The effect of L1 orthography on non-native vowel perception.

PubMed

Escudero, Paola; Wanrooij, Karin

2010-01-01

Previous research has shown that orthography influences the learning and processing of spoken non-native words. In this paper, we examine the effect of L1 orthography on non-native sound perception. In Experiment 1, 204 Spanish learners of Dutch and a control group of 20 native speakers of Dutch were asked to classify Dutch vowel tokens by choosing from auditorily presented options, in one task, and from the orthographic representations of Dutch vowels, in a second task. The results show that vowel categorization varied across tasks: the most difficult vowels in the purely auditory task were the easiest in the orthographic task and, conversely, vowels with a relatively high success rate in the purely auditory task were poorly classified in the orthographic task. The results of Experiment 2 with 22 monolingual Peruvian Spanish listeners replicated the main results of Experiment 1 and confirmed the existence of orthographic effects. Together, the two experiments show that when listening to auditory stimuli only, native speakers of Spanish have great difficulty classifying certain Dutch vowels, regardless of the amount of experience they may have with the Dutch language. Importantly, the pairing of auditory stimuli with orthographic labels can help or hinder Spanish listeners' sound categorization, depending on the specific sound contrast.

Complex, multi-scale small intestinal topography replicated in cellular growth substrates fabricated via chemical vapor deposition of Parylene C.

PubMed

Koppes, Abigail N; Kamath, Megha; Pfluger, Courtney A; Burkey, Daniel D; Dokmeci, Mehmet; Wang, Lin; Carrier, Rebecca L

2016-08-22

Native small intestine possesses distinct multi-scale structures (e.g., crypts, villi) not included in traditional 2D intestinal culture models for drug delivery and regenerative medicine. The known impact of structure on cell function motivates exploration of the influence of intestinal topography on the phenotype of cultured epithelial cells, but the irregular, macro- to submicron-scale features of native intestine are challenging to precisely replicate in cellular growth substrates. Herein, we utilized chemical vapor deposition of Parylene C on decellularized porcine small intestine to create polymeric intestinal replicas containing biomimetic irregular, multi-scale structures. These replicas were used as molds for polydimethylsiloxane (PDMS) growth substrates with macro to submicron intestinal topographical features. Resultant PDMS replicas exhibit multiscale resolution including macro- to micro-scale folds, crypt and villus structures, and submicron-scale features of the underlying basement membrane. After 10 d of human epithelial colorectal cell culture on PDMS substrates, the inclusion of biomimetic topographical features enhanced alkaline phosphatase expression 2.3-fold compared to flat controls, suggesting biomimetic topography is important in induced epithelial differentiation. This work presents a facile, inexpensive method for precisely replicating complex hierarchal features of native tissue, towards a new model for regenerative medicine and drug delivery for intestinal disorders and diseases.

Light-use efficiency of native and hybrid poplar genotypes at high levels of intracanopy competition

Treesearch

D. Scott Green; Eric L. Kruger; Glen R, Stanosz; J. G. Isebrands

2001-01-01

In southern Wisconsin, U.S.A., tree growth and associated canopy traits were compared among five native and hybrid genotypes of poplar (Populus spp.) in replicated, monoclonal stands planted at a 1 x 1 m spacing. The overall objective of this study was to assess clonal suitability to cultural conditions entailing high levels of intracanopy...

Purification, crystallization and X-ray diffraction analysis of the C-terminal protease domain of Venezuelan equine encephalitis virus nsP2

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

Russo, Andrew T.; Watowich, Stanley J., E-mail: watowich@xray.utmb.edu

2006-06-01

The C-terminal protease domain of Venezuelan equine encephalitis virus (VEEV) nsP2 has been overexpressed in E. coli, purified and successfully crystallized. Native crystals diffract to beyond 2.5 Å resolution and isomorphous heavy-atom derivatives suitable for phase analysis have been identified. The C-terminal region of Venezuelan equine encephalitis virus (VEEV) nsP2 is responsible for proteolytic processing of the VEEV polyprotein replication complex. This action regulates the activity of the replication complex and is essential for viral replication, thus making nsP2 a very attractive target for development of VEEV therapeutics. The 338-amino-acid C-terminal region of VEEV nsP2 has been overexpressed in Escherichiamore » coli, purified and crystallized. Crystals diffract to beyond 2.5 Å resolution and belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}. Isomorphous heavy-atom derivatives suitable for phase analysis have been obtained and work on building a complete structural model is under way.« less

Proficiency and sentence constraint effects on second language word learning.

PubMed

Ma, Tengfei; Chen, Baoguo; Lu, Chunming; Dunlap, Susan

2015-07-01

This paper presents an experiment that investigated the effects of L2 proficiency and sentence constraint on semantic processing of unknown L2 words (pseudowords). All participants were Chinese native speakers who learned English as a second language. In the experiment, we used a whole sentence presentation paradigm with a delayed semantic relatedness judgment task. Both higher and lower-proficiency L2 learners could make use of the high-constraint sentence context to judge the meaning of novel pseudowords, and higher-proficiency L2 learners outperformed lower-proficiency L2 learners in all conditions. These results demonstrate that both L2 proficiency and sentence constraint affect subsequent word learning among second language learners. We extended L2 word learning into a sentence context, replicated the sentence constraint effects previously found among native speakers, and found proficiency effects in L2 word learning. Copyright © 2015 Elsevier B.V. All rights reserved.

Engineered disc-like angle-ply structures for intervertebral disc replacement.

PubMed

Nerurkar, Nandan L; Sen, Sounok; Huang, Alice H; Elliott, Dawn M; Mauck, Robert L

2010-04-15

To develop a construction algorithm in which electrospun nanofibrous scaffolds are coupled with a biocompatible hydrogel to engineer a mesenchymal stem cell (MSC)-based disc replacement. To engineer a disc-like angle-ply structure (DAPS) that replicates the multiscale architecture of the intervertebral disc. Successful engineering of a replacement for the intervertebral disc requires replication of its mechanical function and anatomic form. Despite many attempts to engineer a replacement for ailing and degenerated discs, no prior study has replicated the multiscale hierarchical architecture of the native disc, and very few have assessed the mechanical function of formed neo-tissues. A new algorithm for the construction of a disc analogue was developed, using agarose to form a central nucleus pulposus (NP) and oriented electrospun nanofibrous scaffolds to form the anulus fibrosus region (AF). Bovine MSCs were seeded into both regions and biochemical, histologic, and mechanical maturation were evaluated with in vitro culture. We show that mechanical testing in compression and torsion, loading methods commonly used to assess disc mechanics, reveal equilibrium and time-dependent behaviors that are qualitatively similar to native tissue, although lesser in magnitude. Further, we demonstrate that cells seeded into both AF and NP regions adopt distinct morphologies that mirror those seen in native tissue, and that, in the AF region, this ordered community of cells deposit matrix that is organized in an angle-ply configuration. Finally, constructs demonstrate functional development with long-term in vitro culture. These findings provide a new approach for disc tissue engineering that replicates multi-scale form and function of the intervertebral disc, providing a foundation from which to build a multi-scale, biologic, anatomically and hierarchically relevant composite disc analogue for eventual disc replacement.

Using eye-tracking to study the on-line processing of case-marking information among intermediate L2 learners of German

PubMed Central

Jackson, Carrie N.; Dussias, Paola E.; Hristova, Adelina

2012-01-01

This study uses eye-tracking to examine the processing of case-marking information in ambiguous subject- and object-first wh-questions in German. The position of the lexical verb was also manipulated via verb tense to investigate whether verb location influences how intermediate L2 learners process L2 sentences. Results show that intermediate L2 German learners were sensitive to case-marking information, exhibiting longer processing times on subject-first than object-first sentences, regardless of verb location. German native speakers exhibited the opposite word order preference, with longer processing times on object-first than subject-first sentences, replicating previous findings. These results are discussed in light of current L2 processing research, highlighting how methodological constraints influence researchers’ abilities to measure the on-line processing of morphosyntactic information among intermediate L2 learners. PMID:23493761

Performance and lipid profiles of native chickens fed diet containing skipjack fish oil as by-product of fish canning factory

NASA Astrophysics Data System (ADS)

Leke, J. R.; Mandey, J. S.; Laihad, J. T.; Tinangon, R. M.; Tangkau, L.; Junus, C.

2018-01-01

The study was conducted to determine the use of fish oil as by-product of fish canning factory in diet on the performance and lipid profiles of native chickens. The experiment used 100 native chicken with an average initial body weight of 48,9 gram (sd + 9.9), was used in this study for 8 weeks experiment. These were arranged by a completely randomized design with 5 treatments, 5 replications and 4 hens in replication each. The diets were: R0 = 100% Based Diet (BD) + 0% Fish Oil (FO); R1 = 98.5% BD + 1.5% FO; R2 = 98% BD + 2% FO; R3 = 97.5% BD + 2.5% FO; R4 = 97 % BD + 3% FO. Feed and water were provided ad libitum. Variables were performance parameters and lipid profiles. Results showed that fish oil inclusion in diets were significantly increased feed intake, body weight gain, carcass percentage, liver, breast and thigh weight, and decreased blood cholesterol, carbohydrate and meat cholesterol, and also tended to decrease abdominal fat. However, there were no affected on feed conversion, water, protein, fat and ash of breast meat. It can be concluded that the use of fish oil in diet up to 3% could improved performance parameters of native chickens.

Climate modifies response of non-native and native species richness to nutrient enrichment.

PubMed

Flores-Moreno, Habacuc; Reich, Peter B; Lind, Eric M; Sullivan, Lauren L; Seabloom, Eric W; Yahdjian, Laura; MacDougall, Andrew S; Reichmann, Lara G; Alberti, Juan; Báez, Selene; Bakker, Jonathan D; Cadotte, Marc W; Caldeira, Maria C; Chaneton, Enrique J; D'Antonio, Carla M; Fay, Philip A; Firn, Jennifer; Hagenah, Nicole; Harpole, W Stanley; Iribarne, Oscar; Kirkman, Kevin P; Knops, Johannes M H; La Pierre, Kimberly J; Laungani, Ramesh; Leakey, Andrew D B; McCulley, Rebecca L; Moore, Joslin L; Pascual, Jesus; Borer, Elizabeth T

2016-05-19

Ecosystem eutrophication often increases domination by non-natives and causes displacement of native taxa. However, variation in environmental conditions may affect the outcome of interactions between native and non-native taxa in environments where nutrient supply is elevated. We examined the interactive effects of eutrophication, climate variability and climate average conditions on the success of native and non-native plant species using experimental nutrient manipulations replicated at 32 grassland sites on four continents. We hypothesized that effects of nutrient addition would be greatest where climate was stable and benign, owing to reduced niche partitioning. We found that the abundance of non-native species increased with nutrient addition independent of climate; however, nutrient addition increased non-native species richness and decreased native species richness, with these effects dampened in warmer or wetter sites. Eutrophication also altered the time scale in which grassland invasion responded to climate, decreasing the importance of long-term climate and increasing that of annual climate. Thus, climatic conditions mediate the responses of native and non-native flora to nutrient enrichment. Our results suggest that the negative effect of nutrient addition on native abundance is decoupled from its effect on richness, and reduces the time scale of the links between climate and compositional change. © 2016 The Author(s).

Climate modifies response of non-native and native species richness to nutrient enrichment

PubMed Central

Flores-Moreno, Habacuc; Reich, Peter B.; Lind, Eric M.; Sullivan, Lauren L.; Seabloom, Eric W.; Yahdjian, Laura; MacDougall, Andrew S.; Reichmann, Lara G.; Alberti, Juan; Báez, Selene; Bakker, Jonathan D.; Cadotte, Marc W.; Caldeira, Maria C.; Chaneton, Enrique J.; D'Antonio, Carla M.; Fay, Philip A.; Firn, Jennifer; Hagenah, Nicole; Harpole, W. Stanley; Iribarne, Oscar; Kirkman, Kevin P.; Knops, Johannes M. H.; La Pierre, Kimberly J.; Laungani, Ramesh; Leakey, Andrew D. B.; McCulley, Rebecca L.; Moore, Joslin L.; Pascual, Jesus; Borer, Elizabeth T.

2016-01-01

Ecosystem eutrophication often increases domination by non-natives and causes displacement of native taxa. However, variation in environmental conditions may affect the outcome of interactions between native and non-native taxa in environments where nutrient supply is elevated. We examined the interactive effects of eutrophication, climate variability and climate average conditions on the success of native and non-native plant species using experimental nutrient manipulations replicated at 32 grassland sites on four continents. We hypothesized that effects of nutrient addition would be greatest where climate was stable and benign, owing to reduced niche partitioning. We found that the abundance of non-native species increased with nutrient addition independent of climate; however, nutrient addition increased non-native species richness and decreased native species richness, with these effects dampened in warmer or wetter sites. Eutrophication also altered the time scale in which grassland invasion responded to climate, decreasing the importance of long-term climate and increasing that of annual climate. Thus, climatic conditions mediate the responses of native and non-native flora to nutrient enrichment. Our results suggest that the negative effect of nutrient addition on native abundance is decoupled from its effect on richness, and reduces the time scale of the links between climate and compositional change. PMID:27114575

Plasmid replication initiator RepB forms a hexamer reminiscent of ring helicases and has mobile nuclease domains

PubMed Central

Boer, D Roeland; Ruíz-Masó, José A; López-Blanco, José R; Blanco, Alexander G; Vives-Llàcer, Mireia; Chacón, Pablo; Usón, Isabel; Gomis-Rüth, F Xavier; Espinosa, Manuel; Llorca, Oscar; del Solar, Gloria; Coll, Miquel

2009-01-01

RepB initiates plasmid rolling-circle replication by binding to a triple 11-bp direct repeat (bind locus) and cleaving the DNA at a specific distant site located in a hairpin loop within the nic locus of the origin. The structure of native full-length RepB reveals a hexameric ring molecule, where each protomer has two domains. The origin-binding and catalytic domains show a three-layer α–β–α sandwich fold. The active site is positioned at one of the faces of the β-sheet and coordinates a Mn2+ ion at short distance from the essential nucleophilic Y99. The oligomerization domains (ODs), each consisting of four α-helices, together define a compact ring with a central channel, a feature found in ring helicases. The toroidal arrangement of RepB suggests that, similar to ring helicases, it encircles one of the DNA strands during replication to confer processivity to the replisome complex. The catalytic domains appear to be highly mobile with respect to ODs. This mobility may account for the adaptation of the protein to two distinct DNA recognition sites. PMID:19440202

Plant species' origin predicts dominance and response to nutrient enrichment and herbivores in global grasslands.

PubMed

Seabloom, Eric W; Borer, Elizabeth T; Buckley, Yvonne M; Cleland, Elsa E; Davies, Kendi F; Firn, Jennifer; Harpole, W Stanley; Hautier, Yann; Lind, Eric M; MacDougall, Andrew S; Orrock, John L; Prober, Suzanne M; Adler, Peter B; Anderson, T Michael; Bakker, Jonathan D; Biederman, Lori A; Blumenthal, Dana M; Brown, Cynthia S; Brudvig, Lars A; Cadotte, Marc; Chu, Chengjin; Cottingham, Kathryn L; Crawley, Michael J; Damschen, Ellen I; Dantonio, Carla M; DeCrappeo, Nicole M; Du, Guozhen; Fay, Philip A; Frater, Paul; Gruner, Daniel S; Hagenah, Nicole; Hector, Andy; Hillebrand, Helmut; Hofmockel, Kirsten S; Humphries, Hope C; Jin, Virginia L; Kay, Adam; Kirkman, Kevin P; Klein, Julia A; Knops, Johannes M H; La Pierre, Kimberly J; Ladwig, Laura; Lambrinos, John G; Li, Qi; Li, Wei; Marushia, Robin; McCulley, Rebecca L; Melbourne, Brett A; Mitchell, Charles E; Moore, Joslin L; Morgan, John; Mortensen, Brent; O'Halloran, Lydia R; Pyke, David A; Risch, Anita C; Sankaran, Mahesh; Schuetz, Martin; Simonsen, Anna; Smith, Melinda D; Stevens, Carly J; Sullivan, Lauren; Wolkovich, Elizabeth; Wragg, Peter D; Wright, Justin; Yang, Louie

2015-07-15

Exotic species dominate many communities; however the functional significance of species' biogeographic origin remains highly contentious. This debate is fuelled in part by the lack of globally replicated, systematic data assessing the relationship between species provenance, function and response to perturbations. We examined the abundance of native and exotic plant species at 64 grasslands in 13 countries, and at a subset of the sites we experimentally tested native and exotic species responses to two fundamental drivers of invasion, mineral nutrient supplies and vertebrate herbivory. Exotic species are six times more likely to dominate communities than native species. Furthermore, while experimental nutrient addition increases the cover and richness of exotic species, nutrients decrease native diversity and cover. Native and exotic species also differ in their response to vertebrate consumer exclusion. These results suggest that species origin has functional significance, and that eutrophication will lead to increased exotic dominance in grasslands.

Plant species' origin predicts dominance and response to nutrient enrichment and herbivores in global grasslands

PubMed Central

Seabloom, Eric W.; Borer, Elizabeth T.; Buckley, Yvonne M.; Cleland, Elsa E.; Davies, Kendi F.; Firn, Jennifer; Harpole, W. Stanley; Hautier, Yann; Lind, Eric M.; MacDougall, Andrew S.; Orrock, John L.; Prober, Suzanne M.; Adler, Peter B.; Anderson, T. Michael; Bakker, Jonathan D.; Biederman, Lori A.; Blumenthal, Dana M.; Brown, Cynthia S.; Brudvig, Lars A.; Cadotte, Marc; Chu, Chengjin; Cottingham, Kathryn L.; Crawley, Michael J.; Damschen, Ellen I.; Dantonio, Carla M.; DeCrappeo, Nicole M.; Du, Guozhen; Fay, Philip A.; Frater, Paul; Gruner, Daniel S.; Hagenah, Nicole; Hector, Andy; Hillebrand, Helmut; Hofmockel, Kirsten S.; Humphries, Hope C.; Jin, Virginia L.; Kay, Adam; Kirkman, Kevin P.; Klein, Julia A.; Knops, Johannes M. H.; La Pierre, Kimberly J.; Ladwig, Laura; Lambrinos, John G.; Li, Qi; Li, Wei; Marushia, Robin; McCulley, Rebecca L.; Melbourne, Brett A.; Mitchell, Charles E.; Moore, Joslin L.; Morgan, John; Mortensen, Brent; O'Halloran, Lydia R.; Pyke, David A.; Risch, Anita C.; Sankaran, Mahesh; Schuetz, Martin; Simonsen, Anna; Smith, Melinda D.; Stevens, Carly J.; Sullivan, Lauren; Wolkovich, Elizabeth; Wragg, Peter D.; Wright, Justin; Yang, Louie

2015-01-01

Exotic species dominate many communities; however the functional significance of species' biogeographic origin remains highly contentious. This debate is fuelled in part by the lack of globally replicated, systematic data assessing the relationship between species provenance, function and response to perturbations. We examined the abundance of native and exotic plant species at 64 grasslands in 13 countries, and at a subset of the sites we experimentally tested native and exotic species responses to two fundamental drivers of invasion, mineral nutrient supplies and vertebrate herbivory. Exotic species are six times more likely to dominate communities than native species. Furthermore, while experimental nutrient addition increases the cover and richness of exotic species, nutrients decrease native diversity and cover. Native and exotic species also differ in their response to vertebrate consumer exclusion. These results suggest that species origin has functional significance, and that eutrophication will lead to increased exotic dominance in grasslands. PMID:26173623

Categorical Perception Beyond the Basic Level: The Case of Warm and Cool Colors.

PubMed

Holmes, Kevin J; Regier, Terry

2017-05-01

Categories can affect our perception of the world, rendering between-category differences more salient than within-category ones. Across many studies, such categorical perception (CP) has been observed for the basic-level categories of one's native language. Other research points to categorical distinctions beyond the basic level, but it does not demonstrate CP for such distinctions. Here we provide such a demonstration. Specifically, we show CP in English speakers for the non-basic distinction between "warm" and "cool" colors, claimed to represent the earliest stage of color lexicon evolution. Notably, the advantage for discriminating colors that straddle the warm-cool boundary was restricted to the right visual field-the same behavioral signature previously observed for basic-level categories. This pattern held in a replication experiment with increased power. Our findings show that categorical distinctions beyond the basic-level repertoire of one's native language are psychologically salient and may be spontaneously accessed during normal perceptual processing. Copyright © 2016 Cognitive Science Society, Inc.

A Functional Approach Reveals a Genetic and Physical Interaction between Ribonucleotide Reductase and CHK1 in Mammalian Cells

PubMed Central

Taricani, Lorena; Shanahan, Frances; Malinao, Maria-Christina; Beaumont, Maribel; Parry, David

2014-01-01

Ribonucleotide reductase (RNR) enzyme is composed of the homodimeric RRM1 and RRM2 subunits, which together form a heterotetramic active enzyme that catalyzes the de novo reduction of ribonucleotides to generate deoxyribonucleotides (dNTPs), which are required for DNA replication and DNA repair processes. In this study, we show that ablation of RRM1 and RRM2 by siRNA induces G1/S phase arrest, phosphorylation of Chk1 on Ser345 and phosphorylation of γ-H2AX on S139. Combinatorial ablation of RRM1 or RRM2 and Chk1 causes a dramatic accumulation of γ-H2AX, a marker of double-strand DNA breaks, suggesting that activation of Chk1 in this context is essential for suppression of DNA damage. Significantly, we demonstrate for the first time that Chk1 and RNR subunits co-immunoprecipitate from native cell extracts. These functional genomic studies suggest that RNR is a critical mediator of replication checkpoint activation. PMID:25375241

Engineering a collagen matrix that replicates the biological properties of native extracellular matrix.

PubMed

Nam, Kwangwoo; Sakai, Yuuki; Funamoto, Seiichi; Kimura, Tsuyoshi; Kishida, Akio

2011-01-01

In this study, we aimed to replicate the function of native tissues that can be used in tissue engineering and regenerative medicine. The key to such replication is the preparation of an artificial collagen matrix that possesses a structure resembling that of the extracellular matrix. We, therefore, prepared a collagen matrix by fibrillogenesis in a NaCl/Na(2)HPO(4) aqueous solution using a dialysis cassette and investigated its biological behavior in vitro and in vivo. The in vitro cell adhesion and proliferation did not show any significant differences. The degradation rate in the living body could be controlled according to the preparation condition, where the collagen matrix with high water content (F-collagen matrix, >98%) showed fast degradation and collagen matrix with lower water content (T-collagen matrix, >80%) showed no degradation for 8 weeks. The degradation did not affect the inflammatory response at all and relatively faster wound healing response was observed. Comparing this result with that of collagen gel and decellularized cornea, it can be concluded that the structural factor is very important and no cell abnormal behavior would be observed for quaternary structured collagen matrix.

Learning to Read Words in a New Language Shapes the Neural Organization of the Prior Languages

PubMed Central

Mei, Leilei; Xue, Gui; Lu, Zhong-Lin; Chen, Chuansheng; Zhang, Mingxia; He, Qinghua; Wei, Miao; Dong, Qi

2014-01-01

Learning a new language entails interactions with one's prior language(s). Much research has shown how native language affects the cognitive and neural mechanisms of a new language, but little is known about whether and how learning a new language shapes the neural mechanisms of prior language(s). In two experiments in the current study, we used an artificial language training paradigm in combination with fMRI to examine (1) the effects of different linguistic components (phonology and semantics) of a new language on the neural process of prior languages (i.e., native and second languages), and (2) whether such effects were modulated by the proficiency level in the new language. Results of Experiment 1 showed that when the training in a new language involved semantics (as opposed to only visual forms and phonology), neural activity during word reading in the native language (Chinese) was reduced in several reading-related regions, including the left pars opercularis, pars triangularis, bilateral inferior temporal gyrus, fusiform gyrus, and inferior occipital gyrus. Results of Experiment 2 replicated the results of Experiment 1 and further found that semantic training also affected neural activity during word reading in the subjects’ second language (English). Furthermore, we found that the effects of the new language were modulated by the subjects’ proficiency level in the new language. These results provide critical imaging evidence for the influence of learning to read words in a new language on word reading in native and second languages. PMID:25447375

Destabilization of the PCNA trimer mediated by its interaction with the NEIL1 DNA glycosylase

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

Prakash, Aishwarya; Moharana, Kedar; Wallace, Susan S.

The base excision repair (BER) pathway repairs oxidized lesions in the DNA that result from reactive oxygen species generated in cells. If left unrepaired, these damaged DNA bases can disrupt cellular processes such as replication. NEIL1 is one of the 11 human DNA glycosylases that catalyze the first step of the BER pathway, i.e. recognition and excision of DNA lesions. NEIL1 interacts with essential replication proteins such as the ring-shaped homotrimeric proliferating cellular nuclear antigen (PCNA). We isolated a complex formed between NEIL1 and PCNA (±DNA) using size exclusion chromatography (SEC). This interaction was confirmed using native gel electrophoresis andmore » mass spectrometry. Stokes radii measured by SEC hinted that PCNA in complex with NEIL1 (±DNA) was no longer a trimer. Height measurements and images obtained by atomic force microscopy also demonstrated the dissociation of the PCNA homotrimer in the presence of NEIL1 and DNA, while small-angle X-ray scattering analysis confirmed the NEIL1 mediated PCNA trimer dissociation and formation of a 1:1:1 NEIL1-DNA-PCNA(monomer) complex. Furthermore, ab initio shape reconstruction provides insights into the solution structure of this previously unreported complex. Together, these data point to a potential mechanistic switch between replication and BER.« less

Insights into the homo-oligomerization properties of N-terminal coiled-coil domain of Ebola virus VP35 protein.

PubMed

Ramaswamy, Venkata Krishnan; Di Palma, Francesco; Vargiu, Attilio V; Corona, Angela; Piano, Dario; Ruggerone, Paolo; Zinzula, Luca; Tramontano, Enzo

2018-03-02

The multifunctional Ebola virus (EBOV) VP35 protein is a key determinant of virulence. VP35 is essential for EBOV replication, is a component of the viral RNA polymerase and participates in nucleocapsid formation. Furthermore, VP35 contributes to EBOV evasion of the host innate immune response by suppressing RNA silencing and blocking RIG-I like receptors' pathways that lead to type I interferon (IFN) production. VP35 homo-oligomerization has been reported to be critical for its replicative function and to increase its IFN-antagonism properties. Moreover, homo-oligomerization is mediated by a predicted coiled-coil (CC) domain located within its N-terminal region. Here we report the homo-oligomerization profile of full-length recombinant EBOV VP35 (rVP35) assessed by size-exclusion chromatography and native polyacrylamide gel electrophoresis. Based on our biochemical results and in agreement with previous experimental observations, we have built an in silico 3D model of the so-far structurally unsolved EBOV VP35 CC domain and performed self-assembly homo-oligomerization simulations by means of molecular dynamics. Our model advances the understanding of how VP35 may associate in different homo-oligomeric species, a crucial process for EBOV replication and pathogenicity. Copyright © 2018 Elsevier B.V. All rights reserved.

Processing of human cytomegalovirus glycoprotein B in recombinant adenovirus-infected cells.

PubMed

Marshall, G S; Fenger, D P; Stout, G G; Knights, M E; Hunt, L A

1996-07-01

Intracellular processing of human cytomegalovirus (HCMV) glycoprotein B (gB; gpUL55) expressed by a recombinant adenovirus (Ad-gB) was studied in human A549 cells as processing events could affect immunogenicity when such viruses are used as live-recombinant vaccines. Cleavage of [35S]methionine-labelled gp13O into gp93 and gp55 reached a maximum after a 3 h chase. Cleavage was completely inhibited by brefeldin A, suggesting that processing normally occurs as a late Golgi or post-Golgi event. Uncleaved gp 130 remained completely sensitive to endo-beta-N-acetylglucosaminidase H (Endo-H) in untreated cells following long chase periods, indicating high-mannose oligosaccharides at all of the 18 N-linked glycosylation sites (Asn-X-Ser/Thr) and retention in the endoplasmic reticulum. Endo-H analysis of gp55 from swainsonine-treated and untreated cells was consistent with glycosylation at all three potential sites, with two oligosaccharides remaining sensitive to Endo-H and one being processed to Endo-H resistance. The heavily glycosylated N-terminal gp93 subunit was not detected by [35S]methionine-labelling but was easily detected along with gp55 after labelling with [3H]mannose. No cleavage of gp 130 was observed in analogous pulse-chase radiolabelling of Ad-gB-infected human fibroblasts, even though these cells are permissive for HCMV replication and can process the native gB molecule. Processing of gB in recombinant adenovirus-infected A549 cells was generally similar to that previously reported for native gB in HCMV-infected fibroblasts.

Interactions of slimy sculpin (Cottus cognatus) with native and nonnative trout: Consequences for growth

USGS Publications Warehouse

Zimmerman, J.K.H.; Vondracek, B.

2006-01-01

We examined growth of native slimy sculpin (Cottus cognatus), native brook trout (Salvelinus fontinalis), and nonnative brown trout (Salmo trutta) to investigate potential interactions of a native nongame fish with native and nonnative trout. Enclosures (1 m2) were stocked with five treatments (juvenile brown trout with sculpin, juvenile brook trout with sculpin, and single species controls) at three densities. Treatments (with replication) were placed in riffles in Valley Creek, Minnesota, and growth rates were measured for six experiments. We examined the difference in growth of each species in combined species treatments compared with each species alone. We did not find evidence of interactions between brook trout and sculpin, regardless of density or fish size. However, sculpin gained greater mass when alone than with brown trout when sculpin were >16 g. Likewise, brown trout grew more when alone than with sculpin when brown trout were >24 g. In contrast, brown trout ???5 g grew more with sculpin compared with treatments alone. We suggest that native brook trout and sculpin coexist without evidence of competition, whereas nonnative brown trout may compete with sculpin. ?? 2006 NRC.

Dissociation of recombinant prion autocatalysis from infectivity.

PubMed

Noble, Geoffrey P; Supattapone, Surachai

2015-01-01

Within the mammalian prion field, the existence of recombinant prion protein (PrP) conformers with self-replicating (ie. autocatalytic) activity in vitro but little to no infectious activity in vivo challenges a key prediction of the protein-only hypothesis of prion replication--that autocatalytic PrP conformers should be infectious. To understand this dissociation of autocatalysis from infectivity, we recently performed a structural and functional comparison between a highly infectious and non-infectious pair of autocatalytic recombinant PrP conformers derived from the same initial prion strain. (1) We identified restricted, C-terminal structural differences between these 2 conformers and provided evidence that these relatively subtle differences prevent the non-infectious conformer from templating the conversion of native PrP(C) substrates containing a glycosylphosphatidylinositol (GPI) anchor. (1) In this article we discuss a model, consistent with these findings, in which recombinant PrP, lacking post-translational modifications and associated folding constraints, is capable of adopting a wide variety of autocatalytic conformations. Only a subset of these recombinant conformers can be adopted by post-translationally modified native PrP(C), and this subset represents the recombinant conformers with high specific infectivity. We examine this model's implications for the generation of highly infectious recombinant prions and the protein-only hypothesis of prion replication.

A macro-level fetal alcohol syndrome prevention program for Native Americans and Alaska Natives: description and evaluation.

PubMed

May, P A; Hymbaugh, K J

1989-11-01

Presented here are a detailed description and outcome evaluation of a comprehensive, macro-level Fetal Alcohol Syndrome prevention program for Native Americans and Alaska Natives. The program was designed to provide native communities throughout the United States with the knowledge, skills and strategies to initiate primary, secondary and tertiary prevention measures on their own. The key to the program was the training of a cadre of trainers/advocates in all local Native American and Alaska Native communities served by the Indian Health Service. These people were then supported and assisted in their efforts through a variety of means. Evaluation results of knowledge gained indicate that the local trainers had substantial success in imparting FAS information to a variety of audiences (prenatal groups, school children and community groups). Further, the evaluation samples also indicate that the knowledge was retained by the groups over time (2-4 months) and that there may have been some general diffusion of knowledge among peers in local communities. This program is presented in the hope that it will be replicated and improved upon by similar programs using this model as a base.

SELECTION, WITH MINIMAL BIAS, OF AN EXPERIMENTAL CONTROL FROM NATURAL WETLAND ENVIRONMENTS

EPA Science Inventory

This report is of the National Network for Environmental Management studies conducted under the auspices of the Office of Cooperative Environmental Management--U.S. Environmental Protection Agency. The goal of wetland restoration and creation projects is to replicate the native w...

Structural and functional analysis of virus factories purified from Rabbit vesivirus-infected Vero cells.

PubMed

Casais, Rosa; Molleda, Lorenzo González; Machín, Angeles; del Barrio, Gloria; Manso, Alberto García; Dalton, Kevin P; Coto, Ana; Alonso, José Manuel Martín; Prieto, Miguel; Parra, Francisco

2008-10-01

Rabbit vesivirus infection induces membrane modifications and accumulation of vesicular structures in the cytoplasm of infected Vero cells. Crude RaV replication complexes (RCs) have been purified and their structural and functional properties have been characterized. We show that calnexin, an ER-resident protein, RaV non-structural proteins 2AB-, 2C-, 3A-, 3B- and 3CD-like as well as viral RNAs co-localize within membranous structures which are able to replicate the endogenous RNA templates. The purified virus factories protected their viral RNA contents from microccocal nuclease degradation and were inaccessible to exogenously added synthetic transcripts. In addition, we have shown that RCs can be used to investigate uridylylation of native endogenous VPg. In contrast to the observation that the virus factories were inaccessible to RNAs, RCs were accessible to added recombinant VPg which was subsequently nucleotidylylated. Nevertheless no elongation of an RNA chain attached to native or recombinant VPg could be demonstrated.

Proteolytic Processing of Turnip Yellow Mosaic Virus Replication Proteins and Functional Impact on Infectivity▿

PubMed Central

Jakubiec, Anna; Drugeon, Gabrièle; Camborde, Laurent; Jupin, Isabelle

2007-01-01

Turnip yellow mosaic virus (TYMV), a positive-strand RNA virus belonging to the alphavirus-like supergroup, encodes its nonstructural replication proteins as a 206K precursor with domains indicative of methyltransferase (MT), proteinase (PRO), NTPase/helicase (HEL), and polymerase (POL) activities. Subsequent processing of 206K generates a 66K protein encompassing the POL domain and uncharacterized 115K and 85K proteins. Here, we demonstrate that TYMV proteinase mediates an additional cleavage between the PRO and HEL domains of the polyprotein, generating the 115K protein and a 42K protein encompassing the HEL domain that can be detected in plant cells using a specific antiserum. Deletion and substitution mutagenesis experiments and sequence comparisons indicate that the scissile bond is located between residues Ser879 and Gln880. The 85K protein is generated by a host proteinase and is likely to result from nonspecific proteolytic degradation occurring during protein sample extraction or analysis. We also report that TYMV proteinase has the ability to process substrates in trans in vivo. Finally, we examined the processing of the 206K protein containing native, mutated, or shuffled cleavage sites and analyzed the effects of cleavage mutations on viral infectivity and RNA synthesis by performing reverse-genetics experiments. We present evidence that PRO/HEL cleavage is critical for productive virus infection and that the impaired infectivity of PRO/HEL cleavage mutants is due mainly to defective synthesis of positive-strand RNA. PMID:17686855

Learning to read words in a new language shapes the neural organization of the prior languages.

PubMed

Mei, Leilei; Xue, Gui; Lu, Zhong-Lin; Chen, Chuansheng; Zhang, Mingxia; He, Qinghua; Wei, Miao; Dong, Qi

2014-12-01

Learning a new language entails interactions with one׳s prior language(s). Much research has shown how native language affects the cognitive and neural mechanisms of a new language, but little is known about whether and how learning a new language shapes the neural mechanisms of prior language(s). In two experiments in the current study, we used an artificial language training paradigm in combination with an fMRI to examine (1) the effects of different linguistic components (phonology and semantics) of a new language on the neural process of prior languages (i.e., native and second languages), and (2) whether such effects were modulated by the proficiency level in the new language. Results of Experiment 1 showed that when the training in a new language involved semantics (as opposed to only visual forms and phonology), neural activity during word reading in the native language (Chinese) was reduced in several reading-related regions, including the left pars opercularis, pars triangularis, bilateral inferior temporal gyrus, fusiform gyrus, and inferior occipital gyrus. Results of Experiment 2 replicated the results of Experiment 1 and further found that semantic training also affected neural activity during word reading in the subjects׳ second language (English). Furthermore, we found that the effects of the new language were modulated by the subjects׳ proficiency level in the new language. These results provide critical imaging evidence for the influence of learning to read words in a new language on word reading in native and second languages. Copyright © 2014 Elsevier Ltd. All rights reserved.

Community-level plant-soil feedbacks explain landscape distribution of native and non-native plants.

PubMed

Kulmatiski, Andrew

2018-02-01

Plant-soil feedbacks (PSFs) have gained attention for their potential role in explaining plant growth and invasion. While promising, most PSF research has measured plant monoculture growth on different soils in short-term, greenhouse experiments. Here, five soil types were conditioned by growing one native species, three non-native species, or a mixed plant community in different plots in a common-garden experiment. After 4 years, plants were removed and one native and one non-native plant community were planted into replicate plots of each soil type. After three additional years, the percentage cover of each of the three target species in each community was measured. These data were used to parameterize a plant community growth model. Model predictions were compared to native and non-native abundance on the landscape. Native community cover was lowest on soil conditioned by the dominant non-native, Centaurea diffusa , and non-native community cover was lowest on soil cultivated by the dominant native, Pseudoroegneria spicata . Consistent with plant growth on the landscape, the plant growth model predicted that the positive PSFs observed in the common-garden experiment would result in two distinct communities on the landscape: a native plant community on native soils and a non-native plant community on non-native soils. In contrast, when PSF effects were removed, the model predicted that non-native plants would dominate all soils, which was not consistent with plant growth on the landscape. Results provide an example where PSF effects were large enough to change the rank-order abundance of native and non-native plant communities and to explain plant distributions on the landscape. The positive PSFs that contributed to this effect reflected the ability of the two dominant plant species to suppress each other's growth. Results suggest that plant dominance, at least in this system, reflects the ability of a species to suppress the growth of dominant competitors through soil-mediated effects.

Origin Replication Complex Binding, Nucleosome Depletion Patterns, and a Primary Sequence Motif Can Predict Origins of Replication in a Genome with Epigenetic Centromeres

PubMed Central

Tsai, Hung-Ji; Baller, Joshua A.; Liachko, Ivan; Koren, Amnon; Burrack, Laura S.; Hickman, Meleah A.; Thevandavakkam, Mathuravani A.; Rusche, Laura N.

2014-01-01

ABSTRACT Origins of DNA replication are key genetic elements, yet their identification remains elusive in most organisms. In previous work, we found that centromeres contain origins of replication (ORIs) that are determined epigenetically in the pathogenic yeast Candida albicans. In this study, we used origin recognition complex (ORC) binding and nucleosome occupancy patterns in Saccharomyces cerevisiae and Kluyveromyces lactis to train a machine learning algorithm to predict the position of active arm (noncentromeric) origins in the C. albicans genome. The model identified bona fide active origins as determined by the presence of replication intermediates on nondenaturing two-dimensional (2D) gels. Importantly, these origins function at their native chromosomal loci and also as autonomously replicating sequences (ARSs) on a linear plasmid. A “mini-ARS screen” identified at least one and often two ARS regions of ≥100 bp within each bona fide origin. Furthermore, a 15-bp AC-rich consensus motif was associated with the predicted origins and conferred autonomous replicating activity to the mini-ARSs. Thus, while centromeres and the origins associated with them are epigenetic, arm origins are dependent upon critical DNA features, such as a binding site for ORC and a propensity for nucleosome exclusion. PMID:25182328

The introduced tree Prosopis juliflora is a serious threat to native species of the Brazilian Caatinga vegetation.

PubMed

de Souza Nascimento, Clóvis Eduardo; Tabarelli, Marcelo; da Silva, Carlos Alberto Domingues; Leal, Inara Roberta; de Souza Tavares, Wagner; Serrão, José Eduardo; Zanuncio, José Cola

2014-05-15

Despite its economic importance in the rural context, the Prosopis juliflora tree species has already invaded millions of hectares globally (particularly rangelands), threatening native biodiversity and rural sustainability. Here we examine seedling growth (leaf area, stem diameter, plant height) and seedling mortality across five native plant species of the Caatinga vegetation in response to competition with P. juliflora. Two sowing treatments with 10 replications were adopted within a factorial 2 × 5 randomized block design. Treatments consisted of P. juliflora seeds sowed with seeds of Caesalpinia ferrea, Caesalpinia microphylla, Erythrina velutina, Mimosa bimucronata and Mimosa tenuiflora (one single native species per treatment), while seeds of native species sowed without P. juliflora were adopted as controls. Overall, our results suggest that P. juliflora can reduce seedling growth by half and cause increased seedling mortality among woody plant species. Moreover, native species exhibit different levels of susceptibility to competition with P. juliflora, particularly in terms of plant growth. Such a superior competitive ability apparently permits P. juliflora to establish monospecific stands of adult trees, locally displacing native species or limiting their recruitment. The use of less sensitive species, such as C. ferrea and M. tenuiflora, to restore native vegetation before intensive colonization by P. juliflora should be investigated as an effective approach for avoiding its continuous spread across the Caatinga region. Copyright © 2014 Elsevier B.V. All rights reserved.

Mitochondrial nucleoid clusters protect newly synthesized mtDNA during Doxorubicin- and Ethidium Bromide-induced mitochondrial stress

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

Alán, Lukáš, E-mail: lukas.alan@fgu.cas.cz; Špaček

Mitochondrial DNA (mtDNA) is compacted in ribonucleoprotein complexes called nucleoids, which can divide or move within the mitochondrial network. Mitochondrial nucleoids are able to aggregate into clusters upon reaction with intercalators such as the mtDNA depletion agent Ethidium Bromide (EB) or anticancer drug Doxorobicin (DXR). However, the exact mechanism of nucleoid clusters formation remains unknown. Resolving these processes may help to elucidate the mechanisms of DXR-induced cardiotoxicity. Therefore, we addressed the role of two key nucleoid proteins; mitochondrial transcription factor A (TFAM) and mitochondrial single-stranded binding protein (mtSSB); in the formation of mitochondrial nucleoid clusters during the action of intercalators.more » We found that both intercalators cause numerous aberrations due to perturbing their native status. By blocking mtDNA replication, both agents also prevented mtDNA association with TFAM, consequently causing nucleoid aggregation into large nucleoid clusters enriched with TFAM, co-existing with the normal nucleoid population. In the later stages of intercalation (> 48 h), TFAM levels were reduced to 25%. In contrast, mtSSB was released from mtDNA and freely distributed within the mitochondrial network. Nucleoid clusters mostly contained nucleoids with newly replicated mtDNA, however the nucleoid population which was not in replication mode remained outside the clusters. Moreover, the nucleoid clusters were enriched with p53, an anti-oncogenic gatekeeper. We suggest that mitochondrial nucleoid clustering is a mechanism for protecting nucleoids with newly replicated DNA against intercalators mediating genotoxic stress. These results provide new insight into the common mitochondrial response to mtDNA stress and can be implied also on DXR-induced mitochondrial cytotoxicity. - Highlights: • The mechanism for mitochondrial nucleoid clustering is proposed. • DNA intercalators (Doxorubicin or Ethidium Bromide) prevent TFAM binding to mtDNA. • Replicating nucleoids are less prone to DNA intercalator and preserve more TFAM. • Nucleoid clusters mostly contain nucleoids with newly replicated mtDNA. • Recently replicated nucleoids are protected in clusters by increased TFAM and p53.« less

In vivo performance of an acellular disc-like angle ply structure (DAPS) for total disc replacement in a small animal model.

PubMed

Martin, John T; Kim, Dong Hwa; Milby, Andrew H; Pfeifer, Christian G; Smith, Lachlan J; Elliott, Dawn M; Smith, Harvey E; Mauck, Robert L

2017-01-01

Total intervertebral disc replacement with a biologic engineered disc may be an alternative to spinal fusion for treating end-stage disc disease. In previous work, we developed disc-like angle ply structures (DAPS) that replicate the structure and function of the native disc and a rat tail model to evaluate DAPS in vivo. Here, we evaluated a strategy in which, after in vivo implantation, endogenous cells could colonize the acellular DAPS and form an extracellular matrix organized by the DAPS topographical template. To do so, acellular DAPS were implanted into the caudal spines of rats and evaluated over 12 weeks by mechanical testing, histology, and microcomputed tomography. An external fixation device was used to stabilize the implant site and various control groups were included to evaluate the effect of immobilization. There was robust tissue formation within the DAPS after implantation and compressive mechanical properties of the implant matched that of the native motion segment. Immobilization provided a stable site for fibrous tissue formation after either a discectomy or a DAPS implantation, but bony fusion eventually resulted, with segments showing intervertebral bridging after long-term implantation, a process that was accelerated by the implanted DAPS. Thus, while compressive mechanical properties were replicated after DAPS implantation, methods to actively prevent fusion must be developed. Future work will focus on limiting fusion by remobilizing the motion segment after a period of integration, delivering pro-chondrogenic factors, and pre-seeding DAPS with cells prior to implantation. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:23-31, 2017. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

Landscape corridors can increase invasion by an exotic species and reduce diversity of native species.

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

Resasco, Julian; et al,

2014-04-01

Abstract. Landscape corridors are commonly used to mitigate negative effects of habitat fragmentation, but concerns persist that they may facilitate the spread of invasive species. In a replicated landscape experiment of open habitat, we measured effects of corridors on the invasive fire ant, Solenopsis invicta, and native ants. Fire ants have two social forms: polygyne, which tend to disperse poorly but establish at high densities, and monogyne, which disperse widely but establish at lower densities. In landscapes dominated by polygyne fire ants, fire ant abundance was higher and native ant diversity was lower in habitat patches connected by corridors thanmore » in unconnected patches. Conversely, in landscapes dominated by monogyne fire ants, connectivity had no influence on fire ant abundance and native ant diversity. Polygyne fire ants dominated recently created landscapes, suggesting that these corridor effects may be transient. Our results suggest that corridors can facilitate invasion and they highlight the importance of considering species’ traits when assessing corridor utility.« less

Vegetation response to invasive Tamarix control in southwestern U.S. rivers: a collaborative study including 416 sites.

PubMed

González, Eduardo; Sher, Anna A; Anderson, Robert M; Bay, Robin F; Bean, Daniel W; Bissonnete, Gabriel J; Bourgeois, Bérenger; Cooper, David J; Dohrenwend, Kara; Eichhorst, Kim D; El Waer, Hisham; Kennard, Deborah K; Harms-Weissinger, Rebecca; Henry, Annie L; Makarick, Lori J; Ostoja, Steven M; Reynolds, Lindsay V; Robinson, W Wright; Shafroth, Patrick B

2017-09-01

Most studies assessing vegetation response following control of invasive Tamarix trees along southwestern U.S. rivers have been small in scale (e.g., river reach), or at a regional scale but with poor spatial-temporal replication, and most have not included testing the effects of a now widely used biological control. We monitored plant composition following Tamarix control along hydrologic, soil, and climatic gradients in 244 treated and 172 reference sites across six U.S. states. This represents the largest comprehensive assessment to date on the vegetation response to the four most common Tamarix control treatments. Biocontrol by a defoliating beetle (treatment 1) reduced the abundance of Tamarix less than active removal by mechanically using hand and chain-saws (2), heavy machinery (3) or burning (4). Tamarix abundance also decreased with lower temperatures, higher precipitation, and follow-up treatments for Tamarix resprouting. Native cover generally increased over time in active Tamarix removal sites, however, the increases observed were small and was not consistently increased by active revegetation. Overall, native cover was correlated to permanent stream flow, lower grazing pressure, lower soil salinity and temperatures, and higher precipitation. Species diversity also increased where Tamarix was removed. However, Tamarix treatments, especially those generating the highest disturbance (burning and heavy machinery), also often promoted secondary invasions of exotic forbs. The abundance of hydrophytic species was much lower in treated than in reference sites, suggesting that management of southwestern U.S. rivers has focused too much on weed control, overlooking restoration of fluvial processes that provide habitat for hydrophytic and floodplain vegetation. These results can help inform future management of Tamarix-infested rivers to restore hydrogeomorphic processes, increase native biodiversity and reduce abundance of noxious species. © 2017 by the Ecological Society of America.

Review of Research--Sex Differences in Intellectual Functioning: Myth or Reality.

ERIC Educational Resources Information Center

Glickman, Judith R.

Sex difference research has been plagued with a myriad of problems,. Specifically, intelligence testing, if dependent on measurement of spatial or verbal proficiency, may not be an accurate indicator of native ability. Similarly, infrequent replication of studies, studies that only include subjects of one sex yet imply sex differences, and poor…

Formal Schema Theory and Teaching EFL Reading

ERIC Educational Resources Information Center

Young, Barbara N; Man, Zhou

2005-01-01

Inquirers designed and conducted a study investigating whether or not results derived from previous research focusing on teaching and learning English as a native or foreign language would be replicated in a learning environment in which English is taught as a foreign language as in China. Because activation of formal schemata plays an important…

Biophysical stimulation for in vitro engineering of functional cardiac tissues.

PubMed

Korolj, Anastasia; Wang, Erika Yan; Civitarese, Robert A; Radisic, Milica

2017-07-01

Engineering functional cardiac tissues remains an ongoing significant challenge due to the complexity of the native environment. However, our growing understanding of key parameters of the in vivo cardiac microenvironment and our ability to replicate those parameters in vitro are resulting in the development of increasingly sophisticated models of engineered cardiac tissues (ECT). This review examines some of the most relevant parameters that may be applied in culture leading to higher fidelity cardiac tissue models. These include the biochemical composition of culture media and cardiac lineage specification, co-culture conditions, electrical and mechanical stimulation, and the application of hydrogels, various biomaterials, and scaffolds. The review will also summarize some of the recent functional human tissue models that have been developed for in vivo and in vitro applications. Ultimately, the creation of sophisticated ECT that replicate native structure and function will be instrumental in advancing cell-based therapeutics and in providing advanced models for drug discovery and testing. © 2017 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

Hybrid Methods Reveal Multiple Flexibly Linked DNA Polymerases within the Bacteriophage T7 Replisome

DOE PAGES

Wallen, Jamie R.; Zhang, Hao; Weis, Caroline; ...

2017-01-03

The physical organization of DNA enzymes at a replication fork enables efficient copying of two antiparallel DNA strands, yet dynamic protein interactions within the replication complex complicate replisome structural studies. We employed a combination of crystallographic, native mass spectrometry and small-angle X-ray scattering experiments to capture alternative structures of a model replication system encoded by bacteriophage T7. then, the two molecules of DNA polymerase bind the ring-shaped primase-helicase in a conserved orientation and provide structural insight into how the acidic C-terminal tail of the primase-helicase contacts the DNA polymerase to facilitate loading of the polymerase onto DNA. A third DNA polymerasemore » binds the ring in an offset manner that may enable polymerase exchange during replication. Alternative polymerase binding modes are also detected by small-angle X-ray scattering with DNA substrates present. The collective results unveil complex motions within T7 replisome higher-order structures that are underpinned by multivalent protein-protein interactions with functional implications.« less

Hybrid Methods Reveal Multiple Flexibly Linked DNA Polymerases within the Bacteriophage T7 Replisome

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

Wallen, Jamie R.; Zhang, Hao; Weis, Caroline

The physical organization of DNA enzymes at a replication fork enables efficient copying of two antiparallel DNA strands, yet dynamic protein interactions within the replication complex complicate replisome structural studies. We employed a combination of crystallographic, native mass spectrometry and small-angle X-ray scattering experiments to capture alternative structures of a model replication system encoded by bacteriophage T7. then, the two molecules of DNA polymerase bind the ring-shaped primase-helicase in a conserved orientation and provide structural insight into how the acidic C-terminal tail of the primase-helicase contacts the DNA polymerase to facilitate loading of the polymerase onto DNA. A third DNA polymerasemore » binds the ring in an offset manner that may enable polymerase exchange during replication. Alternative polymerase binding modes are also detected by small-angle X-ray scattering with DNA substrates present. The collective results unveil complex motions within T7 replisome higher-order structures that are underpinned by multivalent protein-protein interactions with functional implications.« less

Archaeal DNA replication.

PubMed

Kelman, Lori M; Kelman, Zvi

2014-01-01

DNA replication is essential for all life forms. Although the process is fundamentally conserved in the three domains of life, bioinformatic, biochemical, structural, and genetic studies have demonstrated that the process and the proteins involved in archaeal DNA replication are more similar to those in eukaryal DNA replication than in bacterial DNA replication, but have some archaeal-specific features. The archaeal replication system, however, is not monolithic, and there are some differences in the replication process between different species. In this review, the current knowledge of the mechanisms governing DNA replication in Archaea is summarized. The general features of the replication process as well as some of the differences are discussed.

Tuning in and tuning out: Speech perception in native- and foreign-talker babble

NASA Astrophysics Data System (ADS)

van Heukelem, Kristin; Bradlow, Ann R.

2005-09-01

Studies on speech perception in multitalker babble have revealed asymmetries in the effects of noise on native versus foreign-accented speech intelligibility for native listeners [Rogers et al., Lang Speech 47(2), 139-154 (2004)] and on sentence-in-noise perception by native versus non-native listeners [Mayo et al., J. Speech Lang. Hear. Res., 40, 686-693 (1997)], suggesting that the linguistic backgrounds of talkers and listeners contribute to the effects of noise on speech perception. However, little attention has been paid to the language of the babble. This study tested whether the language of the noise also has asymmetrical effects on listeners. Replicating previous findings [e.g., Bronkhorst and Plomp, J. Acoust. Soc. Am., 92, 3132-3139 (1992)], the results showed poorer English sentence recognition by native English listeners in six-talker babble than in two-talker babble regardless of the language of the babble, demonstrating the effect of increased psychoacoustic/energetic masking. In addition, the results showed that in the two-talker babble condition, native English listeners were more adversely affected by English than Chinese babble. These findings demonstrate informational/cognitive masking on sentence-in-noise recognition in the form of linguistic competition. Whether this competition is at the lexical or sublexical level and whether it is modulated by the phonetic similarity between the target and noise languages remains to be determined.

DNA Unwinding Functions of Minute Virus of Mice NS1 Protein Are Modulated Specifically by the Lambda Isoform of Protein Kinase C

PubMed Central

Dettwiler, Sabine; Rommelaere, Jean; Nüesch, Jürg P. F.

1999-01-01

The parvovirus minute virus of mice NS1 protein is a multifunctional protein involved in a variety of processes during virus propagation, ranging from viral DNA replication to promoter regulation and cytotoxic action to the host cell. Since NS1 becomes phosphorylated during infection, it was proposed that the different tasks of this protein might be regulated in a coordinated manner by phosphorylation. Indeed, comparing biochemical functions of native NS1 with its dephosphorylated counterpart showed that site-specific nicking of the origin and the helicase and ATPase activities are remarkably reduced upon NS1 dephosphorylation while site-specific affinity of the protein to the origin became enhanced. As a consequence, the dephosphorylated polypeptide is deficient for initiation of DNA replication. By adding fractionated cell extracts to a kinase-free in vitro replication system, the combination of two protein components containing members of the protein kinase C (PKC) family was found to rescue the replication activity of the dephosphorylated NS1 protein upon addition of PKC cofactors. One of these components, termed HA-1, also stimulated NS1 helicase function in response to acidic lipids but not phorbol esters, indicating the involvement of atypical PKC isoforms in the modulation of this NS1 function (J. P. F. Nüesch, S. Dettwiler, R. Corbau, and J. Rommelaere, J. Virol. 72:9966–9977, 1998). The present study led to the identification of atypical PKCλ/ι as the active component of HA-1 responsible for the regulation of NS1 DNA unwinding and replicative functions. Moreover, a target PKCλ phosphorylation site was localized at S473 of NS1. By site-directed mutagenesis, we showed that this residue is essential for NS1 helicase activity but not promoter regulation, suggesting a possible modulation of NS1 functions by PKCλ phosphorylation at residue S473. PMID:10438831

Real, Relevant, Meaningful Learning: Community-Based Education in Native Communities.

ERIC Educational Resources Information Center

Enos, Anya Dozier

The Community-Based Education Model (CBEM) at Santa Fe Indian School (SFIS) in New Mexico was studied to determine the elements that contribute to its success and that may be replicated in other community education projects. The CBEM engages students and tribal communities in issues related to their environment, natural resources, and health in an…

Deep functional analysis of synII, a 770 kb synthetic yeast chromosome

PubMed Central

Gao, Feng; Gong, Jianhui; Abramczyk, Dariusz; Walker, Roy; Zhao, Hongcui; Chen, Shihong; Liu, Wei; Luo, Yisha; Müller, Carolin A.; Paul-Dubois-Taine, Adrien; Alver, Bonnie; Stracquadanio, Giovanni; Mitchell, Leslie A.; Luo, Zhouqing; Fan, Yanqun; Zhou, Baojin; Wen, Bo; Tan, Fengji; Wang, Yujia; Zi, Jin; Xie, Zexiong; Li, Bingzhi; Yang, Kun; Richardson, Sarah M.; Jiang, Hui; French, Christopher E.; Nieduszynski, Conrad A.; Koszul, Romain; Marston, Adele L.; Yuan, Yingjin; Wang, Jian; Bader, Joel S.; Dai, Junbiao; Boeke, Jef D.; Xu, Xun; Cai, Yizhi; Yang, Huanming

2017-01-01

Herein we report the successful design, construction and characterization of a 770 kb synthetic yeast chromosome II (synII). Our study incorporates characterization at multiple levels, including phenomics, transcriptomics, proteomics, chromosome segregation and replication analysis to provide a thorough and comprehensive analysis of a synthetic chromosome. Our “Trans-Omics” analyses reveal a modest but potentially significant pervasive up-regulation of translational machinery observed in synII is mainly caused by the deletion of 13 tRNAs. By both complementation assays and SCRaMbLE, we targeted and debuged the origin of a growth defect at 37°C in glycerol medium, which is related to misregulation of the HOG response. Despite the subtle differences, the synII strain shows highly consistent biological processes comparable to the native strain. PMID:28280153

Don't Underestimate the Benefits of Being Misunderstood.

PubMed

Gibson, Edward; Tan, Caitlin; Futrell, Richard; Mahowald, Kyle; Konieczny, Lars; Hemforth, Barbara; Fedorenko, Evelina

2017-06-01

Being a nonnative speaker of a language poses challenges. Individuals often feel embarrassed by the errors they make when talking in their second language. However, here we report an advantage of being a nonnative speaker: Native speakers give foreign-accented speakers the benefit of the doubt when interpreting their utterances; as a result, apparently implausible utterances are more likely to be interpreted in a plausible way when delivered in a foreign than in a native accent. Across three replicated experiments, we demonstrated that native English speakers are more likely to interpret implausible utterances, such as "the mother gave the candle the daughter," as similar plausible utterances ("the mother gave the candle to the daughter") when the speaker has a foreign accent. This result follows from the general model of language interpretation in a noisy channel, under the hypothesis that listeners assume a higher error rate in foreign-accented than in nonaccented speech.

Tubular inverse opal scaffolds for biomimetic vessels

NASA Astrophysics Data System (ADS)

Zhao, Ze; Wang, Jie; Lu, Jie; Yu, Yunru; Fu, Fanfan; Wang, Huan; Liu, Yuxiao; Zhao, Yuanjin; Gu, Zhongze

2016-07-01

There is a clinical need for tissue-engineered blood vessels that can be used to replace or bypass damaged arteries. The success of such grafts depends strongly on their ability to mimic native arteries; however, currently available artificial vessels are restricted by their complex processing, controversial integrity, or uncontrollable cell location and orientation. Here, we present new tubular scaffolds with specific surface microstructures for structural vessel mimicry. The tubular scaffolds are fabricated by rotationally expanding three-dimensional tubular inverse opals that are replicated from colloidal crystal templates in capillaries. Because of the ordered porous structure of the inverse opals, the expanded tubular scaffolds are imparted with circumferentially oriented elliptical pattern microstructures on their surfaces. It is demonstrated that these tailored tubular scaffolds can effectively make endothelial cells to form an integrated hollow tubular structure on their inner surface and induce smooth muscle cells to form a circumferential orientation on their outer surface. These features of our tubular scaffolds make them highly promising for the construction of biomimetic blood vessels.There is a clinical need for tissue-engineered blood vessels that can be used to replace or bypass damaged arteries. The success of such grafts depends strongly on their ability to mimic native arteries; however, currently available artificial vessels are restricted by their complex processing, controversial integrity, or uncontrollable cell location and orientation. Here, we present new tubular scaffolds with specific surface microstructures for structural vessel mimicry. The tubular scaffolds are fabricated by rotationally expanding three-dimensional tubular inverse opals that are replicated from colloidal crystal templates in capillaries. Because of the ordered porous structure of the inverse opals, the expanded tubular scaffolds are imparted with circumferentially oriented elliptical pattern microstructures on their surfaces. It is demonstrated that these tailored tubular scaffolds can effectively make endothelial cells to form an integrated hollow tubular structure on their inner surface and induce smooth muscle cells to form a circumferential orientation on their outer surface. These features of our tubular scaffolds make them highly promising for the construction of biomimetic blood vessels. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr03173k

“Ins” and “Outs” of mesenchymal stem cell osteogenesis in regenerative medicine

PubMed Central

Yamaguchi, Dean T

2014-01-01

Repair and regeneration of bone requires mesenchymal stem cells that by self-renewal, are able to generate a critical mass of cells with the ability to differentiate into osteoblasts that can produce bone protein matrix (osteoid) and enable its mineralization. The number of human mesenchymal stem cells (hMSCs) diminishes with age and ex vivo replication of hMSCs has limited potential. While propagating hMSCs under hypoxic conditions may maintain their ability to self-renew, the strategy of using human telomerase reverse transcriptase (hTERT) to allow for hMSCs to prolong their replicative lifespan is an attractive means of ensuring a critical mass of cells with the potential to differentiate into various mesodermal structural tissues including bone. However, this strategy must be tempered by the oncogenic potential of TERT-transformed cells, or their ability to enhance already established cancers, the unknown differentiating potential of high population doubling hMSCs and the source of hMSCs (e.g., bone marrow, adipose-derived, muscle-derived, umbilical cord blood, etc.) that may provide peculiarities to self-renewal, differentiation, and physiologic function that may differ from non-transformed native cells. Tissue engineering approaches to use hMSCs to repair bone defects utilize the growth of hMSCs on three-dimensional scaffolds that can either be a base on which hMSCs can attach and grow or as a means of sequestering growth factors to assist in the chemoattraction and differentiation of native hMSCs. The use of whole native extracellular matrix (ECM) produced by hMSCs, rather than individual ECM components, appear to be advantageous in not only being utilized as a three-dimensional attachment base but also in appropriate orientation of cells and their differentiation through the growth factors that native ECM harbor or in simulating growth factor motifs. The origin of native ECM, whether from hMSCs from young or old individuals is a critical factor in “rejuvenating” hMSCs from older individuals grown on ECM from younger individuals. PMID:24772237

Foreign Languages Sound Fast: Evidence from Implicit Rate Normalization.

PubMed

Bosker, Hans Rutger; Reinisch, Eva

2017-01-01

Anecdotal evidence suggests that unfamiliar languages sound faster than one's native language. Empirical evidence for this impression has, so far, come from explicit rate judgments. The aim of the present study was to test whether such perceived rate differences between native and foreign languages (FLs) have effects on implicit speech processing. Our measure of implicit rate perception was "normalization for speech rate": an ambiguous vowel between short /a/ and long /a:/ is interpreted as /a:/ following a fast but as /a/ following a slow carrier sentence. That is, listeners did not judge speech rate itself; instead, they categorized ambiguous vowels whose perception was implicitly affected by the rate of the context. We asked whether a bias towards long /a:/ might be observed when the context is not actually faster but simply spoken in a FL. A fully symmetrical experimental design was used: Dutch and German participants listened to rate matched (fast and slow) sentences in both languages spoken by the same bilingual speaker. Sentences were followed by non-words that contained vowels from an /a-a:/ duration continuum. Results from Experiments 1 and 2 showed a consistent effect of rate normalization for both listener groups. Moreover, for German listeners, across the two experiments, foreign sentences triggered more /a:/ responses than (rate matched) native sentences, suggesting that foreign sentences were indeed perceived as faster. Moreover, this FL effect was modulated by participants' ability to understand the FL: those participants that scored higher on a FL translation task showed less of a FL effect. However, opposite effects were found for the Dutch listeners. For them, their native rather than the FL induced more /a:/ responses. Nevertheless, this reversed effect could be reduced when additional spectral properties of the context were controlled for. Experiment 3, using explicit rate judgments, replicated the effect for German but not Dutch listeners. We therefore conclude that the subjective impression that FLs sound fast may have an effect on implicit speech processing, with implications for how language learners perceive spoken segments in a FL.

Native plant recovery in study plots after fennel (Foeniculum vulgare) control on Santa Cruz Island

USGS Publications Warehouse

Power, Paula; Stanley, Thomas R.; Cowan, Clark; Robertson, James R.

2014-01-01

Santa Cruz Island is the largest of the California Channel Islands and supports a diverse and unique flora which includes 9 federally listed species. Sheep, cattle, and pigs, introduced to the island in the mid-1800s, disturbed the soil, browsed native vegetation, and facilitated the spread of exotic invasive plants. Recent removal of introduced herbivores on the island led to the release of invasive fennel (Foeniculum vulgare), which expanded to become the dominant vegetation in some areas and has impeded the recovery of some native plant communities. In 2007, Channel Islands National Park initiated a program to control fennel using triclopyr on the eastern 10% of the island. We established replicate paired plots (seeded and nonseeded) at Scorpion Anchorage and Smugglers Cove, where notably dense fennel infestations (>10% cover) occurred, to evaluate the effectiveness of native seed augmentation following fennel removal. Five years after fennel removal, vegetative cover increased as litter and bare ground cover decreased significantly (P < 0.0001) on both plot types. Vegetation cover of both native and other (nonfennel) exotic species increased at Scorpion Anchorage in both seeded and nonseeded plots. At Smugglers Cove, exotic cover decreased significantly (P = 0.0001) as native cover comprised of Eriogonum arborescensand Leptosyne gigantea increased significantly (P < 0.0001) in seeded plots only. Nonseeded plots at Smugglers Cove were dominated by exotic annual grasses, primarily Avena barbata. The data indicate that seeding with appropriate native seed is a critical step in restoration following fennel control in areas where the native seed bank is depauperate.

Competition, salinity, and clonal growth in native and introduced irises.

PubMed

Mopper, Susan; Wiens, Karen C; Goranova, Greta A

2016-09-01

Iris pseudacorus spread rapidly into North America after introduction from Europe in the 1800s and now co-occurs with native I. hexagona in freshwater Louisiana wetlands. Native irises support and interact with multiple trophic levels, whereas I. pseudacorus is classified an invasive pest because it grows aggressively, reduces biodiversity, and displaces native vegetation. Salinity levels are increasing in coastal wetlands worldwide. We examined how salt-stress affects competitive interactions between these conspecifics. We established a three-way full-factorial common-garden experiment that included species (I. pseudacorus, I. hexagona), competition (no competition, intraspecific competition, and interspecific competition), and salinity (0, 4, 8 parts per thousand NaCl), with six replicates per treatment. After 18 mo, Iris pseudacorus produced much more biomass than the native species did (F1, 92 = 71.5, P < 0.0001). Interspecific competition did not affect the introduced iris, but biomass of the native was strongly reduced (competition × species interaction: F2, 95 = 76.7, P = 0.002). Salinity significantly reduced biomass of both species (F2, 92 = 21.8, P < 0.0001), with no species × salinity interaction (F2, 84 = 1.85, P = 0.16). Our results demonstrate that salt stress strongly reduced clonal reproduction in native and introduced irises; however, the introduced iris had a competitive advantage over the native, regardless of environmental salinity levels. Based on patterns in clonal reproduction, the introduced iris could potentially threaten native iris populations. We are currently investigating seed production and mortality during competition and stress because both clonal and sexual reproduction must be considered when predicting long-term population dynamics. © 2016 Botanical Society of America.

Yeast prions are useful for studying protein chaperones and protein quality control.

PubMed

Masison, Daniel C; Reidy, Michael

2015-01-01

Protein chaperones help proteins adopt and maintain native conformations and play vital roles in cellular processes where proteins are partially folded. They comprise a major part of the cellular protein quality control system that protects the integrity of the proteome. Many disorders are caused when proteins misfold despite this protection. Yeast prions are fibrous amyloid aggregates of misfolded proteins. The normal action of chaperones on yeast prions breaks the fibers into pieces, which results in prion replication. Because this process is necessary for propagation of yeast prions, even small differences in activity of many chaperones noticeably affect prion phenotypes. Several other factors involved in protein processing also influence formation, propagation or elimination of prions in yeast. Thus, in much the same way that the dependency of viruses on cellular functions has allowed us to learn much about cell biology, the dependency of yeast prions on chaperones presents a unique and sensitive way to monitor the functions and interactions of many components of the cell's protein quality control system. Our recent work illustrates the utility of this system for identifying and defining chaperone machinery interactions.

