calculus formation. The mouthrinse test product contained 0.03% triclosan and 0.13% PVM/MA copolymer with the absence of fluoride. The subjects were initially examined for calculus using the Volpe-Manhold procedure. All subjects received an oral prophylaxis and were assigned to the use of either 1) a triclosan-copolymer mouthrinse, or 2) a matching flavored/colored water placebo mouthrinse. Subjects were instructed to rinse twice daily with 10 cc of the assigned mouthrinse for 1 minute, followed by brushing with the provided toothpaste containing fluoride for 45 seconds. After three months of using the assigned mouthrinse, the subjects were reexamined for calculus formation. The results indicated that the subjects using triclosan/copolymer mouthrinse had 23.17% less supragingival calculus than the placebo mouthrinse subjects. This reduction was statistically significant at the 99% or greater (F = 24.35, p<0.001) level of confidence.

AMPK Inhibits ULK1-Dependent Autophagosome Formation and Lysosomal Acidification via Distinct Mechanisms.

PubMed

Nwadike, Chinwendu; Williamson, Leon E; Gallagher, Laura E; Guan, Jun-Lin; Chan, Edmond Y W

2018-05-15

Autophagy maintains metabolism in response to starvation, but each nutrient is sensed distinctly. Amino acid deficiency suppresses mechanistic target of rapamycin complex 1 (MTORC1), while glucose deficiency promotes AMP-activated protein kinase (AMPK). The MTORC1 and AMPK signaling pathways converge onto the ULK1/2 autophagy initiation complex. Here, we show that amino acid starvation promoted formation of ULK1- and sequestosome 1/p62-positive early autophagosomes. Autophagosome initiation was controlled by MTORC1 sensing glutamine, leucine, and arginine levels together. In contrast, glucose starvation promoted AMPK activity, phosphorylation of ULK1 Ser555, and LC3-II accumulation, but with dynamics consistent with a block in autophagy flux. We studied the flux pathway and found that starvation of amino acid but not of glucose activated lysosomal acidification, which occurred independently of autophagy and ULK1. In addition to lack of activation, glucose starvation inhibited the ability of amino acid starvation to activate both autophagosome formation and the lysosome. Activation of AMPK and phosphorylation of ULK1 were determined to specifically inhibit autophagosome formation. AMPK activation also was sufficient to prevent lysosome acidification. These results indicate concerted but distinct AMPK-dependent mechanisms to suppress early and late phases of autophagy. Copyright © 2018 Nwadike et al.

Modulation of methylmercury uptake by methionine: Prevention of mitochondrial dysfunction in rat liver slices by a mimicry mechanism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roos, Daniel Henrique; Puntel, Robson Luiz; Farina, Marcelo

2011-04-01

Methylmercury (MeHg) is an ubiquitous environmental pollutant which is transported into the mammalian cells when present as the methylmercury-cysteine conjugate (MeHg-Cys). With special emphasis on hepatic cells, due to their particular propensity to accumulate an appreciable amount of Hg after exposure to MeHg, this study was performed to evaluate the effects of methionine (Met) on Hg uptake, reactive species (RS) formation, oxygen consumption and mitochondrial function/cellular viability in both liver slices and mitochondria isolated from these slices, after exposure to MeHg or the MeHg-Cys complex. The liver slices were pre-treated with Met (250 {mu}M) 15 min before being exposed tomore » MeHg (25 {mu}M) or MeHg-Cys (25 {mu}M each) for 30 min at 37 {sup o}C. The treatment with MeHg caused a significant increase in the Hg concentration in both liver slices and mitochondria isolated from liver slices. Moreover, the Hg uptake was higher in the group exposed to the MeHg-Cys complex. In the DCF (dichlorofluorescein) assay, the exposure to MeHg and MeHg-Cys produced a significant increase in DFC reactive species (DFC-RS) formation only in the mitochondria isolated from liver slices. As observed with Hg uptake, DFC-RS levels were significantly higher in the mitochondria treated with the MeHg-Cys complex compared to MeHg alone. MeHg exposure also caused a marked decrease in the oxygen consumption of liver slices when compared to the control group, and this effect was more pronounced in the liver slices treated with the MeHg-Cys complex. Similarly, the loss of mitochondrial activity/cell viability was greater in liver slices exposed to the MeHg-Cys complex when compared to slices treated only with MeHg. In all studied parameters, Met pre-treatment was effective in preventing the MeHg- and/or MeHg-Cys-induced toxicity in both liver slices and mitochondria. Part of the protection afforded by Met against MeHg may be related to a direct interaction with MeHg or to the competition of Met with the complex formed between MeHg and endogenous cysteine. In summary, our results show that Met pre-treatment produces pronounced protection against the toxic effects induced by MeHg and/or the MeHg-Cys complex on mitochondrial function and cell viability. Consequently, this amino acid offers considerable promise as a potential agent for treating acute MeHg exposure.« less

Assessment of autophagosome formation by transmission electron microscopy

USDA-ARS?s Scientific Manuscript database

Autophagy is a complex degradative process by which cytosolic material, including organelles, is randomly sequestered within double-membrane bound vesicles termed autophagosomes and targeted for degradation. Initially described as a nutrient stress adaptation response, the process of autophagy is n...

The Regulation of Coenzyme Q Biosynthesis in Eukaryotic Cells: All That Yeast Can Tell Us

PubMed Central

González-Mariscal, Isabel; García-Testón, Elena; Padilla, Sergio; Martín-Montalvo, Alejandro; Pomares Viciana, Teresa; Vazquez-Fonseca, Luis; Gandolfo Domínguez, Pablo; Santos-Ocaña, Carlos

2014-01-01

Coenzyme Q (CoQ) is a mitochondrial lipid, which functions mainly as an electron carrier from complex I or II to complex III at the mitochondrial inner membrane, and also as antioxidant in cell membranes. CoQ is needed as electron acceptor in β-oxidation of fatty acids and pyridine nucleotide biosynthesis, and it is responsible for opening the mitochondrial permeability transition pore. The yeast model has been very useful to analyze the synthesis of CoQ, and therefore, most of the knowledge about its regulation was obtained from the Saccharomyces cerevisiae model. CoQ biosynthesis is regulated to support 2 processes: the bioenergetic metabolism and the antioxidant defense. Alterations of the carbon source in yeast, or in nutrient availability in yeasts or mammalian cells, upregulate genes encoding proteins involved in CoQ synthesis. Oxidative stress, generated by chemical or physical agents or by serum deprivation, modifies specifically the expression of some COQ genes by means of stress transcription factors such as Msn2/4p, Yap1p or Hsf1p. In general, the induction of COQ gene expression produced by metabolic changes or stress is modulated downstream by other regulatory mechanisms such as the protein import to mitochondria, the assembly of a multi-enzymatic complex composed by Coq proteins and also the existence of a phosphorylation cycle that regulates the last steps of CoQ biosynthesis. The CoQ biosynthetic complex assembly starts with the production of a nucleating lipid such as HHB by the action of the Coq2 protein. Then, the Coq4 protein recognizes the precursor HHB acting as the nucleus of the complex. The activity of Coq8p, probably as kinase, allows the formation of an initial pre-complex containing all Coq proteins with the exception of Coq7p. This pre-complex leads to the synthesis of 5-demethoxy-Q6 (DMQ6), the Coq7p substrate. When de novo CoQ biosynthesis is required, Coq7p becomes dephosphorylated by the action of Ptc7p increasing the synthesis rate of CoQ6. This critical model is needed for a better understanding of CoQ biosynthesis. Taking into account that patients with CoQ10 deficiency maintain to some extent the machinery to synthesize CoQ, new promising strategies for the treatment of CoQ10 deficiency will require a better understanding of the regulation of CoQ biosynthesis in the future. PMID:25126044

IceAge: Chemical Evolution of Ices during Star Formation

NASA Astrophysics Data System (ADS)

McClure, Melissa; Bailey, J.; Beck, T.; Boogert, A.; Brown, W.; Caselli, P.; Chiar, J.; Egami, E.; Fraser, H.; Garrod, R.; Gordon, K.; Ioppolo, S.; Jimenez-Serra, I.; Jorgensen, J.; Kristensen, L.; Linnartz, H.; McCoustra, M.; Murillo, N.; Noble, J.; Oberg, K.; Palumbo, M.; Pendleton, Y.; Pontoppidan, K.; Van Dishoeck, E.; Viti, S.

2017-11-01

Icy grain mantles are the main reservoir for volatile elements in star-forming regions across the Universe, as well as the formation site of pre-biotic complex organic molecules (COMs) seen in our Solar System. We propose to trace the evolution of pristine and complex ice chemistry in a representative low-mass star-forming region through observations of a: pre-stellar core, Class 0 protostar, Class I protostar, and protoplanetary disk. Comparing high spectral resolution (R 1500-3000) and sensitivity (S/N 100-300) observations from 3 to 15 um to template spectra, we will map the spatial distribution of ices down to 20-50 AU in these targets to identify when, and at what visual extinction, the formation of each ice species begins. Such high-resolution spectra will allow us to search for new COMs, as well as distinguish between different ice morphologies,thermal histories, and mixing environments. The analysis of these data will result in science products beneficial to Cycle 2 proposers. A newly updated public laboratory ice database will provide feature identifications for all of the expected ices, while a chemical model fit to the observed ice abundances will be released publically as a grid, with varied metallicity and UV fields to simulate other environments. We will create improved algorithms to extract NIRCAM WFSS spectra in crowded fields with extended sources as well as optimize the defringing of MIRI LRS spectra in order to recover broad spectral features. We anticipate that these resources will be particularly useful for astrochemistry and spectroscopy of fainter, extended targets like star forming regions of the SMC/LMC or more distant galaxies.

76 FR 28994 - Submission for OMB Review; Comment Request; A Generic Submission for Formative Research, Pre...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-19

... quantitative (paper, phone, in-person, and web surveys) methodologies to conduct this research, allowing NCI to...; Comment Request; A Generic Submission for Formative Research, Pre-Testing, Stakeholder Measures and... Formative Research, Pre-testing, Stakeholder Measures and Advocate Forms at NCI. Type of Information...

Mechanisms for secondary eyewall formation, and cold-air damming: Tropical cyclone interactions

NASA Astrophysics Data System (ADS)

Garcia-Rivera, Jose Manuel

This dissertation consists of two topics, the mechanisms leading to secondary eyewall formation in tropical cyclones, and effects of tropical cyclone---cold-air interactions on heavy precipitation. The first research topic involves a proposed coupled mechanism for secondary eyewall formation (SEF; initiation of an eyewall replacement cycle), using a WRF-ARW simulation of Hurricane Katrina (2005). The storm underwent a series of structural changes that were deemed necessary for the cycle to begin. These included a significant increase of rainband activity in the SEF region and the eventual vertical coupling of azimuthal-mean updrafts that led to cycle initiation. Increased rainband activity outside the primary eyewall in the hours before was mostly related to an intensifying main feeder band. Close to initiation, an updraft (explained by a pre-existing hypothesis) emerged outside the primary eyewall near the top of the boundary layer (BL). This updraft then intensified and extended both upward and outward, while the storm intensified and approached SEF. Eventually, the updraft coupled with the upward motion associated with rainband-related convection near the SEF radius. Once the alignment occurred, the deep updraft quickly organized to support deep convection that led to SEF within hours of initiation. The coupling of updrafts emanating from the BL with the environmental upward motion associated with the pre-existing rainband activity is proposed to be the key for SEF initiation in this case. The second topic investigates the interactions between an Appalachian cold-air damming event and the near-passage of Tropical Storm Kyle (2002) along the coastal Carolinas, as assessed by using a numerical weather prediction model. While the storm moved along the coastline, it began extra-tropical transition, bringing heavy rains to both the coastal region and inland towards the Piedmont of North Carolina. Our goal is to quantify the effects of both interacting weather systems on heavy precipitation in order to improve the dynamical understanding of such effects, as well as precipitation forecasts in the study region. A series of sensitivity tests were performed to isolate and quantify the effects of both systems on the total accumulated precipitation. It was found that (a) for this type of along-coast track, the pre-existing cold-air damming played only a minor role on the total accumulated precipitation, (b) the outer circulation of Kyle weakened the cold-air damming due to a redirection of the mean flow away from the east side of the Appalachian Mountains, and (c) the combination of Kyle with a shortwave mid to upper-level trough and a surface coastal front were responsible for the heavy precipitation experienced in the study area through the advection of moisture, vorticity, and the forcing of upward motion.

Re-evaluating the Cu K pre-edge XAS transition in complexes with covalent metal–ligand interactions† †Electronic supplementary information (ESI) available: Experimental methods; UV-vis absorption spectrum and crystallographic data for 3; fits to Cu K pre-edge XANES spectra; details of DFT, CASSCF, and MR-DDCI3 computational experiments; optimized atomic coordinates for all complexes. CCDC 1031118 and 1031119. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4sc03294b Click here for additional data file. Click here for additional data file.

PubMed Central

Williams, Kamille D.; Dai, Xuliang; Sproules, Stephen; DeBeer, Serena

2015-01-01

Three [Me2NN]Cu(η2-L2) complexes (Me2NN = HC[C(Me)NAr]2; L2 = PhNO (2), (3), PhCH 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 CH2 (4); Ar = 2,6-Me2-C6H3; ArF = 3,5-(CF3)2-C6H3) have been studied by Cu K-edge X-ray absorption spectroscopy, as well as single- and multi-reference computational methods (DFT, TD-DFT, CASSCF, MRCI, and OVB). The study was extended to a range of both known and theoretical compounds bearing 2p-element donors as a means of deriving a consistent view of how the pre-edge transition energy responds in systems with significant ground state covalency. The ground state electronic structures of many of the compounds under investigation were found to be strongly influenced by correlation effects, resulting in ground state descriptions with majority contributions from a configuration comprised of a Cu(ii) metal center anti-ferromagentically coupled to radical anion O2, PhNO, and ligands. In contrast, the styrene complex 4, which displays a Cu K pre-edge transition despite its formal d10 electron configuration, exhibits what can best be described as a Cu(i):(styrene)0 ground state with strong π-backbonding. The Cu K pre-edge features for these complexes increase in energy from 1 to 4, a trend that was tracked to the percent Cu(ii)-character in the ground state. The unexpected shift to higher pre-edge transition energies with decreasing charge on copper (Q Cu) contributed to an assignment of the pre-edge features for these species as arising from metal-to-ligand charge transfer instead of the traditional Cu1s → Cu3d designation. PMID:29308158

Downstream DNA Tension Regulates the Stability of the T7 RNA Polymerase Initiation Complex

PubMed Central

Skinner, Gary M.; Kalafut, Bennett S.; Visscher, Koen

2011-01-01

Gene transcription by the enzyme RNA polymerase is tightly regulated. In many cases, such as in the lac operon in Escherichia coli, this regulation is achieved through the action of protein factors on DNA. Because DNA is an elastic polymer, its response to enzymatic processing can lead to mechanical perturbations (e.g., linear stretching and supercoiling) that can affect the operation of other DNA processing complexes acting elsewhere on the same substrate molecule. Using an optical-tweezers assay, we measured the binding kinetics between single molecules of bacteriophage T7 RNA polymerase and DNA, as a function of tension. We found that increasing DNA tension under conditions that favor formation of the open complex results in destabilization of the preinitiation complex. Furthermore, with zero ribonucleotides present, when the closed complex is favored, we find reduced tension sensitivity, implying that it is predominantly the open complex that is sensitive. This result strongly supports the “scrunching” model for T7 transcription initiation, as the applied tension acts against the movement of the DNA into the scrunched state, and introduces linear DNA tension as a potential regulatory quantity for transcription initiation. PMID:21320448

Cell proteins bind to multiple sites within the 5' untranslated region of poliovirus RNA.

PubMed Central

del Angel, R M; Papavassiliou, A G; Fernández-Tomás, C; Silverstein, S J; Racaniello, V R

1989-01-01

The 5' noncoding region of poliovirus RNA contains sequences necessary for translation and replication. These functions are probably carried out by recognition of poliovirus RNA by cellular and/or viral proteins. Using a mobility-shift electrophoresis assay and 1,10-phenanthroline/Cu+ footprinting, we demonstrate specific binding of cytoplasmic factors with a sequence from nucleotides 510-629 within the 5' untranslated region (UTR). Complex formation was also observed with a second sequence (nucleotides 97-182) within the 5' UTR. These two regions of the 5' UTR appear to be recognized by distinct cell factors as determined by competition analysis and the effects of ionic strength on complex formation. However, both complexes contain eukaryotic initiation factor 2 alpha, as revealed by their reaction with specific antibody. Images PMID:2554308

SOA formation from photooxidation of naphthalene and methylnaphthalenes with m-xylene and surrogate mixtures

NASA Astrophysics Data System (ADS)

Chen, Chia-Li; Li, Lijie; Tang, Ping; Cocker, David R.

2018-05-01

SOA formation is not well predicted in current models in urban area. The interaction among multiple anthropogenic volatile organic compounds is essential for the SOA formation in the complex urban atmosphere. Secondary organic aerosol (SOA) from the photooxidation of naphthalene, 1-methylnaphthalene, and 2-methylnaphthalene as well as individual polycyclic aromatic hydrocarbons (PAHs) mixed with m-xylene or an atmospheric surrogate mixture was explored in the UCR CE-CERT environmental chamber under urban relevant low NOx and extremely low NOx (H2O2) conditions. Addition of m-xylene suppressed SOA formation from the individual PAH precursor. A similar suppression effect on SOA formation was observed during the surrogate mixture photooxidation suggesting the importance of gas-phase chemical reactivity to SOA formation. The SOA growth rate for different PAH-m-xylene mixtures was strongly correlated with initial [HO2]/[RO2] ratio but negatively correlated with initial m-xylene/NO ratio. Decreasing SOA formation was observed for increasing m-xylene/PAHs ratios and increasing initial m-xylene/NO ratio. The SOA chemical composition characteristics such as f44 versus f43, H/C ratio, O/C ratio, and the oxidation state of the carbon OSbarc were consistent with a continuously aging with the SOA exhibiting characteristics of both individual precursors. SOA formation from PAHs was also suppressed within an atmospheric surrogate mixture compared to the SOA formed from individual PAHs, indicating that atmospheric reactivity directly influences SOA formation from PAHs.

Initiation of DNA replication: functional and evolutionary aspects

PubMed Central

Bryant, John A.; Aves, Stephen J.

2011-01-01

Background The initiation of DNA replication is a very important and highly regulated step in the cell division cycle. It is of interest to compare different groups of eukaryotic organisms (a) to identify the essential molecular events that occur in all eukaryotes, (b) to start to identify higher-level regulatory mechanisms that are specific to particular groups and (c) to gain insights into the evolution of initiation mechanisms. Scope This review features a wide-ranging literature survey covering replication origins, origin recognition and usage, modification of origin usage (especially in response to plant hormones), assembly of the pre-replication complex, loading of the replisome, genomics, and the likely origin of these mechanisms and proteins in Archaea. Conclusions In all eukaryotes, chromatin is organized for DNA replication as multiple replicons. In each replicon, replication is initiated at an origin. With the exception of those in budding yeast, replication origins, including the only one to be isolated so far from a plant, do not appear to embody a specific sequence; rather, they are AT-rich, with short tracts of locally bent DNA. The proteins involved in initiation are remarkably similar across the range of eukaryotes. Nevertheless, their activity may be modified by plant-specific mechanisms, including regulation by plant hormones. The molecular features of initiation are seen in a much simpler form in the Archaea. In particular, where eukaryotes possess a number of closely related proteins that form ‘hetero-complexes’ (such as the origin recognition complex and the MCM complex), archaeans typically possess one type of protein (e.g. one MCM) that forms a homo-complex. This suggests that several eukaryotic initiation proteins have evolved from archaeal ancestors by gene duplication and divergence. PMID:21508040

Birth order dependent growth cone segregation determines synaptic layer identity in the Drosophila visual system.

PubMed

Kulkarni, Abhishek; Ertekin, Deniz; Lee, Chi-Hon; Hummel, Thomas

2016-03-17

The precise recognition of appropriate synaptic partner neurons is a critical step during neural circuit assembly. However, little is known about the developmental context in which recognition specificity is important to establish synaptic contacts. We show that in the Drosophila visual system, sequential segregation of photoreceptor afferents, reflecting their birth order, lead to differential positioning of their growth cones in the early target region. By combining loss- and gain-of-function analyses we demonstrate that relative differences in the expression of the transcription factor Sequoia regulate R cell growth cone segregation. This initial growth cone positioning is consolidated via cell-adhesion molecule Capricious in R8 axons. Further, we show that the initial growth cone positioning determines synaptic layer selection through proximity-based axon-target interactions. Taken together, we demonstrate that birth order dependent pre-patterning of afferent growth cones is an essential pre-requisite for the identification of synaptic partner neurons during visual map formation in Drosophila.

Acyl-CoA synthetase 3 promotes lipid droplet biogenesis in ER microdomains

PubMed Central

Kassan, Adam; Herms, Albert; Fernández-Vidal, Andrea; Bosch, Marta; Schieber, Nicole L.; Reddy, Babu J.N.; Fajardo, Alba; Gelabert-Baldrich, Mariona; Tebar, Francesc; Enrich, Carlos; Gross, Steven P.

2013-01-01

Control of lipid droplet (LD) nucleation and copy number are critical, yet poorly understood, processes. We use model peptides that shift from the endoplasmic reticulum (ER) to LDs in response to fatty acids to characterize the initial steps of LD formation occurring in lipid-starved cells. Initially, arriving lipids are rapidly packed in LDs that are resistant to starvation (pre-LDs). Pre-LDs are restricted ER microdomains with a stable core of neutral lipids. Subsequently, a first round of “emerging” LDs is nucleated, providing additional lipid storage capacity. Finally, in proportion to lipid concentration, new rounds of LDs progressively assemble. Confocal microscopy and electron tomography suggest that emerging LDs are nucleated in a limited number of ER microdomains after a synchronized stepwise process of protein gathering, lipid packaging, and recognition by Plin3 and Plin2. A comparative analysis demonstrates that the acyl-CoA synthetase 3 is recruited early to the assembly sites, where it is required for efficient LD nucleation and lipid storage. PMID:24368806

PreTIS: A Tool to Predict Non-canonical 5’ UTR Translational Initiation Sites in Human and Mouse

PubMed Central

Reuter, Kerstin; Helms, Volkhard

2016-01-01

Translation of mRNA sequences into proteins typically starts at an AUG triplet. In rare cases, translation may also start at alternative non–AUG codons located in the annotated 5’ UTR which leads to an increased regulatory complexity. Since ribosome profiling detects translational start sites at the nucleotide level, the properties of these start sites can then be used for the statistical evaluation of functional open reading frames. We developed a linear regression approach to predict in–frame and out–of–frame translational start sites within the 5’ UTR from mRNA sequence information together with their translation initiation confidence. Predicted start codons comprise AUG as well as near–cognate codons. The underlying datasets are based on published translational start sites for human HEK293 and mouse embryonic stem cells that were derived by the original authors from ribosome profiling data. The average prediction accuracy of true vs. false start sites for HEK293 cells was 80%. When applied to mouse mRNA sequences, the same model predicted translation initiation sites observed in mouse ES cells with an accuracy of 76%. Moreover, we illustrate the effect of in silico mutations in the flanking sequence context of a start site on the predicted initiation confidence. Our new webservice PreTIS visualizes alternative start sites and their respective ORFs and predicts their ability to initiate translation. Solely, the mRNA sequence is required as input. PreTIS is accessible at http://service.bioinformatik.uni-saarland.de/pretis. PMID:27768687

Effect of ZnSe/GaAs interface treatment in ZnSe quality control for optoelectronic device applications

DOE PAGES

Park, Kwangwook; Beaton, Daniel; Steirer, Kenneth X.; ...

2017-01-27

Here, we investigate the role of interface initiation conditions on the growth of ZnSe/GaAs heterovalent heterostructures. ZnSe epilayers were grown on a GaAs surface with various degrees of As-termination and the application of either a Zn or Se pre-treatment. Structural analysis revealed that Zn pre-treatment of an As-rich GaAs surface suppresses Ga 2Se 3 formation at the interface and promotes the growth of high crystal quality ZnSe. This is confirmed with low-temperature photoluminescence. However, moderation of Ga-Se bonding through a Se pre-treatment of an As-rich GaAs surface can prevent excessive intermixing at the interface and promote excitonic emission in themore » underlying GaAs layer. These results provide guidance on how best to prepare heterovalent interfaces for various applications.« less

THE SPATIAL DISTRIBUTION OF COMPLEX ORGANIC MOLECULES IN THE L1544 PRE-STELLAR CORE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiménez-Serra, Izaskun; Vasyunin, Anton I.; Caselli, Paola

The detection of complex organic molecules (COMs) toward cold sources such as pre-stellar cores (with T < 10 K) has challenged our understanding of the formation processes of COMs in the interstellar medium. Recent modeling on COM chemistry at low temperatures has provided new insight into these processes predicting that COM formation depends strongly on parameters such as visual extinction and the level of CO freeze out. We report deep observations of COMs toward two positions in the L1544 pre-stellar core: the dense, highly extinguished continuum peak with A{sub V}≥ 30 mag within the inner 2700 au; and a low-densitymore » shell with average A{sub V}∼ 7.5–8 mag located at 4000 au from the core’s center and bright in CH{sub 3}OH. Our observations show that CH{sub 3}O, CH{sub 3}OCH{sub 3}, and CH{sub 3}CHO are more abundant (by factors of ∼2–10) toward the low-density shell than toward the continuum peak. Other COMs such as CH{sub 3}OCHO, c-C{sub 3}H{sub 2}O, HCCCHO, CH{sub 2}CHCN, and HCCNC show slight enhancements (by factors ≤3), but the associated uncertainties are large. This suggests that COMs are actively formed and already present in the low-density shells of pre-stellar cores. The modeling of the chemistry of O-bearing COMs in L1544 indicates that these species are enhanced in this shell because (i) CO starts freezing out onto dust grains driving an active surface chemistry; (ii) the visual extinction is sufficiently high to prevent the UV photo-dissociation of COMs by the external interstellar radiation field; and (iii) the density is still moderate to prevent severe depletion of COMs onto grains.« less

Determination of sub-ng g-1 levels of total inorganic arsenic and selenium in foods by hydride-generation atomic absorption spectrometry after pre-concentration.

PubMed

Altunay, Nail; Gürkan, Ramazan

2017-03-01

A new and simple ultrasonic-assisted extraction (UAE) procedure was developed for the determination of inorganic arsenic and selenium in foods by hydride-generation atomic absorption spectrometry (HG-AAS). The various analytical variables affecting complex formation and extraction efficiency were investigated and optimised. The method is based on selective complex formation of As(III) and Se(IV) in the presence of excess As(V) and Se(VI) with toluidine red in the presence of tartaric acid at pH 4.5, and then extraction of the resulting condensation products into the micellar phase of non-ionic surfactant, polyethylene glycol dodecyl ether, Brij 35. Under optimised conditions, good linear relationships were obtained in the ranges of 4-225 and 12-400 ng l - 1 with limits of detection of 1.1 and 3.5 ng l - 1 for As(III) and Se(IV), respectively. The repeatability was better than 3.9% for both analytes (n = 10, 25 ng l - 1 ) while reproducibility ranged from 4.2% to 4.8%. The recoveries of As(III) and Se(IV) spiked at 25-100 ng l - 1 were in the range of 94.2-104.8%. After pre-concentration of a 5.0 ml sample, the sensitivity enhancement factors for As(III) and Se(IV) were 185 and 140, respectively. Accuracy was assessed by analysis of two standard reference materials (SRMs) and spiked recovery experiments. The method was successfully applied to the accurate and reliable determination of total As and total Se by HG-AAS after pre-reduction with a mixture of L-cysteine and tartaric acid. Finally, the method was shown to be rapid and sensitive, with good results for extraction, pre-concentration and determination of total As and Se contents (as As(III) and Se(IV)) from food samples.

Pre-mRNA Processing Factor Prp18 Is a Stimulatory Factor of Influenza Virus RNA Synthesis and Possesses Nucleoprotein Chaperone Activity.

PubMed

Minakuchi, M; Sugiyama, K; Kato, Y; Naito, T; Okuwaki, M; Kawaguchi, A; Nagata, K

2017-02-01

The genome of influenza virus (viral RNA [vRNA]) is associated with the nucleoprotein (NP) and viral RNA-dependent RNA polymerases and forms helical viral ribonucleoprotein (vRNP) complexes. The NP-vRNA complex is the biologically active template for RNA synthesis by the viral polymerase. Previously, we identified human pre-mRNA processing factor 18 (Prp18) as a stimulatory factor for viral RNA synthesis using a Saccharomyces cerevisiae replicon system and a single-gene deletion library of Saccharomyces cerevisiae (T. Naito, Y. Kiyasu, K. Sugiyama, A. Kimura, R. Nakano, A. Matsukage, and K. Nagata, Proc Natl Acad Sci USA, 104:18235-18240, 2007, https://doi.org/10.1073/pnas.0705856104). In infected Prp18 knockdown (KD) cells, the synthesis of vRNA, cRNA, and viral mRNAs was reduced. Prp18 was found to stimulate in vitro viral RNA synthesis through its interaction with NP. Analyses using in vitro RNA synthesis reactions revealed that Prp18 dissociates newly synthesized RNA from the template after the early elongation step to stimulate the elongation reaction. We found that Prp18 functions as a chaperone for NP to facilitate the formation of NP-RNA complexes. Based on these results, it is suggested that Prp18 accelerates influenza virus RNA synthesis as an NP chaperone for the processive elongation reaction. Templates for viral RNA synthesis of negative-stranded RNA viruses are not naked RNA but rather RNA encapsidated by viral nucleocapsid proteins forming vRNP complexes. However, viral basic proteins tend to aggregate under physiological ionic strength without chaperones. We identified the pre-mRNA processing factor Prp18 as a stimulatory factor for influenza virus RNA synthesis. We found that one of the targets of Prp18 is NP. Prp18 facilitates the elongation reaction of viral polymerases by preventing the deleterious annealing of newly synthesized RNA to the template. Prp18 functions as a chaperone for NP to stimulate the formation of NP-RNA complexes. Based on these results, we propose that Prp18 may be required to maintain the structural integrity of vRNP for processive template reading. Copyright © 2017 American Society for Microbiology.

HPLC enantioseparation of racemic bupropion, baclofen and etodolac: modification of conventional ligand exchange approach by pre-column formation of chiral ligand exchange complexes.

PubMed

Singh, Manisha; Bhushan, Ravi

2016-11-01

Separation of racemic mixture of (RS)-bupropion, (RS)-baclofen and (RS)-etodolac, commonly marketed racemic drugs, has been achieved by modifying the conventional ligand exchange approach. The Cu(II) complexes were first prepared with a few l-amino acids, namely, l-proline, l-histidine, l-phenylalanine and l-tryptophan, and to these was introduced a mixture of the enantiomer pair of (RS)-bupropion, or (RS)-baclofen or (RS)-etodolac. As a result, formation of a pair of diastereomeric complexes occurred by 'chiral ligand exchange' via the competition between the chelating l-amino acid and each of the two enantiomers from a given pair. The diastereomeric mixture formed in the pre-column process was loaded onto HPLC column. Thus, both the phases during chromatographic separation process were achiral (i.e. neither the stationary phase had any chiral structural feature of its own nor did the mobile phase have any chiral additive). Separation of diastereomers was successful using a C 18 column and a binary mixture of MeCN and TEAP buffer of pH 4.0 (60:40, v/v) as mobile phase at a flow rate of 1 mL/min and UV detection at 230 nm for (RS)-Bup, 220 nm for (RS)-Bac and 223 nm for (RS)-Etd. Baseline separation of the two enantiomers was obtained with a resolution of 6.63 in <15 min. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Characteristics of place identity as part of professional identity development among pre-service teachers

NASA Astrophysics Data System (ADS)

Gross, Michal; Hochberg, Nurit

2016-12-01

How do pre-service teachers perceive place identity, and is there a connection between their formative place identity and the development of their professional teaching identity? These questions are probed among pre-service teachers who participated in a course titled "Integrating Nature into Preschool." The design of the course was based on a multidimensional teaching model that yields a matrix of students' perceptions and the practical aspects derived from them as the students undergo a range of experiences in the course of an academic year. The profile of perceptions uses a mixed-methods analysis that presents statements attesting to four indicators of place identity: familiarity, belonging, involvement, and meaningfulness. These indicators point to a broad spectrum of perceptions arrayed on a continual time axes as well as differences in perception and its complexity. A connection between the development of place identity and that of professional teaching identity is found.

Cryo-EM structure of a late pre-40S ribosomal subunit from Saccharomyces cerevisiae

PubMed Central

Schmidt, Christian; Berninghausen, Otto; Becker, Thomas

2017-01-01

Mechanistic understanding of eukaryotic ribosome formation requires a detailed structural knowledge of the numerous assembly intermediates, generated along a complex pathway. Here, we present the structure of a late pre-40S particle at 3.6 Å resolution, revealing in molecular detail how assembly factors regulate the timely folding of pre-18S rRNA. The structure shows that, rather than sterically blocking 40S translational active sites, the associated assembly factors Tsr1, Enp1, Rio2 and Pno1 collectively preclude their final maturation, thereby preventing untimely tRNA and mRNA binding and error prone translation. Moreover, the structure explains how Pno1 coordinates the 3’end cleavage of the 18S rRNA by Nob1 and how the late factor’s removal in the cytoplasm ensures the structural integrity of the maturing 40S subunit. PMID:29155690

A combined acidification/PEO flocculation process to improve the lignin removal from the pre-hydrolysis liquor of kraft-based dissolving pulp production process.

PubMed

Shi, Haiqiang; Fatehi, Pedram; Xiao, Huining; Ni, Yonghao

2011-04-01

The presence of lignin impairs the utilization of the hemicelluloses dissolved in the pre-hydrolysis liquor (PHL) of the kraft-based dissolving pulp production process. In this paper, a novel process was developed by combining the acidification and poly ethylene oxide (PEO) flocculation concepts to improve the lignin removal. The results showed that the lignin removal was improved by the addition of PEO to the acidified PHL, particularly at a low pH of 1.5. The main mechanisms involved are the lignin/PEO complex formation and the bridging of the formed complexes. This hypothesis was supported by the turbidity, FTIR and particle size measurements. Interestingly, the hemicelluloses removal from the acidification/PEO flocculation was marginal, which would be beneficial for the down-stream ethanol production from the PHL. Additionally, a process flow diagram was proposed that incorporates this new concept into the existing configuration of kraft-based dissolving pulp production process. Copyright © 2011 Elsevier Ltd. All rights reserved.

DNA sequence templates adjacent nucleosome and ORC sites at gene amplification origins in Drosophila

PubMed Central

Liu, Jun; Zimmer, Kurt; Rusch, Douglas B.; Paranjape, Neha; Podicheti, Ram; Tang, Haixu; Calvi, Brian R.

2015-01-01

Eukaryotic origins of DNA replication are bound by the origin recognition complex (ORC), which scaffolds assembly of a pre-replicative complex (pre-RC) that is then activated to initiate replication. Both pre-RC assembly and activation are strongly influenced by developmental changes to the epigenome, but molecular mechanisms remain incompletely defined. We have been examining the activation of origins responsible for developmental gene amplification in Drosophila. At a specific time in oogenesis, somatic follicle cells transition from genomic replication to a locus-specific replication from six amplicon origins. Previous evidence indicated that these amplicon origins are activated by nucleosome acetylation, but how this affects origin chromatin is unknown. Here, we examine nucleosome position in follicle cells using micrococcal nuclease digestion with Ilumina sequencing. The results indicate that ORC binding sites and other essential origin sequences are nucleosome-depleted regions (NDRs). Nucleosome position at the amplicons was highly similar among developmental stages during which ORC is or is not bound, indicating that being an NDR is not sufficient to specify ORC binding. Importantly, the data suggest that nucleosomes and ORC have opposite preferences for DNA sequence and structure. We propose that nucleosome hyperacetylation promotes pre-RC assembly onto adjacent DNA sequences that are disfavored by nucleosomes but favored by ORC. PMID:26227968

A Design Principle for an Autonomous Post-translational Pattern Formation.

PubMed

Sugai, Shuhei S; Ode, Koji L; Ueda, Hiroki R

2017-04-25

Previous autonomous pattern-formation models often assumed complex molecular and cellular networks. This theoretical study, however, shows that a system composed of one substrate with multisite phosphorylation and a pair of kinase and phosphatase can generate autonomous spatial information, including complex stripe patterns. All (de-)phosphorylation reactions are described with a generic Michaelis-Menten scheme, and all species freely diffuse without pre-existing gradients. Computational simulation upon >23,000,000 randomly generated parameter sets revealed the design motifs of cyclic reaction and enzyme sequestration by slow-diffusing substrates. These motifs constitute short-range positive and long-range negative feedback loops to induce Turing instability. The width and height of spatial patterns can be controlled independently by distinct reaction-diffusion processes. Therefore, multisite reversible post-translational modification can be a ubiquitous source for various patterns without requiring other complex regulations such as autocatalytic regulation of enzymes and is applicable to molecular mechanisms for inducing subcellular localization of proteins driven by post-translational modifications. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Rational design of a molecularly imprinted polymer for dinotefuran: theoretical and experimental studies aimed at the development of an efficient adsorbent for microextraction by packed sorbent.

