Soluble Non-ammonia Nitrogen in Ruminal and Omasal Digesta of Korean Native Steers Supplemented with Soluble Proteins

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C. W. Choi

2012-09-01

Full Text Available An experiment was conducted to study the effect of soluble protein supplements on concentration of soluble non-ammonia nitrogen (SNAN in the liquid phase of ruminal (RD and omasal digesta (OD of Korean native steers, and to investigate diurnal pattern in SNAN concentration in RD and OD. Three ruminally cannulated Korean native steers in a 3×3 Latin square design consumed a basal diet of rice straw and corn-based concentrate (control, and that supplemented (kg/d DM basis with intact casein (0.24; IC or acid hydrolyzed casein (0.46; AHC. Ruminal digesta was sampled using a vacuum pump, whereas OD was collected using an omasal sampling system at 2.0 h intervals after a morning feeding. The SNAN fractions (free amino acid (AA, peptide and soluble protein in RD and OD were assessed using the ninhydrin assay. Concentrations of free AA and total SNAN in RD were significantly (p<0.05 lower than those in OD. Although free AA concentration was relatively high, mean peptide was quantitatively the most important fraction of total SNAN in both RD and OD, indicating that degradation of peptide to AA rather than hydrolysis of soluble protein to peptide or deamination may be the most limiting step in rumen proteolysis of Korean native steers. Diurnal variation in peptide concentration in OD for the soluble protein supplemented diets during the feeding cycle peaked 2 h post-feeding and decreased thereafter whereas that for the control was relatively constant during the entire feeding cycle. Diurnal variation in peptide concentration was rather similar between RD and OD.

Periphyton density is similar on native and non-native plant species

NARCIS (Netherlands)

Grutters, B.M.C.; Gross, Elisabeth M.; van Donk, E.; Bakker, E.S.

2017-01-01

Non-native plants increasingly dominate the vegetation in aquatic ecosystems and thrive in eutrophic conditions. In eutrophic conditions, submerged plants risk being overgrown by epiphytic algae; however, if non-native plants are less susceptible to periphyton than natives, this would contribute to

Do native brown trout and non-native brook trout interact reproductively?

Science.gov (United States)

Cucherousset, J.; Aymes, J. C.; Poulet, N.; Santoul, F.; Céréghino, R.

2008-07-01

Reproductive interactions between native and non-native species of fish have received little attention compared to other types of interactions such as predation or competition for food and habitat. We studied the reproductive interactions between non-native brook trout ( Salvelinus fontinalis) and native brown trout ( Salmo trutta) in a Pyrenees Mountain stream (SW France). We found evidence of significant interspecific interactions owing to consistent spatial and temporal overlap in redd localizations and spawning periods. We observed mixed spawning groups composed of the two species, interspecific subordinate males, and presence of natural hybrids (tiger trout). These reproductive interactions could be detrimental to the reproduction success of both species. Our study shows that non-native species might have detrimental effects on native species via subtle hybridization behavior.

Ecological impacts of non-native species: Chapter 2

Science.gov (United States)

Pilliod, David S.; Griffiths, R.A.; Kuzmin, S.L.; Heatwole, Harold; Wilkinson, John W.

2012-01-01

Non-native species are considered one of the greatest threats to freshwater biodiversity worldwide (Drake et al. 1989; Allen and Flecker 1993; Dudgeon et al. 2005). Some of the first hypotheses proposed to explain global patterns of amphibian declines included the effects of non-native species (Barinaga 1990; Blaustein and Wake 1990; Wake and Morowitz 1991). Evidence for the impact of non-native species on amphibians stems (1) from correlative research that relates the distribution or abundance of a species to that of a putative non-native species, and (2) from experimental tests of the effects of a non-native species on survival, growth, development or behaviour of a target species (Kats and Ferrer 2003). Over the past two decades, research on the effects of non-native species on amphibians has mostly focused on introduced aquatic predators, particularly fish. Recent research has shifted to more complex ecological relationships such as influences of sub-lethal stressors (e.g. contaminants) on the effects of non-native species (Linder et al. 2003; Sih et al. 2004), non-native species as vectors of disease (Daszak et al. 2004; Garner et al. 2006), hybridization between non-natives and native congeners (Riley et al. 2003; Storfer et al. 2004), and the alteration of food-webs by non-native species (Nystrom et al. 2001). Other research has examined the interaction of non-native species in terms of facilitation (i.e. one non-native enabling another to become established or spread) or the synergistic effects of multiple non-native species on native amphibians, the so-called invasional meltdown hypothesis (Simerloff and Von Holle 1999). Although there is evidence that some non-native species may interact (Ricciardi 2001), there has yet to be convincing evidence that such interactions have led to an accelerated increase in the number of non-native species and cumulative impacts are still uncertain (Simberloff 2006). Applied research on the control, eradication, and