Replicating DNA by cell factories: roles of central carbon metabolism and transcription in the control of DNA replication in microbes, and implications for understanding this process in human cells

PubMed Central

2013-01-01

Precise regulation of DNA replication is necessary to ensure the inheritance of genetic features by daughter cells after each cell division. Therefore, determining how the regulatory processes operate to control DNA replication is crucial to our understanding and application to biotechnological processes. Contrary to early concepts of DNA replication, it appears that this process is operated by large, stationary nucleoprotein complexes, called replication factories, rather than by single enzymes trafficking along template molecules. Recent discoveries indicated that in bacterial cells two processes, central carbon metabolism (CCM) and transcription, significantly and specifically influence the control of DNA replication of various replicons. The impact of these discoveries on our understanding of the regulation of DNA synthesis is discussed in this review. It appears that CCM may influence DNA replication by either action of specific metabolites or moonlighting activities of some enzymes involved in this metabolic pathway. The role of transcription in the control of DNA replication may arise from either topological changes in nucleic acids which accompany RNA synthesis or direct interactions between replication and transcription machineries. Due to intriguing similarities between some prokaryotic and eukaryotic regulatory systems, possible implications of studies on regulation of microbial DNA replication on understanding such a process occurring in human cells are discussed. PMID:23714207

Amplified Self-replication of DNA Origami Nanostructures through Multi-cycle Fast-annealing Process

NASA Astrophysics Data System (ADS)

Zhou, Feng; Zhuo, Rebecca; He, Xiaojin; Sha, Ruojie; Seeman, Nadrian; Chaikin, Paul

We have developed a non-biological self-replication process using templated reversible association of components and irreversible linking with annealing and UV cycles. The current method requires a long annealing time, up to several days, to achieve the specific self-assembly of DNA nanostructures. In this work, we accomplished the self-replication with a shorter time and smaller replication rate per cycle. By decreasing the ramping time, we obtained the comparable replication yield within 90 min. Systematic studies show that the temperature and annealing time play essential roles in the self-replication process. In this manner, we can amplify the self-replication process to a factor of 20 by increasing the number of cycles within the same amount of time.

Co-generating synthetic parts toward a self-replicating system

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

Li, Jun; Haas, Wilhelm; Jackson, Kirsten

To build replicating systems with new functions, the engineering of existing biological machineries requires a sensible strategy. Protein synthesis Using Recombinant Elements (PURE) system consists of the desired components for transcription, translation, aminoacylation and energy regeneration. PURE, might be the basis for a radically alterable, lifelike system after optimization. Here, we regenerated 54 E. coli ribosomal (r-) proteins individually from DNA templates in the PURE system. We show that using stable isotope labeling with amino acids, mass spectrometry based quantitative proteomics could detect 26 of the 33 50S and 20 of the 21 30S subunit r-proteins when co-expressed in batchmore » format PURE system. By optimizing DNA template concentrations and adapting a miniaturized Fluid Array Device with optimized feeding solution, we were able to cogenerate and detect at least 29 of the 33 50S and all of the 21 30S subunit r-proteins in one pot. The boost on yield of a single r-protein in co-expression pool varied from ~1.5 to 5-fold compared to the batch mode, with up to ~ 2.4 µM yield for a single r-protein. Reconstituted ribosomes under physiological condition from PURE system synthesized 30S r-proteins and native 16S rRNA showed ~13% activity of native 70S ribosomes, which increased to 21% when supplemented with GroEL/ES. As a result, this work also points to what is still needed to obtain self-replicating synthetic ribosomes in-situ in the PURE system.« less

Co-generating synthetic parts toward a self-replicating system

DOE PAGES

Li, Jun; Haas, Wilhelm; Jackson, Kirsten; ...

2017-03-23

To build replicating systems with new functions, the engineering of existing biological machineries requires a sensible strategy. Protein synthesis Using Recombinant Elements (PURE) system consists of the desired components for transcription, translation, aminoacylation and energy regeneration. PURE, might be the basis for a radically alterable, lifelike system after optimization. Here, we regenerated 54 E. coli ribosomal (r-) proteins individually from DNA templates in the PURE system. We show that using stable isotope labeling with amino acids, mass spectrometry based quantitative proteomics could detect 26 of the 33 50S and 20 of the 21 30S subunit r-proteins when co-expressed in batchmore » format PURE system. By optimizing DNA template concentrations and adapting a miniaturized Fluid Array Device with optimized feeding solution, we were able to cogenerate and detect at least 29 of the 33 50S and all of the 21 30S subunit r-proteins in one pot. The boost on yield of a single r-protein in co-expression pool varied from ~1.5 to 5-fold compared to the batch mode, with up to ~ 2.4 µM yield for a single r-protein. Reconstituted ribosomes under physiological condition from PURE system synthesized 30S r-proteins and native 16S rRNA showed ~13% activity of native 70S ribosomes, which increased to 21% when supplemented with GroEL/ES. As a result, this work also points to what is still needed to obtain self-replicating synthetic ribosomes in-situ in the PURE system.« less

Should the position of the patellar component replicate the vertical median ridge of the native patella?

PubMed

Lee, Rae Hyeong; Jeong, Hae Won; Lee, Jin Kyu; Choi, Choong Hyeok

2017-01-01

In total knee arthroplasty (TKA), the position of the patellar component can affect patellar tracking. However, the patellar component cannot always replicate the original high point of the patella because of anatomical variance. This study investigated whether altering the highest point of the patella can affect outcomes of primary TKA, especially in patients having a patella with a far-medialized median ridge. A retrospective review was performed for 177 knees (143 patients) treated with primary TKA between July 2011 and March 2014. Group 1 (34 knees) had the patellar component displaced over three millimeters from the median ridge, while Group 2 (143 knees) had the patellar component placed on the original median ridge position. The one-year follow-up outcomes were reviewed, including: patellar tilt angle, Knee Society Score, Feller Patellar Score, and modified Kujala Anterior Knee Pain Score. Mean (±standard deviation) displacement of the patellar component in Group 1 was 3.97±0.97mm lateral to the original position of the median ridge, with a significant decrease in lateral patellar tilt angle (P<0.001). Lateral patellar tilt showed a positive correlation with the medialization of the patellar component (P<0.001, r=0.401). Ability to rise from a chair was better in Group 1 (P=0.025). There were no other between-group differences in other clinical outcomes. There should be no need for the patellar component to replicate the original highest point of the native patella in primary TKA. Copyright © 2016 Elsevier B.V. All rights reserved.

Invasive lionfish reduce native fish abundance on a regional scale

NASA Astrophysics Data System (ADS)

Ballew, Nicholas G.; Bacheler, Nathan M.; Kellison, G. Todd; Schueller, Amy M.

2016-08-01

Invasive lionfish pose an unprecedented threat to biodiversity and fisheries throughout Atlantic waters off of the southeastern United States, the Caribbean, and the Gulf of Mexico. Here, we employ a spatially replicated Before-After-Control-Impact analysis with temporal pairing to quantify for the first time the impact of the lionfish invasion on native fish abundance across a broad regional scale and over the entire duration of the lionfish invasion (1990-2014). Our results suggest that 1) lionfish-impacted areas off of the southeastern United States are most prevalent off-shore near the continental shelf-break but are also common near-shore and 2) in impacted areas, lionfish have reduced tomtate (a native forage fish) abundance by 45% since the invasion began. Tomtate served as a model native fish species in our analysis, and as such, it is likely that the lionfish invasion has had similar impacts on other species, some of which may be of economic importance. Barring the development of a control strategy that reverses the lionfish invasion, the abundance of lionfish in the Atlantic, Caribbean, and Gulf of Mexico will likely remain at or above current levels. Consequently, the effect of lionfish on native fish abundance will likely continue for the foreseeable future.

Invasive lionfish reduce native fish abundance on a regional scale.

PubMed

Ballew, Nicholas G; Bacheler, Nathan M; Kellison, G Todd; Schueller, Amy M

2016-08-31

Invasive lionfish pose an unprecedented threat to biodiversity and fisheries throughout Atlantic waters off of the southeastern United States, the Caribbean, and the Gulf of Mexico. Here, we employ a spatially replicated Before-After-Control-Impact analysis with temporal pairing to quantify for the first time the impact of the lionfish invasion on native fish abundance across a broad regional scale and over the entire duration of the lionfish invasion (1990-2014). Our results suggest that 1) lionfish-impacted areas off of the southeastern United States are most prevalent off-shore near the continental shelf-break but are also common near-shore and 2) in impacted areas, lionfish have reduced tomtate (a native forage fish) abundance by 45% since the invasion began. Tomtate served as a model native fish species in our analysis, and as such, it is likely that the lionfish invasion has had similar impacts on other species, some of which may be of economic importance. Barring the development of a control strategy that reverses the lionfish invasion, the abundance of lionfish in the Atlantic, Caribbean, and Gulf of Mexico will likely remain at or above current levels. Consequently, the effect of lionfish on native fish abundance will likely continue for the foreseeable future.

Invasive lionfish reduce native fish abundance on a regional scale

PubMed Central

Ballew, Nicholas G.; Bacheler, Nathan M.; Kellison, G. Todd; Schueller, Amy M.

2016-01-01

Invasive lionfish pose an unprecedented threat to biodiversity and fisheries throughout Atlantic waters off of the southeastern United States, the Caribbean, and the Gulf of Mexico. Here, we employ a spatially replicated Before-After-Control-Impact analysis with temporal pairing to quantify for the first time the impact of the lionfish invasion on native fish abundance across a broad regional scale and over the entire duration of the lionfish invasion (1990–2014). Our results suggest that 1) lionfish-impacted areas off of the southeastern United States are most prevalent off-shore near the continental shelf-break but are also common near-shore and 2) in impacted areas, lionfish have reduced tomtate (a native forage fish) abundance by 45% since the invasion began. Tomtate served as a model native fish species in our analysis, and as such, it is likely that the lionfish invasion has had similar impacts on other species, some of which may be of economic importance. Barring the development of a control strategy that reverses the lionfish invasion, the abundance of lionfish in the Atlantic, Caribbean, and Gulf of Mexico will likely remain at or above current levels. Consequently, the effect of lionfish on native fish abundance will likely continue for the foreseeable future. PMID:27578096

Palm Reversal Errors in Native-Signing Children with Autism

PubMed Central

Shield, Aaron; Meier, Richard P.

2012-01-01

Children with autism spectrum disorder (ASD) who have native exposure to a sign language such as American Sign Language (ASL) have received almost no scientific attention. This paper reports the first studies on a sample of five native-signing children (four deaf children of deaf parents and one hearing child of deaf parents; ages 4;6 to 7;5) diagnosed with ASD. A domain-general deficit in the ability of children with ASD to replicate the gestures of others is hypothesized to be a source of palm orientation reversal errors in sign. In Study 1, naturalistic language samples were collected from three native-signing children with ASD and were analyzed for errors in handshape, location, movement and palm orientation. In Study 2, four native-signing children with ASD were compared to 12 typically-developing deaf children (ages 3;7 to 6;9, all born to deaf parents) on a fingerspelling task. In both studies children with ASD showed a tendency to reverse palm orientation on signs specified for inward/outward orientation. Typically-developing deaf children did not produce any such errors in palm orientation. We conclude that this kind of palm reversal has a perceptual rather than a motoric source, and is further evidence of a “self-other mapping” deficit in ASD. PMID:22981637

Rapid evolution accelerates plant population spread in fragmented experimental landscapes.

PubMed

Williams, Jennifer L; Kendall, Bruce E; Levine, Jonathan M

2016-07-29

Predicting the speed of biological invasions and native species migrations requires an understanding of the ecological and evolutionary dynamics of spreading populations. Theory predicts that evolution can accelerate species' spread velocity, but how landscape patchiness--an important control over traits under selection--influences this process is unknown. We manipulated the response to selection in populations of a model plant species spreading through replicated experimental landscapes of varying patchiness. After six generations of change, evolving populations spread 11% farther than nonevolving populations in continuously favorable landscapes and 200% farther in the most fragmented landscapes. The greater effect of evolution on spread in patchier landscapes was consistent with the evolution of dispersal and competitive ability. Accounting for evolutionary change may be critical when predicting the velocity of range expansions. Copyright © 2016, American Association for the Advancement of Science.

Variation in Wolbachia effects on Aedes mosquitoes as a determinant of invasiveness and vectorial capacity.

PubMed

King, Jessica G; Souto-Maior, Caetano; Sartori, Larissa M; Maciel-de-Freitas, Rafael; Gomes, M Gabriela M

2018-04-16

Wolbachia has been introduced into Aedes aegypti mosquitoes to control the spread of arboviruses, such as dengue, chikungunya and Zika. Studies showed that certain Wolbachia strains (such as wMel) reduce replication of dengue viruses in the laboratory, prompting the release of mosquitoes carrying the bacterium into the field, where vectorial capacity can be realistically assessed in relation to native non-carriers. Here we apply a new analysis to two published datasets, and show that wMel increases the mean and the variance in Ae. aegypti susceptibility to dengue infection when introgressed into Brazil and Vietnam genetic backgrounds. In the absence of other processes, higher mean susceptibility should lead to enhanced viral transmission. The increase in variance, however, widens the basis for selection imposed by unexplored natural forces, retaining the potential for reducing transmission overall.

Two-year effects of aminopyralid on an invaded meadow in the Washington Cascades

Treesearch

Timothy B. Harrington; David H. Peter; Warren D. Devine

2014-01-01

Four rates of aminopyralid (30, 60, 90, and 120 g ae ha-1 [0.4, 0.9, 1.3, and 1.8 oz ae acre-1]) were compared for their ability to reduce abundance of nonnative dicot species and favor native species in an invaded Cascade Mountain meadow near Trout Lake, WA. Treatments were applied in two replicated studies (June 2009 and...

On the Second Language Acquisition of Spanish Reflexive Passives and Reflexive Impersonals by French- and English-Speaking Adults

ERIC Educational Resources Information Center

Tremblay, Annie

2006-01-01

This study, a partial replication of Bruhn de Garavito (1999a; 1999b), investigates the second language (L2) acquisition of Spanish reflexive passives and reflexive impersonals by French- and English-speaking adults at an advanced level of proficiency. The L2 acquisition of Spanish reflexive passives and reflexive impersonals by native French and…

Auditory detection of non-speech and speech stimuli in noise: Effects of listeners' native language background.

PubMed

Liu, Chang; Jin, Su-Hyun

2015-11-01

This study investigated whether native listeners processed speech differently from non-native listeners in a speech detection task. Detection thresholds of Mandarin Chinese and Korean vowels and non-speech sounds in noise, frequency selectivity, and the nativeness of Mandarin Chinese and Korean vowels were measured for Mandarin Chinese- and Korean-native listeners. The two groups of listeners exhibited similar non-speech sound detection and frequency selectivity; however, the Korean listeners had better detection thresholds of Korean vowels than Chinese listeners, while the Chinese listeners performed no better at Chinese vowel detection than the Korean listeners. Moreover, thresholds predicted from an auditory model highly correlated with behavioral thresholds of the two groups of listeners, suggesting that detection of speech sounds not only depended on listeners' frequency selectivity, but also might be affected by their native language experience. Listeners evaluated their native vowels with higher nativeness scores than non-native listeners. Native listeners may have advantages over non-native listeners when processing speech sounds in noise, even without the required phonetic processing; however, such native speech advantages might be offset by Chinese listeners' lower sensitivity to vowel sounds, a characteristic possibly resulting from their sparse vowel system and their greater cognitive and attentional demands for vowel processing.

Nation, Face, and Identity: An Initial Investigation of National Face in East Asia

PubMed Central

Chen, Rong; Hwang, Kwang-Kuo

2016-01-01

This research investigates a key concept in East Asia, face, and represents the first attempt to empirically examine the concept of face at the national level. Controlling for the level of national identification, Study 1 employed the scenario experiment method among samples of native Chinese and Taiwanese populations and revealed that national face exhibits patterns reverse of personal face. Using the experimental method, Study 2 replicated the findings of Study 1 and provided support for the different mechanisms underneath national face and personal face. Study 3 replicated the findings of Study 2 and additionally showed that national face exerts a significant inhibitory effect on face process. Findings are discussed in terms of possible implications for intergroup and international relations. Expanding on extant scholarship on face and across three studies with different experimental paradigms, this research turns our attention from face at the personal level to face at the national level by introducing the construct of national face and examining its manifestations in East Asia. The results advance our understanding of the psychological mechanism driving face concern in East Asia. They make a strong and unique case for the psychological existence of national face as an empirically distinct construct and an important psychological resource for East Asians. PMID:27774081

Students classified as LD who received course substitutions for the college foreign language requirement: a replication study.

PubMed

Sparks, Richard L; Philips, Lois G; Javorsky, James

2002-01-01

This replication study examined whether 158 college students classified as learning disabled (LD) who were granted course substitutions for the foreign language (FL) requirement would display significant cognitive and academic achievement differences when grouped by levels of IQ-achievement and achievement-achievement discrepancy and by level of performance on an FL aptitude test (Modern Language Aptitude Test; MLAT), phonological/orthographic processing measures, and in FL courses. The results showed that there were few differences among groups with differing levels of IQ-achievement or achievement-achievement discrepancy (i.e., < 1.0 SD, 1.0-1.49 SD, and > 1.50 SD) on MLAT and American College Testing (ACT) scores, graduating grade point average (GPA), or college FL GPA. The results also showed that between groups who scored at or above versus below the 15th percentile (i.e., < 1.0 SD) on the MLAT, there were no differences on measures of graduating GPA, college FL GPA, native language skill, ACT score, and Verbal IQ. Demographic findings showed that 44% of these petition students met a minimum IQ-achievement discrepancy criterion (> or = 1.0 SD) for classification as LD. These findings suggest that many traditional assumptions about LD and FL learning are likely to be false.

Shifts in an invasive rodent community favoring black rats (Rattus rattus) following restoration of native forest

USGS Publications Warehouse

Shiels, Aaron B.; Medeiros, Arthur C.; von Allmen, Erica I.

2017-01-01

One potential, unintended ecological consequence accompanying forest restoration is a shift in invasive animal populations, potentially impacting conservation targets. Eighteen years after initial restoration (ungulate exclusion, invasive plant control, and out planting native species) at a 4 ha site on Maui, Hawai'i, we compared invasive rodent communities in a restored native dry forest and adjacent non-native grassland. Quarterly for 1 year, we trapped rodents on three replicate transects (107 rodent traps) in each habitat type for three consecutive nights. While repeated trapping may have reduced the rat (Black rat, Rattus rattus) population in the forest, it did not appear to reduce the mouse (House mouse, Mus musculus) population in the grassland. In unrestored grassland, mouse captures outnumbered rat captures 220:1, with mice averaging 54.9 indiv./night versus rats averaging 0.25 indiv./night. In contrast, in restored native forest, rat captures outnumbered mouse captures by nearly 5:1, averaging 9.0 indiv./night versus 1.9 indiv./night for mice. Therefore, relatively recent native forest restoration increased Black rat abundance and also increased their total biomass in the restored ecosystem 36-fold while reducing House mouse biomass 35-fold. Such a community shift is worrisome because Black rats pose a much greater threat than do mice to native birds and plants, perhaps especially to large-seeded tree species. Land managers should be aware that forest restoration (i.e. converting grassland to native forest) can invoke shifts in invasive rodent populations, potentially favoring Black rats. Without intervention, this shift may pose risks for intended conservation targets and modify future forest restoration trajectories.

Native-language N400 and P600 predict dissociable language-learning abilities in adults

PubMed Central

Qi, Zhenghan; Beach, Sara D.; Finn, Amy S.; Minas, Jennifer; Goetz, Calvin; Chan, Brian; Gabrieli, John D.E.

2018-01-01

Language learning aptitude during adulthood varies markedly across individuals. An individual’s native-language ability has been associated with success in learning a new language as an adult. However, little is known about how native-language processing affects learning success and what neural markers of native-language processing, if any, are related to success in learning. We therefore related variation in electrophysiology during native-language processing to success in learning a novel artificial language. Event-related potentials (ERPs) were recorded while native English speakers judged the acceptability of English sentences prior to learning an artificial language. There was a trend towards a double dissociation between native-language ERPs and their relationships to novel syntax and vocabulary learning. Individuals who exhibited a greater N400 effect when processing English semantics showed better future learning of the artificial language overall. The N400 effect was related to syntax learning via its specific relationship to vocabulary learning. In contrast, the P600 effect size when processing English syntax predicted future syntax learning but not vocabulary learning. These findings show that distinct neural signatures of native-language processing relate to dissociable abilities for learning novel semantic and syntactic information. PMID:27737775

Vegetation response to invasive Tamarix control in southwestern U.S. rivers: A collaborative study including 416 sites

USGS Publications Warehouse

González, Eduardo; Sher, Anna A; Anderson, Robert M.; Bay, Robin F.; Bean, Daniel W.; Bissonnete, Gabriel J.; Bourgeois, Bérenger; Cooper, David J.; Dohrenwend, Kara; Eichhorst, Kim D.; El Waer, Hisham; Kennard, Deborah K.; Harms-Weissinger, Rebecca; Henry, Annie L.; Makarick, Lori J.; Ostoja, Steven M.; Reynolds, Lindsay V.; Robinson, W. Wright; Shafroth, Patrick B.

2017-01-01

Most studies assessing vegetation response following control of invasive Tamarix trees along southwestern U.S. rivers have been small in scale (e.g., river reach), or at a regional scale but with poor spatial-temporal replication, and most have not included testing the effects of a now widely used biological control. We monitored plant composition following Tamarix control along hydrologic, soil, and climatic gradients in 244 treated and 172 reference sites across six U.S. states. This represents the largest comprehensive assessment to date on the vegetation response to the four most common Tamarix control treatments. Biocontrol by a defoliating beetle (treatment 1) reduced the abundance of Tamarix less than active removal by mechanically using hand and chain-saws (2), heavy machinery (3) or burning (4). Tamarix abundance also decreased with lower temperatures, higher precipitation, and follow-up treatments for Tamarix resprouting. Native cover generally increased over time in active Tamarix removal sites, however, the increases observed were small and was not consistently increased by active revegetation. Overall, native cover was correlated to permanent stream flow, lower grazing pressure, lower soil salinity and temperatures, and higher precipitation. Species diversity also increased where Tamarix was removed. However, Tamarix treatments, especially those generating the highest disturbance (burning and heavy machinery), also often promoted secondary invasions of exotic forbs. The abundance of hydrophytic species was much lower in treated than in reference sites, suggesting that management of southwestern U.S. rivers has focused too much on weed control, overlooking restoration of fluvial processes that provide habitat for hydrophytic and floodplain vegetation. These results can help inform future management of Tamarix-infested rivers to restore hydrogeomorphic processes, increase native biodiversity and reduce abundance of noxious species.

Infants' Selectively Pay Attention to the Information They Receive from a Native Speaker of Their Language.

PubMed

Marno, Hanna; Guellai, Bahia; Vidal, Yamil; Franzoi, Julia; Nespor, Marina; Mehler, Jacques

2016-01-01

From the first moments of their life, infants show a preference for their native language, as well as toward speakers with whom they share the same language. This preference appears to have broad consequences in various domains later on, supporting group affiliations and collaborative actions in children. Here, we propose that infants' preference for native speakers of their language also serves a further purpose, specifically allowing them to efficiently acquire culture specific knowledge via social learning. By selectively attending to informants who are native speakers of their language and who probably also share the same cultural background with the infant, young learners can maximize the possibility to acquire cultural knowledge. To test whether infants would preferably attend the information they receive from a speaker of their native language, we familiarized 12-month-old infants with a native and a foreign speaker, and then presented them with movies where each of the speakers silently gazed toward unfamiliar objects. At test, infants' looking behavior to the two objects alone was measured. Results revealed that infants preferred to look longer at the object presented by the native speaker. Strikingly, the effect was replicated also with 5-month-old infants, indicating an early development of such preference. These findings provide evidence that young infants pay more attention to the information presented by a person with whom they share the same language. This selectivity can serve as a basis for efficient social learning by influencing how infants' allocate attention between potential sources of information in their environment.

Accessory genes confer a high replication rate to virulent feline immunodeficiency virus.

PubMed

Troyer, Ryan M; Thompson, Jesse; Elder, John H; VandeWoude, Sue

2013-07-01

Feline immunodeficiency virus (FIV) is a lentivirus that causes AIDS in domestic cats, similar to human immunodeficiency virus (HIV)/AIDS in humans. The FIV accessory protein Vif abrogates the inhibition of infection by cat APOBEC3 restriction factors. FIV also encodes a multifunctional OrfA accessory protein that has characteristics similar to HIV Tat, Vpu, Vpr, and Nef. To examine the role of vif and orfA accessory genes in FIV replication and pathogenicity, we generated chimeras between two FIV molecular clones with divergent disease potentials: a highly pathogenic isolate that replicates rapidly in vitro and is associated with significant immunopathology in vivo, FIV-C36 (referred to here as high-virulence FIV [HV-FIV]), and a less-pathogenic strain, FIV-PPR (referred to here as low-virulence FIV [LV-FIV]). Using PCR-driven overlap extension, we produced viruses in which vif, orfA, or both genes from virulent HV-FIV replaced equivalent genes in LV-FIV. The generation of these chimeras is more straightforward in FIV than in primate lentiviruses, since FIV accessory gene open reading frames have very little overlap with other genes. All three chimeric viruses exhibited increased replication kinetics in vitro compared to the replication kinetics of LV-FIV. Chimeras containing HV-Vif or Vif/OrfA had replication rates equivalent to those of the virulent HV-FIV parental virus. Furthermore, small interfering RNA knockdown of feline APOBEC3 genes resulted in equalization of replication rates between LV-FIV and LV-FIV encoding HV-FIV Vif. These findings demonstrate that Vif-APOBEC interactions play a key role in controlling the replication and pathogenicity of this immunodeficiency-inducing virus in its native host species and that accessory genes act as mediators of lentiviral strain-specific virulence.

Memory for non-native language: the role of lexical processing in the retention of surface form.

PubMed

Sampaio, Cristina; Konopka, Agnieszka E

2013-01-01

Research on memory for native language (L1) has consistently shown that retention of surface form is inferior to that of gist (e.g., Sachs, 1967). This paper investigates whether the same pattern is found in memory for non-native language (L2). We apply a model of bilingual word processing to more complex linguistic structures and predict that memory for L2 sentences ought to contain more surface information than L1 sentences. Native and non-native speakers of English were tested on a set of sentence pairs with different surface forms but the same meaning (e.g., "The bullet hit/struck the bull's eye"). Memory for these sentences was assessed with a cued recall procedure. Responses showed that native and non-native speakers did not differ in the accuracy of gist-based recall but that non-native speakers outperformed native speakers in the retention of surface form. The results suggest that L2 processing involves more intensive encoding of lexical level information than L1 processing.

When one person's mistake is another's standard usage: the effect of foreign accent on syntactic processing.

PubMed

Hanulíková, Adriana; van Alphen, Petra M; van Goch, Merel M; Weber, Andrea

2012-04-01

How do native listeners process grammatical errors that are frequent in non-native speech? We investigated whether the neural correlates of syntactic processing are modulated by speaker identity. ERPs to gender agreement errors in sentences spoken by a native speaker were compared with the same errors spoken by a non-native speaker. In line with previous research, gender violations in native speech resulted in a P600 effect (larger P600 for violations in comparison with correct sentences), but when the same violations were produced by the non-native speaker with a foreign accent, no P600 effect was observed. Control sentences with semantic violations elicited comparable N400 effects for both the native and the non-native speaker, confirming no general integration problem in foreign-accented speech. The results demonstrate that the P600 is modulated by speaker identity, extending our knowledge about the role of speaker's characteristics on neural correlates of speech processing.

Tolerance of Sir1p/Origin Recognition Complex-Dependent Silencing for Enhanced Origin Firing at HMRa

PubMed Central

McConnell, Kristopher H.; Müller, Philipp; Fox, Catherine A.

2006-01-01

The HMR-E silencer is a DNA element that directs the formation of silent chromatin at the HMRa locus in Saccharomyces cerevisiae. Sir1p is one of four Sir proteins required for silent chromatin formation at HMRa. Sir1p functions by binding the origin recognition complex (ORC), which binds to HMR-E, and recruiting the other Sir proteins (Sir2p to -4p). ORCs also bind to hundreds of nonsilencer positions distributed throughout the genome, marking them as replication origins, the sites for replication initiation. HMR-E also acts as a replication origin, but compared to many origins in the genome, it fires extremely inefficiently and late during S phase. One postulate to explain this observation is that ORC's role in origin firing is incompatible with its role in binding Sir1p and/or the formation of silent chromatin. Here we examined a mutant HMR-E silencer and fusions between robust replication origins and HMR-E for HMRa silencing, origin firing, and replication timing. Origin firing within HMRa and from the HMR-E silencer itself could be significantly enhanced, and the timing of HMRa replication during an otherwise normal S phase advanced, without a substantial reduction in SIR1-dependent silencing. However, although the robust origin/silencer fusions silenced HMRa quite well, they were measurably less effective than a comparable silencer containing HMR-E's native ORC binding site. PMID:16479013

A study of an adaptive replication framework for orchestrated composite web services.

PubMed

Mohamed, Marwa F; Elyamany, Hany F; Nassar, Hamed M

2013-01-01

Replication is considered one of the most important techniques to improve the Quality of Services (QoS) of published Web Services. It has achieved impressive success in managing resource sharing and usage in order to moderate the energy consumed in IT environments. For a robust and successful replication process, attention should be paid to suitable time as well as the constraints and capabilities in which the process runs. The replication process is time-consuming since outsourcing some new replicas into other hosts is lengthy. Furthermore, nowadays, most of the business processes that might be implemented over the Web are composed of multiple Web services working together in two main styles: Orchestration and Choreography. Accomplishing a replication over such business processes is another challenge due to the complexity and flexibility involved. In this paper, we present an adaptive replication framework for regular and orchestrated composite Web services. The suggested framework includes a number of components for detecting unexpected and unhappy events that might occur when consuming the original published web services including failure or overloading. It also includes a specific replication controller to manage the replication process and select the best host that would encapsulate a new replica. In addition, it includes a component for predicting the incoming load in order to decrease the time needed for outsourcing new replicas, enhancing the performance greatly. A simulation environment has been created to measure the performance of the suggested framework. The results indicate that adaptive replication with prediction scenario is the best option for enhancing the performance of the replication process in an online business environment.

The native-language benefit for talker identification is robust in 7.5-month-old infants.

PubMed

Fecher, Natalie; Johnson, Elizabeth K

2018-04-26

Adults recognize talkers better when the talkers speak a familiar language than when they speak an unfamiliar language. This language familiarity effect (LFE) demonstrates the inseparable nature of linguistic and indexical information in adult spoken language processing. Relatively little is known about children's integration of linguistic and indexical information in speech. For example, to date, only one study has explored the LFE in infants. Here, we sought to better understand the maturation of speech processing abilities in infants by replicating this earlier study using a more stringent experimental design (eliminating a potential voice-language confound), a different test population (English- rather than Dutch-learning infants), and a new language pairing (English vs. Polish rather than Dutch vs. Italian or Japanese). Furthermore, we explored the language exposure conditions required for infants to develop an LFE for a formerly unfamiliar language. We hypothesized based on previous studies (including the perceptual narrowing literature) that infants might develop an LFE more readily than would adults. Although our findings replicate those of the earlier study-demonstrating that the LFE is robust in 7.5-month-olds-we found no evidence that infants need less language exposure than do adults to develop an LFE. We concluded that both infants and adults need extensive (potentially live) exposure to an unfamiliar language before talker identification in that language improves. Moreover, our study suggests that the LFE is likely rooted in early emerging phonology rather than shared lexical knowledge and that infants already closely resemble adults in their processing of linguistic and indexical information. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

The Inherent Asymmetry of DNA Replication.

PubMed

Snedeker, Jonathan; Wooten, Matthew; Chen, Xin

2017-10-06

Semiconservative DNA replication has provided an elegant solution to the fundamental problem of how life is able to proliferate in a way that allows cells, organisms, and populations to survive and replicate many times over. Somewhat lost, however, in our admiration for this mechanism is an appreciation for the asymmetries that occur in the process of DNA replication. As we discuss in this review, these asymmetries arise as a consequence of the structure of the DNA molecule and the enzymatic mechanism of DNA synthesis. Increasing evidence suggests that asymmetries in DNA replication are able to play a central role in the processes of adaptation and evolution by shaping the mutagenic landscape of cells. Additionally, in eukaryotes, recent work has demonstrated that the inherent asymmetries in DNA replication may play an important role in the process of chromatin replication. As chromatin plays an essential role in defining cell identity, asymmetries generated during the process of DNA replication may play critical roles in cell fate decisions related to patterning and development.

Demonstrating the Ecosystem Effects of Armored Suckermouth Catfishes (Loricariidae): A Feasibility Study Using Mesocosms

DTIC Science & Technology

2013-11-01

Figure 2. Native fish used in the mesocosm study: golden topminnow (Fundulus chrysotus). Photo by Mark Binkley, jonahsaquarium.com. Cover in each...Suckermouth Catfishes (Loricariidae): A Feasibility Study Using Mesocosms by Jan Jeffrey Hoover, Nicky M. Hahn, and Jay A. Collins PURPOSE: The...armored suckermouth catfishes, or simply suckermouth catfishes. The authors’ solution is to use mesocosms, medium-sized containers that replicate aquatic

A field experiment demonstrating plant life-history evolution and its eco-evolutionary feedback to seed predator populations.

PubMed

Agrawal, Anurag A; Johnson, Marc T J; Hastings, Amy P; Maron, John L

2013-05-01

The extent to which evolutionary change occurs in a predictable manner under field conditions and how evolutionary changes feed back to influence ecological dynamics are fundamental, yet unresolved, questions. To address these issues, we established eight replicate populations of native common evening primrose (Oenothera biennis). Each population was planted with 18 genotypes in identical frequency. By tracking genotype frequencies with microsatellite DNA markers over the subsequent three years (up to three generations, ≈5,000 genotyped plants), we show rapid and consistent evolution of two heritable plant life-history traits (shorter life span and later flowering time). This rapid evolution was only partially the result of differential seed production; genotypic variation in seed germination also contributed to the observed evolutionary response. Since evening primrose genotypes exhibited heritable variation for resistance to insect herbivores, which was related to flowering time, we predicted that evolutionary changes in genotype frequencies would feed back to influence populations of a seed predator moth that specializes on O. biennis. By the conclusion of the experiment, variation in the genotypic composition among our eight replicate field populations was highly predictive of moth abundance. These results demonstrate how rapid evolution in field populations of a native plant can influence ecological interactions.

ERP evidence for different strategies in the processing of case markers in native speakers and non-native learners

PubMed Central

Mueller, Jutta L; Hirotani, Masako; Friederici, Angela D

2007-01-01

Background The present experiments were designed to test how the linguistic feature of case is processed in Japanese by native and non-native listeners. We used a miniature version of Japanese as a model to compare sentence comprehension mechanisms in native speakers and non-native learners who had received training until they had mastered the system. In the first experiment we auditorily presented native Japanese speakers with sentences containing incorrect double nominatives and incorrect double accusatives, and with correct sentences. In the second experiment we tested trained non-natives with the same material. Based on previous research in German we expected an N400-P600 biphasic ERP response with specific modulations depending on the violated case and whether the listeners were native or non-native. Results For native Japanese participants the general ERP response to the case violations was an N400-P600 pattern. Double accusatives led to an additional enhancement of the P600 amplitude. For the learners a native-like P600 was present for double accusatives and for double nominatives. The additional negativity, however, was present in learners only for double nominative violations, and it was characterized by a different topographical distribution. Conclusion The results indicate that native listeners use case markers for thematic as well as syntactic structure building during incremental sentence interpretation. The modulation of the P600 component for double accusatives possibly reflects case specific syntactic restrictions in Japanese. For adult language learners later processes, as reflected in the P600, seem to be more native-like compared to earlier processes. The anterior distribution of the negativity and its selective emergence for canonical sentences were taken to suggest that the non-native learners resorted to a rather formal processing strategy whereby they relied to a large degree on the phonologically salient nominative case marker. PMID:17331265

Infant diet-related changes in syllable processing between 4 and 5 months: Implications for developing native language sensitivity

USDA-ARS?s Scientific Manuscript database

Since maturational processes triggering increased attunement to native language features in early infancy are sensitive to dietary factors, infant-diet related differences in brain processing of native-language speech stimuli might indicate variations in onset of this tuning process. We measured cor...

Native-language N400 and P600 predict dissociable language-learning abilities in adults.

PubMed

Qi, Zhenghan; Beach, Sara D; Finn, Amy S; Minas, Jennifer; Goetz, Calvin; Chan, Brian; Gabrieli, John D E

2017-04-01

Language learning aptitude during adulthood varies markedly across individuals. An individual's native-language ability has been associated with success in learning a new language as an adult. However, little is known about how native-language processing affects learning success and what neural markers of native-language processing, if any, are related to success in learning. We therefore related variation in electrophysiology during native-language processing to success in learning a novel artificial language. Event-related potentials (ERPs) were recorded while native English speakers judged the acceptability of English sentences prior to learning an artificial language. There was a trend towards a double dissociation between native-language ERPs and their relationships to novel syntax and vocabulary learning. Individuals who exhibited a greater N400 effect when processing English semantics showed better future learning of the artificial language overall. The N400 effect was related to syntax learning via its specific relationship to vocabulary learning. In contrast, the P600 effect size when processing English syntax predicted future syntax learning but not vocabulary learning. These findings show that distinct neural signatures of native-language processing relate to dissociable abilities for learning novel semantic and syntactic information. Copyright © 2016 Elsevier Ltd. All rights reserved.

Understanding how replication processes can maintain systems away from equilibrium using Algorithmic Information Theory.

PubMed

Devine, Sean D

2016-02-01

Replication can be envisaged as a computational process that is able to generate and maintain order far-from-equilibrium. Replication processes, can self-regulate, as the drive to replicate can counter degradation processes that impact on a system. The capability of replicated structures to access high quality energy and eject disorder allows Landauer's principle, in conjunction with Algorithmic Information Theory, to quantify the entropy requirements to maintain a system far-from-equilibrium. Using Landauer's principle, where destabilising processes, operating under the second law of thermodynamics, change the information content or the algorithmic entropy of a system by ΔH bits, replication processes can access order, eject disorder, and counter the change without outside interventions. Both diversity in replicated structures, and the coupling of different replicated systems, increase the ability of the system (or systems) to self-regulate in a changing environment as adaptation processes select those structures that use resources more efficiently. At the level of the structure, as selection processes minimise the information loss, the irreversibility is minimised. While each structure that emerges can be said to be more entropically efficient, as such replicating structures proliferate, the dissipation of the system as a whole is higher than would be the case for inert or simpler structures. While a detailed application to most real systems would be difficult, the approach may well be useful in understanding incremental changes to real systems and provide broad descriptions of system behaviour. Copyright © 2016 The Author. Published by Elsevier Ireland Ltd.. All rights reserved.

An exotic invasive plant selects for increased competitive tolerance, but not competitive suppression, in a native grass.

PubMed

Fletcher, Rebecca A; Callaway, Ragan M; Atwater, Daniel Z

2016-06-01

Exotic invasive plants can exert strong selective pressure for increased competitive ability in native plants. There are two fundamental components of competitive ability: suppression and tolerance, and the current paradigm that these components have equal influences on a species' overall competitive ability has been recently questioned. If these components do not have equal influences on overall ability, then selection on competitive tolerance and suppression may be disproportionate. We used naturally invaded communities to study the effects of selection caused by an invasive forb, Centaurea stoebe, on a native grass, Pseudoroegneria spicata. P. spicata plants were harvested from within dense C. stoebe patches and from nearby uninvaded areas, divided clonally into replicates, then transplanted into a common garden where they grew alone or competed with C. stoebe. We found that P. spicata plants collected from within C. stoebe patches were significantly more tolerant of competition with C. stoebe than P. spicata plants collected from uninvaded areas, but plants from inside invaded patches were not superior at suppressing C. stoebe. These results are consistent with the hypothesis that strong competitors may select for tolerance to competition more than for the ability to suppress neighbors. This has important implications for how native plant communities may respond to invasion over time, and how invasive and native species may ultimately coexist.

Absence of the Asian-specific region V mitochondrial marker in Native Beringians.

PubMed Central

Shields, G F; Hecker, K; Voevoda, M I; Reed, J K

1992-01-01

The Asian-specific 9-bp deletion between the genes for mitochondrial cytochrome oxidase II and lysine transfer RNA has been used to trace aboriginal human movements out of Southeast Asia and into portions of the South Pacific. Although it has been used to estimate the number of independent lineages that occur in the New World, it has not been studied in native peoples of the Beringian region. Thus, we have used PCR to amplify and compare the lengths of DNA segments surrounding this deletion in native peoples of Beringia and the adjacent regions, as well as natives of the Altai Mountains of Southwestern Siberia. Of the 176 individuals analyzed here, the deletion was found in only 3 of 25 individuals from the Ust-Kan region of the Altai Mountains. We comment on the distribution of this marker and on potential relationships between Beringians and other Native American groups in which this marker has been surveyed. One Chukchi possessed three copies of the 9-bp sequence, which suggests (1) that the number of copies of this sequence in humans may be more variable than had been believed and (2) that a mechanism of replication based on tandem duplication may be a potential explanation for the origin of this length mutation in humans. Images Figure 2 Figure 3 Figure 4 PMID:1550120

Adding More Fuel to the Fire: An Eye-Tracking Study of Idiom Processing by Native and Non-Native Speakers

ERIC Educational Resources Information Center

Siyanova-Chanturia, Anna; Conklin, Kathy; Schmitt, Norbert

2011-01-01

Using eye-tracking, we investigate on-line processing of idioms in a biasing story context by native and non-native speakers of English. The stimuli are idioms used figuratively ("at the end of the day"--"eventually"), literally ("at the end of the day"--"in the evening"), and novel phrases ("at the end of the war"). Native speaker results…

ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing.

PubMed

Chen, Xingqi; Shen, Ying; Draper, Will; Buenrostro, Jason D; Litzenburger, Ulrike; Cho, Seung Woo; Satpathy, Ansuman T; Carter, Ava C; Ghosh, Rajarshi P; East-Seletsky, Alexandra; Doudna, Jennifer A; Greenleaf, William J; Liphardt, Jan T; Chang, Howard Y

2016-12-01

Spatial organization of the genome plays a central role in gene expression, DNA replication, and repair. But current epigenomic approaches largely map DNA regulatory elements outside of the native context of the nucleus. Here we report assay of transposase-accessible chromatin with visualization (ATAC-see), a transposase-mediated imaging technology that employs direct imaging of the accessible genome in situ, cell sorting, and deep sequencing to reveal the identity of the imaged elements. ATAC-see revealed the cell-type-specific spatial organization of the accessible genome and the coordinated process of neutrophil chromatin extrusion, termed NETosis. Integration of ATAC-see with flow cytometry enables automated quantitation and prospective cell isolation as a function of chromatin accessibility, and it reveals a cell-cycle dependence of chromatin accessibility that is especially dynamic in G1 phase. The integration of imaging and epigenomics provides a general and scalable approach for deciphering the spatiotemporal architecture of gene control.

Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome.

PubMed

Shen, Yue; Wang, Yun; Chen, Tai; Gao, Feng; Gong, Jianhui; Abramczyk, Dariusz; Walker, Roy; Zhao, Hongcui; Chen, Shihong; Liu, Wei; Luo, Yisha; Müller, Carolin A; Paul-Dubois-Taine, Adrien; Alver, Bonnie; Stracquadanio, Giovanni; Mitchell, Leslie A; Luo, Zhouqing; Fan, Yanqun; Zhou, Baojin; Wen, Bo; Tan, Fengji; Wang, Yujia; Zi, Jin; Xie, Zexiong; Li, Bingzhi; Yang, Kun; Richardson, Sarah M; Jiang, Hui; French, Christopher E; Nieduszynski, Conrad A; Koszul, Romain; Marston, Adele L; Yuan, Yingjin; Wang, Jian; Bader, Joel S; Dai, Junbiao; Boeke, Jef D; Xu, Xun; Cai, Yizhi; Yang, Huanming

2017-03-10

Here, we report the successful design, construction, and characterization of a 770-kilobase synthetic yeast chromosome II (synII). Our study incorporates characterization at multiple levels-including phenomics, transcriptomics, proteomics, chromosome segregation, and replication analysis-to provide a thorough and comprehensive analysis of a synthetic chromosome. Our Trans-Omics analyses reveal a modest but potentially relevant pervasive up-regulation of translational machinery observed in synII, mainly caused by the deletion of 13 transfer RNAs. By both complementation assays and SCRaMbLE (synthetic chromosome rearrangement and modification by loxP -mediated evolution), we targeted and debugged the origin of a growth defect at 37°C in glycerol medium, which is related to misregulation of the high-osmolarity glycerol response. Despite the subtle differences, the synII strain shows highly consistent biological processes comparable to the native strain. Copyright © 2017, American Association for the Advancement of Science.

Host range diversification within the IncP-1 plasmid group

PubMed Central

Yano, Hirokazu; Rogers, Linda M.; Knox, Molly G.; Heuer, Holger; Smalla, Kornelia; Brown, Celeste J.

2013-01-01

Broad-host-range plasmids play a critical role in the spread of antibiotic resistance and other traits. In spite of increasing information about the genomic diversity of closely related plasmids, the relationship between sequence divergence and host range remains unclear. IncP-1 plasmids are currently classified into six subgroups based on the genetic distance of backbone genes. We investigated whether plasmids from two subgroups exhibit a different host range, using two IncP-1γ plasmids, an IncP-1β plasmid and their minireplicons. Efficiencies of plasmid establishment and maintenance were compared using five species that belong to the Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria. The IncP-1β plasmid replicated and persisted in all five hosts in the absence of selection. Of the two IncP-1γ plasmids, both were unable to replicate in alphaproteobacterial host Sphingobium japonicum, and one established itself in Agrobacterium tumefaciens but was very unstable. In contrast, both IncP-1γ minireplicons, which produced higher levels of replication initiation protein than the wild-type plasmids, replicated in all strains, suggesting that poor establishment of the native plasmids is in part due to suboptimal replication initiation gene regulation. The findings suggest that host ranges of distinct IncP-1 plasmids only partially overlap, which may limit plasmid recombination and thus result in further genome divergence. PMID:24002747

Quantitative Analysis of HIV-1 Preintegration Complexes

PubMed Central

Engelman, Alan; Oztop, Ilker; Vandegraaff, Nick; Raghavendra, Nidhanapati K.

2009-01-01

Retroviral replication proceeds through the formation of a provirus, an integrated DNA copy of the viral RNA genome. The linear cDNA product of reverse transcription is the integration substrate and two different integrase activities, 3′ processing and DNA strand transfer, are required for provirus formation. Integrase nicks the cDNA ends adjacent to phylogenetically-conserved CA dinucleotides during 3′ processing. After nuclear entry and locating a suitable chromatin acceptor site, integrase joins the recessed 3′-OHs to the 5′-phosphates of a double-stranded staggered cut in the DNA target. Integrase functions in the context of a large nucleoprotein complex, called the preintegration complex (PIC), and PICs are analyzed to determine levels of integrase 3′ processing and DNA strand transfer activities that occur during acute virus infection. Denatured cDNA end regions are monitored by indirect end-labeling to measure the extent of 3′ processing. Native PICs can efficiently integrate their viral cDNA into exogenously added target DNA in vitro, and Southern blotting or nested PCR assays are used to quantify the resultant DNA strand transfer activity. This study details HIV-1 infection, PIC extraction, partial purification, and quantitative analyses of integrase 3′ processing and DNA strand transfer activities. PMID:19233280

Spatiotemporal Evolution of the Wound Repairing Process in a 3D Human Dermis Equivalent.

PubMed

Lombardi, Bernadette; Casale, Costantino; Imparato, Giorgia; Urciuolo, Francesco; Netti, Paolo Antonio

2017-07-01

Several skin equivalent models have been developed to investigate in vitro the re-epithelialization process occurring during wound healing. Although these models recapitulate closure dynamics of epithelial cells, they fail to capture how a wounded connective tissue rebuilds its 3D architecture until the evolution in a scar. Here, the in vitro tissue repair dynamics of a connective tissue is replicated by using a 3D human dermis equivalent (3D-HDE) model composed of fibroblasts embedded in their own extracellular matrix (ECM). After inducing a physical damage, 3D-HDE undergoes a series of cellular and extracellular events quite similar to those occurring in the native dermis. In particular, fibroblasts differentiation toward myofibroblasts phenotype and neosynthesis of hyaluronic acid, fibronectin, and collagen during the repair process are assessed. Moreover, tissue reorganization after physical damage is investigated by measuring the diameter of bundles and the orientation of fibers of the newly formed ECM network. Finally, the ultimate formation of a scar-like tissue as physiological consequence of the repair and closure process is demonstrated. Taking together, the results highlight that the presence of cell-assembled and responsive stromal components enables quantitative and qualitative in vitro evaluation of the processes involved in scarring during wound healing. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Real-Time Processing of Gender-Marked Articles by Native and Non-Native Spanish Speakers

ERIC Educational Resources Information Center

Lew-Williams, Casey; Fernald, Anne

2010-01-01

Three experiments using online-processing measures explored whether native and non-native Spanish-speaking adults use gender-marked articles to identify referents of target nouns more rapidly, as shown previously with 3-year-old children learning Spanish as L1 (Lew-Williams & Fernald, 2007). In Experiment 1, participants viewed familiar objects…

The Processing of Subject-Object Ambiguities in Native and Near-Native Mexican Spanish

ERIC Educational Resources Information Center

Jegerski, Jill

2012-01-01

This self-paced reading study first tested the prediction that the garden path effect previously observed during the processing of subject-object ambiguities in native English would not obtain in a null subject language like Spanish. The investigation then further explored whether the effect would be evident among near-native readers of Spanish…

Musical ability and non-native speech-sound processing are linked through sensitivity to pitch and spectral information.

PubMed

Kempe, Vera; Bublitz, Dennis; Brooks, Patricia J

2015-05-01

Is the observed link between musical ability and non-native speech-sound processing due to enhanced sensitivity to acoustic features underlying both musical and linguistic processing? To address this question, native English speakers (N = 118) discriminated Norwegian tonal contrasts and Norwegian vowels. Short tones differing in temporal, pitch, and spectral characteristics were used to measure sensitivity to the various acoustic features implicated in musical and speech processing. Musical ability was measured using Gordon's Advanced Measures of Musical Audiation. Results showed that sensitivity to specific acoustic features played a role in non-native speech-sound processing: Controlling for non-verbal intelligence, prior foreign language-learning experience, and sex, sensitivity to pitch and spectral information partially mediated the link between musical ability and discrimination of non-native vowels and lexical tones. The findings suggest that while sensitivity to certain acoustic features partially mediates the relationship between musical ability and non-native speech-sound processing, complex tests of musical ability also tap into other shared mechanisms. © 2014 The British Psychological Society.

Native and Non-Native Speakers' Brain Responses to Filled Indirect Object Gaps

ERIC Educational Resources Information Center

Jessen, Anna; Festman, Julia; Boxell, Oliver; Felser, Claudia

2017-01-01

We examined native and non-native English speakers' processing of indirect object "wh"-dependencies using a filled-gap paradigm while recording event-related potentials (ERPs). The non-native group was comprised of native German-speaking, proficient non-native speakers of English. Both participant groups showed evidence of linking…

Single-molecule comparison of DNA Pol I activity with native and analog nucleotides

NASA Astrophysics Data System (ADS)

Gul, Osman; Olsen, Tivoli; Choi, Yongki; Corso, Brad; Weiss, Gregory; Collins, Philip

2014-03-01

DNA polymerases are critical enzymes for DNA replication, and because of their complex catalytic cycle they are excellent targets for investigation by single-molecule experimental techniques. Recently, we studied the Klenow fragment (KF) of DNA polymerase I using a label-free, electronic technique involving single KF molecules attached to carbon nanotube transistors. The electronic technique allowed long-duration monitoring of a single KF molecule while processing thousands of template strands. Processivity of up to 42 nucleotide bases was directly observed, and statistical analysis of the recordings determined key kinetic parameters for the enzyme's open and closed conformations. Subsequently, we have used the same technique to compare the incorporation of canonical nucleotides like dATP to analogs like 1-thio-2'-dATP. The analog had almost no affect on duration of the closed conformation, during which the nucleotide is incorporated. On the other hand, the analog increased the rate-limiting duration of the open conformation by almost 40%. We propose that the thiolated analog interferes with KF's recognition and binding, two key steps that determine its ensemble turnover rate.

Distinct functions of human RecQ helicases during DNA replication.

PubMed

Urban, Vaclav; Dobrovolna, Jana; Janscak, Pavel

2017-06-01

DNA replication is the most vulnerable process of DNA metabolism in proliferating cells and therefore it is tightly controlled and coordinated with processes that maintain genomic stability. Human RecQ helicases are among the most important factors involved in the maintenance of replication fork integrity, especially under conditions of replication stress. RecQ helicases promote recovery of replication forks being stalled due to different replication roadblocks of either exogenous or endogenous source. They prevent generation of aberrant replication fork structures and replication fork collapse, and are involved in proper checkpoint signaling. The essential role of human RecQ helicases in the genome maintenance during DNA replication is underlined by association of defects in their function with cancer predisposition. Copyright © 2016 Elsevier B.V. All rights reserved.

Stylistic Change in Classroom Native Music.

ERIC Educational Resources Information Center

Johnston, Thomas F.

1981-01-01

Discusses the teaching of native music in classes for Native Americans. Highlights the ways in which changes in musical style evolve and the disparities between the teaching process and the music itself. Suggests methods for successfully uniting process and product. (MK)

Word order processing in a second language: from VO to OV.

PubMed

Erdocia, Kepa; Zawiszewski, Adam; Laka, Itziar

2014-12-01

Event-related potential studies on second language processing reveal that L1/L2 differences are due either to proficiency, age of acquisition or grammatical differences between L1 and L2 (Kotz in Brain Lang 109(2-3):68-74, 2009). However, the relative impact of these and other factors in second language processing is still not well understood. Here we present evidence from behavioral and ERP experiments on Basque sentence word order processing by L1Spanish-L2Basque early bilinguals (Age of Aquisition [Formula: see text] 3 years) with very high proficiency in their L2. Results reveal that these L2 speakers have a preference towards canonical Subject-Object-Verb word order, which they processed faster and with greater ease than non-canonical Object-Subject-Verb. This result converges with the processing preferences shown by natives and reported in Erdocia et al. (Brain Lang 109(1):1-17, 2009). However, electrophysiological measures associated to canonical (SOV) and non-canonical (OSV) sentences revealed a different pattern in the non-natives, as compared to that reported previously for natives. The non-native group elicited a P600 component that native group did not show when comparing S and O at sentence's second position. This pattern of results suggests that, despite high proficiency, non-native language processing recruits neural resources that are different from those employed in native languages.

Effectiveness duckweed (Lemna minor) as an alternative native chicken feed native chicken (Gallus domesticus)

NASA Astrophysics Data System (ADS)

Putra, A.; Ritonga, M. Z.

2018-02-01

This study aimed to know the effectiveness duckweed as feed as native chicken (Gallus domesticus) on growth period (weight gain, feed intake and feed conversion). This research was conducted in Desa Telaga Jernih Kabupaten Langkat. The study was conducted in February 2017 until May 2017. This study use completely randomized design (CRD) with 4 treatments and 5 Replication, where each treatment consisting of 5 Native chickens unsexing. The treatment was used P0 = control (feed manufacturing), P1 = ration conventional with 10% duckweed, P2 = ration conventional with 20% duckweed, P3 = ration conventional with 30% duckweed. The parameters observed were weight gain, feed consumption and feed conversion. The results showed not significantly effect in body weight gain, feed consumption and feed conversion. Where the average of best weight gain on treatment P0 (control), P2 (20% duckweed), P3 (30% duckweed) and P1 (10% duckweed), average of best feed consumption in P0 (control), P2 (20% duckweed ) Of P1 (10% duckweed) and P3 (30% duckweed), P1 (10% duckweed) and P3 (30% duckweed), average of best feed conversion rate in P0 (control), P2 (20% duckweed) P1 (10% duckweed) and P3 (30% duckweed).

Virus like particles as a platform for cancer vaccine development.

PubMed

Ong, Hui Kian; Tan, Wen Siang; Ho, Kok Lian

2017-01-01

Cancers have killed millions of people in human history and are still posing a serious health problem worldwide. Therefore, there is an urgent need for developing preventive and therapeutic cancer vaccines. Among various cancer vaccine development platforms, virus-like particles (VLPs) offer several advantages. VLPs are multimeric nanostructures with morphology resembling that of native viruses and are mainly composed of surface structural proteins of viruses but are devoid of viral genetic materials rendering them neither infective nor replicative. In addition, they can be engineered to display multiple, highly ordered heterologous epitopes or peptides in order to optimize the antigenicity and immunogenicity of the displayed entities. Like native viruses, specific epitopes displayed on VLPs can be taken up, processed, and presented by antigen-presenting cells to elicit potent specific humoral and cell-mediated immune responses. Several studies also indicated that VLPs could overcome the immunosuppressive state of the tumor microenvironment and break self-tolerance to elicit strong cytotoxic lymphocyte activity, which is crucial for both virus clearance and destruction of cancerous cells. Collectively, these unique characteristics of VLPs make them optimal cancer vaccine candidates. This review discusses current progress in the development of VLP-based cancer vaccines and some potential drawbacks of VLPs in cancer vaccine development. Extracellular vesicles with close resembling to viral particles are also discussed and compared with VLPs as a platform in cancer vaccine developments.

Mechanisms of bacterial DNA replication restart

PubMed Central

Windgassen, Tricia A; Wessel, Sarah R; Bhattacharyya, Basudeb

2018-01-01

Abstract Multi-protein DNA replication complexes called replisomes perform the essential process of copying cellular genetic information prior to cell division. Under ideal conditions, replisomes dissociate only after the entire genome has been duplicated. However, DNA replication rarely occurs without interruptions that can dislodge replisomes from DNA. Such events produce incompletely replicated chromosomes that, if left unrepaired, prevent the segregation of full genomes to daughter cells. To mitigate this threat, cells have evolved ‘DNA replication restart’ pathways that have been best defined in bacteria. Replication restart requires recognition and remodeling of abandoned replication forks by DNA replication restart proteins followed by reloading of the replicative DNA helicase, which subsequently directs assembly of the remaining replisome subunits. This review summarizes our current understanding of the mechanisms underlying replication restart and the proteins that drive the process in Escherichia coli (PriA, PriB, PriC and DnaT). PMID:29202195

Genetic engineering of Lactobacillus diolivorans.

PubMed

Pflügl, Stefan; Marx, Hans; Mattanovich, Diethard; Sauer, Michael

2013-07-01

In this study, we developed a toolbox for genetic manipulation of Lactobacillus diolivorans, a promising production organism for 1,3-propanediol from glycerol. Two major findings play a key role for successful transformation of this organism: (1) the absence of a native plasmid, because a native plasmid is a major obstacle for transformation of L. diolivorans, and (2) the absence of DNA methylation. A suitable expression plasmid, pSHM, for homologous and heterologous protein expression in L. diolivorans was constructed. This plasmid is based on the replication origin repA of L. diolivorans. The native glyceraldehyde-3-phosphate dehydrogenase promoter is used for constitutive expression of the genes of interest. Functional expression of genes in L. diolivorans was shown with two examples: production of green fluorescent protein resulted in a 40- to 60-fold higher fluorescence of the obtained clones compared with the wild-type strain. Finally, the homologous overexpression of a putatively NADPH-dependent 1,3-propanediol oxidoreductase improved 1,3-propanediol production by 20% in batch cultures. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

In Vitro Maturation and In Vivo Integration and Function of an Engineered Cell-Seeded Disc-like Angle Ply Structure (DAPS) for Total Disc Arthroplasty.

PubMed

Martin, J T; Gullbrand, S E; Kim, D H; Ikuta, K; Pfeifer, C G; Ashinsky, B G; Smith, L J; Elliott, D M; Smith, H E; Mauck, R L

2017-11-17

Total disc replacement with an engineered substitute is a promising avenue for treating advanced intervertebral disc disease. Toward this goal, we developed cell-seeded disc-like angle ply structures (DAPS) and showed through in vitro studies that these constructs mature to match native disc composition, structure, and function with long-term culture. We then evaluated DAPS performance in an in vivo rat model of total disc replacement; over 5 weeks in vivo, DAPS maintained their structure, prevented intervertebral bony fusion, and matched native disc mechanical function at physiologic loads in situ. However, DAPS rapidly lost proteoglycan post-implantation and did not integrate into adjacent vertebrae. To address this, we modified the design to include polymer endplates to interface the DAPS with adjacent vertebrae, and showed that this modification mitigated in vivo proteoglycan loss while maintaining mechanical function and promoting integration. Together, these data demonstrate that cell-seeded engineered discs can replicate many characteristics of the native disc and are a viable option for total disc arthroplasty.

Real-Time Processing of Gender-Marked Articles by Native and Non-Native Spanish-Speaking Children and Adults

ERIC Educational Resources Information Center

Lew-Williams, Casey

2009-01-01

Six experiments explored how native and non-native Spanish speakers process article-noun sequences in real time, using eye movements as a response measure. Can listeners use gender-marked articles ("la" and "el", the feminine and masculine forms of "the") to rapidly identify familiar and novel nouns? In Experiment 1, adults who learned Spanish as…

Fidelity of DNA Replication in Normal and Malignant Human Breast Cells

DTIC Science & Technology

1998-07-01

synthesome has been extensively demonstrated to carry out full length DNA replication in vitro, and to accurately depict the DNA replication process as it...occurs in the intact cell. By examining the fidelity of the DNA replication process carried out by the DNA synthesome from a number of breast cell types...we have demonstrated for the first time, that the cellular DNA replication machinery of malignant human breast cells is significantly more error-prone than that of non- malignant human breast cells.

Construction of novel shuttle expression vectors for gene expression in Bacillus subtilis and Bacillus pumilus.

PubMed

Shao, Huanhuan; Cao, Qinghua; Zhao, Hongyan; Tan, Xuemei; Feng, Hong

2015-01-01

A native plasmid (pSU01) was detected by genome sequencing of Bacillus subtilis strain S1-4. Two pSU01-based shuttle expression vectors pSU02-AP and pSU03-AP were constructed enabling stable replication in B. subtilis WB600. These vectors contained the reporter gene aprE, encoding an alkaline protease from Bacillus pumilus BA06. The expression vector pSU03-AP only possessed the minimal replication elements (rep, SSO, DSO) and exhibited more stability on structure, suggesting that the rest of the genes in pSU01 (ORF1, ORF2, mob, hsp) were unessential for the structural stability of plasmid in B. subtilis. In addition, recombinant production of the alkaline protease was achieved more efficiently with pSU03-AP whose copy number was estimated to be more than 100 per chromosome. Furthermore, pSU03-AP could also be used to transform and replicate in B. pumilus BA06 under selective pressure. In conclusion, pSU03-AP is expected to be a useful tool for gene expression in Bacillus subtilis and B. pumilus.

Electrophysiological Correlates of Second-Language Syntactic Processes Are Related to Native and Second Language Distance Regardless of Age of Acquisition

PubMed Central

Díaz, Begoña; Erdocia, Kepa; de Menezes, Robert F.; Mueller, Jutta L.; Sebastián-Gallés, Núria; Laka, Itziar

2016-01-01

In the present study, we investigate how early and late L2 learners process L2 grammatical traits that are either present or absent in their native language (L1). Thirteen early (AoA = 4 years old) and 13 late (AoA = 18 years old) Spanish learners of Basque performed a grammatical judgment task on auditory Basque sentences while their event-related brain potentials (ERPs) were recorded. The sentences contained violations of a syntactic property specific to participants' L2, i.e., ergative case, or violations of a syntactic property present in both of the participants' languages, i.e., verb agreement. Two forms of verb agreement were tested: subject agreement, found in participants' L1 and L2, and object agreement, present only in participants' L2. Behaviorally, early bilinguals were more accurate in the judgment task than late L2 learners. Early bilinguals showed native-like ERPs for verb agreement, which differed from the late learners' ERP pattern. Nonetheless, approximation to native-likeness was greater for the subject-verb agreement processing, the type of verb-agreement present in participants' L1, compared to object-verb agreement, the type of verb-agreement present only in participants' L2. For the ergative argument alignment, unique to L2, the two non-native groups showed similar ERP patterns which did not correspond to the natives' ERP pattern. We conclude that non-native syntactic processing approximates native processing for early L2 acquisition and high proficiency levels when the syntactic property is common to the L1 and L2. However, syntactic traits that are not present in the L1 do not rely on native-like processing, despite early AoA and high proficiency. PMID:26903930

Implant Size Availability Affects Reproduction of Distal Femoral Anatomy.

PubMed

Morris, William Z; Gebhart, Jeremy J; Goldberg, Victor M; Wera, Glenn D

2016-07-01

A total knee arthroplasty system offers more distal femoral implant anterior-posterior (AP) sizes than its predecessor. The purpose of this study is to investigate the impact of increased size availability on an implant system's ability to reproduce the AP dimension of the native distal femur. We measured 200 cadaveric femora with the AP-sizing guides of Zimmer (Warsaw, IN) NexGen (8 sizes) and Zimmer Persona (12 sizes) total knee arthroplasty systems. We defined "size deviation" as the difference in the AP dimension between the anatomic size of the native femur and the closest implant size. We defined satisfactory reproduction of distal femoral dimensions as < 1 mm difference between the implant and native femur size. The NexGen system was associated with a mean 0.46 mm greater implant size deviation than Persona (p < 0.001). When using a 1 mm size deviation as a cutoff for satisfactory replication of the native distal femoral anatomy, 85/200 specimens (42.5%) were a poor fit by NexGen, but a satisfactory fit by Persona. Only 1/200 specimens (0.5%) was a poor fit by Persona, but a satisfactory fit by NexGen (p < 0.001). The novel knee system with 12 versus 8 sizes reproduces the AP dimension of the native distal femur more closely than its predecessor. Further study is needed to determine the clinical impact of these differences. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

Distinct contributions of replication and transcription to mutation rate variation of human genomes.

PubMed

Cui, Peng; Ding, Feng; Lin, Qiang; Zhang, Lingfang; Li, Ang; Zhang, Zhang; Hu, Songnian; Yu, Jun

2012-02-01

Here, we evaluate the contribution of two major biological processes--DNA replication and transcription--to mutation rate variation in human genomes. Based on analysis of the public human tissue transcriptomics data, high-resolution replicating map of Hela cells and dbSNP data, we present significant correlations between expression breadth, replication time in local regions and SNP density. SNP density of tissue-specific (TS) genes is significantly higher than that of housekeeping (HK) genes. TS genes tend to locate in late-replicating genomic regions and genes in such regions have a higher SNP density compared to those in early-replication regions. In addition, SNP density is found to be positively correlated with expression level among HK genes. We conclude that the process of DNA replication generates stronger mutational pressure than transcription-associated biological processes do, resulting in an increase of mutation rate in TS genes while having weaker effects on HK genes. In contrast, transcription-associated processes are mainly responsible for the accumulation of mutations in highly-expressed HK genes. Copyright © 2012 Beijing Genomics Institute. Published by Elsevier Ltd. All rights reserved.

Replicative Functions of Minute Virus of Mice NS1 Protein Are Regulated In Vitro by Phosphorylation through Protein Kinase C

PubMed Central

Nüesch, Jürg P. F.; Dettwiler, Sabine; Corbau, Romuald; Rommelaere, Jean

1998-01-01

NS1, the major nonstructural protein of the parvovirus minute virus of mice, is a multifunctional phosphoprotein which is involved in cytotoxicity, transcriptional regulation, and initiation of viral DNA replication. For coordination of these various functions during virus propagation, NS1 has been proposed to be regulated by posttranslational modifications, in particular phosphorylation. Recent in vitro studies (J. P. F. Nüesch, R. Corbau, P. Tattersall, and J. Rommelaere, J. Virol. 72:8002–8012, 1998) provided evidence that distinct NS1 activities, notably the intrinsic helicase function, are modulated by the phosphorylation state of the protein. In order to study the dependence of the initiation of viral DNA replication on NS1 phosphorylation and to identify the protein kinases involved, we established an in vitro replication system that is devoid of endogenous protein kinases and is based on plasmid substrates containing the minimal left-end origins of replication. Cellular components necessary to drive NS1-dependent rolling-circle replication (RCR) were freed from endogenous serine/threonine protein kinases by affinity chromatography, and the eukaryotic DNA polymerases were replaced by the bacteriophage T4 DNA polymerase. While native NS1 (NS1P) supported RCR under these conditions, dephosphorylated NS1 (NS1O) was impaired. Using fractionated HeLa cell extracts, we identified two essential protein components which are able to phosphorylate NS1O, are enriched in protein kinase C (PKC), and, when present together, reactivate NS1O for replication. One of these components, containing atypical PKC, was sufficient to restore NS1O helicase activity. The requirement of NS1O reactivation for characteristic PKC cofactors such as Ca2+/phosphatidylserine or phorbol esters strongly suggests the involvement of this protein kinase family in regulation of NS1 replicative functions in vitro. PMID:9811734

Narrative Comprehension Processes: A Study of Native and Non-Native Readers of Japanese.