PubMed

Silva, Camilla Fonseca; Borges, Keyller Bastos; do Nascimento, Clebio Soares

2017-12-18

In this work, we studied theoretically the formation process of a molecularly imprinted polymer (MIP) for dinotefuran (DNF), testing distinct functional monomers (FM) in various solvents through density functional theory calculations. The results revealed that the best conditions for MIP synthesis were established with methacrylic acid (MAA) as FM in a 1 : 4 stoichiometry and with chloroform as the solvent. This protocol showed the most favourable stabilization energies for the pre-polymerization complexes. Furthermore, the formation of the FM/template complex is enthalpy driven and the occurrence of hydrogen bonds between the DNF and MAA plays a major role in the complex stability. To confirm the theoretical results, MIP was experimentally synthesized considering the best conditions found at the molecular level and characterized by scanning electron microscopy and thermogravimetric analysis. After that, the synthesized material was efficiently employed in microextraction by packed sorbent combined with high-performance liquid chromatography in a preliminary study of the recovery of DNF from water and artificial saliva samples.

Transient Receptor Potential Channels TRPM4 and TRPC3 Critically Contribute to Respiratory Motor Pattern Formation but not Rhythmogenesis in Rodent Brainstem Circuits

PubMed Central

Tariq, Mohammad F.; Phillips, Ryan S.; Mosher, Bryan; Thompson, Ryan; Zhang, Ruli

2018-01-01

Abstract Transient receptor potential channel, TRPM4, the putative molecular substrate for Ca2+-activated nonselective cation current (ICAN), is hypothesized to generate bursting activity of pre-Bötzinger complex (pre-BötC) inspiratory neurons and critically contribute to respiratory rhythmogenesis. Another TRP channel, TRPC3, which mediates Na+/Ca2+ fluxes, may be involved in regulating Ca2+-related signaling, including affecting TRPM4/ICAN in respiratory pre-BötC neurons. However, TRPM4 and TRPC3 expression in pre-BötC inspiratory neurons and functional roles of these channels remain to be determined. By single-cell multiplex RT-PCR, we show mRNA expression for these channels in pre-BötC inspiratory neurons in rhythmically active medullary in vitro slices from neonatal rats and mice. Functional contributions were analyzed with pharmacological inhibitors of TRPM4 or TRPC3 in vitro as well as in mature rodent arterially perfused in situ brainstem–spinal cord preparations. Perturbations of respiratory circuit activity were also compared with those by a blocker of ICAN. Pharmacologically attenuating endogenous activation of TRPM4, TRPC3, or ICAN in vitro similarly reduced the amplitude of inspiratory motoneuronal activity without significant perturbations of inspiratory frequency or variability of the rhythm. Amplitude perturbations were correlated with reduced inspiratory glutamatergic pre-BötC neuronal activity, monitored by multicellular dynamic calcium imaging in vitro. In more intact circuits in situ, the reduction of pre-BötC and motoneuronal inspiratory activity amplitude was accompanied by reduced post-inspiratory motoneuronal activity, without disruption of rhythm generation. We conclude that endogenously activated TRPM4, which likely mediates ICAN, and TRPC3 channels in pre-BötC inspiratory neurons play fundamental roles in respiratory pattern formation but are not critically involved in respiratory rhythm generation. PMID:29435486

Effect of angular momentum alignment and strong magnetic fields on the formation of protostellar discs

NASA Astrophysics Data System (ADS)

Gray, William J.; McKee, Christopher F.; Klein, Richard I.

2018-01-01

Star-forming molecular clouds are observed to be both highly magnetized and turbulent. Consequently, the formation of protostellar discs is largely dependent on the complex interaction between gravity, magnetic fields, and turbulence. Studies of non-turbulent protostellar disc formation with realistic magnetic fields have shown that these fields are efficient in removing angular momentum from the forming discs, preventing their formation. However, once turbulence is included, discs can form in even highly magnetized clouds, although the precise mechanism remains uncertain. Here, we present several high-resolution simulations of turbulent, realistically magnetized, high-mass molecular clouds with both aligned and random turbulence to study the role that turbulence, misalignment, and magnetic fields have on the formation of protostellar discs. We find that when the turbulence is artificially aligned so that the angular momentum is parallel to the initial uniform field, no rotationally supported discs are formed, regardless of the initial turbulent energy. We conclude that turbulence and the associated misalignment between the angular momentum and the magnetic field are crucial in the formation of protostellar discs in the presence of realistic magnetic fields.

Enzymology below 200 K: The kinetics and thermodynamics of the photochemistry catalyzed by protochlorophyllide oxidoreductase

PubMed Central

Heyes, Derren J.; Ruban, Alexander V.; Wilks, Helen M.; Hunter, C. Neil

2002-01-01

The chlorophyll biosynthesis enzyme protochlorophyllide reductase (POR) catalyzes the light-dependent reduction of protochlorophyllide (Pchlide) into chlorophyllide in the presence of NADPH. As POR is light-dependent, catalysis can be initiated by illumination of the enzyme-substrate complex at low temperatures, making it an attractive model for studying aspects of biological proton and hydride transfers. The early stages in the photoreduction, involving Pchlide binding and an initial photochemical reaction, have been studied in vitro by using low-temperature fluorescence and absorbance measurements. Formation of the ternary POR-NADPH-Pchlide complex produces red shifts in the fluorescence and absorbance maxima of Pchlide, allowing the dissociation constant for Pchlide binding to be measured. We demonstrate that the product of an initial photochemical reaction, which can occur below 200 K, is a nonfluorescent intermediate with a broad absorbance band at 696 nm (A696) that is suggested to represent an ion radical complex. The temperature dependence of the rate of A696 formation has allowed the activation energy for the photochemical step to be calculated and has shown that POR catalysis can proceed at much lower temperatures than previously thought. Calculations of differences in free energy between various reaction intermediates have been calculated; these, together with the quantum efficiency for Pchlide conversion, suggest a quantitative model for the thermodynamics of the light-driven step of Pchlide reduction. PMID:12177453

Interactions between HIV-1 Reverse Transcriptase and the Downstream Template Strand in Stable Complexes with Primer-Template

PubMed Central

Rutvisuttinunt, Wiriya; Meyer, Peter R.; Scott, Walter A.

2008-01-01

Background Human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) forms stable ternary complexes in which RT is bound tightly at fixed positions on the primer-template (P/T). We have probed downstream interactions between RT and the template strand in the complex containing the incoming dNTP (+1 dNTP•RT•P/T complex) and in the complex containing the pyrophosphate analog, foscarnet (foscarnet•RT•P/T complex). Methods and Results UV-induced cross-linking between RT and the DNA template strand was most efficient when a bromodeoxyuridine residue was placed in the +2 position (the first template position downstream from the incoming dNTP). Furthermore, formation of the +1 dNTP•RT•P/T complex on a biotin-containing template inhibited binding of streptavidin when biotin was in the +2 position on the template but not when the biotin was in the +3 position. Streptavidin pre-bound to a biotin residue in the template caused RT to stall two to three nucleotides upstream from the biotin residue. The downstream border of the complex formed by the stalled RT was mapped by digestion with exonuclease RecJF. UV-induced cross-linking of the complex formed by the pyrophosphate analog, foscarnet, with RT and P/T occurred preferentially with bromodeoxyuridine in the +1 position on the template in keeping with the location of RT one base upstream in the foscarnet•RT•P/T complex (i.e., in the pre-translocation position). Conclusions For +1 dNTP•RT•P/T and foscarnet•RT•P/T stable complexes, tight interactions were observed between RT and the first unpaired template nucleotide following the bound dNTP or the primer terminus, respectively. PMID:18974785

RIPK3 regulates p62-LC3 complex formation via the caspase-8-dependent cleavage of p62.

PubMed

Matsuzawa, Yu; Oshima, Shigeru; Nibe, Yoichi; Kobayashi, Masanori; Maeyashiki, Chiaki; Nemoto, Yasuhiro; Nagaishi, Takashi; Okamoto, Ryuichi; Tsuchiya, Kiichiro; Nakamura, Tetsuya; Watanabe, Mamoru

2015-01-02

RIPK3 is a key molecule for necroptosis, initially characterized by necrotic cell death morphology and the activation of autophagy. Cell death and autophagic signaling are believed to tightly regulate each other. However, the associated recruitment of signaling proteins remains poorly understood. p62/sequestosome-1 is a selective autophagy substrate and a selective receptor for ubiquitinated proteins. In this study, we illustrated that both mouse and human RIPK3 mediate p62 cleavage and that RIPK3 interacts with p62, resulting in complex formation. In addition, RIPK3-dependent p62 cleavage is restricted by the inhibition of caspases, especially caspase-8. Moreover, overexpression of A20, a ubiquitin-editing enzyme and an inhibitor of caspase-8 activity, inhibits RIPK3-dependent p62 cleavage. To further investigate the potential role of RIPK3 in selective autophagy, we analyzed p62-LC3 complex formation, revealing that RIPK3 prevents the localization of LC3 and ubiquitinated proteins to the p62 complex. In addition, RIPK3-dependent p62-LC3 complex disruption is regulated by caspase inhibition. Taken together, these results demonstrated that RIPK3 interacts with p62 and regulates p62-LC3 complex formation. These findings suggested that RIPK3 serves as a negative regulator of selective autophagy and provides new insights into the mechanism by which RIPK3 regulates autophagic signaling. Copyright © 2014 Elsevier Inc. All rights reserved.

A Study of a Compound Solar Eruption with Two Consecutive Erupting Magnetic Structures

NASA Astrophysics Data System (ADS)

Dhakal, Suman K.; Chintzoglou, Georgios; Zhang, Jie

2018-06-01

We report a study of a compound solar eruption that was associated with two consecutively erupting magnetic structures and correspondingly two distinct peaks, during impulsive phase, of an M-class flare (M8.5). Simultaneous multi-viewpoint observations from SDO, GOES and STEREO-A show that this compound eruption originated from two pre-existing sigmoidal magnetic structures lying along the same polarity inversion line. Observations of the associated pre-existing filaments further show that these magnetic structures are lying one on top of the other, separated by 12 Mm in height, in a so-called “double-decker” configuration. The high-lying magnetic structure became unstable and erupted first, appearing as an expanding hot channel seen at extreme ultraviolet wavelengths. About 12 minutes later, the low-lying structure also started to erupt and moved at an even faster speed compared to the high-lying one. As a result, the two erupting structures interacted and merged with each other, appearing as a single coronal mass ejection in the outer corona. We find that the double-decker configuration is likely caused by the persistent shearing motion and flux cancellation along the source active region’s strong-gradient polarity inversion line. The successive destabilization of these two separate but closely spaced magnetic structures, possibly in the form of magnetic flux ropes, led to a compound solar eruption. The study of the compound eruption provides a unique opportunity to reveal the formation process, initiation, and evolution of complex eruptive structures in solar active regions.

The successful implementation of a licensed data management interface between a Sunquest(®) laboratory information system and an AB SCIEX™ mass spectrometer.

PubMed

French, Deborah; Terrazas, Enrique

2013-01-01

Interfacing complex laboratory equipment to laboratory information systems (LIS) has become a more commonly encountered problem in clinical laboratories, especially for instruments that do not have an interface provided by the vendor. Liquid chromatography-tandem mass spectrometry is a great example of such complex equipment, and has become a frequent addition to clinical laboratories. As the testing volume on such instruments can be significant, manual data entry will also be considerable and the potential for concomitant transcription errors arises. Due to this potential issue, our aim was to interface an AB SCIEX™ mass spectrometer to our Sunquest(®) LIS. WE LICENSED SOFTWARE FOR THE DATA MANAGEMENT INTERFACE FROM THE UNIVERSITY OF PITTSBURGH, BUT EXTENDED THIS WORK AS FOLLOWS: The interface was designed so that it would accept a text file exported from the AB SCIEX™ × 5500 QTrap(®) mass spectrometer, pre-process the file (using newly written code) into the correct format and upload it into Sunquest(®) via file transfer protocol. The licensed software handled the majority of the interface tasks with the exception of converting the output from the Analyst(®) software to the required Sunquest(®) import format. This required writing of a "pre-processor" by one of the authors which was easily integrated with the supplied software. We successfully implemented the data management interface licensed from the University of Pittsburgh. Given the coding that was required to write the pre-processor, and alterations to the source code that were performed when debugging the software, we would suggest that before a laboratory decides to implement such an interface, it would be necessary to have a competent computer programmer available.

Characterization of active reverse transcriptase and nucleoprotein complexes of the yeast retrotransposon Ty3 in vitro.

PubMed

Cristofari, G; Gabus, C; Ficheux, D; Bona, M; Le Grice, S F; Darlix, J L

1999-12-17

Human immunodeficiency virus (HIV) and the distantly related yeast Ty3 retrotransposon encode reverse transcriptase (RT) and a nucleic acid-binding protein designated nucleocapsid protein (NCp) with either one or two zinc fingers, required for HIV-1 replication and Ty3 transposition, respectively. In vitro binding of HIV-1 NCp7 to viral 5' RNA and primer tRNA(3)(Lys) catalyzes formation of nucleoprotein complexes resembling the virion nucleocapsid. Nucleocapsid complex formation functions in viral RNA dimerization and tRNA annealing to the primer binding site (PBS). RT is recruited in these nucleoprotein complexes and synthesizes minus-strand cDNA initiated at the PBS. Recent results on yeast Ty3 have shown that the homologous NCp9 promotes annealing of primer tRNA(i)(Met) to a 5'-3' bipartite PBS, allowing RNA:tRNA dimer formation and initiation of cDNA synthesis at the 5' PBS (). To compare specific cDNA synthesis in a retrotransposon and HIV-1, we have established a Ty3 model system comprising Ty3 RNA with the 5'-3' PBS, primer tRNA(i)(Met), NCp9, and for the first time, highly purified Ty3 RT. Here we report that Ty3 RT is as active as retroviral HIV-1 or murine leukemia virus RT using a synthetic template-primer system. Moreover, and in contrast to what was found with retroviral RTs, retrotransposon Ty3 RT was unable to direct cDNA synthesis by self-priming. We also show that Ty3 nucleoprotein complexes were formed in vitro and that the N terminus of NCp9, but not the zinc finger, is required for complex formation, tRNA annealing to the PBS, RNA dimerization, and primer tRNA-directed cDNA synthesis by Ty3 RT. These results indicate that NCp9 chaperones bona fide cDNA synthesis by RT in the yeast Ty3 retrotransposon, as illustrated for NCp7 in HIV-1, reinforcing the notion that Ty3 NCp9 is an ancestor of HIV-1 NCp7.

Differences and Comparisons of the Properties and Reactivities of Iron(III)–hydroperoxo Complexes with Saturated Coordination Sphere

PubMed Central

Faponle, Abayomi S; Quesne, Matthew G; Sastri, Chivukula V; Banse, Frédéric; de Visser, Sam P

2015-01-01

Heme and nonheme monoxygenases and dioxygenases catalyze important oxygen atom transfer reactions to substrates in the body. It is now well established that the cytochrome P450 enzymes react through the formation of a high-valent iron(IV)–oxo heme cation radical. Its precursor in the catalytic cycle, the iron(III)–hydroperoxo complex, was tested for catalytic activity and found to be a sluggish oxidant of hydroxylation, epoxidation and sulfoxidation reactions. In a recent twist of events, evidence has emerged of several nonheme iron(III)–hydroperoxo complexes that appear to react with substrates via oxygen atom transfer processes. Although it was not clear from these studies whether the iron(III)–hydroperoxo reacted directly with substrates or that an initial O–O bond cleavage preceded the reaction. Clearly, the catalytic activity of heme and nonheme iron(III)–hydroperoxo complexes is substantially different, but the origins of this are still poorly understood and warrant a detailed analysis. In this work, an extensive computational analysis of aromatic hydroxylation by biomimetic nonheme and heme iron systems is presented, starting from an iron(III)–hydroperoxo complex with pentadentate ligand system (L52). Direct C–O bond formation by an iron(III)–hydroperoxo complex is investigated, as well as the initial heterolytic and homolytic bond cleavage of the hydroperoxo group. The calculations show that [(L52)FeIII(OOH)]2+ should be able to initiate an aromatic hydroxylation process, although a low-energy homolytic cleavage pathway is only slightly higher in energy. A detailed valence bond and thermochemical analysis rationalizes the differences in chemical reactivity of heme and nonheme iron(III)–hydroperoxo and show that the main reason for this particular nonheme complex to be reactive comes from the fact that they homolytically split the O–O bond, whereas a heterolytic O–O bond breaking in heme iron(III)–hydroperoxo is found. PMID:25399782

A Constraint on the Formation Timescale of the Young Open Cluster NGC 2264: Lithium Abundance of Pre-main Sequence Stars

NASA Astrophysics Data System (ADS)

Lim, Beomdu; Sung, Hwankyung; Kim, Jinyoung S.; Bessell, Michael S.; Hwang, Narae; Park, Byeong-Gon

2016-11-01

The timescale of cluster formation is an essential parameter in order to understand the formation process of star clusters. Pre-main sequence (PMS) stars in nearby young open clusters reveal a large spread in brightness. If the spread were considered to be a result of a real spread in age, the corresponding cluster formation timescale would be about 5-20 Myr. Hence it could be interpreted that star formation in an open cluster is prolonged for up to a few tens of Myr. However, difficulties in reddening correction, observational errors, and systematic uncertainties introduced by imperfect evolutionary models for PMS stars can result in an artificial age spread. Alternatively, we can utilize Li abundance as a relative age indicator of PMS star to determine the cluster formation timescale. The optical spectra of 134 PMS stars in NGC 2264 have been obtained with MMT/Hectochelle. The equivalent widths have been measured for 86 PMS stars with a detectable Li line (3500\\lt {T}{eff}[{{K}}]≤slant 6500). Li abundance under the condition of local thermodynamic equilibrium (LTE) was derived using the conventional curve of growth method. After correction for non-LTE effects, we find that the initial Li abundance of NGC 2264 is A({Li})=3.2+/- 0.2. From the distribution of the Li abundances, the underlying age spread of the visible PMS stars is estimated to be about 3-4 Myr and this, together with the presence of embedded populations in NGC 2264, suggests that the cluster formed on a timescale shorter than 5 Myr.

Activation of intentional mechanisms through utilization of nonsymbolic movements in aphasia rehabilitation.

PubMed

Richards, Katherine; Singletary, Floris; Rothi, Leslie J Gonzalez; Koehler, Shirley; Crosson, Bruce

2002-01-01

Intentional mechanisms play an important role in complex self-initiated actions, such as language and gesturing. Deficits demonstrated in nonfluent aphasia may be a result of a disconnection between or damage to the initiation (intention) and production mechanisms in the left hemisphere. In chronic nonfluent aphasias, damaged language production mechanisms in the left hemisphere may switch to homologous regions in the right hemisphere while the initiation mechanisms remain active in the left hemisphere. A treatment was developed to prime right-hemisphere initiation mechanisms with movements of the nondominant hand, thereby bringing initiation into the right hemisphere where the language production mechanisms have been shifted. Three subjects with stable, chronic nonfluent aphasias were trained in daily sessions with a therapist to perform a complex nonsymbolic movement sequence with their nondominant hand to initiate naming trials of simple line drawings. Naming probes were administered during pre treatment baseline sessions and before each treatment session. All three subjects demonstrated a stable baseline and a significant increase over baseline performance in the percentage correct on naming probes during the treatment. Findings indicate that more extensive investigations of this newly developed treatment are justified and suggest that activation of right-hemisphere initiation mechanisms may enhance word production accuracy in stable, chronic nonfluent aphasias.

Insights into the Li Intercalation and SEI Formation on LiSi Nanoclusters

DOE PAGES

Hankins, Kie; Soto, Fernando A.; Balbuena, Perla B.

2017-01-01

We report a first-principles atomic level assessment of the lithiation and reactivity of pre-lithiated Si clusters. Density functional theory formation energy calculations reveal that the pre-lithiated Li 16Si 16 cluster exposed to two different Li fluxes can store Li between the concentrations of Li 2.5Si and Li 3.5Si. This increase in storage capacity is attributed to the start of an amorphization process in the cluster, and more importantly these results show that the intercalation reaction can be controlled by the flux of the Li-ions. However, in a real battery, the lithiation of the anode occurs simultaneously to the electrode-electrolyte reactions.more » Here we simulate the solid-electrolyte interphase (SEI) formation and simultaneous lithiation of a Li 16Si 16 cluster in contact with two different electrolyte solutions: one with pure ethylene carbonate (EC), and another with a 1 M solution of LiPF 6 in EC. Our ab initio molecular dynamics simulations show that the solvent and salt are decomposed leading to the initial stages of the SEI layer formation and large part of the added Li becomes part of the SEI. Interestingly, the pure EC solution results in lower storage capacity and higher reactivity, whereas the presence of the salt causes the opposite effect: higher lithiation and reduced reactivity.« less

Development of the Hippocampal Cognitive Map in Pre-weanling Rats

PubMed Central

Wills, Tom; Cacucci, Francesca; Burgess, Neil; O’Keefe, John

2011-01-01

Orienting in large-scale space depends on the interaction of environmental experience and pre-configured, possibly innate, constructs. Place, head-direction and grid cells in the hippocampal formation provide allocentric representations of space. Here we show how these cognitive representations emerge and develop as rat pups first begin to explore their environment. Directional, locational and rhythmic organization of firing are present during initial exploration, including adult-like directional firing. The stability and precision of place cell firing continues to develop throughout juvenility. Stable grid cell firing appears later but matures rapidly to adult levels. Our results demonstrate the presence of three neuronal representations of space prior to extensive experience, and show how they develop with age. PMID:20558720

Reduction of plasma density in the Helicity Injected Torus with Steady Inductance experiment by using a helicon pre-ionization source.

PubMed

Hossack, Aaron C; Firman, Taylor; Jarboe, Thomas R; Prager, James R; Victor, Brian S; Wrobel, Jonathan S; Ziemba, Timothy

2013-10-01

A helicon based pre-ionization source has been developed and installed on the Helicity Injected Torus with Steady Inductance (HIT-SI) spheromak. The source initiates plasma breakdown by injecting impurity-free, unmagnetized plasma into the HIT-SI confinement volume. Typical helium spheromaks have electron density reduced from (2-3) × 10(19) m(-3) to 1 × 10(19) m(-3). Deuterium spheromak formation is possible with density as low as 2 × 10(18) m(-3). The source also enables HIT-SI to be operated with only one helicity injector at injector frequencies above 14.5 kHz. A theory explaining the physical mechanism driving the reduction of breakdown density is presented.

Exploring Pre-Service Science Teachers' Pedagogical Capacity for Formative Assessment through Analyses of Student Answers

ERIC Educational Resources Information Center

Aydeniz, Mehmet; Dogan, Alev

2016-01-01

Background: There has been an increasing emphasis on empowering pre-service and in-service science teachers to attend student reasoning and use formative assessments to guide student learning in recent years. Purpose: The purpose of this study was to explore pre-service science teachers' pedagogical capacity for formative assessment. Sample: This…

Kinetics and thermochemistry of 2,5-dimethyltetrahydrofuran and related oxolanes: next next-generation biofuels.

PubMed

Simmie, John M

2012-05-10

The enthalpies of formation, entropies, specific heats at constant pressure, enthalpy functions, and all carbon-hydrogen and carbon-methyl bond dissociation energies have been computed using high-level methods for the cyclic ethers (oxolanes) tetrahydrofuran, 2-methyltetrahydrofuran, and 2,5-dimethyltetrahydrofuran. Barrier heights for hydrogen-abstraction reactions by hydrogen atoms and the methyl radical are also computed and shown to correlate with reaction energy change. The results show a pleasing consistency and considerably expands the available data for these important compounds. Abstraction by ȮH is accompanied by formation of both pre- and postreaction weakly bound complexes. The resulting radicals formed after abstraction undergo ring-opening reactions leading to readily recognizable intermediates, while competitive H-elimination reactions result in formation of dihydrofurans. Formation enthalpies of all 2,3- and 2,5-dihydrofurans and associated radicals are also reported. It is probable that the compounds at the center of this study will be relatively clean-burning biofuels, although formation of intermediate aldehydes might be problematic.

Styrene Polymerization under Ambient Conditions by using a Transient 1,3,2-Diazaphospholane-2-oxyl Complex.

PubMed

Heurich, Tobias; Qu, Zheng-Wang; Kunzmann, Robert; Schnakenburg, Gregor; Engeser, Marianne; Nožinović, Senada; Streubel, Rainer

2018-04-25

A combined theoretical and experimental study on the formation and reactivity of a P-OTEMP (P-bound TEMPO (TEMPO=2,2,6,6-tetramethyl-piperidin-1-oxyl)) substituted 1,3,2-diazaphospholane W(CO) 5 complex is presented, including DFT-based mechanistic details. The complex possesses a thermally labile O-N bond that cleaves homolytically yielding the transient 1,3,2-diazaphospholane-2-oxyl complex [(CO) 5 W(R 2 PO . )], which acts as a radical initiator for styrene polymerization under ambient conditions. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structures and mechanisms of vesicle coat components and multisubunit tethering complexes

PubMed Central

Jackson, Lauren P; Kümmel, Daniel; Reinisch, Karin M; Owen, David J

2012-01-01

Eukaryotic cells face a logistical challenge in ensuring prompt and precise delivery of vesicular cargo to specific organelles within the cell. Coat protein complexes select cargo and initiate vesicle formation, while multisubunit tethering complexes participate in the delivery of vesicles to target membranes. Understanding these macromolecular assemblies has greatly benefited from their structural characterization. Recent structural data highlight principles in coat recruitment and uncoating in both the endocytic and retrograde pathways, and studies on the architecture of tethering complexes provide a framework for how they might link vesicles to the respective acceptor compartments and the fusion machinery. PMID:22728063

Regulated Eukaryotic DNA Replication Origin Firing with Purified Proteins

PubMed Central

Yeeles, Joseph T.P.; Deegan, Tom D.; Janska, Agnieszka; Early, Anne; Diffley, John F. X.

2016-01-01

Eukaryotic cells initiate DNA replication from multiple origins, which must be tightly regulated to promote precise genome duplication in every cell cycle. To accomplish this, initiation is partitioned into two temporally discrete steps: a double hexameric MCM complex is first loaded at replication origins during G1 phase, and then converted to the active CMG (Cdc45, MCM, GINS) helicase during S phase. Here we describe the reconstitution of budding yeast DNA replication initiation with 16 purified replication factors, made from 42 polypeptides. Origin-dependent initiation recapitulates regulation seen in vivo. Cyclin dependent kinase (CDK) inhibits MCM loading by phosphorylating the origin recognition complex (ORC) and promotes CMG formation by phosphorylating Sld2 and Sld3. Dbf4 dependent kinase (DDK) promotes replication by phosphorylating MCM, and can act either before or after CDK. These experiments define the minimum complement of proteins, protein kinase substrates and co-factors required for regulated eukaryotic DNA replication. PMID:25739503

Regulated eukaryotic DNA replication origin firing with purified proteins.

PubMed

Yeeles, Joseph T P; Deegan, Tom D; Janska, Agnieszka; Early, Anne; Diffley, John F X

2015-03-26

Eukaryotic cells initiate DNA replication from multiple origins, which must be tightly regulated to promote precise genome duplication in every cell cycle. To accomplish this, initiation is partitioned into two temporally discrete steps: a double hexameric minichromosome maintenance (MCM) complex is first loaded at replication origins during G1 phase, and then converted to the active CMG (Cdc45-MCM-GINS) helicase during S phase. Here we describe the reconstitution of budding yeast DNA replication initiation with 16 purified replication factors, made from 42 polypeptides. Origin-dependent initiation recapitulates regulation seen in vivo. Cyclin-dependent kinase (CDK) inhibits MCM loading by phosphorylating the origin recognition complex (ORC) and promotes CMG formation by phosphorylating Sld2 and Sld3. Dbf4-dependent kinase (DDK) promotes replication by phosphorylating MCM, and can act either before or after CDK. These experiments define the minimum complement of proteins, protein kinase substrates and co-factors required for regulated eukaryotic DNA replication.

Protective effects of a topical antioxidant complex containing vitamins C and E and ferulic acid against ultraviolet irradiation-induced photodamage in Chinese women.

PubMed

Wu, Yan; Zheng, Xin; Xu, Xue-Gang; Li, Yuan-Hong; Wang, Bin; Gao, Xing-Hua; Chen, Hong-Duo; Yatskayer, Margarita; Oresajo, Christian

2013-04-01

The objective of the study was to investigate whether a topical antioxidant complex containing vitamins C and E and ferulic acid can protect solar-simulated ultraviolet irradiation (ssUVR)-induced acute photodamage in human skin. Twelve healthy female Chinese subjects were enrolled in this study. Four unexposed sites on dorsal skin were marked for the experiment. The products containing antioxidant complex and vehicle were applied onto 2 sites, respectively, for 4 consecutive days. On day 4, the antioxidant complex-treated site, the vehicle-treated site, and the untreated site (positive control) received ssUVR (5 times the minimal erythema dose). The fourth site (negative control) received neither ssUVR nor treatment. Digital photographs were taken, and skin color was measured pre- and postirradiation. Skin biopsies were obtained 24 hours after exposure to ssUVR, for hematoxylin and eosin and immunohistochemical staining. A single, 5 times the minimal erythema dose of ssUVR substantially induced large amounts of sunburn cell formation, thymine dimer formation, overexpression of p53 protein, and depletion of CD1a+ Langerhans cells. The antioxidant complex containing vitamins C and E and ferulic acid conferred significant protection against biological events compared with other irradiated sites. A topical antioxidant complex containing vitamins C and E and ferulic acid has potential photoprotective effects against ssUVR-induced acute photodamage in human skin.

Spectroscopic Studies of Pre-Biotic Carbon Chemistry

NASA Technical Reports Server (NTRS)

Blake, Geoffrey A.

2002-01-01

As described in the original proposal and in our progress reports, research in the Blake group supported by the Exobiology program seeks to understand the pre-biotic chemistry of carbon along with that of other first- and second-row elements from the earliest stages of star formation through the development of planetary systems. The major tool used is spectroscopy, and the program has observational, laboratory, and theoretical components. The observational and theoretical programs are concerned primarily with a quantitative assessment of the chemical budgets of the biogenic elements in star-forming molecular cloud cores, while the laboratory work is focused on the complex species that characterize the prebiotic chemistry of carbon. We outline below our results over the past two years acquired, in part, with Exobiology support.

Rrp12 and the Exportin Crm1 participate in late assembly events in the nucleolus during 40S ribosomal subunit biogenesis.

PubMed

Moriggi, Giulia; Nieto, Blanca; Dosil, Mercedes

2014-12-01

During the biogenesis of small ribosomal subunits in eukaryotes, the pre-40S particles formed in the nucleolus are rapidly transported to the cytoplasm. The mechanisms underlying the nuclear export of these particles and its coordination with other biogenesis steps are mostly unknown. Here we show that yeast Rrp12 is required for the exit of pre-40S particles to the cytoplasm and for proper maturation dynamics of upstream 90S pre-ribosomes. Due to this, in vivo elimination of Rrp12 leads to an accumulation of nucleoplasmic 90S to pre-40S transitional particles, abnormal 35S pre-rRNA processing, delayed elimination of processing byproducts, and no export of intermediate pre-40S complexes. The exportin Crm1 is also required for the same pre-ribosome maturation events that involve Rrp12. Thus, in addition to their implication in nuclear export, Rrp12 and Crm1 participate in earlier biosynthetic steps that take place in the nucleolus. Our results indicate that, in the 40S subunit synthesis pathway, the completion of early pre-40S particle assembly, the initiation of byproduct degradation and the priming for nuclear export occur in an integrated manner in late 90S pre-ribosomes.

Long-term avoidance memory formation is associated with a transient increase in mushroom body synaptic complexes in leaf-cutting ants

PubMed Central

Falibene, Agustina; Roces, Flavio; Rössler, Wolfgang

2015-01-01

Long-term behavioral changes related to learning and experience have been shown to be associated with structural remodeling in the brain. Leaf-cutting ants learn to avoid previously preferred plants after they have proved harmful for their symbiotic fungus, a process that involves long-term olfactory memory. We studied the dynamics of brain microarchitectural changes after long-term olfactory memory formation following avoidance learning in Acromyrmex ambiguus. After performing experiments to control for possible neuronal changes related to age and body size, we quantified synaptic complexes (microglomeruli, MG) in olfactory regions of the mushroom bodies (MBs) at different times after learning. Long-term avoidance memory formation was associated with a transient change in MG densities. Two days after learning, MG density was higher than before learning. At days 4 and 15 after learning—when ants still showed plant avoidance—MG densities had decreased to the initial state. The structural reorganization of MG triggered by long-term avoidance memory formation clearly differed from changes promoted by pure exposure to and collection of novel plants with distinct odors. Sensory exposure by the simultaneous collection of several, instead of one, non-harmful plant species resulted in a decrease in MG densities in the olfactory lip. We hypothesize that while sensory exposure leads to MG pruning in the MB olfactory lip, the formation of long-term avoidance memory involves an initial growth of new MG followed by subsequent pruning. PMID:25904854

Secondary organic aerosol formation from low-NO(x) photooxidation of dodecane: evolution of multigeneration gas-phase chemistry and aerosol composition.

PubMed

Yee, Lindsay D; Craven, Jill S; Loza, Christine L; Schilling, Katherine A; Ng, Nga Lee; Canagaratna, Manjula R; Ziemann, Paul J; Flagan, Richard C; Seinfeld, John H

2012-06-21

The extended photooxidation of and secondary organic aerosol (SOA) formation from dodecane (C(12)H(26)) under low-NO(x) conditions, such that RO(2) + HO(2) chemistry dominates the fate of the peroxy radicals, is studied in the Caltech Environmental Chamber based on simultaneous gas and particle-phase measurements. A mechanism simulation indicates that greater than 67% of the initial carbon ends up as fourth and higher generation products after 10 h of reaction, and simulated trends for seven species are supported by gas-phase measurements. A characteristic set of hydroperoxide gas-phase products are formed under these low-NO(x) conditions. Production of semivolatile hydroperoxide species within three generations of chemistry is consistent with observed initial aerosol growth. Continued gas-phase oxidation of these semivolatile species produces multifunctional low volatility compounds. This study elucidates the complex evolution of the gas-phase photooxidation chemistry and subsequent SOA formation through a novel approach comparing molecular level information from a chemical ionization mass spectrometer (CIMS) and high m/z ion fragments from an Aerodyne high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS). Combination of these techniques reveals that particle-phase chemistry leading to peroxyhemiacetal formation is the likely mechanism by which these species are incorporated in the particle phase. The current findings are relevant toward understanding atmospheric SOA formation and aging from the "unresolved complex mixture," comprising, in part, long-chain alkanes.

Backbone conformation affects duplex initiation and duplex propagation in hybridisation of synthetic H-bonding oligomers.

PubMed

Iadevaia, Giulia; Núñez-Villanueva, Diego; Stross, Alexander E; Hunter, Christopher A

2018-06-06

Synthetic oligomers equipped with complementary H-bond donor and acceptor side chains form multiply H-bonded duplexes in organic solvents. Comparison of the duplex forming properties of four families of oligomers with different backbones shows that formation of an extended duplex with three or four inter-strand H-bonds is more challenging than formation of complexes that make only two H-bonds. The stabilities of 1 : 1 complexes formed between length complementary homo-oligomers equipped with either phosphine oxide or phenol recognition modules were measured in toluene. When the backbone is very flexible (pentane-1,5-diyl thioether), the stability increases uniformly by an order of magnitude for each additional base-pair added to the duplex: the effective molarities for formation of the first intramolecular H-bond (duplex initiation) and subsequent intramolecular H-bonds (duplex propagation) are similar. This flexible system is compared with three more rigid backbones that are isomeric combinations of an aromatic ring and methylene groups. One of the rigid systems behaves in exactly the same way as the flexible backbone, but the other two do not. For these systems, the effective molarity for formation of the first intramolecular H-bond is the same as that found for the other two backbones, but additional H-bonds are not formed between the longer oligomers. The effective molarities are too low for duplex propagation in these systems, because the oligomer backbones cannot adopt conformations compatible with formation of an extended duplex.

Pre-Implementation Strategies to Adapt and Implement a Veteran Peer Coaching Intervention to Improve Mental Health Treatment Engagement Among Rural Veterans.

PubMed

Koenig, Christopher J; Abraham, Traci; Zamora, Kara A; Hill, Coleen; Kelly, P Adam; Uddo, Madeline; Hamilton, Michelle; Pyne, Jeffrey M; Seal, Karen H

2016-09-01

Telephone motivational coaching has been shown to increase urban veteran mental health treatment initiation. However, no studies have tested telephone motivational coaching delivered by veteran peers to facilitate mental health treatment initiation and engagement. This study describes pre-implementation strategies with 8 Veterans Affairs (VA) community-based outpatient clinics in the West and Mid-South United States to adapt and implement a multisite pragmatic randomized controlled trial of telephone peer motivational coaching for rural veterans. We used 2 pre-implementation strategies, Formative Evaluation (FE) research and Evidence-Based Quality Improvement (EBQI) meetings to adapt the intervention to stakeholders' needs and cultural contexts. FE data were qualitative, semi-structured interviews with rural veterans and VA clinic staff. Results were rapidly analyzed and presented to stakeholders during EBQI meetings to optimize the intervention implementation. FE research results showed that VA clinic providers felt overwhelmed by veterans' mental health needs and acknowledged limited mental health services at VA clinics. Rural veteran interviews indicated geographical, logistical, and cultural barriers to VA mental health treatment initiation and a preference for self-care to cope with mental health symptoms. EBQI meetings resulted in several intervention adaptations, including veteran study recruitment, peer veteran coach training, and an expanded definition of mental health care outcomes. As the VA moves to cultivate community partnerships in order to personalize and expand access to care for rural veterans, pre-implementation processes with engaged stakeholders, such as those described here, can help guide other researchers and clinicians to achieve proactive and veteran-centered health care services. © 2016 National Rural Health Association.

Cost effectiveness of the Oregon quitline "free patch initiative".

PubMed

Fellows, Jeffrey L; Bush, Terry; McAfee, Tim; Dickerson, John

2007-12-01

We estimated the cost effectiveness of the Oregon tobacco quitline's "free patch initiative" compared to the pre-initiative programme. Using quitline utilisation and cost data from the state, intervention providers and patients, we estimated annual programme use and costs for media promotions and intervention services. We also estimated annual quitline registration calls and the number of quitters and life years saved for the pre-initiative and free patch initiative programmes. Service utilisation and 30-day abstinence at six months were obtained from 959 quitline callers. We compared the cost effectiveness of the free patch initiative (media and intervention costs) to the pre-initiative service offered to insured and uninsured callers. We conducted sensitivity analyses on key programme costs and outcomes by estimating a best case and worst case scenario for each intervention strategy. Compared to the pre-intervention programme, the free patch initiative doubled registered calls, increased quitting fourfold and reduced total costs per quit by $2688. We estimated annual paid media costs were $215 per registered tobacco user for the pre-initiative programme and less than $4 per caller during the free patch initiative. Compared to the pre-initiative programme, incremental quitline promotion and intervention costs for the free patch initiative were $86 (range $22-$353) per life year saved. Compared to the pre-initiative programme, the free patch initiative was a highly cost effective strategy for increasing quitting in the population.

Oxidative stress in duckweed (Lemna minor L.) induced by glyphosate: Is the mitochondrial electron transport chain a target of this herbicide?

PubMed

Gomes, Marcelo Pedrosa; Juneau, Philippe

2016-11-01

We investigated the physiological responses of Lemna minor plants exposed to glyphosate. The deleterious effects of this herbicide on photosynthesis, respiration, and pigment concentrations were related to glyphosate-induced oxidative stress through hydrogen peroxide (H 2 O 2 ) accumulation. By using photosynthetic and respiratory electron transport chain (ETC) inhibitors we located the primary site of reactive oxygen species (ROS) production in plants exposed to 500 mg glyphosate l -1 . Inhibition of mitochondrial ETC Complex I by rotenone reduced H 2 O 2 concentrations in glyphosate-treated plants. Complex III activity was very sensitive to glyphosate which appears to act much like antimycin A (an inhibitor of mitochondrial ETC Complex III) by shunting electrons from semiquinone to oxygen, with resulting ROS formation. Confocal evaluations for ROS localization showed that ROS are initially produced outside of the chloroplasts upon initial glyphosate exposure. Our results indicate that in addition to interfering with the shikimate pathway, glyphosate can induce oxidative stress in plants through H 2 O 2 formation by targeting the mitochondrial ETC, which would explain its observed effects on non-target organisms. Copyright © 2016 Elsevier Ltd. All rights reserved.

Developing interprofessional education online: An ecological systems theory analysis.

PubMed

Bluteau, Patricia; Clouder, Lynn; Cureton, Debra

2017-07-01

This article relates the findings of a discourse analysis of an online asynchronous interprofessional learning initiative involving two UK universities. The impact of the initiative is traced over three intensive periods of online interaction, each of several-weeks duration occurring over a three-year period, through an analysis of a random sample of discussion forum threads. The corpus of rich data drawn from the forums is interpreted using ecological systems theory, which highlights the complexity of interaction of individual, social and cultural elements. Ecological systems theory adopts a life course approach to understand how development occurs through processes of progressively more complex reciprocal interaction between people and their environment. This lens provides a novel approach for analysis and interpretation of findings with respect to the impact of pre-registration interprofessional education and the interaction between the individual and their social and cultural contexts as they progress through 3/4 years of their programmes. Development is mapped over time (the chronosystem) to highlight the complexity of interaction across microsystems (individual), mesosystems (curriculum and institutional/care settings), exosystems (community/wider local context), and macrosystems (national context and culture). This article illustrates the intricacies of students' interprofessional development over time and the interactive effects of social ecological components in terms of professional knowledge and understanding, wider appreciation of health and social care culture and identity work. The implications for contemporary pre-registration interprofessional education and the usefulness and applicability of ecological systems theory for future research and development are considered.

Hsp90 is required for the activity of a hepatitis B virus reverse transcriptase.

PubMed Central

Hu, J; Seeger, C

1996-01-01

The heat shock protein Hsp90 is known as an essential component of several signal transduction pathways and has now been identified as an essential host factor for hepatitis B virus replication. Hsp90 interacts with the viral reverse transcriptase to facilitate the formation of a ribonucleoprotein (RNP) complex between the polymerase and an RNA ligand. This RNP complex is required early in replication for viral assembly and initiation of DNA synthesis through a protein-priming mechanism. These results thus invoke a role for the Hsp90 pathway in the formation of an RNP. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 Fig. 6 PMID:8577714

Examination of the formation process of pre-solvated and solvated electron in n-alcohol using femtosecond pulse radiolysis

NASA Astrophysics Data System (ADS)

Toigawa, Tomohiro; Gohdo, Masao; Norizawa, Kimihiro; Kondoh, Takafumi; Kan, Koichi; Yang, Jinfeng; Yoshida, Yoichi

2016-06-01

The formation process of pre-solvated and solvated electron in methanol (MeOH), ethanol (EtOH), n-butanol (BuOH), and n-octanol (OcOH) were investigated using a fs-pulse radiolysis technique by observing the pre-solvated electron at 1400 nm. The formation time constants of the pre-solvated electrons were determined to be 1.2, 2.2, 3.1, and 6.3 ps for MeOH, EtOH, BuOH, and OcOH, respectively. The formation time constants of the solvated electrons were determined to be 6.7, 13.6, 22.2, and 32.9 ps for MeOH, EtOH, BuOH, and OcOH, respectively. The formation dynamics and structure of the pre-solvated and solvated electrons in n-alcohols were discussed based on relation between the obtained time constant and dielectric relaxation time constant from the view point of kinetics. The observed formation time constants of the solvated electrons seemed to be strongly correlated with the second component of the dielectric relaxation time constants, which are related to single molecule motion. On the other hand, the observed formation time constants of the pre-solvated electrons seemed to be strongly correlated with the third component of the dielectric relaxation time constants, which are related to dynamics of hydrogen bonds.

Blood Hemostatic Changes During an Ultraendurance Road Cycling Event in a Hot Environment.

PubMed

Kupchak, Brian R; Kazman, Josh B; Vingren, Jakob L; Levitt, Danielle E; Lee, Elaine C; Williamson, Keith H; Armstrong, Lawrence E; Deuster, Patricia A

2017-09-01

This study aims to examine blood hemostatic responses to completing a 164-km road cycling event in a hot environment. Thirty-seven subjects (28 men and 9 women; 51.8±9.5 [mean±SD] y) completed the ride in 6.6±1.1 hours. Anthropometrics (height, body mass [taken also during morning of the ride], percent body fat [%]) were collected the day before the ride. Blood samples were collected on the morning of the ride (PRE) and immediately after (IP) the subject completed the ride. Concentrations of platelet, platelet activation, coagulation, and fibrinolytic markers (platelet factor 4, β-thromboglobulin, von Willebrand factor antigen, thrombin-antithrombin complex, thrombomodulin, and D-Dimer) were measured. Associations between changes from PRE- to IP-ride were examined as a function of event completion time and subject characteristics (demographics and anthropometrics). All blood hemostatic markers increased significantly (P < .001) from PRE to IP. After controlling for PRE values, finishing time was negatively correlated with platelet factor 4 (r = 0.40; P = .017), while percent body fat (%BF) was negatively correlated with thrombin-antithrombin complex (r = -0.35; P = .038) and to thrombomodulin (r = -0.36; P = .036). In addition, male subjects had greater concentrations of thrombin-antithrombin complex (d = 0.63; P < .05) and natural logarithm thrombomodulin (d = 6.42; P < .05) than female subjects. Completing the 164-km road cycling event in hot conditions resulted in increased concentrations of platelet, platelet activation, coagulation, and fibrinolytic markers in both men and women. Although platelet activation and coagulation occurred, the fibrinolytic system markers also increased, which appears to balance blood hemostasis and may prevent clot formation during exercise in a hot environment. Published by Elsevier Inc.

Proteomic Identification of Carbonylated Proteins in 1,3-Dinitrobenzene Neurotoxicity

PubMed Central

Steiner, Stephen R.; Philbert, Martin A.

2011-01-01

This study demonstrated that 1,3-dinitrobenzene-induced (1,3-DNB) oxidative stress led to the oxidative carbonlyation of specific protein targets in DI TNC1 cells. 1,3-DNB-induced mitochondrial dysfunction, as indicated by loss of tetramethyl rhodamine methyl ester (TMRM) fluorescence, was initially observed at 5 h and coincided with peak reactive oxygen species (ROS) production. ROS production was inhibited in cells pre-treated with the mitochondrial permeability transition (MPT) inhibitor, bonkrekic acid (BkA). Pre-incubation with the antioxidant deferoxamine inhibited loss of TMRM fluorescence until 24 h after initial exposure to 1,3-DNB. Two-dimensional polyacrylamide gel electrophoresis (2D PAGE) and subsequent Oxyblot analysis were used to determine if 1,3-DNB exposure led to the formation of protein carbonyls. Exposing DI TNC1 cells to 1,3-DNB led to marked protein carbonylation 45 min following initial exposure. Pre-treatment with deferoxamine or Trolox reduced the intensity of protein carbonylation in DI TNC1 cells exposed to 1mM 1,3-DNB. Tandem MS/MS performed on protein samples isolated from 1,3-DNB-treated cells revealed that specific proteins within the mitochondria, endoplasmic reticulum (ER), and cytosol are targets of protein carbonylation. The results presented in this study are the first to suggest that the molecular mechanism of 1,3-DNB neurotoxicity may occur through selective carbonylation of protein targets found within certain intracellular compartments of susceptible cells. PMID:21402099

Stepwise assembly of multiple Lin28 proteins on the terminal loop of let-7 miRNA precursors

PubMed Central

Desjardins, Alexandre; Bouvette, Jonathan; Legault, Pascale

2014-01-01

Lin28 inhibits the biogenesis of let-7 miRNAs through direct interactions with let-7 precursors. Previous studies have described seemingly inconsistent Lin28 binding sites on pre-let-7 RNAs. Here, we reconcile these data by examining the binding mechanism of Lin28 to the terminal loop of pre-let-7g (TL-let-7g) using biochemical and biophysical methods. First, we investigate Lin28 binding to TL-let-7g variants and short RNA fragments and identify three independent binding sites for Lin28 on TL-let-7g. We then determine that Lin28 assembles in a stepwise manner on TL-let-7g to form a stable 1:3 complex. We show that the cold-shock domain (CSD) of Lin28 is responsible for remodelling the terminal loop of TL-let-7g, whereas the NCp7-like domain facilitates the initial binding of Lin28 to TL-let-7g. This stable binding of multiple Lin28 molecules to the terminal loop of pre-let-7g extends to other precursors of the let-7 family, but not to other pre-miRNAs tested. We propose a model for stepwise assembly of the 1:1, 1:2 and 1:3 pre-let-7g/Lin28 complexes. Stepwise multimerization of Lin28 on pre-let-7 is required for maximum inhibition of Dicer cleavage for a least one member of the let-7 family and may be important for orchestrating the activity of the several factors that regulate let-7 biogenesis. PMID:24452802

Unilateral ablation of pre-Botzinger complex disrupts breathing during sleep but not wakefulness.

PubMed

McKay, Leanne C; Feldman, Jack L

2008-07-01

In adult rats, bilateral ablation of pre-Bötzinger complex (preBötC) neurokinin 1-expressing (NK1R) neurons leads to a progressive and irreversible disruption in breathing pattern, initially during sleep, eventually resulting in an ataxic breathing pattern during wakefulness. Here we determine whether ablation of fewer preBötC NK1R neurons leads to a persistent pattern of disordered breathing during sleep but not during wakefulness. Adult male Sprague-Dawley rats (n = 12) were instrumented to record diaphragmatic, abdominal, and neck EMG, and EEG. Fourteen days later, a second surgery was performed to stereotaxically microinject into the preBötC on one side the toxin saporin conjugated to substance P (SP-SAP), which selectively ablates NK1R neurons. Postinjection, rats were monitored within a plethysmograph until they were killed (Days 21-51). At Days 6-9 post-unilateral SP-SAP injection, respiratory pattern during sleep, particularly REM sleep, became increasingly disordered, characterized by an increase in frequency of central sleep apnea and hypopneas (36.8 +/- 7.4 episodes/h of REM vs. 6 +/- 2.0 episodes/h in preinjection controls; P < 0.05), whereas breathing during resting wakefulness remained stable. Unlike bilateral SP-SAP-injected rats, an ataxic breathing pattern did not develop during wakefulness. Rats that were monitored up to 51 days post-SP-SAP injection continued to have sleep-disordered breathing; breathing during wakefulness remained relatively stable. Histologic analysis of the ventrolateral medulla confirmed that NK1R neurons within the preBötC on the injected but not on the contralateral side of the medulla were ablated. Gradual loss of preBötC NK1R neurons may be an underlying factor of sleep-disordered breathing, in particular of central sleep apnea.

Kinetic analysis of pre-ribosome structure in vivo

PubMed Central

Swiatkowska, Agata; Wlotzka, Wiebke; Tuck, Alex; Barrass, J. David; Beggs, Jean D.; Tollervey, David

2012-01-01

Pre-ribosomal particles undergo numerous structural changes during maturation, but their high complexity and short lifetimes make these changes very difficult to follow in vivo. In consequence, pre-ribosome structure and composition have largely been inferred from purified particles and analyzed in vitro. Here we describe techniques for kinetic analyses of the changes in pre-ribosome structure in living cells of Saccharomyces cerevisiae. To allow this, in vivo structure probing by DMS modification was combined with affinity purification of newly synthesized 20S pre-rRNA over a time course of metabolic labeling with 4-thiouracil. To demonstrate that this approach is generally applicable, we initially analyzed the accessibility of the region surrounding cleavage site D site at the 3′ end of the mature 18S rRNA region of the pre-rRNA. This revealed a remarkably flexible structure throughout 40S subunit biogenesis, with little stable RNA–protein interaction apparent. Analysis of folding in the region of the 18S central pseudoknot was consistent with previous data showing U3 snoRNA–18S rRNA interactions. Dynamic changes in the structure of the hinge between helix 28 (H28) and H44 of pre-18S rRNA were consistent with recently reported interactions with the 3′ guide region of U3 snoRNA. Finally, analysis of the H18 region indicates that the RNA structure matures early, but additional protection appears subsequently, presumably reflecting protein binding. The structural analyses described here were performed on total, affinity-purified, newly synthesized RNA, so many classes of RNA and RNA–protein complex are potentially amenable to this approach. PMID:23093724

CDK1 Prevents Unscheduled PLK4-STIL Complex Assembly in Centriole Biogenesis.

PubMed

Zitouni, Sihem; Francia, Maria E; Leal, Filipe; Montenegro Gouveia, Susana; Nabais, Catarina; Duarte, Paulo; Gilberto, Samuel; Brito, Daniela; Moyer, Tyler; Kandels-Lewis, Steffi; Ohta, Midori; Kitagawa, Daiju; Holland, Andrew J; Karsenti, Eric; Lorca, Thierry; Lince-Faria, Mariana; Bettencourt-Dias, Mónica

2016-05-09

Centrioles are essential for the assembly of both centrosomes and cilia. Centriole biogenesis occurs once and only once per cell cycle and is temporally coordinated with cell-cycle progression, ensuring the formation of the right number of centrioles at the right time. The formation of new daughter centrioles is guided by a pre-existing, mother centriole. The proximity between mother and daughter centrioles was proposed to restrict new centriole formation until they separate beyond a critical distance. Paradoxically, mother and daughter centrioles overcome this distance in early mitosis, at a time when triggers for centriole biogenesis Polo-like kinase 4 (PLK4) and its substrate STIL are abundant. Here we show that in mitosis, the mitotic kinase CDK1-CyclinB binds STIL and prevents formation of the PLK4-STIL complex and STIL phosphorylation by PLK4, thus inhibiting untimely onset of centriole biogenesis. After CDK1-CyclinB inactivation upon mitotic exit, PLK4 can bind and phosphorylate STIL in G1, allowing pro-centriole assembly in the subsequent S phase. Our work shows that complementary mechanisms, such as mother-daughter centriole proximity and CDK1-CyclinB interaction with centriolar components, ensure that centriole biogenesis occurs once and only once per cell cycle, raising parallels to the cell-cycle regulation of DNA replication and centromere formation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Variations in the degree of crustal extension during formation of a back-arc basin

NASA Astrophysics Data System (ADS)

de Wit, Maarten J.; Stern, Charles R.

1981-02-01

Ophiolite complexes in southern Chile represent the remnants of the mafic portion of the floor of a Cretaceous back-arc basin which widened markedly from north to south over a length of 600 km. Detailed field and geochemical studies of ophiolites in the northern (Sarmiento complex) and southern (Tortuga complex) extremities of the originally wedge-shaped back-arc basin floor, indicate significant north—south differences in the mode of emplacement of basaltic magmas into the pre-existing continental crust, during the formation of the basin. In the northern narrow extremity of the original basin, mafic melts intruded into the continental crust over a diffuse zone causing extensive remobilization and reconstitution of the sialic continental crust. In the southern wider part of the original basin, mafic magmas appear to have been emplaced at a localized oceanic-type spreading centre. The observed north—south variations resulted in formation of back-arc floor with crustal characteristics ranging from intermediate between continental and oceanic to typically oceanic. These variations are interpreted as representing different stages of evolution of a back-arc basin which formed due to a subtle interplay between subduction induced back-arc mantle convection and the release of stress across the convergent plate boundary, possibly related to ridge subduction. Prior to the release of stress, heat transferred from mantle diapirs to the base of crust caused widespread silicic volcanism in South America. With the release of stress, mantle derived melts erupted to the surface along structural pathways resulting in extensive basaltic volcanism in a linear belt behind the island arc and the cessation of silicic volcanism. Initially, basaltic magmas intruded the continental crust over a diffuse region causing reconstitution of sialic crustal rocks. Progressive localization of the zone of intrusion of mafic magmas from the mantle eventually resulted in the development of an oceanic-type spreading centre. Observations in southern Chile and elsewhere suggest that variability in horizontal stress across a convergent plate boundary may be the overriding factor in determining the regional response of continental crust to subduction induced back-arc convection, and hence the mechanism of emplacement into the crust of mafic mantle melts. The various lithologies observed in southern Chile could also be expected to form during the opening phase of major ocean basins and to currently underlie Atlantic-type continental margins.

Wolff-Parkinson-White syndrome: a single exercise stress test might be misleading.

PubMed

Salavitabar, Arash; Silver, Eric S; Liberman, Leonardo

2017-05-01

Risk stratification of patients with Wolff-Parkinson-White syndrome for sudden death is a complex process, particularly in understanding the utility of the repeat exercise stress test. We report a case of an 18-year-old patient who was found to have a high-risk pathway by both invasive and exercise stress testing after an initial exercise stress test showing beat-to-beat loss of pre-excitation.

A TBP-containing multiprotein complex (TIF-IB) mediates transcription specificity of murine RNA polymerase I.

PubMed

Eberhard, D; Tora, L; Egly, J M; Grummt, I

1993-09-11

TIF-IB is a transcription factor which interacts with the mouse ribosomal gene promoter and nucleates the formation of an initiation complex containing RNA polymerase I (Pol I). We have purified this factor to near homogeneity and demonstrate that TIF-IB is a large complex (< 200 kDa) which contains several polypeptides. One of the subunits present in this protein complex is the TATA-binding protein (TBP) as revealed by copurification of TIF-IB activity and TBP over different chromatographic steps including immunoaffinity purification. In addition to TBP, three tightly associated proteins (TAFs-I) with apparent molecular weights of 95, 68, and 48 kDa are contained in this multimeric complex. This subunit composition is similar--but not identical--to the analogous human factor SL1. Depletion of TBP from TIF-IB-containing fractions by immunoprecipitation eliminates TIF-IB activity. Neither TBP alone nor fractions containing other TBP complexes are capable of substituting for TIF-IB activity. Therefore, TIF-IB is a unique complex with Pol I-specific TAFs distinct from other TBP-containing complexes. The identification of TBP as an integral part of the murine rDNA promoter-specific transcription initiation factor extends the previously noted similarity of transcriptional initiation by the three nuclear RNA polymerases and underscores the importance of TAFs in determining promoter specificity.

A TBP-containing multiprotein complex (TIF-IB) mediates transcription specificity of murine RNA polymerase I.

PubMed Central

Eberhard, D; Tora, L; Egly, J M; Grummt, I

1993-01-01

TIF-IB is a transcription factor which interacts with the mouse ribosomal gene promoter and nucleates the formation of an initiation complex containing RNA polymerase I (Pol I). We have purified this factor to near homogeneity and demonstrate that TIF-IB is a large complex (< 200 kDa) which contains several polypeptides. One of the subunits present in this protein complex is the TATA-binding protein (TBP) as revealed by copurification of TIF-IB activity and TBP over different chromatographic steps including immunoaffinity purification. In addition to TBP, three tightly associated proteins (TAFs-I) with apparent molecular weights of 95, 68, and 48 kDa are contained in this multimeric complex. This subunit composition is similar--but not identical--to the analogous human factor SL1. Depletion of TBP from TIF-IB-containing fractions by immunoprecipitation eliminates TIF-IB activity. Neither TBP alone nor fractions containing other TBP complexes are capable of substituting for TIF-IB activity. Therefore, TIF-IB is a unique complex with Pol I-specific TAFs distinct from other TBP-containing complexes. The identification of TBP as an integral part of the murine rDNA promoter-specific transcription initiation factor extends the previously noted similarity of transcriptional initiation by the three nuclear RNA polymerases and underscores the importance of TAFs in determining promoter specificity. Images PMID:8414971

MCM5: a new actor in the link between DNA replication and Meier-Gorlin syndrome.

PubMed

Vetro, Annalisa; Savasta, Salvatore; Russo Raucci, Annalisa; Cerqua, Cristina; Sartori, Geppo; Limongelli, Ivan; Forlino, Antonella; Maruelli, Silvia; Perucca, Paola; Vergani, Debora; Mazzini, Giuliano; Mattevi, Andrea; Stivala, Lucia Anna; Salviati, Leonardo; Zuffardi, Orsetta

2017-05-01

Meier-Gorlin syndrome (MGORS) is a rare disorder characterized by primordial dwarfism, microtia, and patellar aplasia/hypoplasia. Recessive mutations in ORC1, ORC4, ORC6, CDT1, CDC6, and CDC45, encoding members of the pre-replication (pre-RC) and pre-initiation (pre-IC) complexes, and heterozygous mutations in GMNN, a regulator of cell-cycle progression and DNA replication, have already been associated with this condition. We performed whole-exome sequencing (WES) in a patient with a clinical diagnosis of MGORS and identified biallelic variants in MCM5. This gene encodes a subunit of the replicative helicase complex, which represents a component of the pre-RC. Both variants, a missense substitution within a conserved domain critical for the helicase activity, and a single base deletion causing a frameshift and a premature stop codon, were predicted to be detrimental for the MCM5 function. Although variants of MCM5 have never been reported in specific human diseases, defect of this gene in zebrafish causes a phenotype of growth restriction overlapping the one associated with orc1 depletion. Complementation experiments in yeast showed that the plasmid carrying the missense variant was unable to rescue the lethal phenotype caused by mcm5 deletion. Moreover cell-cycle progression was delayed in patient's cells, as already shown for mutations in the ORC1 gene. Altogether our findings support the role of MCM5 as a novel gene involved in MGORS, further emphasizing that this condition is caused by impaired DNA replication.

Characterizing the Protostars in the Herschel Survey of Cygnus-X

NASA Astrophysics Data System (ADS)

Kirk, James; Hora, J. L.; Smith, H. A.; Herschel Cygnus-X Group

2014-01-01

The Cygnus-X complex is an extremely active region of massive star formation at a distance of ~1.4 kpc which can be studied with higher sensitivity and less confusion than more distant regions. The study of this region is important in improving our understanding of the formation processes and protostellar phases of massive stars. A previous Spitzer Legacy survey of Cygnus-X mapped the distributions of Class I and Class II YSOs within the region and studied the interaction between massive young stars and clusters of YSOs. Using data from the recent Herschel survey of the region, taken with the PACS and SPIRE instrument (70-500 microns), we are expanding this study of star formation to the youngest and most deeply embedded objects. Using these data we will expand the sample of massive protostars and YSOs in Cygnus-X, analyze the population of infrared dark clouds and their embedded objects, construct Spectral Energy Distributions (SEDs) using pre-existing Spitzer and near-IR data sets (1-500 microns), and fit these sources with models of protostars to derive luminosities and envelope masses. The derived luminosities and masses will enable us to create evolutionary diagrams and test models of high-mass star formation. We will also investigate what role OB associations, such as Cyg OB2, play in causing subsequent star formation in neighboring clouds, providing us with a comprehensive picture of star formation within this extremely active complex.

Modeling the Pre-Industrial Roots of Modern Super-Exponential Population Growth

PubMed Central

Stutz, Aaron Jonas

2014-01-01

To Malthus, rapid human population growth—so evident in 18th Century Europe—was obviously unsustainable. In his Essay on the Principle of Population, Malthus cogently argued that environmental and socioeconomic constraints on population rise were inevitable. Yet, he penned his essay on the eve of the global census size reaching one billion, as nearly two centuries of super-exponential increase were taking off. Introducing a novel extension of J. E. Cohen's hallmark coupled difference equation model of human population dynamics and carrying capacity, this article examines just how elastic population growth limits may be in response to demographic change. The revised model involves a simple formalization of how consumption costs influence carrying capacity elasticity over time. Recognizing that complex social resource-extraction networks support ongoing consumption-based investment in family formation and intergenerational resource transfers, it is important to consider how consumption has impacted the human environment and demography—especially as global population has become very large. Sensitivity analysis of the consumption-cost model's fit to historical population estimates, modern census data, and 21st Century demographic projections supports a critical conclusion. The recent population explosion was systemically determined by long-term, distinctly pre-industrial cultural evolution. It is suggested that modern globalizing transitions in technology, susceptibility to infectious disease, information flows and accumulation, and economic complexity were endogenous products of much earlier biocultural evolution of family formation's embeddedness in larger, hierarchically self-organizing cultural systems, which could potentially support high population elasticity of carrying capacity. Modern super-exponential population growth cannot be considered separately from long-term change in the multi-scalar political economy that connects family formation and intergenerational resource transfers to wider institutions and social networks. PMID:25141019

Structure, Dynamics, and Deuterium Fractionation of Massive Pre-stellar Cores

NASA Astrophysics Data System (ADS)

Goodson, Matthew D.; Kong, Shuo; Tan, Jonathan C.; Heitsch, Fabian; Caselli, Paola

2016-12-01

High levels of deuterium fraction in N2H+ are observed in some pre-stellar cores. Single-zone chemical models find that the timescale required to reach observed values ({D}{frac}{{{N}}2{{{H}}}+}\\equiv {{{N}}}2{{{D}}}+/{{{N}}}2{{{H}}}+≳ 0.1) is longer than the free-fall time, possibly 10 times longer. Here, we explore the deuteration of turbulent, magnetized cores with 3D magnetohydrodynamics simulations. We use an approximate chemical model to follow the growth in abundances of N2H+ and N2D+. We then examine the dynamics of the core using each tracer for comparison to observations. We find that the velocity dispersion of the core as traced by N2D+ appears slightly sub-virial compared to predictions of the Turbulent Core Model of McKee & Tan, except at late times just before the onset of protostar formation. By varying the initial mass surface density, the magnetic energy, the chemical age, and the ortho-to-para ratio of H2, we also determine the physical and temporal properties required for high deuteration. We find that low initial ortho-to-para ratios (≲ 0.01) and/or multiple free-fall times (≳ 3) of prior chemical evolution are necessary to reach the observed values of deuterium fraction in pre-stellar cores.

Copper Complex in Poly(vinyl chloride) as a Nitric Oxide-Generating Catalyst for the Control of Nitrifying Bacterial Biofilms.

PubMed

Wonoputri, Vita; Gunawan, Cindy; Liu, Sanly; Barraud, Nicolas; Yee, Lachlan H; Lim, May; Amal, Rose

2015-10-14

In this study, catalytic generation of nitric oxide by a copper(II) complex embedded within a poly(vinyl chloride) matrix in the presence of nitrite (source of nitric oxide) and ascorbic acid (reducing agent) was shown to effectively control the formation and dispersion of nitrifying bacteria biofilms. Amperometric measurements indicated increased and prolonged generation of nitric oxide with the addition of the copper complex when compared to that with nitrite and ascorbic acid alone. The effectiveness of the copper complex-nitrite-ascorbic acid system for biofilm control was quantified using protein analysis, which showed enhanced biofilm suppression when the copper complex was used in comparison to that with nitrite and ascorbic acid treatment alone. Confocal laser scanning microscopy (CLSM) and LIVE/DEAD staining revealed a reduction in cell surface coverage without a loss of viability with the copper complex and up to 5 mM of nitrite and ascorbic acid, suggesting that the nitric oxide generated from the system inhibits proliferation of the cells on surfaces. Induction of nitric oxide production by the copper complex system also triggered the dispersal of pre-established biofilms. However, the addition of a high concentration of nitrite and ascorbic acid to a pre-established biofilm induced bacterial membrane damage and strongly decreased the metabolic activity of planktonic and biofilm cells, as revealed by CLSM with LIVE/DEAD staining and intracellular adenosine triphosphate measurements, respectively. This study highlights the utility of the catalytic generation of nitric oxide for the long-term suppression and removal of nitrifying bacterial biofilms.

Theoretical investigation on functional monomer and solvent selection for molecular imprinting of tramadol

NASA Astrophysics Data System (ADS)

Fonseca, Matheus C.; Nascimento, Clebio S.; Borges, Keyller B.

2016-02-01

The purpose of this Letter was to study for the first time the interaction process of tramadol (TRM) with distinct functional monomers (FM) in the formation of molecular imprinted polymer (MIP), using density functional theory (DFT) calculations at B3LYP/6-31G(d,p). As result we were able to establish that the best MIP synthesis conditions are obtained with acrylic acid as FM in 1:3 molar ratio and with chloroform as solvent. This condition presented the lowest stabilization energy for the pre-polymerization complexes. Besides, the intermolecular hydrogen bonds found between the template molecule and functional monomers play a primary role to the complex stability.

Deep sequencing reveals complex mechanisms of diapause preparation in the invasive mosquito, Aedes albopictus.

PubMed

Poelchau, Monica F; Reynolds, Julie A; Elsik, Christine G; Denlinger, David L; Armbruster, Peter A

2013-05-22

Seasonal environments present fundamental physiological challenges to a wide range of insects. Many temperate insects surmount the exigencies of winter by undergoing photoperiodic diapause, in which photoperiod provides a token cue that initiates an alternative developmental programme leading to dormancy. Pre-diapause is a crucial preparatory phase of this process, preceding developmental arrest. However, the regulatory and physiological mechanisms of diapause preparation are largely unknown. Using high-throughput gene expression profiling in the Asian tiger mosquito, Aedes albopictus, we reveal major shifts in endocrine signalling, cell proliferation, metabolism, energy production and cellular structure across pre-diapause development. While some hallmarks of diapause, such as insulin signalling and stress response, were not important at the transcriptional level, two genes, Pepck and PCNA, appear to show diapause-induced transcriptional changes across insect taxa. These processes demonstrate physiological commonalities between Ae. albopictus pre-diapause and diapause strategies across insects, and support the idea of a genetic 'toolkit' for diapause. Observations of gene expression trends from a comparative developmental perspective suggest that individual physiological processes are delayed against a background of a fixed morphological ontogeny. Our results demonstrate how deep sequencing can provide new insights into elusive molecular bases of complex ecological adaptations.

Preparation of cell-free splicing extracts from Saccharomyces cerevisiae.

PubMed

Ares, Manuel

2013-10-01

Much of our understanding of the mechanism of splicing comes from the analysis of cell extracts able to carry out splicing complex formation and splicing reactions in vitro using exogenously added synthetic model pre-mRNA transcripts. This protocol describes the preparation of whole-cell extracts from the budding yeast Saccharomyces cerevisiae. These extracts can be used to dissect the biochemical steps of the splicing reaction and to determine the macromolecules, cofactors, and substrate features necessary for successful splicing.

Rocket launcher mechanism of collaborative actin assembly defined by single-molecule imaging.

PubMed

Breitsprecher, Dennis; Jaiswal, Richa; Bombardier, Jeffrey P; Gould, Christopher J; Gelles, Jeff; Goode, Bruce L

2012-06-01

Interacting sets of actin assembly factors work together in cells, but the underlying mechanisms have remained obscure. We used triple-color single-molecule fluorescence microscopy to image the tumor suppressor adenomatous polyposis coli (APC) and the formin mDia1 during filament assembly. Complexes consisting of APC, mDia1, and actin monomers initiated actin filament formation, overcoming inhibition by capping protein and profilin. Upon filament polymerization, the complexes separated, with mDia1 moving processively on growing barbed ends while APC remained at the site of nucleation. Thus, the two assembly factors directly interact to initiate filament assembly and then separate but retain independent associations with either end of the growing filament.

The founder-cell transcriptome in the Arabidopsis apetala1 cauliflower inflorescence meristem.

PubMed

Frerichs, Anneke; Thoma, Rahere; Abdallah, Ali Taleb; Frommolt, Peter; Werr, Wolfgang; Chandler, John William

2016-11-03

Although the pattern of lateral organ formation from apical meristems establishes species-specific plant architecture, the positional information that confers cell fate to cells as they transit to the meristem flanks where they differentiate, remains largely unknown. We have combined fluorescence-activated cell sorting and RNA-seq to characterise the cell-type-specific transcriptome at the earliest developmental time-point of lateral organ formation using DORNRÖSCHEN-LIKE::GFP to mark founder-cell populations at the periphery of the inflorescence meristem (IM) in apetala1 cauliflower double mutants, which overproliferate IMs. Within the lateral organ founder-cell population at the inflorescence meristem, floral primordium identity genes are upregulated and stem-cell identity markers are downregulated. Additional differentially expressed transcripts are involved in polarity generation and boundary formation, and in epigenetic and post-translational changes. However, only subtle transcriptional reprogramming within the global auxin network was observed. The transcriptional network of differentially expressed genes supports the hypothesis that lateral organ founder-cell specification involves the creation of polarity from the centre to the periphery of the IM and the establishment of a boundary from surrounding cells, consistent with bract initiation. However, contrary to the established paradigm that sites of auxin response maxima pre-pattern lateral organ initiation in the IM, auxin response might play a minor role in the earliest stages of lateral floral initiation.

ArrayInitiative - a tool that simplifies creating custom Affymetrix CDFs

PubMed Central

2011-01-01

Background Probes on a microarray represent a frozen view of a genome and are quickly outdated when new sequencing studies extend our knowledge, resulting in significant measurement error when analyzing any microarray experiment. There are several bioinformatics approaches to improve probe assignments, but without in-house programming expertise, standardizing these custom array specifications as a usable file (e.g. as Affymetrix CDFs) is difficult, owing mostly to the complexity of the specification file format. However, without correctly standardized files there is a significant barrier for testing competing analysis approaches since this file is one of the required inputs for many commonly used algorithms. The need to test combinations of probe assignments and analysis algorithms led us to develop ArrayInitiative, a tool for creating and managing custom array specifications. Results ArrayInitiative is a standalone, cross-platform, rich client desktop application for creating correctly formatted, custom versions of manufacturer-provided (default) array specifications, requiring only minimal knowledge of the array specification rules and file formats. Users can import default array specifications, import probe sequences for a default array specification, design and import a custom array specification, export any array specification to multiple output formats, export the probe sequences for any array specification and browse high-level information about the microarray, such as version and number of probes. The initial release of ArrayInitiative supports the Affymetrix 3' IVT expression arrays we currently analyze, but as an open source application, we hope that others will contribute modules for other platforms. Conclusions ArrayInitiative allows researchers to create new array specifications, in a standard format, based upon their own requirements. This makes it easier to test competing design and analysis strategies that depend on probe definitions. Since the custom array specifications are easily exported to the manufacturer's standard format, researchers can analyze these customized microarray experiments using established software tools, such as those available in Bioconductor. PMID:21548938

The formation and distribution of hippocampal synapses on patterned neuronal networks

NASA Astrophysics Data System (ADS)

Dowell-Mesfin, Natalie M.