ERIC Educational Resources Information Center

Horiba, Yukie

1990-01-01

Comparison of the reading strategies and resulting reading comprehension and recall of native and advanced non-native adult speakers of Japanese found that reading strategy significantly affected comprehension and recall, with non-native readers with limited language command paying more attention to vocabulary and grammar than native readers, who…

Women finding the way: American Indian women leading intervention research in Native communities.

PubMed

Brave Heart, Maria Yellow Horse; Chase, Josephine; Elkins, Jennifer; Martin, Jennifer; Nanez, Jennifer; Mootz, Jennifer

2016-01-01

Although there is literature concentrating on cross-cultural approaches to academic and community partnerships with Native communities, few address the process and experiences of American Indian women leading federally funded and culturally grounded behavioral health intervention research in Native communities. This paper summarizes relevant literature on community-engaged research with Native communities, examines traditional roles and modern challenges for American Indian women, describes the culturally grounded collaborative process for the authors' behavioral health intervention development with Native communities, and considers emergent themes from our own research experiences navigating competing demands from mainstream and Native communities. It concludes with recommendations for supporting and enhancing resilience.

WOMEN FINDING THE WAY: AMERICAN INDIAN WOMEN LEADING INTERVENTION RESEARCH IN NATIVE COMMUNITIES

PubMed Central

Brave Heart, Maria Yellow Horse; Chase, Josephine; Elkins, Jennifer; Martin, Jennifer; Nanez, Jennifer S.; Mootz, Jennifer J.

2017-01-01

Although there is literature concentrating on cross-cultural approaches to academic and community partnerships with Native communities, few address the process and experiences of American Indian women leading federally funded and culturally grounded behavioral health intervention research in Native communities. This paper summarizes relevant literature on community-engaged research with Native communities, examines traditional roles and modern challenges for American Indian women, describes the culturally grounded collaborative process for the authors’ behavioral health intervention development with Native communities, and considers emergent themes from our own research experiences navigating competing demands from mainstream and Native communities. It concludes with recommendations for supporting and enhancing resilience. PMID:27383085

Syntactic learning by mere exposure - An ERP study in adult learners

PubMed Central

Mueller, Jutta L; Oberecker, Regine; Friederici, Angela D

2009-01-01

Background Artificial language studies have revealed the remarkable ability of humans to extract syntactic structures from a continuous sound stream by mere exposure. However, it remains unclear whether the processes acquired in such tasks are comparable to those applied during normal language processing. The present study compares the ERPs to auditory processing of simple Italian sentences in native and non-native speakers after brief exposure to Italian sentences of a similar structure. The sentences contained a non-adjacent dependency between an auxiliary and the morphologically marked suffix of the verb. Participants were presented four alternating learning and testing phases. During learning phases only correct sentences were presented while during testing phases 50 percent of the sentences contained a grammatical violation. Results The non-native speakers successfully learned the dependency and displayed an N400-like negativity and a subsequent anteriorily distributed positivity in response to rule violations. The native Italian group showed an N400 followed by a P600 effect. Conclusion The presence of the P600 suggests that native speakers applied a grammatical rule. In contrast, non-native speakers appeared to use a lexical form-based processing strategy. Thus, the processing mechanisms acquired in the language learning task were only partly comparable to those applied by competent native speakers. PMID:19640301

Syntactic learning by mere exposure--an ERP study in adult learners.

PubMed

Mueller, Jutta L; Oberecker, Regine; Friederici, Angela D

2009-07-29

Artificial language studies have revealed the remarkable ability of humans to extract syntactic structures from a continuous sound stream by mere exposure. However, it remains unclear whether the processes acquired in such tasks are comparable to those applied during normal language processing. The present study compares the ERPs to auditory processing of simple Italian sentences in native and non-native speakers after brief exposure to Italian sentences of a similar structure. The sentences contained a non-adjacent dependency between an auxiliary and the morphologically marked suffix of the verb. Participants were presented four alternating learning and testing phases. During learning phases only correct sentences were presented while during testing phases 50 percent of the sentences contained a grammatical violation. The non-native speakers successfully learned the dependency and displayed an N400-like negativity and a subsequent anteriorily distributed positivity in response to rule violations. The native Italian group showed an N400 followed by a P600 effect. The presence of the P600 suggests that native speakers applied a grammatical rule. In contrast, non-native speakers appeared to use a lexical form-based processing strategy. Thus, the processing mechanisms acquired in the language learning task were only partly comparable to those applied by competent native speakers.

Nativization Processes in L1 Esperanto.

ERIC Educational Resources Information Center

Bergen, Benjamin K.

2001-01-01

Describes characteristics of the Native Esperanto of eight speakers, ranging from age 6 to 14 years. Found bilingualism and nativization effects, differentiating native from non-native Esperanto speech. Among these effects are loss or modification of the accusative case, phonological reduction, attrition of tense/aspect system, and pronominal…

Precise replication of antireflective nanostructures from biotemplates

NASA Astrophysics Data System (ADS)

Gao, Hongjun; Liu, Zhongfan; Zhang, Jin; Zhang, Guoming; Xie, Guoyong

2007-03-01

The authors report herein a new type of nanonipple structures on the cicada's eye and the direct structural replication of the complex micro- and nanostructures for potential functional emulation. A two-step direct molding process is developed to replicate these natural micro- and nanostructures using epoxy resin with high fidelity, which demonstrates a general way of fabricating functional nanostructures by direct replication of natural biotemplates via a suitable physicochemical process. Measurements of spectral reflectance showed that this kind of replicated nanostructure has remarkable antireflective property, suggestive of its potential applications to optical devices.

Interim results of quality-control sampling of surface water for the Upper Colorado River National Water-Quality Assessment Study Unit, water years 1995-96

USGS Publications Warehouse

Spahr, N.E.; Boulger, R.W.

1997-01-01

Quality-control samples provide part of the information needed to estimate the bias and variability that result from sample collection, processing, and analysis. Quality-control samples of surface water collected for the Upper Colorado River National Water-Quality Assessment study unit for water years 1995?96 are presented and analyzed in this report. The types of quality-control samples collected include pre-processing split replicates, concurrent replicates, sequential replicates, post-processing split replicates, and field blanks. Analysis of the pre-processing split replicates, concurrent replicates, sequential replicates, and post-processing split replicates is based on differences between analytical results of the environmental samples and analytical results of the quality-control samples. Results of these comparisons indicate that variability introduced by sample collection, processing, and handling is low and will not affect interpretation of the environmental data. The differences for most water-quality constituents is on the order of plus or minus 1 or 2 lowest rounding units. A lowest rounding unit is equivalent to the magnitude of the least significant figure reported for analytical results. The use of lowest rounding units avoids some of the difficulty in comparing differences between pairs of samples when concentrations span orders of magnitude and provides a measure of the practical significance of the effect of variability. Analysis of field-blank quality-control samples indicates that with the exception of chloride and silica, no systematic contamination of samples is apparent. Chloride contamination probably was the result of incomplete rinsing of the dilute cleaning solution from the outlet ports of the decaport sample splitter. Silica contamination seems to have been introduced by the blank water. Sampling and processing procedures for water year 1997 have been modified as a result of these analyses.

Geographic variation in apparent competition between native and invasive Phragmites australis.

PubMed

Bhattarai, Ganesh P; Meyerson, Laura A; Cronin, James T

2017-02-01

Apparent competition, the negative interaction between species mediated by shared natural enemies, is thought to play an important role in shaping the structure and dynamics of natural communities. However, its importance in driving species invasions, and whether the strength of this indirect interaction varies across the latitudinal range of the invasion, has not been fully explored. We performed replicated field experiments at four sites spanning 900 km along the Atlantic Coast of the United States to assess the presence and strength of apparent competition between sympatric native and invasive lineages of Phragmites australis. Four herbivore guilds were considered: stem-feeders, leaf-miners, leaf-chewers and aphids. We also tested the hypothesis that the strength of this interaction declines with increasing latitude. Within each site, native and invasive plants of P. australis were cross-transplanted between co-occurring native and invasive patches in the same marsh habitat and herbivore damage was evaluated at the end of the growing season. Apparent competition was evident for both lineages and involved all but the leaf-chewer guild. For native plants, total aphids per plant was 296% higher and the incidence of stem-feeding and leaf-mining herbivores was 34% and 221% higher, respectively, when transplanted into invasive than native patches. These data suggest that invasive P. australis has a negative effect on native P. australis via apparent competition. Averaged among herbivore types, the indirect effects of the invasive lineage on the native lineage was 57% higher than the reverse situation, suggesting that apparent competition was asymmetric. We also found that the strength of apparent competition acting against the native lineage was comparable to the benefits to the invasive lineage from enemy release (i.e., proportionately lower mean herbivory of the invasive relative to the native taxa). Finally, we found the first evidence that the strength of apparent competition acting against the native lineage (from stem-feeders only) decreased with increasing latitude. These results suggest that not only could apparent competition be of tantamount importance to enemy release in enhancing the establishment and spread of invasive taxa, but also that these indirect and direct herbivore effects could vary over the invasion range. © 2016 by the Ecological Society of America.

Dissociating Cortical Activity during Processing of Native and Non-Native Audiovisual Speech from Early to Late Infancy

PubMed Central

Fava, Eswen; Hull, Rachel; Bortfeld, Heather

2014-01-01

Initially, infants are capable of discriminating phonetic contrasts across the world’s languages. Starting between seven and ten months of age, they gradually lose this ability through a process of perceptual narrowing. Although traditionally investigated with isolated speech sounds, such narrowing occurs in a variety of perceptual domains (e.g., faces, visual speech). Thus far, tracking the developmental trajectory of this tuning process has been focused primarily on auditory speech alone, and generally using isolated sounds. But infants learn from speech produced by people talking to them, meaning they learn from a complex audiovisual signal. Here, we use near-infrared spectroscopy to measure blood concentration changes in the bilateral temporal cortices of infants in three different age groups: 3-to-6 months, 7-to-10 months, and 11-to-14-months. Critically, all three groups of infants were tested with continuous audiovisual speech in both their native and another, unfamiliar language. We found that at each age range, infants showed different patterns of cortical activity in response to the native and non-native stimuli. Infants in the youngest group showed bilateral cortical activity that was greater overall in response to non-native relative to native speech; the oldest group showed left lateralized activity in response to native relative to non-native speech. These results highlight perceptual tuning as a dynamic process that happens across modalities and at different levels of stimulus complexity. PMID:25116572

The fluctuating resource hypothesis explains invasibility, but not exotic advantage following disturbance.

PubMed

Pearson, Dean E; Ortega, Yvette K; Villarreal, Diego; Lekberg, Ylva; Cock, Marina C; Eren, Özkan; Hierro, José L

2018-06-01

Invasibility is a key indicator of community susceptibility to changes in structure and function. The fluctuating resource hypothesis (FRH) postulates that invasibility is an emergent community property, a manifestation of multiple processes that cannot be reliably predicted by individual community attributes like diversity or productivity. Yet, research has emphasized the role of these individual attributes, with the expectation that diversity should deter invasibility and productivity enhance it. In an effort to explore how these and other factors may influence invasibility, we evaluated the relationship between invasibility and species richness, productivity, resource availability, and resilience in experiments crossing disturbance with exotic seed addition in 1-m 2 plots replicated over large expanses of grasslands in Montana, USA and La Pampa, Argentina. Disturbance increased invasibility as predicted by FRH, but grasslands were more invasible in Montana than La Pampa whether disturbed or not, despite Montana's higher species richness and lower productivity. Moreover, invasibility correlated positively with nitrogen availability and negatively with native plant cover. These patterns suggested that resource availability and the ability of the community to recover from disturbance (resilience) better predicted invasibility than either species richness or productivity, consistent with predictions from FRH. However, in ambient, unseeded plots in Montana, disturbance reduced native cover by >50% while increasing exotic cover >200%. This provenance bias could not be explained by FRH, which predicts that colonization processes act on species' traits independent of origins. The high invasibility of Montana grasslands following disturbance was associated with a strong shift from perennial to annual species, as predicted by succession theory. However, this shift was driven primarily by exotic annuals, which were more strongly represented than perennials in local exotic vs. native species pools. We attribute this provenance bias to extrinsic biogeographic factors such as disparate evolutionary histories and/or introduction filters selecting for traits that favor exotics following disturbance. Our results suggest that (1) invasibility is an emergent property best explained by a community's efficiency in utilizing resources, as predicted by FRH but (2) understanding provenance biases in biological invasions requires moving beyond FRH to incorporate extrinsic biogeographic factors that may favor exotics in community assembly. © 2018 by the Ecological Society of America.

Natural and Heterologous Production of Bacteriocins

NASA Astrophysics Data System (ADS)

Cintas, Luis M.; Herranz, Carmen; Hernández, Pablo E.

Bacteriocins are ribosomally synthesized antimicrobial peptides produced by bacteria, and their use as natural and nontoxic food preservatives has been the source of considerable interest for the research community. In addition, bacteriocins have been investigated for their potential use in human and veterinary applications and in the animal production field. In the native bacterial strain, most bacteriocins are synthesized as biologically inactive precursors, with N-terminal extensions, that are cleaved concomitantly during export of the bacteriocin by dedicated ABC transporters, or the general secretory pathway (GSP) or Sec-dependent pathway. However, a few bacteriocins are synthesized without an N-terminal extension, and others are circularized through a head-to-tail peptide bond, complicating the elucidation of their processing and transport across the cytoplasmic membrane. The high cost of synthetic bacteriocin synthesis and their low yields from many natural producers recommends the exploration of recombinant microbial systems for the heterologous production of bacteriocins. Other advantages of such systems include production of bacteriocins in safer hosts, increased bacteriocin production, control of bacteriocin gene expression, production of food ingredients with antimicrobial activity, construction of multibacteriocinogenic strains with a wider antagonistic spectrum, a better adaptation of the selected hosts to food environments, and providing antagonistic properties to lactic acid bacteria (LAB) used as starter, protective, or probiotic cultures. The recombinant production of bacteriocins mostly relies on the use of expression vectors that replicate in Gram-negative bacteria, Gram-positive bacteria, and yeasts, whereas the production of bacteriocins in heterologous LAB hosts may be essentially based on the expression of native biosynthetic genes, by exchanging or replacing leader peptides and/or dedicated processing and secretion systems (ABC transporters), or by fusion of mature bacteriocins to signal peptides that act as secretion signals.

Speech-sound duration processing in a second language is specific to phonetic categories.

PubMed

Nenonen, Sari; Shestakova, Anna; Huotilainen, Minna; Näätänen, Risto

2005-01-01

The mismatch negativity (MMN) component of the auditory event-related potential was used to determine the effect of native language, Russian, on the processing of speech-sound duration in a second language, Finnish, that uses duration as a cue for phonological distinction. The native-language effect was compared with Finnish vowels that either can or cannot be categorized using the Russian phonological system. The results showed that the duration-change MMN for the Finnish sounds that could be categorized through Russian was reduced in comparison with that for the Finnish sounds having no Russian equivalent. In the Finnish sounds that can be mapped through the Russian phonological system, the facilitation of the duration processing may be inhibited by the native Russian language. However, for the sounds that have no Russian equivalent, new vowel categories independent of the native Russian language have apparently been established, enabling a native-like duration processing of Finnish.

A novel 3D template for mandible and maxilla reconstruction: Rapid prototyping using stereolithography

PubMed Central

Kumta, Samir; Kumta, Monica; Jain, Leena; Purohit, Shrirang; Ummul, Rani

2015-01-01

Introduction: Replication of the exact three-dimensional (3D) structure of the maxilla and mandible is now a priority whilst attempting reconstruction of these bones to attain a complete functional and aesthetic rehabilitation. We hereby present the process of rapid prototyping using stereolithography to produce templates for modelling bone grafts and implants for maxilla/mandible reconstructions, its applications in tumour/trauma, and outcomes for primary and secondary reconstruction. Materials and Methods: Stereolithographic template-assisted reconstruction was used on 11 patients for the reconstruction of the mandible/maxilla primarily following tumour excision and secondarily for the realignment of post-traumatic malunited fractures or deformity corrections. Data obtained from the computed tomography (CT) scans with 1-mm resolution were converted into a computer-aided design (CAD) using the CT Digital Imaging and Communications in Medicine (DICOM) data. Once a CAD model was constructed, it was converted into a stereolithographic format and then processed by the rapid prototyping technology to produce the physical anatomical model using a resin. This resin model replicates the native mandible, which can be thus used off table as a guide for modelling the bone grafts. Discussion: This conversion of two-dimensional (2D) data from CT scan into 3D models is a very precise guide to shaping the bone grafts. Further, this CAD can reconstruct the defective half of the mandible using the mirror image principle, and the normal anatomical model can be created to aid secondary reconstructions. Conclusion: This novel approach allows a precise translation of the treatment plan directly to the surgical field. It is also an important teaching tool for implant moulding and fixation, and helps in patient counselling. PMID:26933279

A novel 3D template for mandible and maxilla reconstruction: Rapid prototyping using stereolithography.

PubMed

Kumta, Samir; Kumta, Monica; Jain, Leena; Purohit, Shrirang; Ummul, Rani

2015-01-01

Replication of the exact three-dimensional (3D) structure of the maxilla and mandible is now a priority whilst attempting reconstruction of these bones to attain a complete functional and aesthetic rehabilitation. We hereby present the process of rapid prototyping using stereolithography to produce templates for modelling bone grafts and implants for maxilla/mandible reconstructions, its applications in tumour/trauma, and outcomes for primary and secondary reconstruction. Stereolithographic template-assisted reconstruction was used on 11 patients for the reconstruction of the mandible/maxilla primarily following tumour excision and secondarily for the realignment of post-traumatic malunited fractures or deformity corrections. Data obtained from the computed tomography (CT) scans with 1-mm resolution were converted into a computer-aided design (CAD) using the CT Digital Imaging and Communications in Medicine (DICOM) data. Once a CAD model was constructed, it was converted into a stereolithographic format and then processed by the rapid prototyping technology to produce the physical anatomical model using a resin. This resin model replicates the native mandible, which can be thus used off table as a guide for modelling the bone grafts. This conversion of two-dimensional (2D) data from CT scan into 3D models is a very precise guide to shaping the bone grafts. Further, this CAD can reconstruct the defective half of the mandible using the mirror image principle, and the normal anatomical model can be created to aid secondary reconstructions. This novel approach allows a precise translation of the treatment plan directly to the surgical field. It is also an important teaching tool for implant moulding and fixation, and helps in patient counselling.

Direct Visualization of DNA Replication Dynamics in Zebrafish Cells.

PubMed

Kuriya, Kenji; Higashiyama, Eriko; Avşar-Ban, Eriko; Tamaru, Yutaka; Ogata, Shin; Takebayashi, Shin-ichiro; Ogata, Masato; Okumura, Katsuzumi

2015-12-01

Spatiotemporal regulation of DNA replication in the S-phase nucleus has been extensively studied in mammalian cells because it is tightly coupled with the regulation of other nuclear processes such as transcription. However, little is known about the replication dynamics in nonmammalian cells. Here, we analyzed the DNA replication processes of zebrafish (Danio rerio) cells through the direct visualization of replicating DNA in the nucleus and on DNA fiber molecules isolated from the nucleus. We found that zebrafish chromosomal DNA at the nuclear interior was replicated first, followed by replication of DNA at the nuclear periphery, which is reminiscent of the spatiotemporal regulation of mammalian DNA replication. However, the relative duration of interior DNA replication in zebrafish cells was longer compared to mammalian cells, possibly reflecting zebrafish-specific genomic organization. The rate of replication fork progression and ori-to-ori distance measured by the DNA combing technique were ∼ 1.4 kb/min and 100 kb, respectively, which are comparable to those in mammalian cells. To our knowledge, this is a first report that measures replication dynamics in zebrafish cells.

Novel apo E-derived ABCA1 agonist peptide (CS-6253) promotes reverse cholesterol transport and induces formation of preβ-1 HDL in vitro

DOE PAGES

Hafiane, Anouar; Bielicki, John K.; Johansson, Jan O.; ...

2015-07-24

Apolipoprotein (apo) mimetic peptides replicate some aspects of HDL function. We have previously reported the effects of compound ATI-5261 on its ability to replicate many functions of native apo A-I in the process of HDL biogenesis. ATI-5261 induced muscle toxicity in wild type C57Bl/6 mice, increased CPK, ALT and AST and increase in triglyceride (Tg) levels. Aromatic phenylalanine residues on the non-polar face of ATI-5261, together with positively charged arginine residues at the lipid-water interface were responsible for these effects. This information was used to create a novel analog (CS-6253) that was non-toxic. We evaluated this peptide designed from themore » carboxyl terminus of apo E, in its ability to mimic apo A-I functionality. Our data shows that the lipidated particles generated by incubating cells overexpressing ABCA1 with lipid free CS-6253 enhances the rate of ABCA1 lipid efflux with high affinity interactions with native ABCA1 oligomeric forms and plasma membrane micro-domains. Interaction between ABCA1 and lipid free CS-6253 resulted in formation of nascent HDL-CS-6253 particles that are actively remodeled in plasma. Mature HDL-CS-6253 particles deliver cholesterol to liver cells via SR-BI in-vitro. CS-6253 significantly increases cholesterol efflux in murine macrophages and in human THP-1 macrophage-derived foam cells expressing ABCA1. Addition of CS-6253 to plasma dose-dependently displaced apo A-I from α-HDL particles and led to de novo formation of preβ-1 HDL that stimulates ABCA1 dependent cholesterol efflux efficiently. When incubated with human plasma CS-6253 was also found to bind with HDL and LDL and promoted the transfer of cholesterol from HDL to LDL predominantly. Our data shows that CS-6253 mimics apo A-I in its ability to promote ABCA1-mediated formation of nascent HDL particles, and enhances formation of preβ-1 HDL with increase in the cycling of apo A-I between the preβ and α-HDL particles in-vitro. These mechanisms are potentially anti-atherogenic.« less

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

Hafiane, Anouar; Bielicki, John K.; Johansson, Jan O.

Apolipoprotein (apo) mimetic peptides replicate some aspects of HDL function. We have previously reported the effects of compound ATI-5261 on its ability to replicate many functions of native apo A-I in the process of HDL biogenesis. ATI-5261 induced muscle toxicity in wild type C57Bl/6 mice, increased CPK, ALT and AST and increase in triglyceride (Tg) levels. Aromatic phenylalanine residues on the non-polar face of ATI-5261, together with positively charged arginine residues at the lipid-water interface were responsible for these effects. This information was used to create a novel analog (CS-6253) that was non-toxic. We evaluated this peptide designed from themore » carboxyl terminus of apo E, in its ability to mimic apo A-I functionality. Our data shows that the lipidated particles generated by incubating cells overexpressing ABCA1 with lipid free CS-6253 enhances the rate of ABCA1 lipid efflux with high affinity interactions with native ABCA1 oligomeric forms and plasma membrane micro-domains. Interaction between ABCA1 and lipid free CS-6253 resulted in formation of nascent HDL-CS-6253 particles that are actively remodeled in plasma. Mature HDL-CS-6253 particles deliver cholesterol to liver cells via SR-BI in-vitro. CS-6253 significantly increases cholesterol efflux in murine macrophages and in human THP-1 macrophage-derived foam cells expressing ABCA1. Addition of CS-6253 to plasma dose-dependently displaced apo A-I from α-HDL particles and led to de novo formation of preβ-1 HDL that stimulates ABCA1 dependent cholesterol efflux efficiently. When incubated with human plasma CS-6253 was also found to bind with HDL and LDL and promoted the transfer of cholesterol from HDL to LDL predominantly. Our data shows that CS-6253 mimics apo A-I in its ability to promote ABCA1-mediated formation of nascent HDL particles, and enhances formation of preβ-1 HDL with increase in the cycling of apo A-I between the preβ and α-HDL particles in-vitro. These mechanisms are potentially anti-atherogenic.« less

Novel Apo E-Derived ABCA1 Agonist Peptide (CS-6253) Promotes Reverse Cholesterol Transport and Induces Formation of preβ-1 HDL In Vitro

PubMed Central

Hafiane, Anouar; Bielicki, John K.; Johansson, Jan O.; Genest, Jacques

2015-01-01

Apolipoprotein (apo) mimetic peptides replicate some aspects of HDL function. We have previously reported the effects of compound ATI-5261 on its ability to replicate many functions of native apo A-I in the process of HDL biogenesis. ATI-5261 induced muscle toxicity in wild type C57Bl/6 mice, increased CPK, ALT and AST and increase in triglyceride (Tg) levels. Aromatic phenylalanine residues on the non-polar face of ATI-5261, together with positively charged arginine residues at the lipid-water interface were responsible for these effects. This information was used to create a novel analog (CS-6253) that was non-toxic. We evaluated this peptide designed from the carboxyl terminus of apo E, in its ability to mimic apo A-I functionality. Our data shows that the lipidated particles generated by incubating cells overexpressing ABCA1 with lipid free CS-6253 enhances the rate of ABCA1 lipid efflux with high affinity interactions with native ABCA1 oligomeric forms and plasma membrane micro-domains. Interaction between ABCA1 and lipid free CS-6253 resulted in formation of nascent HDL-CS-6253 particles that are actively remodeled in plasma. Mature HDL-CS-6253 particles deliver cholesterol to liver cells via SR-BI in-vitro. CS-6253 significantly increases cholesterol efflux in murine macrophages and in human THP-1 macrophage-derived foam cells expressing ABCA1. Addition of CS-6253 to plasma dose-dependently displaced apo A-I from α-HDL particles and led to de novo formation of preβ-1 HDL that stimulates ABCA1 dependent cholesterol efflux efficiently. When incubated with human plasma CS-6253 was also found to bind with HDL and LDL and promoted the transfer of cholesterol from HDL to LDL predominantly. Our data shows that CS-6253 mimics apo A-I in its ability to promote ABCA1-mediated formation of nascent HDL particles, and enhances formation of preβ-1 HDL with increase in the cycling of apo A-I between the preβ and α-HDL particles in-vitro. These mechanisms are potentially anti-atherogenic. PMID:26207756

Semantic and phonetic enhancements for speech-in-noise recognition by native and non-native listeners.

PubMed

Bradlow, Ann R; Alexander, Jennifer A

2007-04-01

Previous research has shown that speech recognition differences between native and proficient non-native listeners emerge under suboptimal conditions. Current evidence has suggested that the key deficit that underlies this disproportionate effect of unfavorable listening conditions for non-native listeners is their less effective use of compensatory information at higher levels of processing to recover from information loss at the phoneme identification level. The present study investigated whether this non-native disadvantage could be overcome if enhancements at various levels of processing were presented in combination. Native and non-native listeners were presented with English sentences in which the final word varied in predictability and which were produced in either plain or clear speech. Results showed that, relative to the low-predictability-plain-speech baseline condition, non-native listener final word recognition improved only when both semantic and acoustic enhancements were available (high-predictability-clear-speech). In contrast, the native listeners benefited from each source of enhancement separately and in combination. These results suggests that native and non-native listeners apply similar strategies for speech-in-noise perception: The crucial difference is in the signal clarity required for contextual information to be effective, rather than in an inability of non-native listeners to take advantage of this contextual information per se.

Fleshy fruit removal and nutritional composition of winter-fruiting plants: a comparison of non-native invasive and native species

Treesearch

Cathryn H. Greenberg; Scott T. Walter

2010-01-01

Invasive, non-native plants threaten forest ecosystems by reducing native plant species richness and potentially altering ecosystem processes. Seed dispersal is critical for successful invasion and range expansion by non-native plants; dispersal is likely to be enhanced if they can successfully compete with native plants for disperser services. Fruit production by non-...

Kasai hepatoportoenterostomy in South Australia: a case for 'centralized decentralization'.

PubMed

Tu, Chen Gang; Khurana, Sanjeev; Couper, Richard; Ford, Andrew W D

2015-11-01

Recent follow-up studies have demonstrated significant improvement in overall survival as well as survival with native liver following geographic centralization of services to three centres in the UK. However, this model has not been replicated in countries with relatively low population density such as Australia and Canada. Retrospective evaluation of all patients born with biliary atresia (BA) in South Australia from 1989 to 2010 was performed. Thirty-one patients with BA were discovered. Two patients were excluded because the initial Kasai procedure (KP) was performed interstate. Outcome parameters measured were (i) clearance of jaundice (bilirubin of less than 20 μmol/L, by 6 months); (ii) survival with native liver; and (iii) overall survival. Kaplan-Meier survival curves were plotted for both survival with native liver and overall survival. The incidence of BA in South Australia between 1989 and 2010 was 7.48 per 100,000 live births. Following KP, clearance of jaundice was achieved in 42.9% of patients. Five-year actuarial survival with native liver was 55.2%, and overall 5-year actuarial survival was 89.3%. The results of KP performed at Women's and Children's Hospital from 1989 to 2010 can be considered comparable with international benchmarks. Based on these results, we propose the creation of a 'centralized' pool of surgeons in Australia to help continue providing 'decentralized' care of BA. © 2014 Royal Australasian College of Surgeons.

Impacts of large herbivorous mammals on bird diversity and abundance in an African savanna.

PubMed

Ogada, D L; Gadd, M E; Ostfeld, R S; Young, T P; Keesing, F

2008-05-01

Large native mammals are declining dramatically in abundance across Africa, with strong impacts on both plant and animal community dynamics. However, the net effects of this large-scale loss in megafauna are poorly understood because responses by several ecologically important groups have not been assessed. We used a large-scale, replicated exclusion experiment in Kenya to investigate the impacts of different guilds of native and domestic large herbivores on the diversity and abundance of birds over a 2-year period. The exclusion of large herbivorous native mammals, including zebras (Equus burchelli), giraffes (Giraffa camelopardalis), elephants (Loxodonta africana), and buffalos (Syncerus caffer), increased the diversity of birds by 30%. Most of this effect was attributable to the absence of elephants and giraffes; these megaherbivores reduced both the canopy area of subdominant woody vegetation and the biomass of ground-dwelling arthropods, and both of these factors were good predictors of the diversity of birds. The canopy area of subdominant trees was positively correlated with the diversity of granivorous birds. The biomass of ground-dwelling arthropods was positively correlated with the diversity of insectivorous birds. Our results suggest that most native large herbivores are compatible with an abundant and diverse bird fauna, as are cattle if they are at a relatively low stocking rate. Future research should focus on determining the spatial arrangements and densities of megaherbivores that will optimize both megaherbivore abundance and bird diversity.

Predicting invasion in grassland ecosystems: Is exotic dominance the real embarrassment of richness?

USGS Publications Warehouse

Seabloom, Eric; Borer, Elizabeth; Buckley, Yvonne; Cleland, Elsa E.; Davies, Kendi; Firn, Jennifer; Harpole, W. Stanley; Hautier, Yann; Lind, Eric M.; MacDougall, Andrew; Orrock, John L.; Prober, Suzanne M.; Adler, Peter; Alberti, Juan; Anderson, T. Michael; Bakker, Jonathan D.; Biederman, Lori A.; Blumenthal, Dana; Brown, Cynthia S.; Brudvig, Lars A.; Caldeira, Maria; Chu, Cheng-Jin; Crawley, Michael J.; Daleo, Pedro; Damschen, Ellen Ingman; D'Antonio, Carla M.; DeCrappeo, Nicole M.; Dickman, Chris R.; Du, Guozhen; Fay, Philip A.; Frater, Paul; Gruner, Daniel S.; Hagenah, Nicole; Hector, Andrew; Helm, Aveliina; Hillebrand, Helmut; Hofmockel, Kirsten S.; Humphries, Hope C.; Iribarne, Oscar; Jin, Virginia L.; Kay, Adam; Kirkman, Kevin P.; Klein, Julia A.; Knops, Johannes M.H.; La Pierre, Kimberly J.; Ladwig, Laura M.; ,; John, G.; Leakey, Andrew D.B.; Li, Qi; Li, Wei; McCulley, Rebecca; Melbourne, Brett; ,; Charles, E.; Moore, Joslin L.; Morgan, John; Mortensen, Brent; O'Halloran, Lydia R.; Pärtel, Meelis; Pascual, Jesús; Pyke, David A.; Risch, Anita C.; Salguero-Gómez, Roberto; Sankaran, Mahesh; Schuetz, Martin; Simonsen, Anna; Smith, Melinda; Stevens, Carly; Sullivan, Lauren; Wardle, Glenda M.; Wolkovich, Elizabeth M.; Wragg, Peter D.; Wright, Justin; Yang, Louie

2013-01-01

Invasions have increased the size of regional species pools, but are typically assumed to reduce native diversity. However, global-scale tests of this assumption have been elusive because of the focus on exotic species richness, rather than relative abundance. This is problematic because low invader richness can indicate invasion resistance by the native community or, alternatively, dominance by a single exotic species. Here, we used a globally replicated study to quantify relationships between exotic richness and abundance in grass-dominated ecosystems in 13 countries on six continents, ranging from salt marshes to alpine tundra. We tested effects of human land use, native community diversity, herbivore pressure, and nutrient limitation on exotic plant dominance. Despite its widespread use, exotic richness was a poor proxy for exotic dominance at low exotic richness, because sites that contained few exotic species ranged from relatively pristine (low exotic richness and cover) to almost completely exotic-dominated ones (low exotic richness but high exotic cover). Both exotic cover and richness were predicted by native plant diversity (native grass richness) and land use (distance to cultivation). Although climate was important for predicting both exotic cover and richness, climatic factors predicting cover (precipitation variability) differed from those predicting richness (maximum temperature and mean temperature in the wettest quarter). Herbivory and nutrient limitation did not predict exotic richness or cover. Exotic dominance was greatest in areas with low native grass richness at the site- or regional-scale. Although this could reflect native grass displacement, a lack of biotic resistance is a more likely explanation, given that grasses comprise the most aggressive invaders. These findings underscore the need to move beyond richness as a surrogate for the extent of invasion, because this metric confounds monodominance with invasion resistance. Monitoring species' relative abundance will more rapidly advance our understanding of invasions

Race and Beliefs about Mental Health Treatment Among Anxious Primary Care Patients

PubMed Central

Hunt, Justin; Sullivan, Greer; Chavira, Denise A.; Stein, Murray B.; Craske, Michelle G.; Golinelli, Daniella; Roy-Byrne, Peter P.; Sherbourne, Cathy D.

2013-01-01

Large racial disparities in the utilization of mental health care persist. Differences in treatment preferences could partially explain the differences in care between minority and non-minority populations. We compared beliefs about mental illness and treatment preferences among adult African Americans, Hispanics, Asian Americans, Native Americans, and whites, with diagnosed anxiety disorders. Measures of beliefs about mental illness and treatment were drawn from the National Comorbidity Survey Replication and from our previous work. There were no significant differences between African-Americans’ and whites’ beliefs. Hispanics’ and Native Americans’ beliefs were most distinctive, but the differences were small in magnitude. Across race/ethnicity, the associations between beliefs and service use were generally weak and statistically insignificant. Differences in illness beliefs and treatment preferences do not fully explain the large, persistent racial disparities in mental health care. Other crucial barriers to quality care exist in our health care system and our society as a whole. PMID:23407203

Detection of Wolbachia in Aedes albopictus and Their Effects on Chikungunya Virus

PubMed Central

Ahmad, Noor Afizah; Vythilingam, Indra; Lim, Yvonne A. L.; Zabari, Nur Zatil Aqmar M.; Lee, Han Lim

2017-01-01

Wolbachia-based vector control strategies have been proposed as a means to augment the currently existing measures for controlling dengue and chikungunya vectors. Prior to utilizing Wolbachia as a novel vector control strategy, it is crucial to understand the Wolbachia–mosquito interactions. In this study, field surveys were conducted to screen for the infection status of Wolbachia in field-collected Aedes albopictus. The effects of Wolbachia in its native host toward the replication and dissemination of chikungunya virus (CHIKV) was also studied. The prevalence of Wolbachia-infected field-collected Ae. albopictus was estimated to be 98.6% (N = 142) for females and 95.1% (N = 102) for males in the population studied. The Ae. albopictus were naturally infected with both wAlbA and wAlbB strains. We also found that the native Wolbachia has no impact on CHIKV infection and minimal effect on CHIKV dissemination to secondary organs. PMID:27920393

Morphosyntactic Processing in Advanced Second Language (L2) Learners: An Event-Related Potential Investigation of the Effects of L1-l2 Similarity and Structural Distance

ERIC Educational Resources Information Center

Alemán Bañón, José; Fiorentino, Robert; Gabriele, Alison

2014-01-01

Different theoretical accounts of second language (L2) acquisition differ with respect to whether or not advanced learners are predicted to show native-like processing for features not instantiated in the native language (L1). We examined how native speakers of English, a language with number but not gender agreement, process number and gender…

Replication of a Continuing Education Workshop in the Evidence-Based Practice Process

ERIC Educational Resources Information Center

Gromoske, Andrea N.; Berger, Lisa K.

2017-01-01

Objective: To replicate the results of Parrish and Rubin's continuing education workshop in the evidence-based practice (EBP) process utilizing different workshop facilitators with participants in a different geographic location. Methods: We used a replicated, one-group pretest-posttest design with 3-month follow-up to evaluate the effectiveness…

A Replication-incompetent Rift Valley Fever Vaccine: Chimeric Virus-like Particles Protect Mice and Rats Against Lethal Challenge

PubMed Central

Mandell, Robert B.; Koukuntla, Ramesh; Mogler, Laura J. K.; Carzoli, Andrea K.; Freiberg, Alexander N.; Holbrook, Michael R.; Martin, Brian K.; Staplin, William R.; Vahanian, Nicholas N.; Link, Charles J.; Flick, Ramon

2009-01-01

Virus-like particles (VLPs) present viral antigens in a native conformation and are effectively recognized by the immune system and therefore are considered as suitable and safe vaccine candidates against many viral diseases. Here we demonstrate that chimeric VLPs containing Rift Valley fever virus (RVFV) glycoproteins GN and GC, nucleoprotein N and the gag protein of Moloney murine leukemia virus represent an effective vaccine candidate against Rift Valley fever, a deadly disease in humans and livestock. Long-lasting humoral and cellular immune responses are demonstrated in a mouse model by the analysis of neutralizing antibody titers and cytokine secretion profiles. Vaccine efficacy studies were performed in mouse and rat lethal challenge models resulting in high protection rates. Taken together, these results demonstrate that replication-incompetent chimeric RVF VLPs are an efficient RVFV vaccine candidate. PMID:19932911

Soil, vegetation, and seed bank of a Sonoran Desert ecosystem along an exotic plant (Pennisetum ciliare) treatment gradient.

PubMed

Abella, Scott R; Chiquoine, Lindsay P; Backer, Dana M

2013-10-01

Ecological conditions following removal of exotic plants are a key part of comprehensive environmental management strategies to combat exotic plant invasions. We examined ecological conditions following removal of the management-priority buffelgrass (Pennisetum ciliare) in Saguaro National Park of the North American Sonoran Desert. We assessed soil, vegetation, and soil seed banks on seven buffelgrass site types: five different frequencies of buffelgrass herbicide plus hand removal treatments (ranging from 5 years of annual treatment to a single year of treatment), untreated sites, and non-invaded sites, with three replicates for each of the seven site types. The 22 measured soil properties (e.g., pH) differed little among sites. Regarding vegetation, buffelgrass cover was low (≤1% median cover), or absent, across all treated sites but was high (10-70%) in untreated sites. Native vegetation cover, diversity, and composition were indistinguishable across site types. Species composition was dominated by native species (>93% relative cover) across all sites except untreated buffelgrass sites. Most (38 species, 93%) of the 41 species detected in soil seed banks were native, and native seed density did not differ significantly across sites. Results suggest that: (1) buffelgrass cover was minimal across treated sites; (2) aside from high buffelgrass cover in untreated sites, ecological conditions were largely indistinguishable across sites; (3) soil seed banks harbored ≥12 species that were frequent in the aboveground vegetation; and (4) native species dominated post-treatment vegetation composition, and removing buffelgrass did not result in replacement by other exotic species.

Soil, Vegetation, and Seed Bank of a Sonoran Desert Ecosystem Along an Exotic Plant ( Pennisetum ciliare) Treatment Gradient

NASA Astrophysics Data System (ADS)

Abella, Scott R.; Chiquoine, Lindsay P.; Backer, Dana M.

2013-10-01

Ecological conditions following removal of exotic plants are a key part of comprehensive environmental management strategies to combat exotic plant invasions. We examined ecological conditions following removal of the management-priority buffelgrass ( Pennisetum ciliare) in Saguaro National Park of the North American Sonoran Desert. We assessed soil, vegetation, and soil seed banks on seven buffelgrass site types: five different frequencies of buffelgrass herbicide plus hand removal treatments (ranging from 5 years of annual treatment to a single year of treatment), untreated sites, and non-invaded sites, with three replicates for each of the seven site types. The 22 measured soil properties (e.g., pH) differed little among sites. Regarding vegetation, buffelgrass cover was low (≤1 % median cover), or absent, across all treated sites but was high (10-70 %) in untreated sites. Native vegetation cover, diversity, and composition were indistinguishable across site types. Species composition was dominated by native species (>93 % relative cover) across all sites except untreated buffelgrass sites. Most (38 species, 93 %) of the 41 species detected in soil seed banks were native, and native seed density did not differ significantly across sites. Results suggest that: (1) buffelgrass cover was minimal across treated sites; (2) aside from high buffelgrass cover in untreated sites, ecological conditions were largely indistinguishable across sites; (3) soil seed banks harbored ≥12 species that were frequent in the aboveground vegetation; and (4) native species dominated post-treatment vegetation composition, and removing buffelgrass did not result in replacement by other exotic species.

Structure and content of Native American stereotypic subgroups: Not just (ig)noble.

PubMed

Burkley, Edward; Durante, Federica; Fiske, Susan T; Burkley, Melissa; Andrade, Angela

2017-04-01

Prejudice against Native Americans as an overall group generally polarizes into positive and negative stereotypic extremes, but distinct subgroups may explain this variability. Using college student samples (Study 1), a preliminary study identified common Native American subgroups and then a main study (N = 153, 74% women, 73% White, mean age = 19 years) had participants rate these subgroups on basic dimensions of stereotype content (i.e., warmth and competence), elicited emotions (e.g., admiration, contempt), and elicited behaviors (e.g., facilitation, harm). In Study 2, these preliminary study and main study procedures were replicated using nationwide samples (main study: N = 139, 51% women, 78% White, mean age = 35 years). For the most part, similar Native American subgroups emerged in both samples. Using the stereotype content model (SCM; Fiske, Cuddy, Glick, & Xu, 2002), the subgroups were found to vary along a competence-by-warmth space. The majority of subgroups (e.g., alcoholics, lazy) were judged low in both competence and warmth. Additional subgroups (e.g., casino operators, warriors) were ambivalently judged as high on competence but low on warmth. Subgroups perceived as high in both competence and warmth elicited more admiration, those low in both competence and warmth elicited more contempt, those high in competence elicited more passive facilitation and less passive harm, and those high in warmth elicited more active facilitation and less active harm. Native American stereotypes are apparently characterized by both noble and ignoble subgroups, highlighting the importance of studying stereotypes at the subgroup level. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

A Comparison of Conservation Reserve Program Habitat Plantings with Respect to Arthropod Prey for Grassland Birds

USGS Publications Warehouse

McIntyre, N.E.; Thompson, Thomas R.

2003-01-01

The Conservation Reserve Program (CRP) was designed to reduce soil erosion and curb agricultural overproduction by converting highly erodible agricultural land to various forms of perennial habitat. It has had an incidental benefit of providing habitat for wildlife and has been beneficial in reversing population declines of several grassland bird species. However, the mechanisms behind these reversals remain unknown. One such mechanism may be differences in food availability on CRP vs. non-CRP land or between different types of CRP. The influence of CRP habitat type on the abundance of arthropod prey used by grassland birds has not been previously explored. We compared the abundance and diversity of arthropods among four CRP habitat types in Texas [replicated plots of exotic lovegrass (Eragrostis curvula), Old World bluestem (Bothriochloa ischaemum), mixed native grasses with buffalograss (Buchloe?? dactyloides) and mixed native grasses without buffalograss] and native shortgrass prairie. Attention was focused on adult and juvenile spiders (Order Araneae), beetles (Coleoptera), orthopterans (Orthroptera: grasshoppers and crickets) and lepidopterans (Lepidoptera: butterflies and moths), as these taxa are the primary prey items of grassland birds during the breeding season. Arthropod diversity and abundance were higher on indigenous prairie compared to CRP, reflecting differences in vegetative diversity and structure, but there were no differences in arthropod richness or abundance among CRP types. These results indicate that, although CRP is not equivalent to native prairie in terms of vegetation or arthropod diversity, CRP lands do support arthropod prey for grassland birds. More direct assays of the survivorship and fitness of birds on CRP compared to native shortgrass prairie are clearly warranted.

In vitro assessment of the contact mechanics of reverse-engineered distal humeral hemiarthroplasty prostheses.

PubMed

Willing, Ryan; Lapner, Michael; King, Graham J W; Johnson, James A

2014-11-01

Distal humeral hemiarthroplasty alters cartilage contact mechanics, which may predispose to osteoarthritis. Current prostheses do not replicate the native anatomy, and therefore contribute to these changes. We hypothesized that prostheses reverse-engineered from the native bone shape would provide similar contact patterns as the native articulation. Reverse-engineered hemiarthroplasty prostheses were manufactured for five cadaveric elbows based on CT images of the distal humerus. Passive flexion trials with constant muscle forces were performed with the native articulation intact while bone motions were recorded using a motion tracking system. Motion trials were then repeated after the distal humerus was replaced with a corresponding reverse-engineered prosthesis. Contact areas and patterns were reconstructed using computer models created from CT scan images combined with the motion tracker data. The total contact areas, as well as the contact area within smaller sub-regions of the ulna and radius, were analyzed for changes resulting from hemiarthroplasty using repeated-measures ANOVAs. Contact area at the ulna and radius decreased on average 42% (SD 19%, P=.008) and 41% (SD 42%, P=.096), respectively. Contact area decreases were not uniform throughout the different sub-regions, suggesting that contact patterns were also altered. Reverse-engineered prostheses did not reproduce the same contact pattern as the native joints, possibly because the thickness of the distal humerus cartilage layer was neglected when generating the prosthesis shapes or as a consequence of the increased stiffness of the metallic implants. Alternative design strategies and materials for hemiarthroplasty should be considered in future work. Copyright © 2014 Elsevier Ltd. All rights reserved.

Biaxial mechanics and inter-lamellar shearing of stem-cell seeded electrospun angle-ply laminates for annulus fibrosus tissue engineering.

PubMed

Driscoll, Tristan P; Nakasone, Ryan H; Szczesny, Spencer E; Elliott, Dawn M; Mauck, Robert L

2013-06-01

The annulus fibrosus (AF) of the intervertebral disk plays a critical role in vertebral load transmission that is heavily dependent on the microscale structure and composition of the tissue. With degeneration, both structure and composition are compromised, resulting in a loss of AF mechanical function. Numerous tissue engineering strategies have addressed the issue of AF degeneration, but few have focused on recapitulation of AF microstructure and function. One approach that allows for generation of engineered AF with appropriate (+/-)30° lamellar microstructure is the use of aligned electrospun scaffolds seeded with mesenchymal stem cells (MSCs) and assembled into angle-ply laminates (APL). Previous work indicates that opposing lamellar orientation is necessary for development of near native uniaxial tensile properties. However, most native AF tensile loads are applied biaxially, as the disk is subjected to multi-axial loads and is constrained by its attachments to the vertebral bodies. Thus, the objective of this study was to evaluate the biaxial mechanical response of engineered AF bilayers, and to determine the importance of opposing lamellar structure under this loading regime. Opposing bilayers, which replicate native AF structure, showed a significantly higher modulus in both testing directions compared to parallel bilayers, and reached ∼60% of native AF biaxial properties. Associated with this increase in biaxial properties, significantly less shear, and significantly higher stretch in the fiber direction, was observed. These results provide additional insight into native tissue structure-function relationships, as well as new benchmarks for engineering functional AF tissue constructs. Copyright © 2013 Orthopaedic Research Society.

Tubular inverse opal scaffolds for biomimetic vessels.

PubMed

Zhao, Ze; Wang, Jie; Lu, Jie; Yu, Yunru; Fu, Fanfan; Wang, Huan; Liu, Yuxiao; Zhao, Yuanjin; Gu, Zhongze

2016-07-14

There is a clinical need for tissue-engineered blood vessels that can be used to replace or bypass damaged arteries. The success of such grafts depends strongly on their ability to mimic native arteries; however, currently available artificial vessels are restricted by their complex processing, controversial integrity, or uncontrollable cell location and orientation. Here, we present new tubular scaffolds with specific surface microstructures for structural vessel mimicry. The tubular scaffolds are fabricated by rotationally expanding three-dimensional tubular inverse opals that are replicated from colloidal crystal templates in capillaries. Because of the ordered porous structure of the inverse opals, the expanded tubular scaffolds are imparted with circumferentially oriented elliptical pattern microstructures on their surfaces. It is demonstrated that these tailored tubular scaffolds can effectively make endothelial cells to form an integrated hollow tubular structure on their inner surface and induce smooth muscle cells to form a circumferential orientation on their outer surface. These features of our tubular scaffolds make them highly promising for the construction of biomimetic blood vessels.

Shaping the Skin: The Interplay of Mesoscale Geometry and Corneocyte Swelling

NASA Astrophysics Data System (ADS)

Evans, Myfanwy E.; Roth, Roland

2014-01-01

The stratum corneum, the outer layer of mammalian skin, provides a remarkable barrier to the external environment, yet it has highly variable permeability properties where it actively mediates between inside and out. On prolonged exposure to water, swelling of the corneocytes (skin cells composed of keratin intermediate filaments) is the key process by which the stratum corneum controls permeability and mechanics. As for many biological systems with intricate function, the mesoscale geometry is optimized to provide functionality from basic physical principles. Here we show that a key mechanism of corneocyte swelling is the interplay of mesoscale geometry and thermodynamics: given helical tubes with woven geometry equivalent to the keratin intermediate filament arrangement, the balance of solvation free energy and elasticity induces swelling of the system, importantly with complete reversibility. Our result remarkably replicates macroscopic experimental data of native through to fully hydrated corneocytes. This finding not only highlights the importance of patterns and morphology in nature but also gives valuable insight into the functionality of skin.

Age of Acquisition and Proficiency in a Second Language Independently Influence the Perception of Non-Native Speech

ERIC Educational Resources Information Center

Archila-Suerte, Pilar; Zevin, Jason; Bunta, Ferenc; Hernandez, Arturo E.

2012-01-01

Sensorimotor processing in children and higher-cognitive processing in adults could determine how non-native phonemes are acquired. This study investigates how age-of-acquisition (AOA) and proficiency-level (PL) predict native-like perception of statistically dissociated L2 categories, i.e., within-category and between-category. In a similarity…

Native and L2 Processing of Homonyms in Sentential Context

ERIC Educational Resources Information Center

Elston-Guttler, K.E.; Friederici, A.D.

2005-01-01

We compare native and non-native processing of homonyms in sentence context whose two most frequent meanings are nouns (e.g., sentence) or a noun and a verb (e.g., trip). With both participant groups, we conducted a combined reaction time (RT)/event-related brain potential (ERP) lexical decision experiment with two stimulus-onset asynchronies…

Widening the Circle: Culturally Relevant Pedagogy for American Indian Children.

ERIC Educational Resources Information Center

Klug, Beverly J.; Whitfield, Patricia T.

This book provides non-Native teachers with information about Native American cultures and offers a pedagogical model that blends Native and non-Native worldviews and methodologies. The book aims to describe the process of becoming bicultural as it relates to success in teaching Native students; provide a short history of American Indian nations,…

Germination responses of an invasive species in native and non-native ranges

Treesearch

Jose L. Hierro; Ozkan Eren; Liana Khetsuriani; Alecu Diaconu; Katalin Torok; Daniel Montesinos; Krikor Andonian; David Kikodze; Levan Janoian; Diego Villarreal; Maria Estanga-Mollica; Ragan M. Callaway

2009-01-01

Studying germination in the native and non-native range of a species can provide unique insights into processes of range expansion and adaptation; however, traits related to germination have rarely been compared between native and nonnative populations. In a series of common garden experiments, we explored whether differences in the seasonality of precipitation,...

Syntactic Constraints and Individual Differences in Native and Non-Native Processing of Wh-Movement

PubMed Central

Johnson, Adrienne; Fiorentino, Robert; Gabriele, Alison

2016-01-01

There is a debate as to whether second language (L2) learners show qualitatively similar processing profiles as native speakers or whether L2 learners are restricted in their ability to use syntactic information during online processing. In the realm of wh-dependency resolution, research has examined whether learners, similar to native speakers, attempt to resolve wh-dependencies in grammatically licensed contexts but avoid positing gaps in illicit contexts such as islands. Also at issue is whether the avoidance of gap filling in islands is due to adherence to syntactic constraints or whether islands simply present processing bottlenecks. One approach has been to examine the relationship between processing abilities and the establishment of wh-dependencies in islands. Grammatical accounts of islands do not predict such a relationship as the parser should simply not predict gaps in illicit contexts. In contrast, a pattern of results showing that individuals with more processing resources are better able to establish wh-dependencies in islands could conceivably be compatible with certain processing accounts. In a self-paced reading experiment which examines the processing of wh-dependencies, we address both questions, examining whether native English speakers and Korean learners of English show qualitatively similar patterns and whether there is a relationship between working memory, as measured by counting span and reading span, and processing in both island and non-island contexts. The results of the self-paced reading experiment suggest that learners can use syntactic information on the same timecourse as native speakers, showing qualitative similarity between the two groups. Results of regression analyses did not reveal a significant relationship between working memory and the establishment of wh-dependencies in islands but we did observe significant relationships between working memory and the processing of licit wh-dependencies. As the contexts in which these relationships emerged differed for learners and native speakers, our results call for further research examining individual differences in dependency resolution in both populations. PMID:27148152

Syntactic Constraints and Individual Differences in Native and Non-Native Processing of Wh-Movement.

PubMed

Johnson, Adrienne; Fiorentino, Robert; Gabriele, Alison

2016-01-01

There is a debate as to whether second language (L2) learners show qualitatively similar processing profiles as native speakers or whether L2 learners are restricted in their ability to use syntactic information during online processing. In the realm of wh-dependency resolution, research has examined whether learners, similar to native speakers, attempt to resolve wh-dependencies in grammatically licensed contexts but avoid positing gaps in illicit contexts such as islands. Also at issue is whether the avoidance of gap filling in islands is due to adherence to syntactic constraints or whether islands simply present processing bottlenecks. One approach has been to examine the relationship between processing abilities and the establishment of wh-dependencies in islands. Grammatical accounts of islands do not predict such a relationship as the parser should simply not predict gaps in illicit contexts. In contrast, a pattern of results showing that individuals with more processing resources are better able to establish wh-dependencies in islands could conceivably be compatible with certain processing accounts. In a self-paced reading experiment which examines the processing of wh-dependencies, we address both questions, examining whether native English speakers and Korean learners of English show qualitatively similar patterns and whether there is a relationship between working memory, as measured by counting span and reading span, and processing in both island and non-island contexts. The results of the self-paced reading experiment suggest that learners can use syntactic information on the same timecourse as native speakers, showing qualitative similarity between the two groups. Results of regression analyses did not reveal a significant relationship between working memory and the establishment of wh-dependencies in islands but we did observe significant relationships between working memory and the processing of licit wh-dependencies. As the contexts in which these relationships emerged differed for learners and native speakers, our results call for further research examining individual differences in dependency resolution in both populations.

Semantic processing in native and second language: evidence from hemispheric differences in fine and coarse semantic coding.

PubMed

Faust, Miriam; Ben-Artzi, Elisheva; Vardi, Nili

2012-12-01

Previous studies suggest that whereas the left hemisphere (LH) is involved in fine semantic processing, the right hemisphere (RH) is uniquely engaged in coarse semantic coding including the comprehension of distinct types of language such as figurative language, lexical ambiguity and verbal humor (e.g., Chiarello, 2003; Faust, 2012). The present study examined the patterns of hemispheric involvement in fine/coarse semantic processing in native and non-native languages using a split visual field priming paradigm. Thirty native Hebrew speaking students made lexical decision judgments of Hebrew and English target words preceded by strongly, weakly, or unrelated primes. Results indicated that whereas for Hebrew pairs, priming effect for the weakly-related word pairs was obtained only for RH presented target words, for English pairs, no priming effect for the weakly-related pairs emerged for either LH or RH presented targets, suggesting that coarse semantic coding is much weaker for a non-native than native language. Copyright © 2012 Elsevier Inc. All rights reserved.

Biomorphous porous hydroxyapatite-ceramics from rattan (Calamus Rotang).

PubMed

Eichenseer, Christiane; Will, Julia; Rampf, Markus; Wend, Süsen; Greil, Peter

2010-01-01

The three-dimensional, highly oriented pore channel anatomy of native rattan (Calamus rotang) was used as a template to fabricate biomorphous hydroxyapatite (Ca(5)(PO(4))(3)OH) ceramics designed for bone regeneration scaffolds. A low viscous hydroxyapatite-sol was prepared from triethyl phosphite and calcium nitrate tetrahydrate and repeatedly vacuum infiltrated into the native template. The template was subsequently pyrolysed at 800 degrees C to form a biocarbon replica of the native tissue. Heat treatment at 1,300 degrees C in air atmosphere caused oxidation of the carbon skeleton and sintering of the hydroxyapatite. SEM analysis confirmed detailed replication of rattan anatomy. Porosity of the samples measured by mercury porosimetry showed a multimodal pore size distribution in the range of 300 nm to 300 microm. Phase composition was determined by XRD and FT-IR revealing hydroxyapatite as the dominant phase with minimum fractions of CaO and Ca(3)(PO(4))(2). The biomorphous scaffolds with a total porosity of 70-80% obtained a compressive strength of 3-5 MPa in axial direction and 1-2 MPa in radial direction of the pore channel orientation. Bending strength was determined in a coaxial double ring test resulting in a maximum bending strength of approximately 2 MPa.

Evolutionary dynamics of nationalism and migration

NASA Astrophysics Data System (ADS)

Barreira da Silva Rocha, André

2013-08-01

I present a dynamic evolutionary game model to address the relation between nationalism against immigrants and assimilation of the latter into the host country culture. I assume a country composed of two different large polymorphic populations, one of native citizens and the other of immigrants. A native citizen may behave nationalistically or may welcome immigrants. Immigrants may have an interest in learning the host country language or not. Evolution is modeled using replicator dynamics (RD). I also account for the presence of an enclave of immigrants in the host country. In the RD, the latter represents the immigrants’ own population effect, which contribution to fitness is controlled using a parameter ρ, 0≤ρ≤1, that represents the enclave size. In line with the empirical literature on migration, the existence of an enclave of immigrants makes assimilation less likely to occur. For large values of ρ, complete assimilation may not occur even if immigrants and natives share very close cultures and norms. Government policy regarding nationalism is modeled both exogenously and endogenously. A single or multiple asymptotically stable states exist for all cases studied but one in which the dynamics is similar to that found in the predator-prey model of Lotka-Volterra for competing species.

Introduced birds incompletely replace seed dispersal by a native frugivore

PubMed Central

Pejchar, Liba

2015-01-01

The widespread loss of native species and the introduction of non-native species has important consequences for island ecosystems. Non-native species may or may not functionally replace the role of native species in ecological processes such as seed dispersal. Although the majority of Hawaii's native plants require bird-mediated seed dispersal, only one native frugivore, Omao (Myadestes obscurus), persists in sufficient numbers to fill this functional role. Omao are restricted to less than half their original range, but two introduced frugivores are abundant throughout Hawaii. Given large-scale extinctions on islands, it is important to understand whether introduced birds serve as functional replacements or whether the absence of native frugivores alters plant communities. To assess seed dispersal by native and introduced birds, seed rain, vegetation characteristics, bird diet, density and habitat use were measured at three sites with Omao and three sites without Omao on Hawaii Island. The diet of native and introduced birds overlapped substantially, but Omao dispersed a variety of native species (n = 6) relatively evenly. In contrast, introduced birds dispersed an invasive species and fewer native species (n = 4), and >90 % of seeds dispersed by introduced birds were from two ubiquitous small-seeded species. Seed rain was significantly greater and more species rich at sites with Omao. These findings suggest that patterns of seed dispersal are altered following the local extinction of a native island frugivore. To more directly evaluate the relative roles of native and introduced frugivores in ecological processes, future studies could include reintroducing Omao to a suitable habitat within its historic range, or novel introductions to nearby islands where closely related species are now extinct. In an era of widespread extinction and invasion of island ecosystems, understanding the consequences of novel animal assemblages for processes like seed dispersal will be critical for maintaining diverse and self-regenerating plant communities. PMID:26139183

Aggregate and Individual Replication Probability within an Explicit Model of the Research Process

ERIC Educational Resources Information Center

Miller, Jeff; Schwarz, Wolf

2011-01-01

We study a model of the research process in which the true effect size, the replication jitter due to changes in experimental procedure, and the statistical error of effect size measurement are all normally distributed random variables. Within this model, we analyze the probability of successfully replicating an initial experimental result by…

Recombinant dengue 2 virus NS3 protein conserves structural antigenic and immunological properties relevant for dengue vaccine design.

PubMed

Ramírez, Rosa; Falcón, Rosabel; Izquierdo, Alienys; García, Angélica; Alvarez, Mayling; Pérez, Ana Beatriz; Soto, Yudira; Muné, Mayra; da Silva, Emiliana Mandarano; Ortega, Oney; Mohana-Borges, Ronaldo; Guzmán, María G

2014-10-01

The NS3 protein is a multifunctional non-structural protein of flaviviruses implicated in the polyprotein processing. The predominance of cytotoxic T cell lymphocytes epitopes on the NS3 protein suggests a protective role of this protein in limiting virus replication. In this work, we studied the antigenicity and immunogenicity of a recombinant NS3 protein of the Dengue virus 2. The full-length NS3 gene was cloned and expressed as a His-tagged fusion protein in Escherichia coli. The pNS3 protein was purified by two chromatography steps. The recombinant NS3 protein was recognized by anti-protease NS3 polyclonal antibody and anti-DENV2 HMAF by Western Blot. This purified protein was able to stimulate the secretion of high levels of gamma interferon and low levels of interleukin-10 and tumor necrosis factor-α in mice splenocytes, suggesting a predominantly Th-1-type T cell response. Immunized BALB/c mice with the purified NS3 protein showed a strong induction of anti-NS3 IgG antibodies, essentially IgG2b, as determined by ELISA. Immunized mice sera with recombinant NS3 protein showed specific recognition of native dengue protein by Western blotting and immunofluorescence techniques. The successfully purified recombinant protein was able to preserv the structural and antigenic determinants of the native dengue protein. The antigenicity shown by the recombinant NS3 protein suggests its possible inclusion into future DENV vaccine preparations.

Anthropocene rockfalls travel farther than prehistoric predecessors

PubMed Central

Borella, Josh Walter; Quigley, Mark; Vick, Louise

2016-01-01

Human modification of natural landscapes has influenced surface processes in many settings on Earth. Quantitative data comparing the distribution and behavior of geologic phenomena before and after human arrival are sparse but urgently required to evaluate possible anthropogenic influences on geologic hazards. We conduct field and imagery-based mapping, statistical analysis, and numerical modeling of rockfall boulders triggered by the fatal 2011 Christchurch earthquakes (n = 285) and newly identified prehistoric (Holocene and Pleistocene) boulders (n = 1049). Prehistoric and modern boulders are lithologically equivalent, derived from the same source cliff, and yield consistent power-law frequency-volume distributions. However, a significant population of modern boulders (n = 26) traveled farther downslope (>150 m) than their most-traveled prehistoric counterparts, causing extensive damage to residential dwellings at the foot of the hillslope. Replication of prehistoric boulder distributions using three-dimensional rigid-body numerical models that incorporate lidar-derived digital topography and realistic boulder trajectories and volumes requires the application of a drag coefficient, attributed to moderate to dense slope vegetation, to account for their spatial distribution. Incorporating a spatially variable native forest into the models successfully predicts prehistoric rockfall distributions. Radiocarbon dating provides evidence for 17th to early 20th century deforestation at the study site during Polynesian and European colonization and after emplacement of prehistoric rockfall. Anthropocene deforestation enabled modern rockfalls to exceed the limits of their prehistoric predecessors, highlighting a shift in the geologic expression of rockfalls due to anthropogenic activity. Reforestation of hillslopes by mature native vegetation could help reduce future rockfall hazard. PMID:27652344

A systematic review on in vitro 3D bone metastases models: A new horizon to recapitulate the native clinical scenario?

PubMed

Salamanna, Francesca; Contartese, Deyanira; Maglio, Melania; Fini, Milena

2016-07-12

While the skeleton is not the only organ where metastasis can occur, it is one of the preferred sites, with a significant impact in patients' quality of life. With the aim of delineating the cellular and molecular mechanisms of bone metastasis, numerous studies have been employed to identify any contributing factors that trigger cancer progression. One of the major limitations of studying cancer-bone metastasis is the multifaceted nature of the native bone environment and the lack of reliable, simple, and not expensive models that strictly mimic the biological processes occurring in vivo allowing a correct translation of results. Currently, with the growing acceptance of in vitro models as effective tools for studying cancer biology, three-dimensional (3D) models have emerged as a compromise between two-dimensional cultures of isolated cancer cells and the complexity of human cancer xenografts in immunocompromised animal hosts. This descriptive systematic literature review summarizes the current status of advanced and alternative 3D in vitro bone metastases models. We have also reviewed the strategies employed by researchers to set-up these models with special reference to recent promising developments trying to better replicate the complexity and heterogeneity of a human metastasis in situ, with an outlook at their use in medicine. All these aspects will greatly contribute to the existing knowledge on bone metastases, providing a specific link to clinical scenarios and thus making 3D in vitro bone metastasis models an attractive tool for multidisciplinary experts.

Systematic Determination of Replication Activity Type Highlights Interconnections between Replication, Chromatin Structure and Nuclear Localization

PubMed Central

Polten, Andreas; Hezroni, Hadas; Eldar, Yonina C.; Meshorer, Eran; Yakhini, Zohar; Simon, Itamar

2012-01-01

DNA replication is a highly regulated process, with each genomic locus replicating at a distinct time of replication (ToR). Advances in ToR measurement technology enabled several genome-wide profiling studies that revealed tight associations between ToR and general genomic features and a remarkable ToR conservation in mammals. Genome wide studies further showed that at the hundreds kb-to-megabase scale the genome can be divided into constant ToR regions (CTRs) in which the replication process propagates at a faster pace due to the activation of multiple origins and temporal transition regions (TTRs) in which the replication process propagates at a slower pace. We developed a computational tool that assigns a ToR to every measured locus and determines its replication activity type (CTR versus TTR). Our algorithm, ARTO (Analysis of Replication Timing and Organization), uses signal processing methods to fit a constant piece-wise linear curve to the measured raw data. We tested our algorithm and provide performance and usability results. A Matlab implementation of ARTO is available at http://bioinfo.cs.technion.ac.il/people/zohar/ARTO/. Applying our algorithm to ToR data measured in multiple mouse and human samples allowed precise genome-wide ToR determination and replication activity type characterization. Analysis of the results highlighted the plasticity of the replication program. For example, we observed significant ToR differences in 10–25% of the genome when comparing different tissue types. Our analyses also provide evidence for activity type differences in up to 30% of the probes. Integration of the ToR data with multiple aspects of chromosome organization characteristics suggests that ToR plays a role in shaping the regional chromatin structure. Namely, repressive chromatin marks, are associated with late ToR both in TTRs and CTRs. Finally, characterization of the differences between TTRs and CTRs, with matching ToR, revealed that TTRs are associated with compact chromatin and are located significantly closer to the nuclear envelope. Supplementary material is available. Raw and processed data were deposited in Geo (GSE17236). PMID:23145042

Hemisphericity and information processing in North American Native (Ojibwa) and non-native adolescents.

PubMed

Morton, L L; Allen, J D; Williams, N H

1994-04-01

Thirty-two male and female adolescents of native ancestry (Ojibwa) and 32 controls were tested using (1) four WISC-R subtests and (2) two dichotic listening tasks which employed a focused-attention paradigm for processing consonant-vowel combinations (CVs) and musical melodies. On the WISC-R, natives scored higher than controls on Block Design and Picture Completion subtests but lower on Vocabulary and Similarities subtests. On laterality measures more native males showed a left ear advantage on the CV task and the melody task. For CVs the left ear advantage was due to native males' lower right ear (i.e., left hemisphere) involvement. For melodies, the laterality index pointed to less left hemisphere involvement for native males, however, the raw scores showed that natives were performing lower overall. The findings are consistent with culturally-based strategy differences, possibly linked to "hemisphericity," but additional clarifying research regarding the cause and extent of such differences is warranted. Thus, implications for education are premature but a focus on teaching "left hemisphere type" strategies to all individuals not utilizing such skills, including many native males, may prove beneficial.