Communication within the central nervous system is highly orchestrated with neurons forming trillions of specialized junctions called synapses. In vivo, biochemical and topographical cues can regulate neuronal growth. Biochemical cues also influence synaptogenesis and synaptic plasticity. The effects of topography on the development of synapses have been less studied. In vitro, neuronal growth is unorganized and complex making it difficult to study the development of networks. Patterned topographical cues guide and control the growth of neuronal processes (axons and dendrites) into organized networks. The aim of this dissertation was to determine if patterned topographical cues can influence synapse formation and distribution. Standard fabrication and compression molding procedures were used to produce silicon masters and polystyrene replicas with topographical cues presented as 1 mum high pillars with diameters of 0.5 and 2.0 mum and gaps of 1.0 to 5.0 mum. Embryonic rat hippocampal neurons grown unto patterned surfaces. A developmental analysis with immunocytochemistry was used to assess the distribution of pre- and post-synaptic proteins. Activity-dependent pre-synaptic vesicle uptake using functional imaging dyes was also performed. Adaptive filtering computer algorithms identified synapses by segmenting juxtaposed pairs of pre- and post-synaptic labels. Synapse number and area were automatically extracted from each deconvolved data set. In addition, neuronal processes were traced automatically to assess changes in synapse distribution. The results of these experiments demonstrated that patterned topographic cues can induce organized and functional neuronal networks that can serve as models for the study of synapse formation and plasticity as well as for the development of neuroprosthetic devices.

N-nitrosodimethylamine (NDMA) formation potential of amine-based water treatment polymers: Effects of in situ chloramination, breakpoint chlorination, and pre-oxidation.

PubMed

Park, Sang Hyuck; Padhye, Lokesh P; Wang, Pei; Cho, Min; Kim, Jae-Hong; Huang, Ching-Hua

2015-01-23

Recent studies show that cationic amine-based water treatment polymers may be important precursors that contribute to formation of the probable human carcinogen N-nitrosodimethylamine (NDMA) during water treatment and disinfection. To better understand how water treatment parameters affect NDMA formation from the polymers, the effects of in situ chloramination, breakpoint chlorination, and pre-oxidation on the NDMA formation from the polymers were investigated. NDMA formation potential (NDMA-FP) as well as dimethylamine (DMA) residual concentration were measured from poly(epichlorohydrin dimethylamine) (polyamine) and poly(diallyldimethylammonium chloride) (polyDADMAC) solutions upon reactions with oxidants including free chlorine, chlorine dioxide, ozone, and monochloramine under different treatment conditions. The results supported that dichloramine (NHCl2) formation was the critical factor affecting NDMA formation from the polymers during in situ chloramination. The highest NDMA formation from the polymers occurred near the breakpoint of chlorination. Polymer chain breakdown and transformation of the released DMA and other intermediates were important factors affecting NDMA formation from the polymers in pre-oxidation followed by post-chloramination. Pre-oxidation generally reduced NDMA-FP of the polymers; however, the treatments involving pre-ozonation increased polyDADMAC's NDMA-FP and DMA release. The strategies for reducing NDMA formation from the polymers may include the avoidance of the conditions favorable to NHCl2 formation and the avoidance of polymer exposure to strong oxidants such as ozone. Copyright © 2014 Elsevier B.V. All rights reserved.

A high affinity RIM-binding protein/Aplip1 interaction prevents the formation of ectopic axonal active zones.

PubMed

Siebert, Matthias; Böhme, Mathias A; Driller, Jan H; Babikir, Husam; Mampell, Malou M; Rey, Ulises; Ramesh, Niraja; Matkovic, Tanja; Holton, Nicole; Reddy-Alla, Suneel; Göttfert, Fabian; Kamin, Dirk; Quentin, Christine; Klinedinst, Susan; Andlauer, Till Fm; Hell, Stefan W; Collins, Catherine A; Wahl, Markus C; Loll, Bernhard; Sigrist, Stephan J

2015-08-14

Synaptic vesicles (SVs) fuse at active zones (AZs) covered by a protein scaffold, at Drosophila synapses comprised of ELKS family member Bruchpilot (BRP) and RIM-binding protein (RBP). We here demonstrate axonal co-transport of BRP and RBP using intravital live imaging, with both proteins co-accumulating in axonal aggregates of several transport mutants. RBP, via its C-terminal Src-homology 3 (SH3) domains, binds Aplip1/JIP1, a transport adaptor involved in kinesin-dependent SV transport. We show in atomic detail that RBP C-terminal SH3 domains bind a proline-rich (PxxP) motif of Aplip1/JIP1 with submicromolar affinity. Pointmutating this PxxP motif provoked formation of ectopic AZ-like structures at axonal membranes. Direct interactions between AZ proteins and transport adaptors seem to provide complex avidity and shield synaptic interaction surfaces of pre-assembled scaffold protein transport complexes, thus, favouring physiological synaptic AZ assembly over premature assembly at axonal membranes.

U14 small nucleolar RNA makes multiple contacts with the pre-ribosomal RNA.

PubMed

Morrissey, J P; Tollervey, D

1997-06-01

The small nucleolar RNA (snoRNA) U14 has two regions of extended primary sequence complementarity to the 18S rRNA. The 3' region (domain B) shows the consensus structure for the methylation guide class of snoRNAs, whereas base-pairing between the 5' region (domain A) and the 18S rRNA sequence is required for the formation of functional ribosomes. Between domains A and B lies another essential region (domain Y). Here we report that yeast U14 can be cross-linked in vivo to the pre-rRNA; cross-linking is detected exclusively with the 35S primary transcript. Many nucleotides in U14 that lie outside of domains A and B are cross-linked to the pre-rRNA; in particular the essential domain Y region is cross-linked at several sites. U14 is, therefore, in far more extensive contact with the pre-rRNA than predicted from simple base-pairing models. Moreover, U14 can be cross-linked to other small RNA species. The functional interactions made by U14 during ribosome synthesis are likely to be very complex.

Portfolio Assessment: Production and Reduction of Complexity

ERIC Educational Resources Information Center

Qvortrup, Ane; Keiding, Tina Bering

2015-01-01

Over the last two decades, the education system has witnessed a shift from summative, product-oriented assessment towards formative, process-oriented assessment. Among the different learning and assessment initiatives introduced in the slipstream of this paradigmatic turn, the portfolio seems to have become one of the most popular. By redescribing…

The kinetics of thermal generation of flavour.

PubMed

Parker, Jane K

2013-01-01

Control and optimisation of flavour is the ultimate challenge for the food and flavour industry. The major route to flavour formation during thermal processing is the Maillard reaction, which is a complex cascade of interdependent reactions initiated by the reaction between a reducing sugar and an amino compound. The complexity of the reaction means that researchers turn to kinetic modelling in order to understand the control points of the reaction and to manipulate the flavour profile. Studies of the kinetics of flavour formation have developed over the past 30 years from single- response empirical models of binary aqueous systems to sophisticated multi-response models in food matrices, based on the underlying chemistry, with the power to predict the formation of some key aroma compounds. This paper discusses in detail the development of kinetic models of thermal generation of flavour and looks at the challenges involved in predicting flavour. Copyright © 2012 Society of Chemical Industry.

The prostaglandin receptor EP2 activates multiple signaling pathways and β-arrestin1 complex formation during mouse skin papilloma development

PubMed Central

Chun, Kyung-Soo; Lao, Huei-Chen; Trempus, Carol S.; Okada, Manabu; Langenbach, Robert

2009-01-01

Prostaglandin E2 (PGE2) is elevated in many tumor types, but PGE2's contributions to tumor growth are largely unknown. To investigate PGE2's roles, the contributions of one of its receptors, EP2, were studied using the mouse skin initiation/promotion model. Initial studies indicated that protein kinase A (PKA), epidermal growth factor receptor (EGFR) and several effectors—cyclic adenosine 3′,5′-monophosphate response element-binding protein (CREB), H-Ras, Src, protein kinase B (AKT) and extracellular signal-regulated kinase (ERK)1/2—were activated in 12-O-tetradecanoylphorbol-13-acetate (TPA)-promoted papillomas and that PKA and EGFR inhibition (H89 and AG1478, respectively) decreased papilloma formation. EP2's contributions to the activation of these pathways and papilloma development were determined by inhibiting endogenous TPA-induced PGE2 production with indomethacin (Indo) and concomitantly treating with the EP2 agonist, CAY10399 (CAY). CAY treatment restored papilloma formation in TPA/Indo-treated mice and increased cyclic adenosine 3′,5′-monophosphate and PKA activation as measured by p-CREB formation. CAY treatment also increased EGFR and Src activation and their inhibition by AG1478 and PP2 indicated that Src was upstream of EGFR. CAY also increased H-Ras, ERK1/2 and AKT activation, and AG1478 decreased their activation indicating EGFR being upstream. Supporting EP2's contribution, EP2−/− mice exhibited 65% fewer papillomas and reduced Src, EGFR, H-Ras, AKT and ERK1/2 activation. G protein-coupled receptor (GPCR) activation of EGFR has been reported to involve Src's activation via a GPCR–β-arrestin–Src complex. Indeed, immunoprecipitation of β-arrestin1 or p-Src indicated the presence of an EP2–β-arrestin1–p-Src complex in papillomas. The data indicated that EP2 contributed to tumor formation via activation of PKA and EGFR and that EP2 formed a complex with β-arrestin1 and Src that contributed to signaling and/or EP2 desensitization. PMID:19587094

Pre-pregnancy community-based intervention for couples in Malaysia: application of intervention mapping.

PubMed

Norris, Shane A; Ho, Julius Cheah Chee; Rashed, Aswir Abd; Vinding, Vibeke; Skau, Jutta K H; Biesma, Regien; Aagaard-Hansen, Jens; Hanson, Mark; Matzen, Priya

2016-11-17

Malaysia is experiencing a nutrition transition with burgeoning obesity, particularly in women, and a growing prevalence of non-communicable disease. These health burdens have severe implications not only for adult health but also across generations. Pre-conception health promotion could address the intergenerational risk of metabolic disease. This paper describes the development of the "Jom Mama" intervention using Intervention Mapping (IM). The Jom Mama intervention aims to improve the health of young adult couples in Malaysia prior to conception. IM comprises of five steps prior to the last one, which involves the evaluation of the intervention. We used the five steps to develop the Jom Mama intervention. Both the process and evidence is documented providing the rationale to the selection of the key objectives of the intervention: (i) increasing healthy dietary practice; (ii) increasing physical activity levels, (iii) reducing sedentary activity; and (iv) improving social support to offset stressful lifestyles. From the IM process, Jom Mama will be health-system centred approach that uniquely combines both community health promoters and an electronic-health platform to deliver the complex intervention. IM is an iterative process that systematically gathers "best" evidence, selects appropriate theories of behaviour change, and facilitates formative research so as to develop a complex intervention. Though the IM process is time consuming, complex, and costly, it has enriched the Jom Mama intervention with a number of notable advantages: (i) intervention fashioned on formative work with stakeholders and in the target group; (ii) intervention combines research evidence with theory; (iii) intervention acknowledges multiple dynamics of influence; and (iv) intervention is embedded within health service priorities in Malaysia for greater scale-up possibility.

Carbon-sulfur bond formation by reductive elimination of gold(iii) thiolates.

PubMed

Currie, Lucy; Rocchigiani, Luca; Hughes, David L; Bochmann, Manfred

2018-05-08

Whereas the reaction of the gold(iii) pincer complex (C^N^C)AuCl with 1-adamantyl thiol (AdSH) in the presence of base affords (C^N^C)AuSAd, the same reaction in the absence of base leads to formation of aryl thioethers as the products of reductive elimination of the Au-C and Au-S ligands (C^N^C = dianion of 2-6-diphenylpyridine or 2-6-diphenylpyrazine). Although high chemical stability is usually taken as a characteristic of pincer complexes, results show that thiols are capable of cleaving one of the pincer Au-C bonds. This reaction is not simply a function of S-H acidity, since no cleavage takes place with other more acidic X-H compounds, such as carbazole, amides, phenols and malonates. The reductive C-S elimination follows a second-order rate law, -d[1a]/dt = k[1a][AdSH]. Reductive elimination is enabled by displacement of the N-donor by thiol; this provides the conformational flexibility necessary for C-S bond formation to occur. Alternatively, reductive C-S bond formation can be induced by reaction of pre-formed thiolates (C^N^C)AuSR with a strong Brønsted acid, followed by addition of SMe2 as base. On the other hand, treatment of (C^N^C)AuR (R = Me, aryl, alkynyl) with thiols under similar conditions leads to selective C-C rather than C-S bond formation. The reaction of (C^N^C)AuSAd with H+ in the absence of a donor ligand affords the thiolato-bridged complex [{(C^N-CH)Au(μ-SAd)}2]2+ which was crystallographically characterised.

Interplay between Synaptonemal Complex, Homologous Recombination, and Centromeres during Mammalian Meiosis

PubMed Central

Qiao, Huanyu; Chen, Jefferson K.; Reynolds, April; Höög, Christer; Paddy, Michael; Hunter, Neil

2012-01-01

The intimate synapsis of homologous chromosome pairs (homologs) by synaptonemal complexes (SCs) is an essential feature of meiosis. In many organisms, synapsis and homologous recombination are interdependent: recombination promotes SC formation and SCs are required for crossing-over. Moreover, several studies indicate that initiation of SC assembly occurs at sites where crossovers will subsequently form. However, recent analyses in budding yeast and fruit fly imply a special role for centromeres in the initiation of SC formation. In addition, in budding yeast, persistent SC–dependent centromere-association facilitates the disjunction of chromosomes that have failed to become connected by crossovers. Here, we examine the interplay between SCs, recombination, and centromeres in a mammal. In mouse spermatocytes, centromeres do not serve as SC initiation sites and are invariably the last regions to synapse. However, centromeres are refractory to de-synapsis during diplonema and remain associated by short SC fragments. Since SC–dependent centromere association is lost before diakinesis, a direct role in homolog segregation seems unlikely. However, post–SC disassembly, we find evidence of inter-centromeric connections that could play a more direct role in promoting homolog biorientation and disjunction. A second class of persistent SC fragments is shown to be crossover-dependent. Super-resolution structured-illumination microscopy (SIM) reveals that these structures initially connect separate homolog axes and progressively diminish as chiasmata form. Thus, DNA crossing-over (which occurs during pachynema) and axis remodeling appear to be temporally distinct aspects of chiasma formation. SIM analysis of the synapsis and crossover-defective mutant Sycp1−/− implies that SCs prevent unregulated fusion of homolog axes. We propose that SC fragments retained during diplonema stabilize nascent bivalents and help orchestrate local chromosome reorganization that promotes centromere and chiasma function. PMID:22761591

Formation and fates of nitrosamines and their formation potentials from a surface water source to drinking water treatment plants in Southern Taiwan.

PubMed

Chen, Wei-Hsiang; Wang, Chung-Ya; Huang, Tsung-Hsien

2016-10-01

Nitrosamines are toxic and emerging disinfection byproducts. In this study, three drinking water treatment plants (DWTPs) in southern Taiwan treating the same source water in Gaoping River with comparable technologies were selected. The objective was to evaluate the formation and fates of six nitrosamines and their formation potentials (FPs) from a surface water source to drinking water. Albeit decreased further downstream in the river, four nitrosamine-FPs were observed in the source water due to anthropogenic pollution in the upstream areas. In the DWTPs, nitrosamines were formed and NDMA was the main species. While high organic carbon concentrations indicated elevated nitrosamine-FPs in the source water, NDMA formation in the DWTPs was more positively associated with reductions of water parameters that quantify organic matters with double bonded ring structures. Although precursor removal via pre-oxidation is a viable approach to limit nitrosamine formation during post-disinfection, this study clearly indicates that a great portion of NDMA in treated water has been formed in the 1st oxidation step of drinking water treatment. The pre-oxidation simulations in the lab demonstrated the impact of pre-chlorination on nitrosamine formation. Given the limited removal in conventional treatment processes, avoiding nitrosamine-FPs in sources and/or nitrosamine formation during pre-oxidation become important issues to control the threats of nitrosamines in drinking water. Under current circumstance in which pre-oxidation is widely used to optimize the treatment effectiveness in many DWTPs, its adverse effect by forming nitrosamines needs to be carefully minimized and using technologies other than pre-chlorination (e.g., pre-ozonation) may be considered. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Crc and Hfq proteins of Pseudomonas putida cooperate in catabolite repression and formation of ribonucleic acid complexes with specific target motifs.

PubMed

Moreno, Renata; Hernández-Arranz, Sofía; La Rosa, Ruggero; Yuste, Luis; Madhushani, Anjana; Shingler, Victoria; Rojo, Fernando

2015-01-01

The Crc protein is a global regulator that has a key role in catabolite repression and optimization of metabolism in Pseudomonads. Crc inhibits gene expression post-transcriptionally, preventing translation of mRNAs bearing an AAnAAnAA motif [the catabolite activity (CA) motif] close to the translation start site. Although Crc was initially believed to bind RNA by itself, this idea was recently challenged by results suggesting that a protein co-purifying with Crc, presumably the Hfq protein, could account for the detected RNA-binding activity. Hfq is an abundant protein that has a central role in post-transcriptional gene regulation. Herein, we show that the Pseudomonas putida Hfq protein can recognize the CA motifs of RNAs through its distal face and that Crc facilitates formation of a more stable complex at these targets. Crc was unable to bind RNA in the absence of Hfq. However, pull-down assays showed that Crc and Hfq can form a co-complex with RNA containing a CA motif in vitro. Inactivation of the hfq or the crc gene impaired catabolite repression to a similar extent. We propose that Crc and Hfq cooperate in catabolite repression, probably through forming a stable co-complex with RNAs containing CA motifs to result in inhibition of translation initiation. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

The impact of pre-oxidation with potassium permanganate on cyanobacterial organic matter removal by coagulation.

PubMed

Naceradska, Jana; Pivokonsky, Martin; Pivokonska, Lenka; Baresova, Magdalena; Henderson, Rita K; Zamyadi, Arash; Janda, Vaclav

2017-05-01

The study investigates the effect of permanganate pre-oxidation on the coagulation of peptides/proteins of Microcystis aeruginosa which comprise a major proportion of the organic matter during cyanobacterial bloom decay. Four different permanganate dosages (0.1, 0.2, 0.4 and 0.6 mg KMnO 4 mg -1 DOC) were applied prior to coagulation by ferric sulphate. Moreover, changes in sample characteristics, such as UV 254 , DOC content and molecular weight distribution, after pre-oxidation were monitored. The results showed that permanganate pre-oxidation led to a reduction in coagulant dose, increased organic matter removals by coagulation (by 5-12% depending on permanganate dose), microcystin removal (with reductions of 91-96%) and a shift of the optimum pH range from 4.3 to 6 without to 5.5-7.3 with pre-oxidation. Degradation of organic matter into inorganic carbon and adsorption of organic matter onto hydrous MnO 2 are suggested as the main processes responsible for coagulation improvement. Moreover, permanganate prevented the formation of Fe-peptide/protein complexes that inhibit coagulation at pH about 6.2 without pre-oxidation. The study showed that carefully optimized dosing of permanganate improves cyanobacterial peptide/protein removal, with the benefit of microcystin elimination. Copyright © 2017 Elsevier Ltd. All rights reserved.

Inhibition of Calpains Protects Mn-Induced Neurotransmitter release disorders in Synaptosomes from Mice: Involvement of SNARE Complex and Synaptic Vesicle Fusion.

PubMed

Wang, Can; Xu, Bin; Ma, Zhuo; Liu, Chang; Deng, Yu; Liu, Wei; Xu, Zhao-Fa

2017-06-16

Overexposure to manganese (Mn) could disrupt neurotransmitter release via influencing the formation of SNARE complex, but the underlying mechanisms are still unclear. A previous study demonstrated that SNAP-25 is one of substrate of calpains. The current study investigated whether calpains were involved in Mn-induced disorder of SNARE complex. After mice were treated with Mn for 24 days, Mn deposition increased significantly in basal nuclei in Mn-treated and calpeptin pre-treated groups. Behaviorally, less time spent in the center of the area and decreased average velocity significantly in an open field test after 24 days of Mn exposure. With the increase in MnCl 2 dosage, intracellular Ca 2+ increased significantly, but pretreatment with calpeptin caused a dose-dependent decrease in calpains activity. There were fragments of N-terminal of SNAP-25 protein appearance in Mn-treated groups, but it is decreased with pretreatment of calpeptin. FM1-43-labeled synaptic vesicles also provided evidence that the treatment with Mn resulted in increasing first and then decreasing, which was consistent with Glu release and the 80 kDa protein levels of SNARE complexes. In summary, Mn induced the disorder of neurotransmitter release through influencing the formation of SNARE complex via cleaving SNAP-25 by overactivation of calpains in vivo.

Multi-day convective-environmental evolution prior to tropical cyclone formation from geostationary satellite measurements

NASA Astrophysics Data System (ADS)

Chang, Minhee; Ho, Chang-Hoi; Park, Myung-Sook

2016-04-01

Tropical cyclones (TCs) are developed through persistent latent heating taken from deep convective process. By analyzing aircraft and polar-orbit satellite observations, distinct upper-level warm-core induced by strong updraft was found in pre-TCs while vertically uniform temperature profile is found in non-developers. Precipitation is also broader and more frequent in developing disturbances than in nondeveloping ones. However, large uncertainties remain in determining which disturbance will develop into TC by using observation snap-shots. Here, five-day systematic evolution of deep convection and environments in developing (80) and non-developing (491) disturbances are examined over the western North Pacific for 20072009 by using geostationary satellite observation. Daily, positive tendencies in the hourly time series of the area of the MTSAT-1R infrared (IR) and water vapor (WV) brightness temperature difference < 0 are used to define single diurnal convective burst (CB) event. In terms of single CB properties (duration, expanded convective area, maximum convective area, and expanding rate), developing and nondeveloping disturbances shows significantly different mean values in the statistics, but it is not effective to estimate TC genesis. The presence of continuous CB events more than two days (i.e. multi-day CB; mCB), however, is generally found in developing disturbances. Based on the presence and absence mCB in the IR-WV time series, two different evolutions from Day 1 to Day 5 of TC formation (non-development) are explored, in which Day 6 is set to be a TC formation day (Day5 as non-development vortex decaying day). The majority of developing disturbances with mCB (83 %) initially have stronger large-scale vorticity with low-level maxima, tend to have gradually increasing deep convective area and vorticities at low-to-upper troposphere. By contrast, few developing disturbances (17 %) without mCB are pre-conditioned by much weaker large-scale vorticity. Due to adjacent dry air, resultant intensification was driven only after from Day 3 with rapid increase in relative vorticity and abrupt convective burst. There also exist many non-developing cases with mCB (54 %), which appear to candidates of TC formation as gradually increasing their convective area from Day 1 to Day 4. Due to the initially weak large-scale vorticity, they eventually decay on Day 5. For nondeveloping disturbances without mCB (46%), initially weak large-scale vorticity as well as dry atmosphere resulted in one-time deep convection and decay. Thus, this study suggests that the multiple days of convective burst, which initially accompanies strong low- to mid-troposphere large-scale vorticity, is important in TC formation.

Spectroscopic studies on the interaction of cimetidine drug with biologically significant σ- and π-acceptors

NASA Astrophysics Data System (ADS)

Pandeeswaran, M.; Elango, K. P.

2010-05-01

Spectroscopic studies revealed that the interaction of cimetidine drug with electron acceptors iodine and 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) resulted through the initial formation of ionic intermediate to charge transfer (CT) complex. The CT-complexes of the interactions have been characterized using UV-vis, 1H NMR, FT-IR and GC-MS techniques. The formation of triiodide ion, I 3-, is further confirmed by the observation of the characteristic bands in the far IR spectrum for non-linear I 3- ion with C s symmetry at 156 and 131 cm -1 assigned to νas(I-I) and νs(I-I) of the I-I bond and at 73 cm -1 due to bending δ(I 3-). The rate of formation of the CT-complexes has been measured and discussed as a function of relative permittivity of solvent and temperature. The influence of relative permittivity of the medium on the rate indicated that the intermediate is more polar than the reactants and this observation was further supported by spectral studies. Based on the spectroscopic results plausible mechanisms for the interaction of the drug with the chosen acceptors were proposed and discussed and the point of attachment of the multifunctional cimetidine drug with these acceptors during the formation of CT-complex has been established.

The 28-entity IGES test file results using ComputerVision CADDS 4X

NASA Technical Reports Server (NTRS)

Kuan, Anchyi; Shah, Saurin; Smith, Kevin

1987-01-01

The investigation was based on the following steps: (1) Read the 28 Entity IGES (Initial Graphics Exchange Specification) Test File into the CAD data base with the IGES post-processor; (2) Make the modifications to the displayed geometries, which should produce the normalized front view and the drawing entity defined display; (3) Produce the drawing entity defined display of the file as it appears in the CAD system after modification to the geometry; (4) Translate the file back to IGES format using IGES pre-processor; (5) Read the IGES file produced by the pre-processor back into the CAD data base; (6) Produce another drawing entity defined display of the CAD display; and (7) Compare the plots resulting from steps 3 and 6 - they should be identical to each other.

Understanding the Reaction Chemistry of 2,2':5',2''-Terthiophene Films with Vapor-Deposited Ag, Al, and Ca

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sang, Lingzi; Matz, Dallas L.; Pemberton, Jeanne E.

The reaction chemistry of vapor-deposited 2,2':5',2''-terthiophene (α-3T) solid-state thin films with postdeposited Ag, Al, and Ca is investigated in ultrahigh vacuum using Raman spectroscopy. Vapor-deposited Ag forms nanoparticles on these films and induces considerable surface enhanced Raman scattering (SERS) along with a change in molecular symmetry of adjacent α-3T and formation of Ag–S bonds; no other reaction chemistry is observed. Vapor-deposited Al and Ca undergo chemical reaction with α-3T initiated by metal-to-α-3T electron transfer. For Al, the resulting product is predominantly amorphous carbon through initial radical formation and subsequent decomposition reactions. For Ca, the spectral evidence suggests two pathways: onemore » leading to α-3T polymerization and the other resulting in thiophene ring opening, both initiated by radical formation through Ca-to-α-3T electron transfer. These interfacial reactions reflect the complex chemistry that can occur between low work function metals and thiophene-based oligomers. This reactivity is strongly correlated with metal work function.« less

Understanding the Reaction Chemistry of 2,2':5',2"-Terthiophene Films with Vapor-Deposited Ag, Al, and Ca

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sang, Lingzi; Matz, Dallas L.; Pemberton, Jeanne E.

The reaction chemistry of vapor-deposited 2,2':5',2''-terthiophene (α-3T) solid-state thin films with postdeposited Ag, Al, and Ca is investigated in ultrahigh vacuum using Raman spectroscopy. Vapor-deposited Ag forms nanoparticles on these films and induces considerable surface enhanced Raman scattering (SERS) along with a change in molecular symmetry of adjacent α-3T and formation of Ag–S bonds; no other reaction chemistry is observed. Vapor-deposited Al and Ca undergo chemical reaction with α-3T initiated by metal-to-α-3T electron transfer. For Al, the resulting product is predominantly amorphous carbon through initial radical formation and subsequent decomposition reactions. For Ca, the spectral evidence suggests two pathways: onemore » leading to α-3T polymerization and the other resulting in thiophene ring opening, both initiated by radical formation through Ca-to-α-3T electron transfer. These interfacial reactions reflect the complex chemistry that can occur between low work function metals and thiophene-based oligomers. This reactivity is strongly correlated with metal work function.« less

Formation of singlet oxygen by decomposition of protein hydroperoxide in photosystem II.

PubMed

Pathak, Vinay; Prasad, Ankush; Pospíšil, Pavel

2017-01-01

Singlet oxygen (1O2) is formed by triplet-triplet energy transfer from triplet chlorophyll to O2 via Type II photosensitization reaction in photosystem II (PSII). Formation of triplet chlorophyll is associated with the change in spin state of the excited electron and recombination of triplet radical pair in the PSII antenna complex and reaction center, respectively. Here, we have provided evidence for the formation of 1O2 by decomposition of protein hydroperoxide in PSII membranes deprived of Mn4O5Ca complex. Protein hydroperoxide is formed by protein oxidation initiated by highly oxidizing chlorophyll cation radical and hydroxyl radical formed by Type I photosensitization reaction. Under highly oxidizing conditions, protein hydroperoxide is oxidized to protein peroxyl radical which either cyclizes to dioxetane or recombines with another protein peroxyl radical to tetroxide. These highly unstable intermediates decompose to triplet carbonyls which transfer energy to O2 forming 1O2. Data presented in this study show for the first time that 1O2 is formed by decomposition of protein hydroperoxide in PSII membranes deprived of Mn4O5Ca complex.

Formation of singlet oxygen by decomposition of protein hydroperoxide in photosystem II

PubMed Central

Pathak, Vinay; Prasad, Ankush

2017-01-01

Singlet oxygen (1O2) is formed by triplet-triplet energy transfer from triplet chlorophyll to O2 via Type II photosensitization reaction in photosystem II (PSII). Formation of triplet chlorophyll is associated with the change in spin state of the excited electron and recombination of triplet radical pair in the PSII antenna complex and reaction center, respectively. Here, we have provided evidence for the formation of 1O2 by decomposition of protein hydroperoxide in PSII membranes deprived of Mn4O5Ca complex. Protein hydroperoxide is formed by protein oxidation initiated by highly oxidizing chlorophyll cation radical and hydroxyl radical formed by Type I photosensitization reaction. Under highly oxidizing conditions, protein hydroperoxide is oxidized to protein peroxyl radical which either cyclizes to dioxetane or recombines with another protein peroxyl radical to tetroxide. These highly unstable intermediates decompose to triplet carbonyls which transfer energy to O2 forming 1O2. Data presented in this study show for the first time that 1O2 is formed by decomposition of protein hydroperoxide in PSII membranes deprived of Mn4O5Ca complex. PMID:28732060

Tracing the Origins of Nitrogen Bearing Organics Toward Orion KL with Alma

NASA Astrophysics Data System (ADS)

Carroll, Brandon; Crockett, Nathan; Bergin, Edwin; Blake, Geoffrey

2016-06-01

A comprehensive analysis of a broadband 1.2 THz wide spectral survey of the Orion Kleinmann-Low nebula (Orion KL) from the Herschel Space Telescope has shown that nitrogen bearing complex organics trace systematically hotter gas than O-bearing organics toward this source. The origin of this O/N dichotomy remains a mystery. If complex molecules originate from grain surfaces, N-bearing species may be more difficult to remove from grain surfaces than O-bearing organics. Theoretical studies, however, have shown that hot (T=300 K) gas phase chemistry can produce high abundances of N-bearing organics while suppressing the formation of O-bearing complex molecules. In order to distinguish these distinct formation pathways we have obtained extremely high angular resolution observations of methyl cyanide (CH_3CN) using the Atacama Large Millimeter/Submillimeter Array (ALMA) toward Orion KL. By simultaneously imaging 13CH_3CN and CH_2DCN we map the temperature structure and D/H ratio of CH_3CN. We will present the initial results of these observations and discuss their implications for the formation of N-bearing organics in the interstellar medium.

Large-scale influences on the pre-genesis of tropical cyclone Karl (2010)

NASA Astrophysics Data System (ADS)

Griffin, Kyle S.

The genesis of Tropical Cyclone (TC) Karl (2010) in September 2010 provided a unique opportunity to examine the continuing problem of understanding tropical cyclogenesis. The precursor disturbance to Karl originated from a cluster of showers east of the Windward Islands and was well sampled by ongoing field campaigns, particularly the PRE-Depression Investigation of Cloud-systems in the Tropics (PREDICT), as the targeted disturbance progressed westward. While traditional genesis theories focusing on moisture and mass fields (e.g. top-down showerhead method) can explain the initial spin-up of the disturbance several days prior to its official genesis, additional perspectives are examined in concert with more traditional methods in order to provide a more complete analysis of the synoptic-scale patterns that influenced the pre-Karl disturbance. A surge of westerly winds from northern South America aids the initial spin-up of the pre-Karl disturbance on 8-9 September, leading to the formation of a nearly closed earth-relative circulation. It can be shown that these anomalous westerly winds are tied to the convectively active phase of a convectively coupled Kelvin wave (CCKW). The observed formation of the nearly closed circulation on 10 September is well timed with the passage of this convectively active phase, a relationship that has been shown to hold true in cases of CCKW-TC interactions around the globe. Physically, the CCKW increases deep convection and aids in the generation of low-level relative vorticity on the cyclonic shear side of the low-level westerly wind anomalies, both of which serve to help organize the pre-Karl disturbance. Finally, the passage of the CCKW coincides with an equatorward surge of cold air and southerly winds in the lee of the Andes, triggered by a passing mid-latitude disturbance on 31 August. As the surge passes the equator on 7 September, little temperature perturbation remains with the surge, but terrain-channeled low-level flow acts to turn southerly flow into westerly flow south of the pre-Karl disturbance. By 8-9 September, anomalous westerly winds with the surge merge with and enhance the anomalous westerly winds associated with the CCKW passage, strengthening the low-level vorticity generation in the cyclonic shear of the merged CCKW-wind surge on the pre-Karl disturbance. However, despite this increase in vorticity and convection, the environment surrounding the pre-Karl disturbance remained unfavorable for several more days, with increased vertical wind shear and the convectively suppressed phase of a CCKW inhibiting further development before TC genesis occurred on 14 September. Despite this delayed development, the interplay of both mid-latitude and equatorial wave precursors likely contributed to the eventual genesis of TC Karl.

Forced Ignition Study Based On Wavelet Method

NASA Astrophysics Data System (ADS)

Martelli, E.; Valorani, M.; Paolucci, S.; Zikoski, Z.

2011-05-01

The control of ignition in a rocket engine is a critical problem for combustion chamber design. Therefore it is essential to fully understand the mechanism of ignition during its earliest stages. In this paper the characteristics of flame kernel formation and initial propagation in a hydrogen-argon-oxygen mixing layer are studied using 2D direct numerical simulations with detailed chemistry and transport properties. The flame kernel is initiated by adding an energy deposition source term in the energy equation. The effect of unsteady strain rate is studied by imposing a 2D turbulence velocity field, which is initialized by means of a synthetic field. An adaptive wavelet method, based on interpolating wavelets is used in this study to solve the compressible reactive Navier- Stokes equations. This method provides an alternative means to refine the computational grid points according to local demands of the physical solution. The present simulations show that in the very early instants the kernel perturbed by the turbulent field is characterized by an increased burning area and a slightly increased rad- ical formation. In addition, the calculations show that the wavelet technique yields a significant reduction in the number of degrees of freedom necessary to achieve a pre- scribed solution accuracy.

The subduction-accretion history of the Bangong-Nujiang Ocean: Constraints from provenance and geochronology of the Mesozoic strata near Gaize, central Tibet

NASA Astrophysics Data System (ADS)

Li, Shun; Ding, Lin; Guilmette, Carl; Fu, Jiajun; Xu, Qiang; Yue, Yahui; Henrique-Pinto, Renato

2017-04-01

The Mesozoic strata, within the Bangong-Nujiang suture zone in central Tibet, recorded critical information about the subduction-accretion processes of the Bangong-Nujiang Ocean prior to the Lhasa-Qiangtang collision. This paper reports detailed field observations, petrographic descriptions, sandstone detrital zircon U-Pb ages and Hf isotopic analyses from an accretionary complex (preserved as Mugagangri Group) and the unconformably overlying Shamuluo Formation near Gaize. The youngest detrital zircon ages, together with other age constraints from literature, suggest that the Mugagangri Group was deposited during late Triassic-early Jurassic, while the Shamuluo Formation was deposited during late Jurassic-early Cretaceous. Based on the differences in lithology, age and provenance, the Mugagangri Group is subdivided into the upper, middle and lower subunits. These units are younging structurally downward/southward, consistent with models of progressive off-scrapping and accretion in a southward-facing subduction complex. The upper subunit, comprising mainly quartz-sandstone and siliceous mud/shale, was deposited in abyssal plain environment close to the Qiangtang passive margin during late Triassic, with sediments derived from the southern Qiangtang block. The middle and lower subunits comprise mainly lithic-quartz-sandstone and mud/shale, containing abundant ultramafic/ophiolitic fragments. The middle subunit, of late Triassic-early Jurassic age, records a transition in tectono-depositional setting from abyssal plain to trench-wedge basin, with sudden influx of sediments sourced from the central Qiangtang metamorphic belt and northern Qiangtang magmatic belt. The appearance of ultramafic/ophiolitic fragments in the middle subunit reflects the subduction initiation. The lower subunit was deposited in a trench-wedge basin during early Jurassic, with influx of Jurassic-aged zircons originating from the newly active southern Qiangtang magmatic arc. The lower subunit records the onset of arc magmatism related to the northward subduction of the Bangong-Nujiang Ocean. The Shamuluo Formation, comprising mainly lithic-feldspar-sandstone with limestone interlayers, was deposited in a post-collisional residual-sea or pre-collisional trench-slope basin, with sediments derived entirely from the Qiangtang block.

Beach cusp destruction, formation, and evolution during and subsequent to an extratropical storm, Duck, North Carolina

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miller, J.R.; Miller, S.M.O.; Torzynski, C.A.

Many studies have debated whether beach cusps are erosional or depositional features. The April 12-14, 1988, extratropical storm provided an opportunity to view the direct effects of one of the largest storms of the past decade upon beach sedimentology and morphology on barrier islands near Duck, North Carolina. Prior to the storm, the beach at Duck was characterized by a well-defined pattern of beach cusps with horn-to-horn spacings averaging 35 m. Storm-induced alterations were dominated by an initial period of beach erosion that remobilized the upper 30 to 50 cm of beach sediment, followed by aggradation. Net aggradation was mostmore » prominent along the middle beachface and within the pre-storm cusp bays. These morphologic adjustments resulted in the destruction of cusps, which were replaced with a post-storm planar beachface composed of horizontally bedded fine- to coarse-grained sediments. Within 24 hrs of storm subsidence, new beach cusps formed sequentially along the coast in the direction of longshore transport. Initial cusp formation resulted from beach erosion and the creation of bays in the planar storm-beach surface at positions of preferential post-storm runup. The initial cusp horns were composed of truncated horizontal beds of the planar beach accreted during the storm. After their formation, the cusps sequentially migrated downdrift. Migrating horns were composed of a coarse-grained sediment wedge that thickened toward horn crests, suggesting formation by deposition. It is concluded from these observations that beach cusps are both erosional and depositional in nature.« less

RNA-induced silencing complex (RISC) Proteins PACT, TRBP, and Dicer are SRA binding nuclear receptor coregulators

PubMed Central

Redfern, Andrew D.; Colley, Shane M.; Beveridge, Dianne J.; Ikeda, Naoya; Epis, Michael R.; Li, Xia; Foulds, Charles E.; Stuart, Lisa M.; Barker, Andrew; Russell, Victoria J.; Ramsay, Kerry; Kobelke, Simon J.; Li, Xiaotao; Hatchell, Esme C.; Payne, Christine; Giles, Keith M.; Messineo, Adriana; Gatignol, Anne; Lanz, Rainer B.; O’Malley, Bert W.; Leedman, Peter J.

2013-01-01

The cytoplasmic RNA-induced silencing complex (RISC) contains dsRNA binding proteins, including protein kinase RNA activator (PACT), transactivation response RNA binding protein (TRBP), and Dicer, that process pre-microRNAs into mature microRNAs (miRNAs) that target specific mRNA species for regulation. There is increasing evidence for important functional interactions between the miRNA and nuclear receptor (NR) signaling networks, with recent data showing that estrogen, acting through the estrogen receptor, can modulate initial aspects of nuclear miRNA processing. Here, we show that the cytoplasmic RISC proteins PACT, TRBP, and Dicer are steroid receptor RNA activator (SRA) binding NR coregulators that target steroid-responsive promoters and regulate NR activity and downstream gene expression. Furthermore, each of the RISC proteins, together with Argonaute 2, associates with SRA and specific pre-microRNAs in both the nucleus and cytoplasm, providing evidence for links between NR-mediated transcription and some of the factors involved in miRNA processing. PMID:23550157

RNA-induced silencing complex (RISC) Proteins PACT, TRBP, and Dicer are SRA binding nuclear receptor coregulators.

PubMed

Redfern, Andrew D; Colley, Shane M; Beveridge, Dianne J; Ikeda, Naoya; Epis, Michael R; Li, Xia; Foulds, Charles E; Stuart, Lisa M; Barker, Andrew; Russell, Victoria J; Ramsay, Kerry; Kobelke, Simon J; Li, Xiaotao; Hatchell, Esme C; Payne, Christine; Giles, Keith M; Messineo, Adriana; Gatignol, Anne; Lanz, Rainer B; O'Malley, Bert W; Leedman, Peter J

2013-04-16

The cytoplasmic RNA-induced silencing complex (RISC) contains dsRNA binding proteins, including protein kinase RNA activator (PACT), transactivation response RNA binding protein (TRBP), and Dicer, that process pre-microRNAs into mature microRNAs (miRNAs) that target specific mRNA species for regulation. There is increasing evidence for important functional interactions between the miRNA and nuclear receptor (NR) signaling networks, with recent data showing that estrogen, acting through the estrogen receptor, can modulate initial aspects of nuclear miRNA processing. Here, we show that the cytoplasmic RISC proteins PACT, TRBP, and Dicer are steroid receptor RNA activator (SRA) binding NR coregulators that target steroid-responsive promoters and regulate NR activity and downstream gene expression. Furthermore, each of the RISC proteins, together with Argonaute 2, associates with SRA and specific pre-microRNAs in both the nucleus and cytoplasm, providing evidence for links between NR-mediated transcription and some of the factors involved in miRNA processing.

Structural characterization of ribosome recruitment and translocation by type IV IRES.

PubMed

Murray, Jason; Savva, Christos G; Shin, Byung-Sik; Dever, Thomas E; Ramakrishnan, V; Fernández, Israel S

2016-05-09

Viral mRNA sequences with a type IV IRES are able to initiate translation without any host initiation factors. Initial recruitment of the small ribosomal subunit as well as two translocation steps before the first peptidyl transfer are essential for the initiation of translation by these mRNAs. Using electron cryomicroscopy (cryo-EM) we have structurally characterized at high resolution how the Cricket Paralysis Virus Internal Ribosomal Entry Site (CrPV-IRES) binds the small ribosomal subunit (40S) and the translocation intermediate stabilized by elongation factor 2 (eEF2). The CrPV-IRES restricts tvhe otherwise flexible 40S head to a conformation compatible with binding the large ribosomal subunit (60S). Once the 60S is recruited, the binary CrPV-IRES/80S complex oscillates between canonical and rotated states (Fernández et al., 2014; Koh et al., 2014), as seen for pre-translocation complexes with tRNAs. Elongation factor eEF2 with a GTP analog stabilizes the ribosome-IRES complex in a rotated state with an extra ~3 degrees of rotation. Key residues in domain IV of eEF2 interact with pseudoknot I (PKI) of the CrPV-IRES stabilizing it in a conformation reminiscent of a hybrid tRNA state. The structure explains how diphthamide, a eukaryotic and archaeal specific post-translational modification of a histidine residue of eEF2, is involved in translocation.

Seeding hydrate formation in water-saturated sand with dissolved-phase methane obtained from hydrate dissolution: A progress report

USGS Publications Warehouse

Waite, William F.; Osegovic, J.P.; Winters, William J.; Max, M.D.; Mason, David H.

2008-01-01

An isobaric flow loop added to the Gas Hydrate And Sediment Test Laboratory Instrument (GHASTLI) is being investigated as a means of rapidly forming methane hydrate in watersaturated sand from methane dissolved in water. Water circulates through a relatively warm source chamber, dissolving granular methane hydrate that was pre-made from seed ice, then enters a colder hydrate growth chamber where hydrate can precipitate in a water-saturated sand pack. Hydrate dissolution in the source chamber imparts a known methane concentration to the circulating water, and hydrate particles from the source chamber entrained in the circulating water can become nucleation sites to hasten the onset of hydrate formation in the growth chamber. Initial results suggest hydrate grows rapidly near the growth chamber inlet. Techniques for establishing homogeneous hydrate formation throughout the sand pack are being developed.

SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read

PubMed Central

2010-01-01

Background High-throughput automated sequencing has enabled an exponential growth rate of sequencing data. This requires increasing sequence quality and reliability in order to avoid database contamination with artefactual sequences. The arrival of pyrosequencing enhances this problem and necessitates customisable pre-processing algorithms. Results SeqTrim has been implemented both as a Web and as a standalone command line application. Already-published and newly-designed algorithms have been included to identify sequence inserts, to remove low quality, vector, adaptor, low complexity and contaminant sequences, and to detect chimeric reads. The availability of several input and output formats allows its inclusion in sequence processing workflows. Due to its specific algorithms, SeqTrim outperforms other pre-processors implemented as Web services or standalone applications. It performs equally well with sequences from EST libraries, SSH libraries, genomic DNA libraries and pyrosequencing reads and does not lead to over-trimming. Conclusions SeqTrim is an efficient pipeline designed for pre-processing of any type of sequence read, including next-generation sequencing. It is easily configurable and provides a friendly interface that allows users to know what happened with sequences at every pre-processing stage, and to verify pre-processing of an individual sequence if desired. The recommended pipeline reveals more information about each sequence than previously described pre-processors and can discard more sequencing or experimental artefacts. PMID:20089148

Promoting clinical and laboratory interaction by harmonization.

PubMed

Plebani, Mario; Panteghini, Mauro

2014-05-15

The lack of interchangeable results in current practice among clinical laboratories has underpinned greater attention to standardization and harmonization projects. Although the focus was mainly on the standardization and harmonization of measurement procedures and their results, the scope of harmonization goes beyond method and analytical results: it includes all other aspects of laboratory testing, including terminology and units, report formats, reference limits and decision thresholds, as well as test profiles and criteria for the interpretation of results. In particular, as evidence collected in last decades demonstrates that pre-pre- and post-post-analytical steps are more vulnerable to errors, harmonization initiatives should be performed to improve procedures and processes at the laboratory-clinical interface. Managing upstream demand, down-stream interpretation of laboratory results, and subsequent appropriate action through close relationships between laboratorians and clinicians remains a crucial issue of the laboratory testing process. Therefore, initiatives to improve test demand management from one hand and to harmonize procedures to improve physicians' acknowledgment of laboratory data and their interpretation from the other hand are needed in order to assure quality and safety in the total testing process. © 2013.

Transient surface states during the CBE growth of GaAs

NASA Astrophysics Data System (ADS)

Farrell, T.; Hill, D.; Joyce, T. B.; Bullough, T. J.; Weightman, P.

1997-05-01

We report the occurrence of a transient surface state during the initial stages of CBE GaAs(0 0 1) growth. The state was detected in real-time reflectance ( R) and reflectance anisotropy spectroscopy (RAS) growth monitoring. At low growth rates, less than 1 μm/h, beam equivalent pressure (BEP) of triethylgallium (TEG) < 2.5 × 10 -5 mbar there was no change in R and the RAS signal changed from its pre-growth value under arsenic stabilisation at the growth temperature to its "during growth" value upon admission of the TEG, with the familiar monolayer oscillations. At higher TEG BEPs there was a rapid increase in R at all monitoring wavelengths, followed by a monotonic decay to its pre-growth value. This transient increase in R was accompanied by a change in the RAS signal, the magnitude and sign of which varied with wavelength. The initial increase in R is shown to be associated with the development of a metallic-like surface whereas the changes in the RAS signal are consistent with the formation of Ga dimers.

Birth order dependent growth cone segregation determines synaptic layer identity in the Drosophila visual system

PubMed Central

Kulkarni, Abhishek; Ertekin, Deniz; Lee, Chi-Hon; Hummel, Thomas

2016-01-01

The precise recognition of appropriate synaptic partner neurons is a critical step during neural circuit assembly. However, little is known about the developmental context in which recognition specificity is important to establish synaptic contacts. We show that in the Drosophila visual system, sequential segregation of photoreceptor afferents, reflecting their birth order, lead to differential positioning of their growth cones in the early target region. By combining loss- and gain-of-function analyses we demonstrate that relative differences in the expression of the transcription factor Sequoia regulate R cell growth cone segregation. This initial growth cone positioning is consolidated via cell-adhesion molecule Capricious in R8 axons. Further, we show that the initial growth cone positioning determines synaptic layer selection through proximity-based axon-target interactions. Taken together, we demonstrate that birth order dependent pre-patterning of afferent growth cones is an essential pre-requisite for the identification of synaptic partner neurons during visual map formation in Drosophila. DOI: http://dx.doi.org/10.7554/eLife.13715.001 PMID:26987017

Polerovirus protein P0 prevents the assembly of small RNA-containing RISC complexes and leads to degradation of ARGONAUTE1.

PubMed

Csorba, Tibor; Lózsa, Rita; Hutvágner, György; Burgyán, József

2010-05-01

RNA silencing plays an important role in plants in defence against viruses. To overcome this defence, plant viruses encode suppressors of RNA silencing. The most common mode of silencing suppression is sequestration of double-stranded RNAs involved in the antiviral silencing pathways. Viral suppressors can also overcome silencing responses through protein-protein interaction. The poleroviral P0 silencing suppressor protein targets ARGONAUTE (AGO) proteins for degradation. AGO proteins are the core component of the RNA-induced silencing complex (RISC). We found that P0 does not interfere with the slicer activity of pre-programmed siRNA/miRNA containing AGO1, but prevents de novo formation of siRNA/miRNA containing AGO1. We show that the AGO1 protein is part of a high-molecular-weight complex, suggesting the existence of a multi-protein RISC in plants. We propose that P0 prevents RISC assembly by interacting with one of its protein components, thus inhibiting formation of siRNA/miRNA-RISC, and ultimately leading to AGO1 degradation. Our findings also suggest that siRNAs enhance the stability of co-expressed AGO1 in both the presence and absence of P0.

Pliocene transpressional modification of depositional basins by convergent thrusting adjacent to the "Big Bend" of the San Andreas fault: An example from Lockwood Valley, southern California

USGS Publications Warehouse

Kellogg, K.S.; Minor, S.A.

2005-01-01

The "Big Bend" of the San Andreas fault in the western Transverse Ranges of southern California is a left stepping flexure in the dextral fault system and has long been recognized as a zone of relatively high transpression compared to adjacent regions. The Lockwood Valley region, just south of the Big Bend, underwent a profound change in early Pliocene time (???5 Ma) from basin deposition to contraction, accompanied by widespread folding and thrusting. This change followed the recently determined initiation of opening of the northern Gulf of California and movement along the southern San Andreas fault at about 6.1 Ma, with the concomitant formation of the Big Bend. Lockwood Valley occupies a 6-km-wide, fault-bounded structural basin in which converging blocks of Paleoproterozoic and Cretaceous crystalline basement and upper Oligocene and lower Miocene sedimentary rocks (Plush Ranch Formation) were thrust over Miocene and Pliocene basin-fill sedimentary rocks (in ascending order, Caliente Formation, Lockwood Clay, and Quatal Formation). All the pre-Quatal sedimentary rocks and most of the Pliocene Quatal Formation were deposited during a mid-Tertiary period of regional transtension in a crustal block that underwent little clockwise vertical-axis rotation as compared to crustal blocks to the south. Ensuing Pliocene and Quaternary transpression in the Big Bend region began during deposition of the poorly dated Quatal Formation and was marked by four converging thrust systems, which decreased the areal extent of the sedimentary basin and formed the present Lockwood Valley structural basin. None of the thrusts appears presently active. Estimated shortening across the center of the basin was about 30 percent. The fortnerly defined eastern Big Pine fault, now interpreted to be two separate, oppositely directed, contractional reverse or thrust faults, marks the northwestern structural boundary of Lockwood Valley. The complex geometry of the Lockwood Valley basin is similar to other Tertiary structural basins in southern California, such those that underlie Cuyama Valley, the Ridge basin, and the east Ventura basin.

Rapid Formation of Microbe-Oil Aggregates and Changes in Community Composition in Coastal Surface Water Following Exposure to Oil and the Dispersant Corexit.

PubMed

Doyle, Shawn M; Whitaker, Emily A; De Pascuale, Veronica; Wade, Terry L; Knap, Anthony H; Santschi, Peter H; Quigg, Antonietta; Sylvan, Jason B

2018-01-01

During the Deepwater Horizon (DWH) oil spill, massive quantities of oil were deposited on the seafloor via a large-scale marine oil-snow sedimentation and flocculent accumulation (MOSSFA) event. The role of chemical dispersants (e.g., Corexit) applied during the DWH oil spill clean-up in helping or hindering the formation of this MOSSFA event are not well-understood. Here, we present the first experiment related to the DWH oil spill to specifically investigate the relationship between microbial community structure, oil and Corexit®, and marine oil-snow in coastal surface waters. We observed the formation of micron-scale aggregates of microbial cells around droplets of oil and dispersant and found that their rate of formation was directly related to the concentration of oil within the water column. These micro-aggregates are potentially important precursors to the formation of larger marine oil-snow particles. Therefore, our observation that Corexit® significantly enhanced their formation suggests dispersant application may play a role in the development of MOSSFA events. We also observed that microbial communities in marine surface waters respond to oil and oil plus Corexit® differently and much more rapidly than previously measured, with major shifts in community composition occurring within only a few hours of experiment initiation. In the oil-amended treatments without Corexit®, this manifested as an increase in community diversity due to the outgrowth of several putative aliphatic- and aromatic-hydrocarbon degrading genera, including phytoplankton-associated taxa. In contrast, microbial community diversity was reduced in mesocosms containing chemically dispersed oil. Importantly, different consortia of hydrocarbon degrading bacteria responded to oil and chemically dispersed oil, indicating that functional redundancy in the pre-spill community likely results in hydrocarbon consumption in both undispersed and dispersed oils, but by different bacterial taxa. Taken together, these data improve our understanding of how dispersants influence the degradation and transport of oil in marine surface waters following an oil spill and provide valuable insight into the early response of complex microbial communities to oil exposure.

Rapid Formation of Microbe-Oil Aggregates and Changes in Community Composition in Coastal Surface Water Following Exposure to Oil and the Dispersant Corexit

PubMed Central

Doyle, Shawn M.; Whitaker, Emily A.; De Pascuale, Veronica; Wade, Terry L.; Knap, Anthony H.; Santschi, Peter H.; Quigg, Antonietta; Sylvan, Jason B.

2018-01-01

During the Deepwater Horizon (DWH) oil spill, massive quantities of oil were deposited on the seafloor via a large-scale marine oil-snow sedimentation and flocculent accumulation (MOSSFA) event. The role of chemical dispersants (e.g., Corexit) applied during the DWH oil spill clean-up in helping or hindering the formation of this MOSSFA event are not well-understood. Here, we present the first experiment related to the DWH oil spill to specifically investigate the relationship between microbial community structure, oil and Corexit®, and marine oil-snow in coastal surface waters. We observed the formation of micron-scale aggregates of microbial cells around droplets of oil and dispersant and found that their rate of formation was directly related to the concentration of oil within the water column. These micro-aggregates are potentially important precursors to the formation of larger marine oil-snow particles. Therefore, our observation that Corexit® significantly enhanced their formation suggests dispersant application may play a role in the development of MOSSFA events. We also observed that microbial communities in marine surface waters respond to oil and oil plus Corexit® differently and much more rapidly than previously measured, with major shifts in community composition occurring within only a few hours of experiment initiation. In the oil-amended treatments without Corexit®, this manifested as an increase in community diversity due to the outgrowth of several putative aliphatic- and aromatic-hydrocarbon degrading genera, including phytoplankton-associated taxa. In contrast, microbial community diversity was reduced in mesocosms containing chemically dispersed oil. Importantly, different consortia of hydrocarbon degrading bacteria responded to oil and chemically dispersed oil, indicating that functional redundancy in the pre-spill community likely results in hydrocarbon consumption in both undispersed and dispersed oils, but by different bacterial taxa. Taken together, these data improve our understanding of how dispersants influence the degradation and transport of oil in marine surface waters following an oil spill and provide valuable insight into the early response of complex microbial communities to oil exposure. PMID:29696005

The Gaia-ESO Survey: the present-day radial metallicity distribution of the Galactic disc probed by pre-main-sequence clusters

NASA Astrophysics Data System (ADS)

Spina, L.; Randich, S.; Magrini, L.; Jeffries, R. D.; Friel, E. D.; Sacco, G. G.; Pancino, E.; Bonito, R.; Bravi, L.; Franciosini, E.; Klutsch, A.; Montes, D.; Gilmore, G.; Vallenari, A.; Bensby, T.; Bragaglia, A.; Flaccomio, E.; Koposov, S. E.; Korn, A. J.; Lanzafame, A. C.; Smiljanic, R.; Bayo, A.; Carraro, G.; Casey, A. R.; Costado, M. T.; Damiani, F.; Donati, P.; Frasca, A.; Hourihane, A.; Jofré, P.; Lewis, J.; Lind, K.; Monaco, L.; Morbidelli, L.; Prisinzano, L.; Sousa, S. G.; Worley, C. C.; Zaggia, S.

2017-05-01

Context. The radial metallicity distribution in the Galactic thin disc represents a crucial constraint for modelling disc formation and evolution. Open star clusters allow us to derive both the radial metallicity distribution and its evolution over time. Aims: In this paper we perform the first investigation of the present-day radial metallicity distribution based on [Fe/H] determinations in late type members of pre-main-sequence clusters. Because of their youth, these clusters are therefore essential for tracing the current interstellar medium metallicity. Methods: We used the products of the Gaia-ESO Survey analysis of 12 young regions (age < 100 Myr), covering Galactocentric distances from 6.67 to 8.70 kpc. For the first time, we derived the metal content of star forming regions farther than 500 pc from the Sun. Median metallicities were determined through samples of reliable cluster members. For ten clusters the membership analysis is discussed in the present paper, while for other two clusters (I.e. Chamaeleon I and Gamma Velorum) we adopted the members identified in our previous works. Results: All the pre-main-sequence clusters considered in this paper have close-to-solar or slightly sub-solar metallicities. The radial metallicity distribution traced by these clusters is almost flat, with the innermost star forming regions having [Fe/H] values that are 0.10-0.15 dex lower than the majority of the older clusters located at similar Galactocentric radii. Conclusions: This homogeneous study of the present-day radial metallicity distribution in the Galactic thin disc favours models that predict a flattening of the radial gradient over time. On the other hand, the decrease of the average [Fe/H] at young ages is not easily explained by the models. Our results reveal a complex interplay of several processes (e.g. star formation activity, initial mass function, supernova yields, gas flows) that controlled the recent evolution of the Milky Way. Based on observations made with the ESO/VLT, at Paranal Observatory, under program 188.B-3002 (The Gaia-ESO Public Spectroscopic Survey).Full Table 1 is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/601/A70

Substrate-Induced Formation of Ribosomal Decoding Center for Accurate and Rapid Genetic Code Translation.

PubMed

Pavlov, Michael Y; Ehrenberg, Måns

2018-05-20

Accurate translation of genetic information is crucial for synthesis of functional proteins in all organisms. We use recent experimental data to discuss how induced fit affects accuracy of initial codon selection on the ribosome by aminoacyl transfer RNA in ternary complex ( T 3 ) with elongation factor Tu (EF-Tu) and guanosine-5'-triphosphate (GTP). We define actual accuracy ([Formula: see text]) of a particular protein synthesis system as its current accuracy and the effective selectivity ([Formula: see text]) as [Formula: see text] in the limit of zero ribosomal binding affinity for T 3 . Intrinsic selectivity ([Formula: see text]), defined as the upper thermodynamic limit of [Formula: see text], is determined by the free energy difference between near-cognate and cognate T 3 in the pre-GTP hydrolysis state on the ribosome. [Formula: see text] is much larger than [Formula: see text], suggesting the possibility of a considerable increase in [Formula: see text] and [Formula: see text] at negligible kinetic cost. Induced fit increases [Formula: see text] and [Formula: see text] without affecting [Formula: see text], and aminoglycoside antibiotics reduce [Formula: see text] and [Formula: see text] at unaltered [Formula: see text].

Argus: A W-band 16-pixel focal plane array for the Green Bank Telescope

NASA Astrophysics Data System (ADS)

Devaraj, Kiruthika; Church, Sarah; Cleary, Kieran; Frayer, David; Gawande, Rohit; Goldsmith, Paul; Gundersen, Joshua; Harris, Andrew; Kangaslahti, Pekka; Readhead, Tony; Reeves, Rodrigo; Samoska, Lorene; Sieth, Matt; Voll, Patricia

2015-05-01

We are building Argus, a 16-pixel square-packed focal plane array that will cover the 75-115.3 GHz frequency range on the Robert C. Byrd Green Bank Telescope (GBT). The primary research area for Argus is the study of star formation within our Galaxy and nearby galaxies. Argus will map key molecules that trace star formation, including carbon monoxide (CO) and hydrogen cyanide (HCN). An additional key science area is astrochemistry, which will be addressed by observing complex molecules in the interstellar medium, and the study of formation of solar systems, which will be addressed by identifying dense pre-stellar cores and by observing comets in our solar system. Argus has a highly scalable architecture and will be a technology path finder for larger arrays. The array is modular in construction, which will allow easy replacement of malfunctioning and poorly performing components.

Advances in synapse formation: forging connections in the worm.

PubMed

Cherra, Salvatore J; Jin, Yishi

2015-01-01

Synapse formation is the quintessential process by which neurons form specific connections with their targets to enable the development of functional circuits. Over the past few decades, intense research efforts have identified thousands of proteins that localize to the pre- and postsynaptic compartments. Genetic dissection has provided important insights into the nexus of the molecular and cellular network, and has greatly advanced our knowledge about how synapses form and function physiologically. Moreover, recent studies have highlighted the complex regulation of synapse formation with the identification of novel mechanisms involving cell interactions from non-neuronal sources. In this review, we cover the conserved pathways required for synaptogenesis and place specific focus on new themes of synapse modulation arising from studies in Caenorhabditis elegans. For further resources related to this article, please visit the WIREs website. The authors have declared no conflicts of interest for this article. © 2014 Wiley Periodicals, Inc.

The effects of pre-ionization using a shunt resistor on reproducibility of the x-ray emission in a dense plasma focus device

NASA Astrophysics Data System (ADS)

Piriaei, D.; Yousefi, H. R.; Mahabadi, T. D.; SalarElahi, A.; Ghoranneviss, M.

2017-08-01

In this research, the effects of pre-ionization using a shunt resistor on reproducibility of x-ray emission in a Mather type plasma focus device have been studied. This technique increased the intensities of the emitted x-rays from argon as the filling gas of the device and made the x-ray yields with similar intensities reproducible. A Mirnov coil was also used to record the variations of the plasma's magnetic field, and the wavelet spectrums of these recorded signals showed the reduced instabilities due to the application of the pre-ionization technique. Moreover, it was demonstrated that this technique was capable of reducing the number of initial runaway electrons that could increase the impurities and instabilities inside the plasma. In addition to the above-mentioned features, this technique could improve the uniform formation of the current sheath during the breakdown phase that might later lead to a high quality pinch and high intensity emitted x-rays.

Beyond tRNA cleavage: novel essential function for yeast tRNA splicing endonuclease unrelated to tRNA processing

PubMed Central

Dhungel, Nripesh; Hopper, Anita K.

2012-01-01

Pre-tRNA splicing is an essential process in all eukaryotes. In yeast and vertebrates, the enzyme catalyzing intron removal from pre-tRNA is a heterotetrameric complex (splicing endonuclease [SEN] complex). Although the SEN complex is conserved, the subcellular location where pre-tRNA splicing occurs is not. In yeast, the SEN complex is located at the cytoplasmic surface of mitochondria, whereas in vertebrates, pre-tRNA splicing is nuclear. We engineered yeast to mimic the vertebrate cell biology and demonstrate that all three steps of pre-tRNA splicing, as well as tRNA nuclear export and aminoacylation, occur efficiently when the SEN complex is nuclear. However, nuclear pre-tRNA splicing fails to complement growth defects of cells with defective mitochondrial-located splicing, suggesting that the yeast SEN complex surprisingly serves a novel and essential function in the cytoplasm that is unrelated to tRNA splicing. The novel function requires all four SEN complex subunits and the catalytic core. A subset of pre-rRNAs accumulates when the SEN complex is restricted to the nucleus, indicating that the SEN complex moonlights in rRNA processing. Thus, findings suggest that selection for the subcellular distribution of the SEN complex may reside not in its canonical, but rather in a novel, activity. PMID:22391451

CO(2) incorporation in hydroxide and hydroperoxide containing water clusters--a unifying mechanism for hydrolysis and protolysis.

PubMed

Ryding, Mauritz J; Uggerud, Einar

2014-05-28

The reactions of CO2 with anionic water clusters containing hydroxide, OH(-)(H2O)n, and hydroperoxide, HO2(-)(H2O)n, have been studied in the isolated state using a mass spectrometric technique. The OH(-)(H2O)n clusters were found to react faster for n = 2,3, while for n >3 the HO2(-)(H2O)n clusters are more reactive. Insights from quantum chemical calculations revealed a common mechanism in which the decisive bicarbonate-forming step starts from a pre-reaction complex where OH(-) and CO2 are separated by one water molecule. Proton transfer from the water molecule to OH(-) then effectively moves the hydroxide ion motif next to the CO2 molecule. A new covalent bond is formed between CO2 and the emerging OH(-) in concert with the proton transfer. For larger clusters, successive proton transfers from H2O molecules to neighbouring OH(-) are required to effectively bring about the formation of the pre-reaction complex, upon which bicarbonate formation is accomplished according to the concerted mechanism. In this manner, a general mechanism is suggested, also applicable to bulk water and thereby to CO2 uptake in oceans. Furthermore, this mechanism avoids the intermediate H2CO3 by combining the CO2 hydrolysis step and the protolysis step into one. The general mechanistic picture is consistent with low enthalpy barriers and that the limiting factors are largely of entropic nature.

Fusion Stage of HIV-1 Entry Depends on Virus-Induced Cell Surface Exposure of Phosphatidylserine.

PubMed

Zaitseva, Elena; Zaitsev, Eugene; Melikov, Kamran; Arakelyan, Anush; Marin, Mariana; Villasmil, Rafael; Margolis, Leonid B; Melikyan, Gregory B; Chernomordik, Leonid V

2017-07-12

HIV-1 entry into host cells starts with interactions between the viral envelope glycoprotein (Env) and cellular CD4 receptors and coreceptors. Previous work has suggested that efficient HIV entry also depends on intracellular signaling, but this remains controversial. Here we report that formation of the pre-fusion Env-CD4-coreceptor complexes triggers non-apoptotic cell surface exposure of the membrane lipid phosphatidylserine (PS). HIV-1-induced PS redistribution depends on Ca 2+ signaling triggered by Env-coreceptor interactions and involves the lipid scramblase TMEM16F. Externalized PS strongly promotes Env-mediated membrane fusion and HIV-1 infection. Blocking externalized PS or suppressing TMEM16F inhibited Env-mediated fusion. Exogenously added PS promoted fusion, with fusion dependence on PS being especially strong for cells with low surface density of coreceptors. These findings suggest that cell-surface PS acts as an important cofactor that promotes the fusogenic restructuring of pre-fusion complexes and likely focuses the infection on cells conducive to PS signaling. Published by Elsevier Inc.

Effects of pre-reproductive maternal enrichment on maternal care, offspring's play behavior and oxytocinergic neurons.

PubMed

Cutuli, Debora; Berretta, Erica; Caporali, Paola; Sampedro-Piquero, Patricia; De Bartolo, Paola; Laricchiuta, Daniela; Gelfo, Francesca; Pesoli, Matteo; Foti, Francesca; Farioli Vecchioli, Stefano; Petrosini, Laura

2018-02-17

Potentiating social, cognitive, and sensorimotor stimulations the Environmental Enrichment (EE) increases levels of novelty and complexity experienced by individuals. Growing evidence demonstrates that parental EE experience, even occurring in the pre-reproductive phase, affects behavioral and neural developmental trajectories of the offspring. To discover how the accumulation of early maternal complex experiences may inform and shape the social behavior of the following generation, we examined the effects of pre-reproductive enrichment of dams (post-natal days 21-72) on the play performances of their male and female adolescent offspring. Furthermore, we examined the effects of pre-reproductive enrichment on maternal behavior (during post-partum days 1-10) and male intruder aggression (on post-partum day 11). Since oxytocin modulates maternal care, social bonding, and agonistic behavior, the number of oxytocinergic neurons of the paraventricular (PVN) and supraoptic (SON) nuclei was examined in both dams and offspring. Results revealed that enriched females exhibited higher levels of pup-oriented behaviors, especially Crouching, and initiated pup-retrieval more quickly than standard females after the maternal aggression test. Such behavioral peculiarities were accompanied by increased levels of oxytocinergic neurons in PVN and SON. Moreover, pre-reproductive maternal EE cross-generationally influenced the offspring according to sex. Indeed, male pups born to enriched females exhibited a reduced play fighting associated with a higher number of oxytocinergic neurons in SON in comparison to male pups born to standard-housed females. In conclusion, pre-reproductive EE to the mothers affects their maternal care and has a cross-generational impact on the social behavior of their offspring that do not directly experiences EE. Copyright © 2018 Elsevier Ltd. All rights reserved.

Conditional Inactivation of Upstream Binding Factor Reveals Its Epigenetic Functions and the Existence of a Somatic Nucleolar Precursor Body

PubMed Central

Hamdane, Nourdine; Stefanovsky, Victor Y.; Tremblay, Michel G.; Németh, Attila; Paquet, Eric; Lessard, Frédéric; Sanij, Elaine; Hannan, Ross; Moss, Tom

2014-01-01

Upstream Binding Factor (UBF) is a unique multi-HMGB-box protein first identified as a co-factor in RNA polymerase I (RPI/PolI) transcription. However, its poor DNA sequence selectivity and its ability to generate nucleosome-like nucleoprotein complexes suggest a more generalized role in chromatin structure. We previously showed that extensive depletion of UBF reduced the number of actively transcribed ribosomal RNA (rRNA) genes, but had little effect on rRNA synthesis rates or cell proliferation, leaving open the question of its requirement for RPI transcription. Using gene deletion in mouse, we now show that UBF is essential for embryo development beyond morula. Conditional deletion in cell cultures reveals that UBF is also essential for transcription of the rRNA genes and that it defines the active chromatin conformation of both gene and enhancer sequences. Loss of UBF prevents formation of the SL1/TIF1B pre-initiation complex and recruitment of the RPI-Rrn3/TIF1A complex. It is also accompanied by recruitment of H3K9me3, canonical histone H1 and HP1α, but not by de novo DNA methylation. Further, genes retain penta-acetyl H4 and H2A.Z, suggesting that even in the absence of UBF the rRNA genes can maintain a potentially active state. In contrast to canonical histone H1, binding of H1.4 is dependent on UBF, strongly suggesting that it plays a positive role in gene activity. Unexpectedly, arrest of rRNA synthesis does not suppress transcription of the 5S, tRNA or snRNA genes, nor expression of the several hundred mRNA genes implicated in ribosome biogenesis. Thus, rRNA gene activity does not coordinate global gene expression for ribosome biogenesis. Loss of UBF also unexpectedly induced the formation in cells of a large sub-nuclear structure resembling the nucleolar precursor body (NPB) of oocytes and early embryos. These somatic NPBs contain rRNA synthesis and processing factors but do not associate with the rRNA gene loci (NORs). PMID:25121932

Translation Initiation Factor eIF4B Interacts with a Picornavirus Internal Ribosome Entry Site in both 48S and 80S Initiation Complexes Independently of Initiator AUG Location

PubMed Central

Ochs, Kerstin; Rust, René C.; Niepmann, Michael

1999-01-01

Most eukaryotic initiation factors (eIFs) are required for internal translation initiation at the internal ribosome entry site (IRES) of picornaviruses. eIF4B is incorporated into ribosomal 48S initiation complexes with the IRES RNA of foot-and-mouth disease virus (FMDV). In contrast to the weak interaction of eIF4B with capped cellular mRNAs and its release upon entry of the ribosomal 60S subunit, eIF4B remains tightly associated with the FMDV IRES during formation of complete 80S ribosomes. Binding of eIF4B to the IRES is energy dependent, and binding of the small ribosomal subunit to the IRES requires the previous energy-dependent association of initiation factors with the IRES. The interaction of eIF4B with the IRES in 48S and 80S complexes is independent of the location of the initiator AUG and thus independent of the mechanism by which the small ribosomal subunit is placed at the actual start codon, either by direct internal ribosomal entry or by scanning. eIF4B does not greatly rearrange its binding to the IRES upon entry of the ribosomal subunits, and the interaction of eIF4B with the IRES is independent of the polypyrimidine tract-binding protein, which enhances FMDV translation. PMID:10438840

Methods for applying accurate digital PCR analysis on low copy DNA samples.

PubMed

Whale, Alexandra S; Cowen, Simon; Foy, Carole A; Huggett, Jim F

2013-01-01

Digital PCR (dPCR) is a highly accurate molecular approach, capable of precise measurements, offering a number of unique opportunities. However, in its current format dPCR can be limited by the amount of sample that can be analysed and consequently additional considerations such as performing multiplex reactions or pre-amplification can be considered. This study investigated the impact of duplexing and pre-amplification on dPCR analysis by using three different assays targeting a model template (a portion of the Arabidopsis thaliana alcohol dehydrogenase gene). We also investigated the impact of different template types (linearised plasmid clone and more complex genomic DNA) on measurement precision using dPCR. We were able to demonstrate that duplex dPCR can provide a more precise measurement than uniplex dPCR, while applying pre-amplification or varying template type can significantly decrease the precision of dPCR. Furthermore, we also demonstrate that the pre-amplification step can introduce measurement bias that is not consistent between experiments for a sample or assay and so could not be compensated for during the analysis of this data set. We also describe a model for estimating the prevalence of molecular dropout and identify this as a source of dPCR imprecision. Our data have demonstrated that the precision afforded by dPCR at low sample concentration can exceed that of the same template post pre-amplification thereby negating the need for this additional step. Our findings also highlight the technical differences between different templates types containing the same sequence that must be considered if plasmid DNA is to be used to assess or control for more complex templates like genomic DNA.

Methods for Applying Accurate Digital PCR Analysis on Low Copy DNA Samples

PubMed Central

Whale, Alexandra S.; Cowen, Simon; Foy, Carole A.; Huggett, Jim F.