Adaptation and colonization history affect the evolution of clines in two introduced species.

PubMed

Keller, Stephen R; Sowell, Dexter R; Neiman, Maurine; Wolfe, Lorne M; Taylor, Douglas R

2009-08-01

Phenotypic and genetic clines have long been synonymous with adaptive evolution. However, other processes (for example, migration, range expansion, invasion) may generate clines in traits or loci across geographical and environmental gradients. It is therefore important to distinguish between clines that represent adaptive evolution and those that result from selectively neutral demographic or genetic processes. We tested for the differentiation of phenotypic traits along environmental gradients using two species in the genus Silene, whilst statistically controlling for colonization history and founder effects. We sampled seed families from across the native and introduced ranges, genotyped individuals and estimated phenotypic differentiation in replicated common gardens. The results suggest that post-glacial expansion of S. vulgaris and S. latifolia involved both neutral and adaptive genetic differentiation (clines) of life history traits along major axes of environmental variation in Europe and North America. Phenotypic clines generally persisted when tested against the neutral expectation, although some clines disappeared (and one cline emerged) when the effects of genetic ancestry were statistically removed. Colonization history, estimated using genetic markers, is a useful null model for tests of adaptive trait divergence, especially during range expansion and invasion when selection and gene flow may not have reached equilibrium.

Literacy achievement of children with intellectual disabilities and differing linguistic backgrounds.

PubMed

Verhoeven, L; Vermeer, A

2006-10-01

The aim of the present study was to examine the literacy achievement of 10- to 12-year-old native and non-native children with intellectual disabilities (ID) living in the Netherlands. An intriguing question within this context was whether the second language learning non-native children with ID would show a double disadvantage when compared with their monolingual Dutch peers with no ID. Dutch literacy scores in the domains of word decoding, vocabulary, syntax and text were therefore compared for: (1) intellectually disabled native Dutch children; (2) intellectually disabled non-native children; (3) normally developing native Dutch children; and (4) normally developing non-native children. The interrelations between literacy subskills were also compared for native vs. non-native children with ID. The native and non-native students diagnosed as intellectually disabled produced substantially lower literacy scores than their non-disabled peers. The differences between the native (L1) and non-native (L2) children in regular vs. special education were found to depend on the aspect of literacy considered. Word decoding and language skills turned out to significantly predict the children's reading comprehension, although some differences in the strength of relationships could also be evidenced. The literacy achievement of intellectually disabled children with differing linguistic backgrounds generally falls behind that of their non-disabled peers. For word decoding, the non-native children in regular and special education were generally able to keep up with their native peers. For higher-order literacy abilities closely related to the mental lexicon, sentence processing and text processing, however, significant differences in the performances of the native (L1) and non-native (L2) children in regular vs. special education were found, suggesting a double disadvantage for the non-native children in special education.

A Drosophila Toolkit for the Visualization and Quantification of Viral Replication Launched from Transgenic Genomes

PubMed Central

Wernet, Mathias F.; Klovstad, Martha; Clandinin, Thomas R.

2014-01-01

Arthropod RNA viruses pose a serious threat to human health, yet many aspects of their replication cycle remain incompletely understood. Here we describe a versatile Drosophila toolkit of transgenic, self-replicating genomes (‘replicons’) from Sindbis virus that allow rapid visualization and quantification of viral replication in vivo. We generated replicons expressing Luciferase for the quantification of viral replication, serving as useful new tools for large-scale genetic screens for identifying cellular pathways that influence viral replication. We also present a new binary system in which replication-deficient viral genomes can be activated ‘in trans’, through co-expression of an intact replicon contributing an RNA-dependent RNA polymerase. The utility of this toolkit for studying virus biology is demonstrated by the observation of stochastic exclusion between replicons expressing different fluorescent proteins, when co-expressed under control of the same cellular promoter. This process is analogous to ‘superinfection exclusion’ between virus particles in cell culture, a process that is incompletely understood. We show that viral polymerases strongly prefer to replicate the genome that encoded them, and that almost invariably only a single virus genome is stochastically chosen for replication in each cell. Our in vivo system now makes this process amenable to detailed genetic dissection. Thus, this toolkit allows the cell-type specific, quantitative study of viral replication in a genetic model organism, opening new avenues for molecular, genetic and pharmacological dissection of virus biology and tool development. PMID:25386852

Maynard Participation in Alaska Forum on the Environment Panel Discussion on Increasing Input to the US National Climate Assessment (NCA) and the Intergovernmental Panel on Climate Change (IPCC) Processes from Alaska, with Emphasis on Indigenous Peoples Issues

NASA Technical Reports Server (NTRS)

Maynard, Nancy G.

2012-01-01

Dr. Nancy Maynard was invited by the Alaska Forum on the Environment to participate in a Panel Discussion to discuss (1) background about what the US NCA and International IPCC assessments are, (2) the impact the assessments have on policy-making, (3) the process for participation in both assessments, (4) how we can increase participation by Indigenous Peoples such as Native Americans and Alaska Natives, (5) How we can increase historical and current impacts input from Native communities through stories, oral history, "grey" literature, etc. The session will be chaired by Dr. Bull Bennett, a cochair of the US NCA's chapter on "Native and Tribal Lands and Resources" and Dr. Maynard is the other co-chair of that chapter and they will discuss the latest activities under the NCA process relevant to Native Americans and Alaska Natives. Dr. Maynard is also a Lead Author of the "Polar Regions" chapter of the IPCC WG2 (5th Assessment) and she will describes some of the latest approaches by the IPCC to entrain more Indigenous peoples into the IPCC process.

Reanalysis and semantic persistence in native and non-native garden-path recovery.

PubMed

Jacob, Gunnar; Felser, Claudia

2016-01-01

We report the results from an eye-movement monitoring study investigating how native and non-native speakers of English process temporarily ambiguous sentences such as While the gentleman was eating the burgers were still being reheated in the microwave, in which an initially plausible direct-object analysis is first ruled out by a syntactic disambiguation (were) and also later on by semantic information (being reheated). Both participant groups showed garden-path effects at the syntactic disambiguation, with native speakers showing significantly stronger effects of ambiguity than non-native speakers in later eye-movement measures but equally strong effects in first-pass reading times. Ambiguity effects at the semantic disambiguation and in participants' end-of-trial responses revealed that for both participant groups, the incorrect direct-object analysis was frequently maintained beyond the syntactic disambiguation. The non-native group showed weaker reanalysis effects at the syntactic disambiguation and was more likely to misinterpret the experimental sentences than the native group. Our results suggest that native language (L1) and non-native language (L2) parsing are similar with regard to sensitivity to syntactic and semantic error signals, but different with regard to processes of reanalysis.

Regulated transport into the nucleus of herpesviridae DNA replication core proteins.

PubMed

Gualtiero, Alvisi; Jans, David A; Camozzi, Daria; Avanzi, Simone; Loregian, Arianna; Ripalti, Alessandro; Palù, Giorgio

2013-09-16

The Herpesvirdae family comprises several major human pathogens belonging to three distinct subfamilies. Their double stranded DNA genome is replicated in the nuclei of infected cells by a number of host and viral products. Among the latter the viral replication complex, whose activity is strictly required for viral replication, is composed of six different polypeptides, including a two-subunit DNA polymerase holoenzyme, a trimeric primase/helicase complex and a single stranded DNA binding protein. The study of herpesviral DNA replication machinery is extremely important, both because it provides an excellent model to understand processes related to eukaryotic DNA replication and it has important implications for the development of highly needed antiviral agents. Even though all known herpesviruses utilize very similar mechanisms for amplification of their genomes, the nuclear import of the replication complex components appears to be a heterogeneous and highly regulated process to ensure the correct spatiotemporal localization of each protein. The nuclear transport process of these enzymes is controlled by three mechanisms, typifying the main processes through which protein nuclear import is generally regulated in eukaryotic cells. These include cargo post-translational modification-based recognition by the intracellular transporters, piggy-back events allowing coordinated nuclear import of multimeric holoenzymes, and chaperone-assisted nuclear import of specific subunits. In this review we summarize these mechanisms and discuss potential implications for the development of antiviral compounds aimed at inhibiting the Herpesvirus life cycle by targeting nuclear import of the Herpesvirus DNA replicating enzymes.

DNA replication components as regulators of epigenetic inheritance--lesson from fission yeast centromere.

PubMed

He, Haijin; Gonzalez, Marlyn; Zhang, Fan; Li, Fei

2014-06-01

Genetic information stored in DNA is accurately copied and transferred to subsequent generations through DNA replication. This process is accomplished through the concerted actions of highly conserved DNA replication components. Epigenetic information stored in the form of histone modifications and DNA methylation, constitutes a second layer of regulatory information important for many cellular processes, such as gene expression regulation, chromatin organization, and genome stability. During DNA replication, epigenetic information must also be faithfully transmitted to subsequent generations. How this monumental task is achieved remains poorly understood. In this review, we will discuss recent advances on the role of DNA replication components in the inheritance of epigenetic marks, with a particular focus on epigenetic regulation in fission yeast. Based on these findings, we propose that specific DNA replication components function as key regulators in the replication of epigenetic information across the genome.

Effector-Triggered Self-Replication in Coupled Subsystems.

PubMed

Komáromy, Dávid; Tezcan, Meniz; Schaeffer, Gaël; Marić, Ivana; Otto, Sijbren

2017-11-13

In living systems processes like genome duplication and cell division are carefully synchronized through subsystem coupling. If we are to create life de novo, similar control over essential processes such as self-replication need to be developed. Here we report that coupling two dynamic combinatorial subsystems, featuring two separate building blocks, enables effector-mediated control over self-replication. The subsystem based on the first building block shows only self-replication, whereas that based on the second one is solely responsive toward a specific external effector molecule. Mixing the subsystems arrests replication until the effector molecule is added, resulting in the formation of a host-effector complex and the liberation of the building block that subsequently engages in self-replication. The onset, rate and extent of self-replication is controlled by the amount of effector present. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cooperative working of bacterial chromosome replication proteins generated by a reconstituted protein expression system

PubMed Central

Fujiwara, Kei; Katayama, Tsutomu; Nomura, Shin-ichiro M.

2013-01-01

Replication of all living cells relies on the multirounds flow of the central dogma. Especially, expression of DNA replication proteins is a key step to circulate the processes of the central dogma. Here we achieved the entire sequential transcription–translation–replication process by autonomous expression of chromosomal DNA replication machineries from a reconstituted transcription–translation system (PURE system). We found that low temperature is essential to express a complex protein, DNA polymerase III, in a single tube using the PURE system. Addition of the 13 genes, encoding initiator, DNA helicase, helicase loader, RNA primase and DNA polymerase III to the PURE system gave rise to a DNA replication system by a coupling manner. An artificial genetic circuit demonstrated that the DNA produced as a result of the replication is able to provide genetic information for proteins, indicating the in vitro central dogma can sequentially undergo two rounds. PMID:23737447

DNA replication machinery is required for development in Drosophila.

PubMed

Kohzaki, Hidetsugu; Asano, Maki; Murakami, Yota

2018-01-01

 In Drosophila , some factors involved in chromosome replication seem to be involved in gene amplification and endoreplication, which are actively utilized in particular tissue development, but direct evidence has not been shown. Therefore, we examined the effect of depletion of replication factors on these processes. First, we confirmed RNAi knockdown can be used for the depletion of replication factors by comparing the phenotypes of RNAi knockdown and deletion or point mutants of the components of DNA licensing factor, MCM2, MCM4 and Cdt1. Next, we found that tissue-specific RNAi knockdown of replication factors caused tissue-specific defects, probably due to defects in DNA replication. In particular, we found that depletion inhibited gene amplification of the chorion gene in follicle cells and endoreplication in salivary glands, showing that chromosomal DNA replication factors are required for these processes. Finally, using RNAi, we screened the genes for chromosomal DNA replication that affected tissue development. Interestingly, wing specific knockdown of Mcm10 induced wing formation defects. These results suggest that some components of chromosomal replication machinery are directly involved in tissue development.

The influence of language deprivation in early childhood on L2 processing: An ERP comparison of deaf native signers and deaf signers with a delayed language acquisition.

PubMed

Skotara, Nils; Salden, Uta; Kügow, Monique; Hänel-Faulhaber, Barbara; Röder, Brigitte

2012-05-03

To examine which language function depends on early experience, the present study compared deaf native signers, deaf non-native signers and hearing German native speakers while processing German sentences. The participants watched simple written sentences while event-related potentials (ERPs) were recorded. At the end of each sentence they were asked to judge whether the sentence was correct or not. Two types of violations were introduced in the middle of the sentence: a semantically implausible noun or a violation of subject-verb number agreement. The results showed a similar ERP pattern after semantic violations (an N400 followed by a positivity) in all three groups. After syntactic violations, native German speakers and native signers of German sign language (DGS) with German as second language (L2) showed a left anterior negativity (LAN) followed by a P600, whereas no LAN but a negativity over the right hemisphere instead was found in deaf participants with a delayed onset of first language (L1) acquisition. The P600 of this group had a smaller amplitude and a different scalp distribution as compared to German native speakers. The results of the present study suggest that language deprivation in early childhood alters the cerebral organization of syntactic language processing mechanisms for L2. Semantic language processing instead was unaffected.

Native American Indians and the Counseling Process: Culture, Adaptation, and Style.

ERIC Educational Resources Information Center

Skouras, Thomas J.

Native Americans constitute a significant population that is growing and has great need for mental health and counseling services. Social problems in Native communities include high rates of alcoholism, alcohol-related deaths, drug use, youth suicide, and sexually transmitted diseases. Despite their mental health needs, Native Americans are…

Chromatin Structure and Replication Origins: Determinants Of Chromosome Replication And Nuclear Organization

PubMed Central

Smith, Owen K.; Aladjem, Mirit I.

2014-01-01

The DNA replication program is, in part, determined by the epigenetic landscape that governs local chromosome architecture and directs chromosome duplication. Replication must coordinate with other biochemical processes occurring concomitantly on chromatin, such as transcription and remodeling, to insure accurate duplication of both genetic and epigenetic features and to preserve genomic stability. The importance of genome architecture and chromatin looping in coordinating cellular processes on chromatin is illustrated by two recent sets of discoveries. First, chromatin-associated proteins that are not part of the core replication machinery were shown to affect the timing of DNA replication. These chromatin-associated proteins could be working in concert, or perhaps in competition, with the transcriptional machinery and with chromatin modifiers to determine the spatial and temporal organization of replication initiation events. Second, epigenetic interactions are mediated by DNA sequences that determine chromosomal replication. In this review we summarize recent findings and current models linking spatial and temporal regulation of the replication program with epigenetic signaling. We discuss these issues in the context of the genome’s three-dimensional structure with an emphasis on events occurring during the initiation of DNA replication. PMID:24905010

Does the speaker matter? Online processing of semantic and pragmatic information in L2 speech comprehension.

PubMed

Foucart, Alice; Garcia, Xavier; Ayguasanosa, Meritxell; Thierry, Guillaume; Martin, Clara; Costa, Albert

2015-08-01

The present study investigated how pragmatic information is integrated during L2 sentence comprehension. We put forward that the differences often observed between L1 and L2 sentence processing may reflect differences on how various types of information are used to process a sentence, and not necessarily differences between native and non-native linguistic systems. Based on the idea that when a cue is missing or distorted, one relies more on other cues available, we hypothesised that late bilinguals favour the cues that they master during sentence processing. To verify this hypothesis we investigated whether late bilinguals take the speaker's identity (inferred by the voice) into account when incrementally processing speech and whether this affects their online interpretation of the sentence. To do so, we adapted Van Berkum, J.J.A., Van den Brink, D., Tesink, C.M.J.Y., Kos, M., Hagoort, P., 2008. J. Cogn. Neurosci. 20(4), 580-591, study in which sentences with either semantic violations or pragmatic inconsistencies were presented. While both the native and the non-native groups showed a similar response to semantic violations (N400), their response to speakers' inconsistencies slightly diverged; late bilinguals showed a positivity much earlier than native speakers (LPP). These results suggest that, like native speakers, late bilinguals process semantic and pragmatic information incrementally; however, what seems to differ between L1 and L2 processing is the time-course of the different processes. We propose that this difference may originate from late bilinguals' sensitivity to pragmatic information and/or their ability to efficiently make use of the information provided by the sentence context to generate expectations in relation to pragmatic information during L2 sentence comprehension. In other words, late bilinguals may rely more on speaker identity than native speakers when they face semantic integration difficulties. Copyright © 2015 Elsevier Ltd. All rights reserved.

Conflict Resolution in the Genome: How Transcription and Replication Make It Work.

PubMed

Hamperl, Stephan; Cimprich, Karlene A

2016-12-01

The complex machineries involved in replication and transcription translocate along the same DNA template, often in opposing directions and at different rates. These processes routinely interfere with each other in prokaryotes, and mounting evidence now suggests that RNA polymerase complexes also encounter replication forks in higher eukaryotes. Indeed, cells rely on numerous mechanisms to avoid, tolerate, and resolve such transcription-replication conflicts, and the absence of these mechanisms can lead to catastrophic effects on genome stability and cell viability. In this article, we review the cellular responses to transcription-replication conflicts and highlight how these inevitable encounters shape the genome and impact diverse cellular processes. Copyright © 2016 Elsevier Inc. All rights reserved.

Chromatin Challenges during DNA Replication: A Systems Representation

PubMed Central

Aladjem, Mirit I.; Weinstein, John N.; Pommier, Yves

2008-01-01

In a recent review, A. Groth and coworkers presented a comprehensive account of nucleosome disassembly in front of a DNA replication fork, assembly behind the replication fork, and the copying of epigenetic information onto the replicated chromatin. Understanding those processes however would be enhanced by a comprehensive graphical depiction analogous to a circuit diagram. Accordingly, we have constructed a molecular interaction map (MIM) that preserves in essentially complete detail the processes described by Groth et al. The MIM organizes and elucidates the information presented by Groth et al. on the complexities of chromatin replication, thereby providing a tool for system-level comprehension of the effects of genetic mutations, altered gene expression, and pharmacologic intervention. PMID:17959828

Statistical physics of self-replication.

PubMed

England, Jeremy L

2013-09-28

Self-replication is a capacity common to every species of living thing, and simple physical intuition dictates that such a process must invariably be fueled by the production of entropy. Here, we undertake to make this intuition rigorous and quantitative by deriving a lower bound for the amount of heat that is produced during a process of self-replication in a system coupled to a thermal bath. We find that the minimum value for the physically allowed rate of heat production is determined by the growth rate, internal entropy, and durability of the replicator, and we discuss the implications of this finding for bacterial cell division, as well as for the pre-biotic emergence of self-replicating nucleic acids.

Electrophysiological correlates of cross-linguistic semantic integration in hearing signers: N400 and LPC.

PubMed

Zachau, Swantje; Korpilahti, Pirjo; Hämäläinen, Jarmo A; Ervast, Leena; Heinänen, Kaisu; Suominen, Kalervo; Lehtihalmes, Matti; Leppänen, Paavo H T

2014-07-01

We explored semantic integration mechanisms in native and non-native hearing users of sign language and non-signing controls. Event-related brain potentials (ERPs) were recorded while participants performed a semantic decision task for priming lexeme pairs. Pairs were presented either within speech or across speech and sign language. Target-related ERP responses were subjected to principal component analyses (PCA), and neurocognitive basis of semantic integration processes were assessed by analyzing the N400 and the late positive complex (LPC) components in response to spoken (auditory) and signed (visual) antonymic and unrelated targets. Semantically-related effects triggered across modalities would indicate a similar tight interconnection between the signers׳ two languages like that described for spoken language bilinguals. Remarkable structural similarity of the N400 and LPC components with varying group differences between the spoken and signed targets were found. The LPC was the dominant response. The controls׳ LPC differed from the LPC of the two signing groups. It was reduced to the auditory unrelated targets and was less frontal for all the visual targets. The visual LPC was more broadly distributed in native than non-native signers and was left-lateralized for the unrelated targets in the native hearing signers only. Semantic priming effects were found for the auditory N400 in all groups, but only native hearing signers revealed a clear N400 effect to the visual targets. Surprisingly, the non-native signers revealed no semantically-related processing effect to the visual targets reflected in the N400 or the LPC; instead they appeared to rely more on visual post-lexical analyzing stages than native signers. We conclude that native and non-native signers employed different processing strategies to integrate signed and spoken semantic content. It appeared that the signers׳ semantic processing system was affected by group-specific factors like language background and/or usage. Copyright © 2014 Elsevier Ltd. All rights reserved.

Directed evolution of DNA polymerase, RNA polymerase and reverse transcriptase activity in a single polypeptide.

PubMed

Ong, Jennifer L; Loakes, David; Jaroslawski, Szymon; Too, Kathleen; Holliger, Philipp

2006-08-18

DNA polymerases enable key technologies in modern biology but for many applications, native polymerases are limited by their stringent substrate recognition. Here we describe short-patch compartmentalized self-replication (spCSR), a novel strategy to expand the substrate spectrum of polymerases in a targeted way. spCSR is based on the previously described CSR, but unlike CSR only a short region (a "patch") of the gene under investigation is diversified and replicated. This allows the selection of polymerases under conditions where catalytic activity and processivity are compromised to the extent that full self-replication is inefficient. We targeted two specific motifs involved in substrate recognition in the active site of DNA polymerase I from Thermus aquaticus (Taq) and selected for incorporation of both ribonucleotide- (NTP) and deoxyribonucleotide-triphosphates (dNTPs) using spCSR. This allowed the isolation of multiple variants of Taq with apparent dual substrate specificity. They were able to synthesize RNA, while still retaining essentially wild-type (wt) DNA polymerase activity as judged by PCR. One such mutant (AA40: E602V, A608V, I614M, E615G) was able to incorporate both NTPs and dNTPs with the same catalytic efficiency as the wt enzyme incorporates dNTPs. AA40 allowed the generation of mixed RNA-DNA amplification products in PCR demonstrating DNA polymerase, RNA polymerase as well as reverse transcriptase activity within the same polypeptide. Furthermore, AA40 displayed an expanded substrate spectrum towards other 2'-substituted nucleotides and was able to synthesize nucleic acid polymers in which each base bore a different 2'-substituent. Our results suggest that spCSR will be a powerful strategy for the generation of polymerases with altered substrate specificity for applications in nano- and biotechnology and in the enzymatic synthesis of antisense and RNAi probes.

Assessing Competence in ESL: Reading.

ERIC Educational Resources Information Center

Oller, John W., Jr.

Results from research with eye movement photography (EMP) are discussed with a view to defining differences between native-speaker and non-native reading processes. The greatest contrast is in terms of the duration of eye fixations; non-native speakers at the college level require about as much time for a fixation as an average native-speaker at…

Water guns affect abundance and behavior of bigheaded carp and native fish differently

USGS Publications Warehouse

Rivera, Jose; Glover, David C.; Kocovsky, Patrick; Garvey, James E.; Gaikowski, Mark; Jensen, Nathan R.; Adams, Ryan F.

2018-01-01

Water guns have shown the potential to repel nuisance aquatic organisms. This study examines the effects of exposure to a 1966.4 cm3 seismic water gun array (two guns) on the abundance and behavior of Bighead Carp Hypophthalmichthys nobilis, Silver Carp H. molitrix (collectively referred to as bigheaded carp) and native fishes (e.g., Smallmouth Buffalo Ictiobus bubalus). Water guns were deployed in a channel that connects the Illinois River to backwater quarry pits that contained a large transient population of bigheaded carp. To evaluate the effect of water guns, mobile side-looking split-beam hydroacoustic surveys were conducted before, during and between replicated water gun firing periods. Water guns did not affect abundance of bigheaded carp, but abundance of native fish detected during the firing treatment was 43 and 34% lower than the control and water guns off treatments, respectively. The proximity of bigheaded carp to the water gun array was similar between the water guns on and water guns off treatments. In contrast, the closest detected native fish were detected farther from the water guns during the water guns on treatment (mean ± SE, 32.38 ± 3.32 m) than during the water guns off treatment (15.04 ± 1.59 m). The water gun array had a greater impact on native fish species than on bigheaded carp. Caution should be taken to the extrapolation of these results to other fish species and to fish exposed to water guns in different environments (e.g., reduced shoreline interaction) or exposure to a larger array of water guns, or for use of water guns for purposes other than a barrier.

A common-garden study of resource-island effects on a native and an exotic, annual grass after fire

USGS Publications Warehouse

Hoover, Amber N.; Germino, Matthew J.

2012-01-01

Plant-soil variation related to perennial-plant resource islands (coppices) interspersed with relatively bare interspaces is a major source of heterogeneity in desert rangelands. Our objective was to determine how native and exotic grasses vary on coppice mounds and interspaces (microsites) in unburned and burned sites and underlying factors that contribute to the variation in sagebrush-steppe rangelands of the Idaho National Lab, where interspaces typically have abiotic crusts. We asked how the exotic cheatgrass (Bromus tectorum L.) and native bluebunch wheatgrass (Pseudoroegneria spicata [Pursh] A. Löve) were distributed among the microsites and measured their abundances in three replicate wildfires and nearby unburned areas. We conducted a common-garden study in which soil cores from each burned microsite type were planted with seed of either species to determine microsite effects on establishment and growth of native and exotic grasses. We assessed soil physical properties in the common-garden study to determine the intrinsic properties of each microsite surface and the retention of microsite soil differences following transfer of soils to the garden, to plant growth, and to wetting/drying cycles. In the field study, only bluebunch wheatgrass density was greater on coppice mounds than interspaces, in both unburned and burned areas. In the common-garden experiment, there were microsite differences in soil physical properties, particularly in crust hardness and its relationship to moisture, but soil properties were unaffected by plant growth. Also in the experiment, both species had equal densities yet greater dry mass production on coppice-mound soils compared to interspace soils, suggesting microsite differences in growth but not establishment (likely related to crust weakening resulting from watering). Coppice-interspace patterning and specifically native-herb recovery on coppices is likely important for postfire resistance of this rangeland to cheatgrass.

Quantitative Proteomic Analysis of Mosquito C6/36 Cells Reveals Host Proteins Involved in Zika Virus Infection.

PubMed

Xin, Qi-Lin; Deng, Cheng-Lin; Chen, Xi; Wang, Jun; Wang, Shao-Bo; Wang, Wei; Deng, Fei; Zhang, Bo; Xiao, Gengfu; Zhang, Lei-Ke

2017-06-15

Zika virus (ZIKV) is an emerging arbovirus belonging to the genus Flavivirus of the family Flaviviridae During replication processes, flavivirus manipulates host cell systems to facilitate its replication, while the host cells activate antiviral responses. Identification of host proteins involved in the flavivirus replication process may lead to the discovery of antiviral targets. The mosquitoes Aedes aegypti and Aedes albopictus are epidemiologically important vectors for ZIKV, and effective restrictions of ZIKV replication in mosquitoes will be vital in controlling the spread of virus. In this study, an iTRAQ-based quantitative proteomic analysis of ZIKV-infected Aedes albopictus C6/36 cells was performed to investigate host proteins involved in the ZIKV infection process. A total of 3,544 host proteins were quantified, with 200 being differentially regulated, among which CHCHD2 can be upregulated by ZIKV infection in both mosquito C6/36 and human HeLa cells. Our further study indicated that CHCHD2 can promote ZIKV replication and inhibit beta interferon (IFN-β) production in HeLa cells, suggesting that ZIKV infection may upregulate CHCHD2 to inhibit IFN-I production and thus promote virus replication. Bioinformatics analysis of regulated host proteins highlighted several ZIKV infection-regulated biological processes. Further study indicated that the ubiquitin proteasome system (UPS) plays roles in the ZIKV entry process and that an FDA-approved inhibitor of the 20S proteasome, bortezomib, can inhibit ZIKV infection in vivo Our study illustrated how host cells respond to ZIKV infection and also provided a candidate drug for the control of ZIKV infection in mosquitoes and treatment of ZIKV infection in patients. IMPORTANCE ZIKV infection poses great threats to human health, and there is no FDA-approved drug available for the treatment of ZIKV infection. During replication, ZIKV manipulates host cell systems to facilitate its replication, while host cells activate antiviral responses. Identification of host proteins involved in the ZIKV replication process may lead to the discovery of antiviral targets. In this study, the first quantitative proteomic analysis of ZIKV-infected cells was performed to investigate host proteins involved in the ZIKV replication process. Bioinformatics analysis highlighted several ZIKV infection-regulated biological processes. Further study indicated that the ubiquitin proteasome system (UPS) plays roles in the ZIKV entry process and that an FDA-approved inhibitor of the UPS, bortezomib, can inhibit ZIKV infection in vivo Our study not only illustrated how host cells respond to ZIKV infection but also provided a candidate drug for the control of ZIKV infection in mosquitoes and treatment of ZIKV infection in patients. Copyright © 2017 American Society for Microbiology.

Prioritizing islands for the eradication of invasive vertebrates in the United Kingdom overseas territories.

PubMed

Dawson, Jeffrey; Oppel, Steffen; Cuthbert, Richard J; Holmes, Nick; Bird, Jeremy P; Butchart, Stuart H M; Spatz, Dena R; Tershy, Bernie

2015-02-01

Invasive alien species are one of the primary threats to native biodiversity on islands worldwide. Consequently, eradicating invasive species from islands has become a mainstream conservation practice. Deciding which islands have the highest priority for eradication is of strategic importance to allocate limited resources to achieve maximum conservation benefit. Previous island prioritizations focused either on a narrow set of native species or on a small geographic area. We devised a prioritization approach that incorporates all threatened native terrestrial vertebrates and all invasive terrestrial vertebrates occurring on 11 U.K. overseas territories, which comprise over 2000 islands ranging from the sub-Antarctic to the tropics. Our approach includes eradication feasibility and distinguishes between the potential and realistic conservation value of an eradication, which reflects the benefit that would accrue following eradication of either all invasive species or only those species for which eradication techniques currently exist. We identified the top 25 priority islands for invasive species eradication that together would benefit extant populations of 155 native species including 45 globally threatened species. The 5 most valuable islands included the 2 World Heritage islands Gough (South Atlantic) and Henderson (South Pacific) that feature unique seabird colonies, and Anegada, Little Cayman, and Guana Island in the Caribbean that feature a unique reptile fauna. This prioritization can be rapidly repeated if new information or techniques become available, and the approach could be replicated elsewhere in the world. © 2014 Crown copyright. Conservation Biology © 2014 Society for Conservation Biology.

Mechanics of oriented electrospun nanofibrous scaffolds for annulus fibrosus tissue engineering.

PubMed

Nerurkar, Nandan L; Elliott, Dawn M; Mauck, Robert L

2007-08-01

Engineering a functional replacement for the annulus fibrosus (AF) of the intervertebral disc is contingent upon recapitulation of AF structure, composition, and mechanical properties. In this study, we propose a new paradigm for AF tissue engineering that focuses on the reconstitution of anatomic fiber architecture and uses constitutive modeling to evaluate construct function. A modified electrospinning technique was utilized to generate aligned nanofibrous polymer scaffolds for engineering the basic functional unit of the AF, a single lamella. Scaffolds were tested in uniaxial tension at multiple fiber orientations, demonstrating a nonlinear dependence of modulus on fiber angle that mimicked the nonlinearity and anisotropy of native AF. A homogenization model previously applied to native AF successfully described scaffold mechanical response, and parametric studies demonstrated that nonfibrillar matrix, along with fiber connectivity, are key contributors to tensile mechanics for engineered AF. We demonstrated that AF cells orient themselves along the aligned scaffolds and deposit matrix that contributes to construct mechanics under loading conditions relevant to the in vivo environment. The homogenization model was applied to cell-seeded constructs and provided quantitative measures for the evolution of matrix and interfibrillar interactions. Finally, the model demonstrated that at fiber angles of the AF (28 degrees -44 degrees ), engineered material behaved much like native tissue, suggesting that engineered constructs replicate the physiologic behavior of the single AF lamella. Constitutive modeling provides a powerful tool for analysis of engineered AF neo-tissue and native AF tissue alike, highlighting key mechanical design criteria for functional AF tissue engineering.

Community-based participatory research with Native American communities: the Chronic Disease Self-Management Program.

PubMed

Jernigan, Valarie Blue Bird

2010-11-01

Health disparities among Native Americans persist despite efforts to translate evidence-based programs from research to practice. Few evidence-based, theory-driven prevention and management interventions have been successfully translated within Native American communities. The use of community-based participatory research (CBPR) has shown promise in this process. This article provides an overview of the use of CBPR with Native American communities and discusses the translation of the Stanford Chronic Disease Self-Management Program, using a CBPR approach, with an urban Native American community. This article highlights not only how the CBPR process facilitates the successful translation of the Stanford program but also how CBPR is used within this community to build community capacity.

The Role of Native-Language Knowledge in the Perception of Casual Speech in a Second Language

PubMed Central

Mitterer, Holger; Tuinman, Annelie

2012-01-01

Casual speech processes, such as /t/-reduction, make word recognition harder. Additionally, word recognition is also harder in a second language (L2). Combining these challenges, we investigated whether L2 learners have recourse to knowledge from their native language (L1) when dealing with casual speech processes in their L2. In three experiments, production and perception of /t/-reduction was investigated. An initial production experiment showed that /t/-reduction occurred in both languages and patterned similarly in proper nouns but differed when /t/ was a verbal inflection. Two perception experiments compared the performance of German learners of Dutch with that of native speakers for nouns and verbs. Mirroring the production patterns, German learners’ performance strongly resembled that of native Dutch listeners when the reduced /t/ was part of a word stem, but deviated where /t/ was a verbal inflection. These results suggest that a casual speech process in a second language is problematic for learners when the process is not known from the leaner’s native language, similar to what has been observed for phoneme contrasts. PMID:22811675

Processing changes when listening to foreign-accented speech

PubMed Central

Romero-Rivas, Carlos; Martin, Clara D.; Costa, Albert

2015-01-01

This study investigates the mechanisms responsible for fast changes in processing foreign-accented speech. Event Related brain Potentials (ERPs) were obtained while native speakers of Spanish listened to native and foreign-accented speakers of Spanish. We observed a less positive P200 component for foreign-accented speech relative to native speech comprehension. This suggests that the extraction of spectral information and other important acoustic features was hampered during foreign-accented speech comprehension. However, the amplitude of the N400 component for foreign-accented speech comprehension decreased across the experiment, suggesting the use of a higher level, lexical mechanism. Furthermore, during native speech comprehension, semantic violations in the critical words elicited an N400 effect followed by a late positivity. During foreign-accented speech comprehension, semantic violations only elicited an N400 effect. Overall, our results suggest that, despite a lack of improvement in phonetic discrimination, native listeners experience changes at lexical-semantic levels of processing after brief exposure to foreign-accented speech. Moreover, these results suggest that lexical access, semantic integration and linguistic re-analysis processes are permeable to external factors, such as the accent of the speaker. PMID:25859209

Umyuangcaryaraq "Reflecting": multidimensional assessment of reflective processes on the consequences of alcohol use among rural Yup'ik Alaska Native youth.

PubMed

Allen, James; Fok, Carlotta Ching Ting; Henry, David; Skewes, Monica

2012-09-01

Concerns in some settings regarding the accuracy and ethics of employing direct questions about alcohol use suggest need for alternative assessment approaches with youth. Umyuangcaryaraq is a Yup'ik Alaska Native word meaning "Reflecting." The Reflective Processes Scale was developed as a youth measure tapping awareness and thinking over potential negative consequences of alcohol misuse as a protective factor that includes cultural elements often shared by many other Alaska Native and American Indian cultures. This study assessed multidimensional structure, item functioning, and validity. Responses from 284 rural Alaska Native youth allowed bifactor analysis to assess structure, estimates of location and discrimination parameters, and convergent and discriminant validity. A bifactor model of the scale items with three content factors provided excellent fit to observed data. Item response theory analysis suggested a binary response format as optimal. Evidence of convergent and discriminant validity was established. The measure provides an assessment of reflective processes about alcohol that Alaska Native youth engage in when thinking about reasons not to drink. The concept of reflective processes has potential to extend understandings of cultural variation in mindfulness, alcohol expectancies research, and culturally mediated protective factors in Alaska Native and American Indian youth.

Hemispheric asymmetry of emotion words in a non-native mind: a divided visual field study.

PubMed

Jończyk, Rafał

2015-05-01

This study investigates hemispheric specialization for emotional words among proficient non-native speakers of English by means of the divided visual field paradigm. The motivation behind the study is to extend the monolingual hemifield research to the non-native context and see how emotion words are processed in a non-native mind. Sixty eight females participated in the study, all highly proficient in English. The stimuli comprised 12 positive nouns, 12 negative nouns, 12 non-emotional nouns and 36 pseudo-words. To examine the lateralization of emotion, stimuli were presented unilaterally in a random fashion for 180 ms in a go/no-go lexical decision task. The perceptual data showed a right hemispheric advantage for processing speed of negative words and a complementary role of the two hemispheres in the recognition accuracy of experimental stimuli. The data indicate that processing of emotion words in non-native language may require greater interhemispheric communication, but at the same time demonstrates a specific role of the right hemisphere in the processing of negative relative to positive valence. The results of the study are discussed in light of the methodological inconsistencies in the hemifield research as well as the non-native context in which the study was conducted.

Selective replication of oncolytic virus M1 results in a bystander killing effect that is potentiated by Smac mimetics.

PubMed

Cai, Jing; Lin, Yuan; Zhang, Haipeng; Liang, Jiankai; Tan, Yaqian; Cavenee, Webster K; Yan, Guangmei

2017-06-27

Oncolytic virotherapy is a treatment modality that uses native or genetically modified viruses that selectively replicate in and kill tumor cells. Viruses represent a type of pathogen-associated molecular pattern and thereby induce the up-regulation of dozens of cytokines via activating the host innate immune system. Second mitochondria-derived activator of caspases (Smac) mimetic compounds (SMCs), which antagonize the function of inhibitor of apoptosis proteins (IAPs) and induce apoptosis, sensitize tumor cells to multiple cytokines. Therefore, we sought to determine whether SMCs sensitize tumor cells to cytokines induced by the oncolytic M1 virus, thus enhancing a bystander killing effect. Here, we report that SMCs potentiate the oncolytic effect of M1 in vitro, in vivo, and ex vivo. This strengthened oncolytic efficacy resulted from the enhanced bystander killing effect caused by the M1 virus via cytokine induction. Through a microarray analysis and subsequent validation using recombinant cytokines, we identified IL-8, IL-1A, and TRAIL as the key cytokines in the bystander killing effect. Furthermore, SMCs increased the replication of M1, and the accumulation of virus protein induced irreversible endoplasmic reticulum stress- and c-Jun N-terminal kinase-mediated apoptosis. Nevertheless, the combined treatment with M1 and SMCs had little effect on normal and human primary cells. Because SMCs selectively and significantly enhance the bystander killing effect and the replication of oncolytic virus M1 specifically in cancer cells, this combined treatment may represent a promising therapeutic strategy.

The Perception and Representation of Segmental and Prosodic Mandarin Contrasts in Native Speakers of Cantonese

PubMed Central

Zhang, Xujin; Samuel, Arthur G.; Liu, Siyun

2011-01-01

Previous research has found that a speaker’s native phonological system has a great influence on perception of another language. In three experiments, we tested the perception and representation of Mandarin phonological contrasts by Guangzhou Cantonese speakers, and compared their performance to that of native Mandarin speakers. Despite their rich experience using Mandarin Chinese, the Cantonese speakers had problems distinguishing specific Mandarin segmental and tonal contrasts that do not exist in Guangzhou Cantonese. However, we found evidence that the subtle differences between two members of a contrast were nonetheless represented in the lexicon. We also found different processing patterns for non-native segmental versus non-native tonal contrasts. The results provide substantial new information about the representation and processing of segmental and prosodic information by individuals listening to a closely-related, very well-learned, but still non-native language. PMID:22707849

Aggregate and individual replication probability within an explicit model of the research process.

PubMed

Miller, Jeff; Schwarz, Wolf

2011-09-01

We study a model of the research process in which the true effect size, the replication jitter due to changes in experimental procedure, and the statistical error of effect size measurement are all normally distributed random variables. Within this model, we analyze the probability of successfully replicating an initial experimental result by obtaining either a statistically significant result in the same direction or any effect in that direction. We analyze both the probability of successfully replicating a particular experimental effect (i.e., the individual replication probability) and the average probability of successful replication across different studies within some research context (i.e., the aggregate replication probability), and we identify the conditions under which the latter can be approximated using the formulas of Killeen (2005a, 2007). We show how both of these probabilities depend on parameters of the research context that would rarely be known in practice. In addition, we show that the statistical uncertainty associated with the size of an initial observed effect would often prevent accurate estimation of the desired individual replication probability even if these research context parameters were known exactly. We conclude that accurate estimates of replication probability are generally unattainable.

Are Local Filters Blind to Provenance? Ant Seed Predation Suppresses Exotic Plants More than Natives

PubMed Central

Pearson, Dean E.; Icasatti, Nadia S.; Hierro, Jose L.; Bird, Benjamin J.

2014-01-01

The question of whether species’ origins influence invasion outcomes has been a point of substantial debate in invasion ecology. Theoretically, colonization outcomes can be predicted based on how species’ traits interact with community filters, a process presumably blind to species’ origins. Yet, exotic plant introductions commonly result in monospecific plant densities not commonly seen in native assemblages, suggesting that exotic species may respond to community filters differently than natives. Here, we tested whether exotic and native species differed in their responses to a local community filter by examining how ant seed predation affected recruitment of eighteen native and exotic plant species in central Argentina. Ant seed predation proved to be an important local filter that strongly suppressed plant recruitment, but ants suppressed exotic recruitment far more than natives (89% of exotic species vs. 22% of natives). Seed size predicted ant impacts on recruitment independent of origins, with ant preference for smaller seeds resulting in smaller seeded plant species being heavily suppressed. The disproportionate effects of provenance arose because exotics had generally smaller seeds than natives. Exotics also exhibited greater emergence and earlier peak emergence than natives in the absence of ants. However, when ants had access to seeds, these potential advantages of exotics were negated due to the filtering bias against exotics. The differences in traits we observed between exotics and natives suggest that higher-order introduction filters or regional processes preselected for certain exotic traits that then interacted with the local seed predation filter. Our results suggest that the interactions between local filters and species traits can predict invasion outcomes, but understanding the role of provenance will require quantifying filtering processes at multiple hierarchical scales and evaluating interactions between filters. PMID:25099535

Reciprocal Effects of Litter from Exotic and Congeneric Native Plant Species via Soil Nutrients

PubMed Central

Meisner, Annelein; de Boer, Wietse; Cornelissen, Johannes H. C.; van der Putten, Wim H.

2012-01-01

Invasive exotic plant species are often expected to benefit exclusively from legacy effects of their litter inputs on soil processes and nutrient availability. However, there are relatively few experimental tests determining how litter of exotic plants affects their own growth conditions compared to congeneric native plant species. Here, we test how the legacy of litter from three exotic plant species affects their own performance in comparison to their congeneric natives that co-occur in the invaded habitat. We also analyzed litter effects on soil processes. In all three comparisons, soil with litter from exotic plant species had the highest respiration rates. In two out of the three exotic-native species comparisons, soil with litter from exotic plant species had higher inorganic nitrogen concentrations than their native congener, which was likely due to higher initial litter quality of the exotics. When litter from an exotic plant species had a positive effect on itself, it also had a positive effect on its native congener. We conclude that exotic plant species develop a legacy effect in soil from the invaded range through their litter inputs. This litter legacy effect results in altered soil processes that can promote both the exotic plant species and their native congener. PMID:22359604

Soil Seed Bank Responses to Postfire Herbicide and Native Seeding Treatments Designed to Control Bromus tectorum in a Pinyon–Juniper Woodland at Zion National Park, USA

USGS Publications Warehouse

Brooks, Matthew L.; Hondo Brisbin, graduate student; Andrea Thode, Associate Professor; Karen Weber, graduate student

2013-01-01

The continued threat of an invasive, annual brome (Bromus) species in the western United States has created the need for integrated approaches to postfire restoration. Additionally, the high germination rate, high seed production, and seed bank carryover of annual bromes points to the need to assay soil seed banks as part of monitoring programs. We sampled the soil seed bank to help assess the effectiveness of treatments utilizing the herbicide Plateau® (imazapic) and a perennial native seed mix to control annual Bromus species and enhance perennial native plant establishment following a wildfire in Zion National Park, Utah. This study is one of few that have monitored the effects of imazapic and native seeding on a soil seed bank community and the only one that we know of that has done so in a pinyon–juniper woodland. The study made use of untreated, replicated controls, which is not common for seed bank studies. One year posttreatment, Bromus was significantly reduced in plots sprayed with herbicide. By the second year posttreatment, the effects of imazapic were less evident and convergence with the controls was evident. Emergence of seeded species was low for the duration of the study. Dry conditions and possible interactions with imazapic probably contributed to the lack of emergence of seeded native species. The perennial grass sand dropseed outperformed the other species included in the seed mix. We also examined how the treatments affected the soil seed bank community as a whole. We found evidence that the herbicide was reducing several native annual forbs and one nonnative annual forb. However, overall effects on the community were not significant. The results of our study were similar to what others have found in that imazapic is effective in providing a short-term reduction in Bromus density, although it can impact emergence of nontarget species.

Predicting invasion in grassland ecosystems: is exotic dominance the real embarrassment of richness?

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

Seabloom, Eric W.; Borer, Elizabeth T.; Buckley, Yvonne

2013-10-16

Invasions have increased the size of regional species pools, but are typically assumed to reduce native diversity. However, global-scale tests of this assumption have been elusive because of the focus on exotic species richness, rather than relative abundance. This is problematic because low invader richness can indicate invasion resistance by the native community or, alternatively, dominance by a single exotic species. Here, we used a globally replicated study to quantify relationships between exotic richness and abundance in grass-dominated ecosystems in 13 countries on six continents, ranging from salt marshes to alpine tundra. We tested effects of human land use, nativemore » community diversity, herbivore pressure, and nutrient limitation on exotic plant dominance. Despite its widespread use, exotic richness was a poor proxy for exotic dominance at low exotic richness, because sites that contained few exotic species ranged from relatively pristine (low exotic richness and cover) to almost completely exotic-dominated ones (low exotic richness but high exotic cover). Both exotic cover and richness were predicted by native plant diversity (native grass richness) and land use (distance to cultivation). Although climate was important for predicting both exotic cover and richness, climatic factors predicting cover (precipitation variability) differed from those predicting richness (maximum temperature and mean temperature in the wettest quarter). Herbivory and nutrient limitation did not predict exotic richness or cover. Exotic dominance was greatest in areas with low native grass richness at the site- or regional-scale. Although this could reflect native grass displacement, a lack of biotic resistance is a more likely explanation, given that grasses comprise the most aggressive invaders. These findings underscore the need to move beyond richness as a surrogate for the extent of invasion, because this metric confounds monodominance with invasion resistance. Monitoring species’ relative abundance will more rapidly advance our understanding of invasions.« less

Second Language Processing in Reading and Translation

ERIC Educational Resources Information Center

Lim, Jung Hyun

2011-01-01

The purpose of this dissertation is to investigate the processing mechanisms of non-native English speakers at both the sentence level and the morphological level, addressing the issue of whether adult second language (L2) learners qualitatively differ from native speakers in processing linguistic input. Using psycholinguistic on-line techniques…

Genome instabilities arising from ribonucleotides in DNA.

PubMed

Klein, Hannah L

2017-08-01

Genomic DNA is transiently contaminated with ribonucleotide residues during the process of DNA replication through misincorporation by the replicative DNA polymerases α, δ and ε, and by the normal replication process on the lagging strand, which uses RNA primers. These ribonucleotides are efficiently removed during replication by RNase H enzymes and the lagging strand synthesis machinery. However, when ribonucleotides remain in DNA they can distort the DNA helix, affect machineries for DNA replication, transcription and repair, and can stimulate genomic instabilities which are manifest as increased mutation, recombination and chromosome alterations. The genomic instabilities associated with embedded ribonucleotides are considered here, along with a discussion of the origin of the lesions that stimulate particular classes of instabilities. Copyright © 2017 Elsevier B.V. All rights reserved.

G-Quadruplexes in DNA Replication: A Problem or a Necessity?

PubMed

Valton, Anne-Laure; Prioleau, Marie-Noëlle

2016-11-01

DNA replication is a highly regulated process that ensures the correct duplication of the genome at each cell cycle. A precise cell type-specific temporal program controls the duplication of complex vertebrate genomes in an orderly manner. This program is based on the regulation of both replication origin firing and replication fork progression. G-quadruplexes (G4s), DNA secondary structures displaying noncanonical Watson-Crick base pairing, have recently emerged as key controllers of genome duplication. Here we discuss the various means by which G4s affect this fundamental cellular process. Copyright © 2016 Elsevier Ltd. All rights reserved.

Replication and Pedagogy in the History of Psychology V: The Metronome and Wilhelm Wundt's Search for the Components of Consciousness

NASA Astrophysics Data System (ADS)

Ayala, Christopher; Borawski, Steven; Miller, Jonathon

2008-05-01

Wilhelm Wundt (1832 1920) believed that consciousness was represented by the interconnection of psychical processes comprised of temporal elements and compounds. To explore these processes, Wundt used a metronome to measure the amount of information that passed into consciousness across time. The current project replicated some of his procedures, to better understand the role of introspection and the complexity of the metronome task for experimenters and observers. The results of the replication were mixed, but the replication helped provide insights into Wundt’s procedures and their relationship to his theories.

Perturbation of ribosome biogenesis drives cells into senescence through 5S RNP-mediated p53 activation.

PubMed

Nishimura, Kazuho; Kumazawa, Takuya; Kuroda, Takao; Katagiri, Naohiro; Tsuchiya, Mai; Goto, Natsuka; Furumai, Ryohei; Murayama, Akiko; Yanagisawa, Junn; Kimura, Keiji

2015-03-03

The 5S ribonucleoprotein particle (RNP) complex, consisting of RPL11, RPL5, and 5S rRNA, is implicated in p53 regulation under ribotoxic stress. Here, we show that the 5S RNP contributes to p53 activation and promotes cellular senescence in response to oncogenic or replicative stress. Oncogenic stress accelerates rRNA transcription and replicative stress delays rRNA processing, resulting in RPL11 and RPL5 accumulation in the ribosome-free fraction, where they bind MDM2. Experimental upregulation of rRNA transcription or downregulation of rRNA processing, mimicking the nucleolus under oncogenic or replicative stress, respectively, also induces RPL11-mediated p53 activation and cellular senescence. We demonstrate that exogenous expression of certain rRNA-processing factors rescues the processing defect, attenuates p53 accumulation, and increases replicative lifespan. To summarize, the nucleolar-5S RNP-p53 pathway functions as a senescence inducer in response to oncogenic and replicative stresses. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Lexical Encoding of L2 Tones: The Role of L1 Stress, Pitch Accent and Intonation

ERIC Educational Resources Information Center

Braun, Bettina; Galts, Tobias; Kabak, Baris

2014-01-01

Native language prosodic structure is known to modulate the processing of non-native suprasegmental information. It has been shown that native speakers of French, a language without lexical stress, have difficulties storing non-native stress contrasts. We investigated whether the ability to store lexical tone (as in Mandarin Chinese) also depends…

An Authentic Voice in the Technocratic Wilderness: Alaskan Natives and the "Tundra Times."

ERIC Educational Resources Information Center

Daley, Patrick; James, Beverly

1986-01-01

Examines a pair of critical challenges to the cultural integrity of Alaskan Natives around 1960 as pivotal episodes in the process of native resistance to U. S. dominance. Historically evaluates the fragility of native culture in terms of the political, scientific, and economic interests expressed in the mainstream Alaskan press, particularly the…

Mathematics and Science Curricula in Elementary and Secondary Education for American Indian and Alaska Native Students.

ERIC Educational Resources Information Center

Preston, Vera

Issues related to the improvement of mathematics and science education pertain to Native students as well as to the general population. Native students are most successful at tasks that use visual and spatial abilities and that involve simultaneous processing. Instruction should build on Native students' strengths. Experiential learning and…

Conversion of native terrestrial ecosystems in Hawai‘i to novel grazing systems: a review

USGS Publications Warehouse

Leopold, Christina R.; Hess, Steven C.

2017-01-01

The remote oceanic islands of Hawai‘i exemplify the transformative effects that non-native herbivorous mammals can bring to isolated terrestrial ecosystems. We reviewed published literature containing systematically collected, analyzed, and peer-reviewed original data specifically addressing direct effects of non-native hoofed mammals (ungulates) on terrestrial ecosystems, and indirect effects and interactions on ecosystem processes in Hawai‘i. The effects of ungulates on native vegetation and ecosystems were addressed in 58 original studies and mostly showed strong short-term regeneration of dominant native trees and understory ferns after ungulate removal, but unassisted recovery was dependent on the extent of previous degradation. Ungulates were associated with herbivory, bark-stripping, disturbance by hoof action, soil erosion, enhanced nutrient cycling from the interaction of herbivory and grasses, and increased pyrogenicity and competition between native plants and pasture grasses. No studies demonstrated that ungulates benefitted native ecosystems except in short-term fire-risk reduction. However, non-native plants became problematic and continued to proliferate after release from herbivory, including at least 11 species of non-native pasture grasses that had become established prior to ungulate removal. Competition from non-native grasses inhibited native species regeneration where degradation was extensive. These processes have created novel grazing systems which, in some cases, have irreversibly altered Hawaii’s terrestrial ecology. Non-native plant control and outplanting of rarer native species will be necessary for recovery where degradation has been extensive. Lack of unassisted recovery in some locations should not be construed as a reason to not attempt restoration of other ecosystems.

Modeling invasive alien plant species in river systems: Interaction with native ecosystem engineers and effects on hydro-morphodynamic processes

NASA Astrophysics Data System (ADS)

van Oorschot, M.; Kleinhans, M. G.; Geerling, G. W.; Egger, G.; Leuven, R. S. E. W.; Middelkoop, H.

2017-08-01

Invasive alien plant species negatively impact native plant communities by out-competing species or changing abiotic and biotic conditions in their introduced range. River systems are especially vulnerable to biological invasions, because waterways can function as invasion corridors. Understanding interactions of invasive and native species and their combined effects on river dynamics is essential for developing cost-effective management strategies. However, numerical models for simulating long-term effects of these processes are lacking. This paper investigates how an invasive alien plant species affects native riparian vegetation and hydro-morphodynamics. A morphodynamic model has been coupled to a dynamic vegetation model that predicts establishment, growth and mortality of riparian trees. We introduced an invasive alien species with life-history traits based on Japanese Knotweed (Fallopia japonica), and investigated effects of low- and high propagule pressure on invasion speed, native vegetation and hydro-morphodynamic processes. Results show that high propagule pressure leads to a decline in native species cover due to competition and the creation of unfavorable native colonization sites. With low propagule pressure the invader facilitates native seedling survival by creating favorable hydro-morphodynamic conditions at colonization sites. With high invader abundance, water levels are raised and sediment transport is reduced during the growing season. In winter, when the above-ground invader biomass is gone, results are reversed and the floodplain is more prone to erosion. Invasion effects thus depend on seasonal above- and below ground dynamic vegetation properties and persistence of the invader, on the characteristics of native species it replaces, and the combined interactions with hydro-morphodynamics.

INITIATION AND REGULATION OF PARAMYXOVIRUS TRANSCRIPTION AND REPLICATION

PubMed Central

Noton, Sarah L.; Fearns, Rachel

2015-01-01

The paramyxovirus family has a genome consisting of a single strand of negative sense RNA. This genome acts as a template for two distinct processes: transcription to generate subgenomic, capped and polyadenylated mRNAs, and genome replication. These viruses only encode one polymerase. Thus, an intriguing question is, how does the viral polymerase initiate and become committed to either transcription or replication? By answering this we can begin to understand how these two processes are regulated. In this review article, we present recent findings from studies on the paramyxovirus, respiratory syncytial virus, which show how its polymerase is able to initiate transcription and replication from a single promoter. We discuss how these findings apply to other paramyxoviruses. Then, we examine how trans-acting proteins and promoter secondary structure might serve to regulate transcription and replication during different phases of the paramyxovirus replication cycle. PMID:25683441

Initiation and regulation of paramyxovirus transcription and replication.

PubMed

Noton, Sarah L; Fearns, Rachel

2015-05-01

The paramyxovirus family has a genome consisting of a single strand of negative sense RNA. This genome acts as a template for two distinct processes: transcription to generate subgenomic, capped and polyadenylated mRNAs, and genome replication. These viruses only encode one polymerase. Thus, an intriguing question is, how does the viral polymerase initiate and become committed to either transcription or replication? By answering this we can begin to understand how these two processes are regulated. In this review article, we present recent findings from studies on the paramyxovirus, respiratory syncytial virus, which show how its polymerase is able to initiate transcription and replication from a single promoter. We discuss how these findings apply to other paramyxoviruses. Then, we examine how trans-acting proteins and promoter secondary structure might serve to regulate transcription and replication during different phases of the paramyxovirus replication cycle. Copyright © 2015 Elsevier Inc. All rights reserved.

Strategic role of the ubiquitin-dependent segregase p97 (VCP or Cdc48) in DNA replication.

PubMed

Ramadan, Kristijan; Halder, Swagata; Wiseman, Katherine; Vaz, Bruno

2017-02-01

Genome amplification (DNA synthesis) is one of the most demanding cellular processes in all proliferative cells. The DNA replication machinery (also known as the replisome) orchestrates genome amplification during S-phase of the cell cycle. Genetic material is particularly vulnerable to various events that can challenge the replisome during its assembly, activation (firing), progression (elongation) and disassembly from chromatin (termination). Any disturbance of the replisome leads to stalling of the DNA replication fork and firing of dormant replication origins, a process known as DNA replication stress. DNA replication stress is considered to be one of the main causes of sporadic cancers and other pathologies related to tissue degeneration and ageing. The mechanisms of replisome assembly and elongation during DNA synthesis are well understood. However, once DNA synthesis is complete, the process of replisome disassembly, and its removal from chromatin, remains unclear. In recent years, a growing body of evidence has alluded to a central role in replisome regulation for the ubiquitin-dependent protein segregase p97, also known as valosin-containing protein (VCP) in metazoans and Cdc48 in lower eukaryotes. By orchestrating the spatiotemporal turnover of the replisome, p97 plays an essential role in DNA replication. In this review, we will summarise our current knowledge about how p97 controls the replisome from replication initiation, to elongation and finally termination. We will also further examine the more recent findings concerning the role of p97 and how mutations in p97 cofactors, also known as adaptors, cause DNA replication stress induced genomic instability that leads to cancer and accelerated ageing. To our knowledge, this is the first comprehensive review concerning the mechanisms involved in the regulation of DNA replication by p97.

Collective Framework and Performance Optimizations to Open MPI for Cray XT Platforms

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

Ladd, Joshua S; Gorentla Venkata, Manjunath; Shamis, Pavel

2011-01-01

The performance and scalability of collective operations plays a key role in the performance and scalability of many scientific applications. Within the Open MPI code base we have developed a general purpose hierarchical collective operations framework called Cheetah, and applied it at large scale on the Oak Ridge Leadership Computing Facility's Jaguar (OLCF) platform, obtaining better performance and scalability than the native MPI implementation. This paper discuss Cheetah's design and implementation, and optimizations to the framework for Cray XT 5 platforms. Our results show that the Cheetah's Broadcast and Barrier perform better than the native MPI implementation. For medium data,more » the Cheetah's Broadcast outperforms the native MPI implementation by 93% for 49,152 processes problem size. For small and large data, it out performs the native MPI implementation by 10% and 9%, respectively, at 24,576 processes problem size. The Cheetah's Barrier performs 10% better than the native MPI implementation for 12,288 processes problem size.« less

The Influence of Hydroxylation on Maintaining CpG Methylation Patterns: A Hidden Markov Model Approach.

PubMed

Giehr, Pascal; Kyriakopoulos, Charalampos; Ficz, Gabriella; Wolf, Verena; Walter, Jörn

2016-05-01

DNA methylation and demethylation are opposing processes that when in balance create stable patterns of epigenetic memory. The control of DNA methylation pattern formation by replication dependent and independent demethylation processes has been suggested to be influenced by Tet mediated oxidation of 5mC. Several alternative mechanisms have been proposed suggesting that 5hmC influences either replication dependent maintenance of DNA methylation or replication independent processes of active demethylation. Using high resolution hairpin oxidative bisulfite sequencing data, we precisely determine the amount of 5mC and 5hmC and model the contribution of 5hmC to processes of demethylation in mouse ESCs. We develop an extended hidden Markov model capable of accurately describing the regional contribution of 5hmC to demethylation dynamics. Our analysis shows that 5hmC has a strong impact on replication dependent demethylation, mainly by impairing methylation maintenance.

Prevalence of Buggy Creek Virus (Togaviridae: Alphavirus) in Insect Vectors Increases Over Time in the Presence of an Invasive Avian Host

PubMed Central

Moore, Amy T.; O'Brien, Valerie A.

2012-01-01

Abstract Invasive species can disrupt natural disease dynamics by altering pathogen transmission among native hosts and vectors. The relatively recent occupancy of cliff swallow (Petrochelidon pyrrhonota) nesting colonies in western Nebraska by introduced European house sparrows (Passer domesticus) has led to yearly increases in the prevalence of an endemic arbovirus, Buggy Creek virus (BCRV), in its native swallow bug (Oeciacus vicarius) vector at sites containing both the invasive sparrow host and the native swallow host. At sites without the invasive host, no long-term changes in prevalence have occurred. The percentage of BCRV isolates exhibiting cytopathicity in Vero-cell culture assays increased significantly with year at sites with sparrows but not at swallow-only sites, suggesting that the virus is becoming more virulent to vertebrates in the presence of the invasive host. Increased BCRV prevalence in bug vectors at mixed-species colonies may reflect high virus replication rates in house sparrow hosts, resulting in frequent virus transmission between sparrows and swallow bugs. This case represents a rare empirical example of a pathogen effectively switching to an invasive host, documented in the early phases of the host's arrival in a specialized ecosystem and illustrating how an invasive species can promote long-term changes in host–parasite transmission dynamics. PMID:21923265

MECHANICAL DESIGN CRITERIA FOR INTERVERTEBRAL DISC TISSUE ENGINEERING

PubMed Central

Nerurkar, Nandan L.; Elliott, Dawn M.; Mauck, Robert L.

2009-01-01

Due to the inability of current clinical practices to restore function to degenerated intervertebral discs, the arena of disc tissue engineering has received substantial attention in recent years. Despite tremendous growth and progress in this field, translation to clinical implementation has been hindered by a lack of well-defined functional benchmarks. Because successful replacement of the disc is contingent upon replication of some or all of its complex mechanical behaviour, it is critically important that disc mechanics be well characterized in order to establish discrete functional goals for tissue engineering. In this review, the key functional signatures of the intervertebral disc are discussed and used to propose a series of native tissue benchmarks to guide the development of engineered replacement tissues. These benchmarks include measures of mechanical function under tensile, compressive and shear deformations for the disc and its substructures. In some cases, important functional measures are identified that have yet to be measured in the native tissue. Ultimately, native tissue benchmark values are compared to measurements that have been made on engineered disc tissues, identifying measures where functional equivalence was achieved, and others where there remain opportunities for advancement. Several excellent reviews exist regarding disc composition and structure, as well as recent tissue engineering strategies; therefore this review will remain focused on the functional aspects of disc tissue engineering. PMID:20080239

Adaptive restoration of river terrace vegetation through iterative experiments

USGS Publications Warehouse

Dela Cruz, Michelle P.; Beauchamp, Vanessa B.; Shafroth, Patrick B.; Decker, Cheryl E.; O’Neil, Aviva

2014-01-01

Restoration projects can involve a high degree of uncertainty and risk, which can ultimately result in failure. An adaptive restoration approach can reduce uncertainty through controlled, replicated experiments designed to test specific hypotheses and alternative management approaches. Key components of adaptive restoration include willingness of project managers to accept the risk inherent in experimentation, interest of researchers, availability of funding for experimentation and monitoring, and ability to restore sites as iterative experiments where results from early efforts can inform the design of later phases. This paper highlights an ongoing adaptive restoration project at Zion National Park (ZNP), aimed at reducing the cover of exotic annual Bromus on riparian terraces, and revegetating these areas with native plant species. Rather than using a trial-and-error approach, ZNP staff partnered with academic, government, and private-sector collaborators to conduct small-scale experiments to explicitly address uncertainties concerning biomass removal of annual bromes, herbicide application rates and timing, and effective seeding methods for native species. Adaptive restoration has succeeded at ZNP because managers accept the risk inherent in experimentation and ZNP personnel are committed to continue these projects over a several-year period. Techniques that result in exotic annual Bromus removal and restoration of native plant species at ZNP can be used as a starting point for adaptive restoration projects elsewhere in the region.

Replication in Mobile Environments

DTIC Science & Technology

2007-12-01

control number. 1. REPORT DATE 01 DEC 2007 2. REPORT TYPE N/A 3. DATES COVERED 4. TITLE AND SUBTITLE Data Replication Over Disadvantaged ...Communication, Information Processing, and Ergonomics KIE What is the Problem? Data replication among distributed databases occurring over disadvantaged

Incorporation of an invasive plant into a native insect herbivore food web

PubMed Central

Santos Pimenta, Lúcia P.; Lammers, Youri; Steenbergen, Peter J.; Flohil, Marco; Beveridge, Nils G.P.; van Duijn, Pieter T.; Meulblok, Marjolein M.; Sosef, Nils; van de Ven, Robin; Werring, Ralf; Beentjes, Kevin K.; Meijer, Kim; Vos, Rutger A.; Vrieling, Klaas; Gravendeel, Barbara; Choi, Young; Verpoorte, Robert; Smit, Chris; Beukeboom, Leo W.

2016-01-01

The integration of invasive species into native food webs represent multifarious dynamics of ecological and evolutionary processes. We document incorporation of Prunus serotina (black cherry) into native insect food webs. We find that P. serotina harbours a herbivore community less dense but more diverse than its native relative, P. padus (bird cherry), with similar proportions of specialists and generalists. While herbivory on P. padus remained stable over the past century, that on P. serotina gradually doubled. We show that P. serotina may have evolved changes in investment in cyanogenic glycosides compared with its native range. In the leaf beetle Gonioctena quinquepunctata, recently shifted from native Sorbus aucuparia to P. serotina, we find divergent host preferences on Sorbus- versus Prunus-derived populations, and weak host-specific differentiation among 380 individuals genotyped for 119 SNP loci. We conclude that evolutionary processes may generate a specialized herbivore community on an invasive plant, allowing prognoses of reduced invasiveness over time. On the basis of the results presented here, we would like to caution that manual control might have the adverse effect of a slowing down of processes of adaptation, and a delay in the decline of the invasive character of P. serotina. PMID:27190702

Influences of Native American land use on the Colonial Euro-American settlement of the South Carolina Piedmont

PubMed Central

Nelson, Donald R.

2018-01-01

We test the hypothesis that prehistoric Native American land use influenced the Euro-American settlement process in a South Carolina Piedmont landscape. Long term ecological studies demonstrate that land use legacies influence processes and trajectories in complex, coupled social and ecological systems. Native American land use likely altered the ecological and evolutionary feedback and trajectories of many North American landscapes. Yet, considerable debate revolves around the scale and extent of land use legacies of prehistoric Native Americans. At the core of this debate is the question of whether or not European colonists settled a mostly “wild” landscape or an already “humanized” landscape. We use statistical event analysis to model the effects of prehistoric Native American settlement on the rate of Colonial land grants (1749–1775). Our results reveal how abandoned Native American settlements were among the first areas claimed and homesteaded by Euro-Americans. We suggest that prehistoric land use legacies served as key focal nodes in the Colonial era settlement process. As a consequence, localized prehistoric land use legacies likely helped structure the long term, landscape- to regional-level ecological inheritances that resulted from Euro-American settlement. PMID:29596504

Influences of Native American land use on the Colonial Euro-American settlement of the South Carolina Piedmont.

PubMed

Coughlan, Michael R; Nelson, Donald R

2018-01-01

We test the hypothesis that prehistoric Native American land use influenced the Euro-American settlement process in a South Carolina Piedmont landscape. Long term ecological studies demonstrate that land use legacies influence processes and trajectories in complex, coupled social and ecological systems. Native American land use likely altered the ecological and evolutionary feedback and trajectories of many North American landscapes. Yet, considerable debate revolves around the scale and extent of land use legacies of prehistoric Native Americans. At the core of this debate is the question of whether or not European colonists settled a mostly "wild" landscape or an already "humanized" landscape. We use statistical event analysis to model the effects of prehistoric Native American settlement on the rate of Colonial land grants (1749-1775). Our results reveal how abandoned Native American settlements were among the first areas claimed and homesteaded by Euro-Americans. We suggest that prehistoric land use legacies served as key focal nodes in the Colonial era settlement process. As a consequence, localized prehistoric land use legacies likely helped structure the long term, landscape- to regional-level ecological inheritances that resulted from Euro-American settlement.