2013-01-01

Digital PCR (dPCR) is a highly accurate molecular approach, capable of precise measurements, offering a number of unique opportunities. However, in its current format dPCR can be limited by the amount of sample that can be analysed and consequently additional considerations such as performing multiplex reactions or pre-amplification can be considered. This study investigated the impact of duplexing and pre-amplification on dPCR analysis by using three different assays targeting a model template (a portion of the Arabidopsis thaliana alcohol dehydrogenase gene). We also investigated the impact of different template types (linearised plasmid clone and more complex genomic DNA) on measurement precision using dPCR. We were able to demonstrate that duplex dPCR can provide a more precise measurement than uniplex dPCR, while applying pre-amplification or varying template type can significantly decrease the precision of dPCR. Furthermore, we also demonstrate that the pre-amplification step can introduce measurement bias that is not consistent between experiments for a sample or assay and so could not be compensated for during the analysis of this data set. We also describe a model for estimating the prevalence of molecular dropout and identify this as a source of dPCR imprecision. Our data have demonstrated that the precision afforded by dPCR at low sample concentration can exceed that of the same template post pre-amplification thereby negating the need for this additional step. Our findings also highlight the technical differences between different templates types containing the same sequence that must be considered if plasmid DNA is to be used to assess or control for more complex templates like genomic DNA. PMID:23472156

High fluorescence emission of carboxylic acid functionalized polystyrene/BaTiO{sub 3} nanocomposites and rare earth metal complexes: Preparation and characterization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cao, X. T.; Showkat, A. M.; Wang, Z.

2015-03-30

Noble fluorescence nanocomposite compound based on barium titanate nanoparticles (BTO), polystyrene (PSt), and terbium ion (Tb{sup 3+}) was synthesized by a combination of surface-initiated reversible addition-fragmentation chain transfer (RAFT) polymerization, Friedel-Crafts alkylation reaction and coordinate chemistry. Initially, a modification of surface of BTO was conducted by an exchange process with S-benzyl S’-trimethoxysilylpropyltrithiocarbonate to create macro-initiator for polymerization of styrene. Subsequently, aryl carboxylic acid functionalized polystyrene grafted barium titanate (BTO-g-PSt-COOH) was generated by substitution reaction between 4-(Chloromethyl) benzoic acid and PSt chains. The coordination of the nanohybrids with Tb{sup 3+} ions afforded fluorescent Tb{sup 3+} tagged aryl carboxylic acid functionalized polystyrenemore » grafted barium titanate (BTO-g-PSt-Tb{sup 3+}) complexes. Structure, morphology, and fluorescence properties of nanohybrid complexes were investigated by respective physical and spectral studies. FT-IR and SEM analyses confirmed the formation of BTO-g-PSt-Tb{sup 3+}nanohybrids. Furthermore, TGA profiles demonstrated the grafting of aryl carboxylic acid functionalized polystyrene on BTO surface. Optical properties of BTO-g-PSt-Tb{sup 3+} complexes were investigated by fluorescence spectroscopy.« less

Chemical Impact of Solar Energetic Particle Event From The Young Sun: Implications for the Origin of Prebiotic Chemistry and the Fain Young Sun Paradox

NASA Astrophysics Data System (ADS)

Airapetian, V.; Gronoff, G.; Hébrard, E.; Danchi, W.

2015-12-01

Understanding how the simple molecules present on the early Earth and possibly Mars may have set a path for complex biological molecules, the building blocks of life, represents one of greatest unsolved questions. Here we present a new model of the rise of the abiotic nitrogen fixation and associated pre-biotic chemistry in the early Earth and Mars atmosphere mediated by solar eruptive events. Our physical models of interaction of magnetic clouds ejected from the young Sun with magnetospheres of the early Earth show significant perturbations of geomagnetic fields that produce extended polar caps. These polar caps provide pathways for energetic particles associated with magnetic clouds to penetrate into the nitrogen-rich weakly reducing atmosphere and initiate the reactive chemistry by breaking molecular nitrogen, carbon dioxide, methane and producing hydrogen cyanide, the essential compound for life. The model also shows that contrary to the current models of warming of early Earth and Mars, major atmospheric constituents, CO2 and CH4 will be destroyed due to collisional dissociation with energetic particles. Instead, efficient formation of the potent greenhouse gas, nitrous oxide, as a by-product of these processes is expected. This mechanism can consistently explain the Faint Young Sun's paradox for the early atmospheres of Earth and Mars. Our new model provides insight into how life may have initiated on Earth and Mars and how to search for the spectral signatures on planets "pregnant" with the potential for life.

Patient participation in cancer clinical trials: A pilot test of lay navigation.

PubMed

Cartmell, Kathleen B; Bonilha, Heather S; Matson, Terri; Bryant, Debbie C; Zapka, Jane G; Bentz, Tricia A; Ford, Marvella E; Hughes-Halbert, Chanita; Simpson, Kit N; Alberg, Anthony J

2016-08-15

Clinical trials (CT) represent an important treatment option for cancer patients. Unfortunately, patients face challenges to enrolling in CTs, such as logistical barriers, poor CT understanding and complex clinical regimens. Patient navigation is a strategy that may help to improve the delivery of CT education and support services. We examined the feasibility and initial effect of one navigation strategy, use of lay navigators. A lay CT navigation intervention was evaluated in a prospective cohort study among 40 lung and esophageal cancer patients. The intervention was delivered by a trained lay navigator who viewed a 17-minute CT educational video with each patient, assessed and answered their questions about CT participation and addressed reported barriers to care and trial participation. During this 12-month pilot project, 85% (95% CI: 72%-93%) of patients eligible for a therapeutic CT consented to participate in the CT navigation intervention. Among navigated patients, CT understanding improved between pre- and post-test (means 3.54 and 4.40, respectively; p-value 0.004), and 95% (95% CI: 82%-98%) of navigated patients consented to participate in a CT. Navigated patients reported being satisfied with patient navigation services and CT participation. In this formative single-arm pilot project, initial evidence was found for the potential effect of a lay navigation intervention on CT understanding and enrollment. A randomized controlled trial is needed to examine the efficacy of the intervention for improving CT education and enrollment.

Subsolidus migmatization in high-grade meta-tuffs (Kurkijärvi, southwest Finland)

NASA Astrophysics Data System (ADS)

Blom, K. A.

1988-07-01

The phenomenon of migmatization was studied in Precambrian metavolcanic gneisses of calc-alkaline chemistry, outcropping along a prograde amphibolite/granulite facies transition in the West Uusimaa Complex of SW Finland. This paper discusses one of the studied gneiss levels (a garnet-bearing Qtz/Plag/Ksp/Bio-gneiss) which was observed to transsect the metamorphic isograd pattern at almost right angle. The gneiss was studied for structures, whole-rock chemistry (major, trace and REE), mineral content, microtextures, plagioclase anorthite content and fluid inclusions. Data concerning the latter four subjects are presented. Migmatization proved to: (1) have occurred parallel to compositional banding of the rocks; (2) have produced identical leucosome/melanosome/mesosome mineral parageneses; (3) have initiated feldspar/garnet-poikiloblasthesis (and occasionally biotite porphyroblasthesis) in leucosome, and biotite-/garnet-poikiloblasthesis in melanosome; (4) have caused entrapment of unstrained quartz blebs carrying isolated (primary) two-phase pure H 2O fluid inclusions of unique filling degree range in the above-mentioned feldspar- and garnet-poikiloblasts; (5) have occurred post-D 1/pre-D 2, synchronous to amphibolitefacies metamorphism, in the subsolidus regime; (6) have been affected by D 2 in the way of localized mylonitization of the melanosome, and quartz migration (exudation) from adjacent mesosome into leucosome; and (7) have had some control by the biotite content of the original compositionally banded rock. Initial leucosome formation appears to have been controlled by the pre-leucosome biotite content: the recalculated modal biotite content of the leucosome/melanosome combination conspicuously is in the range of 5-20 vol.% of biotite. Final extent of the leucosome shows on its turn a marked correlation with mesosome modal biotite content. Because leucosomes occur carrying a recalculated modal biotite content equalling adjacent mesosome biotite content, a second factor is held responsible for the onset of migmatization in the buried and sheared rock: deficient water balance. Migmatization, initiated at {P}/{T} conditions fit for feldspar recrystallization and almandine formation, was induced during prograde metamorphism to cancel an established zonation in water pressure or water content parallel to compositional banding. Zones of low PH 2O or wt.% H 2O thereby were converted into leucosomes, while zones of higher PH 2O or wt.% H 2O remained unaffected (and became mesosome). That XH 2O did not vary at the onset of migmatization is recorded in the isolated pure H 2O fluid inclusions contained in the quartz blebs enclosed in the studied leucosome- and melanosome-poikiloblasts. Restore of water balance (either by internally controlled factors or externally introduced ones) halted migmatization and its obliteration of compositional banding.

Architecture of human translation initiation factor 3

PubMed Central

Querol-Audi, Jordi; Sun, Chaomin; Vogan, Jacob M.; Smith, Duane; Gu, Yu; Cate, Jamie; Nogales, Eva

2013-01-01

SUMMARY Eukaryotic translation initiation factor 3 (eIF3) plays a central role in protein synthesis by organizing the formation of the 43S preinitiation complex. Using genetic tag visualization by electron microscopy, we reveal the molecular organization of ten human eIF3 subunits, including an octameric core. The structure of eIF3 bears a close resemblance to that of the proteasome lid, with a conserved spatial organization of eight core subunits containing PCI and MPN domains that coordinate functional interactions in both complexes. We further show that eIF3 subunits a and c interact with initiation factors eIF1 and eIF1A, which control the stringency of start codon selection. Finally, we find that subunit j, which modulates messenger RNA interactions with the small ribosomal subunit, makes multiple independent interactions with the eIF3 octameric core. These results highlight the conserved architecture of eIF3 and how it scaffolds key factors that control translation initiation in higher eukaryotes, including humans. PMID:23623729

A world of opportunities with nanopore sequencing.

PubMed

Leggett, Richard M; Clark, Matthew D

2017-11-28

Oxford Nanopore Technologies' MinION sequencer was launched in pre-release form in 2014 and represents an exciting new sequencing paradigm. The device offers multi-kilobase reads and a streamed mode of operation that allows processing of reads as they are generated. Crucially, it is an extremely compact device that is powered from the USB port of a laptop computer, enabling it to be taken out of the lab and facilitating previously impossible in-field sequencing experiments to be undertaken. Many of the initial publications concerning the platform focused on provision of tools to access and analyse the new sequence formats and then demonstrating the assembly of microbial genomes. More recently, as throughput and accuracy have increased, it has been possible to begin work involving more complex genomes and metagenomes. With the release of the high-throughput GridION X5 and PromethION platforms, the sequencing of large genomes will become more cost efficient, and enable the leveraging of extremely long (>100 kb) reads for resolution of complex genomic structures. This review provides a brief overview of nanopore sequencing technology, describes the growing range of nanopore bioinformatics tools, and highlights some of the most influential publications that have emerged over the last 2 years. Finally, we look to the future and the potential the platform has to disrupt work in human, microbiome, and plant genomics. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

The Arctic Regional Communications Small SATellite (ARCSAT)

NASA Technical Reports Server (NTRS)

Casas, Joseph; Kress, Martin; Sims, William; Spehn, Stephen; Jaeger, Talbot; Sanders, Devon

2013-01-01

Traditional satellite missions are extremely complex and expensive to design, build, test, launch and operate. Consequently many complementary operational, exploration and research satellite missions are being formulated as a growing part of the future space community capabilities using formations of small, distributed, simple to launch and inexpensive highly capable small scale satellites. The Arctic Regional Communications small SATellite (ARCSAT) initiative would launch a Mini-Satellite "Mothership" into Polar or Sun Sync low-earth-orbit (LEO). Once on orbit, the Mothership would perform orbital insertion of four internally stored independently maneuverable nanosatellites, each containing electronically steerable antennas and reconfigurable software-defined radios. Unlike the traditional geostationary larger complex satellite communication systems, this LEO communications system will be comprised of initially a five small satellite formation that can be later incrementally increased in the total number of satellites for additional data coverage. ARCSAT will provide significant enabling capabilities in the Arctic for autonomous voice and data communications relay, Maritime Domain Awareness (MDA), data-extraction from unattended sensors, and terrestrial Search & Rescue (SAR) beacon detection missions throughout the "data starved desert" of the Arctic Region.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Horn, Paul R., E-mail: prhorn@berkeley.edu; Mao, Yuezhi; Head-Gordon, Martin, E-mail: mhg@cchem.berkeley.edu

In energy decomposition analysis of Kohn-Sham density functional theory calculations, the so-called frozen (or pre-polarization) interaction energy contains contributions from permanent electrostatics, dispersion, and Pauli repulsion. The standard classical approach to separate them suffers from several well-known limitations. We introduce an alternative scheme that employs valid antisymmetric electronic wavefunctions throughout and is based on the identification of individual fragment contributions to the initial supersystem wavefunction as determined by an energetic optimality criterion. The density deformations identified with individual fragments upon formation of the initial supersystem wavefunction are analyzed along with the distance dependence of the new and classical terms formore » test cases that include the neon dimer, ammonia borane, water-Na{sup +}, water-Cl{sup −}, and the naphthalene dimer.« less

Pre-Columbian agricultural landscapes, ecosystem engineers, and self-organized patchiness in Amazonia.

PubMed

McKey, Doyle; Rostain, Stéphen; Iriarte, José; Glaser, Bruno; Birk, Jago Jonathan; Holst, Irene; Renard, Delphine

2010-04-27

The scale and nature of pre-Columbian human impacts in Amazonia are currently hotly debated. Whereas pre-Columbian people dramatically changed the distribution and abundance of species and habitats in some parts of Amazonia, their impact in other parts is less clear. Pioneer research asked whether their effects reached even further, changing how ecosystems function, but few in-depth studies have examined mechanisms underpinning the resilience of these modifications. Combining archeology, archeobotany, paleoecology, soil science, ecology, and aerial imagery, we show that pre-Columbian farmers of the Guianas coast constructed large raised-field complexes, growing on them crops including maize, manioc, and squash. Farmers created physical and biogeochemical heterogeneity in flat, marshy environments by constructing raised fields. When these fields were later abandoned, the mosaic of well-drained islands in the flooded matrix set in motion self-organizing processes driven by ecosystem engineers (ants, termites, earthworms, and woody plants) that occur preferentially on abandoned raised fields. Today, feedbacks generated by these ecosystem engineers maintain the human-initiated concentration of resources in these structures. Engineer organisms transport materials to abandoned raised fields and modify the structure and composition of their soils, reducing erodibility. The profound alteration of ecosystem functioning in these landscapes coconstructed by humans and nature has important implications for understanding Amazonian history and biodiversity. Furthermore, these landscapes show how sustainability of food-production systems can be enhanced by engineering into them follows that maintain ecosystem services and biodiversity. Like anthropogenic dark earths in forested Amazonia, these self-organizing ecosystems illustrate the ecological complexity of the legacy of pre-Columbian land use.

Pre-Columbian agricultural landscapes, ecosystem engineers, and self-organized patchiness in Amazonia

PubMed Central

McKey, Doyle; Rostain, Stéphen; Iriarte, José; Glaser, Bruno; Birk, Jago Jonathan; Holst, Irene; Renard, Delphine

2010-01-01

The scale and nature of pre-Columbian human impacts in Amazonia are currently hotly debated. Whereas pre-Columbian people dramatically changed the distribution and abundance of species and habitats in some parts of Amazonia, their impact in other parts is less clear. Pioneer research asked whether their effects reached even further, changing how ecosystems function, but few in-depth studies have examined mechanisms underpinning the resilience of these modifications. Combining archeology, archeobotany, paleoecology, soil science, ecology, and aerial imagery, we show that pre-Columbian farmers of the Guianas coast constructed large raised-field complexes, growing on them crops including maize, manioc, and squash. Farmers created physical and biogeochemical heterogeneity in flat, marshy environments by constructing raised fields. When these fields were later abandoned, the mosaic of well-drained islands in the flooded matrix set in motion self-organizing processes driven by ecosystem engineers (ants, termites, earthworms, and woody plants) that occur preferentially on abandoned raised fields. Today, feedbacks generated by these ecosystem engineers maintain the human-initiated concentration of resources in these structures. Engineer organisms transport materials to abandoned raised fields and modify the structure and composition of their soils, reducing erodibility. The profound alteration of ecosystem functioning in these landscapes coconstructed by humans and nature has important implications for understanding Amazonian history and biodiversity. Furthermore, these landscapes show how sustainability of food-production systems can be enhanced by engineering into them fallows that maintain ecosystem services and biodiversity. Like anthropogenic dark earths in forested Amazonia, these self-organizing ecosystems illustrate the ecological complexity of the legacy of pre-Columbian land use. PMID:20385814

Structural development of the Red Hill portion of the Feather River ultramafic complex, Pulmas County, California

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weisenberg, C.W.

1979-01-01

The Feather River Ultramafic Complex is a partially serpentinized body of metamorphosed alpine peridotite and gabbro that lies along the northern part of the Melones fault zone, a NNW trending belt in the Northern Sierra Nevada. The complex was studied in the area of Red Hill, near the canyon of the North Fork, Feather River. The complex is separated from the Calaveras Terrain and Arlington Formation country rocks by steep faults; the Melones Fault on the east and the Rich Bar Fault on the west. Units recognized within the complex include Rich Bar metamorphic rocks, peridotite, metaperidotite, tremolite-olivine schist, hornblendemore » schist, and layered metagabbro. The Rich Bar metamorphic rocks are tectonic slices of amphibolite grade hornblende schist, mica schist, and quartzite found along the Rich Bar Fault. The complex shows evidence of 4 major events. E-1 (Pennsylvania-Permian) was formation of the peridotite-gabbro complex. E-2 (Permo-Triassic) consisted of pervasive shearing parallel to the Rich Bar Fault associated with initial emplacement within the Sierra Nevada. E-3 is believed to be compression and metamorphism (serpentinization) associated with the Nevadan orogeny. E-4 was associated with intrusion of nearby plutons. The regional association of the complex with late paleozoic arc volcanics of the Taylorsville area suggest formation near or under an island arc. Metamorphism during emplacement indicates association with the arc at that time. Left-lateral shear during emplacement along the Rich Bar Fault indicates NW directed thrusting when the layering in metagabbro is rotated to horizontal.« less

A Supramolecular Approach for Liver Radioembolization

PubMed Central

Spa, Silvia J.; Welling, Mick M.; van Oosterom, Matthias N.; Rietbergen, Daphne D. D.; Burgmans, Mark C.; Verboom, Willem; Huskens, Jurriaan; Buckle, Tessa; van Leeuwen, Fijs W. B.

2018-01-01

Hepatic radioembolization therapies can suffer from discrepancies between diagnostic planning (scout-scan) and the therapeutic delivery itself, resulting in unwanted side-effects such as pulmonary shunting. We reasoned that a nanotechnology-based pre-targeting strategy could help overcome this shortcoming by directly linking pre-interventional diagnostics to the local delivery of therapy. Methods: The host-guest interaction between adamantane and cyclodextrin was employed in an in vivo pre-targeting set-up. Adamantane (guest)-functionalized macro albumin aggregates (MAA-Ad; d = 18 μm) and (radiolabeled) Cy5 and β-cyclodextrin (host)-containing PIBMA polymers (99mTc-Cy50.5CD10PIBMA39; MW ~ 18.8 kDa) functioned as the reactive pair. Following liver or lung embolization with (99mTc)-MAA-Ad or (99mTc)-MAA (control), the utility of the pre-targeting concept was evaluated after intravenous administration of 99mTc-Cy50.5CD10PIBMA39. Results: Interactions between MAA-Ad and Cy50.5CD10PIBMA39 could be monitored in solution using confocal microscopy and were quantified by radioisotope-based binding experiments. In vivo the accumulation of the MAA-Ad particles in the liver or lungs yielded an approximate ten-fold increase in accumulation of 99mTc-Cy50.5CD10PIBMA39 in these organs (16.2 %ID/g and 10.5 %ID/g, respectively) compared to the control. Pre-targeting with MAA alone was shown to be only half as efficient. Uniquely, for the first time, this data demonstrates that the formation of supramolecular interactions between cyclodextrin and adamantane can be used to drive complex formation in the chemically challenging in vivo environment. Conclusion: The in vivo distribution pattern of the cyclodextrin host could be guided by the pre-administration of the adamantane guest, thereby creating a direct link between the scout-scan (MAA-Ad) and delivery of therapy. PMID:29721086

New insights from an old mutant: SPADIX4 governs fruiting body development but not hyphal fusion in Sordaria macrospora.

PubMed

Teichert, Ines; Lutomski, Miriam; Märker, Ramona; Nowrousian, Minou; Kück, Ulrich

2017-02-01

During the sexual life cycle of filamentous fungi, multicellular fruiting bodies are generated for the dispersal of spores. The filamentous ascomycete Sordaria macrospora has a long history as a model system for studying fruiting body formation, and two collections of sterile mutants have been generated. However, for most of these mutants, the underlying genetic defect remains unknown. Here, we investigated the mutant spadix (spd) that was generated by X-ray mutagenesis in the 1950s and terminates sexual development after the formation of pre-fruiting bodies (protoperithecia). We sequenced the spd genome and found a 22 kb deletion affecting four genes, which we termed spd1-4. Generation of deletion strains revealed that only spd4 is required for fruiting body formation. Although sterility in S. macrospora is often coupled with a vegetative hyphal fusion defect, Δspd4 was still capable of fusion. This feature distinguishes SPD4 from many other regulators of sexual development. Remarkably, GFP-tagged SPD4 accumulated in the nuclei of vegetative hyphae and fruiting body initials, the ascogonial coils, but not in sterile tissue from the developing protoperithecium. Our results point to SPD4 as a specific determinant of fruiting body formation. Research on SPD4 will, therefore, contribute to understanding cellular reprogramming during initiation of sexual development in fungi.

Rate and yield relationships in the production of xanthan gum by batch fermentations using complex and chemically defined growth media

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pinches, A.; Pallent, L.J.

1986-10-01

Rate and yield information relating to biomass and product formation and to nitrogen, glucose and oxygen consumption are described for xanthan gum batch fermentations in which both chemically defined (glutamate nitrogen) and complex (peptone nitrogen) media are employed. Simple growth and product models are used for data interpretation. For both nitrogen sources, rate and yield parameter estimates are shown to be independent of initial nitrogen concentrations. For stationary phases, specific rates of gum production are shown to be independent of nitrogen source but dependent on initial nitrogen concentration. The latter is modeled empirically and suggests caution in applying simple productmore » models to xanthan gum fermentations. 13 references.« less

Modelling Fault Zone Evolution: Implications for fluid flow.

NASA Astrophysics Data System (ADS)

Moir, H.; Lunn, R. J.; Shipton, Z. K.

2009-04-01

Flow simulation models are of major interest to many industries including hydrocarbon, nuclear waste, sequestering of carbon dioxide and mining. One of the major uncertainties in these models is in predicting the permeability of faults, principally in the detailed structure of the fault zone. Studying the detailed structure of a fault zone is difficult because of the inaccessible nature of sub-surface faults and also because of their highly complex nature; fault zones show a high degree of spatial and temporal heterogeneity i.e. the properties of the fault change as you move along the fault, they also change with time. It is well understood that faults influence fluid flow characteristics. They may act as a conduit or a barrier or even as both by blocking flow across the fault while promoting flow along it. Controls on fault hydraulic properties include cementation, stress field orientation, fault zone components and fault zone geometry. Within brittle rocks, such as granite, fracture networks are limited but provide the dominant pathway for flow within this rock type. Research at the EU's Soultz-sous-Forệt Hot Dry Rock test site [Evans et al., 2005] showed that 95% of flow into the borehole was associated with a single fault zone at 3490m depth, and that 10 open fractures account for the majority of flow within the zone. These data underline the critical role of faults in deep flow systems and the importance of achieving a predictive understanding of fault hydraulic properties. To improve estimates of fault zone permeability, it is important to understand the underlying hydro-mechanical processes of fault zone formation. In this research, we explore the spatial and temporal evolution of fault zones in brittle rock through development and application of a 2D hydro-mechanical finite element model, MOPEDZ. The authors have previously presented numerical simulations of the development of fault linkage structures from two or three pre-existing joints, the results of which compare well to features observed in mapped exposures. For these simple simulations from a small number of pre-existing joints the fault zone evolves in a predictable way: fault linkage is governed by three key factors: Stress ratio of s1 (maximum compressive stress) to s3(minimum compressive stress), original geometry of the pre-existing structures (contractional vs. dilational geometries) and the orientation of the principle stress direction (σ1) to the pre-existing structures. In this paper we present numerical simulations of the temporal and spatial evolution of fault linkage structures from many pre-existing joints. The initial location, size and orientations of these joints are based on field observations of cooling joints in granite from the Sierra Nevada. We show that the constantly evolving geometry and local stress field perturbations contribute significantly to fault zone evolution. The location and orientations of linkage structures previously predicted by the simple simulations are consistent with the predicted geometries in the more complex fault zones, however, the exact location at which individual structures form is not easily predicted. Markedly different fault zone geometries are predicted when the pre-existing joints are rotated with respect to the maximum compressive stress. In particular, fault surfaces range from evolving smooth linear structures to producing complex ‘stepped' fault zone geometries. These geometries have a significant effect on simulations of along and across-fault flow.

Influence of riparian vegetation on channel widening and subsequent contraction on a sand-bed stream since European settlement: Widden Brook, Australia

NASA Astrophysics Data System (ADS)

Erskine, Wayne; Keene, Annabelle; Bush, Richard; Cheetham, Michael; Chalmers, Anita

2012-04-01

Widden Brook in the Hunter Valley, Australia, was first settled by Europeans in 1831 and had widened substantially by the 1870s due to frequent floods during a flood-dominated regime impacting on highly disturbed banks whose riparian trees had been either ringbarked or cleared, and whose understorey had been grazed. Catastrophic floods in 1950 (many), two in August 1952 and one in February 1955 effected the final phase of channel widening at the onset of a second flood-dominated regime more than half a century after the initial widening. Contraction has been active since 1963 by a combination of five biogeomorphic processes. Firstly, rapid channel widening, migration and cutoffs totally reworked the pre-European floodplain and were followed by active floodplain formation. Initial bar formation was replaced by sand splay and overbank deposition which constructed a new floodplain and narrower channel. Secondly, overwidened channel segments that were produced by the catastrophic 1955 flood have contracted since 1963 by the formation of up to four bank-attached, discontinuous benches below the floodplain. Each bench has a bar nucleus of pebbly coarse sand overlain by stratified fine-medium sand and mud. Colonisation by River Sheoaks (Casuarina cunninghamiana subsp. cunninghamiana) or grasses (Cynodon dactylon, Paspalum distichum, Pennisetum clandestinum) is important in converting bars to benches. Thirdly, narrower segments which developed since 1963 have contracted by small-scale accretion on both banks. These deposits are steeply dipping, interbedded sand and mud trapped by stoloniferous and rhizomatous grasses (C. dactylon, P. distichum, P. clandestinum) which also rapidly stabilise the deposits. Fourthly, rare laterally migrating, small radius bends have contracted by recent point bar formation greatly exceeding cutbank recession rates. Point bar formation is controlled by secondary currents producing inclined stratified coarse sands without the influence of vegetation. Lastly, rare, overwidened, non-migrating, large radius bends have greatly contracted by the infilling of dissecting chutes across the convex bank. Establishment of stoloniferous and rhizomatous clonal grasses (Phragmites australis, C. dactylon, P. distichum, P. clandestinum) is important in inducing sedimentation of the chutes. Contraction has produced a much narrower channel than the design width between river training fences which were installed progressively between the 1960s and 1990s. The recent flood history of Widden Brook has not included any catastrophic floods of a size similar to February 1955. Our work demonstrates that both trees and grasses can be associated with narrower channel widths and that the causal link between width and vegetation type is more complex than usually acknowledged.

Aluminum and Fenton reaction: how can the reaction be modulated by speciation? A computational study using citrate as a test case.

PubMed

Mujika, Jon I; Dalla Torre, Gabriele; Lopez, Xabier

2018-06-13

The pro-oxidant ability of aluminum is behind many of the potential toxic effects of this exogenous element in the human organism. Although the overall process is still far from being understood at the molecular level, the well known ability of aluminum to promote the Fenton reaction is mediated through the formation of stable aluminum-superoxide radical complexes. However, the properties of metal complexes are highly influenced by the speciation of the metal. In this paper, we investigate the effect that speciation could have on the pro-oxidant activity of aluminum. We choose citrate as a test case, because it is the main low-molecular-mass chelator of aluminum in blood serum, forming very stable aluminum-citrate complexes. The influence of citrate in the interaction of aluminum with the superoxide radical is investigated, determining how the formation of aluminum-citrate complexes affects the promotion of the Fenton reaction. The results indicate that citrate increases the stability of the aluminum-superoxide complexes through the formation of ternary compounds, and that the Fenton reaction is even more favorable when aluminum is chelated to citrate. Nevertheless, our results demonstrate that overall, citrate may prevent the pro-oxidant activity of aluminum: on one hand, in an excess of citrate, the formation of 1 : 2 aluminum-citrate complexes is expected. On the other hand, the chelation of iron by citrate makes the reduction of iron thermodynamically unfavorable. In summary, the results suggest that citrate can have both a promotion and protective role, depending on subtle factors, such as initial concentration, non-equilibrium behavior and the exchange rate of ligands in the first shell of the metals.

Cdc6 localizes to S- and G2-phase centrosomes in a cell cycle-dependent manner

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Gwang Su; Kang, Jeeheon; Bang, Sung Woong

2015-01-16

Highlights: • Cdc6 protein is a component of the pre-replicative complex required for chromosomal replication initiation. • Cdc6 localized to centrosomes of S and G2 phases in a cell cycle-dependent manner. • The centrosomal localization was governed by centrosomal localization signal sequences of Cdc6. • Deletions or substitution mutations on the centrosomal localization signal interfered with centrosomal localization of the Cdc6 proteins. - Abstract: The Cdc6 protein has been primarily investigated as a component of the pre-replicative complex for the initiation of chromosome replication, which contributes to maintenance of chromosomal integrity. Here, we show that Cdc6 localized to the centrosomesmore » during S and G2 phases of the cell cycle. The centrosomal localization was mediated by Cdc6 amino acid residues 311–366, which are conserved within other Cdc6 homologues and contains a putative nuclear export signal. Deletions or substitutions of the amino acid residues did not allow the proteins to localize to centrosomes. In contrast, DsRed tag fused to the amino acid residues localized to centrosomes. These results indicated that a centrosome localization signal is contained within amino acid residues 311–366. The cell cycle-dependent centrosomal localization of Cdc6 in S and G2 phases suggest a novel function of Cdc6 in centrosomes.« less

Triggering and dynamic evolution of the LUSI mud volcano, Indonesia

NASA Astrophysics Data System (ADS)

Svensen, H.; Mazzini, A.; Akhmanov, G. G.; Aloisi, G.; Planke, S.; Sørenssen, A.; Istadi, B.

2007-12-01

Mud volcanoes are geologically important manifestations of vertical fluid flow and mud eruption in sedimentary basins worldwide. Their formation is predominantly ascribed to release of overpressure from clay- and organic- rich sediments, leading to impressive buildup of mud mountains in submarine and subaerial settings. Here we report data from two fieldworks on a newly born mud volcano named LUSI eruption in Eastern Java (Indonesia). The eruption site appears close to an active magmatic complex in a backarc sedimentary basin in Indonesia. Its specific location results in a high background temperature gradient that triggers mineralogical transformations and geochemical reactions at shallow depth. The eruption of 100 deg.C mud and gas that started the 29th of May 2006 flooded a large area within the Sidoarjo village in Northeast Java. Thousands of people have so far been evacuated and, since the initial eruption, the flow rate escalated from 5000 to 120,000 m3/d during the first eleven weeks. Then the erupted volume started to pulsate between almost zero and 120,000 m3/d in the period August-September, whereas it increased dramatically following swarms of earthquakes in September, before reaching almost 180,000 m3/d in December 2006. Fifteen months after the initial burst, LUSI is still vigorously erupting up to 111,000 m3/d, the average subsidence of the area reached 11 m. Seismic images show that a pre-existing structure was present before the eruption. Based on geochemical and field results, we propose a mechanism where the eruptions started following the 27th of May earthquake due to fracturing and accompanied depressurization of >100 deg.C pore fluids from > 1700 m depth released from a structure in already critical conditions. This resulted in the formation of a quasi-hydrothermal system with a geyser-like surface expression and with an activity influenced by the regional seismicity.

Bursting Transition Dynamics Within the Pre-Bötzinger Complex

NASA Astrophysics Data System (ADS)

Duan, Lixia; Chen, Xi; Tang, Xuhui; Su, Jianzhong

The pre-Bötzinger complex of the mammalian brain stem plays a crucial role in the respiratory rhythms generation. Neurons within the pre-Bötzinger complex have been found experimentally to yield different firing activities. In this paper, we study the spiking and bursting activities related to the respiratory rhythms in the pre-Bötzinger complex based on a mathematical model proposed by Butera. Using the one-dimensional first recurrence map induced by dynamics, we investigate the different bursting patterns and their transition of the pre-Bötzinger complex neurons based on the Butera model, after we derived a one-dimensional map from the dynamical characters of the differential equations, and we obtained conditions for the transition of different bursting patterns. These analytical results were verified through numerical simulations. We conclude that the one-dimensional map contains similar rhythmic patterns as the Butera model and can be used as a simpler modeling tool to study fast-slow models like pre-Bötzinger complex neural circuit.

Hierarchical Model for the Evolution of Cloud Complexes

NASA Astrophysics Data System (ADS)

Sánchez D., Néstor M.; Parravano, Antonio

1999-01-01

The structure of cloud complexes appears to be well described by a tree structure (i.e., a simplified ``stick man'') representation when the image is partitioned into ``clouds.'' In this representation, the parent-child relationships are assigned according to containment. Based on this picture, a hierarchical model for the evolution of cloud complexes, including star formation, is constructed. The model follows the mass evolution of each substructure by computing its mass exchange with its parent and children. The parent-child mass exchange (evaporation or condensation) depends on the radiation density at the interphase. At the end of the ``lineage,'' stars may be born or die, so that there is a nonstationary mass flow in the hierarchical structure. For a variety of parameter sets the system follows the same series of steps to transform diffuse gas into stars, and the regulation of the mass flux in the tree by previously formed stars dominates the evolution of the star formation. For the set of parameters used here as a reference model, the system tends to produce initial mass functions (IMFs) that have a maximum at a mass that is too high (~2 Msolar) and the characteristic times for evolution seem too long. We show that these undesired properties can be improved by adjusting the model parameters. The model requires further physics (e.g., allowing for multiple stellar systems and clump collisions) before a definitive comparison with observations can be made. Instead, the emphasis here is to illustrate some general properties of this kind of complex nonlinear model for the star formation process. Notwithstanding the simplifications involved, the model reveals an essential feature that will likely remain if additional physical processes are included, that is, the detailed behavior of the system is very sensitive to the variations on the initial and external conditions, suggesting that a ``universal'' IMF is very unlikely. When an ensemble of IMFs corresponding to a variety of initial or external conditions is examined, the slope of the IMF at high masses shows variations comparable to the range derived from observational data. These facts suggest that the considered physical processes (phase transitions regulated by the radiation field) may play a role in the global evolution of molecular complexes.

Baseline groundwater chemistry characterization in an area of future Marcellus shale gas development

NASA Astrophysics Data System (ADS)

Eisenhauer, P.; Zegre, N.; Edwards, P. J.; Strager, M.

2012-12-01

The recent increase in development of the Marcellus shale formation for natural gas in the mid-Atlantic can be attributed to advances in unconventional extraction methods, namely hydraulic fracturing, a process that uses water to pressurize and fracture relatively impermeable shale layers to release natural gas. In West Virginia, the Department of Energy estimates 95 to 105 trillion cubic feet (TCF) of expected ultimately recovery (EUR) of natural gas for this formation. With increased development of the Marcellus shale formation comes concerns for the potential of contamination to groundwater resources that serve as primary potable water sources for many rural communities. However, the impacts of this practice on water resources are poorly understood because of the lack of controlled pre versus post-drilling experiments attributed to the rapid development of this resource. To address the knowledge gaps of the potential impacts of Marcellus shale development on groundwater resources, a pre versus post-drilling study has been initiated by the USFS Fernow Experimental Forest in the Monongahela National Forest. Drilling is expected to start at three locations within the next year. Pre-drilling water samples were collected and analyzed from two groundwater wells, a shallow spring, a nearby lake, and river to characterize background water chemistry and identify potential end-members. Geochemical analysis includes major ions, methane, δ13C-CH4, δ2H-CH4, 226Radium, and δ13C-DIC. In addition, a GIS-based conceptual ground water flow model was developed to identify possible interactions between shallow groundwater and natural gas wells given gas well construction failure. This model is used to guide management decisions regarding groundwater resources in an area of increasing shale gas development.

The Effects of Pre-Task Planning and On-line Planning on Fluency, Complexity, and Accuracy in L2 Monologic Oral Production.

ERIC Educational Resources Information Center

Yuan, Fangyuan; Ellis, Rod

2003-01-01

Investigated the effects of both pre-task and on-line planning on second language (L2) oral production. Results show that pre-task planning enhances grammatical complexity while on-line planning positively influences accuracy and grammatical complexity. Pre-task planners also produced more fluent and lexically varied language than the on-line…

18 CFR 50.3 - Applications/pre-filing; rules and format.

Code of Federal Regulations, 2010 CFR

2010-04-01

... filings must be signed in compliance with § 385.2005 of this chapter. (e) The Commission will conduct a... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Applications/pre-filing... INTERSTATE ELECTRIC TRANSMISSION FACILITIES § 50.3 Applications/pre-filing; rules and format. (a) Filings are...