Replication and Transmission of the Novel Bovine Influenza D Virus in a Guinea Pig Model

PubMed Central

Sreenivasan, Chithra; Thomas, Milton; Sheng, Zizhang; Hause, Ben M.; Collin, Emily A.; Knudsen, David E. B.; Pillatzki, Angela; Nelson, Eric; Wang, Dan; Kaushik, Radhey S.

2015-01-01

ABSTRACT Influenza D virus (FLUDV) is a novel influenza virus that infects cattle and swine. The goal of this study was to investigate the replication and transmission of bovine FLUDV in guinea pigs. Following direct intranasal inoculation of animals, the virus was detected in nasal washes of infected animals during the first 7 days postinfection. High viral titers were obtained from nasal turbinates and lung tissues of directly inoculated animals. Further, bovine FLUDV was able to transmit from the infected guinea pigs to sentinel animals by means of contact and not by aerosol dissemination under the experimental conditions tested in this study. Despite exhibiting no clinical signs, infected guinea pigs developed seroconversion and the viral antigen was detected in lungs of animals by immunohistochemistry. The observation that bovine FLUDV replicated in the respiratory tract of guinea pigs was similar to observations described previously in studies of gnotobiotic calves and pigs experimentally infected with bovine FLUDV but different from those described previously in experimental infections in ferrets and swine with a swine FLUDV, which supported virus replication only in the upper respiratory tract and not in the lower respiratory tract, including lung. Our study established that guinea pigs could be used as an animal model for studying this newly emerging influenza virus. IMPORTANCE Influenza D virus (FLUDV) is a novel emerging pathogen with bovine as its primary host. The epidemiology and pathogenicity of the virus are not yet known. FLUDV also spreads to swine, and the presence of FLUDV-specific antibodies in humans could indicate that there is a potential for zoonosis. Our results showed that bovine FLUDV replicated in the nasal turbinate and lungs of guinea pigs at high titers and was also able to transmit from an infected animal to sentinel animals by contact. The fact that bovine FLUDV replicated productively in both the upper and lower respiratory tracts of guinea pigs, similarly to virus infection in its native host, demonstrates that guinea pigs would be a suitable model host to study the replication and transmission potential of bovine FLUDV. PMID:26378161

Replication and Transmission of the Novel Bovine Influenza D Virus in a Guinea Pig Model.

PubMed

Sreenivasan, Chithra; Thomas, Milton; Sheng, Zizhang; Hause, Ben M; Collin, Emily A; Knudsen, David E B; Pillatzki, Angela; Nelson, Eric; Wang, Dan; Kaushik, Radhey S; Li, Feng

2015-12-01

Influenza D virus (FLUDV) is a novel influenza virus that infects cattle and swine. The goal of this study was to investigate the replication and transmission of bovine FLUDV in guinea pigs. Following direct intranasal inoculation of animals, the virus was detected in nasal washes of infected animals during the first 7 days postinfection. High viral titers were obtained from nasal turbinates and lung tissues of directly inoculated animals. Further, bovine FLUDV was able to transmit from the infected guinea pigs to sentinel animals by means of contact and not by aerosol dissemination under the experimental conditions tested in this study. Despite exhibiting no clinical signs, infected guinea pigs developed seroconversion and the viral antigen was detected in lungs of animals by immunohistochemistry. The observation that bovine FLUDV replicated in the respiratory tract of guinea pigs was similar to observations described previously in studies of gnotobiotic calves and pigs experimentally infected with bovine FLUDV but different from those described previously in experimental infections in ferrets and swine with a swine FLUDV, which supported virus replication only in the upper respiratory tract and not in the lower respiratory tract, including lung. Our study established that guinea pigs could be used as an animal model for studying this newly emerging influenza virus. Influenza D virus (FLUDV) is a novel emerging pathogen with bovine as its primary host. The epidemiology and pathogenicity of the virus are not yet known. FLUDV also spreads to swine, and the presence of FLUDV-specific antibodies in humans could indicate that there is a potential for zoonosis. Our results showed that bovine FLUDV replicated in the nasal turbinate and lungs of guinea pigs at high titers and was also able to transmit from an infected animal to sentinel animals by contact. The fact that bovine FLUDV replicated productively in both the upper and lower respiratory tracts of guinea pigs, similarly to virus infection in its native host, demonstrates that guinea pigs would be a suitable model host to study the replication and transmission potential of bovine FLUDV. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Exploring the Digital Natives among Pre-Service Teachers in Turkey: A Cross-Cultural Validation of the Digital Native Assessment Scale

ERIC Educational Resources Information Center

Teo, Timothy; Kabakçi Yurdakul, Isil; Ursavas, Ömer Faruk

2016-01-01

This study aims to explore the digital natives among a sample of pre-service teachers and in the process, examine the validity of a Turkish adaptation of the digital native assessment scale (DNAS) [Teo, T., & Fan, X. (2013). "Coefficient alpha and beyond: Issues and alternatives for educational research." "The Asia-Pacific…

Can native annual forbs reduce Bromus tectorum biomass and indirectly facilitate establishment of a native perennial grass?

Treesearch

Elizabeth A. Leger; Erin M. Goergen; Tara Forbis de Queiroz

2014-01-01

Restoration is challenging in systems invaded by competitive, disturbance oriented plants, but greater success may be achieved by mimicking natural successional processes and including disturbanceoriented natives in a seed mix. We asked whether seven native annual forbs from the Great Basin Desert, USA, were capable of reducing biomass of the invasive annual grass...

Alfalfa mosaic virus replicase proteins, P1 and P2, localize to the tonoplast in the presence of virus RNA

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

Ibrahim, Amr; Present address: Genomics Facility, Agricultural Genetic Engineering Research Institute, Agricultural Research Center, Giza 12619; Hutchens, Heather M.

2012-11-25

To identify the virus components important for assembly of the Alfalfa mosaic virus replicase complex, we used live cell imaging of Arabidopsis thaliana protoplasts that expressed various virus cDNAs encoding native and GFP-fusion proteins of P1 and P2 replicase proteins and full-length virus RNAs. Expression of P1-GFP alone resulted in fluorescent vesicle-like bodies in the cytoplasm that colocalized with FM4-64, an endocytic marker, and RFP-AtVSR2, RabF2a/Rha1-mCherry, and RabF2b/Ara7-mCherry, all of which localize to multivesicular bodies (MVBs), which are also called prevacuolar compartments, that mediate traffic to the lytic vacuole. GFP-P2 was driven from the cytosol to MVBs when expressed withmore » P1 indicating that P1 recruited GFP-P2. P1-GFP localized on the tonoplast, which surrounds the vacuole, in the presence of infectious virus RNA, replication competent RNA2, or P2 and replication competent RNA1 or RNA3. This suggests that a functional replication complex containing P1, P2, and a full-length AMV RNA assembles on MVBs to traffic to the tonoplast.« less

Race and beliefs about mental health treatment among anxious primary care patients.

PubMed

Hunt, Justin; Sullivan, Greer; Chavira, Denise A; Stein, Murray B; Craske, Michelle G; Golinelli, Daniela; Roy-Byrne, Peter P; Sherbourne, Cathy D

2013-03-01

Large racial disparities in the use of mental health care persist. Differences in treatment preferences could partially explain the differences in care between minority and nonminority populations. We compared beliefs about mental illness and treatment preferences between adult African-Americans, Hispanics, Asian Americans, Native Americans, and White Americans with diagnosed anxiety disorders. Measures of beliefs about mental illness and treatment were drawn from the National Comorbidity Survey Replication and from our previous work. There were no significant differences in beliefs between the African-Americans and the White Americans. The beliefs of the Hispanics and the Native Americans were most distinctive, but the differences were small in magnitude. Across race/ethnicity, the associations between beliefs and service use were generally weak and statistically insignificant. The differences in illness beliefs and treatment preferences do not fully explain the large, persistent racial disparities in mental health care. Other crucial barriers to quality care exist in our health care system and our society as a whole.

A biomimetic three-dimensional woven composite scaffold for functional tissue engineering of cartilage

NASA Astrophysics Data System (ADS)

Moutos, Franklin T.; Freed, Lisa E.; Guilak, Farshid

2007-02-01

Tissue engineering seeks to repair or regenerate tissues through combinations of implanted cells, biomaterial scaffolds and biologically active molecules. The rapid restoration of tissue biomechanical function remains an important challenge, emphasizing the need to replicate structural and mechanical properties using novel scaffold designs. Here we present a microscale 3D weaving technique to generate anisotropic 3D woven structures as the basis for novel composite scaffolds that are consolidated with a chondrocyte-hydrogel mixture into cartilage tissue constructs. Composite scaffolds show mechanical properties of the same order of magnitude as values for native articular cartilage, as measured by compressive, tensile and shear testing. Moreover, our findings showed that porous composite scaffolds could be engineered with initial properties that reproduce the anisotropy, viscoelasticity and tension-compression nonlinearity of native articular cartilage. Such scaffolds uniquely combine the potential for load-bearing immediately after implantation in vivo with biological support for cell-based tissue regeneration without requiring cultivation in vitro.

Optimization of Native and Formaldehyde iPOND Techniques for Use in Suspension Cells.

PubMed

Wiest, Nathaniel E; Tomkinson, Alan E

2017-01-01

The isolation of proteins on nascent DNA (iPOND) technique developed by the Cortez laboratory allows a previously unparalleled ability to examine proteins associated with replicating and newly synthesized DNA in mammalian cells. Both the original, formaldehyde-based iPOND technique and a more recent derivative, accelerated native iPOND (aniPOND), have mostly been performed in adherent cell lines. Here, we describe modifications to both protocols for use with suspension cell lines. These include cell culture, pulse, and chase conditions that optimize sample recovery in both protocols using suspension cells and several key improvements to the published aniPOND technique that reduce sample loss, increase signal to noise, and maximize sample recovery. Additionally, we directly and quantitatively compare the iPOND and aniPOND protocols to test the strengths and limitations of both. Finally, we present a detailed protocol to perform the optimized aniPOND protocol in suspension cell lines. © 2017 Elsevier Inc. All rights reserved.

Membrane-bound SIV envelope trimers are immunogenic in ferrets after intranasal vaccination with a replication-competent canine distemper virus vector.

PubMed

Zhang, Xinsheng; Wallace, Olivia; Wright, Kevin J; Backer, Martin; Coleman, John W; Koehnke, Rebecca; Frenk, Esther; Domi, Arban; Chiuchiolo, Maria J; DeStefano, Joanne; Narpala, Sandeep; Powell, Rebecca; Morrow, Gavin; Boggiano, Cesar; Zamb, Timothy J; Richter King, C; Parks, Christopher L

2013-11-01

We are investigating canine distemper virus (CDV) as a vaccine vector for the delivery of HIV envelope (Env) that closely resembles the native trimeric spike. We selected CDV because it will promote vaccine delivery to lymphoid tissues, and because human exposure is infrequent, reducing potential effects of pre-existing immunity. Using SIV Env as a model, we tested a number of vector and gene insert designs. Vectors containing a gene inserted between the CDV H and L genes, which encoded Env lacking most of its cytoplasmic tail, propagated efficiently in Vero cells, expressed the immunogen on the cell surface, and incorporated the SIV glycoprotein into progeny virus particles. When ferrets were vaccinated intranasally, there were no signs of distress, vector replication was observed in the gut-associated lymphoid tissues, and the animals produced anti-SIV Env antibodies. These data show that live CDV-SIV Env vectors can safely induce anti-Env immune responses following intranasal vaccination. © 2013 Elsevier Inc. All rights reserved.

Effects of plausibility on structural priming.

PubMed

Christianson, Kiel; Luke, Steven G; Ferreira, Fernanda

2010-03-01

We report a replication and extension of Ferreira (2003), in which it was observed that native adult English speakers misinterpret passive sentences that relate implausible but not impossible semantic relationships (e.g., The angler was caught by the fish) significantly more often than they do plausible passives or plausible or implausible active sentences. In the experiment reported here, participants listened to the same plausible and implausible passive and active sentences as in Ferreira (2003), answered comprehension questions, and then orally described line drawings of simple transitive actions. The descriptions were analyzed as a measure of structural priming (Bock, 1986). Question accuracy data replicated Ferreira (2003). Production data yielded an interaction: Passive descriptions were produced more often after plausible passives and implausible actives. We interpret these results as indicative of a language processor that proceeds along differentiated morphosyntactic and semantic routes. The processor may end up adjudicating between conflicting outputs from these routes by settling on a "good enough" representation that is not completely faithful to the input.

Eukaryotic DNA Replication Fork.

PubMed

Burgers, Peter M J; Kunkel, Thomas A

2017-06-20

This review focuses on the biogenesis and composition of the eukaryotic DNA replication fork, with an emphasis on the enzymes that synthesize DNA and repair discontinuities on the lagging strand of the replication fork. Physical and genetic methodologies aimed at understanding these processes are discussed. The preponderance of evidence supports a model in which DNA polymerase ε (Pol ε) carries out the bulk of leading strand DNA synthesis at an undisturbed replication fork. DNA polymerases α and δ carry out the initiation of Okazaki fragment synthesis and its elongation and maturation, respectively. This review also discusses alternative proposals, including cellular processes during which alternative forks may be utilized, and new biochemical studies with purified proteins that are aimed at reconstituting leading and lagging strand DNA synthesis separately and as an integrated replication fork.

Legacy effects overwhelm the short-term effects of exotic plant invasion and restoration on soil microbial community structure, enzyme activities, and nitrogen cycling.

PubMed

Elgersma, Kenneth J; Ehrenfeld, Joan G; Yu, Shen; Vor, Torsten

2011-11-01

Plant invasions can have substantial consequences for the soil ecosystem, altering microbial community structure and nutrient cycling. However, relatively little is known about what drives these changes, making it difficult to predict the effects of future invasions. In addition, because most studies compare soils from uninvaded areas to long-established dense invasions, little is known about the temporal dependence of invasion impacts. We experimentally manipulated forest understory vegetation in replicated sites dominated either by exotic Japanese barberry (Berberis thunbergii), native Viburnums, or native Vacciniums, so that each vegetation type was present in each site-type. We compared the short-term effect of vegetation changes to the lingering legacy effects of the previous vegetation type by measuring soil microbial community structure (phospholipid fatty acids) and function (extracellular enzymes and nitrogen mineralization). We also replaced the aboveground litter in half of each plot with an inert substitute to determine if changes in the soil microbial community were driven by aboveground or belowground plant inputs. We found that after 2 years, the microbial community structure and function was largely determined by the legacy effect of the previous vegetation type, and was not affected by the current vegetation. Aboveground litter removal had only weak effects, suggesting that changes in the soil microbial community and nutrient cycling were driven largely by belowground processes. These results suggest that changes in the soil following either invasion or restoration do not occur quickly, but rather exhibit long-lasting legacy effects from previous belowground plant inputs.

10 CFR 74.45 - Measurements and measurement control.

Code of Federal Regulations, 2013 CFR

2013-01-01

... measurements, obtaining samples, and performing laboratory analyses for element concentration and isotope... of random error behavior. On a predetermined schedule, the program shall include, as appropriate: (i) Replicate analyses of individual samples; (ii) Analysis of replicate process samples; (iii) Replicate volume...

10 CFR 74.45 - Measurements and measurement control.

Code of Federal Regulations, 2014 CFR

2014-01-01

... measurements, obtaining samples, and performing laboratory analyses for element concentration and isotope... of random error behavior. On a predetermined schedule, the program shall include, as appropriate: (i) Replicate analyses of individual samples; (ii) Analysis of replicate process samples; (iii) Replicate volume...

10 CFR 74.45 - Measurements and measurement control.

Code of Federal Regulations, 2012 CFR

2012-01-01

... measurements, obtaining samples, and performing laboratory analyses for element concentration and isotope... of random error behavior. On a predetermined schedule, the program shall include, as appropriate: (i) Replicate analyses of individual samples; (ii) Analysis of replicate process samples; (iii) Replicate volume...

Impacts of Carpobrotus edulis (L.) N.E.Br. on the Germination, Establishment and Survival of Native Plants: A Clue for Assessing Its Competitive Strength

PubMed Central

Novoa, Ana; González, Luís

2014-01-01

Does Carpobrotus edulis have an impact on native plants? How do C. edulis’ soil residual effects affect the maintenance of native populations? What is the extent of interspecific competition in its invasion process? In order to answer those questions, we established pure and mixed cultures of native species and C. edulis on soil collected from invaded and native areas of Mediterranean coastal dunes in the Iberian Peninsula. We examined the impact of the invader on the germination, growth and survival of seeds and adult plants of two native plant species (Malcolmia littorea (L.) R.Br, and Scabiosa atropurpurea L.) growing with ramets or seeds of C. edulis. Residual effects of C. edulis on soils affected the germination process and early growth of native plants in different ways, depending on plant species and density. Interspecific competition significantly reduced the germination and early growth of native plants but this result was soil, density, timing and plant species dependent. Also, at any density of adult individuals of C. edulis, established native adult plants were not competitive. Moreover, ramets of C. edulis had a lethal effect on native plants, which died in a short period of time. Even the presence of C. edulis seedlings prevents the recruitment of native species. In conclusion, C. edulis have strong negative impacts on the germination, growth and survival of the native species M. littorea and S. atropurpurea. These impacts were highly depended on the development stages of native and invasive plants. Our findings are crucial for new strategies of biodiversity conservation in coastal habitats. PMID:25210924

Impacts of Carpobrotus edulis (L.) N.E.Br. on the germination, establishment and survival of native plants: a clue for assessing its competitive strength.

PubMed

Novoa, Ana; González, Luís

2014-01-01

Does Carpobrotus edulis have an impact on native plants? How do C. edulis' soil residual effects affect the maintenance of native populations? What is the extent of interspecific competition in its invasion process? In order to answer those questions, we established pure and mixed cultures of native species and C. edulis on soil collected from invaded and native areas of Mediterranean coastal dunes in the Iberian Peninsula. We examined the impact of the invader on the germination, growth and survival of seeds and adult plants of two native plant species (Malcolmia littorea (L.) R.Br, and Scabiosa atropurpurea L.) growing with ramets or seeds of C. edulis. Residual effects of C. edulis on soils affected the germination process and early growth of native plants in different ways, depending on plant species and density. Interspecific competition significantly reduced the germination and early growth of native plants but this result was soil, density, timing and plant species dependent. Also, at any density of adult individuals of C. edulis, established native adult plants were not competitive. Moreover, ramets of C. edulis had a lethal effect on native plants, which died in a short period of time. Even the presence of C. edulis seedlings prevents the recruitment of native species. In conclusion, C. edulis have strong negative impacts on the germination, growth and survival of the native species M. littorea and S. atropurpurea. These impacts were highly depended on the development stages of native and invasive plants. Our findings are crucial for new strategies of biodiversity conservation in coastal habitats.

Combination process of diamond machining and roll-to-roll UV-replication for thin film micro- and nanostructures

NASA Astrophysics Data System (ADS)

Väyrynen, J.; Mönkkönen, K.; Siitonen, S.

2016-09-01

Roll-to-roll (R2R) ultraviolet (UV) curable embossing replication process is a highly accurate and cost effective way to replicate large quantities of thin film polymer parts. These structures can be used for microfluidics, LED-optics, light guides, displays, cameras, diffusers, decorative, laser sensing and measuring devices. In the R2R UV-process, plastic thin film coated with UV-curable lacquer, passes through an imprinting embossing drum and is then hardened by an UV-lamp. One key element for mastering this process is the ability to manufacture a rotating drum containing micro- and nanostructures. Depending on the pattern shapes, the drum can be directly machined by diamond machining or it can be done through wafer level lithographical process. Due to the shrinkage of UV-curable lacquer, the R2R drum pattern process needs to be prototyped few times, in order to get the desired performance and shape from the R2R produced part. To speed up the prototyping and overall process we have developed a combination process where planar diamond machining patterns are being turned into a drum roller. Initially diamond machined patterns from a planar surface are replicated on a polymer sheet using UV-replication. Secondly, a nickel stamper shim is grown form the polymer sheet and at the end the stamper is turned into a roller and used in the R2R process. This process allows various micro milled, turned, grooved and ruled structures to be made at thin film products through the R2R process. In this paper, the process flow and examples of fabricating R2R embossed UVcurable thin film micro- and nanostructures from planar diamond machined patterns, is reported.

Clitic pronouns reveal the time course of processing gender and number in a second language

PubMed Central

Rossi, Eleonora; Kroll, Judith F.; Dussias, Paola E.

2014-01-01

This study investigates grammatical gender and number processing marked on clitic pronouns in native Spanish speakers and in late English-Spanish bilinguals using ERPs. Spanish clitic pronouns were chosen as a critical grammatical structure which is absent in English, and which encodes both grammatical gender and number. Number, but not grammatical gender, is present in English, making this structure a prime one to investigate second language processing. Results reveal a P600 effect in native speakers for violations of both gender and number. Late but relatively proficient English-Spanish bilinguals show a P600 effect only for number violations occurring at the clitic pronoun, but not for gender violations. However a post-hoc analysis reveals that a subset of highly proficient late bilinguals does reveal sensitivity to violations of grammatical gender marked on clitic pronouns. Taken together these results suggest that native-like processing is possible for highly proficient late second language learners for grammatical features that are not present in the speakers' native language, even when those features are encoded on a grammatical morpheme which itself is absent in the speakers' native language. PMID:25036762

Monitoring of the spatial and temporal dynamics of BER/SSBR pathway proteins, including MYH, UNG2, MPG, NTH1 and NEIL1-3, during DNA replication.

PubMed

Bj Rås, Karine Ø; Sousa, Mirta M L; Sharma, Animesh; Fonseca, Davi M; S Gaard, Caroline K; Bj Rås, Magnar; Otterlei, Marit

2017-08-21

Base lesions in DNA can stall the replication machinery or induce mutations if bypassed. Consequently, lesions must be repaired before replication or in a post-replicative process to maintain genomic stability. Base excision repair (BER) is the main pathway for repair of base lesions and is known to be associated with DNA replication, but how BER is organized during replication is unclear. Here we coupled the iPOND (isolation of proteins on nascent DNA) technique with targeted mass-spectrometry analysis, which enabled us to detect all proteins required for BER on nascent DNA and to monitor their spatiotemporal orchestration at replication forks. We demonstrate that XRCC1 and other BER/single-strand break repair (SSBR) proteins are enriched in replisomes in unstressed cells, supporting a cellular capacity of post-replicative BER/SSBR. Importantly, we identify for the first time the DNA glycosylases MYH, UNG2, MPG, NTH1, NEIL1, 2 and 3 on nascent DNA. Our findings suggest that a broad spectrum of DNA base lesions are recognized and repaired by BER in a post-replicative process. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Replication protein A: directing traffic at the intersection of replication and repair.

PubMed

Oakley, Greg G; Patrick, Steve M

2010-06-01

Since the initial discovery of replication protein A (RPA) as a DNA replication factor, much progress has been made on elucidating critical roles for RPA in other DNA metabolic pathways. RPA has been shown to be required for DNA replication, DNA repair, DNA recombination, and the DNA damage response pathway with roles in checkpoint activation. This review summarizes the current understanding of RPA structure, phosphorylation and protein-protein interactions in mediating these DNA metabolic processes.

Rational Deletion Cloze Processing Strategies: ESL and Native English.

ERIC Educational Resources Information Center

Markham, Paul L.

1987-01-01

Explores cloze sensitivity to global comprehension by means of retrospective interview techniques. No significant differences were found between English as a second language (ESL) college students (N=14) and native English-speaking students (N=14) in their processing strategies. (Author/CB)

Bidirectional clear speech perception benefit for native and high-proficiency non-native talkers and listeners: Intelligibility and accentednessa

PubMed Central

Smiljanić, Rajka; Bradlow, Ann R.

2011-01-01

This study investigated how native language background interacts with speaking style adaptations in determining levels of speech intelligibility. The aim was to explore whether native and high proficiency non-native listeners benefit similarly from native and non-native clear speech adjustments. The sentence-in-noise perception results revealed that fluent non-native listeners gained a large clear speech benefit from native clear speech modifications. Furthermore, proficient non-native talkers in this study implemented conversational-to-clear speaking style modifications in their second language (L2) that resulted in significant intelligibility gain for both native and non-native listeners. The results of the accentedness ratings obtained for native and non-native conversational and clear speech sentences showed that while intelligibility was improved, the presence of foreign accent remained constant in both speaking styles. This suggests that objective intelligibility and subjective accentedness are two independent dimensions of non-native speech. Overall, these results provide strong evidence that greater experience in L2 processing leads to improved intelligibility in both production and perception domains. These results also demonstrated that speaking style adaptations along with less signal distortion can contribute significantly towards successful native and non-native interactions. PMID:22225056

Words and pictures: An electrophysiological investigation of domain specific processing in native Chinese and English speakers

PubMed Central

Yum, Yen Na; Holcomb, Phillip J.; Grainger, Jonathan

2011-01-01

Comparisons of word and picture processing using Event-Related Potentials (ERPs) are contaminated by gross physical differences between the two types of stimuli. In the present study, we tackle this problem by comparing picture processing with word processing in an alphabetic and a logographic script, that are also characterized by gross physical differences. Native Mandarin Chinese speakers viewed pictures (line drawings) and Chinese characters (Experiment 1), native English speakers viewed pictures and English words (Experiment 2), and naïve Chinese readers (native English speakers) viewed pictures and Chinese characters (Experiment 3) in a semantic categorization task. The varying pattern of differences in the ERPs elicited by pictures and words across the three experiments provided evidence for i) script-specific processing arising between 150–200 ms post-stimulus onset, ii) domain-specific but script-independent processing arising between 200–300 ms post-stimulus onset, and iii) processing that depended on stimulus meaningfulness in the N400 time window. The results are interpreted in terms of differences in the way visual features are mapped onto higher-level representations for pictures and words in alphabetic and logographic writing systems. PMID:21439991

Investigating Auditory Processing of Syntactic Gaps with L2 Speakers Using Pupillometry

ERIC Educational Resources Information Center

Fernandez, Leigh; Höhle, Barbara; Brock, Jon; Nickels, Lyndsey

2018-01-01

According to the Shallow Structure Hypothesis (SSH), second language (L2) speakers, unlike native speakers, build shallow syntactic representations during sentence processing. In order to test the SSH, this study investigated the processing of a syntactic movement in both native speakers of English and proficient late L2 speakers of English using…

ATR-like kinase Mec1 facilitates both chromatin accessibility at DNA replication forks and replication fork progression during replication stress

PubMed Central

Rodriguez, Jairo; Tsukiyama, Toshio

2013-01-01

Faithful DNA replication is essential for normal cell division and differentiation. In eukaryotic cells, DNA replication takes place on chromatin. This poses the critical question as to how DNA replication can progress through chromatin, which is inhibitory to all DNA-dependent processes. Here, we developed a novel genome-wide method to measure chromatin accessibility to micrococcal nuclease (MNase) that is normalized for nucleosome density, the NCAM (normalized chromatin accessibility to MNase) assay. This method enabled us to discover that chromatin accessibility increases specifically at and ahead of DNA replication forks in normal S phase and during replication stress. We further found that Mec1, a key regulatory ATR-like kinase in the S-phase checkpoint, is required for both normal chromatin accessibility around replication forks and replication fork rate during replication stress, revealing novel functions for the kinase in replication stress response. These results suggest a possibility that Mec1 may facilitate DNA replication fork progression during replication stress by increasing chromatin accessibility around replication forks. PMID:23307868

Fabrication of flexible grating sensing waveguide based on nano-imprint lithography and micro-replication process

NASA Astrophysics Data System (ADS)

Liu, Yueming; Tian, Weijian; Zhang, Shaojun

2009-05-01

Soft and flexible grating sensing waveguides is urgently demanded in application of micro-bending sensing and surface distortion sensing in medical catheter and smart skin sensing unit etc. Based on Nano-imprint Lithography and micro-replication process, polymer grating waveguides with core size 4μm×20μm and pitch 0.75μm are fabricated successfully in this paper. This novel grating waveguides is soft and flexible enough for related application and with the bio-medical safe feature when used in human body catheter. Fabricated processes are presented including the fabrication of micro mould and UV-replication process, and relative skills are discussed also in this paper.

Corridors Increase Plant Species Richness at Large Scales

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

Damschen, Ellen I.; Haddad, Nick M.; Orrock,John L.

2006-09-01

Habitat fragmentation is one of the largest threats to biodiversity. Landscape corridors, which are hypothesized to reduce the negative consequences of fragmentation, have become common features of ecological management plans worldwide. Despite their popularity, there is little evidence documenting the effectiveness of corridors in preserving biodiversity at large scales. Using a large-scale replicated experiment, we showed that habitat patches connected by corridors retain more native plant species than do isolated patches, that this difference increases over time, and that corridors do not promote invasion by exotic species. Our results support the use of corridors in biodiversity conservation.

Corridors increase plant species richness at large scales.

PubMed

Damschen, Ellen I; Haddad, Nick M; Orrock, John L; Tewksbury, Joshua J; Levey, Douglas J

2006-09-01

Habitat fragmentation is one of the largest threats to biodiversity. Landscape corridors, which are hypothesized to reduce the negative consequences of fragmentation, have become common features of ecological management plans worldwide. Despite their popularity, there is little evidence documenting the effectiveness of corridors in preserving biodiversity at large scales. Using a large-scale replicated experiment, we showed that habitat patches connected by corridors retain more native plant species than do isolated patches, that this difference increases over time, and that corridors do not promote invasion by exotic species. Our results support the use of corridors in biodiversity conservation.

Alpha-Synuclein Expression Restricts RNA Viral Infections in the Brain.

PubMed

Beatman, Erica L; Massey, Aaron; Shives, Katherine D; Burrack, Kristina S; Chamanian, Mastooreh; Morrison, Thomas E; Beckham, J David

2015-12-30

We have discovered that native, neuronal expression of alpha-synuclein (Asyn) inhibits viral infection, injury, and disease in the central nervous system (CNS). Enveloped RNA viruses, such as West Nile virus (WNV), invade the CNS and cause encephalitis, yet little is known about the innate neuron-specific inhibitors of viral infections in the CNS. Following WNV infection of primary neurons, we found that Asyn protein expression is increased. The infectious titer of WNV and Venezuelan equine encephalitis virus (VEEV) TC83 in the brains of Asyn-knockout mice exhibited a mean increase of 10(4.5) infectious viral particles compared to the titers in wild-type and heterozygote littermates. Asyn-knockout mice also exhibited significantly increased virus-induced mortality compared to Asyn heterozygote or homozygote control mice. Virus-induced Asyn localized to perinuclear, neuronal regions expressing viral envelope protein and the endoplasmic reticulum (ER)-associated trafficking protein Rab1. In Asyn-knockout primary neuronal cultures, the levels of expression of ER signaling pathways, known to support WNV replication, were significantly elevated before and during viral infection compared to those in Asyn-expressing primary neuronal cultures. We propose a model in which virus-induced Asyn localizes to ER-derived membranes, modulates virus-induced ER stress signaling, and inhibits viral replication, growth, and injury in the CNS. These data provide a novel and important functional role for the expression of native alpha-synuclein, a protein that is closely associated with the development of Parkinson's disease. Neuroinvasive viruses such as West Nile virus are able to infect neurons and cause severe disease, such as encephalitis, or infection of brain tissue. Following viral infection in the central nervous system, only select neurons are infected, implying that neurons exhibit innate resistance to viral infections. We discovered that native neuronal expression of alpha-synuclein inhibited viral infection in the central nervous system. When the gene for alpha-synuclein was deleted, mice exhibited significantly decreased survival, markedly increased viral growth in the brain, and evidence of increased neuron injury. Virus-induced alpha-synuclein localized to intracellular neuron membranes, and in the absence of alpha-synuclein expression, specific endoplasmic reticulum stress signaling events were significantly increased. We describe a new neuron-specific inhibitor of viral infections in the central nervous system. Given the importance of alpha-synuclein as a cause of Parkinson's disease, these data also ascribe a novel functional role for the native expression of alpha-synuclein in the CNS. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Effect of extraction temperature on characteristics of chicken legskin gelatin

NASA Astrophysics Data System (ADS)

Sompie, M.; Triasih, A.

2018-01-01

Gelatin is a denaturalized protein that is derived from collagen by acidic or alkaline hydrolysis and is an important functional biopolymer that has a very broad application in many industrial fields. Its functional properties depend on processing conditions as well as the raw material. The objective of the research was to study effect of extraction temperature on characteristics of native chicken legskin gelatin. This study used Completely Randomized Design (CRD) with four treatments (T1 = 500C, T2 = 550C, T3 = 600C, T4 = 650C) and five replications. Statistical analysis were carried out by one Anova and the mean difference was tested using Duncan’s Multiple Range Test. The result of research indicated that, extraction temperature had significant effect (P<0.05) on yield, gel strength, viscocity and protein content of chicken legskin gelatin, but it had no significant effect (P>0.05) on water content. It was concluded that the use of extraction temperature 600C was (yields 13.75, gel strength 78.75 g bloom, viscosity 6.52 cP, protein content 84.23% and water content 6.20%).

Native language shapes automatic neural processing of speech.

PubMed

Intartaglia, Bastien; White-Schwoch, Travis; Meunier, Christine; Roman, Stéphane; Kraus, Nina; Schön, Daniele

2016-08-01

The development of the phoneme inventory is driven by the acoustic-phonetic properties of one's native language. Neural representation of speech is known to be shaped by language experience, as indexed by cortical responses, and recent studies suggest that subcortical processing also exhibits this attunement to native language. However, most work to date has focused on the differences between tonal and non-tonal languages that use pitch variations to convey phonemic categories. The aim of this cross-language study is to determine whether subcortical encoding of speech sounds is sensitive to language experience by comparing native speakers of two non-tonal languages (French and English). We hypothesized that neural representations would be more robust and fine-grained for speech sounds that belong to the native phonemic inventory of the listener, and especially for the dimensions that are phonetically relevant to the listener such as high frequency components. We recorded neural responses of American English and French native speakers, listening to natural syllables of both languages. Results showed that, independently of the stimulus, American participants exhibited greater neural representation of the fundamental frequency compared to French participants, consistent with the importance of the fundamental frequency to convey stress patterns in English. Furthermore, participants showed more robust encoding and more precise spectral representations of the first formant when listening to the syllable of their native language as compared to non-native language. These results align with the hypothesis that language experience shapes sensory processing of speech and that this plasticity occurs as a function of what is meaningful to a listener. Copyright © 2016 Elsevier Ltd. All rights reserved.

Persistence of native and exotic plants 10 years after prairie reconstruction

USGS Publications Warehouse

Larson, Diane L.; Bright, J. B.; Drobney, Pauline; Larson, Jennifer L.; Vacek, Sara

2017-01-01

Prairie reconstructions are a critical component of preservation of the imperiled tallgrass prairie ecosystem in the Midwestern United States. Sustainability of this endeavor depends on establishment of persistent cover of planted native species and resistance to noxious weeds. The goal of this study was to understand the influence of early reconstruction practices on long-term outcomes. Twelve replicates of three planting methods (dormant-season broadcast, growing-season broadcast, and growing-season drill) and three seed mix richness levels (10, 20, or 34 species), fully crossed in a completely randomized design were planted in 2005 on nine former agricultural fields located in Iowa and Minnesota. Cover by species was estimated in 2005–2007, 2010, and 2015. In 2015, cover of planted species, native nonplanted species, and exotic species were similar to those recorded in 2010. Cover of the noxious weed Cirsium arvense had also declined by an average of 49% without herbicide from a peak in 2007 to low stable levels from 2010 to 2015. Richness of planted forbs, on the other hand, were still increasing in high-richness broadcast treatments (e.g. 17–59% increase 2010–1015 in Minnesota). Two results in 2015 are reasons for concern: cover of planted species is only slightly over 50% in both Minnesota and Iowa, though with forbs still increasing, this may improve; and the cool-season exotic grasses Poa pratensis and Bromus inermis are increasing at both Minnesota and Iowa sites. Control of these invasive grasses will be necessary, but care will be needed to avoid negative impacts of control methods on natives.

Few effects of invasive plants Reynoutria japonica, Rudbeckia laciniata and Solidago gigantea on soil physical and chemical properties.

PubMed

Stefanowicz, Anna M; Stanek, Małgorzata; Nobis, Marcin; Zubek, Szymon

2017-01-01

Biological invasions are an important problem of human-induced changes at a global scale. Invasive plants can modify soil nutrient pools and element cycling, creating feedbacks that potentially stabilize current or accelerate further invasion, and prevent re-establishment of native species. The aim of this study was to compare the effects of Reynoutria japonica, Rudbeckia laciniata and Solidago gigantea, invading non-forest areas located within or outside river valleys, on soil physical and chemical parameters, including soil moisture, element concentrations, organic matter content and pH. Additionally, invasion effects on plant species number and total plant cover were assessed. The concentrations of elements in shoots and roots of invasive and native plants were also measured. Split-plot ANOVA revealed that the invasions significantly reduced plant species number, but did not affect most soil physical and chemical properties. The invasions decreased total P concentration and increased N-NO 3 concentration in soil in comparison to native vegetation, though the latter only in the case of R. japonica. The influence of invasion on soil properties did not depend on location (within- or outside valleys). The lack of invasion effects on most soil properties does not necessarily imply the lack of influence of invasive plants, but may suggest that the direction of the changes varies among replicate sites and there are no general patterns of invasion-induced alterations for these parameters. Tissue element concentrations, with the exception of Mg, did not differ between invasive and native plants, and were not related to soil element concentrations. Copyright © 2016 Elsevier B.V. All rights reserved.

Hard X-Ray and Wide Focusing Telescopes

NASA Technical Reports Server (NTRS)

Gorenstein, Paul

1998-01-01

Studies are being carried out to compare the performance of several different separation materials used in the replication process. This report presents the results obtained during the second year of a program which consists of replicating smooth, thin substrates, depositing multilayer coatings upon them, and evaluating their performance. Replication and multilayer coatings are both critically important to the development of focussing hard X-ray telescopes that function up to 100 keV. The activities of the current year include extending the comparison between sputtered amorphous carbon and evaporated gold to include sputtered as well as evaporated gold. The figure of merit being the smoothness of the replica which has a direct effect on the specular reflectivity. These results were obtained with epoxy replication, but they should be applicable to electroformed nickel, the process we expect to use for the ultimate replicated optics.

Changes in bacterial and eukaryotic communities during sewage decomposition in Mississippi river water.

PubMed

Korajkic, Asja; Parfrey, Laura Wegener; McMinn, Brian R; Baeza, Yoshiki Vazquez; VanTeuren, Will; Knight, Rob; Shanks, Orin C

2015-02-01

Microbial decay processes are one of the mechanisms whereby sewage contamination is reduced in the environment. This decomposition process involves a highly complex array of bacterial and eukaryotic communities from both sewage and ambient waters. However, relatively little is known about how these communities change due to mixing and subsequent decomposition of the sewage contaminant. We investigated decay of sewage in upper Mississippi River using Illumina sequencing of 16S and 18S rRNA gene hypervariable regions and qPCR for human-associated and general fecal Bacteroidales indicators. Mixtures of primary treated sewage and river water were placed in dialysis bags and incubated in situ under ambient conditions for seven days. We assessed changes in microbial community composition under two treatments in a replicated factorial design: sunlight exposure versus shaded and presence versus absence of native river microbiota. Initial diversity was higher in sewage compared to river water for 16S sequences, but the reverse was observed for 18S sequences. Both treatments significantly shifted community composition for eukaryotes and bacteria (P < 0.05). Data indicated that the presence of native river microbiota, rather than exposure to sunlight, accounted for the majority of variation between treatments for both 16S (R = 0.50; P > 0.001) and 18S (R = 0.91; P = 0.001) communities. A comparison of 16S sequence data and fecal indicator qPCR measurements indicated that the latter was a good predictor of overall bacterial community change over time (rho: 0.804-0.814, P = 0.001). These findings suggest that biotic interactions, such as predation by bacterivorous protozoa, can be critical factors in the decomposition of sewage in freshwater habitats and support the use of Bacteroidales genetic markers as indicators of fecal pollution. Published by Elsevier Ltd.

Multiscale analysis of replication technique efficiency for 3D roughness characterization of manufactured surfaces

NASA Astrophysics Data System (ADS)

Jolivet, S.; Mezghani, S.; El Mansori, M.

2016-09-01

The replication of topography has been generally restricted to optimizing material processing technologies in terms of statistical and single-scale features such as roughness. By contrast, manufactured surface topography is highly complex, irregular, and multiscale. In this work, we have demonstrated the use of multiscale analysis on replicates of surface finish to assess the precise control of the finished replica. Five commercial resins used for surface replication were compared. The topography of five standard surfaces representative of common finishing processes were acquired both directly and by a replication technique. Then, they were characterized using the ISO 25178 standard and multiscale decomposition based on a continuous wavelet transform, to compare the roughness transfer quality at different scales. Additionally, atomic force microscope force modulation mode was used in order to compare the resins’ stiffness properties. The results showed that less stiff resins are able to replicate the surface finish along a larger wavelength band. The method was then tested for non-destructive quality control of automotive gear tooth surfaces.

CMG helicase and DNA polymerase ε form a functional 15-subunit holoenzyme for eukaryotic leading-strand DNA replication.

PubMed

Langston, Lance D; Zhang, Dan; Yurieva, Olga; Georgescu, Roxana E; Finkelstein, Jeff; Yao, Nina Y; Indiani, Chiara; O'Donnell, Mike E

2014-10-28

DNA replication in eukaryotes is asymmetric, with separate DNA polymerases (Pol) dedicated to bulk synthesis of the leading and lagging strands. Pol α/primase initiates primers on both strands that are extended by Pol ε on the leading strand and by Pol δ on the lagging strand. The CMG (Cdc45-MCM-GINS) helicase surrounds the leading strand and is proposed to recruit Pol ε for leading-strand synthesis, but to date a direct interaction between CMG and Pol ε has not been demonstrated. While purifying CMG helicase overexpressed in yeast, we detected a functional complex between CMG and native Pol ε. Using pure CMG and Pol ε, we reconstituted a stable 15-subunit CMG-Pol ε complex and showed that it is a functional polymerase-helicase on a model replication fork in vitro. On its own, the Pol2 catalytic subunit of Pol ε is inefficient in CMG-dependent replication, but addition of the Dpb2 protein subunit of Pol ε, known to bind the Psf1 protein subunit of CMG, allows stable synthesis with CMG. Dpb2 does not affect Pol δ function with CMG, and thus we propose that the connection between Dpb2 and CMG helps to stabilize Pol ε on the leading strand as part of a 15-subunit leading-strand holoenzyme we refer to as CMGE. Direct binding between Pol ε and CMG provides an explanation for specific targeting of Pol ε to the leading strand and provides clear mechanistic evidence for how strand asymmetry is maintained in eukaryotes.

CMG helicase and DNA polymerase ε form a functional 15-subunit holoenzyme for eukaryotic leading-strand DNA replication

PubMed Central

Langston, Lance D.; Zhang, Dan; Yurieva, Olga; Georgescu, Roxana E.; Finkelstein, Jeff; Yao, Nina Y.; Indiani, Chiara; O’Donnell, Mike E.

2014-01-01

DNA replication in eukaryotes is asymmetric, with separate DNA polymerases (Pol) dedicated to bulk synthesis of the leading and lagging strands. Pol α/primase initiates primers on both strands that are extended by Pol ε on the leading strand and by Pol δ on the lagging strand. The CMG (Cdc45-MCM-GINS) helicase surrounds the leading strand and is proposed to recruit Pol ε for leading-strand synthesis, but to date a direct interaction between CMG and Pol ε has not been demonstrated. While purifying CMG helicase overexpressed in yeast, we detected a functional complex between CMG and native Pol ε. Using pure CMG and Pol ε, we reconstituted a stable 15-subunit CMG–Pol ε complex and showed that it is a functional polymerase–helicase on a model replication fork in vitro. On its own, the Pol2 catalytic subunit of Pol ε is inefficient in CMG-dependent replication, but addition of the Dpb2 protein subunit of Pol ε, known to bind the Psf1 protein subunit of CMG, allows stable synthesis with CMG. Dpb2 does not affect Pol δ function with CMG, and thus we propose that the connection between Dpb2 and CMG helps to stabilize Pol ε on the leading strand as part of a 15-subunit leading-strand holoenzyme we refer to as CMGE. Direct binding between Pol ε and CMG provides an explanation for specific targeting of Pol ε to the leading strand and provides clear mechanistic evidence for how strand asymmetry is maintained in eukaryotes. PMID:25313033

Biochemical Activities of Minute Virus of Mice Nonstructural Protein NS1 Are Modulated In Vitro by the Phosphorylation State of the Polypeptide

PubMed Central

Nüesch, Jürg P. F.; Corbau, Romuald; Tattersall, Peter; Rommelaere, Jean

1998-01-01

NS1, the 83-kDa major nonstructural protein of minute virus of mice (MVM), is a multifunctional nuclear phosphoprotein which is required in a variety of steps during progeny virus production, early as well as late during infection. NS1 is the initiator protein for viral DNA replication. It binds specifically to target DNA motifs; has site-specific single-strand nickase, intrinsic ATPase, and helicase activities; trans regulates viral and cellular promoters; and exerts cytotoxic stress on the host cell. To investigate whether these multiple activities of NS1 depend on posttranslational modifications, in particular phosphorylation, we expressed His-tagged NS1 in HeLa cells by using recombinant vaccinia viruses, dephosphorylated it at serine and threonine residues with calf intestine alkaline phosphatase, and compared the biochemical activities of the purified un(der)phosphorylated (NS1O) and the native (NS1P) polypeptides. Biochemical analyses of replicative functions of NS1O revealed a severe reduction of intrinsic helicase activity and, to a minor extent, of ATPase and nickase activities, whereas its affinity for the target DNA sequence [ACCA]2–3 was enhanced compared to that of NS1P. In the presence of endogenous protein kinases found in replication extracts, NS1O showed all functions necessary for resolution and replication of the 3′ dimer bridge, indicating reactivation of NS1O by rephosphorylation. Partial reactivation of the helicase activity was found as well when NS1O was incubated with protein kinase C. PMID:9733839

A Novel Self-Replicating Chimeric Lentivirus-Like Particle

PubMed Central

Young, Kelly R.; Madden, Victoria J.; Johnson, Philip R.; Johnston, Robert E.

2012-01-01

Successful live attenuated vaccines mimic natural exposure to pathogens without causing disease and have been successful against several viruses. However, safety concerns prevent the development of attenuated human immunodeficiency virus (HIV) as a vaccine candidate. If a safe, replicating virus vaccine could be developed, it might have the potential to offer significant protection against HIV infection and disease. Described here is the development of a novel self-replicating chimeric virus vaccine candidate that is designed to provide natural exposure to a lentivirus-like particle and to incorporate the properties of a live attenuated virus vaccine without the inherent safety issues associated with attenuated lentiviruses. The genome from the alphavirus Venezuelan equine encephalitis virus (VEE) was modified to express SHIV89.6P genes encoding the structural proteins Gag and Env. Expression of Gag and Env from VEE RNA in primate cells led to the assembly of particles that morphologically and functionally resembled lentivirus virions and that incorporated alphavirus RNA. Infection of CD4+ cells with chimeric lentivirus-like particles was specific and productive, resulting in RNA replication, expression of Gag and Env, and generation of progeny chimeric particles. Further genome modifications designed to enhance encapsidation of the chimeric virus genome and to express an attenuated simian immunodeficiency virus (SIV) protease for particle maturation improved the ability of chimeric lentivirus-like particles to propagate in cell culture. This study provides proof of concept for the feasibility of creating chimeric virus genomes that express lentivirus structural proteins and assemble into infectious particles for presentation of lentivirus immunogens in their native and functional conformation. PMID:22013035

A novel self-replicating chimeric lentivirus-like particle.

PubMed

Jurgens, Christy K; Young, Kelly R; Madden, Victoria J; Johnson, Philip R; Johnston, Robert E

2012-01-01

Successful live attenuated vaccines mimic natural exposure to pathogens without causing disease and have been successful against several viruses. However, safety concerns prevent the development of attenuated human immunodeficiency virus (HIV) as a vaccine candidate. If a safe, replicating virus vaccine could be developed, it might have the potential to offer significant protection against HIV infection and disease. Described here is the development of a novel self-replicating chimeric virus vaccine candidate that is designed to provide natural exposure to a lentivirus-like particle and to incorporate the properties of a live attenuated virus vaccine without the inherent safety issues associated with attenuated lentiviruses. The genome from the alphavirus Venezuelan equine encephalitis virus (VEE) was modified to express SHIV89.6P genes encoding the structural proteins Gag and Env. Expression of Gag and Env from VEE RNA in primate cells led to the assembly of particles that morphologically and functionally resembled lentivirus virions and that incorporated alphavirus RNA. Infection of CD4⁺ cells with chimeric lentivirus-like particles was specific and productive, resulting in RNA replication, expression of Gag and Env, and generation of progeny chimeric particles. Further genome modifications designed to enhance encapsidation of the chimeric virus genome and to express an attenuated simian immunodeficiency virus (SIV) protease for particle maturation improved the ability of chimeric lentivirus-like particles to propagate in cell culture. This study provides proof of concept for the feasibility of creating chimeric virus genomes that express lentivirus structural proteins and assemble into infectious particles for presentation of lentivirus immunogens in their native and functional conformation.

Grazing Incidence Neutron Optics

NASA Technical Reports Server (NTRS)

Gubarev, Mikhail V. (Inventor); Ramsey, Brian D. (Inventor); Engelhaupt, Darell E. (Inventor)

2013-01-01

Neutron optics based on the two-reflection geometries are capable of controlling beams of long wavelength neutrons with low angular divergence. The preferred mirror fabrication technique is a replication process with electroform nickel replication process being preferable. In the preliminary demonstration test an electroform nickel optics gave the neutron current density gain at the focal spot of the mirror at least 8 for neutron wavelengths in the range from 6 to 20.ANG.. The replication techniques can be also be used to fabricate neutron beam controlling guides.

Grazing incidence neutron optics

NASA Technical Reports Server (NTRS)

Gubarev, Mikhail V. (Inventor); Ramsey, Brian D. (Inventor); Engelhaupt, Darell E. (Inventor)

2012-01-01

Neutron optics based on the two-reflection geometries are capable of controlling beams of long wavelength neutrons with low angular divergence. The preferred mirror fabrication technique is a replication process with electroform nickel replication process being preferable. In the preliminary demonstration test an electroform nickel optics gave the neutron current density gain at the focal spot of the mirror at least 8 for neutron wavelengths in the range from 6 to 20 .ANG.. The replication techniques can be also be used to fabricate neutron beam controlling guides.

Chaperone-Assisted Protein Folding Is Critical for Yellow Fever Virus NS3/4A Cleavage and Replication.

PubMed

Bozzacco, Leonia; Yi, Zhigang; Andreo, Ursula; Conklin, Claire R; Li, Melody M H; Rice, Charles M; MacDonald, Margaret R

2016-01-06

DNAJC14, a heat shock protein 40 (Hsp40) cochaperone, assists with Hsp70-mediated protein folding. Overexpressed DNAJC14 is targeted to sites of yellow fever virus (YFV) replication complex (RC) formation, where it interacts with viral nonstructural (NS) proteins and inhibits viral RNA replication. How RCs are assembled and the roles of chaperones in this coordinated process are largely unknown. We hypothesized that chaperones are diverted from their normal cellular protein quality control function to play similar roles during viral infection. Here, we show that DNAJC14 overexpression affects YFV polyprotein processing and alters RC assembly. We monitored YFV NS2A-5 polyprotein processing by the viral NS2B-3 protease in DNAJC14-overexpressing cells. Notably, DNAJC14 mutants that did not inhibit YFV replication had minimal effects on polyprotein processing, while overexpressed wild-type DNAJC14 affected the NS3/4A and NS4A/2K cleavage sites, resulting in altered NS3-to-NS3-4A ratios. This suggests that DNAJC14's folding activity normally modulates NS3/4A/2K cleavage events to liberate appropriate levels of NS3 and NS4A and promote RC formation. We introduced amino acid substitutions at the NS3/4A site to alter the levels of the NS3 and NS4A products and examined their effects on YFV replication. Residues with reduced cleavage efficiency did not support viral RNA replication, and only revertant viruses with a restored wild-type arginine or lysine residue at the NS3/4A site were obtained. We conclude that DNAJC14 inhibition of RC formation upon DNAJC14 overexpression is likely due to chaperone dysregulation and that YFV probably utilizes DNAJC14's cochaperone function to modulate processing at the NS3/4A site as a mechanism ensuring virus replication. Flaviviruses are single-stranded RNA viruses that cause a wide range of illnesses. Upon host cell entry, the viral genome is translated on endoplasmic reticulum (ER) membranes to produce a single polyprotein, which is cleaved by host and viral proteases to generate viral proteins required for genome replication and virion production. Several studies suggest a role for molecular chaperones during these processes. While the details of chaperone roles have been elusive, in this report we show that overexpression of the ER-resident cochaperone DNAJC14 affects YFV polyprotein processing at the NS3/4A site. This work reveals that DNAJC14 modulation of NS3/4A site processing is an important mechanism to ensure virus replication. Our work highlights the importance of finely regulating flavivirus polyprotein processing. In addition, it suggests future studies to address similarities and/or differences among flaviviruses and to interrogate the precise mechanisms employed for polyprotein processing, a critical step that can ultimately be targeted for novel drug development. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Chaperone-Assisted Protein Folding Is Critical for Yellow Fever Virus NS3/4A Cleavage and Replication

PubMed Central

Bozzacco, Leonia; Yi, Zhigang; Andreo, Ursula; Conklin, Claire R.; Li, Melody M. H.; Rice, Charles M.

2016-01-01

ABSTRACT DNAJC14, a heat shock protein 40 (Hsp40) cochaperone, assists with Hsp70-mediated protein folding. Overexpressed DNAJC14 is targeted to sites of yellow fever virus (YFV) replication complex (RC) formation, where it interacts with viral nonstructural (NS) proteins and inhibits viral RNA replication. How RCs are assembled and the roles of chaperones in this coordinated process are largely unknown. We hypothesized that chaperones are diverted from their normal cellular protein quality control function to play similar roles during viral infection. Here, we show that DNAJC14 overexpression affects YFV polyprotein processing and alters RC assembly. We monitored YFV NS2A-5 polyprotein processing by the viral NS2B-3 protease in DNAJC14-overexpressing cells. Notably, DNAJC14 mutants that did not inhibit YFV replication had minimal effects on polyprotein processing, while overexpressed wild-type DNAJC14 affected the NS3/4A and NS4A/2K cleavage sites, resulting in altered NS3-to-NS3-4A ratios. This suggests that DNAJC14's folding activity normally modulates NS3/4A/2K cleavage events to liberate appropriate levels of NS3 and NS4A and promote RC formation. We introduced amino acid substitutions at the NS3/4A site to alter the levels of the NS3 and NS4A products and examined their effects on YFV replication. Residues with reduced cleavage efficiency did not support viral RNA replication, and only revertant viruses with a restored wild-type arginine or lysine residue at the NS3/4A site were obtained. We conclude that DNAJC14 inhibition of RC formation upon DNAJC14 overexpression is likely due to chaperone dysregulation and that YFV probably utilizes DNAJC14's cochaperone function to modulate processing at the NS3/4A site as a mechanism ensuring virus replication. IMPORTANCE Flaviviruses are single-stranded RNA viruses that cause a wide range of illnesses. Upon host cell entry, the viral genome is translated on endoplasmic reticulum (ER) membranes to produce a single polyprotein, which is cleaved by host and viral proteases to generate viral proteins required for genome replication and virion production. Several studies suggest a role for molecular chaperones during these processes. While the details of chaperone roles have been elusive, in this report we show that overexpression of the ER-resident cochaperone DNAJC14 affects YFV polyprotein processing at the NS3/4A site. This work reveals that DNAJC14 modulation of NS3/4A site processing is an important mechanism to ensure virus replication. Our work highlights the importance of finely regulating flavivirus polyprotein processing. In addition, it suggests future studies to address similarities and/or differences among flaviviruses and to interrogate the precise mechanisms employed for polyprotein processing, a critical step that can ultimately be targeted for novel drug development. PMID:26739057

Termination of DNA replication forks: "Breaking up is hard to do".

PubMed

Bailey, Rachael; Priego Moreno, Sara; Gambus, Agnieszka

2015-01-01

To ensure duplication of the entire genome, eukaryotic DNA replication initiates from thousands of replication origins. The replication forks move through the chromatin until they encounter forks from neighboring origins. During replication fork termination forks converge, the replisomes disassemble and topoisomerase II resolves the daughter DNA molecules. If not resolved efficiently, terminating forks result in genomic instability through the formation of pathogenic structures. Our recent findings shed light onto the mechanism of replisome disassembly upon replication fork termination. We have shown that termination-specific polyubiquitylation of the replicative helicase component - Mcm7, leads to dissolution of the active helicase in a process dependent on the p97/VCP/Cdc48 segregase. The inhibition of terminating helicase disassembly resulted in a replication termination defect. In this extended view we present hypothetical models of replication fork termination and discuss remaining and emerging questions in the DNA replication termination field.

Repetition Suppression in the Left Inferior Frontal Gyrus Predicts Tone Learning Performance.

PubMed

Asaridou, Salomi S; Takashima, Atsuko; Dediu, Dan; Hagoort, Peter; McQueen, James M

2016-06-01

Do individuals differ in how efficiently they process non-native sounds? To what extent do these differences relate to individual variability in sound-learning aptitude? We addressed these questions by assessing the sound-learning abilities of Dutch native speakers as they were trained on non-native tone contrasts. We used fMRI repetition suppression to the non-native tones to measure participants' neuronal processing efficiency before and after training. Although all participants improved in tone identification with training, there was large individual variability in learning performance. A repetition suppression effect to tone was found in the bilateral inferior frontal gyri (IFGs) before training. No whole-brain effect was found after training; a region-of-interest analysis, however, showed that, after training, repetition suppression to tone in the left IFG correlated positively with learning. That is, individuals who were better in learning the non-native tones showed larger repetition suppression in this area. Crucially, this was true even before training. These findings add to existing evidence that the left IFG plays an important role in sound learning and indicate that individual differences in learning aptitude stem from differences in the neuronal efficiency with which non-native sounds are processed. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Postaccess processes in the open vs. closed class distinction.

PubMed

Matthei, E H; Kean, M L

1989-02-01

We present the results of two auditory lexical decision experiments in which we attempted to replicate findings originally presented in Bradley (1978, Computational distinctions of vocabulary type, Ph.D. dissertation, MIT). The results obtained by Bradley were used as evidence for a processing distinction between the open and the closed class vocabularies; this distinction then used as part of an explanation for agrammatism in the comprehension and production of Broca's aphasics. In our first experiment we failed to replicate Bradley's result of frequency insensitivity in the closed class. Our second experiment, however, replicates Bradley's finding that closed class based nonwords (e.g., thanage) fail to induce interference effects in nonword decisions. We argue that our results, together with the various other reported failures to replicate Bradley's frequency insensitivity result, indicate that the open and closed classes may play distinct roles in postaccess phenomena involving the processing of morphological information but that such studies cannot address the question of whether the open vs. closed class distinction plays a role in syntactic processing.

Host cell processes that influence the intracellular survival of Legionella pneumophila.

PubMed

Shin, Sunny; Roy, Craig R

2008-06-01

Key to the pathogenesis of intracellular pathogens is their ability to manipulate host cell processes, permitting the establishment of an intracellular replicative niche. In turn, the host cell deploys defence mechanisms that limit intracellular infection. The bacterial pathogen Legionella pneumophila, the aetiological agent of Legionnaire's Disease, has evolved virulence mechanisms that allow it to replicate within protozoa, its natural host. Many of these tactics also enable L. pneumophila's survival and replication inside macrophages within a membrane-bound compartment known as the Legionella-containing vacuole. One of the virulence factors indispensable for L. pneumophila's intracellular survival is a type IV secretion system, which translocates a large repertoire of bacterial effectors into the host cell. These effectors modulate multiple host cell processes and in particular, redirect trafficking of the L. pneumophila phagosome and mediate its conversion into an ER-derived organelle competent for intracellular bacterial replication. In this review, we discuss how L. pneumophila manipulates host cells, as well as host cell processes that either facilitate or impede its intracellular survival.

Theoretical models for the regulation of DNA replication in fast-growing bacteria

NASA Astrophysics Data System (ADS)

Creutziger, Martin; Schmidt, Mischa; Lenz, Peter

2012-09-01

Growing in always changing environments, Escherichia coli cells are challenged by the task to coordinate growth and division. In particular, adaption of their growth program to the surrounding medium has to guarantee that the daughter cells obtain fully replicated chromosomes. Replication is therefore to be initiated at the right time, which is particularly challenging in media that support fast growth. Here, the mother cell initiates replication not only for the daughter but also for the granddaughter cells. This is possible only if replication occurs from several replication forks that all need to be correctly initiated. Despite considerable efforts during the last 40 years, regulation of this process is still unknown. Part of the difficulty arises from the fact that many details of the relevant molecular processes are not known. Here, we develop a novel theoretical strategy for dealing with this general problem: instead of analyzing a single model, we introduce a wide variety of 128 different models that make different assumptions about the unknown processes. By comparing the predictions of these models we are able to identify the key quantities that allow the experimental discrimination of the different models. Analysis of these quantities yields that out of the 128 models 94 are not consistent with available experimental data. From the remaining 34 models we are able to conclude that mass growth and DNA replication need either to be truly coupled, by coupling DNA replication initiation to the event of cell division, or to the amount of accumulated mass. Finally, we make suggestions for experiments to further reduce the number of possible regulation scenarios.

Dissociation of working memory processing associated with native and second languages: PET investigation.

PubMed

Kim, Jae-Jin; Kim, Myung Sun; Lee, Jae Sung; Lee, Dong Soo; Lee, Myung Chul; Kwon, Jun Soo

2002-04-01

Verbal working memory plays a significant role in language comprehension and problem-solving. The prefrontal cortex has been suggested as a critical area in working memory. Given that domain-specific dissociations of working memory may exist within the prefrontal cortex, it is possible that there may also be further functional divisions within the verbal working memory processing. While differences in the areas of the brain engaged in native and second languages have been demonstrated, little is known about the dissociation of verbal working memory associated with native and second languages. We have used H2(15)O positron emission tomography in 14 normal subjects in order to identify the neural correlates selectively involved in working memory of native (Korean) and second (English) languages. All subjects were highly proficient in the native language but poorly proficient in the second language. Cognitive tasks were a two-back task for three kinds of visually presented objects: simple pictures, English words, and Korean words. The anterior portion of the right dorsolateral prefrontal cortex and the left superior temporal gyrus were activated in working memory for the native language, whereas the posterior portion of the right dorsolateral prefrontal cortex and the left inferior temporal gyrus were activated in working memory for the second language. The results suggest that the right dorsolateral prefrontal cortex and left temporal lobe may be organized into two discrete, language-related functional systems. Internal phonological processing seems to play a predominant role in working memory processing for the native language with a high proficiency, whereas visual higher order control does so for the second language with a low proficiency. (C)2002 Elsevier Science (USA).

7 CFR 1780.49 - Rural or Native Alaskan villages.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 12 2010-01-01 2010-01-01 false Rural or Native Alaskan villages. 1780.49 Section..., DEPARTMENT OF AGRICULTURE (CONTINUED) WATER AND WASTE LOANS AND GRANTS Loan and Grant Application Processing § 1780.49 Rural or Native Alaskan villages. (a) General. (1) This section contains regulations for...

Education and the Native American.

ERIC Educational Resources Information Center

Iannucilli, Mary V.

Traditionally, Native Americans educated their children through the oral transmission of beliefs and values. Christian missions dominated Indian education from the 16th to the 19th century and began the process of erasing Native American identity and culture. After the Civil War, control of 73 Indian agencies was assigned to 13 religious…

H4K20me0 marks post-replicative chromatin and recruits the TONSL₋MMS22L DNA repair complex

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

Saredi, Giulia; Huang, Hongda; Hammond, Colin M.

Here, we report that after DNA replication, chromosomal processes including DNA repair and transcription take place in the context of sister chromatids. While cell cycle regulation can guide these processes globally, mechanisms to distinguish pre- and post-replicative states locally remain unknown. In this paper we reveal that new histones incorporated during DNA replication provide a signature of post-replicative chromatin, read by the human TONSL–MMS22L 1, 2, 3, 4 homologous recombination complex. We identify the TONSL ankyrin repeat domain (ARD) as a reader of histone H4 tails unmethylated at K20 (H4K20me0), which are specific to new histones incorporated during DNA replicationmore » and mark post-replicative chromatin until the G2/M phase of the cell cycle. Accordingly, TONSL–MMS22L binds new histones H3–H4 both before and after incorporation into nucleosomes, remaining on replicated chromatin until late G2/M. H4K20me0 recognition is required for TONSL–MMS22L binding to chromatin and accumulation at challenged replication forks and DNA lesions. Consequently, TONSL ARD mutants are toxic, compromising genome stability, cell viability and resistance to replication stress. Finally, together, these data reveal a histone-reader-based mechanism for recognizing the post-replicative state, offering a new angle to understand DNA repair with the potential for targeted cancer therapy.« less

Mechanisms of DNA replication termination.

PubMed

Dewar, James M; Walter, Johannes C

2017-08-01

Genome duplication is carried out by pairs of replication forks that assemble at origins of replication and then move in opposite directions. DNA replication ends when converging replication forks meet. During this process, which is known as replication termination, DNA synthesis is completed, the replication machinery is disassembled and daughter molecules are resolved. In this Review, we outline the steps that are likely to be common to replication termination in most organisms, namely, fork convergence, synthesis completion, replisome disassembly and decatenation. We briefly review the mechanism of termination in the bacterium Escherichia coli and in simian virus 40 (SV40) and also focus on recent advances in eukaryotic replication termination. In particular, we discuss the recently discovered E3 ubiquitin ligases that control replisome disassembly in yeast and higher eukaryotes, and how their activity is regulated to avoid genome instability.

Role of the Adenovirus DNA-Binding Protein in In Vitro Adeno-Associated Virus DNA Replication

PubMed Central

Ward, Peter; Dean, Frank B.; O’Donnell, Michael E.; Berns, Kenneth I.

1998-01-01

A basic question in adeno-associated virus (AAV) biology has been whether adenovirus (Ad) infection provided any function which directly promoted replication of AAV DNA. Previously in vitro assays for AAV DNA replication, using linear duplex AAV DNA as the template, uninfected or Ad-infected HeLa cell extracts, and exogenous AAV Rep protein, demonstrated that Ad infection provides a direct helper effect for AAV DNA replication. It was shown that the nature of this helper effect was to increase the processivity of AAV DNA replication. Left unanswered was the question of whether this effect was the result of cellular factors whose activity was enhanced by Ad infection or was the result of direct participation of Ad proteins in AAV DNA replication. In this report, we show that in the in vitro assay, enhancement of processivity occurs with the addition of either the Ad DNA-binding protein (Ad-DBP) or the human single-stranded DNA-binding protein (replication protein A [RPA]). Clearly Ad-DBP is present after Ad infection but not before, whereas the cellular level of RPA is not apparently affected by Ad infection. However, we have not measured possible modifications of RPA which might occur after Ad infection and affect AAV DNA replication. When the substrate for replication was an AAV genome inserted into a plasmid vector, RPA was not an effective substitute for Ad-DBP. Extracts supplemented with Ad-DBP preferentially replicated AAV sequences rather than adjacent vector sequences; in contrast, extracts supplemented with RPA preferentially replicated vector sequences. PMID:9420241

New Views on Strand Asymmetry in Insect Mitochondrial Genomes

PubMed Central

Wei, Shu-Jun; Shi, Min; Chen, Xue-Xin; Sharkey, Michael J.; van Achterberg, Cornelis; Ye, Gong-Yin; He, Jun-Hua

2010-01-01

Strand asymmetry in nucleotide composition is a remarkable feature of animal mitochondrial genomes. Understanding the mutation processes that shape strand asymmetry is essential for comprehensive knowledge of genome evolution, demographical population history and accurate phylogenetic inference. Previous studies found that the relative contributions of different substitution types to strand asymmetry are associated with replication alone or both replication and transcription. However, the relative contributions of replication and transcription to strand asymmetry remain unclear. Here we conducted a broad survey of strand asymmetry across 120 insect mitochondrial genomes, with special reference to the correlation between the signs of skew values and replication orientation/gene direction. The results show that the sign of GC skew on entire mitochondrial genomes is reversed in all species of three distantly related families of insects, Philopteridae (Phthiraptera), Aleyrodidae (Hemiptera) and Braconidae (Hymenoptera); the replication-related elements in the A+T-rich regions of these species are inverted, confirming that reversal of strand asymmetry (GC skew) was caused by inversion of replication origin; and finally, the sign of GC skew value is associated with replication orientation but not with gene direction, while that of AT skew value varies with gene direction, replication and codon positions used in analyses. These findings show that deaminations during replication and other mutations contribute more than selection on amino acid sequences to strand compositions of G and C, and that the replication process has a stronger affect on A and T content than does transcription. Our results may contribute to genome-wide studies of replication and transcription mechanisms. PMID:20856815

RepExplore: addressing technical replicate variance in proteomics and metabolomics data analysis.

PubMed

Glaab, Enrico; Schneider, Reinhard

2015-07-01

High-throughput omics datasets often contain technical replicates included to account for technical sources of noise in the measurement process. Although summarizing these replicate measurements by using robust averages may help to reduce the influence of noise on downstream data analysis, the information on the variance across the replicate measurements is lost in the averaging process and therefore typically disregarded in subsequent statistical analyses.We introduce RepExplore, a web-service dedicated to exploit the information captured in the technical replicate variance to provide more reliable and informative differential expression and abundance statistics for omics datasets. The software builds on previously published statistical methods, which have been applied successfully to biomedical omics data but are difficult to use without prior experience in programming or scripting. RepExplore facilitates the analysis by providing a fully automated data processing and interactive ranking tables, whisker plot, heat map and principal component analysis visualizations to interpret omics data and derived statistics. Freely available at http://www.repexplore.tk enrico.glaab@uni.lu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

The Regulatory Interactions of p21 and PCNA in Human Breast Cancer

DTIC Science & Technology

2002-07-01

Proliferating cell nuclear antigen (PCNA) is a multifunctional enzyme involved in multiple cellular processes including DNA replication and repair...During DNA replication , PCNA function as an accessory factor- for the DNA polymerases E arid and are part of a multiprotein DNA replication complex...a cyclin-dependent kinase inhibitor, p21WAF1 ability to inhibit DNA replication in response to DNA damage has been wall characterized. Interestingly

Fidelity of DNA Replication in Normal and Malignant Human Breast Cells.

DTIC Science & Technology

1996-08-01

In order to better understand the extent to which the intact DNA replication machinery contributes to the overall mutation frequencies observed in...normal and malignant breast cells, I have designed experiments to examine the degree of fidelity exhibited during the DNA replication process in both...normal and cancerous breast cells. To accomplish this goal I have isolated a multiprotein DNA replication complex (which we have designated the DNA

Political Status of Native Indian Women: Contradictory Implications of Canadian State Policy.

ERIC Educational Resources Information Center

Fiske, Jo-Anne

1995-01-01

Explores the ambiguous nature of Canadian Native women's political status in relation to men within the internal political processes of Indian reserve communities. Examines linkages among economic factors, domestic organization, and political process, and the disruption of Indian women's lives by state intervention (particularly federal laws…

A COMPARISON OF VECTOR AND RASTER GIS METHODS FOR CALCULATING LANDSCAPE METRICS USED IN ENVIRONMENTAL ASSESSMENTS

EPA Science Inventory

GIS-based measurements that combine native raster and native vector data are commonly used to assess environmental quality. Most of these measurements can be calculated using either raster or vector data formats and processing methods. Raster processes are more commonly used beca...

Comprehension Process of Second Language Indirect Requests.

ERIC Educational Resources Information Center

Takahashi, Satomi; Roitblat, Herbert L.

1994-01-01

Examines the comprehension of English conventional indirect requests by native English speakers and Japanese learners of English. Subjects read stories inducing either a conventional or a literal interpretation of a priming sentence. Results suggest that both native and nonnative speakers process both meanings of an ambiguous conventional request.…

Phosphorylated SIRT1 associates with replication origins to prevent excess replication initiation and preserve genomic stability

PubMed Central

Utani, Koichi; Fu, Haiqing; Jang, Sang-Min; Marks, Anna B.; Smith, Owen K.; Zhang, Ya; Redon, Christophe E.; Shimizu, Noriaki

2017-01-01

Abstract Chromatin structure affects DNA replication patterns, but the role of specific chromatin modifiers in regulating the replication process is yet unclear. We report that phosphorylation of the human SIRT1 deacetylase on Threonine 530 (T530-pSIRT1) modulates DNA synthesis. T530-pSIRT1 associates with replication origins and inhibits replication from a group of ‘dormant’ potential replication origins, which initiate replication only when cells are subject to replication stress. Although both active and dormant origins bind T530-pSIRT1, active origins are distinguished from dormant origins by their unique association with an open chromatin mark, histone H3 methylated on lysine 4. SIRT1 phosphorylation also facilitates replication fork elongation. SIRT1 T530 phosphorylation is essential to prevent DNA breakage upon replication stress and cells harboring SIRT1 that cannot be phosphorylated exhibit a high prevalence of extrachromosomal elements, hallmarks of perturbed replication. These observations suggest that SIRT1 phosphorylation modulates the distribution of replication initiation events to insure genomic stability. PMID:28549174

A Successful Replication of the River Visitor Inventory and Monitoring Process for Capacity Management

Treesearch

Kenneth Chilman; James Vogel; Greg Brown; John H. Burde

2004-01-01

This paper has 3 purposes: to discuss 1. case study research and its utility for recreation management decisionmaking, 2. the recreation visitor inventory and monitoring process developed from case study research, and 3. a successful replication of the process in a large-scale, multi-year application. Although case study research is discussed in research textbooks as...

Specific functions of the Rep and Rep׳ proteins of porcine circovirus during copy-release and rolling-circle DNA replication.

PubMed

Cheung, Andrew K

2015-07-01

The roles of two porcine circovirus replication initiator proteins, Rep and Rep׳, in generating copy-release and rolling-circle DNA replication intermediates were determined. Rep uses the supercoiled closed-circular genome (ccc) to initiate leading-strand synthesis (identical to copy-release replication) and generates the single-stranded circular (ssc) genome from the displaced DNA strand. In the process, a minus-genome primer (MGP) necessary for complementary-strand synthesis, from ssc to ccc, is synthesized. Rep׳ cleaves the growing nascent-strand to regenerate the parent ccc molecule. In the process, a Rep׳-DNA hybrid containing the right palindromic sequence (at the origin of DNA replication) is generated. Analysis of the virus particle showed that it is composed of four components: ssc, MGP, capsid protein and a novel Rep-related protein (designated Protein-3). Copyright © 2015. Published by Elsevier Inc.

Federal repatriation legislation and the role of physical anthropology in repatriation.

PubMed

Ousley, Stephen D; Billeck, William T; Hollinger, R Eric

2005-01-01

Two laws governing the disposition of Native American human remains in museums and institutions have had a profound impact on anthropology, and especially physical anthropology. In contrast to the perception of constant conflict between Native Americans and physical anthropologists, the repatriation process based on these laws has been in large part harmonious between institutions and Native peoples in the US. Despite misconceptions, the Native American Graves Protection and Repatriation Act (NAPGRA; 25 United States Code (U.S.C.) 3001-3013) was not intended to halt further research on Native American remains in museums. In fact, court decisions have affirmed that the documentation of human remains produces information no other methods can provide, and provides necessary evidence to be incorporated and weighed, along with other evidence, in evaluating "cultural affiliation," the legal term for the required connection from federally recognized Native American groups to their ancestors. The wide variety of osteological data collected at the National Museum of Natural History (NMNH), Smithsonian Institution, have proven indispensable when evaluating cultural affiliation, especially when other information sources are unhelpful or ambiguous, and provide an empirical basis for determining the ancestry of individuals whose remains will be discovered in the future. To date, the claim-driven process at the NMNH has resulted in the affiliation and repatriation of more Native American remains than any other institution in the country. Repatriation experiences at the NMNH demonstrate the changing relationships between museums and Native peoples, the continuing important contributions that physical anthropology makes to the repatriation process, and the importance of physical anthropology in understanding the recent and ancient history of North America. (c) 2005 Wiley-Liss, Inc.

Estimating replicate time shifts using Gaussian process regression

PubMed Central

Liu, Qiang; Andersen, Bogi; Smyth, Padhraic; Ihler, Alexander

2010-01-01

Motivation: Time-course gene expression datasets provide important insights into dynamic aspects of biological processes, such as circadian rhythms, cell cycle and organ development. In a typical microarray time-course experiment, measurements are obtained at each time point from multiple replicate samples. Accurately recovering the gene expression patterns from experimental observations is made challenging by both measurement noise and variation among replicates' rates of development. Prior work on this topic has focused on inference of expression patterns assuming that the replicate times are synchronized. We develop a statistical approach that simultaneously infers both (i) the underlying (hidden) expression profile for each gene, as well as (ii) the biological time for each individual replicate. Our approach is based on Gaussian process regression (GPR) combined with a probabilistic model that accounts for uncertainty about the biological development time of each replicate. Results: We apply GPR with uncertain measurement times to a microarray dataset of mRNA expression for the hair-growth cycle in mouse back skin, predicting both profile shapes and biological times for each replicate. The predicted time shifts show high consistency with independently obtained morphological estimates of relative development. We also show that the method systematically reduces prediction error on out-of-sample data, significantly reducing the mean squared error in a cross-validation study. Availability: Matlab code for GPR with uncertain time shifts is available at http://sli.ics.uci.edu/Code/GPRTimeshift/ Contact: ihler@ics.uci.edu PMID:20147305

Development of plasmid vector and electroporation condition for gene transfer in sporogenic lactic acid bacterium, Bacillus coagulans.

PubMed

Rhee, Mun Su; Kim, Jin-Woo; Qian, Yilei; Ingram, L O; Shanmugam, K T

2007-07-01

Bacillus coagulans is a sporogenic lactic acid bacterium that ferments glucose and xylose, major components of plant biomass, a potential feedstock for cellulosic ethanol. The temperature and pH for optimum rate of growth of B. coagulans (50 to 55 degrees C, pH 5.0) are very similar to that of commercially developed fungal cellulases (50 degrees C; pH 4.8). Due to this match, simultaneous saccharification and fermentation (SSF) of cellulose to products by B. coagulans is expected to require less cellulase than needed if the SSF is conducted at a sub-optimal temperature, such as 30 degrees C, the optimum for yeast, the main biocatalyst used by the ethanol industry. To fully exploit B. coagulans as a platform organism, we have developed an electroporation method to transfer plasmid DNA into this genetically recalcitrant bacterium. We also constructed a B. coagulans/E. coli shuttle vector, plasmid pMSR10 that contains the rep region from a native plasmid (pMSR0) present in B. coagulans strain P4-102B. The native plasmid, pMSR0 (6823bp), has 9 ORFs, and replicates by rolling-circle mode of replication. Plasmid pNW33N, developed for Geobacillus stearothermophilus, was also transformed into this host and stably maintained while several other Bacillus/Escherichia coli shuttle vector plasmids were not transformed into B. coagulans. The transformation efficiency of B. coagulans strain P4-102B using the plasmids pNW33N or pMSR10 was about 1.5x10(16) per mole of DNA. The availability of shuttle vectors and an electroporation method is expected to aid in genetic and metabolic engineering of B. coagulans.

It's the deceiver, not the receiver: No individual differences when detecting deception in a foreign and a native language.

PubMed

Law, Marvin K H; Jackson, Simon A; Aidman, Eugene; Geiger, Mattis; Olderbak, Sally; Kleitman, Sabina

2018-01-01

Individual differences in lie detection remain poorly understood. Bond and DePaulo's meta-analysis examined judges (receivers) who were ascertaining lies from truths and senders (deceiver) who told these lies and truths. Bond and DePaulo found that the accuracy of detecting deception depended more on the characteristics of senders rather than the judges' ability to detect lies/truths. However, for many studies in this meta-analysis, judges could hear and understand senders. This made language comprehension a potential confound. This paper presents the results of two studies. Extending previous work, in Study 1, we removed language comprehension as a potential confound by having English-speakers (N = 126, mean age = 19.86) judge the veracity of German speakers (n = 12) in a lie detection task. The twelve lie-detection stimuli included emotional and non-emotional content, and were presented in three modalities-audio only, video only, and audio and video together. The intelligence (General, Auditory, Emotional) and personality (Dark Triads and Big 6) of participants was also assessed. In Study 2, a native German-speaking sample (N = 117, mean age = 29.10) were also tested on a similar lie detection task to provide a control condition. Despite significantly extending research design and the selection of constructs employed to capture individual differences, both studies replicated Bond and DePaulo's findings. The results of Study1 indicated that removing language comprehension did not amplify individual differences in judge's ability to ascertain lies from truths. Study 2 replicated these results confirming a lack of individual differences in judge's ability to detect lies. The results of both studies suggest that Sender (deceiver) characteristics exerted a stronger influence on the outcomes of lie detection than the judge's attributes.

The Temporal Regulation of S Phase Proteins During G1

PubMed Central

Grant, Gavin D.; Cook, Jeanette G.

2018-01-01

Successful DNA replication requires intimate coordination with cell cycle progression. Prior to DNA replication initiation in S phase, a series of essential preparatory events in G1 phase ensures timely, complete, and precise genome duplication. Among the essential molecular processes are regulated transcriptional upregulation of genes that encode replication proteins, appropriate post-transcriptional control of replication factor abundance and activity, and the assembly of DNA-loaded protein complexes to license replication origins. In this chapter we describe these critical G1 events necessary for DNA replication and their regulation in the context of both cell cycle entry and cell cycle progression. PMID:29357066

From structure to mechanism—understanding initiation of DNA replication

PubMed Central

Riera, Alberto; Barbon, Marta; Noguchi, Yasunori; Reuter, L. Maximilian; Schneider, Sarah; Speck, Christian

2017-01-01

DNA replication results in the doubling of the genome prior to cell division. This process requires the assembly of 50 or more protein factors into a replication fork. Here, we review recent structural and biochemical insights that start to explain how specific proteins recognize DNA replication origins, load the replicative helicase on DNA, unwind DNA, synthesize new DNA strands, and reassemble chromatin. We focus on the minichromosome maintenance (MCM2–7) proteins, which form the core of the eukaryotic replication fork, as this complex undergoes major structural rearrangements in order to engage with DNA, regulate its DNA-unwinding activity, and maintain genome stability. PMID:28717046

Alternative Lengthening of Telomeres Mediated by Mitotic DNA Synthesis Engages Break-Induced Replication Processes

PubMed Central

Min, Jaewon; Wright, Woodring E.

2017-01-01

ABSTRACT Alternative lengthening of telomeres (ALT) is a telomerase-independent telomere maintenance mechanism that occurs in a subset of cancers. By analyzing telomerase-positive cells and their human TERC knockout-derived ALT human cell lines, we show that ALT cells harbor more fragile telomeres representing telomere replication problems. ALT-associated replication defects trigger mitotic DNA synthesis (MiDAS) at telomeres in a RAD52-dependent, but RAD51-independent, manner. Telomeric MiDAS is a conservative DNA synthesis process, potentially mediated by break-induced replication, similar to type II ALT survivors in Saccharomyces cerevisiae. Replication stresses induced by ectopic oncogenic expression of cyclin E, G-quadruplexes, or R-loop formation facilitate the ALT pathway and lead to telomere clustering, a hallmark of ALT cancers. The TIMELESS/TIPIN complex suppresses telomere clustering and telomeric MiDAS, whereas the SMC5/6 complex promotes them. In summary, ALT cells exhibit more telomere replication defects that result in persistent DNA damage responses at telomeres, leading to the engagement of telomeric MiDAS (spontaneous mitotic telomere synthesis) that is triggered by DNA replication stress, a potential driver of genomic duplications in cancer. PMID:28760773

A highly aggregated geographical distribution of forest pest invasions in the USA

Treesearch

Andrew M. Liebhold; Deborah G. McCullough; Laura M. Blackburn; Susan J. Frankel; Betsy Von Holle; Juliann E. Aukema

2013-01-01

Geographical variation in numbers of established non-native species provides clues to the underlying processes driving biological invasions. Specifically, this variation reflects landscape characteristics that drive non-native species arrival, establishment and spread. Here, we investigate spatial variation in damaging non-native forest insect and pathogen species to...

Effects of Lips and Hands on Auditory Learning of Second-Language Speech Sounds

ERIC Educational Resources Information Center

Hirata, Yukari; Kelly, Spencer D.

2010-01-01

Purpose: Previous research has found that auditory training helps native English speakers to perceive phonemic vowel length contrasts in Japanese, but their performance did not reach native levels after training. Given that multimodal information, such as lip movement and hand gesture, influences many aspects of native language processing, the…

36 CFR 219.15 - Interaction with American Indian tribes and Alaska Natives.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 36 Parks, Forests, and Public Property 2 2010-07-01 2010-07-01 false Interaction with American Indian tribes and Alaska Natives. 219.15 Section 219.15 Parks, Forests, and Public Property FOREST... Indian tribes and Alaska Natives to participate in the planning process to assist in: (1) The early...

Native Alaska's Floating Factoryship--She Plies the Pacific Ocean for Native Alaska.

ERIC Educational Resources Information Center

Wassaja, The Indian Historian, 1980

1980-01-01

Describes the history of the Al-Ind-Esk-A Sea, a floating fish processing factory representing a major hope for the economic independence of Alaska Natives residing outside the state. Discusses employment practices in effect on the ship. Notes interesting facts about the ship's engines and fittings. (SB)

University Students' Perceptions of Native and Non-Native Teachers

ERIC Educational Resources Information Center

Ustunluoglu, Evrim

2007-01-01

The employment of native teachers of English in countries where English is a foreign language, coupled with a growing concern over teaching effectiveness, has led to collecting data about teachers' performance through student feedback. Not much research has been carried out in Turkey to evaluate the process and output of language teaching by…

Proteasome-dependent degradation of replisome components regulates faithful DNA replication.

PubMed

Roseaulin, Laura C; Noguchi, Chiaki; Noguchi, Eishi

2013-08-15

The replication machinery, or the replisome, collides with a variety of obstacles during the normal process of DNA replication. In addition to damaged template DNA, numerous chromosome regions are considered to be difficult to replicate owing to the presence of DNA secondary structures and DNA-binding proteins. Under these conditions, the replication fork stalls, generating replication stress. Stalled forks are prone to collapse, posing serious threats to genomic integrity. It is generally thought that the replication checkpoint functions to stabilize the replisome and replication fork structure upon replication stress. This is important in order to allow DNA replication to resume once the problem is solved. However, our recent studies demonstrated that some replisome components undergo proteasome-dependent degradation during DNA replication in the fission yeast Schizosaccharomyces pombe. Our investigation has revealed the involvement of the SCF(Pof3) (Skp1-Cullin/Cdc53-F-box) ubiquitin ligase in replisome regulation. We also demonstrated that forced accumulation of the replisome components leads to abnormal DNA replication upon replication stress. Here we review these findings and present additional data indicating the importance of replisome degradation for DNA replication. Our studies suggest that cells activate an alternative pathway to degrade replisome components in order to preserve genomic integrity.

Mechanical design criteria for intervertebral disc tissue engineering.

PubMed

Nerurkar, Nandan L; Elliott, Dawn M; Mauck, Robert L

2010-04-19

Due to the inability of current clinical practices to restore function to degenerated intervertebral discs, the arena of disc tissue engineering has received substantial attention in recent years. Despite tremendous growth and progress in this field, translation to clinical implementation has been hindered by a lack of well-defined functional benchmarks. Because successful replacement of the disc is contingent upon replication of some or all of its complex mechanical behaviors, it is critically important that disc mechanics be well characterized in order to establish discrete functional goals for tissue engineering. In this review, the key functional signatures of the intervertebral disc are discussed and used to propose a series of native tissue benchmarks to guide the development of engineered replacement tissues. These benchmarks include measures of mechanical function under tensile, compressive, and shear deformations for the disc and its substructures. In some cases, important functional measures are identified that have yet to be measured in the native tissue. Ultimately, native tissue benchmark values are compared to measurements that have been made on engineered disc tissues, identifying where functional equivalence was achieved, and where there remain opportunities for advancement. Several excellent reviews exist regarding disc composition and structure, as well as recent tissue engineering strategies; therefore this review will remain focused on the functional aspects of disc tissue engineering. Copyright 2009 Elsevier Ltd. All rights reserved.

Fabrication and characterization of biomimetic multichanneled crosslinked-urethane-doped polyester tissue engineered nerve guides.

PubMed

Tran, Richard T; Choy, Wai Man; Cao, Hung; Qattan, Ibrahim; Chiao, Jung-Chih; Ip, Wing Yuk; Yeung, Kelvin Wai Kwok; Yang, Jian

2014-08-01

Biomimetic scaffolds that replicate the native architecture and mechanical properties of target tissues have been recently shown to be a very promising strategy to guide cellular growth and facilitate tissue regeneration. In this study, porous, soft, and elastic crosslinked urethane-doped polyester (CUPE) tissue engineered nerve guides were fabricated with multiple longitudinally oriented channels and an external non-porous sheath to mimic the native endoneurial microtubular and epineurium structure, respectively. The fabrication technique described herein is highly adaptable and allows for fine control over the resulting nerve guide architecture in terms of channel number, channel diameter, porosity, and mechanical properties. Biomimetic multichanneled CUPE guides were fabricated with various channel numbers and displayed an ultimate peak stress of 1.38 ± 0.22 MPa with a corresponding elongation at break of 122.76 ± 42.17%, which were comparable to that of native nerve tissue. The CUPE nerve guides were also evaluated in vivo for the repair of a 1 cm rat sciatic nerve defect. Although histological evaluations revealed collapse of the inner structure from CUPE TENGs, the CUPE nerve guides displayed fiber populations and densities comparable with nerve autograft controls after 8 weeks of implantation. These studies are the first report of a CUPE-based biomimetic multichanneled nerve guide and warrant future studies towards optimization of the channel geometry for use in neural tissue engineering. © 2013 Wiley Periodicals, Inc.

Control of Scar Tissue Formation in the Cornea: Strategies in Clinical and Corneal Tissue Engineering

PubMed Central

Wilson, Samantha L.; El Haj, Alicia J.; Yang, Ying

2012-01-01

Corneal structure is highly organized and unified in architecture with structural and functional integration which mediates transparency and vision. Disease and injury are the second most common cause of blindness affecting over 10 million people worldwide. Ninety percent of blindness is permanent due to scarring and vascularization. Scarring caused via fibrotic cellular responses, heals the tissue, but fails to restore transparency. Controlling keratocyte activation and differentiation are key for the inhibition and prevention of fibrosis. Ophthalmic surgery techniques are continually developing to preserve and restore vision but corneal regression and scarring are often detrimental side effects and long term continuous follow up studies are lacking or discouraging. Appropriate corneal models may lead to a reduced need for corneal transplantation as presently there are insufficient numbers or suitable tissue to meet demand. Synthetic optical materials are under development for keratoprothesis although clinical use is limited due to implantation complications and high rejection rates. Tissue engineered corneas offer an alternative which more closely mimic the morphological, physiological and biomechanical properties of native corneas. However, replication of the native collagen fiber organization and retaining the phenotype of stromal cells which prevent scar-like tissue formation remains a challenge. Careful manipulation of culture environments are under investigation to determine a suitable environment that simulates native ECM organization and stimulates keratocyte migration and generation. PMID:24955637

USP37 deubiquitinates Cdt1 and contributes to regulate DNA replication.

PubMed

Hernández-Pérez, Santiago; Cabrera, Elisa; Amoedo, Hugo; Rodríguez-Acebes, Sara; Koundrioukoff, Stephane; Debatisse, Michelle; Méndez, Juan; Freire, Raimundo

2016-10-01

DNA replication control is a key process in maintaining genomic integrity. Monitoring DNA replication initiation is particularly important as it needs to be coordinated with other cellular events and should occur only once per cell cycle. Crucial players in the initiation of DNA replication are the ORC protein complex, marking the origin of replication, and the Cdt1 and Cdc6 proteins, that license these origins to replicate by recruiting the MCM2-7 helicase. To accurately achieve its functions, Cdt1 is tightly regulated. Cdt1 levels are high from metaphase and during G1 and low in S/G2 phases of the cell cycle. This control is achieved, among other processes, by ubiquitination and proteasomal degradation. In an overexpression screen for Cdt1 deubiquitinating enzymes, we isolated USP37, to date the first ubiquitin hydrolase controlling Cdt1. USP37 overexpression stabilizes Cdt1, most likely a phosphorylated form of the protein. In contrast, USP37 knock down destabilizes Cdt1, predominantly during G1 and G1/S phases of the cell cycle. USP37 interacts with Cdt1 and is able to de-ubiquitinate Cdt1 in vivo and, USP37 is able to regulate the loading of MCM complexes onto the chromatin. In addition, downregulation of USP37 reduces DNA replication fork speed. Taken together, here we show that the deubiquitinase USP37 plays an important role in the regulation of DNA replication. Whether this is achieved via Cdt1, a central protein in this process, which we have shown to be stabilized by USP37, or via additional factors, remains to be tested. Copyright © 2016 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

A novel environmental DNA approach to quantify the cryptic invasion of non-native genotypes.

PubMed

Uchii, Kimiko; Doi, Hideyuki; Minamoto, Toshifumi

2016-03-01

The invasion of non-native species that are closely related to native species can lead to competitive elimination of the native species and/or genomic extinction through hybridization. Such invasions often become serious before they are detected, posing unprecedented threats to biodiversity. A Japanese native strain of common carp (Cyprinus carpio) has become endangered owing to the invasion of non-native strains introduced from the Eurasian continent. Here, we propose a rapid environmental DNA-based approach to quantitatively monitor the invasion of non-native genotypes. Using this system, we developed a method to quantify the relative proportion of native and non-native DNA based on a single-nucleotide polymorphism using cycling probe technology in real-time PCR. The efficiency of this method was confirmed in aquarium experiments, where the quantified proportion of native and non-native DNA in the water was well correlated to the biomass ratio of native and non-native genotypes. This method provided quantitative estimates for the proportion of native and non-native DNA in natural rivers and reservoirs, which allowed us to estimate the degree of invasion of non-native genotypes without catching and analysing individual fish. Our approach would dramatically facilitate the process of quantitatively monitoring the invasion of non-native conspecifics in aquatic ecosystems, thus revealing a promising method for risk assessment and management in biodiversity conservation. © 2015 John Wiley & Sons Ltd.

Inhibition of Poliovirus-Induced Cleavage of Cellular Protein PCBP2 Reduces the Levels of Viral RNA Replication

PubMed Central

Chase, Amanda J.; Daijogo, Sarah

2014-01-01

ABSTRACT Due to their small genome size, picornaviruses must utilize host proteins to mediate cap-independent translation and viral RNA replication. The host RNA-binding protein poly(rC) binding protein 2 (PCBP2) is involved in both processes in poliovirus infected cells. It has been shown that the viral proteinase 3CD cleaves PCBP2 and contributes to viral translation inhibition. However, cleaved PCBP2 remains active in viral RNA replication. This would suggest that both cleaved and intact forms of PCBP2 have a role in the viral RNA replication cycle. The picornavirus genome must act as a template for both translation and RNA replication. However, a template that is actively being translated cannot function as a template for RNA replication, suggesting that there is a switch in template usage from translation to RNA replication. We demonstrate that the cleavage of PCBP2 by the poliovirus 3CD proteinase is a necessary step for efficient viral RNA replication and, as such, may be important for mediating a switch in template usage from translation to RNA replication. IMPORTANCE Poliovirus, like all positive-strand RNA viruses that replicate in the cytoplasm of eukaryotic cells, uses its genomic RNA as a template for both viral protein synthesis and RNA replication. Given that these processes cannot occur simultaneously on the same template, poliovirus has evolved a mechanism(s) to facilitate the switch from using templates for translation to using them for RNA synthesis. This study explores one possible scenario for how the virus alters the functions of a host cell RNA binding protein to mediate, in part, this important transition. PMID:24371074

Variation in salinity tolerance among larval anurans: implications for community composition and the spread of an invasive, non-native species

USGS Publications Warehouse

Brown, Mary E.; Walls, Susan C.

2013-01-01

Amphibians in freshwater coastal wetlands periodically experience acute exposure to salinity from hurricane-related overwash events, as well as chronic exposure associated with rising sea levels. In a comparative experimental approach, we examined whether seven species of anuran amphibians vary in their tolerance to changes in salinity. In a laboratory study, we exposed larval Hyla cinerea (Green Treefrog), H. squirella (Squirrel Treefrog), Lithobates catesbeianus (American Bullfrog), L. sphenocephalus (Southern Leopard Frog), Anaxyrus terrestris (Southern Toad), and Gastrophryne carolinensis (Eastern Narrow-mouthed Toad) from an inland population in north central Florida, USA, and Osteopilus septentrionalis (Cuban Treefrog) tadpoles from an inland population in southwest Florida, to acute salinity for 72 h. For each species, we replicated trials in which tadpoles were exposed to salinities of 0.2 (control), 5, 10, 12, 14, and 16 ppt. For all species, tadpoles reared in the control and 5 ppt treatments had 96.7–100% survival. No individuals of G. carolinensis survived at salinities exceeding 5 ppt and no individuals of any species survived in the 14 or 16 ppt treatments. For all other native species, survival at 10 ppt ranged from 46.7 to 80%, but declined to 0% at 12 ppt (except for H. cinerea, of which only 3.3% survived at 12 ppt). In contrast, all individuals of the invasive, non-native O. septentrionalis survived exposure to a salinity of 10 ppt, and survival in this species remained relatively high at 12 ppt. Our results illustrate that the non-native O. septentrionalis has a higher salinity tolerance than the native species tested, which may contribute to its invasion potential. Moreover, species commonly associated with coastal freshwater wetlands differ in their salinity tolerances, suggesting that salt water intrusion due to storm surges and sea level rise may affect the species composition of these ecosystems.

Theoretical Implications of Contemporary Brain Science for Japanese EFL Learning

ERIC Educational Resources Information Center

Clayton, John Lloyd

2015-01-01

Recent advances in brain science show that adult native Japanese speakers utilize a different balance of language processing routes in the brain as compared to native English speakers. Biologically this represents the remarkable flexibility of the human brain to adapt universal human cognitive processes to fit the specific needs of linguistic and…

L2 Processing of Plural Inflection in English

ERIC Educational Resources Information Center

Song, Yoonsang

2015-01-01

This study investigates (1) whether late second language (L2) learners can attain native-like knowledge of English plural inflection even when their first language (L1) lacks an equivalent and (2) whether they construct hierarchically structured representations during online sentence processing like native speakers. In a self-paced reading task,…

Young Learners' Response Processes When Taking Computerized Tasks for Speaking Assessment

ERIC Educational Resources Information Center

Lee, Shinhye; Winke, Paula

2018-01-01

We investigated how young language learners process their responses on and perceive a computer-mediated, timed speaking test. Twenty 8-, 9-, and 10-year-old non-native English-speaking children (NNSs) and eight same-aged, native English-speaking children (NSs) completed seven computerized sample TOEFL® Primary™ speaking test tasks. We investigated…

Plasmid Vectors for Xylella fastidiosa Utilizing a Toxin-Antitoxin System for Stability in the Absence of Antibiotic Selection.

PubMed

Burbank, Lindsey P; Stenger, Drake C

2016-08-01

The phytopathogen Xylella fastidiosa causes disease in a variety of important crop and landscape plants. Functional genetic studies have led to a broader understanding of virulence mechanisms used by this pathogen in the grapevine host. Plasmid shuttle vectors are important tools in studies of bacterial genetics but there are only a limited number of plasmid vectors available that replicate in X. fastidiosa, and even fewer that are retained without antibiotic selection. Two plasmids are described here that show stable replication in X. fastidiosa and are effective for gene complementation both in vitro and in planta. Plasmid maintenance is facilitated by incorporation of the PemI/PemK plasmid addiction system, consisting of PemK, an endoribonuclease toxin, and its cognate antitoxin, PemI. Vector pXf20pemIK utilizes a native X. fastidiosa replication origin as well as a high-copy-number pUC origin for propagation in Escherichia coli cloning strains. Broad-host-range vector pBBR5pemIK is a medium- to low-copy-number plasmid based on the pBBR1 backbone. Both plasmids are maintained for extended periods of time in the absence of antibiotic selection, as well as up to 14 weeks in grapevine, without affecting bacterial fitness. These plasmids present an alternative to traditional complementation and expression vectors which rely on antibiotic selection for plasmid retention.

Statistical analysis of native contact formation in the folding of designed model proteins

NASA Astrophysics Data System (ADS)

Tiana, Guido; Broglia, Ricardo A.

2001-02-01

The time evolution of the formation probability of native bonds has been studied for designed sequences which fold fast into the native conformation. From this analysis a clear hierarchy of bonds emerge: (a) local, fast forming highly stable native bonds built by some of the most strongly interacting amino acids of the protein; (b) nonlocal bonds formed late in the folding process, in coincidence with the folding nucleus, and involving essentially the same strongly interacting amino acids already participating in the fast bonds; (c) the rest of the native bonds whose behavior is subordinated, to a large extent, to that of the strong local and nonlocal native contacts.

Overlap and Differences in Brain Networks Underlying the Processing of Complex Sentence Structures in Second Language Users Compared with Native Speakers.

PubMed

Weber, Kirsten; Luther, Lisa; Indefrey, Peter; Hagoort, Peter

2016-05-01

When we learn a second language later in life, do we integrate it with the established neural networks in place for the first language or is at least a partially new network recruited? While there is evidence that simple grammatical structures in a second language share a system with the native language, the story becomes more multifaceted for complex sentence structures. In this study, we investigated the underlying brain networks in native speakers compared with proficient second language users while processing complex sentences. As hypothesized, complex structures were processed by the same large-scale inferior frontal and middle temporal language networks of the brain in the second language, as seen in native speakers. These effects were seen both in activations and task-related connectivity patterns. Furthermore, the second language users showed increased task-related connectivity from inferior frontal to inferior parietal regions of the brain, regions related to attention and cognitive control, suggesting less automatic processing for these structures in a second language.

Replication of Special Education Research: Necessary but Far Too Rare

ERIC Educational Resources Information Center

Makel, Matthew C.; Plucker, Jonathan A.; Freeman, Jennifer; Lombardi, Allison; Simonsen, Brandi; Coyne, Michael

2016-01-01

Increased calls for rigor in special education have often revolved around the use of experimental research design. However, the replicability of research results is also a central tenet to the scientific research process. To assess the prevalence, success rate, and authorship history of replications in special education, we investigated the…

A Replication of Failure, Not a Failure to Replicate

ERIC Educational Resources Information Center

Holden, Gary; Barker, Kathleen; Kuppens, Sofie; Rosenberg, Gary; LeBreton, Jonathan

2015-01-01

Purpose: The increasing role of systematic reviews in knowledge production demands greater rigor in the literature search process. The performance of the Social Work Abstracts (SWA) database has been examined multiple times over the past three decades. The current study is a replication within this line of research. Method: Issue-level coverage…

High resolution approach to the native state ensemble kinetics and thermodynamics.

PubMed

Wu, Sangwook; Zhuravlev, Pavel I; Papoian, Garegin A

2008-12-15

Many biologically interesting functions such as allosteric switching or protein-ligand binding are determined by the kinetics and mechanisms of transitions between various conformational substates of the native basin of globular proteins. To advance our understanding of these processes, we constructed a two-dimensional free energy surface (FES) of the native basin of a small globular protein, Trp-cage. The corresponding order parameters were defined using two native substructures of Trp-cage. These calculations were based on extensive explicit water all-atom molecular dynamics simulations. Using the obtained two-dimensional FES, we studied the transition kinetics between two Trp-cage conformations, finding that switching process shows a borderline behavior between diffusive and weakly-activated dynamics. The transition is well-characterized kinetically as a biexponential process. We also introduced a new one-dimensional reaction coordinate for the conformational transition, finding reasonable qualitative agreement with the two-dimensional kinetics results. We investigated the distribution of all the 38 native nuclear magnetic resonance structures on the obtained FES, analyzing interactions that stabilize specific low-energy conformations. Finally, we constructed a FES for the same system but with simple dielectric model of water instead of explicit water, finding that the results were surprisingly similar in a small region centered on the native conformations. The dissimilarities between the explicit and implicit model on the larger-scale point to the important role of water in mediating interactions between amino acid residues.

Parasite-mediated predation between native and invasive amphipods.

PubMed Central

MacNeil, Calum; Dick, Jaimie T A; Hatcher, Melanie J; Terry, Rebecca S; Smith, Judith E; Dunn, Alison M

2003-01-01

Parasites can structure biological communities directly through population regulation and indirectly by processes such as apparent competition. However, the role of parasites in the process of biological invasion is less well understood and mechanisms of parasite mediation of predation among hosts are unclear. Mutual predation between native and invading species is an important factor in determining the outcome of invasions in freshwater amphipod communities. Here, we show that parasites mediate mutual intraguild predation among native and invading species and may thereby facilitate the invasion process. We find that the native amphipod Gammarus duebeni celticus is host to a microsporidian parasite, Pleistophora sp. (new species), with a frequency of infection of 0-90%. However, the parasite does not infect three invading species, G. tigrinus, G. pulex and Crangonyx pseudogracilis. In field and laboratory manipulations, we show that the parasite exhibits cryptic virulence: the parasite does not affect host fitness in single-species populations, but virulence becomes apparent when the native and invading species interact. That is, infection has no direct effect on G. d. celticus survivorship, size or fecundity; however, in mixed-species experiments, parasitized natives show a reduced capacity to prey on the smaller invading species and are more likely to be preyed upon by the largest invading species. Thus, by altering dominance relationships and hierarchies of mutual predation, parasitism strongly influences, and has the potential to change, the outcome of biological invasions. PMID:12816645

Fast and cheap fabrication of molding tools for polymer replication

NASA Astrophysics Data System (ADS)

Richter, Christiane; Kirschner, Nadine; Worgull, Matthias; Rapp, Bastian E.

2017-02-01

Polymer replication is a prerequisite for low-cost microstructure components for consumer and end user market. The production of cost-effective microstructure in polymers requires metal molding tools which are often fabricated by direct structuring methods like milling or laser machining both of which are time-consuming and cost-intensive. We present an alternative fabrication method based on replication processes which allows the cheap ( 50 €) and fast ( 12 h) replication of complex microstructures into metal. The process comprises three steps: 1. Generation of the microstructure in a photoresist via lithography. 2. Casting of the structure into a high-temperature silicone which serves as original mold for creation of the metal molding tool. 3. Melting of an eutectic alloy of Sn, Ag and Cu under light pressure directly inside of the silicone within an oven. After cooling to room temperature the metal molding tool can be used for polymer replication into conventional thermoplastic polymers. As a first example we structured polymethylmethacrylate (PMMA) foils with a thickness of 1 mm via hot embossing and feature sizes of 100 μm could be replicated with high fidelity.

Cancer therapy and replication stress: forks on the road to perdition.

PubMed

Kotsantis, Panagiotis; Jones, Rebecca M; Higgs, Martin R; Petermann, Eva

2015-01-01

Deregulated DNA replication occurs in cancer where it contributes to genomic instability. This process is a target of cytotoxic therapies. Chemotherapies exploit high DNA replication in cancer cells by modifying the DNA template or by inhibiting vital enzymatic activities that lead to slowing or stalling replication fork progression. Stalled replication forks can be converted into toxic DNA double-strand breaks resulting in cell death, i.e., replication stress. While likely crucial for many cancer treatments, replication stress is poorly understood due to its complexity. While we still know relatively little about the role of replication stress in cancer therapy, technical advances in recent years have shed new light on the effect that cancer therapeutics have on replication forks and the molecular mechanisms that lead from obstructed fork progression to cell death. This chapter will give an overview of our current understanding of replication stress in the context of cancer therapy. © 2015 Elsevier Inc. All rights reserved.

Mechanisms and regulation of DNA replication initiation in eukaryotes

PubMed Central

Parker, Matthew W.; Botchan, Michael R.; Berger, James M.

2017-01-01

Cellular DNA replication is initiated through the action of multiprotein complexes that recognize replication start sites in the chromosome (termed origins) and facilitate duplex DNA melting within these regions. In a given cell cycle, initiation occurs only once per origin and each round of replication is tightly coupled to cell division. To avoid aberrant origin firing and re-replication, eukaryotes tightly regulate two events in the initiation process: loading of the replicative helicase, MCM2-7, onto chromatin by the Origin Recognition Complex (ORC), and subsequent activation of the helicase by incorporation into a complex known as the CMG. Recent work has begun to reveal the details of an orchestrated and sequential exchange of initiation factors on DNA that give rise to a replication-competent complex, the replisome. Here we review the molecular mechanisms that underpin eukaryotic DNA replication initiation – from selecting replication start sites to replicative helicase loading and activation – and describe how these events are often distinctly regulated across different eukaryotic model organisms. PMID:28094588

Mechanisms and regulation of DNA replication initiation in eukaryotes.

PubMed

Parker, Matthew W; Botchan, Michael R; Berger, James M

2017-04-01

Cellular DNA replication is initiated through the action of multiprotein complexes that recognize replication start sites in the chromosome (termed origins) and facilitate duplex DNA melting within these regions. In a typical cell cycle, initiation occurs only once per origin and each round of replication is tightly coupled to cell division. To avoid aberrant origin firing and re-replication, eukaryotes tightly regulate two events in the initiation process: loading of the replicative helicase, MCM2-7, onto chromatin by the origin recognition complex (ORC), and subsequent activation of the helicase by its incorporation into a complex known as the CMG. Recent work has begun to reveal the details of an orchestrated and sequential exchange of initiation factors on DNA that give rise to a replication-competent complex, the replisome. Here, we review the molecular mechanisms that underpin eukaryotic DNA replication initiation - from selecting replication start sites to replicative helicase loading and activation - and describe how these events are often distinctly regulated across different eukaryotic model organisms.

Bilingualism affects audiovisual phoneme identification

PubMed Central

Burfin, Sabine; Pascalis, Olivier; Ruiz Tada, Elisa; Costa, Albert; Savariaux, Christophe; Kandel, Sonia

2014-01-01

We all go through a process of perceptual narrowing for phoneme identification. As we become experts in the languages we hear in our environment we lose the ability to identify phonemes that do not exist in our native phonological inventory. This research examined how linguistic experience—i.e., the exposure to a double phonological code during childhood—affects the visual processes involved in non-native phoneme identification in audiovisual speech perception. We conducted a phoneme identification experiment with bilingual and monolingual adult participants. It was an ABX task involving a Bengali dental-retroflex contrast that does not exist in any of the participants' languages. The phonemes were presented in audiovisual (AV) and audio-only (A) conditions. The results revealed that in the audio-only condition monolinguals and bilinguals had difficulties in discriminating the retroflex non-native phoneme. They were phonologically “deaf” and assimilated it to the dental phoneme that exists in their native languages. In the audiovisual presentation instead, both groups could overcome the phonological deafness for the retroflex non-native phoneme and identify both Bengali phonemes. However, monolinguals were more accurate and responded quicker than bilinguals. This suggests that bilinguals do not use the same processes as monolinguals to decode visual speech. PMID:25374551

Genetic origin, admixture, and asymmetry in maternal and paternal human lineages in Cuba

PubMed Central

2008-01-01

Background Before the arrival of Europeans to Cuba, the island was inhabited by two Native American groups, the Tainos and the Ciboneys. Most of the present archaeological, linguistic and ancient DNA evidence indicates a South American origin for these populations. In colonial times, Cuban Native American people were replaced by European settlers and slaves from Africa. It is still unknown however, to what extent their genetic pool intermingled with and was 'diluted' by the arrival of newcomers. In order to investigate the demographic processes that gave rise to the current Cuban population, we analyzed the hypervariable region I (HVS-I) and five single nucleotide polymorphisms (SNPs) in the mitochondrial DNA (mtDNA) coding region in 245 individuals, and 40 Y-chromosome SNPs in 132 male individuals. Results The Native American contribution to present-day Cubans accounted for 33% of the maternal lineages, whereas Africa and Eurasia contributed 45% and 22% of the lineages, respectively. This Native American substrate in Cuba cannot be traced back to a single origin within the American continent, as previously suggested by ancient DNA analyses. Strikingly, no Native American lineages were found for the Y-chromosome, for which the Eurasian and African contributions were around 80% and 20%, respectively. Conclusion While the ancestral Native American substrate is still appreciable in the maternal lineages, the extensive process of population admixture in Cuba has left no trace of the paternal Native American lineages, mirroring the strong sexual bias in the admixture processes taking place during colonial times. PMID:18644108

Second Language Processing Shows Increased Native-Like Neural Responses after Months of No Exposure

PubMed Central

Morgan-Short, Kara; Finger, Ingrid; Grey, Sarah; Ullman, Michael T.

2012-01-01

Although learning a second language (L2) as an adult is notoriously difficult, research has shown that adults can indeed attain native language-like brain processing and high proficiency levels. However, it is important to then retain what has been attained, even in the absence of continued exposure to the L2—particularly since periods of minimal or no L2 exposure are common. This event-related potential (ERP) study of an artificial language tested performance and neural processing following a substantial period of no exposure. Adults learned to speak and comprehend the artificial language to high proficiency with either explicit, classroom-like, or implicit, immersion-like training, and then underwent several months of no exposure to the language. Surprisingly, proficiency did not decrease during this delay. Instead, it remained unchanged, and there was an increase in native-like neural processing of syntax, as evidenced by several ERP changes—including earlier, more reliable, and more left-lateralized anterior negativities, and more robust P600s, in response to word-order violations. Moreover, both the explicitly and implicitly trained groups showed increased native-like ERP patterns over the delay, indicating that such changes can hold independently of L2 training type. The results demonstrate that substantial periods with no L2 exposure are not necessarily detrimental. Rather, benefits may ensue from such periods of time even when there is no L2 exposure. Interestingly, both before and after the delay the implicitly trained group showed more native-like processing than the explicitly trained group, indicating that type of training also affects the attainment of native-like processing in the brain. Overall, the findings may be largely explained by a combination of forgetting and consolidation in declarative and procedural memory, on which L2 grammar learning appears to depend. The study has a range of implications, and suggests a research program with potentially important consequences for second language acquisition and related fields. PMID:22470434

Measuring effectiveness of semantic cues in degraded English sentences in non-native listeners.

PubMed

Shi, Lu-Feng

2014-01-01

This study employed Boothroyd and Nittrouer's k (1988) to directly quantify effectiveness in native versus non-native listeners' use of semantic cues. Listeners were presented speech-perception-in-noise sentences processed at three levels of concurrent multi-talker babble and reverberation. For each condition, 50 sentences with multiple semantic cues and 50 with minimum semantic cues were randomly presented. Listeners verbally reported and wrote down the target words. The metric, k, was derived from percent-correct scores for sentences with and without semantics. Ten native and 33 non-native listeners participated. The presence of semantics increased recognition benefit by over 250% for natives, but access to semantics remained limited for non-native listeners (90-135%). The k was comparable across conditions for native listeners, but level-dependent for non-natives. The k for non-natives was significantly different from 1 in all conditions, suggesting semantic cues, though reduced in importance in difficult conditions, were helpful for non-natives. Non-natives as a group were not as effective in using semantics to facilitate English sentence recognition as natives. Poor listening conditions were particularly adverse to the use of semantics in non-natives, who may rely on clear acoustic-phonetic cues before benefitting from semantic cues when recognizing connected speech.

Manipulating 3D-Printed and Paper Models Enhances Student Understanding of Viral Replication

ERIC Educational Resources Information Center

Couper, Lisa; Johannes, Kristen; Powers, Jackie; Silberglitt, Matt; Davenport, Jodi

2016-01-01

Understanding key concepts in molecular biology requires reasoning about molecular processes that are not directly observable and, as such, presents a challenge to students and teachers. We ask whether novel interactive physical models and activities can help students understand key processes in viral replication. Our 3D tangible models are…

Development of replicated optics for AXAF-1 XDA testing

NASA Technical Reports Server (NTRS)

Engelhaupt, Darell; Wilson, Michele; Martin, Greg

1995-01-01

Advanced optical systems for applications such as grazing incidence Wolter I x-ray mirror assemblies require extraordinary mirror surfaces in terms of fine finish and surface figure. The impeccable mirror surface is on the inside of the rotational mirror form. One practical method of producing devices with these requirements is to first fabricate an exterior surface for the optical device then replicate that surface to have the inverse component with lightweight characteristics. The replicated optic is not better than the master or mandrel from which it is made. This task identifies methods and materials for forming these extremely low roughness optical components. The objectives of this contract were to (1) prepare replication samples of electroless nickel coated aluminum, and determine process requirements for plating XDA test optic; (2) prepare and assemble plating equipment required to process a demonstration optic; (3) characterize mandrels, replicas and test samples for residual stress, surface contamination and surface roughness and figure using equipment at MSFC and; (4) provide technical expertise in establishing the processes, procedures, supplies and equipment needed to process the XDA test optics.

The foreign language effect on the self-serving bias: A field experiment in the high school classroom.

PubMed

van Hugten, Joeri; van Witteloostuijn, Arjen

2018-01-01

The rise of bilingual education triggers an important question: which language is preferred for a particular school activity? Our field experiment (n = 120) shows that students (aged 13-15) who process feedback in non-native English have greater self-serving bias than students who process feedback in their native Dutch. By contrast, literature on the foreign-language emotionality effect suggests a weaker self-serving bias in the non-native language, so our result adds nuance to that literature. The result is important to schools as it suggests that teachers may be able to reduce students' defensiveness and demotivation by communicating negative feedback in the native language, and teachers may be able to increase students' confidence and motivation by communicating positive feedback in the foreign language.

The American Native Press and American Indian Studies.

ERIC Educational Resources Information Center

Littlefield, Daniel F., Jr.

1986-01-01

As product and process, the Native American press has a long history. The establishment of the first native-run press in 1828 began a press history that continues today. That history is represented by more than 2,000 periodical titles alone, two-thirds of which have been established during the past 20 years. Impressive collections of these…

Culturally Competent Substance Abuse Prevention Research among Rural Native American Communities.

ERIC Educational Resources Information Center

Stubben, Jerry

A study examined the process of evaluating family-oriented substance abuse prevention efforts in three Native American communities. In general, the Native communities exhibited a lack of commitment to academic evaluation research due to concerns over who would gain from such research, how much value was placed on Indian opinions, the level of…

Phrase Frequency, Proficiency and Grammaticality Interact in Non-Native Processing: Implications for Theories of SLA

ERIC Educational Resources Information Center

Shantz, Kailen

2017-01-01

This study reports on a self-paced reading experiment in which native and non-native speakers of English read sentences designed to evaluate the predictions of usage-based and rule-based approaches to second language acquisition (SLA). Critical stimuli were four-word sequences embedded into sentences in which phrase frequency and grammaticality…

Dynamic Architecture of Eukaryotic DNA Replication Forks In Vivo, Visualized by Electron Microscopy.

PubMed

Zellweger, Ralph; Lopes, Massimo

2018-01-01

The DNA replication process can be heavily perturbed by several different conditions of genotoxic stress, particularly relevant for cancer onset and therapy. The combination of psoralen crosslinking and electron microscopy has proven instrumental to reveal the fine architecture of in vivo DNA replication intermediates and to uncover their remodeling upon specific conditions of genotoxic stress. The replication structures are stabilized in vivo (by psoralen crosslinking) prior to extraction and enrichment procedures, allowing their visualization at the transmission electron microscope. This chapter outlines the procedures required to visualize and interpret in vivo replication intermediates of eukaryotic genomic DNA, and includes an improved method for enrichment of replication intermediates, compared to previously used BND-cellulose columns.

From structure to mechanism-understanding initiation of DNA replication.

PubMed

Riera, Alberto; Barbon, Marta; Noguchi, Yasunori; Reuter, L Maximilian; Schneider, Sarah; Speck, Christian

2017-06-01

DNA replication results in the doubling of the genome prior to cell division. This process requires the assembly of 50 or more protein factors into a replication fork. Here, we review recent structural and biochemical insights that start to explain how specific proteins recognize DNA replication origins, load the replicative helicase on DNA, unwind DNA, synthesize new DNA strands, and reassemble chromatin. We focus on the minichromosome maintenance (MCM2-7) proteins, which form the core of the eukaryotic replication fork, as this complex undergoes major structural rearrangements in order to engage with DNA, regulate its DNA-unwinding activity, and maintain genome stability. © 2017 Riera et al.; Published by Cold Spring Harbor Laboratory Press.

Integrating active restoration with environmental flows to improve native riparian tree establishment in the Colorado River Delta

USGS Publications Warehouse

Schlatter, Karen; Grabau, Matthew R.; Shafroth, Patrick B.; Zamora-Arroyo, Francisco

2017-01-01

Drastic alterations to river hydrology, land use change, and the spread of the nonnative shrub, tamarisk (Tamarix spp.), have led to the degradation of riparian habitat in the Colorado River Delta in Mexico. Delivery of environmental flows to promote native cottonwood (Populus spp.) and willow (Salix spp.) recruitment in human-impacted riparian systems can be unsuccessful due to flow-magnitude constraints and altered abiotic–biotic feedbacks. In 2014, an experimental pulse flow of water was delivered to the Colorado River in Mexico as part of the U.S.-Mexico binational agreement, Minute 319. We conducted a field experiment to assess the effects of vegetation removal, seed augmentation, and environmental flows, separately and in combination, on germination and first-year seedling establishment of cottonwood, willow, and tamarisk at five replicate sites along 5 river km. The relatively low-magnitude flow deliveries did not substantively restore natural fluvial processes of erosion, sediment deposition, and vegetation scour, but did provide wetted surface soils, shallow groundwater, and low soil salinity. Cottonwood and willow only established in wetted, cleared treatments, and establishment was variable in these treatments due to variable site conditions and inundation duration and timing. Wetted soils, bare surface availability, soil salinity, and seed availability were significant factors contributing to successful cottonwood and willow germination, while soil salinity and texture affected seedling persistence over the growing season. Tamarisk germinated and persisted in a wider range of environmental conditions than cottonwood and willow, including in un-cleared treatment areas. Our results suggest that site management can increase cottonwood and willow recruitment success from low-magnitude environmental flow events, an approach that can be applied in other portions of the Delta and to other human-impacted riparian systems across the world with similar ecological limitations.

Replication licensing and the DNA damage checkpoint

PubMed Central

Cook, Jeanette Gowen

2011-01-01

Accurate and timely duplication of chromosomal DNA requires that replication be coordinated with processes that ensure genome integrity. Significant advances in determining how the earliest steps in DNA replication are affected by DNA damage have highlighted some of the mechanisms to establish that coordination. Recent insights have expanded the relationship between the ATM and ATR-dependent checkpoint pathways and the proteins that bind and function at replication origins. These findings suggest that checkpoints and replication are more intimately associated than previously appreciated, even in the absence of exogenous DNA damage. This review summarizes some of these developments. PMID:19482602

Amyloid fibrils: formation, replication, and physics behind them

NASA Astrophysics Data System (ADS)

Saric, Andela

The assembly of normally soluble proteins into long fibrils, known as amyloids, is associated with a range of pathologies, including Alzheimer's and Parkinson's diseases. A large number of structurally unrelated proteins form this type of fibrils, and we are in a pursuit of physical principles that underlie the amyloid formation and propagation. We show that small disorders oligomers, which are increasingly believed to be the prime cause for cellular toxicity, serve as nucleation centers for the fibril formation. We then relate experimentally measurable kinetic descriptors of amyloid aggregation to the microscopic mechanisms of the process. Once formed, amyloid fibrils can catalyse the formation of new oligomers and fibrils in a process that resembles self-replication. By combining simulations with biosensing and kinetic measurements of the aggregation of Alzheimer's A β peptide, we propose a mechanistic explanation for the self-replication of protein fibrils, and discuss its thermodynamic signature. Finally, we consider the design of possible inhibitors of the fibril self-replication process. Mechanistic understandings provided here not only have implications for future efforts to control pathological protein aggregation, but are also of interest for the rational assembly of bionanomaterials, where achieving and controlling self-replication is one of the unfulfilled goals.

Social learning and the replication process: an experimental investigation.

PubMed

Derex, Maxime; Feron, Romain; Godelle, Bernard; Raymond, Michel

2015-06-07

Human cultural traits typically result from a gradual process that has been described as analogous to biological evolution. This observation has led pioneering scholars to draw inspiration from population genetics to develop a rigorous and successful theoretical framework of cultural evolution. Social learning, the mechanism allowing information to be transmitted between individuals, has thus been described as a simple replication mechanism. Although useful, the extent to which this idealization appropriately describes the actual social learning events has not been carefully assessed. Here, we used a specifically developed computer task to evaluate (i) the extent to which social learning leads to the replication of an observed behaviour and (ii) the consequences it has for fitness landscape exploration. Our results show that social learning does not lead to a dichotomous choice between disregarding and replicating social information. Rather, it appeared that individuals combine and transform information coming from multiple sources to produce new solutions. As a consequence, landscape exploration was promoted by the use of social information. These results invite us to rethink the way social learning is commonly modelled and could question the validity of predictions coming from models considering this process as replicative. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Sign Perception and Recognition in Non-Native Signers of ASL

PubMed Central

Morford, Jill P.; Carlson, Martina L.

2011-01-01

Past research has established that delayed first language exposure is associated with comprehension difficulties in non-native signers of American Sign Language (ASL) relative to native signers. The goal of the current study was to investigate potential explanations of this disparity: do non-native signers have difficulty with all aspects of comprehension, or are their comprehension difficulties restricted to some aspects of processing? We compared the performance of deaf non-native, hearing L2, and deaf native signers on a handshape and location monitoring and a sign recognition task. The results indicate that deaf non-native signers are as rapid and accurate on the monitoring task as native signers, with differences in the pattern of relative performance across handshape and location parameters. By contrast, non-native signers differ significantly from native signers during sign recognition. Hearing L2 signers, who performed almost as well as the two groups of deaf signers on the monitoring task, resembled the deaf native signers more than the deaf non-native signers on the sign recognition task. The combined results indicate that delayed exposure to a signed language leads to an overreliance on handshape during sign recognition. PMID:21686080

Nuclear DNA Replication in Trypanosomatids: There Are No Easy Methods for Solving Difficult Problems.

PubMed

da Silva, Marcelo S; Pavani, Raphael S; Damasceno, Jeziel D; Marques, Catarina A; McCulloch, Richard; Tosi, Luiz Ricardo Orsini; Elias, Maria Carolina

2017-11-01

In trypanosomatids, etiological agents of devastating diseases, replication is robust and finely controlled to maintain genome stability and function in stressful environments. However, these parasites encode several replication protein components and complexes that show potentially variant composition compared with model eukaryotes. This review focuses on the advances made in recent years regarding the differences and peculiarities of the replication machinery in trypanosomatids, including how such divergence might affect DNA replication dynamics and the replication stress response. Comparing the DNA replication machinery and processes of parasites and their hosts may provide a foundation for the identification of targets that can be used in the development of chemotherapies to assist in the eradication of diseases caused by these pathogens. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Keystone predators (eastern newts, Notophthalmus viridescens) reduce the impacts of an aquatic invasive species

USGS Publications Warehouse

Smith, Kimberly G.

2006-01-01

Predation, competition, and their interaction are known to be important factors that influence the structure of ecological communities. In particular, in those cases where a competitive hierarchy exists among prey species, the presence of certain keystone predators can result in enhanced diversity in the prey community. However, little is known regarding the influence of keystone predator presence on invaded prey communities. Given the widespread occurrence of invasive species and substantial concern regarding their ecological impacts, studies on this topic are needed. In this study I used naturalistic replications of an experimental tadpole assemblage to assess the influence of predatory eastern newts, Notophthalmus viridescens, on the outcome of interspecific competition among native and nonindigenous tadpoles. When newts were absent, the presence of the tadpoles of one invasive species, the Cuban treefrog, Osteopilus septentrionalis, resulted in decreased survival and growth rate of the dominant native species, Bufo terrestris, and dominance of the tadpole assemblage by O. septentrionalis. However, the presence of one adult newt generally reduced or eliminated the negative impacts of O. septentrionalis tadpoles, resulting in comparable survival and performance of native species in invaded and noninvaded treatments. Differential mortality among the tadpole species suggests that newts preyed selectively on O. septentrionalis tadpoles, supporting the hypothesis that newts acted as keystone predators in the invaded assemblage. The presence of nonindigenous larval cane toads, Bufo marinus, did not significantly affect native species, and this species was not negatively affected by the presence of newts. Collectively, these results suggest that eastern newts significantly modified the competitive hierarchy of the invaded tadpole assemblage and reduced the impacts of a competitively superior invasive species. If general, these results suggest that the presence of certain species may be an essential factor regulating the ecological impacts of biological invasions.

A new image-based process for quantifying hemodynamic contributions to long-term morbidity in a rabbit model of aortic coarctation

NASA Astrophysics Data System (ADS)

Wendell, David C.; Dholakia, Ronak J.; Larsen, Paul M.; Menon, Arjun; LaDisa, John F., Jr.

2010-03-01

Coarctation of the aorta (CoA) is associated with reduced life expectancy despite successful surgical treatment. Interestingly, much of the related long-term morbidity can be explained by abnormal hemodynamics, vascular biomechanics and cardiac function. MRI has played an important role in assessing coarctation severity, but the heterogeneity and small number of patients at each center presents an obstacle for determining causality. This work describes optimized imaging parameters to create computational fluid dynamics (CFD) models revealing changes in hemodynamics and vascular biomechanics from a rabbit model. CoA was induced surgically at 10 weeks using silk or dissolvable ligatures to replicate native and end-to-end treatment cases, respectively. Cardiac function was evaluated at 32 weeks using a fastcard SPGR sequence in 6-8 two-chamber short-axis views. Left ventricular (LV) volume, ejection fraction, and mass were quantified and compared to control rabbits. Phase contrast (PC) and angiographic MRI were used to create CFD models. Ascending aortic PCMRI data were mapped to the model inflow and outflow boundary conditions replicated measured pressure (BP) and flow. CFD simulations were performed using a stabilized finite element method to calculate indices including velocity, BP and wall shear stress (WSS). CoA models displayed higher velocity through the coarctation region and decreased velocity elsewhere, leading to decreased WSS above and below the stenosis. Pronounced wall displacement was associated with CoA-induced changes in BP. CoA caused reversible LV hypertrophy. Cardiac function was maintained, but caused a persistent hyperdynamic state. This model may now be used to investigate potential mechanisms of long-term morbidity.

A four-component model of the action potential in mouse detrusor smooth muscle cell

PubMed Central

Brain, Keith L.; Young, John S.; Manchanda, Rohit

2018-01-01

Background and hypothesis Detrusor smooth muscle cells (DSMCs) of the urinary bladder are electrically connected to one another via gap junctions and form a three dimensional syncytium. DSMCs exhibit spontaneous electrical activity, including passive depolarizations and action potentials. The shapes of spontaneous action potentials (sAPs) observed from a single DSM cell can vary widely. The biophysical origins of this variability, and the precise components which contribute to the complex shapes observed are not known. To address these questions, the basic components which constitute the sAPs were investigated. We hypothesized that linear combinations of scaled versions of these basic components can produce sAP shapes observed in the syncytium. Methods and results The basic components were identified as spontaneous evoked junction potentials (sEJP), native AP (nAP), slow after hyperpolarization (sAHP) and very slow after hyperpolarization (vsAHP). The experimental recordings were grouped into two sets: a training data set and a testing data set. A training set was used to estimate the components, and a test set to evaluate the efficiency of the estimated components. We found that a linear combination of the identified components when appropriately amplified and time shifted replicated various AP shapes to a high degree of similarity, as quantified by the root mean square error (RMSE) measure. Conclusions We conclude that the four basic components—sEJP, nAP, sAHP, and vsAHP—identified and isolated in this work are necessary and sufficient to replicate all varieties of the sAPs recorded experimentally in DSMCs. This model has the potential to generate testable hypotheses that can help identify the physiological processes underlying various features of the sAPs. Further, this model also provides a means to classify the sAPs into various shape classes. PMID:29351282

A four-component model of the action potential in mouse detrusor smooth muscle cell.

PubMed

Padmakumar, Mithun; Brain, Keith L; Young, John S; Manchanda, Rohit

2018-01-01

Detrusor smooth muscle cells (DSMCs) of the urinary bladder are electrically connected to one another via gap junctions and form a three dimensional syncytium. DSMCs exhibit spontaneous electrical activity, including passive depolarizations and action potentials. The shapes of spontaneous action potentials (sAPs) observed from a single DSM cell can vary widely. The biophysical origins of this variability, and the precise components which contribute to the complex shapes observed are not known. To address these questions, the basic components which constitute the sAPs were investigated. We hypothesized that linear combinations of scaled versions of these basic components can produce sAP shapes observed in the syncytium. The basic components were identified as spontaneous evoked junction potentials (sEJP), native AP (nAP), slow after hyperpolarization (sAHP) and very slow after hyperpolarization (vsAHP). The experimental recordings were grouped into two sets: a training data set and a testing data set. A training set was used to estimate the components, and a test set to evaluate the efficiency of the estimated components. We found that a linear combination of the identified components when appropriately amplified and time shifted replicated various AP shapes to a high degree of similarity, as quantified by the root mean square error (RMSE) measure. We conclude that the four basic components-sEJP, nAP, sAHP, and vsAHP-identified and isolated in this work are necessary and sufficient to replicate all varieties of the sAPs recorded experimentally in DSMCs. This model has the potential to generate testable hypotheses that can help identify the physiological processes underlying various features of the sAPs. Further, this model also provides a means to classify the sAPs into various shape classes.

Native and exotic plants of fragments of sagebrush steppe produced by geomorphic processes versus land use

USGS Publications Warehouse

Huntly, N.; Bangert, R.; Hanser, S.E.

2011-01-01

Habitat fragmentation and invasion by exotic species are regarded as major threats to the biodiversity of many ecosystems. We surveyed the plant communities of two types of remnant sagebrush-steppe fragments from nearby areas on the Snake River Plain of southeastern Idaho, USA. One type resulted from land use (conversion to dryland agriculture; hereafter AG Islands) and the other from geomorphic processes (Holocene volcanism; hereafter kipukas). We assessed two predictions for the variation in native plant species richness of these fragments, using structural equation models (SEM). First, we predicted that the species richness of native plants would follow the MacArthur-Wilson (M-W) hypothesis of island biogeography, as often is expected for the communities of habitat fragments. Second, we predicted a negative relationship between native and exotic plants, as would be expected if exotic plants are decreasing the diversity of native plants. Finally, we assessed whether exotic species were more strongly associated with the fragments embedded in the agricultural landscape, as would be expected if agriculture had facilitated the introduction and naturalization of non-native species, and whether the communities of the two types of fragments were distinct. Species richness of native plants was not strongly correlated with M-W characteristics for either the AG Islands or the **kipukas. The AG Islands had more species and higher cover of exotics than the kipukas, and exotic plants were good predictors of native plant species richness. Our results support the hypothesis that proximity to agriculture can increase the diversity and abundance of exotic plants in native habitat. In combination with other information, the results also suggest that agriculture and exotic species have caused loss of native diversity and reorganization of the sagebrush-steppe plant community. ?? 2011 Springer Science+Business Media B.V.

Pre-attentive sensitivity to vowel duration reveals native phonology and predicts learning of second-language sounds.

PubMed

Chládková, Kateřina; Escudero, Paola; Lipski, Silvia C

2013-09-01

In some languages (e.g. Czech), changes in vowel duration affect word meaning, while in others (e.g. Spanish) they do not. Yet for other languages (e.g. Dutch), the linguistic role of vowel duration remains unclear. To reveal whether Dutch represents vowel length in its phonology, we compared auditory pre-attentive duration processing in native and non-native vowels across Dutch, Czech, and Spanish. Dutch duration sensitivity patterned with Czech but was larger than Spanish in the native vowel, while it was smaller than Czech and Spanish in the non-native vowel. An interpretation of these findings suggests that in Dutch, duration is used phonemically but it might be relevant for the identity of certain native vowels only. Furthermore, the finding that Spanish listeners are more sensitive to duration in non-native than in native vowels indicates that a lack of duration differences in one's native language could be beneficial for second-language learning. Copyright © 2013 Elsevier Inc. All rights reserved.

Intracellular coordination of potyviral RNA functions in infection

PubMed Central

Mäkinen, Kristiina; Hafrén, Anders

2014-01-01

Establishment of an infection cycle requires mechanisms to allocate the genomes of (+)-stranded RNA viruses in a balanced ratio to translation, replication, encapsidation, and movement, as well as mechanisms to prevent translocation of viral RNA (vRNA) to cellular RNA degradation pathways. The ratio of vRNA allocated to various functions is likely balanced by the availability of regulatory proteins or competition of the interaction sites within regulatory ribonucleoprotein complexes. Due to the transient nature of viral processes and the interdependency between vRNA pathways, it is technically demanding to work out the exact molecular mechanisms underlying vRNA regulation. A substantial number of viral and host proteins have been identified that facilitate the steps that lead to the assembly of a functional potyviral RNA replication complex and their fusion with chloroplasts. Simultaneously with on-going viral replication, part of the replicated potyviral RNA enters movement pathways. Although not much is known about the processes of potyviral RNA release from viral replication complexes, the molecular interactions involved in these processes determine the fate of the replicated vRNA. Some viral and host cell proteins have been described that direct replicated potyviral RNA to translation to enable potyviral gene expression and productive infection. The antiviral defense of the cell causes vRNA degradation by RNA silencing. We hypothesize that also plant pathways involved in mRNA decay may have a role in the coordination of potyviral RNA expression. In this review, we discuss the roles of different potyviral and host proteins in the coordination of various potyviral RNA functions. PMID:24723931

Intracellular coordination of potyviral RNA functions in infection.