Facile NOx interconversion over preoxidized Ag(111)

NASA Astrophysics Data System (ADS)

Klacar, S.; Martin, N. M.; Gustafson, J.; Blomberg, S.; Liu, Z.; Axnanda, S.; Chang, R.; Lundgren, E.; Grönbeck, H.

2013-11-01

X-ray photoelectron spectroscopy and density functional theory calculations are used to investigate NO adsorption at low (100 K) and room temperature (RT) over preoxidized Ag(111). At 100 K, the data indicates presence of NO and N2O2, with little or no nitrite/nitrate formation. This is consistent with the calculated surface core level shifts and the pronounced barrier for nitrite formation. At RT, the recorded spectra indicate a complex interconversion between adsorbed species with an initial formation of a p(4 × 4) nitrate overlayer. With increasing NO pressure, the experimental results are best rationalized by partial nitrate decomposition into nitrites and subsequent NO physisorption, which leads to the formation of N2O3-like species.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Yoosoo; Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791; Kim, Se-Hyun

Highlights: • Membrane fusion driven by SNARE complex is hindered by several polyphenols. • Distinctive inhibitory effect of each polyphenol on SNARE zippering in neuron was examined. • FRET between fluorescence protein-tagged SNAREs probed well SNARE zippering in PC12 cells. • Delphinidin and cyanidin inhibit N-terminal SNARE nucleation in Ca{sup 2+}-independent manner. • Myricetin inhibits Ca{sup 2+}-dependent transmembrane association of SNARE complex. - Abstract: Fusion of synaptic vesicles with the presynaptic plasma membrane in the neuron is mediated by soluble N-ethylmaleimide-sensitive fusion protein-attachment protein receptor (SNARE) proteins. SNARE complex formation is a zippering-like process which initiates at the N-terminus andmore » proceeds to the C-terminal membrane-proximal region. Previously, we showed that this zippering-like process is regulated by several polyphenols, leading to the arrest of membrane fusion and the inhibition of neuroexocytosis. In vitro studies using purified SNARE proteins reconstituted in liposomes revealed that each polyphenol uniquely regulates SNARE zippering. However, the unique regulatory effect of each polyphenol in cells has not yet been examined. In the present study, we observed SNARE zippering in neuronal PC12 cells by measuring the fluorescence resonance energy transfer (FRET) changes of a cyan fluorescence protein (CFP) and a yellow fluorescence protein (YFP) fused to the N-termini or C-termini of SNARE proteins. We show that delphinidin and cyanidin inhibit the initial N-terminal nucleation of SNARE complex formation in a Ca{sup 2+}-independent manner, while myricetin inhibits Ca{sup 2+}-dependent transmembrane domain association of the SNARE complex in the cell. This result explains how polyphenols exhibit botulinum neurotoxin-like activity in vivo.« less

Evolution of Pre-Main Sequence Accretion Disks

NASA Technical Reports Server (NTRS)

Hartmann, Lee W.

2005-01-01

The aim of this project was to develop a comprehensive global picture of the physical conditions in, and evolutionary timescales of, premain sequence accretion disks. The results of this work will help constrain the initial conditions for planet formation. To this end we developed much larger samples of 3-10 Myr-old stars to provide better empirical constraints on protoplanetary disk evolution; measured disk accretion rates in these systems; and constructed detailed model disk structures consistent with observations to infer physical conditions such as grain growth in protoplanetary disks.

Studies of Circumstellar Disk Evolution

NASA Technical Reports Server (NTRS)

Hartmann, Lee W.

2005-01-01

The aim of this project is to develop a comprehensive global picture of the physical conditions in, and evolutionary timescales of, pre-main sequence accretion disks. The results of this work will help constrain the initial conditions for planet formation. To this end we are developing much larger samples of 3-10 Myr-old stars to provide better empirical constraints on protoplanetary disk evolution; measuring disk accretion rates in these systems; and constructing detailed model disk structures consistent with observations to infer physical conditions such as grain growth in protoplanetary disks.

Experimental considerations in metal mobilization from soil by chelating ligands: The influence of soil-solution ratio and pre-equilibration - A case study on Fe acquisition by phytosiderophores.

PubMed

Schenkeveld, W D C; Kimber, R L; Walter, M; Oburger, E; Puschenreiter, M; Kraemer, S M

2017-02-01

The efficiency of chelating ligands in mobilizing metals from soils and sediments is generally examined under conditions remote from those under which they are exuded or applied in the field. This may lead to incorrect estimations of the mobilizing efficiency. The aim of this study was to establish the influence of the soil solution ratio (SSR) and pre-equilibration with electrolyte solution on metal mobilization and metal displacement. For this purpose a series of interaction experiments with a calcareous clay soil and a biogenic chelating agent, the phytosiderophore 2'-deoxymugineic acid (DMA) were carried out. For a fixed ligand concentration, the SSR had a strong influence on metal mobilization and displacement. Metal complexation was faster at higher SSR. Reactive pools of metals that were predominantly mobilized at SSR 6 (in this case Cu), became depleted at SSR 0.1, whereas metals that were marginally mobilized at SSR 6, were dominantly mobilized at SSR 0.1 (in this case Fe), because of large soil reactive pools. For a fixed "amount of ligand"-to-"amount of soil"-ratio, metal complexation scaled linearly with the SSR. The efficiency of ligands in mobilizing metals under field conditions can be predicted with batch experiments, as long as the ligand-to-soil-ratio is matched. In most previously reported studies this criterion was not met. Equivalent metal-complex concentrations under field conditions can be back-calculated using adsorption isotherms for the respective metal-complexes. Drying and dry storage created labile pools of Fe, Cu and Zn, which were rapidly mobilized upon addition of DMA solution to dry soil. Pre-equilibration decreased these labile pools, leading to smaller concentrations of these metals during initial mobilization, but did not reduce the lag time between ligand addition and onset of microbial degradation of the metal-complexes. Hence SSR and pre-equilibration should be carefully considered when testing the metal mobilizing efficiency of chelating ligands. Copyright © 2016. Published by Elsevier B.V.

Kinetic pathway of 40S ribosomal subunit recruitment to hepatitis C virus internal ribosome entry site.

PubMed

Fuchs, Gabriele; Petrov, Alexey N; Marceau, Caleb D; Popov, Lauren M; Chen, Jin; O'Leary, Seán E; Wang, Richard; Carette, Jan E; Sarnow, Peter; Puglisi, Joseph D

2015-01-13

Translation initiation can occur by multiple pathways. To delineate these pathways by single-molecule methods, fluorescently labeled ribosomal subunits are required. Here, we labeled human 40S ribosomal subunits with a fluorescent SNAP-tag at ribosomal protein eS25 (RPS25). The resulting ribosomal subunits could be specifically labeled in living cells and in vitro. Using single-molecule Förster resonance energy transfer (FRET) between RPS25 and domain II of the hepatitis C virus (HCV) internal ribosome entry site (IRES), we measured the rates of 40S subunit arrival to the HCV IRES. Our data support a single-step model of HCV IRES recruitment to 40S subunits, irreversible on the initiation time scale. We furthermore demonstrated that after binding, the 40S:HCV IRES complex is conformationally dynamic, undergoing slow large-scale rearrangements. Addition of translation extracts suppresses these fluctuations, funneling the complex into a single conformation on the 80S assembly pathway. These findings show that 40S:HCV IRES complex formation is accompanied by dynamic conformational rearrangements that may be modulated by initiation factors.

Temporal-contextual processing in working memory: evidence from delayed cued recall and delayed free recall tests.

PubMed

Loaiza, Vanessa M; McCabe, David P

2012-02-01

Three experiments are reported that addressed the nature of processing in working memory by investigating patterns of delayed cued recall and free recall of items initially studied during complex and simple span tasks. In Experiment 1, items initially studied during a complex span task (i.e., operation span) were more likely to be recalled after a delay in response to temporal-contextual cues, relative to items from subspan and supraspan list lengths in a simple span task (i.e., word span). In Experiment 2, items initially studied during operation span were more likely to be recalled from neighboring serial positions during delayed free recall than were items studied during word span trials. Experiment 3 demonstrated that the number of attentional refreshing opportunities strongly predicts episodic memory performance, regardless of whether the information is presented in a spaced or massed format in a modified operation span task. The results indicate that the content-context bindings created during complex span trials reflect attentional refreshing opportunities that are used to maintain items in working memory.

Decapping activators in Saccharomyces cerevisiae act by multiple mechanisms.

PubMed

Nissan, Tracy; Rajyaguru, Purusharth; She, Meipei; Song, Haiwei; Parker, Roy

2010-09-10

Eukaryotic mRNA degradation often occurs in a process whereby translation initiation is inhibited and the mRNA is targeted for decapping. In yeast cells, Pat1, Scd6, Edc3, and Dhh1 all function to promote decapping by an unknown mechanism(s). We demonstrate that purified Scd6 and a region of Pat1 directly repress translation in vitro by limiting the formation of a stable 48S preinitiation complex. Moreover, while Pat1, Edc3, Dhh1, and Scd6 all bind the decapping enzyme, only Pat1 and Edc3 enhance its activity. We also identify numerous direct interactions between Pat1, Dcp1, Dcp2, Dhh1, Scd6, Edc3, Xrn1, and the Lsm1-7 complex. These observations identify three classes of decapping activators that function to directly repress translation initiation and/or stimulate Dcp1/2. Moreover, Pat1 is identified as critical in mRNA decay by first inhibiting translation initiation, then serving as a scaffold to recruit components of the decapping complex, and finally activating Dcp2. Copyright © 2010 Elsevier Inc. All rights reserved.

Some Cenozoic hydrocarbon basins on the continental shelf of Vietnam

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dien, P.T.

1994-07-01

The formation of the East Vietnam Sea basins was related to different geodynamic processes. The pre-Oligocene basement consists of igneous, metamorphic, and metasediment complexes. The Cretaceous-Eocene basement formations are formed by convergence of continents after destruction of the Tethys Ocean. Many Jurassic-Eocene fractured magmatic highs of the Cuulong basin basement constitute important reservoirs that are producing good crude oil. The Paleocene-Eocene formations are characterized by intramountain metamolasses, sometimes interbedded volcanic rocks. Interior structures of the Tertiary basins connect with rifted branches of the widened East Vietnam Sea. Bacbo (Song Hong) basin is predominated by alluvial-rhythmic clastics in high-constructive deltas, whichmore » developed on the rifting and sagging structures of the continental branch. Petroleum plays are constituted from Type III source rocks, clastic reservoirs, and local caprocks. Cuulong basin represents sagging structures and is predominated by fine clastics, with tidal-lagoonal fine sandstone and shalestone in high-destructive deltas that are rich in Type II source rocks. The association of the pre-Cenozoic fractured basement reservoirs and the Oligocene-Miocene clastic reservoir sequences with the Oligocene source rocks and the good caprocks is frequently met in petroleum plays of this basin. Nan Conson basin was formed from complicated structures that are related to spreading of the oceanic branch. This basin is characterized by Oligocene epicontinental fine clastics and Miocene marine carbonates that are rich in Types I, II, and III organic matter. There are both pre-Cenozoic fractured basement reservoirs, Miocene buildup carbonate reservoir rocks and Oligocene-Miocene clastic reservoir sequences, in this basin. Pliocene-Quaternary sediments are sand and mud carbonates in the shelf facies of the East Vietnam Sea back-arc basin. Their great thickness provides good conditions for maturation and trapping.« less

Origins of carbonate spherulites: Implications for Brazilian Aptian pre-salt reservoir

NASA Astrophysics Data System (ADS)

Chafetz, Henry; Barth, Jennifer; Cook, Megan; Guo, Xuan; Zhou, Jie

2018-03-01

Spherulites, spherical to elliptical allochems composed of crystals radiating from a common core, investigated from a variety of depositional settings, e.g., hot springs, ambient water temperature geyser, tufa, and caliche, are all composed of a fine-grained nucleus made-up of carbonate encrusted bacterial bodies, biofilms, and/or EPS and surrounded by a cortex of radiating crystals of either aragonite or calcite. The microbes and their by-products in the nucleus induced the precipitation of carbonate, overcoming the inhibition to initiate crystal formation. The enveloping radiating crystals comprising aragonitic cortices tended to grow abiotically producing well-formed euhedral crystals with a paucity of included bacterial fossils. Whereas those cortical crystals made-up of calcite commonly contained bacterial fossils, indicating that the bacterial colonies contributed to the calcitic cortical crystal precipitation. Similar spherulites form a thick, widespread accumulation in the Aptian Pre-Salt lacustrine deposits in the Campos Basin, offshore Brazil. As with the travertine, tufa, and caliche spherulites, the Pre-Salt spherulites most likely initiated carbonate precipitation around bacterial colonies and/or their bioproducts, probably while afloat in a lacustrine water column before settling to the water-sediment interface. Absence of inter-spherulite sediment and the spherulite-to-spherulite compaction indicate that cortical crystal growth continued while the spherulites were at the sediment-water interface rather than displacively within a sediment.

Surface dynamics and mechanics in liquid crystal polymer coatings

NASA Astrophysics Data System (ADS)

Liu, Danqing; Broer, Dirk J.

2015-03-01

Based on liquid crystal networks we developed `smart' coatings with responsive surface topographies. Either by prepatterning or by the formation of self-organized structures they can be switched on and off in a pre-designed manner. Here we provide an overview of our methods to generate coatings that form surface structures upon the actuation by light. The coating oscillates between a flat surface and a surface with pre-designed 3D micro-patterns by modulating a light source. With recent developments in solid state lighting, light is an attractive trigger medium as it can be integrated in a device for local control or can be used remotely for flood or localized exposure. The basic principle of formation of surface topographies is based on the change of molecular organization in ordered liquid crystal polymer networks. The change in order leads to anisotropic dimensional changes with contraction along the director and expansion to the two perpendicular directions and an increase in volume by the formation of free volume. These two effects work in concert to provide local expansion and contraction in the coating steered by the local direction of molecular orientation. The surface deformation, expressed as the height difference between the activated regions and the non-activated regions divided by the initial film thickness, is of the order of 20%. Switching occurs immediately when the light is switched `on' and `off' and takes several tens of seconds.

CYP4A in tumor-associated macrophages promotes pre-metastatic niche formation and metastasis.

PubMed

Chen, X W; Yu, T J; Zhang, J; Li, Y; Chen, H L; Yang, G F; Yu, W; Liu, Y Z; Liu, X X; Duan, C F; Tang, H L; Qiu, M; Wang, C L; Zheng, H; Yue, J; Guo, A M; Yang, J

2017-08-31

Tumor-associated macrophages (TAMs) play an essential role in metastasis. However, what enables TAMs to have a superior capacity to establish pre-metastatic microenvironment in distant organs is unclear. Here we have begun to uncover the effects of cytochrome P450 (CYP) 4A in TAMs on lung pre-metastatic niche formation and metastasis. CYP4A + TAM infiltration was positively associated with metastasis, pre-metastatic niche formation and poor prognosis in breast cancer patients. The pharmacological inhibition of CYP4A reduced lung pre-metastatic niche formation (evidenced by a decrease in vascular endothelial growth factor receptor 1 positive (VEGFR1 + ) myeloid cell recruitment and pro-metastatic protein expression) and metastatic burden, accompanied with TAM polarization away from the M2 phenotype in spontaneous metastasis models of 4T1 breast cancer and B16F10 melanoma. Co-implantation of 4T1 cells with CYP4A10 high macrophages promoted lung pre-metastatic niche formation and metastasis. Depletion of TAMs disrupted lung pre-metastatic niches and thereby prevented metastasis. Treatment with the CM from CYP4A10 high M2 macrophages (M2) increased pre-metastatic niche formation and metastatic burden in the lungs, whereas CYP4A inhibition attenuated these effects. In vitro TAM polarization away from the M2 phenotype induced by CYP4A inhibition decreased VEGFR1 + myeloid cell migration and fibronectin expression, accompanied with downregulation of STAT3 signaling. Conversely, overexpression of CYP4A or exogenous addition of 20-hydroxyeicosatetraenoic acid promoted M2 polarization and cytokine production of macrophages and thereby enhanced migration of VEGFR1 + myeloid cells, which were reversed by siRNA or pharmacological inhibition of STAT3. Importantly, a combined blocking M2 macrophage-derived factors TGF-β, VEGF and SDF-1 abolished VEGFR1 + myeloid cell migration and fibroblast activation induced by CYP4A. In summary, CYP4A in TAMs is crucial for lung pre-metastatic niche formation and metastasis, and may serve as a potential therapeutic target in human cancer.

Reduction of plasma density in the Helicity Injected Torus with Steady Inductance experiment by using a helicon pre-ionization source

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hossack, Aaron C.; Jarboe, Thomas R.; Victor, Brian S.

2013-10-15

A helicon based pre-ionization source has been developed and installed on the Helicity Injected Torus with Steady Inductance (HIT-SI) spheromak. The source initiates plasma breakdown by injecting impurity-free, unmagnetized plasma into the HIT-SI confinement volume. Typical helium spheromaks have electron density reduced from (2–3) × 10{sup 19} m{sup −3} to 1 × 10{sup 19} m{sup −3}. Deuterium spheromak formation is possible with density as low as 2 × 10{sup 18} m{sup −3}. The source also enables HIT-SI to be operated with only one helicity injector at injector frequencies above 14.5 kHz. A theory explaining the physical mechanism driving the reductionmore » of breakdown density is presented.« less

CYCLIN-DEPENDENT KINASE G1 Is Associated with the Spliceosome to Regulate CALLOSE SYNTHASE5 Splicing and Pollen Wall Formation in Arabidopsis[C][W][OA

PubMed Central

Huang, Xue-Yong; Niu, Jin; Sun, Ming-Xi; Zhu, Jun; Gao, Ju-Fang; Yang, Jun; Zhou, Que; Yang, Zhong-Nan

2013-01-01

Arabidopsis thaliana CYCLIN-DEPEDENT KINASE G1 (CDKG1) belongs to the family of cyclin-dependent protein kinases that were originally characterized as cell cycle regulators in eukaryotes. Here, we report that CDKG1 regulates pre-mRNA splicing of CALLOSE SYNTHASE5 (CalS5) and, therefore, pollen wall formation. The knockout mutant cdkg1 exhibits reduced male fertility with impaired callose synthesis and abnormal pollen wall formation. The sixth intron in CalS5 pre-mRNA, a rare type of intron with a GC 5′ splice site, is abnormally spliced in cdkg1. RNA immunoprecipitation analysis suggests that CDKG1 is associated with this intron. CDKG1 contains N-terminal Ser/Arg (RS) motifs and interacts with splicing factor Arginine/Serine-Rich Zinc Knuckle-Containing Protein33 (RSZ33) through its RS region to regulate proper splicing. CDKG1 and RS-containing Zinc Finger Protein22 (SRZ22), a splicing factor interacting with RSZ33 and U1 small nuclear ribonucleoprotein particle (snRNP) component U1-70k, colocalize in nuclear speckles and reside in the same complex. We propose that CDKG1 is recruited to U1 snRNP through RSZ33 to facilitate the splicing of the sixth intron of CalS5. PMID:23404887

Paleogeography and sedimentology of Upper Cretaceous turbidites, San Diego, California.

USGS Publications Warehouse

Nilsen, T.H.; Abbott, P.L.

1981-01-01

Upper Cretaceous (Campanian and Maestrichtian) marine strata of the Rosario Group in the San Diego area include the Point Loma Formation and overlying Cabrillo Formation. Thes units contain 6 facies associations which define a deep-sea fan deposited by westward-flowing sediment gravity flows that transported sediments derived chiefly from batholithic and pre-batholithic metamorphic rocks of the Peninsular Ranges. The sedimentary basin initially deepened abruptly. The fan then prograded westward into the basin, with a retrogradational phase recorded in the uppermost part of the sequence. The fan was deposited along the eastern edge of a forearc basin similar to that of the Great Valley sequence in northern California. The western part of the fan appears to have been truncated by late Cenozoic strike-slip faulting.-from Authors

Glioblastoma: A Pathogenic Crosstalk between Tumor Cells and Pericytes

PubMed Central

Redondo-Garcia, Carolina; Martinez, Salvador

2014-01-01

Cancers likely originate in progenitor zones containing stem cells and perivascular stromal cells. Much evidence suggests stromal cells play a central role in tumor initiation and progression. Brain perivascular cells (pericytes) are contractile and function normally to regulate vessel tone and morphology, have stem cell properties, are interconvertible with macrophages and are involved in new vessel formation during angiogenesis. Nevertheless, how pericytes contribute to brain tumor infiltration is not known. In this study we have investigated the underlying mechanism by which the most lethal brain cancer, Glioblastoma Multiforme (GBM) interacts with pre-existing blood vessels (co-option) to promote tumor initiation and progression. Here, using mouse xenografts and laminin-coated silicone substrates, we show that GBM malignancy proceeds via specific and previously unknown interactions of tumor cells with brain pericytes. Two-photon and confocal live imaging revealed that GBM cells employ novel, Cdc42-dependent and actin-based cytoplasmic extensions, that we call flectopodia, to modify the normal contractile activity of pericytes. This results in the co-option of modified pre-existing blood vessels that support the expansion of the tumor margin. Furthermore, our data provide evidence for GBM cell/pericyte fusion-hybrids, some of which are located on abnormally constricted vessels ahead of the tumor and linked to tumor-promoting hypoxia. Remarkably, inhibiting Cdc42 function impairs vessel co-option and converts pericytes to a phagocytic/macrophage-like phenotype, thus favoring an innate immune response against the tumor. Our work, therefore, identifies for the first time a key GBM contact-dependent interaction that switches pericyte function from tumor-suppressor to tumor-promoter, indicating that GBM may harbor the seeds of its own destruction. These data support the development of therapeutic strategies directed against co-option (preventing incorporation and modification of pre-existing blood vessels), possibly in combination with anti-angiogenesis (blocking new vessel formation), which could lead to improved vascular targeting not only in Glioblastoma but also for other cancers. PMID:25032689

How does mindfulness modulate self-regulation in pre-adolescent children? An integrative neurocognitive review.

PubMed

Kaunhoven, Rebekah Jane; Dorjee, Dusana

2017-03-01

Pre-adolescence is a key developmental period in which complex intrinsic volitional methods of self-regulation are acquired as a result of rapid maturation within the brain networks underlying the self-regulatory processes of attention control and emotion regulation. Fostering adaptive self-regulation skills during this stage of development has strong implications for physical health, emotional and socio-economic outcomes during adulthood. There is a growing interest in mindfulness-based programmes for pre-adolescents with initial findings suggesting self-regulation improvements, however, neurodevelopmental studies on mindfulness with pre-adolescents are scarce. This analytical review outlines an integrative neuro-developmental approach, which combines self-report and behavioural assessments with event related brain potentials (ERPs) to provide a systemic multilevel understanding of the neurocognitive mechanisms of mindfulness in pre-adolescence. We specifically focus on the N2, error related negativity (ERN), error positivity (Pe), P3a, P3b and late positive potential (LPP) ERP components as indexes of mindfulness related modulations in non-volitional bottom-up self-regulatory processes (salience detection, stimulus driven orienting and mind wandering) and volitional top-down self-regulatory processes (endogenous orienting and executive attention). Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

Pre- and post-remediation characterization of acid-generating fluvial tailings material

USGS Publications Warehouse

Smith, Kathleen S.; Walton-Day, Katherine; Hoal, Karin O.; Driscoll, Rhonda L.; Pietersen, K.

2012-01-01

The upper Arkansas River south of Leadville, Colorado, USA, contains deposits of fluvial tailings from historical mining operations in the Leadville area. These deposits are potential non-point sources of acid and metal contamination to surface- and groundwater systems. We are investigating a site that recently underwent in situ remediation treatment with lime, fertilizer, and compost. Pre- and post-remediation fluvial tailings material was collected from a variety of depths to examine changes in mineralogy, acid generation, and extractable nutrients. Results indicate sufficient nutrient availability in the post-remediation near-surface material, but pyrite and acid generation persist below the depth of lime and fertilizer addition. Mineralogical characterization performed using semi-quantitative X-ray diffraction and quantitative SEM-based micro-mineralogy (Mineral Liberation Analysis, MLA) reveal formation of gypsum, jarosite, and complex coatings surrounding mineral grains in post-remediation samples.

Discrete Molecular Dynamics Can Predict Helical Prestructured Motifs in Disordered Proteins

PubMed Central

Han, Kyou-Hoon; Dokholyan, Nikolay V.; Tompa, Péter; Kalmár, Lajos; Hegedűs, Tamás

2014-01-01

Intrinsically disordered proteins (IDPs) lack a stable tertiary structure, but their short binding regions termed Pre-Structured Motifs (PreSMo) can form transient secondary structure elements in solution. Although disordered proteins are crucial in many biological processes and designing strategies to modulate their function is highly important, both experimental and computational tools to describe their conformational ensembles and the initial steps of folding are sparse. Here we report that discrete molecular dynamics (DMD) simulations combined with replica exchange (RX) method efficiently samples the conformational space and detects regions populating α-helical conformational states in disordered protein regions. While the available computational methods predict secondary structural propensities in IDPs based on the observation of protein-protein interactions, our ab initio method rests on physical principles of protein folding and dynamics. We show that RX-DMD predicts α-PreSMos with high confidence confirmed by comparison to experimental NMR data. Moreover, the method also can dissect α-PreSMos in close vicinity to each other and indicate helix stability. Importantly, simulations with disordered regions forming helices in X-ray structures of complexes indicate that a preformed helix is frequently the binding element itself, while in other cases it may have a role in initiating the binding process. Our results indicate that RX-DMD provides a breakthrough in the structural and dynamical characterization of disordered proteins by generating the structural ensembles of IDPs even when experimental data are not available. PMID:24763499

The role of retrieval mode and retrieval orientation in retrieval practice: insights from comparing recognition memory testing formats and restudying.

PubMed

Gao, Chuanji; Rosburg, Timm; Hou, Mingzhu; Li, Bingbing; Xiao, Xin; Guo, Chunyan

2016-12-01

The effectiveness of retrieval practice for aiding long-term memory, referred to as the testing effect, has been widely demonstrated. However, the specific neurocognitive mechanisms underlying this phenomenon remain unclear. In the present study, we sought to explore the role of pre-retrieval processes at initial testing on later recognition performance by using event-related potentials (ERPs). Subjects studied two lists of words (Chinese characters) and then performed a recognition task or a source memory task, or restudied the word lists. At the end of the experiment, subjects received a final recognition test based on the remember-know paradigm. Behaviorally, initial testing (active retrieval) enhanced memory retention relative to restudying (passive retrieval). The retrieval mode at initial testing was indexed by more positive-going ERPs for unstudied items in the active-retrieval tasks than in passive retrieval from 300 to 900 ms. Follow-up analyses showed that the magnitude of the early ERP retrieval mode effect (300-500 ms) was predictive of the behavioral testing effect later on. In addition, the ERPs for correctly rejected new items during initial testing differed between the two active-retrieval tasks from 500 to 900 ms, and this ERP retrieval orientation effect predicted differential behavioral testing gains between the two active-retrieval conditions. Our findings confirm that initial testing promotes later retrieval relative to restudying, and they further suggest that adopting pre-retrieval processing in the forms of retrieval mode and retrieval orientation might contribute to these memory enhancements.

Research on pre-scientific concept of light in children's cognitive activity

NASA Astrophysics Data System (ADS)

Lan, Zhigao; Yu, Yang; Yan, Dan; Yang, Shulin

2017-08-01

Based on the theory of Ausubel's meaningful learning and cognitive characteristic of childens pre-scientific concept, two students of Huang Gang Middle School have been interviewed continuously about cognition of interaction between light and matter. Comprehension degree of childens pre-scientific concept about interaction between light and matter has been deeply understood, formation of strategy of childens pre-scientific concept has been discussed. Several influence factors related to formation of childens pre-scientific concept have been analyzed, such as sex, family environment, and learning experience of kindergarten and primary school.

Clinical Decision Support Improves Initial Dosing and Monitoring of Tobramycin and Amikacin

PubMed Central

Cox, Zachary L.; Nelsen, Cori L.; Waitman, Lemuel R.; McCoy, Jacob A.; Peterson, Josh F.

2010-01-01

Purpose Clinical decision support (CDS) systems could be valuable tools in reducing aminoglycoside prescribing errors. We evaluated the impact of CDS on initial dosing, interval, and pharmacokinetic outcomes of amikacin and tobramycin therapy. Methods A complex CDS advisor to provide guidance on initial dosing and monitoring, using both traditional and extended interval dosing strategies, was integrated into computerized provider order entry (CPOE) and compared to a control group which featured close pharmacy monitoring of all aminoglycoside orders. A random sample of 118 patients from an academic, tertiary care medical center prescribed amikacin and tobramycin prior to advisor implementation was compared to 98 patients admitted following advisor implementation. Primary outcome was an initial dose within 10% of a dose calculated to be adherent to published dose guidelines. Secondary outcomes were a guideline-adherent interval, trough and peak concentrations in goal range, and incidence of nephrotoxicity. Results Of 216 patients studied, 97 were prescribed amikacin and 119 were prescribed tobramycin. The primary outcome of initial dosing consistent with guideline-based care increased from 40% in the pre-advisor arm to 80% in the post-advisor arm (p<0.001), with a number needed to treat of 3 patients to prevent one incorrect dose. Correct initial interval based on renal function also increased from 63% to 87% (p<0.001). The changes in initial dosing and interval resulted in an increase of trough concentrations in the goal range from 59% pre-advisor to 89% post-advisor implementation (p=0.0004). There was no significant difference in peak concentrations in goal range or incidence of nephrotoxicity (25% vs. 17%, p=0.2). Conclusion An advisor for aminoglycoside dosing and monitoring integrated into CPOE significantly improves initial dosing, selection of interval, and trough concentrations at goal compared to unassisted physician dosing. PMID:21411805

New approach on volatile contents determination in silicate melt inclusions: A coupling X-ray microtomography and geochemical approach in Los Humeros caldera complex (Eastern Mexican Volcanic Belt)

NASA Astrophysics Data System (ADS)

Creon, L.; Levresse, G.; Carrasco Nuñez, G.

2016-12-01

Volatile contents and magma degassing behavior are known to affect the style, frequency, and intensity of near-surface magmatic processes. For this reason, much effort have been devoted to characterize the volatile evolution of shallow magmatic systems to better constrain volcanic history. Silicate melt inclusions (SMI) represent samples of melt that were isolated from the bulk magma at depth, thus preserving the PTX conditions of the pre-eruptive material. SMI are often affected by the formation of a bubble after trapping; this is a natural consequence of the PVTX properties of crystal-melt-volatile systems. Previous workers have recognized that bubble formation is an obstacle, which affects the interpretation of SMI trapping conditions based only on analysis of the glass phase. Indeed, they explained that bubbles can contain a significant percentage of the volatiles, particularly for those with low solubility in the melt (e.g. CO2). In this study, we propose to define the pre-eruptive PTX conditions of Los Humeros magma chamber using SMI from the various eruption events within 460 and 30 Ka. An innovative analytical coupling has been used in order to determine: (1) the volume of the SMI glass and bubble, using high resolution 3D X-ray microtomography; (2) the density and composition of the bubbles, using Raman spectroscopy; (3) the volatile element contents in glass, using NanoSIMS; and, (4) the major elements composition of the glass, using EPMA. The recalculated volatile concentrations of the total SMI (glass + bubble), illustrate clearly that the volatile content determinations using only the glass phase, underestimate drastically the total volatile content and therefore induce significant error on the determination of the pre-eruptive volcanic budget and on the constrain on the volcanic and thermal history. This study had moreover highlighted the complex evolution of Los Humeros composite magma chamber and, gave constrains for geothermal exploration purpose.

A simple and efficient ultrasonic-assisted extraction procedure combined with UV-Vis spectrophotometry for the pre-concentration and determination of folic acid (vitamin B9) in various sample matrices.

PubMed

Gürkan, Ramazan; Altunay, Nail

2016-07-01

A simple and efficient ultrasonic-assisted extraction (UAE) procedure has been proposed for the pre-concentration of (2S)-2-[(4-{[(2-amino-4-hydroxypteridin-yl)methyl]amino}phenyl)formamido]pentanedioic acid (folic acid) in vegetables, pharmaceuticals and foods prior to determination at 540 nm using UV-Vis spectrophotometry. The method is based on hydrophobic ternary complex formation of folic acid with silver ions in the presence of cetyltrimethylammonium bromide (CTAB) as a sensitivity enhancer counter ion at pH 7.0, and then extraction into a micellar phase of polyethylene glycol monoalkyl ether (Genapol X-080). The impacts on the extraction efficiency and complex formation of analytical parameters such as sample pH, concentration of silver, concentration of surfactants and extraction time, ultrasonic time and sample volume, were investigated and optimised in detail. The matrix effect on the pre-concentration and determination of folic acid was investigated, and it was observed that the proposed method was highly selective against possible matrix co-extractives. Under optimised conditions, a good linear relationship between the analytical signal and folic acid concentration was obtained in the range of 0.6-180 μg l(-1) with a detection limit of 0.19 μg l(-1) and quantification limit of 0.63 μg l(-1). The applicability was evaluated using samples fortified at different concentration levels, and recoveries higher than 94.1% were obtained. The precision as the percent relative standard deviation (RSD%) was in range of 2.5-3.8% (10 and 40 μg l(-1), n = 5). The proposed method was validated by analysis of two standard reference materials (SRMs) and various real samples, and satisfactory results were obtained.

Structural Model Development: Branches, Attitudes and Self-Efficacy of Pedagogical Formation Program Pre-Service Teachers

ERIC Educational Resources Information Center

Sivaci, Sadik Yuksel

2017-01-01

In this study, the relationship between attitudes of pedagogical formation program pre-service teachers towards teaching profession and their self-efficacies has been examined. In this case, the effect of graduation branches of the pre-service teachers on teacher self-efficacies and the effect of teacher self-efficacies on attitudes towards…

The Influence of Formal and Informal Formative Pre-Service Experiences on Teacher Self-Efficacy

ERIC Educational Resources Information Center

Tuchman, Elie; Isaacs, Jenny

2011-01-01

Formal pre-service training has been shown to be effective in building teacher self-efficacy beliefs. However, the impact of other, less formal, "teacher-like" pre-service experiences on the formation of efficacy beliefs has not previously been investigated. This study examines the associations between both formal and informal formative…

Formative Assessment and Academic Achievement in Pre-Graduate Students of Health Sciences

ERIC Educational Resources Information Center

Carrillo-de-la-Pena, Maria T.; Bailles, Eva; Caseras, Xavier; Martinez, Alvar; Ortet, Generos; Perez, Jorge

2009-01-01

Although educational experts recommend the use of formative assessment, there is a dearth of empirical studies on its impact on academic achievement. In this research the authors analyse to what extent participation and performance in formative assessment are associated with positive academic outcomes of pre-graduate students of health sciences. A…

Boninites: Characteristics and tectonic constraints, northeastern Appalachians

USGS Publications Warehouse

Kim, J.; Jacobi, R.D.

2002-01-01

Boninites are high Mg andesites that are thought to form in suprasubduction zone tectonic environments as primary melts from refractory mantle. Boninites provide a potential constraint on tectonic models for ancient terranes that contain boninites because the only unequivocal tectonic setting in which "modern" boninites have been recognized is a fore-arc setting. Tectonic models for "modern" boninite genesis include subduction initiation ("infant arc"), fore-arc spreading, and the forearc side of intra-arc rifting (spreading). These models can be differentiated by the relative age of the boninites and to a lesser degree, geochemistry. The distinctive geochemistry of boninites promotes their recognition in ancient terranes. As detailed in this report, several mafic terranes in the northeastern Appalachians contain boninites; these terranes were situated on both sides of Iapetus. The characteristics of these boninites can be used to constrain tectonic models of the evolution of the northeastern Appalachians. On the Laurentian side of Iapetus, "infant arc" boninites were not produced ubiquitously during the Cambrian subduction initiation, unless sampling problems or minimum age dates obscure a more widespread boninite "infant arc". The Cambrian subduction initiation on the Laurentian side was probably characterized by both "infant arc" boninitic arc construction (perhaps the >496 Ma Hawley Formation and the >488 Ma Betts Cove Ophiolite) and "normal" arc construction (Mt. Orford). This duality is consistent with the suggestion that the pre-collisional geometry of the Laurentian margin was complex. The Bay of Islands Complex and Thetford Mines ophiolite boninites are likely associated with forearc/intra-arc spreading during the protracted evolution of the Cambrian arc system. The relatively young boninites in the Bronson Hill Arc suggest that the Taconic continuous eastward subduction tectonic model is less tenable than other models. On the Gondwana side of Iapetus, the Tea Arm boninites of the Exploits Group stratigraphically rest on arc and MORB volcanics. This stratigraphy, and the relatively young age of the boninites (486 Ma), compared to assumed subduction initiation age (>513 Ma), suggest that the boninites may be more consistent with fore-arc spreading/intra-arc spreading. However, an "infant arc" model cannot be dismissed, and is commonly proposed for the nearby boninites in the Wild Bight Group. ?? 2002 Elsevier Science Ltd. All rights reserved.

Unilateral Ablation of Pre-Bötzinger Complex Disrupts Breathing during Sleep but Not Wakefulness

PubMed Central

McKay, Leanne C.; Feldman, Jack L.