PubMed

Mäkinen, Kristiina; Hafrén, Anders

2014-01-01

Establishment of an infection cycle requires mechanisms to allocate the genomes of (+)-stranded RNA viruses in a balanced ratio to translation, replication, encapsidation, and movement, as well as mechanisms to prevent translocation of viral RNA (vRNA) to cellular RNA degradation pathways. The ratio of vRNA allocated to various functions is likely balanced by the availability of regulatory proteins or competition of the interaction sites within regulatory ribonucleoprotein complexes. Due to the transient nature of viral processes and the interdependency between vRNA pathways, it is technically demanding to work out the exact molecular mechanisms underlying vRNA regulation. A substantial number of viral and host proteins have been identified that facilitate the steps that lead to the assembly of a functional potyviral RNA replication complex and their fusion with chloroplasts. Simultaneously with on-going viral replication, part of the replicated potyviral RNA enters movement pathways. Although not much is known about the processes of potyviral RNA release from viral replication complexes, the molecular interactions involved in these processes determine the fate of the replicated vRNA. Some viral and host cell proteins have been described that direct replicated potyviral RNA to translation to enable potyviral gene expression and productive infection. The antiviral defense of the cell causes vRNA degradation by RNA silencing. We hypothesize that also plant pathways involved in mRNA decay may have a role in the coordination of potyviral RNA expression. In this review, we discuss the roles of different potyviral and host proteins in the coordination of various potyviral RNA functions.

Recombination in Enteroviruses Is a Biphasic Replicative Process Involving the Generation of Greater-than Genome Length ‘Imprecise’ Intermediates

PubMed Central

Lowry, Kym; Woodman, Andrew; Cook, Jonathan; Evans, David J.

2014-01-01

Recombination in enteroviruses provides an evolutionary mechanism for acquiring extensive regions of novel sequence, is suggested to have a role in genotype diversity and is known to have been key to the emergence of novel neuropathogenic variants of poliovirus. Despite the importance of this evolutionary mechanism, the recombination process remains relatively poorly understood. We investigated heterologous recombination using a novel reverse genetic approach that resulted in the isolation of intermediate chimeric intertypic polioviruses bearing genomes with extensive duplicated sequences at the recombination junction. Serial passage of viruses exhibiting such imprecise junctions yielded progeny with increased fitness which had lost the duplicated sequences. Mutations or inhibitors that changed polymerase fidelity or the coalescence of replication complexes markedly altered the yield of recombinants (but did not influence non-replicative recombination) indicating both that the process is replicative and that it may be possible to enhance or reduce recombination-mediated viral evolution if required. We propose that extant recombinants result from a biphasic process in which an initial recombination event is followed by a process of resolution, deleting extraneous sequences and optimizing viral fitness. This process has implications for our wider understanding of ‘evolution by duplication’ in the positive-strand RNA viruses. PMID:24945141

Volumetric velocimetry downstream of a percutaneous heart valve

NASA Astrophysics Data System (ADS)

Raghav, Vrishank; Clifford, Christopher; Midha, Prem; Okafor, Ikechukwu; Thurow, Brian; Yoganathan, Ajit; Auburn University Collaboration; Georgia Institute of Technology Collaboration

2017-11-01

Transcatheter aortic valve replacement has emerged as a safe and effective treatment for severe, symptomatic aortic stenosis in intermediate or greater surgical risk patients. However, despite excellent short-term outcomes, improved imaging and awareness has led to the identification of leaflet thrombosis on the aortic side of the prosthesis. Upon implantation, the transcatheter heart valve (THV) becomes enclosed in the native aortic valve leaflet tissue dividing the native sinus into two regions - a smaller anatomical sinus and a neo-sinus. To understand the causes for thrombosis, plenoptic Particle Image Velocimetry (PIV) is used to investigate the pulsatile three-dimensional flow in the sinus and neo-sinus region of the THV. Experiments are conducted on both a real and a transparent THV model in a pulsatile flow loop capable of replicating physiological hemodynamics. Comparisons with planar PIV results demonstrate the feasibility of using Plenoptic PIV to study heart valve fluid dynamics. Large three-dimensional regions of low velocity magnitude and low viscous shear stress were observed near the heart valve which could increase particle residence time potentially leading to formation of clots the THV leaflet.

Infiltration performance of engineered surfaces commonly used for distributed stormwater management

NASA Astrophysics Data System (ADS)

Valinski, Nicholas A.

Engineered porous media are commonly used in low impact development (LID) structures to mitigate excess stormwater in urban environments. Differences in infiltrability of these LID systems arise from the wide variety of materials used to create porous surfaces and subsequent maintenance, debris loading, and physical damage. In this study, infiltration capacity of six common materials was tested by multiple replicate experiments with automated mini-disk infiltrometers. The tested materials included porous asphalt, porous concrete, porous brick pavers, flexible porous pavement, engineered soils, and native soils. Porous asphalt, large porous brick pavers, and curb cutout rain gardens showed the greatest infiltration rates. Most engineered porous pavements and soils performed better than the native silt loam soils. Infiltration performance was found to be related more to site design and environmental factors than material choice. Sediment trap zones in both pavements and engineered soil rain gardens were found to be beneficial to the whole site performance. Winter chloride application had a large negative impact on poured in place concrete, making it a poor choice for heavily salted areas.

Brain potentials reveal unconscious translation during foreign-language comprehension.

PubMed

Thierry, Guillaume; Wu, Yan Jing

2007-07-24

Whether the native language of bilingual individuals is active during second-language comprehension is the subject of lively debate. Studies of bilingualism have often used a mix of first- and second-language words, thereby creating an artificial "dual-language" context. Here, using event-related brain potentials, we demonstrate implicit access to the first language when bilinguals read words exclusively in their second language. Chinese-English bilinguals were required to decide whether English words presented in pairs were related in meaning or not; they were unaware of the fact that half of the words concealed a character repetition when translated into Chinese. Whereas the hidden factor failed to affect behavioral performance, it significantly modulated brain potentials in the expected direction, establishing that English words were automatically and unconsciously translated into Chinese. Critically, the same modulation was found in Chinese monolinguals reading the same words in Chinese, i.e., when Chinese character repetition was evident. Finally, we replicated this pattern of results in the auditory modality by using a listening comprehension task. These findings demonstrate that native-language activation is an unconscious correlate of second-language comprehension.

Infiltration performance of engineered surfaces commonly used for distributed stormwater management.

PubMed

Valinski, N A; Chandler, D G

2015-09-01

Engineered porous media are commonly used in low impact development (LID) structures to mitigate excess stormwater in urban environments. Differences in infiltrability of these LID systems arise from the wide variety of materials used to create porous surfaces and subsequent maintenance, debris loading, and physical damage. In this study, the infiltration capacity of six common materials was tested by multiple replicate experiments with automated mini-disk infiltrometers. The tested materials included porous asphalt, porous concrete, porous brick pavers, flexible porous pavement, engineered soils, and native soils. Porous asphalt, large porous brick pavers, and curb cutout rain gardens showed the greatest infiltration rates. Most engineered porous pavements and soils performed better than the native silt loam soils. Infiltration performance was found to be related more to site design and environmental factors than material choice. Sediment trap zones in both pavements and engineered soil rain gardens were found to be beneficial to the whole site performance. Winter chloride application had a large negative impact on poured in place concrete, making it a poor choice for heavily salted areas. Copyright © 2015 Elsevier Ltd. All rights reserved.

Mechanomimetic hydrogels for vocal fold lamina propria regeneration.

PubMed

Kutty, Jaishankar K; Webb, Ken

2009-01-01

Vocal fold injury commonly leads to reduced vocal quality due to scarring-induced alterations in matrix composition and tissue biomechanics. The long-term hypothesis motivating our work is that rapid restoration of phonation and the associated dynamic mechanical environment will reduce scarring and promote regenerative healing. Toward this end, the objective of this study was to develop mechanomimetic, degradable hydrogels approximating the viscoelastic properties of the vocal ligament and mucosa that may be photopolymerized in situ to restore structural integrity to vocal fold tissues. The tensile and rheological properties of hydrogels (targeting the vocal ligament and mucosa, respectively) were varied as a function of macromer concentration. PEG diacrylate-based hydrogels exhibited linear stress-strain response and elastic modulus consistent with the properties of the vocal ligament at low strains (0-15%), but did not replicate the non-linear behavior observed in native tissue at higher strains. Methacrylated hyaluronic acid hydrogels displayed dynamic viscosity consistent with native vocal mucosa, while elastic shear moduli values were several-fold higher. Cell culture studies indicated that both hydrogels supported spreading, proliferation and collagen/proteoglycan matrix deposition by encapsulated fibroblasts throughout the 3D network.

On "feeling right" in cultural contexts: how person-culture match affects self-esteem and subjective well-being.

PubMed

Fulmer, C Ashley; Gelfand, Michele J; Kruglanski, Arie W; Kim-Prieto, Chu; Diener, Ed; Pierro, Antonio; Higgins, E Tory

2010-11-01

Whether one is in one's native culture or abroad, one's personality can differ markedly from the personalities of the majority, thus failing to match the "cultural norm." Our studies examined how the interaction of individual- and cultural-level personality affects people's self-esteem and well-being. We propose a person-culture match hypothesis that predicts that when a person's personality matches the prevalent personalities of other people in a culture, culture functions as an important amplifier of the positive effect of personality on self-esteem and subjective well-being at the individual level. Across two studies, using data from more than 7,000 individuals from 28 societies, multilevel random-coefficient analyses showed that when a relation between a given personality trait and well-being or self-esteem exists at the individual level, the relation is stronger in cultures characterized by high levels of that personality dimension. Results were replicated across extraversion, promotion focus, and locomotive regulatory mode. Our research has practical implications for the well-being of both cultural natives and migrants.

Cross-lingual neighborhood effects in generalized lexical decision and natural reading.

PubMed

Dirix, Nicolas; Cop, Uschi; Drieghe, Denis; Duyck, Wouter

2017-06-01

The present study assessed intra- and cross-lingual neighborhood effects, using both a generalized lexical decision task and an analysis of a large-scale bilingual eye-tracking corpus (Cop, Dirix, Drieghe, & Duyck, 2016). Using new neighborhood density and frequency measures, the general lexical decision task yielded an inhibitory cross-lingual neighborhood density effect on reading times of second language words, replicating van Heuven, Dijkstra, and Grainger (1998). Reaction times for native language words were not influenced by neighborhood density or frequency but error rates showed cross-lingual neighborhood effects depending on target word frequency. The large-scale eye movement corpus confirmed effects of cross-lingual neighborhood on natural reading, even though participants were reading a novel in a unilingual context. Especially second language reading and to a lesser extent native language reading were influenced by lexical candidates from the nontarget language, although these effects in natural reading were largely facilitatory. These results offer strong and direct support for bilingual word recognition models that assume language-independent lexical access. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Role of the 85-Kilobase Plasmid and Plasmid-Encoded Virulence-Associated Protein A in Intracellular Survival and Virulence of Rhodococcus equi

PubMed Central

Giguère, Steeve; Hondalus, Mary K.; Yager, Julie A.; Darrah, Patricia; Mosser, David M.; Prescott, John F.

1999-01-01

Rhodococcus equi is a facultative intracellular pathogen of macrophages and a cause of pneumonia in young horses (foals) and immunocompromised people. Isolates of R. equi from pneumonic foals typically contain large, 85- or 90-kb plasmids encoding a highly immunogenic virulence-associated protein (VapA). The objective of this study was to determine the role of the 85-kb plasmid and VapA in the intracellular survival and virulence of R. equi. Clinical isolates containing the plasmid and expressing VapA efficiently replicated within mouse macrophages in vitro, while plasmid-cured derivatives of these organisms did not multiply intracellularly. An isolate harboring the large plasmid also replicated in the tissues of experimentally infected mice, whereas its plasmid-cured derivative was rapidly cleared. All foals experimentally infected with a plasmid-containing clinical isolate developed severe bronchopneumonia, whereas the foals infected with its plasmid-cured derivative remained asymptomatic and free of visible lung lesions. By day 14 postinfection, lung bacterial burdens had increased considerably in foals challenged with the plasmid-containing clinical isolate. In contrast, bacteria could no longer be cultured from the lungs of foals challenged with the isogenic plasmid-cured derivative. A recombinant, plasmid-cured derivative expressing wild-type levels of VapA failed to replicate in macrophages and remained avirulent for both mice and foals. These results show that the 85-kb plasmid of R. equi is essential for intracellular replication within macrophages and for development of disease in the native host, the foal. However, expression of VapA alone is not sufficient to restore the virulence phenotype. PMID:10377138

Insect Cell-Derived Cofactors Become Fully Functional after Proteinase K and Heat Treatment for High-Fidelity Amplification of Glycosylphosphatidylinositol-Anchored Recombinant Scrapie and BSE Prion Proteins

PubMed Central

Imamura, Morikazu; Kato, Nobuko; Okada, Hiroyuki; Yoshioka, Miyako; Iwamaru, Yoshifumi; Shimizu, Yoshihisa; Mohri, Shirou; Yokoyama, Takashi; Murayama, Yuichi

2013-01-01

The central event in prion infection is the conformational conversion of host-encoded cellular prion protein (PrPC) into the pathogenic isoform (PrPSc). Diverse mammalian species possess the cofactors required for in vitro replication of PrPSc by protein-misfolding cyclic amplification (PMCA), but lower organisms, such as bacteria, yeasts, and insects, reportedly lack the essential cofactors. Various cellular components, such as RNA, lipids, and other identified cofactor molecules, are commonly distributed in both eukaryotes and prokaryotes, but the reasons for the absence of cofactor activity in lower organisms remain to be elucidated. Previously, we reported that brain-derived factors were necessary for the in vitro replication of glycosylphosphatidylinositol-anchored baculovirus-derived recombinant PrP (Bac-PrP). Here, we demonstrate that following protease digestion and heat treatment, insect cell lysates had the functional cofactor activity required for Bac-PrP replication by PMCA. Mammalian PrPSc seeds and Bac-PrPSc generated by PMCA using Bac-PrP and insect cell-derived cofactors showed similar pathogenicity and produced very similar lesions in the brains of inoculated mice. These results suggested that the essential cofactors required for the high-fidelity replication of mammalian PrPSc were present in the insect cells but that the cofactor activity was masked or inhibited in the native state. We suggest that not only RNA, but also DNA, are the key components of PMCA, although other cellular factors were necessary for the expression of the cofactor activity of nucleic acids. PMCA using only insect cell-derived substances (iPMCA) was highly useful for the ultrasensitive detection of PrPSc of some prion strains. PMID:24367521

Vaccinia virus-free rescue of fluorescent replication-defective vesicular stomatitis virus and pseudotyping with Puumala virus glycoproteins for use in neutralization tests.

PubMed

Paneth Iheozor-Ejiofor, Rommel; Levanov, Lev; Hepojoki, Jussi; Strandin, Tomas; Lundkvist, Åke; Plyusnin, Alexander; Vapalahti, Olli

2016-05-01

Puumala virus (PUUV) grows slowly in cell culture. To study antigenic properties of PUUV, an amenable method for their expression would be beneficial. To achieve this, a replication-defective recombinant vesicular stomatitis virus, rVSVΔG*EGFP, was rescued using BSRT7/5 and encephalomyocarditis virus (EMCV) internal ribosomal entry site (IRES)-enabled rescue plasmids. Using these particles, pseudotypes bearing PUUV Sotkamo strain glycoproteins were produced, with titres in the range 105-108, and were used in pseudotype focus reduction neutralization tests (pFRNTs) with neutralizing monoclonal antibodies and patient sera. The results were compared with those from orthodox focus reduction neutralization tests (oFRNTs) using native PUUV with the same samples and showed a strong positive correlation (rs = 0.82) between the methods. While developing the system we identified three amino acids which were mutated in the Vero E6 cell culture adapted PUUV prototype Sotkamo strain sequence, and changing these residues was critical for expression and neutralizing antibody binding of PUUV glycoproteins.

Lack of close relationship between three strains of human rhinoviruses as determined by their RNA sequences.

PubMed

Yin, F H; Lonberg-Holm, K; Chan, S P

1973-07-01

The possible genomic homologies between three serotypes of human rhinoviruses (HRV 1A, HRV 2, and HRV 14) were investigated. First we confirmed that these viruses were unrelated by the criterion of the absence of common antigenic determinants on the surfaces of the native virions, as detected by cross-neutralization of complementfixation. RNA-RNA hybridization was then examined with purified, highly radioactive, double-stranded, replicative-form RNA and excess single-stranded virion RNA. Single-stranded RNA showed 100% homology with the minus strand from the replicative-form RNA of the same type of virus. HRV 1A, HRV 2, and HRV 14 showed low intertypic homologies; these were not significantly greater than those found between the rhinoviruses and polivirus, which were used as a negative control. The immunological relationship and the RNA homology between HRV 1A and HRV 1B were also examined by the above techniques. It was confirmed that HRV 1A and HRV 1B share some surface determinants and it was also found that HRV 1B RNA shares 70% homology with HRV 1A RNA.

Speech-Sound Duration Processing in a Second Language is Specific to Phonetic Categories

ERIC Educational Resources Information Center

Nenonen, Sari; Shestakova, Anna; Huotilainen, Minna; Naatanen, Risto

2005-01-01

The mismatch negativity (MMN) component of the auditory event-related potential was used to determine the effect of native language, Russian, on the processing of speech-sound duration in a second language, Finnish, that uses duration as a cue for phonological distinction. The native-language effect was compared with Finnish vowels that either can…

U. S. and Canadian Native Voluntary Associations: Continuities Within the Evolution of Culture.

ERIC Educational Resources Information Center

Price, John A.

Evolutionary processes are described for Native (American Indian) voluntary associations in the U.S. and Canada in aboriginal times, in the twentieth century generally, and in cities specifically. These processes at different times and in different social settings are shown to be related to each other through specific historic continuities and…

75 FR 71625 - System Restoration Reliability Standards

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-24

... processing software should be filed in native applications or print-to-PDF format, and not in a scanned... (2006), aff'd sub nom. Alcoa, Inc. v. FERC, 564 F.3d 1342 (D.C. Cir. 2009). 6. On March 16, 2007, the... electronically using word processing software should be filed in native applications or print-to-PDF format, and...

Methamphetamine Use among Rural White and Native American Adolescents: An Application of the Stress Process Model

ERIC Educational Resources Information Center

Eitle, David J.; Eitle, Tamela McNulty

2013-01-01

Methamphetamine use has been identified as having significant adverse health consequences, yet we know little about the correlates of its use. Additionally, research has found that Native Americans are at the highest risk for methamphetamine use. Our exploratory study, informed by the stress process model, examines stress and stress buffering…

A Process Evaluation of the Alaska Native Colorectal Cancer Family Outreach Program

ERIC Educational Resources Information Center

Redwood, Diana; Provost, Ellen; Lopez, Ellen D. S.; Skewes, Monica; Johnson, Rhonda; Christensen, Claudia; Sacco, Frank; Haverkamp, Donald

2016-01-01

This article presents the results of a process evaluation of the Alaska Native (AN) Colorectal Cancer (CRC) Family Outreach Program, which encourages CRC screening among AN first-degree relatives (i.e., parents, siblings, adult children; hereafter referred to as relatives) of CRC patients. Among AN people incidence and death rates from CRC are the…

Perceptions of Refusals to Invitations: Exploring the Minds of Foreign Language Learners

ERIC Educational Resources Information Center

Felix-Brasdefer, J. Cesar

2008-01-01

Descriptions of speech act realisations of native and non-native speakers abound in the cross-cultural and interlanguage pragmatics literature. Yet, what is lacking is an analysis of the cognitive processes involved in the production of speech acts. This study examines the cognitive processes and perceptions of learners of Spanish when refusing…

An Examination of Native and Immigrant Students' Social Networking Using the College Search and Selection Process

ERIC Educational Resources Information Center

Neimeyer, Bruce Carlton

2009-01-01

This dissertation explores the use of formal and informal networks through cyber- and traditional communication methods in the college search and selection process by native and immigrant students to examine various postulates and propositions of social capital theory. In addition, the analysis of cybernetworks used by disadvantaged, college bound…

A Comparison of Vector and Raster GIS Methods for Calculating Landscape Metrics Used in Environmental Assessments

Treesearch

Timothy G. Wade; James D. Wickham; Maliha S. Nash; Anne C. Neale; Kurt H. Riitters; K. Bruce Jones

2003-01-01

AbstractGIS-based measurements that combine native raster and native vector data are commonly used in environmental assessments. Most of these measurements can be calculated using either raster or vector data formats and processing methods. Raster processes are more commonly used because they can be significantly faster computationally...

METHAMPHETAMINE USE AMONG RURAL WHITE AND NATIVE AMERICAN ADOLESCENTS: AN APPLICATION OF THE STRESS PROCESS MODEL

PubMed Central

Eitle, David J.; McNulty Eitle, Tamela

2016-01-01

Methamphetamine use has been identified as having significant adverse health consequences, yet we know little about the correlates of its use. Additionally, research has found that Native Americans are at the highest risk for methamphetamine use. Our exploratory study, informed by the stress process model, examines stress and stress buffering factors associated with methamphetamine use among a cross-sectional sample of rural white and Native American adolescents (n=573). Results of logistic regression analyses revealed mixed support for the stress process model; while stress exposure and family methamphetamine use predicted past year methamphetamine use, the inclusion of these variables failed to attenuate the association between race and past year use. PMID:25445505

Back to the Origin

PubMed Central

Evertts, Adam G.

2012-01-01

In bacteria, replication is a carefully orchestrated event that unfolds the same way for each bacterium and each cell division. The process of DNA replication in bacteria optimizes cell growth and coordinates high levels of simultaneous replication and transcription. In metazoans, the organization of replication is more enigmatic. The lack of a specific sequence that defines origins of replication has, until recently, severely limited our ability to define the organizing principles of DNA replication. This question is of particular importance as emerging data suggest that replication stress is an important contributor to inherited genetic damage and the genomic instability in tumors. We consider here the replication program in several different organisms including recent genome-wide analyses of replication origins in humans. We review recent studies on the role of cytosine methylation in replication origins, the role of transcriptional looping and gene gating in DNA replication, and the role of chromatin’s 3-dimensional structure in DNA replication. We use these new findings to consider several questions surrounding DNA replication in metazoans: How are origins selected? What is the relationship between replication and transcription? How do checkpoints inhibit origin firing? Why are there early and late firing origins? We then discuss whether oncogenes promote cancer through a role in DNA replication and whether errors in DNA replication are important contributors to the genomic alterations and gene fusion events observed in cancer. We conclude with some important areas for future experimentation. PMID:23634256

Calcium and aluminum impacts on sugar maple physiology in a northern hardwood forest.

PubMed

Halman, Joshua M; Schaberg, Paul G; Hawley, Gary J; Pardo, Linda H; Fahey, Timothy J

2013-11-01

Forests of northeastern North America have been exposed to anthropogenic acidic inputs for decades, resulting in altered cation relations and disruptions to associated physiological processes in multiple tree species, including sugar maple (Acer saccharum Marsh.). In the current study, the impacts of calcium (Ca) and aluminum (Al) additions on mature sugar maple physiology were evaluated at the Hubbard Brook Experimental Forest (Thornton, NH, USA) to assess remediation (Ca addition) or exacerbation (Al addition) of current acidified conditions. Fine root cation concentrations and membrane integrity, carbon (C) allocation, foliar cation concentrations and antioxidant activity, foliar response to a spring freezing event and reproductive ability (flowering, seed quantity, filled seed and seed germination) were evaluated for dominant sugar maple trees in a replicated plot study. Root damage and foliar antioxidant activity were highest in Al-treated trees, while growth-associated C, foliar re-flush following a spring frost and reproductive ability were highest in Ca-treated trees. In general, we found that trees on Ca-treated plots preferentially used C resources for growth and reproductive processes, whereas Al-treated trees devoted C to defense-based processes. Similarities between Al-treated and control trees were observed for foliar cation concentrations, C partitioning and seed production, suggesting that sugar maples growing in native forests may be more stressed than previously perceived. Our experiment suggests that disruption of the balance of Ca and Al in sugar maples by acid deposition continues to be an important driver of tree health.

Viral precursor protein P3 and its processed products perform discrete and essential functions in the poliovirus RNA replication complex

USDA-ARS?s Scientific Manuscript database

The differential use of protein precursors and their products is a key strategy used during poliovirus replication. To characterize the role of protein precursors during replication, we examined the complementation profiles of mutants that inhibited 3D polymerase or 3C-RNA binding activity. We showe...

Mouse Norovirus infection promotes autophagy induction to facilitate replication but prevents final autophagosome maturation

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

O’Donnell, Tanya B.; Hyde, Jennifer L.; Mintern, Justine D.

Autophagy is a cellular process used to eliminate intracellular pathogens. Many viruses however are able to manipulate this cellular process for their own advantage. Here we demonstrate that Mouse Norovirus (MNV) infection induces autophagy but does not appear to utilise the autophagosomal membrane for establishment and formation of the viral replication complex. We have observed that MNV infection results in lipidation and recruitment of LC3 to the autophagosome membrane but prevents subsequent fusion of the autophagosomes with lysosomes, as SQSTM1 (an autophagy receptor) accumulates and Lysosome-Associated Membrane Protein1 is sequestered to the MNV replication complex (RC) rather than to autophagosomes.more » We have additionally observed that chemical modulation of autophagy differentially affects MNV replication. From this study we can conclude that MNV infection induces autophagy, however suppresses the final maturation step of this response, indicating that autophagy induction contributes to MNV replication independently of RC biogenesis. - Highlights: • MNV induces autophagy in infected murine macrophages. • MNV does not utilise autophagosomal membranes for replication. • The MNV-induced autophagosomes do not fuse with lysosomes. • MNV sequesters SQSTM1 to prevent autophagy degradation and turnover. • Chemical modulation of autophagy enhances MNV replication.« less

Detoxification of biomass derived acetate via metabolic conversion to ethanol, acetone, isopropanol, or ethyl acetate

DOEpatents

Sillers, William Ryan; Van Dijken, Hans; Licht, Steve; Shaw, IV, Arthur J.; Gilbert, Alan Benjamin; Argyros, Aaron; Froehlich, Allan C.; McBride, John E.; Xu, Haowen; Hogsett, David A.; Rajgarhia, Vineet B.

2017-03-28

One aspect of the invention relates to a genetically modified thermophilic or mesophilic microorganism, wherein a first native gene is partially, substantially, or completely deleted, silenced, inactivated, or down-regulated, which first native gene encodes a first native enzyme involved in the metabolic production of an organic acid or a salt thereof, thereby increasing the native ability of said thermophilic or mesophilic microorganism to produce lactate or acetate as a fermentation product. In certain embodiments, the aforementioned microorganism further comprises a first non-native gene, which first non-native gene encodes a first non-native enzyme involved in the metabolic production of lactate or acetate. Another aspect of the invention relates to a process for converting lignocellulosic biomass to lactate or acetate, comprising contacting lignocellulosic biomass with a genetically modified thermophilic or mesophilic microorganism.

Enquire within: cultural evolution and cognitive science.

PubMed

Heyes, Cecilia

2018-04-05

Cultural evolution and cognitive science need each other. Cultural evolution needs cognitive science to find out whether the conditions necessary for Darwinian evolution are met in the cultural domain. Cognitive science needs cultural evolution to explain the origins of distinctively human cognitive processes. Focusing on the first question, I argue that cultural evolutionists can get empirical traction on third-way cultural selection by rooting the distinction between replication and reconstruction, two modes of cultural inheritance, in the distinction between System 1 and System 2 cognitive processes. This move suggests that cultural epidemiologists are right in thinking that replication has higher fidelity than reconstruction, and replication processes are not genetic adaptations for culture, but wrong to assume that replication is rare. If replication is not rare, an important requirement for third-way cultural selection, one-shot fidelity , is likely to be met. However, there are other requirements, overlooked by dual-inheritance theorists when they conflate strong (Darwinian) and weak (choice) senses of 'cultural selection', including dumb choices and recurrent fidelity In a second excursion into cognitive science, I argue that these requirements can be met by metacognitive social learning strategies , and trace the origins of these distinctively human cognitive processes to cultural evolution. Like other forms of cultural learning, they are not cognitive instincts but cognitive gadgets.This article is part of the theme issue 'Bridging cultural gaps: interdisciplinary studies in human cultural evolution'. © 2018 The Author(s).

Helicobacter pylori shows asymmetric and polar cell divisome assembly associated with DNA replisome.

PubMed

Kamran, Mohammad; Dubey, Priyanka; Verma, Vijay; Dasgupta, Santanu; Dhar, Suman K

2018-05-09

DNA replication and cell division are two fundamental processes in the life cycle of a cell. The majority of prokaryotic cells undergo division by means of binary fission in coordination with replication of the genome. Both processes, but especially their coordination, are poorly understood in Helicobacter pylori. Here, we studied the cell divisome assembly and the subsequent processes of membrane and peptidoglycan synthesis in the bacterium. To our surprise, we found the cell divisome assembly to be polar, which was well-corroborated by the asymmetric membrane and peptidoglycan synthesis at the poles. The divisome components showed its assembly to be synchronous with that of the replisome and the two remained associated throughout the cell cycle, demonstrating a tight coordination among chromosome replication, segregation and cell division in H. pylori. To our knowledge, this is the first report where both DNA replication and cell division along with their possible association have been demonstrated for this pathogenic bacterium. © 2018 Federation of European Biochemical Societies.

Investigation of the Causes of Breast Cancer at the Cellular Level: Isolation of In Vivo Binding Sites of the Human Origin Recognition Complex

DTIC Science & Technology

2002-08-01

We study the process of DNA replication in proliferating human cells. Our efforts are directed to the identification and characterization of proteins...that promote DNA replication (initiators) as well as the DNA sequences recognized by them (replicators) . We have focused in a group of initiator...to be a critical factor for the coordination of DNA replication with the cell division cycle. hOrclp levels are higher between the exit of mitosis and

Human Mitochondrial DNA Replication

PubMed Central

Holt, Ian J.; Reyes, Aurelio

2012-01-01

Elucidation of the process of DNA replication in mitochondria is in its infancy. For many years, maintenance of the mitochondrial genome was regarded as greatly simplified compared to the nucleus. Mammalian mitochondria were reported to lack all DNA repair systems, to eschew DNA recombination, and to possess but a single DNA polymerase, polymerase γ. Polγ was said to replicate mitochondrial DNA exclusively via one mechanism, involving only two priming events and a handful of proteins. In this “strand-displacement model,” leading strand DNA synthesis begins at a specific site and advances approximately two-thirds of the way around the molecule before DNA synthesis is initiated on the “lagging” strand. Although the displaced strand was long-held to be coated with protein, RNA has more recently been proposed in its place. Furthermore, mitochondrial DNA molecules with all the features of products of conventional bidirectional replication have been documented, suggesting that the process and regulation of replication in mitochondria is complex, as befits a genome that is a core factor in human health and longevity. PMID:23143808

Unveiling the mystery of mitochondrial DNA replication in yeasts.

PubMed

Chen, Xin Jie; Clark-Walker, George Desmond

2018-01-01

Conventional DNA replication is initiated from specific origins and requires the synthesis of RNA primers for both the leading and lagging strands. In contrast, the replication of yeast mitochondrial DNA is origin-independent. The replication of the leading strand is likely primed by recombinational structures and proceeded by a rolling circle mechanism. The coexistent linear and circular DNA conformers facilitate the recombination-based initiation. The replication of the lagging strand is poorly understood. Re-evaluation of published data suggests that the rolling circle may also provide structures for the synthesis of the lagging-strand by mechanisms such as template switching. Thus, the coupling of recombination with rolling circle replication and possibly, template switching, may have been selected as an economic replication mode to accommodate the reductive evolution of mitochondria. Such a replication mode spares the need for conventional replicative components, including those required for origin recognition/remodelling, RNA primer synthesis and lagging-strand processing. Copyright © 2017 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

Blood Politics, Ethnic Identity, and Racial Misclassification among American Indians and Alaska Natives

PubMed Central

Haozous, Emily A.; Strickland, Carolyn J.; Palacios, Janelle F.; Solomon, Teshia G. Arambula

2014-01-01

Misclassification of race in medical and mortality records has long been documented as an issue in American Indian/Alaska Native data. Yet, little has been shared in a cohesive narrative which outlines why misclassification of American Indian/Alaska Native identity occurs. The purpose of this paper is to provide a summary of the current state of the science in racial misclassification among American Indians and Alaska Natives. We also provide a historical context on the importance of this problem and describe the ongoing political processes that both affect racial misclassification and contribute to the context of American Indian and Alaska Native identity. PMID:24669226

Blood politics, ethnic identity, and racial misclassification among American Indians and Alaska Natives.

PubMed

Haozous, Emily A; Strickland, Carolyn J; Palacios, Janelle F; Solomon, Teshia G Arambula

2014-01-01

Misclassification of race in medical and mortality records has long been documented as an issue in American Indian/Alaska Native data. Yet, little has been shared in a cohesive narrative which outlines why misclassification of American Indian/Alaska Native identity occurs. The purpose of this paper is to provide a summary of the current state of the science in racial misclassification among American Indians and Alaska Natives. We also provide a historical context on the importance of this problem and describe the ongoing political processes that both affect racial misclassification and contribute to the context of American Indian and Alaska Native identity.

Attacking invasive grasses

USGS Publications Warehouse

Keeley, Jon E.

2015-01-01

In grasslands fire may play a role in the plant invasion process, both by creating disturbances that potentially favour non-native invasions and as a possible tool for controlling alien invasions. Havill et al. (Applied Vegetation Science, 18, 2015, this issue) determine how native and non-native species respond to different fire regimes as a first step in understanding the potential control of invasive grasses.

The Medicine of Coming to Center: Use of the Native American Centering Technique--Ayeli--To Promote Wellness and Healing in Group Work

ERIC Educational Resources Information Center

Garrett, Michael Tlanusta; Brubaker, Michael; Torres-Rivera, Edil; West-Olatunji, Cirecie; Conwill, William L.

2008-01-01

This article provides group counselors a description of Ayeli, a culturally-based centering technique rooted in Native American traditions. Ayeli is a process that allows participants an opportunity to experience and reflect on four crucial elements relevant to wellness from a Native American perspective: belonging, mastery, independence, and…

Structural Correlates for Lexical Efficiency and Number of Languages in Non-Native Speakers of English

ERIC Educational Resources Information Center

Grogan, A.; Parker Jones, O.; Ali, N.; Crinion, J.; Orabona, S.; Mechias, M. L.; Ramsden, S.; Green, D. W.; Price, C. J.

2012-01-01

We used structural magnetic resonance imaging (MRI) and voxel based morphometry (VBM) to investigate whether the efficiency of word processing in the non-native language (lexical efficiency) and the number of non-native languages spoken (2+ versus 1) were related to local differences in the brain structure of bilingual and multilingual speakers.…

Arthropod assemblages on native and nonnative plant species of a coastal reserve in California.

PubMed

Fork, Susanne K

2010-06-01

Biological invasions by nonnative plant species are a widespread phenomenon. Many studies have shown strong ecological impacts of plant invasions on native plant communities and ecosystem processes. Far fewer studies have examined effects on associated animal communities. From the perspective of a reserve's land management, I addressed the question of whether arthropod assemblages on two nonnative plant species of concern were impoverished compared with those assemblages associated with two predominant native plant species of that reserve. If the nonnative plant species, Conium maculatum L., and Phalaris aquatica L., supported highly depauperate arthropod assemblages compared with the native plant species, Baccharis pilularis De Candolle and Leymus triticoides (Buckley) Pilger, this finding would provide additional support for prioritizing removal of nonnatives and restoration of natives. I assessed invertebrate assemblages at the taxonomic levels of arthropod orders, Coleoptera families, and Formicidae species, using univariate analyses to examine community attributes (richness and abundance) and multivariate techniques to assess arthropod assemblage community composition differences among plant species. Arthropod richness estimates by taxonomic level between native and nonnative vegetation showed varying results. Overall, arthropod richness of the selected nonnative plants, examined at higher taxonomic resolution, was not necessarily less diverse than two of common native plants found on the reserve, although differences were found among plant species. Impacts of certain nonnative plant species on arthropod assemblages may be more difficult to elucidate than those impacts shown on native plants and ecosystem processes.

Dynamic Folding Pathway Models of the Trp-Cage Protein

PubMed Central

Kim, Seung-Yeon

2013-01-01

Using action-derived molecular dynamics (ADMD), we study the dynamic folding pathway models of the Trp-cage protein by providing its sequential conformational changes from its initial disordered structure to the final native structure at atomic details. We find that the numbers of native contacts and native hydrogen bonds are highly correlated, implying that the native structure of Trp-cage is achieved through the concurrent formations of native contacts and native hydrogen bonds. In early stage, an unfolded state appears with partially formed native contacts (~40%) and native hydrogen bonds (~30%). Afterward, the folding is initiated by the contact of the side chain of Tyr3 with that of Trp6, together with the formation of the N-terminal α-helix. Then, the C-terminal polyproline structure docks onto the Trp6 and Tyr3 rings, resulting in the formations of the hydrophobic core of Trp-cage and its near-native state. Finally, the slow adjustment processes of the near-native states into the native structure are dominant in later stage. The ADMD results are in agreement with those of the experimental folding studies on Trp-cage and consistent with most of other computational studies. PMID:23865078

Replication Fork Protection Factors Controlling R-Loop Bypass and Suppression.

PubMed

Chang, Emily Yun-Chia; Stirling, Peter C

2017-01-14

Replication-transcription conflicts have been a well-studied source of genome instability for many years and have frequently been linked to defects in RNA processing. However, recent characterization of replication fork-associated proteins has revealed that defects in fork protection can directly or indirectly stabilize R-loop structures in the genome and promote transcription-replication conflicts that lead to genome instability. Defects in essential DNA replication-associated activities like topoisomerase, or the minichromosome maintenance (MCM) helicase complex, as well as fork-associated protection factors like the Fanconi anemia pathway, both appear to mitigate transcription-replication conflicts. Here, we will highlight recent advances that support the concept that normal and robust replisome function itself is a key component of mitigating R-loop coupled genome instability.

The foreign language effect on the self-serving bias: A field experiment in the high school classroom

PubMed Central

van Witteloostuijn, Arjen

2018-01-01

The rise of bilingual education triggers an important question: which language is preferred for a particular school activity? Our field experiment (n = 120) shows that students (aged 13–15) who process feedback in non-native English have greater self-serving bias than students who process feedback in their native Dutch. By contrast, literature on the foreign-language emotionality effect suggests a weaker self-serving bias in the non-native language, so our result adds nuance to that literature. The result is important to schools as it suggests that teachers may be able to reduce students’ defensiveness and demotivation by communicating negative feedback in the native language, and teachers may be able to increase students’ confidence and motivation by communicating positive feedback in the foreign language. PMID:29425224

Analysis of Consumers' Preferences and Price Sensitivity to Native Chickens.

PubMed

Lee, Min-A; Jung, Yoojin; Jo, Cheorun; Park, Ji-Young; Nam, Ki-Chang

2017-01-01

This study analyzed consumers' preferences and price sensitivity to native chickens. A survey was conducted from Jan 6 to 17, 2014, and data were collected from consumers (n=500) living in Korea. Statistical analyses evaluated the consumption patterns of native chickens, preference marketing for native chicken breeds which will be newly developed, and price sensitivity measurement (PSM). Of the subjects who preferred broilers, 24.3% do not purchase native chickens because of the dryness and tough texture, while those who preferred native chickens liked their chewy texture (38.2%). Of the total subjects, 38.2% preferred fried native chickens (38.2%) for processed food, 38.4% preferred direct sales for native chicken distribution, 51.0% preferred native chickens to be slaughtered in specialty stores, and 32.4% wanted easy access to native chickens. Additionally, the price stress range (PSR) was 50 won and the point of marginal cheapness (PMC) and point of marginal expensiveness (PME) were 6,980 won and 12,300 won, respectively. Evaluation of the segmentation market revealed that consumers who prefer broiler to native chicken breeds were more sensitive to the chicken price. To accelerate the consumption of newly developed native chicken meat, it is necessary to develop a texture that each consumer needs, to increase the accessibility of native chickens, and to have diverse menus and recipes as well as reasonable pricing for native chickens.

Analysis of Consumers’ Preferences and Price Sensitivity to Native Chickens

PubMed Central

Lee, Min-A; Jung, Yoojin; Jo, Cheorun

2017-01-01

This study analyzed consumers’ preferences and price sensitivity to native chickens. A survey was conducted from Jan 6 to 17, 2014, and data were collected from consumers (n=500) living in Korea. Statistical analyses evaluated the consumption patterns of native chickens, preference marketing for native chicken breeds which will be newly developed, and price sensitivity measurement (PSM). Of the subjects who preferred broilers, 24.3% do not purchase native chickens because of the dryness and tough texture, while those who preferred native chickens liked their chewy texture (38.2%). Of the total subjects, 38.2% preferred fried native chickens (38.2%) for processed food, 38.4% preferred direct sales for native chicken distribution, 51.0% preferred native chickens to be slaughtered in specialty stores, and 32.4% wanted easy access to native chickens. Additionally, the price stress range (PSR) was 50 won and the point of marginal cheapness (PMC) and point of marginal expensiveness (PME) were 6,980 won and 12,300 won, respectively. Evaluation of the segmentation market revealed that consumers who prefer broiler to native chicken breeds were more sensitive to the chicken price. To accelerate the consumption of newly developed native chicken meat, it is necessary to develop a texture that each consumer needs, to increase the accessibility of native chickens, and to have diverse menus and recipes as well as reasonable pricing for native chickens. PMID:28747834

Problem solving during artificial selection of self-replicating loops

NASA Astrophysics Data System (ADS)

Chou, Hui-Hsien; Reggia, James A.

1998-05-01

Past cellular automata models of self-replication have generally done only one thing: replicate themselves. However, it has recently been demonstrated that such self-replicating structures can be programmed to also carry out a task during the replication process. Past models of this sort have been limited in that the “program” involved is copied unchanged from parent to child, so that each generation of replicants is executing exactly the same program on exactly the same data. Here we take a different approach in which each replicant receives a distinct partial solution that is modified during replication. Under artificial selection, replicants with promising solutions proliferate while those with failed solutions are lost. We show that this approach can be applied successfully to solve an NP-complete problem, the satisfiability problem. Bounds are given on the cellular space size and time needed to solve a given problem, and simulations demonstrate that this approach works effectively. These and other recent results raise the possibility of evolving self-replicating structures that have a simulated metabolism or that carry out useful tasks.

Human CST has independent functions during telomere duplex replication and C-strand fill-in

PubMed Central

Wang, Feng; Stewart, Jason A.; Kasbek, Christopher; Zhao, Yong; Wright, Woodring E.; Price, Carolyn M.

2012-01-01

Summary Human CST (CTC1-STN1-TEN1) is an RPA-like complex that is needed for efficient replication through the telomere duplex and genome-wide replication restart after fork stalling. Here we show that STN1/CST has a second function in telomere replication during G-overhang maturation. Analysis of overhang structure after STN1 depletion revealed normal kinetics for telomerase-mediated extension in S-phase but a delay in subsequent overhang shortening. This delay resulted from a defect in C-strand fill-in. Short telomeres exhibited the fill-in defect but normal telomere duplex replication, indicating that STN1/CST functions independently in these processes. Our work also indicates that the requirement for STN1/CST in telomere duplex replication correlates with increasing telomere length and replication stress. Our results provide the first direct evidence that STN1/CST participates in C-strand fill-in. They also demonstrate that STN1/CST participates in two mechanistically separate steps during telomere replication and identify CST as a novel replication factor that solves diverse replication-associated problems. PMID:23142664

Resource competition in plant invasions: emerging patterns and research needs

PubMed Central

Gioria, Margherita; Osborne, Bruce A.

2014-01-01

Invasions by alien plants provide a unique opportunity to examine competitive interactions among plants. While resource competition has long been regarded as a major mechanism responsible for successful invasions, given a well-known capacity for many invaders to become dominant and reduce plant diversity in the invaded communities, few studies have measured resource competition directly or have assessed its importance relative to that of other mechanisms, at different stages of an invasion process. Here, we review evidence comparing the competitive ability of invasive species vs. that of co-occurring native plants, along a range of environmental gradients, showing that many invasive species have a superior competitive ability over native species, although invasive congeners are not necessarily competitively superior over native congeners, nor are alien dominants are better competitors than native dominants. We discuss how the outcomes of competition depend on a number of factors, such as the heterogeneous distribution of resources, the stage of the invasion process, as well as phenotypic plasticity and evolutionary adaptation, which may result in increased or decreased competitive ability in both invasive and native species. Competitive advantages of invasive species over natives are often transient and only important at the early stages of an invasion process. It remains unclear how important resource competition is relative to other mechanisms (competition avoidance via phenological differences, niche differentiation in space associated with phylogenetic distance, recruitment and dispersal limitation, indirect competition, and allelopathy). Finally, we identify the conceptual and methodological issues characterizing competition studies in plant invasions, and we discuss future research needs, including examination of resource competition dynamics and the impact of global environmental change on competitive interactions between invasive and native species. PMID:25324851

Resource competition in plant invasions: emerging patterns and research needs.

PubMed

Gioria, Margherita; Osborne, Bruce A

2014-01-01

Invasions by alien plants provide a unique opportunity to examine competitive interactions among plants. While resource competition has long been regarded as a major mechanism responsible for successful invasions, given a well-known capacity for many invaders to become dominant and reduce plant diversity in the invaded communities, few studies have measured resource competition directly or have assessed its importance relative to that of other mechanisms, at different stages of an invasion process. Here, we review evidence comparing the competitive ability of invasive species vs. that of co-occurring native plants, along a range of environmental gradients, showing that many invasive species have a superior competitive ability over native species, although invasive congeners are not necessarily competitively superior over native congeners, nor are alien dominants are better competitors than native dominants. We discuss how the outcomes of competition depend on a number of factors, such as the heterogeneous distribution of resources, the stage of the invasion process, as well as phenotypic plasticity and evolutionary adaptation, which may result in increased or decreased competitive ability in both invasive and native species. Competitive advantages of invasive species over natives are often transient and only important at the early stages of an invasion process. It remains unclear how important resource competition is relative to other mechanisms (competition avoidance via phenological differences, niche differentiation in space associated with phylogenetic distance, recruitment and dispersal limitation, indirect competition, and allelopathy). Finally, we identify the conceptual and methodological issues characterizing competition studies in plant invasions, and we discuss future research needs, including examination of resource competition dynamics and the impact of global environmental change on competitive interactions between invasive and native species.

Biomaterial Characterization of Off-the-Shelf Decellularized Porcine Pericardial Tissue for use in Prosthetic Valvular Applications.

PubMed

Choe, Joshua A; Jana, Soumen; Tefft, Brandon J; Hennessy, Ryan S; Go, Jason; Morse, David; Lerman, Amir; Young, Melissa D

2018-05-10

Fixed pericardial tissue is commonly used for commercially available xenograft valve implants, and has proven durability, but lacks the capability to remodel and grow. Decellularized porcine pericardial tissue has the promise to outperform fixed tissue and remodel, but the decellularization process has been shown to damage the collagen structure and reduce mechanical integrity of the tissue. Therefore, a comparison of uniaxial tensile properties was performed on decellularized, decellularized-sterilized, fixed, and native porcine pericardial tissue, versus native valve leaflet cusps. The results of non-parametric analysis showed statistically significant differences (p<0.05) between the stiffness of 1) decellularized vs. native pericardium, and native cusps as well as fixed tissue respectively; however decellularized tissue showed large increases in elastic properties. Porosity testing of the tissues showed no statistical difference between decellularized or decell-sterilized tissue compared to native cusps (p>0.05). SEM confirmed that valvular endothelial and interstitial cells colonized the decellularized pericardial surface when seeded and grown for 30 days in static culture. Collagen assays and TEM analysis showed limited reductions in collagen with processing; yet, GAG assays showed great reductions in the processed pericardium relative to native cusps. Decellularized pericardium had comparatively lower mechanical properties amongst the groups studied; yet, the stiffness was comparatively similar to the native cusps and demonstrated a lack of cytotoxicity. Suture retention, accelerated wear, and hydrodynamic testing of prototype decellularized and decell-sterilized valves showed positive functionality. Sterilized tissue could mimic valvular mechanical environment in vitro, therefore making it a viable potential candidate for off-the-shelf tissue engineered valvular applications. KEYTERMS Decellularization, Sterilization, Pericardial Tissue, Heart Valves, Tissue Engineering, Biomechanics. This article is protected by copyright. All rights reserved.

Replicating Social Programmes: Approaches, Strategies and Conceptual Issues. Management of Social Transformations (MOST) Discussion Paper Series, No. 18.

ERIC Educational Resources Information Center

van Oudenhoven, Nico; Wazir, Rekha

This paper reviews the key issues and methodologies involved in the replication of social programs, as they pertain to non-profit sector development in the United States and in international development. The related process of knowledge transfer and dissemination, as well as the more specific strategies involved in replication and going-to-scale…

Self-replication of chemical systems based on recognition within a double or a triple helix - A realistic hypothesis

NASA Technical Reports Server (NTRS)

Kanavarioti, Anastassia

1992-01-01

A scenario is proposed for the non-enzymatic self-replication of short RNA molecules. The self-replication of an oligopyrimidine strand is considered and the process of template-directed synthesis based on recognition within a double helix is discussed. Replication mechanisms are suggested for selected oligonucleotides. The mechanisms are based on Watson-Crick base pairing between complementary nucleotides as well as Hoogsteen base pairing between a duplex and the complementary third strand. It is suggested that self-replication based on these mechanisms may be accomplished but may result in a substantial amount of misinformation transfer when mixed oligonucleotides are used.

Process of infection with bacteriophage phi chi 174. XL. Viral DNA replication of phi chi 174 mutants blocked in progeny single-stranded DNA synthesis.

PubMed Central

Fukuda, A; Sinsheimer, R L

1976-01-01

Mutation in several different cistrons of bacteriophage phi chi 174 blocks net progeny single-stranded DNA synthesis at the late period of infection (15). For the study of the functions of these cistrons in single-stranded DNA synthesis, asymmetric replication of replicative form DNA was examined at the late period of infection with amber mutants of these cistrons. While the normal, rapid process of asymmetric single-stranded viral DNA synthesis is blocked at the late period of these mutant infections, an asymmetric synthesis of the viral strand of replicative-form DNA is observed in this period, though at a reduced level, together with degradation of prelabeled viral strand. Some intermediate replicative-form molecules were also detected. Asymmetric synthesis of the viral strand of replicative-form DNA at the late period of phi chi infection is completely inhibited in the presence of a low concentration (35mug/ml) of chloramphenicol (which also blocks net single-stranded viral DNA synthesis). These results are discussed in terms of the possible role of the specific viral proteins for normal single-stranded DNA synthesis. PMID:1255871

An Event-Related Potential (ERP) Investigation of Filler-Gap Processing in Native and Second Language Speakers

ERIC Educational Resources Information Center

Dallas, Andrea; DeDe, Gayle; Nicol, Janet

2013-01-01

The current study employed a neuro-imaging technique, Event-Related Potentials (ERP), to investigate real-time processing of sentences containing filler-gap dependencies by late-learning speakers of English as a second language (L2) with a Chinese native language background. An individual differences approach was also taken to examine the role of…

Effect of Visual Experience on Face Processing: A Developmental Study of Inversion and Non-Native Effects

ERIC Educational Resources Information Center

Sangrigoli, Sandy; de Schonen, Scania

2004-01-01

In adults, three phenomena are taken to demonstrate an experience effect on face recognition: an inversion effect, a non-native face effect (so-called "other-race" effect) and their interaction. It is crucial for our understanding of the developmental perception mechanisms of object processing to discover when these effects are present in…

Do grammatical-gender distinctions learned in the second language influence native-language lexical processing?

PubMed Central

Kaushanskaya, Margarita; Smith, Samantha

2015-01-01

How does learning a second language influence native language processing? In the present study, we examined whether knowledge of Spanish – a language that marks grammatical gender on inanimate nouns – influences lexical processing in English – a language that does not mark grammatical gender. We tested three groups of adult English native speakers: monolinguals, emergent bilinguals with high exposure to Spanish, and emergent bilinguals with low exposure to Spanish. Participants engaged in an associative learning task in English where they learned to associate names of inanimate objects with proper names. For half of the pairs, the grammatical gender of the noun’s Spanish translation matched the gender of the proper name (e.g., corn-Patrick). For half of the pairs, the grammatical gender of the noun’s Spanish translation mismatched the gender of the proper noun (e.g., beach-William). High-Spanish-exposure bilinguals (but not monolinguals or low-Spanish-exposure bilinguals) were less accurate at retrieving proper names for gender-incongruent than for gender-congruent pairs. This indicates that second-language morphosyntactic information is activated during native-language processing, even when the second language is acquired later in life. PMID:26977134

Factors influencing microinjection molding replication quality

NASA Astrophysics Data System (ADS)

Vera, Julie; Brulez, Anne-Catherine; Contraires, Elise; Larochette, Mathieu; Trannoy-Orban, Nathalie; Pignon, Maxime; Mauclair, Cyril; Valette, Stéphane; Benayoun, Stéphane

2018-01-01

In recent years, there has been increased interest in producing and providing high-precision plastic parts that can be manufactured by microinjection molding: gears, pumps, optical grating elements, and so on. For all of these applications, the replication quality is essential. This study has two goals: (1) fabrication of high-precision parts using the conventional injection molding machine; (2) identification of robust parameters that ensure production quality. Thus, different technological solutions have been used: cavity vacuuming and the use of a mold coated with DLC or CrN deposits. AFM and SEM analyses were carried out to characterize the replication profile. The replication quality was studied in terms of the process parameters, coated and uncoated molds and crystallinity of the polymer. Specific studies were processed to quantify the replicability of injection molded parts (ABS, PC and PP). Analysis of the Taguchi experimental designs permits prioritization of the impact of each parameter on the replication quality. A discussion taking into account these new parameters and the thermal and spreading properties on the coatings is proposed. It appeared that, in general, increasing the mold temperature improves the molten polymer fill in submicron features except for the steel insert (for which the presence of a vacuum is the most important factor). Moreover, the DLC coating was the best coating to increase the quality of the replication. This result could be explained by the lower thermal diffusivity of this coating. We noted that the viscosity of the polymers is not a primordial factor of the replication quality.

Expression profiling of colorectal cancer cells reveals inhibition of DNA replication licensing by extracellular calcium.

PubMed

Aggarwal, Abhishek; Schulz, Herbert; Manhardt, Teresa; Bilban, Martin; Thakker, Rajesh V; Kallay, Enikö

2017-06-01

Colorectal cancer is one of the most common cancers in industrialised societies. Epidemiological studies, animal experiments, and randomized clinical trials have shown that dietary factors can influence all stages of colorectal carcinogenesis, from initiation through promotion to progression. Calcium is one of the factors with a chemoprophylactic effect in colorectal cancer. The aim of this study was to understand the molecular mechanisms of the anti-tumorigenic effects of extracellular calcium ([Ca 2+ ] o ) in colon cancer cells. Gene expression microarray analysis of colon cancer cells treated for 1, 4, and 24h with 2mM [Ca 2+ ] o identified significant changes in expression of 1571 probe sets (ANOVA, p<10 -5 ). The main biological processes affected by [Ca 2+ ] o were DNA replication, cell division, and regulation of transcription. All factors involved in DNA replication-licensing were significantly downregulated by [Ca 2+ ] o . Furthermore, we show that the calcium-sensing receptor (CaSR), a G protein-coupled receptor is a mediator involved in this process. To test whether these results were physiologically relevant, we fed mice with a standard diet containing low (0.04%), intermediate (0.1%), or high (0.9%) levels of dietary calcium. The main molecules regulating replication licensing were inhibited also in vivo, in the colon of mice fed high calcium diet. We show that among the mechanisms behind the chemopreventive effect of [Ca 2+ ] o is inhibition of replication licensing, a process often deregulated in neoplastic transformation. Our data suggest that dietary calcium is effective in preventing replicative stress, one of the main drivers of cancer and this process is mediated by the calcium-sensing receptor. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Cytomics - importance of multimodal analysis of cell function and proliferation in oncology.

PubMed

Tárnok, A; Bocsi, J; Brockhoff, G

2006-12-01

Cancer is a highly complex and heterogeneous disease involving a succession of genetic changes (frequently caused or accompanied by exogenous trauma), and resulting in a molecular phenotype that in turn results in a malignant specification. The development of malignancy has been described as a multistep process involving self-sufficiency in growth signals, insensitivity to antigrowth signals, evasion of apoptosis, limitless replicative potential, sustained angiogenesis, and finally tissue invasion and metastasis. The quantitative analysis of networking molecules within the cells might be applied to understand native-state tissue signalling biology, complex drug actions and dysfunctional signalling in transformed cells, that is, in cancer cells. High-content and high-throughput single-cell analysis can lead to systems biology and cytomics. The application of cytomics in cancer research and diagnostics is very broad, ranging from the better understanding of the tumour cell biology to the identification of residual tumour cells after treatment, to drug discovery. The ultimate goal is to pinpoint in detail these processes on the molecular, cellular and tissue level. A comprehensive knowledge of these will require tissue analysis, which is multiplex and functional; thus, vast amounts of data are being collected from current genomic and proteomic platforms for integration and interpretation as well as for new varieties of updated cytomics technology. This overview will briefly highlight the most important aspects of this continuously developing field.

Synchronization of DNA array replication kinetics

NASA Astrophysics Data System (ADS)

Manturov, Alexey O.; Grigoryev, Anton V.

2016-04-01

In the present work we discuss the features of the DNA replication kinetics at the case of multiplicity of simultaneously elongated DNA fragments. The interaction between replicated DNA fragments is carried out by free protons that appears at the every nucleotide attachment at the free end of elongated DNA fragment. So there is feedback between free protons concentration and DNA-polymerase activity that appears as elongation rate dependence. We develop the numerical model based on a cellular automaton, which can simulate the elongation stage (growth of DNA strands) for DNA elongation process with conditions pointed above and we study the possibility of the DNA polymerases movement synchronization. The results obtained numerically can be useful for DNA polymerase movement detection and visualization of the elongation process in the case of massive DNA replication, eg, under PCR condition or for DNA "sequencing by synthesis" sequencing devices evaluation.

Replication of plant RNA virus genomes in a cell-free extract of evacuolated plant protoplasts

PubMed Central

Komoda, Keisuke; Naito, Satoshi; Ishikawa, Masayuki

2004-01-01

The replication of eukaryotic positive-strand RNA virus genomes occurs through a complex process involving multiple viral and host proteins and intracellular membranes. Here we report a cell-free system that reproduces this process in vitro. This system uses a membrane-containing extract of uninfected plant protoplasts from which the vacuoles had been removed by Percoll gradient centrifugation. We demonstrate that the system supported translation, negative-strand RNA synthesis, genomic RNA replication, and subgenomic RNA transcription of tomato mosaic virus and two other plant positive-strand RNA viruses. The RNA synthesis, which depended on translation of the genomic RNA, produced virus-related RNA species similar to those that are generated in vivo. This system will aid in the elucidation of the mechanisms of genome replication in these viruses. PMID:14769932

Analysis of mutagenic DNA repair in a thermoconditional mutant of Saccharomyces cerevisiae. IV. Influence of DNA replication and excision repair on REV2 dependent UV-mutagenesis and repair.

PubMed

Siede, W; Eckardt, F

1986-01-01

A double mutant being thermoconditionally defective in mutation induction as well as in repair of pre-lethal UV-induced DNA damage (rev2ts) and deficient in excision repair (rad3-2) was studied in temperature-shift experiments. The influence of inhibitors of DNA replication (hydroxyurea, aphidicolin) was determined. Additionally, an analysis of the dose-response pattern of mutation induction ("mutation kinetics") at several ochre alleles was carried out. It was concluded that the UV-inducible REV2 dependent mutagenic repair process is not induced in excision-deficient cells. In excision-deficient cells, REV2 dependent mutation fixation is slow and mostly post-replicative though not dependent on DNA replication. The REV2 mediated mutagenic process could be separated from the repair function.

Culturally scarred trees in the Bob Marshall Wilderness, Montana, USA - Interpreting Native American historical forest use in a wilderness area

Treesearch

Lars Ostlund; Bob Keane; Steve Arno; Rikard Andersson

2005-01-01

Wilderness areas are primarily set aside to protect natural ecosystems and processes. However, most protected areas have a long history of native peoples' land use predating their protection. The general paucity of evidence in the form of historical records, in combination with romantic views of native peoples' effects on nature, often leads to their impact...

Evaluation of native plant seeds and seeding in the east-side central Cascades ponderosa pine zone

Treesearch

Nan C. Vance

2010-01-01

In dry, open coniferous forests of the montane West, stand-replacing wildfires and land use activities alter the composition and abundance of native grasses and forbs by degrading the habitat and accelerating the invasion of exotic annuals. On these lands, native forbs and grasses delayed or prevented from recovery by natural processes may require intervention through...

The emotional impact of being myself: Emotions and foreign-language processing.

PubMed

Ivaz, Lela; Costa, Albert; Duñabeitia, Jon Andoni

2016-03-01

Native languages are acquired in emotionally rich contexts, whereas foreign languages are typically acquired in emotionally neutral academic environments. As a consequence of this difference, it has been suggested that bilinguals' emotional reactivity in foreign-language contexts is reduced as compared with native language contexts. In the current study, we investigated whether this emotional distance associated with foreign languages could modulate automatic responses to self-related linguistic stimuli. Self-related stimuli enhance performance by boosting memory, speed, and accuracy as compared with stimuli unrelated to the self (the so-called self-bias effect). We explored whether this effect depends on the language context by comparing self-biases in a native and a foreign language. Two experiments were conducted with native Spanish speakers with a high level of English proficiency in which they were asked to complete a perceptual matching task during which they associated simple geometric shapes (circles, squares, and triangles) with the labels "you," "friend," and "other" either in their native or foreign language. Results showed a robust asymmetry in the self-bias in the native- and foreign-language contexts: A larger self-bias was found in the native than in the foreign language. An additional control experiment demonstrated that the same materials administered to a group of native English speakers yielded robust self-bias effects that were comparable in magnitude to the ones obtained with the Spanish speakers when tested in their native language (but not in their foreign language). We suggest that the emotional distance evoked by the foreign-language contexts caused these differential effects across language contexts. These results demonstrate that the foreign-language effects are pervasive enough to affect automatic stages of emotional processing. (c) 2016 APA, all rights reserved).

Replication and Pedagogy in the History of Psychology V: The Metronome and Wilhelm Wundt's Search for the Components of Consciousness

ERIC Educational Resources Information Center

Ayala, Christopher; Borawski, Steven; Miller, Jonathon

2008-01-01

Wilhelm Wundt (1832-1920) believed that consciousness was represented by the interconnection of psychical processes comprised of temporal elements and compounds. To explore these processes, Wundt used a metronome to measure the amount of information that passed into consciousness across time. The current project replicated some of his procedures,…

Making sense of the noise: Replication difficulties of Correll's (2008) modulation of 1/f noise in a racial bias task.

PubMed

Madurski, Christine; LeBel, Etienne P

2015-08-01

Correll (Journal of Personality and Social Psychology, 94, 48-59, 2008; Study 2) found that instructions to use or avoid race information decreased the emission of 1/f noise in a weapon identification task (WIT). These results suggested that 1/f noise in racial bias tasks reflected an effortful deliberative process, providing new insights regarding the mechanisms underlying implicit racial biases. Given the potential theoretical and applied importance of understanding the psychological processes underlying implicit racial biases - and in light of the growing demand for independent direct replications of findings to ensure the cumulative nature of our science - we attempted to replicate Correll's finding in two high-powered studies. Despite considerable effort to closely duplicate all procedural and methodological details of the original study (i.e., same cover story, experimental manipulation, implicit measure task, original stimuli, task instructions, sampling frame, population, and statistical analyses), both replication attempts were unsuccessful in replicating the original finding challenging the theoretical account that 1/f noise in racial bias tasks reflects a deliberative process. However, the emission of 1/f noise did consistently emerge across samples in each of our conditions. Hence, future research is needed to clarify the psychological significance of 1/f noise in racial bias tasks.

An Amino-Terminal Polo Kinase Interaction Motif Acts in the Regulation of Centrosome Formation and Reveals a Novel Function for centrosomin (cnn) in Drosophila

PubMed Central

Eisman, Robert C.; Phelps, Melissa A. S.; Kaufman, Thomas

2015-01-01

The formation of the pericentriolar matrix (PCM) and a fully functional centrosome in syncytial Drosophila melanogaster embryos requires the rapid transport of Cnn during initiation of the centrosome replication cycle. We show a Cnn and Polo kinase interaction is apparently required during embryogenesis and involves the exon 1A-initiating coding exon, suggesting a subset of Cnn splice variants is regulated by Polo kinase. During PCM formation exon 1A Cnn-Long Form proteins likely bind Polo kinase before phosphorylation by Polo for Cnn transport to the centrosome. Loss of either of these interactions in a portion of the total Cnn protein pool is sufficient to remove native Cnn from the pool, thereby altering the normal localization dynamics of Cnn to the PCM. Additionally, Cnn-Short Form proteins are required for polar body formation, a process known to require Polo kinase after the completion of meiosis. Exon 1A Cnn-LF and Cnn-SF proteins, in conjunction with Polo kinase, are required at the completion of meiosis and for the formation of functional centrosomes during early embryogenesis. PMID:26447129

An Amino-Terminal Polo Kinase Interaction Motif Acts in the Regulation of Centrosome Formation and Reveals a Novel Function for centrosomin (cnn) in Drosophila.

PubMed

Eisman, Robert C; Phelps, Melissa A S; Kaufman, Thomas

2015-10-01

The formation of the pericentriolar matrix (PCM) and a fully functional centrosome in syncytial Drosophila melanogaster embryos requires the rapid transport of Cnn during initiation of the centrosome replication cycle. We show a Cnn and Polo kinase interaction is apparently required during embryogenesis and involves the exon 1A-initiating coding exon, suggesting a subset of Cnn splice variants is regulated by Polo kinase. During PCM formation exon 1A Cnn-Long Form proteins likely bind Polo kinase before phosphorylation by Polo for Cnn transport to the centrosome. Loss of either of these interactions in a portion of the total Cnn protein pool is sufficient to remove native Cnn from the pool, thereby altering the normal localization dynamics of Cnn to the PCM. Additionally, Cnn-Short Form proteins are required for polar body formation, a process known to require Polo kinase after the completion of meiosis. Exon 1A Cnn-LF and Cnn-SF proteins, in conjunction with Polo kinase, are required at the completion of meiosis and for the formation of functional centrosomes during early embryogenesis. Copyright © 2015 by the Genetics Society of America.

Atomistic Simulations of the pH Induced Functional Rearrangement of Influenza Hemagglutinin

NASA Astrophysics Data System (ADS)

Lin, Xingcheng; Noel, Jeffrey; Wang, Qinghua; Ma, Jianpeng; Onuchic, Jose

Influenza hemagglutinin (HA), a surface glycoprotein responsible for the entry and replication of flu viruses in their host cells, functions by starting a dramatic conformational rearrangement, which leads to a fusion of the viral and endosomal membranes. It has been claimed that a loop-to-coiled-coil transition of the B-loop domain of HA drives the HA-induced membrane fusion. On the lack of dynamical details, however, the microscopic picture for this proposed ``spring-loaded'' movement is missing. To elaborate on the transition of the B-loop, we performed a set of unbiased all-atom molecular dynamics simulations of the full B-loop structure with the CHARMM36 force field. The complete free-energy profile constructed from our simulations reveals a slow transition rate for the B-loop that is incompatible with a downhill process. Additionally, our simulations indicate two potential sources of kinetic traps in the structural switch of the B-loop: Desolvation barriers and non-native secondary structure formation. The slow timescale of the B-loop transition also confirms our previous discovery from simulations using a coarse-grained structure-based model, which identified two competitive pathways both with a slow B-loop transition for HA to guide the membrane fusion.

The Chinese Lexicon Project: A megastudy of lexical decision performance for 25,000+ traditional Chinese two-character compound words.

PubMed

Tse, Chi-Shing; Yap, Melvin J; Chan, Yuen-Lai; Sze, Wei Ping; Shaoul, Cyrus; Lin, Dan

2017-08-01

Using a megastudy approach, we developed a database of lexical variables and lexical decision reaction times and accuracy rates for more than 25,000 traditional Chinese two-character compound words. Each word was responded to by about 33 native Cantonese speakers in Hong Kong. This resource provides a valuable adjunct to influential mega-databases, such as the Chinese single-character, English, French, and Dutch Lexicon Projects. Three analyses were conducted to illustrate the potential uses of the database. First, we compared the proportion of variance in lexical decision performance accounted for by six word frequency measures and established that the best predictor was Cai and Brysbaert's (PLoS One, 5, e10729, 2010) contextual diversity subtitle frequency. Second, we ran virtual replications of three previously published lexical decision experiments and found convergence between the original experiments and the present megastudy. Finally, we conducted item-level regression analyses to examine the effects of theoretically important lexical variables in our normative data. This is the first publicly available large-scale repository of behavioral responses pertaining to Chinese two-character compound word processing, which should be of substantial interest to psychologists, linguists, and other researchers.