2008-01-01

Rationale: In adult rats, bilateral ablation of pre-Bötzinger complex (preBötC) neurokinin 1–expressing (NK1R) neurons leads to a progressive and irreversible disruption in breathing pattern, initially during sleep, eventually resulting in an ataxic breathing pattern during wakefulness. Objectives: Here we determine whether ablation of fewer preBötC NK1R neurons leads to a persistent pattern of disordered breathing during sleep but not during wakefulness. Methods: Adult male Sprague-Dawley rats (n = 12) were instrumented to record diaphragmatic, abdominal, and neck EMG, and EEG. Fourteen days later, a second surgery was performed to stereotaxically microinject into the preBötC on one side the toxin saporin conjugated to substance P (SP-SAP), which selectively ablates NK1R neurons. Measurements and Main Results: Postinjection, rats were monitored within a plethysmograph until they were killed (Days 21–51). At Days 6–9 post–unilateral SP-SAP injection, respiratory pattern during sleep, particularly REM sleep, became increasingly disordered, characterized by an increase in frequency of central sleep apnea and hypopneas (36.8 ± 7.4 episodes/h of REM vs. 6 ± 2.0 episodes/h in preinjection controls; P < 0.05), whereas breathing during resting wakefulness remained stable. Unlike bilateral SP-SAP–injected rats, an ataxic breathing pattern did not develop during wakefulness. Rats that were monitored up to 51 days post–SP-SAP injection continued to have sleep-disordered breathing; breathing during wakefulness remained relatively stable. Histologic analysis of the ventrolateral medulla confirmed that NK1R neurons within the preBötC on the injected but not on the contralateral side of the medulla were ablated. Conclusions: Gradual loss of preBötC NK1R neurons may be an underlying factor of sleep-disordered breathing, in particular of central sleep apnea. PMID:18420958

Public housing relocations in Atlanta, Georgia, and declines in spatial access to safety net primary care

PubMed Central

Cooper, Hannah LF; Wodarski, Stephanie; Cummings, Janet; Hunter-Jones, Josalin; Karnes, Conny; Ross, Zev; Druss, Ben; Bonney, Loida E

2012-01-01

This analysis investigates changes in spatial access to safety-net primary care in a sample of US public housing residents relocating via the HOPE VI initiative from public housing complexes to voucher-subsidized rental units; substance misusers were oversampled. We used gravity-based models to measure spatial access to care, and used mixed models to assess pre-/post-relocation changes in access. Half the sample experienced declines in spatial access of ≥79.83%; declines did not vary by substance misuse status. Results suggest that future public housing relocation initiatives should partner with relocaters, particularly those in poor health, to help them find housing near safety-net clinics. PMID:23060002

The chemical state of defective uranium-plutonium oxide fuel pins irradiated in sodium cooled reactors

NASA Astrophysics Data System (ADS)

Kleykamp, H.

1997-09-01

Steady-state irradiation experiments were conducted in the sodium loop of the Siloe reactor on artificially failed mixed oxide pins that had been pre-irradiated in fast reactors up to 11.5% burnup. The formation of the predominant reaction product Na 3(U,Pu)O 4 starts on the fuel surface and is terminated when a lower O/(U + Pu) threshold of the fuel is attained. The axial extent of the reaction product depends on the size of the initial cladding defect. The occurrence of secondary cracks is possible. Na(U,Pu)O 3 forms at higher fuel temperatures. The existence of Na 3U 1- xPu xO 4 is shown in pre-irradiated blanket pins after artificial defect formation. Caesium in the oxocompounds is reduced to the metallic state and is dissolved in the coolant. Evidence of a very low chemical potential of oxygen in defective fuel pins is sustained by the occurrence of actinide-platinum metal phases formed by coupled reduction of hypostoichiometric fuel with ɛ-(Mo,Tc,Ru,Rh,Pd) precipitates. Continued operation of defective pins is not hazardous by easy precautions.

[Complex diagnostic of cognitive impairment].

PubMed

Emelin, A Yu; Lobzin, V Yu

2017-01-01

In this article, the authors discussed the various aspects of pre-dementia stages of cognitive impairment, predominantly of neurodegenerative etiology. The modern conception of the pathophysiology of initial stages of cognitive impairment, the potential for lifetime pathological markers of amyloidosis and neurodegeneration are discussed. The authors proposed to use the concept of 'early signs of cognitive impairment'. The algorithm of the complex early diagnosis of cognitive impairment as well as the opportunities and prospects of clinical, neuropsychological, neuroimaging and laboratory examination methods are presented. The data on main diseases characterized by cognitive impairment and prospects for the use of new highly informative methods for early and differential diagnosis of Alzheimer's disease and vascular cognitive impairment are discussed.

Structural characterization of ribosome recruitment and translocation by type IV IRES

PubMed Central

Murray, Jason; Savva, Christos G; Shin, Byung-Sik; Dever, Thomas E; Ramakrishnan, V; Fernández, Israel S

2016-01-01

Viral mRNA sequences with a type IV IRES are able to initiate translation without any host initiation factors. Initial recruitment of the small ribosomal subunit as well as two translocation steps before the first peptidyl transfer are essential for the initiation of translation by these mRNAs. Using electron cryomicroscopy (cryo-EM) we have structurally characterized at high resolution how the Cricket Paralysis Virus Internal Ribosomal Entry Site (CrPV-IRES) binds the small ribosomal subunit (40S) and the translocation intermediate stabilized by elongation factor 2 (eEF2). The CrPV-IRES restricts the otherwise flexible 40S head to a conformation compatible with binding the large ribosomal subunit (60S). Once the 60S is recruited, the binary CrPV-IRES/80S complex oscillates between canonical and rotated states (Fernández et al., 2014; Koh et al., 2014), as seen for pre-translocation complexes with tRNAs. Elongation factor eEF2 with a GTP analog stabilizes the ribosome-IRES complex in a rotated state with an extra ~3 degrees of rotation. Key residues in domain IV of eEF2 interact with pseudoknot I (PKI) of the CrPV-IRES stabilizing it in a conformation reminiscent of a hybrid tRNA state. The structure explains how diphthamide, a eukaryotic and archaeal specific post-translational modification of a histidine residue of eEF2, is involved in translocation. DOI: http://dx.doi.org/10.7554/eLife.13567.001 PMID:27159451

Trapping and desorption of complex organic molecules in water at 20 K

NASA Astrophysics Data System (ADS)

Burke, Daren J.; Puletti, Fabrizio; Woods, Paul M.; Viti, Serena; Slater, Ben; Brown, Wendy A.

2015-10-01

The formation, chemical, and thermal processing of complex organic molecules (COMs) is currently a topic of much interest in interstellar chemistry. The isomers glycolaldehyde, methyl formate, and acetic acid are particularly important because of their role as pre-biotic species. It is becoming increasingly clear that many COMs are formed within interstellar ices which are dominated by water. Hence, the interaction of these species with water ice is crucially important in dictating their behaviour. Here, we present the first detailed comparative study of the adsorption and thermal processing of glycolaldehyde, methyl formate, and acetic acid adsorbed on and in water ices at astrophysically relevant temperatures (20 K). We show that the functional group of the isomer dictates the strength of interaction with water ice, and hence the resulting desorption and trapping behaviour. Furthermore, the strength of this interaction directly affects the crystallization of water, which in turn affects the desorption behaviour. Our detailed coverage and composition dependent data allow us to categorize the desorption behaviour of the three isomers on the basis of the strength of intermolecular and intramolecular interactions, as well as the natural sublimation temperature of the molecule. This categorization is extended to other C, H, and O containing molecules in order to predict and describe the desorption behaviour of COMs from interstellar ices.

A Novel Role for Cytochrome c: Efficient Catalysis of S-Nitrosothiol Formation

PubMed Central

Basu, Swati; Keszler, Agnes; Azarova, Natalia A.; Nwanze, Nneka; Perlegas, Andreas; Shiva, Sruti; Broniowska, Katarzyna A.; Hogg, Neil; Kim-Shapiro, Daniel B.

2009-01-01

While S-nitrosothiols are regarded as important elements of many NO-dependent signal transduction pathways, the physiological mechanism of their formation remains elusive. Here, we demonstrate a novel mechanism by which cytochrome c may represent an efficient catalyst of S-nitrosation in vivo. In this mechanism, initial binding of GSH to ferric cytochrome c is followed by reaction of NO with this complex, yielding ferrous cytochrome c and GSNO. We show that when submitochondrial particles or cell lysates are exposed to NO in the presence of cytochrome c, there is a robust formation of protein S-nitrosothiols. In the case of submitochondrial particles protein S-nitrosation is paralleled with an inhibition of mitochondrial complex I. These observations raise the possibility that cytochrome c is a mediator of S-nitrosation in biological systems, particularly during hypoxia, and that release of cytochrome c in to the cytosol during apoptosis potentially releases a GSNO synthase activity which could modulate apoptotic signaling. PMID:19879353

Complexities of management of a urostomy in Ehlers-Danlos syndrome: a reflective account.

PubMed

Oxenham, Julie

Mary (pseudonym) is a 30-year-old woman who underwent a urinary diversion and formation of an ileal conduit/urostomy (urinary stoma) due to the formation of multiple bladder diverticula, which caused micturition difficulties and recurrent urinary tract infections with associated pain and discomfort. The bladder diverticula were caused by Ehlers-Danlos syndrome (EDS), a hereditary disorder of the connective tissue or, particulary, defective collagen. Surgical intervention in patients with EDS is prone to complications due to poor wound healing, including issues of dehiscence, postoperative bleeding and poor uptake of anaesthesia and analgesia. After an initial presentation of the syndrome of EDS and Mary's history, this article offers a reflective account (informed by Gibbs' Reflective Cycle) and illustrates the complexities of caring for an individual with EDS who undergoes stoma formation. The author, a stoma care nurse, demonstrates how using purposeful reflection resulted in better understanding and awareness of caring for an individual with a rare syndrome and the nursing challenges this presented.

Chaperoning 5S RNA assembly

PubMed Central

Madru, Clément; Lebaron, Simon; Blaud, Magali; Delbos, Lila; Pipoli, Juliana; Pasmant, Eric; Réty, Stéphane; Leulliot, Nicolas

2015-01-01

In eukaryotes, three of the four ribosomal RNAs (rRNAs)—the 5.8S, 18S, and 25S/28S rRNAs—are processed from a single pre-rRNA transcript and assembled into ribosomes. The fourth rRNA, the 5S rRNA, is transcribed by RNA polymerase III and is assembled into the 5S ribonucleoprotein particle (RNP), containing ribosomal proteins Rpl5/uL18 and Rpl11/uL5, prior to its incorporation into preribosomes. In mammals, the 5S RNP is also a central regulator of the homeostasis of the tumor suppressor p53. The nucleolar localization of the 5S RNP and its assembly into preribosomes are performed by a specialized complex composed of Rpf2 and Rrs1 in yeast or Bxdc1 and hRrs1 in humans. Here we report the structural and functional characterization of the Rpf2–Rrs1 complex alone, in complex with the 5S RNA, and within pre-60S ribosomes. We show that the Rpf2–Rrs1 complex contains a specialized 5S RNA E-loop-binding module, contacts the Rpl5 protein, and also contacts the ribosome assembly factor Rsa4 and the 25S RNA. We propose that the Rpf2–Rrs1 complex establishes a network of interactions that guide the incorporation of the 5S RNP in preribosomes in the initial conformation prior to its rotation to form the central protuberance found in the mature large ribosomal subunit. PMID:26159998

Zircon U-Pb ages and Hf-O isotopic composition of migmatites from the Zanjan-Takab complex, NW Iran: Constraints on partial melting of metasediments

NASA Astrophysics Data System (ADS)

Moghadam, Hadi Shafaii; Li, Xian-Hua; Stern, Robert J.; Ghorbani, Ghasem; Bakhshizad, Farzaneh

2016-01-01

We study migmatites and other metamorphic rocks in the Zanjan-Takab region of NW Iran and use these results to report the first evidence of Oligocene core complex formation in Iran. Four samples of migmatites associated with paragneisses, including leucosomes and associated para-amphibolite melanosomes were selected for U-Pb dating and Hf-O isotopic analysis. Zircon cores - interpreted as originally detrital zircons - have variable ages that peak at ca. 100-110 Ma, but their sedimentation age - indicated by the youngest 206Pb/238U ages - is ca. 35-40 Ma. New zircons associated with incipient melting occur as overgrowths around zircon cores and/or as newly grown grains. Morphologies and internal structures suggest that rim growth and formation of new zircons were associated with partial melting. All four samples contain zircons with rims that yield 206Pb/238U ages of 28-25 Ma, indicating that partial melting occurred in Late Oligocene time. δ18O values for zircon rims vary between 8.2 and 12.3‰, significantly higher than expected for mantle inputs (δ18O 6‰) and consistent with equilibrium with surface materials. Zircon rims yield εHf(t) between 2.2 and 12.4 and two-stage Hf model ages of 448-562 Ma, indicating that the region is underlain by Cadomian-Caledonian crust. According to the Hf-O isotopic values, the main mechanism forming zircon rims was dissolution of pre-existing detrital zircons with reprecipitation of new zircon shortly thereafter. Oligocene ages indicate that partial melting accompanied core complex formation in the Zanjan-Takab region. Extension, melting, and core complex formation in south-central Iran are Eocene in age, but younger ages of Oligocene-Miocene in NW Iran and Turkey indicate that extension was distributed throughout the region during Cenozoic time.

Nephrin Regulates Lamellipodia Formation by Assembling a Protein Complex That Includes Ship2, Filamin and Lamellipodin

PubMed Central

Venkatareddy, Madhusudan; Cook, Leslie; Abuarquob, Kamal; Verma, Rakesh; Garg, Puneet

2011-01-01

Actin dynamics has emerged at the forefront of podocyte biology. Slit diaphragm junctional adhesion protein Nephrin is necessary for development of the podocyte morphology and transduces phosphorylation-dependent signals that regulate cytoskeletal dynamics. The present study extends our understanding of Nephrin function by showing in cultured podocytes that Nephrin activation induced actin dynamics is necessary for lamellipodia formation. Upon activation Nephrin recruits and regulates a protein complex that includes Ship2 (SH2 domain containing 5′ inositol phosphatase), Filamin and Lamellipodin, proteins important in regulation of actin and focal adhesion dynamics, as well as lamellipodia formation. Using the previously described CD16-Nephrin clustering system, Nephrin ligation or activation resulted in phosphorylation of the actin crosslinking protein Filamin in a p21 activated kinase dependent manner. Nephrin activation in cell culture results in formation of lamellipodia, a process that requires specialized actin dynamics at the leading edge of the cell along with focal adhesion turnover. In the CD16-Nephrin clustering model, Nephrin ligation resulted in abnormal morphology of actin tails in human podocytes when Ship2, Filamin or Lamellipodin were individually knocked down. We also observed decreased lamellipodia formation and cell migration in these knock down cells. These data provide evidence that Nephrin not only initiates actin polymerization but also assembles a protein complex that is necessary to regulate the architecture of the generated actin filament network and focal adhesion dynamics. PMID:22194892

The structure and evolution of galacto-detonation waves - Some analytic results in sequential star formation models of spiral galaxies

NASA Technical Reports Server (NTRS)

Cowie, L. L.; Rybicki, G. B.

1982-01-01

Waves of star formation in a uniform, differentially rotating disk galaxy are treated analytically as a propagating detonation wave front. It is shown, that if single solitary waves could be excited, they would evolve asymptotically to one of two stable spiral forms, each of which rotates with a fixed pattern speed. Simple numerical solutions confirm these results. However, the pattern of waves that develop naturally from an initially localized disturbance is more complex and dies out within a few rotation periods. These results suggest a conclusive observational test for deciding whether sequential star formation is an important determinant of spiral structure in some class of galaxies.

Antipsychotics reverse abnormal EEG complexity in drug-naïve schizophrenia: A multiscale entropy analysis

PubMed Central

Takahashi, Tetsuya; Cho, Raymond Y.; Mizuno, Tomoyuki; Kikuchi, Mitsuru; Murata, Tetsuhito; Takahashi, Koichi; Wada, Yuji

2010-01-01

Multiscale entropy (MSE) analysis is a novel entropy-based approach for measuring dynamical complexity in physiological systems over a range of temporal scales. To evaluate this analytic approach as an aid to elucidating the pathophysiologic mechanisms in schizophrenia, we examined MSE in EEG activity in drug-naïve schizophrenia subjects pre- and post-treatment with antipsychotics in comparison with traditional EEG analysis. We recorded eyes-closed resting state EEG from frontal, temporal, parietal and occipital regions in drug-naïve 22 schizophrenia and 24 age-matched healthy control subjects. Fifteen patients were re-evaluated within 2–8 weeks after the initiation of antipsychotic treatment. For each participant, MSE was calculated on one continuous 60 second epoch for each experimental session. Schizophrenia subjects showed significantly higher complexity at higher time scales (lower frequencies), than that of healthy controls in fronto-centro-temporal, but not in parieto-occipital regions. Post-treatment, this higher complexity decreased to healthy control subject levels selectively in fronto-central regions, while the increased complexity in temporal sites remained higher. Comparative power analysis identified spectral slowing in frontal regions in pre-treatment schizophrenia subjects, consistent with previous findings, whereas no antipsychotic treatment effect was observed. In summary, multiscale entropy measures identified abnormal dynamical EEG signal complexity in anterior brain areas in schizophrenia that normalized selectively in fronto-central areas with antipsychotic treatment. These findings show that entropy-based analytic methods may serve as a novel approach for characterizing and understanding abnormal cortical dynamics in schizophrenia, and elucidating the therapeutic mechanisms of antipsychotics. PMID:20149880

Effect of Pedagogical Formation Program on Pre-Service History Teachers' Perceived Self-Efficacy

ERIC Educational Resources Information Center

Yazici, Fatih; Yildirim, Tercan

2017-01-01

The purpose of the present study is to investigate pre-service history teachers' perceived self-efficacy and the effect of pedagogical formation training on this perception. The study is based on a one-group pretest-posttest research design, which is a type of pre-experimental design. For the purpose of the study, in the first week of the…

An Investigation of Pre-Service Science Teachers' Level of Efficacy in the Undergraduate Science Teacher Education Program and Pedagogical Formation Program

ERIC Educational Resources Information Center

Çetin, Oguz

2017-01-01

The purpose of this research is to comparatively investigate the efficacy levels of pre-service science (Science, Biology, Physics, and Chemistry) teachers enrolled at the Undergraduate Program of Science Teacher Education and Pedagogical Formation Program. A total of 275 pre-service teachers who were studying in different programmes in the…

The impact of dihydrogen phosphate anions on the excited-state proton transfer of harmane. Effect of β-cyclodextrin on these photoreactions.

PubMed

Reyman, Dolores; Viñas, Montserrat H; Tardajos, Gloria; Mazario, Eva

2012-01-12

Photoinduced proton transfer reactions of harmane (1-methyl-9H-pyrido[3,4-b]indole) (HAR) in the presence of a proton donor/acceptor such as dihydrogen phosphate anions in aqueous solution have been studied by stationary and time-resolved fluorescence spectroscopy. The presence of high amounts of dihydrogen phosphate ions modifies the acid/base properties of this alkaloid. Thus, by keeping the pH constant at pH 8.8 and by increasing the amount of NaH(2)PO(4) in the solution, it is possible to reproduce the same spectral profiles as those obtained in high alkaline solutions (pH >12) in the absence of NaH(2)PO(4). Under these conditions, a new fluorescence profile appears at around 520 nm. This result could be related to the results of a recent investigation which suggests that a high intake of phosphates may promote skin tumorigenesis. The presence of β-cyclodextrin (β-CD) avoids the proton transfer reactions in this alkaloid by means the formation of an inclusion complex between β-CD and HAR. The formation of this complex originates a remarkable enhancement of the emission intensity from the neutral form in contrast to the cationic and zwitterionic forms. A new lifetime was obtained at 360 nm (2.5 ns), which was associated with the emission of this inclusion complex. At this wavelength, the fluorescence intensity decay of HAR can be described by a linear combination of two exponentials. From the ratio between the pre-exponential factors, we have obtained a value of K = 501 M for the equilibrium of formation of this complex.

Non-FG mediated transport of the large pre-ribosomal subunit through the nuclear pore complex by the mRNA export factor Gle2

PubMed Central

Occhipinti, Laura; Chang, Yiming; Altvater, Martin; Menet, Anna M.; Kemmler, Stefan; Panse, Vikram G.

2013-01-01

Multiple export receptors passage bound pre-ribosomes through nuclear pore complexes (NPCs) by transiently interacting with the Phe-Gly (FG) meshwork of their transport channels. Here, we reveal how the non-FG interacting yeast mRNA export factor Gly-Leu-FG lethal 2 (Gle2) functions in the export of the large pre-ribosomal subunit (pre-60S). Structure-guided studies uncovered conserved platforms used by Gle2 to export pre-60S: an uncharacterized basic patch required to bind pre-60S, and a second surface that makes non-FG contacts with the nucleoporin Nup116. A basic patch mutant of Gle2 is able to function in mRNA export, but not pre-60S export. Thus, Gle2 provides a distinct interaction platform to transport pre-60S to the cytoplasm. Notably, Gle2’s interaction platforms become crucial for pre-60S export when FG-interacting receptors are either not recruited to pre-60S or are impaired. We propose that large complex cargos rely on non-FG as well as FG-interactions for their efficient translocation through the nuclear pore complex channel. PMID:23907389

Re-wiring of energy metabolism promotes viability during hyperreplication stress in E. coli

PubMed Central

Campion, Christopher; Weimann, Allan

2017-01-01

Chromosome replication in Escherichia coli is initiated by DnaA. DnaA binds ATP which is essential for formation of a DnaA-oriC nucleoprotein complex that promotes strand opening, helicase loading and replisome assembly. Following initiation, DnaAATP is converted to DnaAADP primarily by the Regulatory Inactivation of DnaA process (RIDA). In RIDA deficient cells, DnaAATP accumulates leading to uncontrolled initiation of replication and cell death by accumulation of DNA strand breaks. Mutations that suppress RIDA deficiency either dampen overinitiation or permit growth despite overinitiation. We characterize mutations of the last group that have in common that distinct metabolic routes are rewired resulting in the redirection of electron flow towards the cytochrome bd-1. We propose a model where cytochrome bd-1 lowers the formation of reactive oxygen species and hence oxidative damage to the DNA in general. This increases the processivity of replication forks generated by overinitiation to a level that sustains viability. PMID:28129339

Pre-registration interprofessional clinical education in the workplace: a realist review.

PubMed

Kent, Fiona; Hayes, Jacinta; Glass, Sharon; Rees, Charlotte E

2017-09-01

The inclusion of interprofessional education opportunities in clinical placements for pre-registration learners has recently been proposed as a strategy to enhance graduates' skills in collaborative practice. A realist review was undertaken to ascertain the contexts, mechanisms and outcomes of formal interprofessional clinical workplace learning. Initial scoping was carried out, after which Ovid MEDLINE, CINAHL and EMBASE were searched from 2005 to April 2016 to identify formal interprofessional workplace educational interventions involving pre-registration learners. Papers reporting studies conducted in dedicated training wards were excluded, leaving a total of 30 papers to be included in the review. Several educational formats that combined students from medicine, nursing, pharmacy and allied health professions were identified. These included: the use of engagement by student teams with a real patient through interview as the basis for discussion and reflection; the use of case studies through which student teams work to promote discussion; structured workshops; ward rounds, and shadowing. Meaningful interprofessional student discussion and reflection comprised the mechanism by which the outcome of learners acquiring knowledge of the roles of other professions and teamwork skills was achieved. The mechanism of dialogue during an interaction with a real patient allowed the patient to provide his or her perspective and contributed to an awareness of the patient's perspective in health care practice. Medication- or safety-focused interprofessional tasks contributed to improved safety awareness. In the absence of trained facilitators or in the context of negative role-modelling, programmes were less successful. In the design of workplace education initiatives, curriculum decisions should take into consideration the contexts of the initiatives and the mechanisms for achieving the education-related outcomes of interest. © 2017 John Wiley & Sons Ltd and The Association for the Study of Medical Education.

Mediator structure and rearrangements required for holoenzyme formation.

PubMed

Tsai, Kuang-Lei; Yu, Xiaodi; Gopalan, Sneha; Chao, Ti-Chun; Zhang, Ying; Florens, Laurence; Washburn, Michael P; Murakami, Kenji; Conaway, Ronald C; Conaway, Joan W; Asturias, Francisco J

2017-04-13

The conserved Mediator co-activator complex has an essential role in the regulation of RNA polymerase II transcription in all eukaryotes. Understanding the structure and interactions of Mediator is crucial for determining how the complex influences transcription initiation and conveys regulatory information to the basal transcription machinery. Here we present a 4.4 Å resolution cryo-electron microscopy map of Schizosaccharomyces pombe Mediator in which conserved Mediator subunits are individually resolved. The essential Med14 subunit works as a central backbone that connects the Mediator head, middle and tail modules. Comparison with a 7.8 Å resolution cryo-electron microscopy map of a Mediator-RNA polymerase II holoenzyme reveals that changes in the structure of Med14 facilitate a large-scale Mediator rearrangement that is essential for holoenzyme formation. Our study suggests that access to different conformations and crosstalk between structural elements are essential for the Mediator regulation mechanism, and could explain the capacity of the complex to integrate multiple regulatory signals.

N-Picolyl Derivatives of Kemp’s Triamine as Potential Antitumor Agents: A Preliminary Investigation

PubMed Central

Regino, Celeste Aida S.; Torti, Suzy V.; Ma, Rong; Yap, Glenn P.A.; Kreisel, Kevin A.; Torti, Frank M.; Planalp, Roy P.; Brechbiel, Martin W.

2008-01-01

Pre-organized tripodal ligands such as the N-picolyl derivatives of cis,cis-1,3,5-triamino-cis,cis-1,3,5-trimethylcyclohexane (Kemp’s triamine) were prepared as analogs to N,N’,N”- tris(2-pyridylmethyl)-cis,cis-1,3,5-triaminocyclohexane (tachpyr) in hopes of enhancing the rate of formation and stability of the metal complexes. A tricyclic bisaminal was formed via the reduction of the Schiff base while the tri(picolyl) derivative was synthesized via reductive amination of pyridine carboxaldehyde. Their cytotoxicities to the HeLa cell line were evaluated and directly compared to tachpyr and N,N’,N”- tris(2-pyridylmethyl)-tris(2-aminoethyl)amine (trenpyr). Results indicate that N,N’,N”-tris(2-pyridylmethyl)-cis,cis-1,3,5-triamino-cis,cis-1,3,5-trimethylcyclohexane (Kemp’s pyr) exhibits cytotoxic activity against the HeLa cancer cell line comparable to tachpyr (IC50 ~ 8.0 µM). Both Kemp’s pyr and tachpyr show higher cytotoxic activity over the aliphatic analogue of trenpyr (IC50 ~ 14 µM) suggesting that the major contributor to the activity is the ligand’s ability to form a stable and tight complex and that the equatorial/axial equilibrium impacting the complex formation for the cyclohexane-based ligands is not significant. PMID:16335923

Genetic variations in the DNA replication origins of human papillomavirus family correlate with their oncogenic potential.

PubMed

Yilmaz, Gulden; Biswas-Fiss, Esther E; Biswas, Subhasis B

2018-04-01

Human papillomaviruses (HPVs) encompass a large family of viruses that range from benign to highly carcinogenic. The crucial differences between benign and carcinogenic types of HPV remain unknown, except that the two HPV types differ in the frequency of DNA replication. We have systematically analyzed the mechanism of HPV DNA replication initiation in low-risk and high-risk HPVs. Our results demonstrate that HPV-encoded E2 initiator protein and its four binding sites in the replication origin play pivotal roles in determining the destiny of the HPV-infected cell. We have identified strain-specific single nucleotide variations in E2 binding sites found only in the high-risk HPVs. We have demonstrated that these variations result in attenuated formation of the E2-DNA complex. E2 binding to these sites is linked to the activation of the DNA replication origin as well as initiation of DNA replication. Both electrophoretic mobility shift assay and atomic force microscopy studies demonstrated that binding of E2 from either low- or high-risk HPVs with variant binding sequences lacked multimeric E2-DNA complex formation in vitro. These results provided a molecular basis of differential DNA replication in the two types of HPVs and pointed to a correlation with the development of cancer. Copyright © 2017. Published by Elsevier B.V.

Hypothesis testing for the validation of the kinetic spectrophotometric methods for the determination of lansoprazole in bulk and drug formulations via Fe(III) and Zn(II) chelates.

PubMed

Rahman, Nafisur; Kashif, Mohammad

2010-03-01

Point and interval hypothesis tests performed to validate two simple and economical, kinetic spectrophotometric methods for the assay of lansoprazole are described. The methods are based on the formation of chelate complex of the drug with Fe(III) and Zn(II). The reaction is followed spectrophotometrically by measuring the rate of change of absorbance of coloured chelates of the drug with Fe(III) and Zn(II) at 445 and 510 nm, respectively. The stoichiometric ratio of lansoprazole to Fe(III) and Zn(II) complexes were found to be 1:1 and 2:1, respectively. The initial-rate and fixed-time methods are adopted for determination of drug concentrations. The calibration graphs are linear in the range 50-200 µg ml⁻¹ (initial-rate method), 20-180 µg ml⁻¹ (fixed-time method) for lansoprazole-Fe(III) complex and 120-300 (initial-rate method), and 90-210 µg ml⁻¹ (fixed-time method) for lansoprazole-Zn(II) complex. The inter-day and intra-day precision data showed good accuracy and precision of the proposed procedure for analysis of lansoprazole. The point and interval hypothesis tests indicate that the proposed procedures are not biased. Copyright © 2010 John Wiley & Sons, Ltd.

Sequential self-assembly of DNA functionalized droplets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yin; McMullen, Angus; Pontani, Lea-Laetitia

Complex structures and devices, both natural and manmade, are often constructed sequentially. From crystallization to embryogenesis, a nucleus or seed is formed and built upon. Sequential assembly allows for initiation, signaling, and logical programming, which are necessary for making enclosed, hierarchical structures. Though biology relies on such schemes, they have not been available in materials science. We demonstrate programmed sequential self-assembly of DNA functionalized emulsions. The droplets are initially inert because the grafted DNA strands are pre-hybridized in pairs. Active strands on initiator droplets then displace one of the paired strands and thus release its complement, which in turn activatesmore » the next droplet in the sequence, akin to living polymerization. This strategy provides time and logic control during the self-assembly process, and offers a new perspective on the synthesis of materials.« less

Robonaut Mobile Autonomy: Initial Experiments

NASA Technical Reports Server (NTRS)

Diftler, M. A.; Ambrose, R. O.; Goza, S. M.; Tyree, K. S.; Huber, E. L.

2006-01-01

A mobile version of the NASA/DARPA Robonaut humanoid recently completed initial autonomy trials working directly with humans in cluttered environments. This compact robot combines the upper body of the Robonaut system with a Segway Robotic Mobility Platform yielding a dexterous, maneuverable humanoid ideal for interacting with human co-workers in a range of environments. This system uses stereovision to locate human teammates and tools and a navigation system that uses laser range and vision data to follow humans while avoiding obstacles. Tactile sensors provide information to grasping algorithms for efficient tool exchanges. The autonomous architecture utilizes these pre-programmed skills to form complex behaviors. The initial behavior demonstrates a robust capability to assist a human by acquiring a tool from a remotely located individual and then following the human in a cluttered environment with the tool for future use.

Sequential self-assembly of DNA functionalized droplets

DOE PAGES

Zhang, Yin; McMullen, Angus; Pontani, Lea-Laetitia; ...

2017-06-16

Complex structures and devices, both natural and manmade, are often constructed sequentially. From crystallization to embryogenesis, a nucleus or seed is formed and built upon. Sequential assembly allows for initiation, signaling, and logical programming, which are necessary for making enclosed, hierarchical structures. Though biology relies on such schemes, they have not been available in materials science. We demonstrate programmed sequential self-assembly of DNA functionalized emulsions. The droplets are initially inert because the grafted DNA strands are pre-hybridized in pairs. Active strands on initiator droplets then displace one of the paired strands and thus release its complement, which in turn activatesmore » the next droplet in the sequence, akin to living polymerization. This strategy provides time and logic control during the self-assembly process, and offers a new perspective on the synthesis of materials.« less

Why we need asteroid sample return mission?

NASA Astrophysics Data System (ADS)

Barucci, Maria Antonietta

2016-07-01

Small bodies retain evidence of the primordial solar nebula and the earliest solar system processes that shaped their evolution. They may also contain pre-solar material as well as complex organic molecules, which could have a major role to the development of life on Earth. For these reasons, asteroids and comets have been targets of interest for missions for over three decades. However, our knowledge of these bodies is still very limited, and each asteroid or comet visited by space mission has revealed unexpected scientific results, e.g. the structure and nature of comet 67P/Churyumov-Gerasimenko (67P/C-G) visited by the Rosetta mission. Only in the laboratory can instruments with the necessary precision and sensitivity be applied to individual components of the complex mixture of materials that forms a small body regolith, to determine their precise chemical and isotopic composition. Such measurements are vital for revealing the evidence of stellar, interstellar medium, pre-solar nebula and parent body processes that are retained in primitive material, unaltered by atmospheric entry or terrestrial contamination. For those reasons, sample return missions are considered a high priority by a number of the leading space agencies. Abundant within the inner Solar System and the main impactors on terrestrial planets, small bodies may have been the principal contributors of the water and organic material essential to create life on Earth. Small bodies can therefore be considered to be equivalent to DNA for unravelling our solar system's history, offering us a unique window to investigate both the formation of planets and the origin of life. A sample return mission to a primitive Near-Earth Asteroid (NEA) has been study at ESA from 2008 in the framework of ESA's Cosmic Vision (CV) programme, with the objective to answer to the fundamental CV questions "How does the Solar System work?" and "What are the conditions for life and planetary formations?". The returned material will allow us to study in terrestrial laboratories some of the most primitive materials available to investigate early solar system formation processes, to explore initial stages of habitable planet formation, to identify and characterize the organics and volatiles in a primitive asteroid. The ideal easy target body for such mission is a D type NEA. D types are the most abundant asteroids beyond the outer edge of the main belt. It is likely that they formed much further out in the Solar System, possibly as far as the transneptunian objects, and were subsequently captured in their present locations following the migration of the gas giants. Spectral features indicate that these bodies are organic rich, contain fine anhydrous minerals but also may be volatile rich and appear to be the most primitive rocky material present in the solar system. In addition to addressing the major science goals, sample return mission from a NEA also involved innovative European technologies. The key sample return capabilities, i.e. asteroid navigation, touch and go, sampling mechanism and the re-entry capsule have reached at ESA a validation status to enter implementation phase. The development of sample return technology represents in Europe a crucial element for planetary science and for the space technology development.

Cilostamide and forskolin treatment during pre-IVM improves preimplantation development of cloned embryos by influencing meiotic progression and gap junction communication in pigs.

PubMed

Park, Bola; Lee, Hanna; Lee, Yongjin; Elahi, Fazle; Lee, Joohyeong; Lee, Seung Tae; Park, Choon-Keun; Hyun, Sang-Hwan; Lee, Eunsong

2016-08-01

This study was conducted to evaluate the effects of treatment with the cAMP modulators cilostamide and/or forskolin during pre-IVM culture on meiotic progression, gap junction communication, intraoocyte cAMP level and glutathione content, embryonic development after parthenogenesis, and somatic cell nuclear transfer in pigs. Cumulus-oocyte complexes were cultured for 24 hours in unsupplemented medium or media containing 20 μM cilostamide and/or 50 μM forskolin. After pre-IVM, oocytes were cultured for 41 to 44 hours in a standard IVM medium to induce oocyte maturation. When the nuclear status of oocytes was examined after pre-IVM for 24 hours, a higher (P < 0.01) proportion of oocytes treated with forskolin (85.5%) and cilostamide + forskolin (92.6%) remained at the germinal vesicle stage compared with untreated (20.6%) and cilostamide-treated oocytes (54.7%). cAMP level in pre-IVM oocytes was significantly increased by combined treatment with cilostamide + forskolin (21.38 fmol/oocyte) relative to the no pre-IVM control, no treatment, cilostamide, and forskolin groups (2.85, 1.88, 1.74, and 8.95 fmol/oocyte, respectively). Forskolin with or without cilostamide significantly maintained open-gap junction communication relative to no treatment. Blastocyst formation in parthenogenesis was significantly (P < 0.01) improved by forskolin (65.3%) relative to other treatments (28.3% to 48.1%). Supplementation of pre-IVM with dibutyryl cAMP showed similar blastocyst formation as forskolin treatment (61.1% and 61.0%, respectively). In somatic cell nuclear transfer, simultaneous treatment with cilostamide + forskolin significantly (P < 0.05) increased embryonic development to the blastocyst stage (42.9%) relative to the no pre-IVM, control, and cilostamide groups (32.3, 28.6, and 32.8%, respectively). The glutathione contents in pre-IVM oocytes were increased by no treatment, forskolin, and cilostamide + forskolin (1.38, 1.39, and 1.27 pixels/oocyte, respectively) compared with no pre-IVM and cilostamide (1.00 and 0.99 pixels/oocyte, respectively; P < 0.05). Our results reported that the meiotic progression of immature pig oocytes could be reversibly attenuated by cAMP, whereas treatment with cilostamide and forskolin during pre-IVM had positive effects on developmental competence of oocytes in pigs, probably by improving cytoplasmic maturation. Copyright © 2016 Elsevier Inc. All rights reserved.