Role of Replication and CpG Methylation in Fragile X Syndrome CGG Deletions in Primate Cells

PubMed Central

Nichol Edamura, Kerrie; Leonard, Michelle R.; Pearson, Christopher E.

2005-01-01

Instability of the fragile X CGG repeat involves both maternally derived expansions and deletions in the gametes of full-mutation males. It has also been suggested that the absence of aberrant CpG methylation may enhance repeat deletions through an unknown process. The effect of CGG tract length, DNA replication direction, location of replication initiation, and CpG methylation upon CGG stability were investigated using an SV40 primate replication system. Replication-dependant deletions with 53 CGG repeats were observed when replication was initiated proximal to the repeat, with CGG as the lagging-strand template. When we initiated replication further from the repeat, while maintaining CGG as the lagging-strand template or using CCG as the lagging-strand template, significant instability was not observed. CpG methylation of the unstable template stabilized the repeat, decreasing both the frequency and the magnitude of deletion events. Furthermore, CpG methylation slowed the efficiency of replication for all templates. Interestingly, replication forks displayed no evidence of a block at the CGG repeat tract, regardless of replication direction or CpG methylation status. Templates with 20 CGG repeats were stable under all circumstances. These results reveal that CGG deletions occur during replication and are sensitive to replication-fork dynamics, tract length, and CpG methylation. PMID:15625623

What Should Researchers Expect When They Replicate Studies? A Statistical View of Replicability in Psychological Science.

PubMed

Patil, Prasad; Peng, Roger D; Leek, Jeffrey T

2016-07-01

A recent study of the replicability of key psychological findings is a major contribution toward understanding the human side of the scientific process. Despite the careful and nuanced analysis reported, the simple narrative disseminated by the mass, social, and scientific media was that in only 36% of the studies were the original results replicated. In the current study, however, we showed that 77% of the replication effect sizes reported were within a 95% prediction interval calculated using the original effect size. Our analysis suggests two critical issues in understanding replication of psychological studies. First, researchers' intuitive expectations for what a replication should show do not always match with statistical estimates of replication. Second, when the results of original studies are very imprecise, they create wide prediction intervals-and a broad range of replication effects that are consistent with the original estimates. This may lead to effects that replicate successfully, in that replication results are consistent with statistical expectations, but do not provide much information about the size (or existence) of the true effect. In this light, the results of the Reproducibility Project: Psychology can be viewed as statistically consistent with what one might expect when performing a large-scale replication experiment. © The Author(s) 2016.

Experimental Replication of an Aeroengine Combustion Instability

NASA Technical Reports Server (NTRS)

Cohen, J. M.; Hibshman, J. R.; Proscia, W.; Rosfjord, T. J.; Wake, B. E.; McVey, J. B.; Lovett, J.; Ondas, M.; DeLaat, J.; Breisacher, K.

2000-01-01

Combustion instabilities in gas turbine engines are most frequently encountered during the late phases of engine development, at which point they are difficult and expensive to fix. The ability to replicate an engine-traceable combustion instability in a laboratory-scale experiment offers the opportunity to economically diagnose the problem (to determine the root cause), and to investigate solutions to the problem, such as active control. The development and validation of active combustion instability control requires that the causal dynamic processes be reproduced in experimental test facilities which can be used as a test bed for control system evaluation. This paper discusses the process through which a laboratory-scale experiment was designed to replicate an instability observed in a developmental engine. The scaling process used physically-based analyses to preserve the relevant geometric, acoustic and thermo-fluid features. The process increases the probability that results achieved in the single-nozzle experiment will be scalable to the engine.

Helicase promotes replication re-initiation from an RNA transcript.

PubMed

Sun, Bo; Singh, Anupam; Sultana, Shemaila; Inman, James T; Patel, Smita S; Wang, Michelle D

2018-06-13

To ensure accurate DNA replication, a replisome must effectively overcome numerous obstacles on its DNA substrate. After encountering an obstacle, a progressing replisome often aborts DNA synthesis but continues to unwind. However, little is known about how DNA synthesis is resumed downstream of an obstacle. Here, we examine the consequences of a non-replicating replisome collision with a co-directional RNA polymerase (RNAP). Using single-molecule and ensemble methods, we find that T7 helicase interacts strongly with a non-replicating T7 DNA polymerase (DNAP) at a replication fork. As the helicase advances, the associated DNAP also moves forward. The presence of the DNAP increases both helicase's processivity and unwinding rate. We show that such a DNAP, together with its helicase, is indeed able to actively disrupt a stalled transcription elongation complex, and then initiates replication using the RNA transcript as a primer. These observations exhibit T7 helicase's novel role in replication re-initiation.

Control of DNA replication: a new facet of Hox proteins?

PubMed

Miotto, Benoit; Graba, Yacine

2010-09-01

Hox proteins are well-known as developmental transcription factors controlling cell and tissue identity, but recent findings suggest that they are also part of the cell replication machinery. Hox-mediated control of transcription and replication may ensure coordinated control of cell growth and differentiation, two processes that need to be tightly and precisely coordinated to allow proper organ formation and patterning. In this review we summarize the available data linking Hox proteins to the replication machinery and discuss the developmental and pathological implications of this new facet of Hox protein function.

Perceiving non-native speech: Word segmentation

NASA Astrophysics Data System (ADS)

Mondini, Michèle; Miller, Joanne L.

2004-05-01

One important source of information listeners use to segment speech into discrete words is allophonic variation at word junctures. Previous research has shown that non-native speakers impose their native-language phonetic norms on their second language; as a consequence, non-native speech may (in some cases) exhibit altered patterns of allophonic variation at word junctures. We investigated the perceptual consequences of this for word segmentation by presenting native-English listeners with English word pairs produced either by six native-English speakers or six highly fluent, native-French speakers of English. The target word pairs had contrastive word juncture involving voiceless stop consonants (e.g., why pink/wipe ink; gray ties/great eyes; we cash/weak ash). The task was to identify randomized instances of each individual target word pair (as well as control pairs) by selecting one of four possible choices (e.g., why pink, wipe ink, why ink, wipe pink). Overall, listeners were more accurate in identifying target word pairs produced by the native-English speakers than by the non-native English speakers. These findings suggest that one contribution to the processing cost associated with listening to non-native speech may be the presence of altered allophonic information important for word segmentation. [Work supported by NIH/NIDCD.

Get on Board the Cost Effective Way: A Tech Prep Replication Process.

ERIC Educational Resources Information Center

Moore, Wayne A.; Szul, Linda F.; Rivosecchi, Karen

1997-01-01

The Northwestern Pennsylvania Tech Prep Consortium model for replicating tech prep programs includes these steps: fact finding, local industry analysis, curriculum development, detailed description, marketing strategies, implementation, and program evaluation. (SK)

Replication landscape of the human genome

PubMed Central

Petryk, Nataliya; Kahli, Malik; d'Aubenton-Carafa, Yves; Jaszczyszyn, Yan; Shen, Yimin; Silvain, Maud; Thermes, Claude; Chen, Chun-Long; Hyrien, Olivier

2016-01-01

Despite intense investigation, human replication origins and termini remain elusive. Existing data have shown strong discrepancies. Here we sequenced highly purified Okazaki fragments from two cell types and, for the first time, quantitated replication fork directionality and delineated initiation and termination zones genome-wide. Replication initiates stochastically, primarily within non-transcribed, broad (up to 150 kb) zones that often abut transcribed genes, and terminates dispersively between them. Replication fork progression is significantly co-oriented with the transcription. Initiation and termination zones are frequently contiguous, sometimes separated by regions of unidirectional replication. Initiation zones are enriched in open chromatin and enhancer marks, even when not flanked by genes, and often border ‘topologically associating domains' (TADs). Initiation zones are enriched in origin recognition complex (ORC)-binding sites and better align to origins previously mapped using bubble-trap than λ-exonuclease. This novel panorama of replication reveals how chromatin and transcription modulate the initiation process to create cell-type-specific replication programs. PMID:26751768

DNA replication fidelity in Mycobacterium tuberculosis is mediated by an ancestral prokaryotic proofreader.

PubMed

Rock, Jeremy M; Lang, Ulla F; Chase, Michael R; Ford, Christopher B; Gerrick, Elias R; Gawande, Richa; Coscolla, Mireia; Gagneux, Sebastien; Fortune, Sarah M; Lamers, Meindert H

2015-06-01

The DNA replication machinery is an important target for antibiotic development in increasingly drug-resistant bacteria, including Mycobacterium tuberculosis. Although blocking DNA replication leads to cell death, disrupting the processes used to ensure replication fidelity can accelerate mutation and the evolution of drug resistance. In Escherichia coli, the proofreading subunit of the replisome, the ɛ exonuclease, is essential for high-fidelity DNA replication; however, we find that the corresponding subunit is completely dispensable in M. tuberculosis. Rather, the mycobacterial replicative polymerase DnaE1 itself encodes an editing function that proofreads DNA replication, mediated by an intrinsic 3'-5' exonuclease activity within its PHP domain. Inactivation of the DnaE1 PHP domain increases the mutation rate by more than 3,000-fold. Moreover, phylogenetic analysis of DNA replication proofreading in the bacterial kingdom suggests that E. coli is a phylogenetic outlier and that PHP domain-mediated proofreading is widely conserved and indeed may be the ancestral prokaryotic proofreader.

USP7/HAUSP: A SUMO deubiquitinase at the heart of DNA replication.

PubMed

Smits, Veronique A J; Freire, Raimundo

2016-09-01

DNA replication is both highly conserved and controlled. Problematic DNA replication can lead to genomic instability and therefore carcinogenesis. Numerous mechanisms work together to achieve this tight control and increasing evidence suggests that post-translational modifications (phosphorylation, ubiquitination, SUMOylation) of DNA replication proteins play a pivotal role in this process. Here we discuss such modifications in the light of a recent article that describes a novel role for the deubiquitinase (DUB) USP7/HAUSP in the control of DNA replication. USP7 achieves this function by an unusual and novel mechanism, namely deubiquitination of SUMOylated proteins at the replication fork, making USP7 also a SUMO DUB (SDUB). This work extends previous observations of increased levels of SUMO and low levels of ubiquitin at the on-going replication fork. Here, we discuss this novel study, its contribution to the DNA replication and genomic stability field and what questions arise from this work. © 2016 WILEY Periodicals, Inc.

DNA Replication Is Required for Circadian Clock Function by Regulating Rhythmic Nucleosome Composition.

PubMed

Liu, Xiao; Dang, Yunkun; Matsu-Ura, Toru; He, Yubo; He, Qun; Hong, Christian I; Liu, Yi

2017-07-20

Although the coupling between circadian and cell cycles allows circadian clocks to gate cell division and DNA replication in many organisms, circadian clocks were thought to function independently of cell cycle. Here, we show that DNA replication is required for circadian clock function in Neurospora. Genetic and pharmacological inhibition of DNA replication abolished both overt and molecular rhythmicities by repressing frequency (frq) gene transcription. DNA replication is essential for the rhythmic changes of nucleosome composition at the frq promoter. The FACT complex, known to be involved in histone disassembly/reassembly, is required for clock function and is recruited to the frq promoter in a replication-dependent manner to promote replacement of histone H2A.Z by H2A. Finally, deletion of H2A.Z uncoupled the dependence of the circadian clock on DNA replication. Together, these results establish circadian clock and cell cycle as interdependent coupled oscillators and identify DNA replication as a critical process in the circadian mechanism. Published by Elsevier Inc.

DNA replication fidelity in Mycobacterium tuberculosis is mediated by an ancestral prokaryotic proofreader

PubMed Central

Rock, Jeremy M.; Lang, Ulla F.; Chase, Michael R.; Ford, Christopher B.; Gerrick, Elias R.; Gawande, Richa; Coscolla, Mireia; Gagneux, Sebastien; Fortune, Sarah M.; Lamers, Meindert H.

2015-01-01

The DNA replication machinery is an important target for antibiotic development for increasingly drug resistant bacteria including Mycobacterium tuberculosis1. While blocking DNA replication leads to cell death, disrupting the processes used to ensure replication fidelity can accelerate mutation and the evolution of drug resistance. In E. coli, the proofreading subunit of the replisome, the ε-exonuclease, is essential for high fidelity DNA replication2; however, we find that it is completely dispensable in M. tuberculosis. Rather, the mycobacterial replicative polymerase, DnaE1, encodes a novel editing function that proofreads DNA replication, mediated by an intrinsic 3′-5′ exonuclease activity within its PHP domain. Inactivation of the DnaE1 PHP domain increases the mutation rate by greater than 3,000 fold. Moreover, phylogenetic analysis of DNA replication proofreading in the bacterial kingdom suggests that E. coli is a phylogenetic outlier and that PHP-domain mediated proofreading is widely conserved and indeed may be the ancestral prokaryotic proofreader. PMID:25894501

Real-time processing of gender-marked articles by native and non-native Spanish speakers

PubMed Central

Lew-Williams, Casey; Fernald, Anne

2010-01-01

Three experiments using online processing measures explored whether native and non-native Spanish-speaking adults use gender-marked articles to identify referents of target nouns more rapidly, as shown previously with 3-year-old children learning Spanish as L1 (Lew-Williams & Fernald, 2007). In Experiment 1, participants viewed familiar objects with names of either the same or different grammatical gender while listening to Spanish sentences referring to one object. L1 adults, like L1 children, oriented to the target more rapidly on different-gender trials, when the article was informative about noun identity; however, L2 adults did not. Experiments 2 and 3 controlled for frequency of exposure to article-noun pairs by using novel nouns. L2 adults could not exploit gender information when different article-noun pairs were used in teaching and testing. Experience-related factors may influence how L1 adults and children and L2 adults—who learned Spanish at different ages and in different settings—use grammatical gender in realtime processing. PMID:21076648

The composition of engineered cartilage at the time of implantation determines the likelihood of regenerating tissue with a normal collagen architecture.

PubMed

Nagel, Thomas; Kelly, Daniel J

2013-04-01

The biomechanical functionality of articular cartilage is derived from both its biochemical composition and the architecture of the collagen network. Failure to replicate this normal Benninghoff architecture in regenerating articular cartilage may in turn predispose the tissue to failure. In this article, the influence of the maturity (or functionality) of a tissue-engineered construct at the time of implantation into a tibial chondral defect on the likelihood of recapitulating a normal Benninghoff architecture was investigated using a computational model featuring a collagen remodeling algorithm. Such a normal tissue architecture was predicted to form in the intact tibial plateau due to the interplay between the depth-dependent extracellular matrix properties, foremost swelling pressures, and external mechanical loading. In the presence of even small empty defects in the articular surface, the collagen architecture in the surrounding cartilage was predicted to deviate significantly from the native state, indicating a possible predisposition for osteoarthritic changes. These negative alterations were alleviated by the implantation of tissue-engineered cartilage, where a mature implant was predicted to result in the formation of a more native-like collagen architecture than immature implants. The results of this study highlight the importance of cartilage graft functionality to maintain and/or re-establish joint function and suggest that engineering a tissue with a native depth-dependent composition may facilitate the establishment of a normal Benninghoff collagen architecture after implantation into load-bearing defects.

The Language of Fairness: how Cross-Linguistic Norms in Spanish and English Influence Reactions to Unfair Treatment.

PubMed

Birk, Sam J; Kausel, Edgar E

2016-11-14

We integrate recent findings from the linguistics literature with the organizational justice literature to examine how the language used to encode justice violations influences fairness perceptions. The study focused on the use of non-agentive syntax to encode mistakes in Spanish ("The vase was broken") versus using agentive syntax in English ("She broke the vase") influences event fairness perceptions. We hypothesized that when justice violations are encoded using Spanish, because the non-agentive syntax makes the responsible party less salient, the event would be perceived as less unfair. In Study 1 (n = 111), English-speaking participants rated the fairness of an event in which a mistake was made and an employee received a negative outcome. They rated it as more unfair (p < .01, η2 = .06) when the scenario was presented in agentive syntax. Experiment 2 (n = 70) used native English- and Spanish-speakers who watched a video of manager making a mistake. We found that Spanish-speakers used less agentive syntax (p < .01, η2 = .21), perceived the event as less unfair (p < .001, η2 = .23), and were more willing to help the manager who made the mistake. In Experiment 3 (n = 101) we replicated this effect controlling for cross-cultural differences and native language; further, we found an interaction between entity fairness (event vs. entity) and native language (Spanish vs. English) on citizenship intentions (p < .01, η2 = .08). These results extend our understanding of how language may influence relevant workplace attitudes.

A Comparison of American Indian and Non-American Indian Parental Involvement in the IEP Process: Perceived Needs for Involvement and Training. Final Report.

ERIC Educational Resources Information Center

Gajar, Anna; Matuszny, Rose Marie

This final report discusses the activities and outcomes of a study that investigated the involvement of American Indian/Alaska Native (AI/AN) and non-American Indian/Alaska Native parents of children with disabilities in the general educational and Individualized Education Program (IEP) processes, and the specific needs of parents that would…

Comparing Ease-of-Processing Values of the Same Set of Words for Native English Speakers and Japanese Learners of English

ERIC Educational Resources Information Center

Takashima, Hiroomi

2009-01-01

Ease of processing of 3,969 English words for native speakers and Japanese learners was investigated using lexical decision and naming latencies taken from the English Lexicon Project (Balota et al. The English Lexicon Project: A web-based repository of descriptive and behavioral measures for 40,481 English words and nonwords, 2002) and accuracy…

Seed rain under native and non-native tree species in the Cabo Rojo National Wildlife Refuge, Puerto Rico.

PubMed

Arias Garcia, Andrea; Chinea, J Danilo

2014-09-01

Seed dispersal is a fundamental process in plant ecology and is of critical importance for the restoration of tropical communities. The lands of the Cabo Rojo National Wildlife Refuge (CRNWR), formerly under agriculture, were abandoned in the 1970s and colonized mainly by non-native tree species of degraded pastures. Here we described the seed rain under the most common native and non-native trees in the refuge in an attempt to determine if focal tree geographic origin (native versus non-native) influences seed dispersal. For this, seed rain was sampled for one year under the canopies of four native and four non-native tree species common in this refuge using 40 seed traps. No significant differences were found for the abundance of seeds, or their diversity, dispersing under native versus non-native focal tree species, nor under the different tree species. A significantly different seed species composition was observed reaching native versus non-native focal species. However, this last result could be more easily explained as a function of distance of the closest adults of the two most abundantly dispersed plant species to the seed traps than as a function of the geographic origin of the focal species. We suggest to continue the practice of planting native tree species, not only as a way to restore the community to a condition similar to the original one, but also to reduce the distances needed for effective dispersal.

Can infants learn phonology in the lab? A meta-analytic answer.

PubMed

Cristia, Alejandrina

2018-01-01

Two of the key tasks facing the language-learning infant lie at the level of phonology: establishing which sounds are contrastive in the native inventory, and determining what their possible syllabic positions and permissible combinations (phonotactics) are. In 2002-2003, two theoretical proposals, one bearing on how infants can learn sounds (Maye, Werker, & Gerken, 2002) and the other on phonotactics (Chambers, Onishi, & Fisher, 2003), were put forward on the pages of Cognition, each supported by two laboratory experiments, wherein a group of infants was briefly exposed to a set of pseudo-words, and plausible phonological generalizations were tested subsequently. These two papers have received considerable attention from the general scientific community, and inspired a flurry of follow-up work. In the context of questions regarding the replicability of psychological science, the present work uses a meta-analytic approach to appraise extant empirical evidence for infant phonological learning in the laboratory. It is found that neither seminal finding (on learning sounds and learning phonotactics) holds up when close methodological replications are integrated, although less close methodological replications do provide some evidence in favor of the sound learning strand of work. Implications for authors and readers of this literature are drawn out. It would be desirable that additional mechanisms for phonological learning be explored, and that future infant laboratory work employ paradigms that rely on constrained and unambiguous links between experimental exposure and measured infant behavior. Copyright © 2017. Published by Elsevier B.V.

Chromatin Controls DNA Replication Origin Selection, Lagging-Strand Synthesis, and Replication Fork Rates.

PubMed

Kurat, Christoph F; Yeeles, Joseph T P; Patel, Harshil; Early, Anne; Diffley, John F X

2017-01-05

The integrity of eukaryotic genomes requires rapid and regulated chromatin replication. How this is accomplished is still poorly understood. Using purified yeast replication proteins and fully chromatinized templates, we have reconstituted this process in vitro. We show that chromatin enforces DNA replication origin specificity by preventing non-specific MCM helicase loading. Helicase activation occurs efficiently in the context of chromatin, but subsequent replisome progression requires the histone chaperone FACT (facilitates chromatin transcription). The FACT-associated Nhp6 protein, the nucleosome remodelers INO80 or ISW1A, and the lysine acetyltransferases Gcn5 and Esa1 each contribute separately to maximum DNA synthesis rates. Chromatin promotes the regular priming of lagging-strand DNA synthesis by facilitating DNA polymerase α function at replication forks. Finally, nucleosomes disrupted during replication are efficiently re-assembled into regular arrays on nascent DNA. Our work defines the minimum requirements for chromatin replication in vitro and shows how multiple chromatin factors might modulate replication fork rates in vivo. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips[OPEN

PubMed Central

LeBlanc, Chantal; Lee, Tae-Jin; Mulvaney, Patrick; Allen, George C.; Martienssen, Robert A.; Thompson, William F.

2017-01-01

All plants and animals must replicate their DNA, using a regulated process to ensure that their genomes are completely and accurately replicated. DNA replication timing programs have been extensively studied in yeast and animal systems, but much less is known about the replication programs of plants. We report a novel adaptation of the “Repli-seq” assay for use in intact root tips of maize (Zea mays) that includes several different cell lineages and present whole-genome replication timing profiles from cells in early, mid, and late S phase of the mitotic cell cycle. Maize root tips have a complex replication timing program, including regions of distinct early, mid, and late S replication that each constitute between 20 and 24% of the genome, as well as other loci corresponding to ∼32% of the genome that exhibit replication activity in two different time windows. Analyses of genomic, transcriptional, and chromatin features of the euchromatic portion of the maize genome provide evidence for a gradient of early replicating, open chromatin that transitions gradually to less open and less transcriptionally active chromatin replicating in mid S phase. Our genomic level analysis also demonstrated that the centromere core replicates in mid S, before heavily compacted classical heterochromatin, including pericentromeres and knobs, which replicate during late S phase. PMID:28842533

Dispersal and selection mediate hybridization between a native and invasive species

USGS Publications Warehouse

Kovach, Ryan P.; Muhlfeld, Clint C.; Boyer, Matthew C.; Lowe, Winsor H.; Allendorf, Fred W.; Luikart, Gordon

2015-01-01

Hybridization between native and non-native species has serious biological consequences, but our understanding of how dispersal and selection interact to influence invasive hybridization is limited. Here, we document the spread of genetic introgression between a native (Oncorhynchus clarkii) and invasive (Oncorhynchus mykiss) trout, and identify the mechanisms influencing genetic admixture. In two populations inhabiting contrasting environments, non-native admixture increased rapidly from 1984 to 2007 and was driven by surprisingly consistent processes. Individual admixture was related to two phenotypic traits associated with fitness: size at spawning and age of juvenile emigration. Fish with higher non-native admixture were larger and tended to emigrate at a younger age—relationships that are expected to confer fitness advantages to hybrid individuals. However, strong selection against non-native admixture was evident across streams and cohorts (mean selection coefficient against genotypes with non-native alleles (s) ¼ 0.60; s.e. ¼ 0.10). Nevertheless, hybridization was promoted in both streams by the continuous immigration of individuals with high levels of non-native admixture from other hybrid source populations. Thus, antagonistic relationships between dispersal and selection are mediating invasive hybridization between these fish, emphasizing that data on dispersal and natural selection are needed to fully understand the dynamics of introgression between native and non-native species. .

Spatial arrangement overrules environmental factors to structure native and non-native assemblages of synanthropic harvestmen.

PubMed

Muster, Christoph; Meyer, Marc; Sattler, Thomas

2014-01-01

Understanding how space affects the occurrence of native and non-native species is essential for inferring processes that shape communities. However, studies considering spatial and environmental variables for the entire community - as well as for the native and non-native assemblages in a single study - are scarce for animals. Harvestmen communities in central Europe have undergone drastic turnovers during the past decades, with several newly immigrated species, and thus provide a unique system to study such questions. We studied the wall-dwelling harvestmen communities from 52 human settlements in Luxembourg and found the assemblages to be largely dominated by non-native species (64% of specimens). Community structure was analysed using Moran's eigenvector maps as spatial variables, and landcover variables at different radii (500 m, 1000 m, 2000 m) in combination with climatic parameters as environmental variables. A surprisingly high portion of pure spatial variation (15.7% of total variance) exceeded the environmental (10.6%) and shared (4%) components of variation, but we found only minor differences between native and non-native assemblages. This could result from the ecological flexibility of both, native and non-native harvestmen that are not restricted to urban habitats but also inhabit surrounding semi-natural landscapes. Nevertheless, urban landcover variables explained more variation in the non-native community, whereas coverage of semi-natural habitats (forests, rivers) at broader radii better explained the native assemblage. This indicates that some urban characteristics apparently facilitate the establishment of non-native species. We found no evidence for competitive replacement of native by invasive species, but a community with novel combination of native and non-native species.

Spatial Arrangement Overrules Environmental Factors to Structure Native and Non-Native Assemblages of Synanthropic Harvestmen

PubMed Central

Muster, Christoph; Meyer, Marc; Sattler, Thomas

2014-01-01

Understanding how space affects the occurrence of native and non-native species is essential for inferring processes that shape communities. However, studies considering spatial and environmental variables for the entire community – as well as for the native and non-native assemblages in a single study – are scarce for animals. Harvestmen communities in central Europe have undergone drastic turnovers during the past decades, with several newly immigrated species, and thus provide a unique system to study such questions. We studied the wall-dwelling harvestmen communities from 52 human settlements in Luxembourg and found the assemblages to be largely dominated by non-native species (64% of specimens). Community structure was analysed using Moran's eigenvector maps as spatial variables, and landcover variables at different radii (500 m, 1000 m, 2000 m) in combination with climatic parameters as environmental variables. A surprisingly high portion of pure spatial variation (15.7% of total variance) exceeded the environmental (10.6%) and shared (4%) components of variation, but we found only minor differences between native and non-native assemblages. This could result from the ecological flexibility of both, native and non-native harvestmen that are not restricted to urban habitats but also inhabit surrounding semi-natural landscapes. Nevertheless, urban landcover variables explained more variation in the non-native community, whereas coverage of semi-natural habitats (forests, rivers) at broader radii better explained the native assemblage. This indicates that some urban characteristics apparently facilitate the establishment of non-native species. We found no evidence for competitive replacement of native by invasive species, but a community with novel combination of native and non-native species. PMID:24595309

To express the policy of the United States regarding the United States relationship with Native Hawaiians, to provide a process for the reorganization of a Native Hawaiian government and the recognition by the United States of the Native Hawaiian government, and for other purposes.

THOMAS, 111th Congress

Rep. Abercrombie, Neil [D-HI-1

2009-02-04

House - 07/23/2009 Referred to the Subcommittee on the Constitution, Civil Rights, and Civil Liberties. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

Methods and materials for the production of L-lactic acid in yeast

DOEpatents

Hause, Ben [Jordan, MN; Rajgarhia, Vineet [Minnetonka, MN; Suominen, Pirkko [Maple Grove, MN

2009-05-19

Recombinant yeast are provided having, in one aspect, multiple exogenous LDH genes integrated into the genome, while leaving native PDC genes intact. In a second aspect, recombinant yeast are provided having an exogenous LDH gene integrated into its genome at the locus of a native PDC gene, with deletion of the native PDC gene. The recombinant yeast are useful in fermentation process for producing lactic acid.

A novel process for direct production of acetone-butanol-ethanol from native starches using granular starch hydrolyzing enzyme by Clostridium saccharoperbutylacetonicum N1-4.

PubMed

Thang, Vu Hong; Kobayashi, Genta

2014-02-01

In this work, a new approach for acetone-butanol-ethanol (ABE) production has been proposed. Direct fermentation of native starches (uncooked process) was investigated by using granular starch hydrolyzing enzyme (GSHE) and Clostridium saccharoperbutylacetonicum N1-4. Even the process was carried out under suboptimal condition for activity of GSHE, the production of ABE was similar with that observed in conventional process or cooked process in terms of final solvent concentration (21.3 ± 0.4 to 22.4 ± 0.4 g/L), butanol concentration (17.5 ± 0.4 to 17.8 ± 0.3 g/L) and butanol yield (0.33 to 0.37 g/g). The production of solvents was significantly dependent on the source of starches. Among investigated starches, corn starch was more susceptible to GSHE while cassava starch was the most resistant to this enzyme. Fermentation using native corn starch resulted in the solvent productivity of 0.47 g/L h, which was about 15 % higher than that achieved in cooked process. On the contrary, uncooked process using cassava and wheat starch resulted in the solvent productivity of 0.30 and 0.37 g/L h, which were respectively about 30 % lower than those obtained in cooked process. No contamination was observed during all trials even fermentation media were prepared without sterilization. During the fermentation using native starches, no formation of foam is observed. This uncooked process does not require cooking starchy material; therefore, the thermal energy consumption for solvent production would remarkably be reduced in comparison with cooked process.

DAMe: a toolkit for the initial processing of datasets with PCR replicates of double-tagged amplicons for DNA metabarcoding analyses.

PubMed

Zepeda-Mendoza, Marie Lisandra; Bohmann, Kristine; Carmona Baez, Aldo; Gilbert, M Thomas P

2016-05-03

DNA metabarcoding is an approach for identifying multiple taxa in an environmental sample using specific genetic loci and taxa-specific primers. When combined with high-throughput sequencing it enables the taxonomic characterization of large numbers of samples in a relatively time- and cost-efficient manner. One recent laboratory development is the addition of 5'-nucleotide tags to both primers producing double-tagged amplicons and the use of multiple PCR replicates to filter erroneous sequences. However, there is currently no available toolkit for the straightforward analysis of datasets produced in this way. We present DAMe, a toolkit for the processing of datasets generated by double-tagged amplicons from multiple PCR replicates derived from an unlimited number of samples. Specifically, DAMe can be used to (i) sort amplicons by tag combination, (ii) evaluate PCR replicates dissimilarity, and (iii) filter sequences derived from sequencing/PCR errors, chimeras, and contamination. This is attained by calculating the following parameters: (i) sequence content similarity between the PCR replicates from each sample, (ii) reproducibility of each unique sequence across the PCR replicates, and (iii) copy number of the unique sequences in each PCR replicate. We showcase the insights that can be obtained using DAMe prior to taxonomic assignment, by applying it to two real datasets that vary in their complexity regarding number of samples, sequencing libraries, PCR replicates, and used tag combinations. Finally, we use a third mock dataset to demonstrate the impact and importance of filtering the sequences with DAMe. DAMe allows the user-friendly manipulation of amplicons derived from multiple samples with PCR replicates built in a single or multiple sequencing libraries. It allows the user to: (i) collapse amplicons into unique sequences and sort them by tag combination while retaining the sample identifier and copy number information, (ii) identify sequences carrying unused tag combinations, (iii) evaluate the comparability of PCR replicates of the same sample, and (iv) filter tagged amplicons from a number of PCR replicates using parameters of minimum length, copy number, and reproducibility across the PCR replicates. This enables an efficient analysis of complex datasets, and ultimately increases the ease of handling datasets from large-scale studies.

Nativization processes in L1 Esperanto.

PubMed

Bergen, B K

2001-10-01

The artificial language Esperanto is spoken not only as a second language, by its proponents, but also as a native language by children of some of those proponents. The present study is a preliminary description of some characteristics of the Native Esperanto (NE) of eight speakers, ranging in age from six to fourteen years. As such, it is the first of its kind--previous works on NE are either theoretical treatises or individual case studies. We find, at least for the eight subjects studied, both bilingualism and nativization effects, differentiating native from non-native Esperanto speech. Among these effects are loss or modification of the accusative case, phonological reduction, attrition of the tense/aspect system, and pronominal cliticization. The theoretical ramifications are discussed, particularly with regard to universals of language acquisition and the effects of expressive requirements of language.

Response-Induced Reversals of Preference in Gambling: An Extended Replication in Las Vegas

ERIC Educational Resources Information Center

Lichtenstein, Sarah; Slovic, Paul

1973-01-01

The present report describes an expanded replication of the previous experiments in a nonlaboratory real-play setting unique to the experimental literature on decision processes - a casino in downtown Las Vegas. (Author)

Effect of Lamina Thickness of Prepreg on the Surface Accuracy of Carbon Fiber Composite Space Mirrors

NASA Astrophysics Data System (ADS)

Yang, Zhiyong; Tang, Zhanwen; Xie, Yongjie; Shi, Hanqiao; Zhang, Boming; Guo, Hongjun

2018-02-01

Composite space mirror can completely replicate the high-precision surface of mould by replication process, but the actual surface accuracy of the replication composite mirror always decreases. Lamina thickness of prepreg affects the layers and layup sequence of composite space mirror, and which would affect surface accuracy of space mirror. In our research, two groups of contrasting cases through finite element analyses (FEA) and comparative experiments were studied; the effect of different lamina thicknesses of prepreg and corresponding lay-up sequences was focused as well. We describe a special analysis model, validated process and result analysis. The simulated and measured surface figures both get the same conclusion. Reducing lamina thickness of prepreg used in replicating composite space mirror is propitious to optimal design of layup sequence for fabricating composite mirror, and could improve its surface accuracy.

Crystallisation and preliminary X-ray diffraction analysis of the protease from Southampton norovirus complexed with a Michael-acceptor inhibitor

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

Coates, Leighton; Cooper, Jon; Hussey, Robert

2008-01-01

Noroviruses are the predominant cause of human epidemic nonbacterial gastroenteritis. Viral replication requires a cysteine protease that cleaves a 200 kDa viral polyprotein into its constituent functional parts. Here, the crystallization of the recombinant protease from the Southampton norovirus is described. While the native crystals were found to diffract only to medium resolution (2.9 {angstrom}), cocrystals of an inhibitor complex diffracted X-rays to 1.7 {angstrom} resolution. The polypeptide inhibitor (Ac-EFQLQ-propenyl ethyl ester) possesses an amino-acid sequence designed to match the substrate specificity of the enzyme, but was synthesized with a reactive Michael acceptor group at the C-terminal end.

Surface cleaning and pure nitridation of GaSb by in-situ plasma processing

NASA Astrophysics Data System (ADS)

Gotow, Takahiro; Fujikawa, Sachie; Fujishiro, Hiroki I.; Ogura, Mutsuo; Chang, Wen Hsin; Yasuda, Tetsuji; Maeda, Tatsuro

2017-10-01

A clean and flat GaSb surface without native oxides has been attained by H2 plasma cleaning and subsequent in-situ N2 plasma nitridation process at 300 oC. The mechanisms of thermal desorption behavior of native oxides on GaSb have been studied by thermal desorption spectroscopy (TDS) analysis. The suitable heat treatment process window for preparing a clean GaSb surface is given. Auger electron spectroscopy (AES) analysis indicates that native oxides were completely removed on the GaSb surface after H2 plasma exposure and the pure nitridation of the clean GaSb surface was obtained at a relatively low temperature of 300 °C. This pure nitridation of GaSb have a possibility to be used as a passivation layer for high quality GaSb MOS devices.

The logic of DNA replication in double-stranded DNA viruses: insights from global analysis of viral genomes

PubMed Central

Kazlauskas, Darius; Krupovic, Mart; Venclovas, Česlovas

2016-01-01

Abstract Genomic DNA replication is a complex process that involves multiple proteins. Cellular DNA replication systems are broadly classified into only two types, bacterial and archaeo-eukaryotic. In contrast, double-stranded (ds) DNA viruses feature a much broader diversity of DNA replication machineries. Viruses differ greatly in both completeness and composition of their sets of DNA replication proteins. In this study, we explored whether there are common patterns underlying this extreme diversity. We identified and analyzed all major functional groups of DNA replication proteins in all available proteomes of dsDNA viruses. Our results show that some proteins are common to viruses infecting all domains of life and likely represent components of the ancestral core set. These include B-family polymerases, SF3 helicases, archaeo-eukaryotic primases, clamps and clamp loaders of the archaeo-eukaryotic type, RNase H and ATP-dependent DNA ligases. We also discovered a clear correlation between genome size and self-sufficiency of viral DNA replication, the unanticipated dominance of replicative helicases and pervasive functional associations among certain groups of DNA replication proteins. Altogether, our results provide a comprehensive view on the diversity and evolution of replication systems in the DNA virome and uncover fundamental principles underlying the orchestration of viral DNA replication. PMID:27112572

Tropical fish community does not recover 45 years after predator introduction.

PubMed

Sharpe, D M T; De León, L F; González, R; Torchin, M E

2017-02-01

Predation is considered to be an important factor structuring natural communities. However, it is often difficult to determine how it may influence long-term, broad-scale, diversity patterns, particularly in diverse tropical systems. Biological introductions can provide powerful insight to test the sustained consequences of predation in natural communities, if pre-introduction data are available. Half a century ago, Zaret and Paine demonstrated strong and immediate community-level effects following the introduction of a novel apex predator (peacock bass, Cichla monoculus) into Lake Gatun, Panama. To test for long-term changes associated with this predator introduction, we followed up on their classic study by replicating historical sampling methods and examining changes in the littoral fish community at two sites in Lake Gatun 45 years post-introduction. To broaden our inference, we complemented this temporal comparison with a spatial analysis, wherein we compared the fish communities from two lakes with and one lake without peacock bass. Comparisons with historical data revealed that the peacock bass remains the most abundant predator in Lake Gatun. Furthermore, the collapse of the littoral prey community observed immediately following the invasion has been sustained over the past 45 years. The mean abundance of native littoral fish is now 96% lower than it was prior to the introduction. Diversity (rarefied species richness) declined by 64% post-introduction, and some native species appear to have been locally extirpated. We observed a similar pattern across invaded and uninvaded lakes: the mean abundance of native fishes was 5-40 times lower in lakes with (Gatun, Alajuela) relative to the lake without peacock bass (Bayano). In particular, small-bodied native fishes (Characidae, Peociliidae), which are common prey of the peacock bass, were more than two orders of magnitude (307 times) less abundant in Gatun and one order of magnitude (28 times) less abundant in Alajuela than in Bayano. However, total native fish diversity did not differ significantly across lakes, suggesting that while many native species have declined in abundance, few have been completely extirpated. Introduced predators can have strong effects on community structure and functional diversity, even in highly diverse tropical communities, and these effects can persist over multiple decades. © 2016 by the Ecological Society of America.

AlphaScreen-based homogeneous assay using a pair of 25-residue artificial proteins for high-throughput analysis of non-native IgG.

PubMed

Senga, Yukako; Imamura, Hiroshi; Miyafusa, Takamitsu; Watanabe, Hideki; Honda, Shinya

2017-09-29

Therapeutic IgG becomes unstable under various stresses in the manufacturing process. The resulting non-native IgG molecules tend to associate with each other and form aggregates. Because such aggregates not only decrease the pharmacological effect but also become a potential risk factor for immunogenicity, rapid analysis of aggregation is required for quality control of therapeutic IgG. In this study, we developed a homogeneous assay using AlphaScreen and AF.2A1. AF.2A1 is a 25-residue artificial protein that binds specifically to non-native IgG generated under chemical and physical stresses. This assay is performed in a short period of time. Our results show that AF.2A1-AlphaScreen may be used to evaluate the various types of IgG, as AF.2A1 recognizes the non-native structure in the constant region (Fc region) of IgG. The assay was effective for detection of non-native IgG, with particle size up to ca. 500 nm, generated under acid, heat, and stirring conditions. In addition, this technique is suitable for analyzing non-native IgG in CHO cell culture supernatant and mixed with large amounts of native IgG. These results indicate the potential of AF.2A1-AlphaScreen to be used as a high-throughput evaluation method for process monitoring as well as quality testing in the manufacturing of therapeutic IgG.

Coexistence via coevolution driven by reduced allelochemical effects and increased tolerance to competition between invasive and native plants.

PubMed

Huang, Fangfang; Lankau, Richard; Peng, Shaolin

2018-04-01

Coevolution can promote long-term coexistence of two competing species if selection acts to reduce the fitness inequality between competitors and/or strengthen negative frequency dependence within each population. However, clear coevolution between plant competitors has been rarely documented. Plant invasions offer opportunities to capture the process of coevolution. Here we investigated how the developing relationship between an invasive forb, Alliaria petiolata, and a native competitor, Pilea pumila, may affect their long-term coexistence, by testing the competitive effects of populations of varying lengths of co-occurrence on each other across a chronosequence of invasion history. Alliaria petiolata and P. pumila tended to develop greater tolerance to competition over invasion history. Their coexistence was promoted more by increases in stabilizing relative to equalizing processes. These changes likely stem in part from reductions in allelopathic traits in the invader and evolution of tolerance in the native. These results suggested that some native species can evolve tolerance against the competitive effects of strong invaders, which likely promoted their persistence in invaded communities. However, the potential for coevolutionary rescue of competing populations is likely to vary across native species, and evolutionary processes should not be expected to compensate for the ecological consequences of exotic invasions. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Essential role of cyclophilin A for hepatitis C virus replication and virus production and possible link to polyprotein cleavage kinetics.

PubMed

Kaul, Artur; Stauffer, Sarah; Berger, Carola; Pertel, Thomas; Schmitt, Jennifer; Kallis, Stephanie; Zayas, Margarita; Lopez, Margarita Zayas; Lohmann, Volker; Luban, Jeremy; Bartenschlager, Ralf

2009-08-01

Viruses are obligate intracellular parasites and therefore their replication completely depends on host cell factors. In case of the hepatitis C virus (HCV), a positive-strand RNA virus that in the majority of infections establishes persistence, cyclophilins are considered to play an important role in RNA replication. Subsequent to the observation that cyclosporines, known to sequester cyclophilins by direct binding, profoundly block HCV replication in cultured human hepatoma cells, conflicting results were obtained as to the particular cyclophilin (Cyp) required for viral RNA replication and the underlying possible mode of action. By using a set of cell lines with stable knock-down of CypA or CypB, we demonstrate in the present work that replication of subgenomic HCV replicons of different genotypes is reduced by CypA depletion up to 1,000-fold whereas knock-down of CypB had no effect. Inhibition of replication was rescued by over-expression of wild type CypA, but not by a mutant lacking isomerase activity. Replication of JFH1-derived full length genomes was even more sensitive to CypA depletion as compared to subgenomic replicons and virus production was completely blocked. These results argue that CypA may target an additional viral factor outside of the minimal replicase contributing to RNA amplification and assembly, presumably nonstructural protein 2. By selecting for resistance against the cyclosporine analogue DEBIO-025 that targets CypA in a dose-dependent manner, we identified two mutations (V2440A and V2440L) close to the cleavage site between nonstructural protein 5A and the RNA-dependent RNA polymerase in nonstructural protein 5B that slow down cleavage kinetics at this site and reduce CypA dependence of viral replication. Further amino acid substitutions at the same cleavage site accelerating processing increase CypA dependence. Our results thus identify an unexpected correlation between HCV polyprotein processing and CypA dependence of HCV replication.

The "Perceptual Wedge Hypothesis" as the Basis for Bilingual Babies' Phonetic Processing Advantage: New insights from fNIRS Brain Imaging

ERIC Educational Resources Information Center

Petitto, L. A.; Berens, M. S.; Kovelman, I.; Dubins, M. H.; Jasinska, K.; Shalinsky, M.

2012-01-01

In a neuroimaging study focusing on young bilinguals, we explored the brains of bilingual and monolingual babies across two age groups (younger 4-6 months, older 10-12 months), using fNIRS in a new event-related design, as babies processed linguistic phonetic (Native English, Non-Native Hindi) and nonlinguistic Tone stimuli. We found that phonetic…

Regulating DNA Replication in Plants

PubMed Central

Sanchez, Maria de la Paz; Costas, Celina; Sequeira-Mendes, Joana; Gutierrez, Crisanto

2012-01-01

Chromosomal DNA replication in plants has requirements and constraints similar to those in other eukaryotes. However, some aspects are plant-specific. Studies of DNA replication control in plants, which have unique developmental strategies, can offer unparalleled opportunities of comparing regulatory processes with yeast and, particularly, metazoa to identify common trends and basic rules. In addition to the comparative molecular and biochemical studies, genomic studies in plants that started with Arabidopsis thaliana in the year 2000 have now expanded to several dozens of species. This, together with the applicability of genomic approaches and the availability of a large collection of mutants, underscores the enormous potential to study DNA replication control in a whole developing organism. Recent advances in this field with particular focus on the DNA replication proteins, the nature of replication origins and their epigenetic landscape, and the control of endoreplication will be reviewed. PMID:23209151

Using Model Replication to Improve the Reliability of Agent-Based Models

NASA Astrophysics Data System (ADS)

Zhong, Wei; Kim, Yushim

The basic presupposition of model replication activities for a computational model such as an agent-based model (ABM) is that, as a robust and reliable tool, it must be replicable in other computing settings. This assumption has recently gained attention in the community of artificial society and simulation due to the challenges of model verification and validation. Illustrating the replication of an ABM representing fraudulent behavior in a public service delivery system originally developed in the Java-based MASON toolkit for NetLogo by a different author, this paper exemplifies how model replication exercises provide unique opportunities for model verification and validation process. At the same time, it helps accumulate best practices and patterns of model replication and contributes to the agenda of developing a standard methodological protocol for agent-based social simulation.

Post-secretion processing influences spider silk performance

PubMed Central

Blamires, Sean J.; Wu, Chung-Lin; Blackledge, Todd A.; Tso, I-Min

2012-01-01

Phenotypic variation facilitates adaptations to novel environments. Silk is an example of a highly variable biomaterial. The two-spidroin (MaSp) model suggests that spider major ampullate (MA) silk is composed of two proteins—MaSp1 predominately contains alanine and glycine and forms strength enhancing β-sheet crystals, while MaSp2 contains proline and forms elastic spirals. Nonetheless, mechanical properties can vary in spider silks without congruent amino acid compositional changes. We predicted that post-secretion processing causes variation in the mechanical performance of wild MA silk independent of protein composition or spinning speed across 10 species of spider. We used supercontraction to remove post-secretion effects and compared the mechanics of silk in this ‘ground state’ with wild native silks. Native silk mechanics varied less among species compared with ‘ground state’ silks. Variability in the mechanics of ‘ground state’ silks was associated with proline composition. However, variability in native silks did not. We attribute interspecific similarities in the mechanical properties of native silks, regardless of amino acid compositions, to glandular processes altering molecular alignment of the proteins prior to extrusion. Such post-secretion processing may enable MA silk to maintain functionality across environments, facilitating its function as a component of an insect-catching web. PMID:22628213

Learning to perceptually organize speech signals in native fashion.

PubMed

Nittrouer, Susan; Lowenstein, Joanna H

2010-03-01

The ability to recognize speech involves sensory, perceptual, and cognitive processes. For much of the history of speech perception research, investigators have focused on the first and third of these, asking how much and what kinds of sensory information are used by normal and impaired listeners, as well as how effective amounts of that information are altered by "top-down" cognitive processes. This experiment focused on perceptual processes, asking what accounts for how the sensory information in the speech signal gets organized. Two types of speech signals processed to remove properties that could be considered traditional acoustic cues (amplitude envelopes and sine wave replicas) were presented to 100 listeners in five groups: native English-speaking (L1) adults, 7-, 5-, and 3-year-olds, and native Mandarin-speaking adults who were excellent second-language (L2) users of English. The L2 adults performed more poorly than L1 adults with both kinds of signals. Children performed more poorly than L1 adults but showed disproportionately better performance for the sine waves than for the amplitude envelopes compared to both groups of adults. Sentence context had similar effects across groups, so variability in recognition was attributed to differences in perceptual organization of the sensory information, presumed to arise from native language experience.

NEIGHBORHOOD IMMIGRATION AND NATIVE OUT-MIGRATION

PubMed Central

Crowder, Kyle; Hall, Matthew; Tolnay, Stewart E.

2011-01-01

This study combines data from the Panel Study of Income Dynamics with data from four censuses to examine the effects of foreign-born populations in the immediate neighborhood of residence and surrounding neighborhoods on the residential mobility decisions of native-born black and white householders. We find that the likelihood of out-mobility for native householders is significantly and positively associated with the relative size of, and increases in, the immigrant population in the neighborhood. Consistent with theoretical arguments related to the distance dependence of mobility, large concentrations of immigrants in surrounding areas reduce native out-mobility, presumably by reducing the attractiveness of the most likely mobility destinations. A sizable share of local immigration effects can be explained by the mobility-related characteristics of native-born individuals living in immigrant-populated areas, but the racial composition of the neighborhood (for native whites) and local housing market conditions (for native blacks) also are important mediating factors. The implications of these patterns for processes of neighborhood change and broader patterns of residential segregation are discussed. PMID:21731082

Does Acacia dealbata express shade tolerance in Mediterranean forest ecosystems of South America?

PubMed Central

Aguilera, Narciso; Sanhueza, Carolina; Guedes, Lubia M; Becerra, José; Carrasco, Sebastián; Hernández, Víctor

2015-01-01

The distribution of Acacia dealbata Link (Fabaceae) in its non-native range is associated with disturbed areas. However, the possibility that it can penetrate the native forest during the invasion process cannot be ruled out. This statement is supported by the fact that this species has been experimentally established successfully under the canopy of native forest. Nonetheless, it is unknown whether A. dealbata can express shade tolerance traits to help increase its invasive potential. We investigated the shade tolerance of A. dealbata under the canopy of two native forests and one non-native for three consecutive years, as well as its early growth and photosynthetic performance at low light intensities (9, 30, and 70 μmol m−2sec−1) under controlled conditions. We found many A. dealbata plants surviving and growing under the canopy of native and non-native forests. The number of plants of this invasive species remained almost constant under the canopy of native forests during the years of study. However, the largest number of A. dealbata plants was found under the canopy of non-native forest. In every case, the distribution pattern varied with a highest density of plants in forest edges decreasing progressively toward the inside. Germination and early growth of A. dealbata were slow but successful at three low light intensities tested under controlled conditions. For all tested light regimes, we observed that in this species, most of the energy was dissipated by photochemical processes, in accordance with the high photosynthetic rates that this plant showed, despite the really low light intensities under which it was grown. Our study reveals that A. dealbata expressed shade tolerance traits under the canopy of native and non-native forests. This behavior is supported by the efficient photosynthetic performance that A. dealbata showed at low light intensities. Therefore, these results suggest that Mediterranean forest ecosystems of South America can become progressively invaded by A. dealbata and provide a basis for estimating the possible impacts that this invasive species can cause in these ecosystems in a timescale. PMID:26380668

Structural Insights into the Coupling of Virion Assembly and Rotavirus Replication

PubMed Central

Trask, Shane D.; McDonald, Sarah M.; Patton, John T.

2013-01-01

Preface Viral replication is rapid and robust, but it is far from a chaotic process. Instead, successful production of infectious progeny requires that events occur in the correct place and at the correct time. Rotavirus, a segmented double-stranded RNA virus of the Reoviridae family, seems to govern its replication through ordered disassembly and assembly of a triple-layered icosahedral capsid. In recent years, high-resolution structural data have provided unprecedented insight into these events. In this Review, we explore the current understanding of rotavirus replication and how it compares to other Reoviridae family members. PMID:22266782

Autonomous replication of nucleic acids by polymerization/nicking enzyme/DNAzyme cascades for the amplified detection of DNA and the aptamer-cocaine complex.

PubMed

Wang, Fuan; Freage, Lina; Orbach, Ron; Willner, Itamar

2013-09-03

The progressive development of amplified DNA sensors and aptasensors using replication/nicking enzymes/DNAzyme machineries is described. The sensing platforms are based on the tailoring of a DNA template on which the recognition of the target DNA or the formation of the aptamer-substrate complex trigger on the autonomous isothermal replication/nicking processes and the displacement of a Mg(2+)-dependent DNAzyme that catalyzes the generation of a fluorophore-labeled nucleic acid acting as readout signal for the analyses. Three different DNA sensing configurations are described, where in the ultimate configuration the target sequence is incorporated into a nucleic acid blocker structure associated with the sensing template. The target-triggered isothermal autonomous replication/nicking process on the modified template results in the formation of the Mg(2+)-dependent DNAzyme tethered to a free strand consisting of the target sequence. This activates additional template units for the nucleic acid self-replication process, resulting in the ultrasensitive detection of the target DNA (detection limit 1 aM). Similarly, amplified aptamer-based sensing platforms for cocaine are developed along these concepts. The modification of the cocaine-detection template by the addition of a nucleic acid sequence that enables the autonomous secondary coupled activation of a polymerization/nicking machinery and DNAzyme generation path leads to an improved analysis of cocaine (detection limit 10 nM).

Research as Spiritual Covenant

PubMed Central

Salois, Emily Matt; Holkup, Patricia A.; Tripp-Reimer, Toni; Weinert, Clarann

2009-01-01

Conducting research with Native American communities poses special challenges from misunderstandings that may arise from the interface of differing cultural worldviews held by the scientific and the Native communities. Although the community-based participatory research approach shows promise for conducting research that can maximize benefits and minimize the risks of harm to Native American people, there is little information related to the practical implementation of culturally appropriate research practices when working with Native American communities. Drawing on the authors' research with three Native American communities in the Northwest, this article describes culturally appropriate processes for engaging Native American communities. The first section identifies and describes the principles that provide the foundation for the authors' research activity as a spiritual covenant and guides the authors' research with the three communities. The second section describes the project phase matrix that was used to organize the approaches employed in this work. PMID:16829635

I "hear" what you're "saying": Auditory perceptual simulation, reading speed, and reading comprehension.

PubMed

Zhou, Peiyun; Christianson, Kiel

2016-01-01

Auditory perceptual simulation (APS) during silent reading refers to situations in which the reader actively simulates the voice of a character or other person depicted in a text. In three eye-tracking experiments, APS effects were investigated as people read utterances attributed to a native English speaker, a non-native English speaker, or no speaker at all. APS effects were measured via online eye movements and offline comprehension probes. Results demonstrated that inducing APS during silent reading resulted in observable differences in reading speed when readers simulated the speech of faster compared to slower speakers and compared to silent reading without APS. Social attitude survey results indicated that readers' attitudes towards the native and non-native speech did not consistently influence APS-related effects. APS of both native speech and non-native speech increased reading speed, facilitated deeper, less good-enough sentence processing, and improved comprehension compared to normal silent reading.

Inhibition and recovery of the replication of depurinated parvovirus DNA in mouse fibroblasts

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

Vos, J.M.; Avalosse, B.; Su, Z.Z.

Apurinic sites were introduced in the single-stranded DNA of parvovirus minute-virus-of-mice (MVM) and their effect on viral DNA synthesis was measured in mouse fibroblasts. Approximately one apurinic site per viral genome, is sufficient to block its replication in untreated cells. The exposure of host cells to a sublethal dose of UV-light 15 hours prior to virus infection, enhances their ability to support the replication of depurinated MVM. Cell preirradiation induces the apparent overcome of 10-15% of viral DNA replication blocks. These results indicate that apurinic sites prevent mammalian cells from replicating single-stranded DNA unless a recovery process is activated bymore » cell UV-irradiation.« less

Quantifying the intelligibility of speech in noise for non-native listeners.

PubMed

van Wijngaarden, Sander J; Steeneken, Herman J M; Houtgast, Tammo

2002-04-01

When listening to languages learned at a later age, speech intelligibility is generally lower than when listening to one's native language. The main purpose of this study is to quantify speech intelligibility in noise for specific populations of non-native listeners, only broadly addressing the underlying perceptual and linguistic processing. An easy method is sought to extend these quantitative findings to other listener populations. Dutch subjects listening to Germans and English speech, ranging from reasonable to excellent proficiency in these languages, were found to require a 1-7 dB better speech-to-noise ratio to obtain 50% sentence intelligibility than native listeners. Also, the psychometric function for sentence recognition in noise was found to be shallower for non-native than for native listeners (worst-case slope around the 50% point of 7.5%/dB, compared to 12.6%/dB for native listeners). Differences between native and non-native speech intelligibility are largely predicted by linguistic entropy estimates as derived from a letter guessing task. Less effective use of context effects (especially semantic redundancy) explains the reduced speech intelligibility for non-native listeners. While measuring speech intelligibility for many different populations of listeners (languages, linguistic experience) may be prohibitively time consuming, obtaining predictions of non-native intelligibility from linguistic entropy may help to extend the results of this study to other listener populations.

Quantifying the intelligibility of speech in noise for non-native listeners

NASA Astrophysics Data System (ADS)

van Wijngaarden, Sander J.; Steeneken, Herman J. M.; Houtgast, Tammo

2002-04-01

When listening to languages learned at a later age, speech intelligibility is generally lower than when listening to one's native language. The main purpose of this study is to quantify speech intelligibility in noise for specific populations of non-native listeners, only broadly addressing the underlying perceptual and linguistic processing. An easy method is sought to extend these quantitative findings to other listener populations. Dutch subjects listening to Germans and English speech, ranging from reasonable to excellent proficiency in these languages, were found to require a 1-7 dB better speech-to-noise ratio to obtain 50% sentence intelligibility than native listeners. Also, the psychometric function for sentence recognition in noise was found to be shallower for non-native than for native listeners (worst-case slope around the 50% point of 7.5%/dB, compared to 12.6%/dB for native listeners). Differences between native and non-native speech intelligibility are largely predicted by linguistic entropy estimates as derived from a letter guessing task. Less effective use of context effects (especially semantic redundancy) explains the reduced speech intelligibility for non-native listeners. While measuring speech intelligibility for many different populations of listeners (languages, linguistic experience) may be prohibitively time consuming, obtaining predictions of non-native intelligibility from linguistic entropy may help to extend the results of this study to other listener populations.

Dispersal and selection mediate hybridization between a native and invasive species.

PubMed

Kovach, Ryan P; Muhlfeld, Clint C; Boyer, Matthew C; Lowe, Winsor H; Allendorf, Fred W; Luikart, Gordon

2015-01-22

Hybridization between native and non-native species has serious biological consequences, but our understanding of how dispersal and selection interact to influence invasive hybridization is limited. Here, we document the spread of genetic introgression between a native (Oncorhynchus clarkii) and invasive (Oncorhynchus mykiss) trout, and identify the mechanisms influencing genetic admixture. In two populations inhabiting contrasting environments, non-native admixture increased rapidly from 1984 to 2007 and was driven by surprisingly consistent processes. Individual admixture was related to two phenotypic traits associated with fitness: size at spawning and age of juvenile emigration. Fish with higher non-native admixture were larger and tended to emigrate at a younger age--relationships that are expected to confer fitness advantages to hybrid individuals. However, strong selection against non-native admixture was evident across streams and cohorts (mean selection coefficient against genotypes with non-native alleles (s) = 0.60; s.e. = 0.10). Nevertheless, hybridization was promoted in both streams by the continuous immigration of individuals with high levels of non-native admixture from other hybrid source populations. Thus, antagonistic relationships between dispersal and selection are mediating invasive hybridization between these fish, emphasizing that data on dispersal and natural selection are needed to fully understand the dynamics of introgression between native and non-native species. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Reasons for the Invasive Success of a Guppy (Poecilia reticulata) Population in Trinidad

PubMed Central

Sievers, Caya; Willing, Eva-Maria; Hoffmann, Margarete; Dreyer, Christine; Ramnarine, Indar; Magurran, Anne

2012-01-01

The introduction of non-native species into new habitats poses a major threat to native populations. Of particular interest, though often overlooked, are introductions of populations that are not fully reproductively isolated from native individuals and can hybridize with them. To address this important topic we used different approaches in a multi-pronged study, combining the effects of mate choice, shoaling behaviour and genetics. Here we present evidence that behavioural traits such as shoaling and mate choice can promote population mixing if individuals do not distinguish between native and foreign conspecifics. We examined this in the context of two guppy (Poecilia reticulata) populations that have been subject to an introduction and subsequent population mixing event in Trinidad. The introduction of Guanapo River guppies into the Turure River more than 50 years ago led to a marked reduction of the original genotype. In our experiments, female guppies did not distinguish between shoaling partners when given the choice between native and foreign individuals. Introduced fish are therefore likely to benefit from the protection of a shoal and will improve their survival chances as a result. The additional finding that male guppies do not discriminate between females on the basis of origin will further increase the process of population mixing, especially if males encounter mixed shoals. In a mesocosm experiment, in which the native and foreign populations were allowed to mate freely, we found, as expected on the basis of these behavioural interactions, that the distribution of offspring genotypes could be predicted from the proportions of the two types of founding fish. This result suggests that stochastic and environmental processes have reinforced the biological ones to bring about the genetic dominance of the invading population in the Turure River. Re-sampling the Turure for genetic analysis using SNP markers confirmed the population mixing process and showed that it is an on-going process in this river and has led to the nearly complete disappearance of the original genotype. PMID:22693621

BRCA2 and RAD51 promote double-strand break formation and cell death in response to gemcitabine.

PubMed

Jones, Rebecca M; Kotsantis, Panagiotis; Stewart, Grant S; Groth, Petra; Petermann, Eva

2014-10-01

Replication inhibitors cause replication fork stalling and double-strand breaks (DSB) that result from processing of stalled forks. During recovery from replication blocks, the homologous recombination (HR) factor RAD51 mediates fork restart and DSB repair. HR defects therefore sensitize cells to replication inhibitors, with clear implications for cancer therapy. Gemcitabine is a potent replication inhibitor used to treat cancers with mutations in HR genes such as BRCA2. Here, we investigate why, paradoxically, mutations in HR genes protect cells from killing by gemcitabine. Using DNA replication and DNA damage assays in mammalian cells, we show that even short gemcitabine treatments cause persistent replication inhibition. BRCA2 and RAD51 are recruited to chromatin early after removal of the drug, actively inhibit replication fork progression, and promote the formation of MUS81- and XPF-dependent DSBs that remain unrepaired. Our data suggest that HR intermediates formed at gemcitabine-stalled forks are converted into DSBs and thus contribute to gemcitabine-induced cell death, which could have implications for the treatment response of HR-deficient tumors. ©2014 American Association for Cancer Research.

BRCA2 and RAD51 promote double-strand break formation and cell death in response to Gemcitabine

PubMed Central

Jones, Rebecca M.; Kotsantis, Panagiotis; Stewart, Grant S.; Groth, Petra; Petermann, Eva

2014-01-01

Replication inhibitors cause replication fork stalling and double-strand breaks (DSBs) that result from processing of stalled forks. During recovery from replication blocks, the homologous recombination (HR) factor RAD51 mediates fork restart and DSB repair. HR defects therefore sensitise cells to replication inhibitors, with clear implications for cancer therapy. Gemcitabine is a potent replication inhibitor used to treat cancers with mutations in HR genes such as BRCA2. Here we investigate why, paradoxically, mutations in HR genes protect cells from killing by Gemcitabine. Using DNA replication and -damage assays in mammalian cells, we show that even short Gemcitabine treatments cause persistent replication inhibition. BRCA2 and RAD51 are recruited to chromatin early after removal of the drug, actively inhibit replication fork progression and promote the formation of MUS81- and XPF-dependent DSBs that remain unrepaired. Our data suggest that HR intermediates formed at Gemcitabine-stalled forks are converted into DSBs and thus contribute to Gemcitabine-induced cell death, which could have implications for the treatment response of HR-deficient tumours. PMID:25053826

Sustainability of a Compartmentalized Host-Parasite Replicator System under Periodic Washout-Mixing Cycles

PubMed Central

Furubayashi, Taro

2018-01-01

The emergence and dominance of parasitic replicators are among the major hurdles for the proliferation of primitive replicators. Compartmentalization of replicators is proposed to relieve the parasite dominance; however, it remains unclear under what conditions simple compartmentalization uncoupled with internal reaction secures the long-term survival of a population of primitive replicators against incessant parasite emergence. Here, we investigate the sustainability of a compartmentalized host-parasite replicator (CHPR) system undergoing periodic washout-mixing cycles, by constructing a mathematical model and performing extensive simulations. We describe sustainable landscapes of the CHPR system in the parameter space and elucidate the mechanism of phase transitions between sustainable and extinct regions. Our findings revealed that a large population size of compartments, a high mixing intensity, and a modest amount of nutrients are important factors for the robust survival of replicators. We also found two distinctive sustainable phases with different mixing intensities. These results suggest that a population of simple host–parasite replicators assumed before the origin of life can be sustained by a simple compartmentalization with periodic washout-mixing processes. PMID:29373536

Efficacy of glyphosate and five surfactants for controlling giant salvinia

USGS Publications Warehouse

Fairchild, J.F.; Allert, A.L.; Riddle, J.S.; Gladwin, D.R.

2002-01-01

Giant salvinia (Salvinia molesta Mitchell) is a non-native, invasive aquatic fern that was recently introduced to the southern United States. The aggressive nature of the species has led to concerns over its potential adverse impacts to native plants, fish, and invertebrates. We conducted a study to determine the efficacy of glyphosate [isopropylamine salt of N-(phosphono-methyl)glycine] and several surfactants for control of giant salvinia. Studies were conducted over a 42-day period using static renewals (twice weekly) with 4% Hoagland's medium (10 mg/L N equivalent) in replicated 2-L containers. Five concentrations of glyphosate (0, 0.45, 0.91, 1.82, and 3.60% v:v) and five surfactants (0.25% concentration, v:v; Optima???, Kinetic???, Mon 0818???, Cygnet Plus???, and LI-700???) were applied with a pressurized sprayer as a single surface application in a fully nested experimental design. Untreated giant salvinia grew rapidly and exhibited an increase of 800% wet weight biomass over the 42-day test duration. Glyphosate, with and without surfactants, exhibited efficacy at concentrations as low as 0.45% of the commercial formulation. Glyphosate with Optima was the only mixture that resulted in complete mortality of plants with no regrowth.

Phytochemical diversity of cranberry (Vaccinium macrocarpon Aiton) cultivars by anthocyanin determination and metabolomic profiling with chemometric analysis.

PubMed

Brown, Paula N; Murch, Susan J; Shipley, Paul

2012-01-11

Originally native to the eastern United States, American cranberry ( Vaccinium macrocarpon Aiton, family Ericaceae) cultivation of native and hybrid varieties has spread across North America. Herein is reported the phytochemical diversity of five cranberry cultivars (Stevens, Ben Lear, Bergman, Pilgrim, and GH1) collected in the Greater Vancouver Regional District, by anthocyanin content and UPLC-TOF-MS metabolomic profiling. The anthocyanin content for biological replicates (n = 5) was determined as 7.98 ± 5.83, Ben Lear; 7.02 ± 1.75, Bergman; 6.05 ± 2.51, GH1; 3.28 ± 1.88, Pilgrim; and 2.81 ± 0.81, Stevens. Using subtractive metabonomic algorithms 6481 compounds were found conserved across all varietals, with 136 (Ben Lear), 84 (Bergman), 91 (GH1), 128 (Pilgrim), and 165 (Stevens) unique compounds observed. Principal component analysis (PCA) did not differentiate varieties, whereas partial least-squares discriminate analysis (PLS-DA) exhibited clustering patterns. Univariate statistical approaches were applied to the data set, establishing significance of values and assessing quality of the models. Metabolomic profiling with chemometric analysis proved to be useful for characterizing metabonomic changes across cranberry varieties.

Adverse birth outcomes among native-born and immigrant women: replicating national evidence regarding Mexicans at the local level.

PubMed

Cervantes, A; Keith, L; Wyshak, G

1999-06-01

For almost two decades, the literature has consistently described an epidemiologic paradox relating to better birth outcomes among high-risk groups, particularly new immigrants from Mexico and Southeast Asia. We hypothesize that regardless of their sociodemographic profile, Mexican immigrants will exhibit lower rates of low birth weight and preterm deliveries than native-(U.S.) born women of Mexican origin, non-Hispanic White and Black women, and Puerto Rican Women. We studied 57,324 live-born singleton infants born to residents in the city of Chicago in a linked data set of 1994 birth-death records. Multivariate logistic regression was used to analyze race/ethnicity differentials in two pregnancy outcome measures, low birth weight and preterm birth. Overall better birth outcome is related to maternal immigrant status regardless of race/ethnic groups. Immigrant Mexican women had a significantly lower risk of both low birth weight [adjusted odds ratio (AOR): 0.78, 95% confidence interval (CI) 0.66-0.91] and preterm births (AOR: 0.75, 95% CI 0.65-0.86) and were at 28% and 33% lower risks of delivering a low birth weight infant or a premature infant, respectively, than non-Hispanic White women.

Developing Native School Boards: Facilitators and Impediments.

ERIC Educational Resources Information Center

Isherwood, Geoffrey B.

1997-01-01

Effective strategies for assisting Canadian Native communities to develop school boards included encouraging an unhurried adaptive learning process, providing guidance to achieve consensus, and allowing for an incubation period. Impediments to development included community members' avoidance of leadership roles, cross-cultural misunderstandings,…