Protein kinase substrate identification on functional protein arrays

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Zhou Fang

2008-02-01

Full Text Available Abstract Background Over the last decade, kinases have emerged as attractive therapeutic targets for a number of different diseases, and numerous high throughput screening efforts in the pharmaceutical community are directed towards discovery of compounds that regulate kinase function. The emerging utility of systems biology approaches has necessitated the development of multiplex tools suitable for proteomic-scale experiments to replace lower throughput technologies such as mass spectroscopy for the study of protein phosphorylation. Recently, a new approach for identifying substrates of protein kinases has applied the miniaturized format of functional protein arrays to characterize phosphorylation for thousands of candidate protein substrates in a single experiment. This method involves the addition of protein kinases in solution to arrays of immobilized proteins to identify substrates using highly sensitive radioactive detection and hit identification algorithms. Results To date, the factors required for optimal performance of protein array-based kinase substrate identification have not been described. In the current study, we have carried out a detailed characterization of the protein array-based method for kinase substrate identification, including an examination of the effects of time, buffer compositions, and protein concentration on the results. The protein array approach was compared to standard solution-based assays for assessing substrate phosphorylation, and a correlation of greater than 80% was observed. The results presented here demonstrate how novel substrates for protein kinases can be quickly identified from arrays containing thousands of human proteins to provide new clues to protein kinase function. In addition, a pooling-deconvolution strategy was developed and applied that enhances characterization of specific kinase-substrate relationships and decreases reagent consumption. Conclusion Functional protein microarrays are an

Simultaneous isolation of mRNA and native protein from minute samples of cells

DEFF Research Database (Denmark)

Petersen, Tonny Studsgaard; Andersen, Claus Yding

2014-01-01

Precious biological samples often lack a sufficient number of cells for multiple procedures, such as extraction of mRNA while maintaining protein in a non-denatured state suitable for subsequent characterization. Here we present a new method for the simultaneous purification of mRNA and native...... in their native state for traditional protein assays. We validated the procedure using neonatal rat ovaries and small numbers of human granulosa cells, demonstrating the extraction of mRNA suitable for gene expression analysis with simultaneous isolation of native proteins suitable for downstream characterization...... proteins from samples containing small numbers of cells. Our approach utilizes oligodeoxythymidylate [oligo(dT)25]-coated paramagnetic beads in an optimized reaction buffer to isolate mRNA comparable in quantity and quality to mRNA isolated with existing methods, while maintaining the proteins...

Aquatic macroinvertebrate responses to native and non-native predators

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Haddaway N. R.

2014-01-01

Full Text Available Non-native species can profoundly affect native ecosystems through trophic interactions with native species. Native prey may respond differently to non-native versus native predators since they lack prior experience. Here we investigate antipredator responses of two common freshwater macroinvertebrates, Gammarus pulex and Potamopyrgus jenkinsi, to olfactory cues from three predators; sympatric native fish (Gasterosteus aculeatus, sympatric native crayfish (Austropotamobius pallipes, and novel invasive crayfish (Pacifastacus leniusculus. G. pulex responded differently to fish and crayfish; showing enhanced locomotion in response to fish, but a preference for the dark over the light in response to the crayfish. P.jenkinsi showed increased vertical migration in response to all three predator cues relative to controls. These different responses to fish and crayfish are hypothesised to reflect the predators’ differing predation types; benthic for crayfish and pelagic for fish. However, we found no difference in response to native versus invasive crayfish, indicating that prey naiveté is unlikely to drive the impacts of invasive crayfish. The Predator Recognition Continuum Hypothesis proposes that benefits of generalisable predator recognition outweigh costs when predators are diverse. Generalised responses of prey as observed here will be adaptive in the presence of an invader, and may reduce novel predators’ potential impacts.

Non-native educators in English language teaching

CERN Document Server

Braine, George

2013-01-01

The place of native and non-native speakers in the role of English teachers has probably been an issue ever since English was taught internationally. Although ESL and EFL literature is awash, in fact dependent upon, the scrutiny of non-native learners, interest in non-native academics and teachers is fairly new. Until recently, the voices of non-native speakers articulating their own concerns have been even rarer. This book is a response to this notable vacuum in the ELT literature, providing a forum for language educators from diverse geographical origins and language backgrounds. In addition to presenting autobiographical narratives, these authors argue sociopolitical issues and discuss implications for teacher education, all relating to the theme of non-native educators in ETL. All of the authors are non-native speakers of English. Some are long established professionals, whereas others are more recent initiates to the field. All but one received part of the higher education in North America, and all excep...

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

Science.gov (United States)

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

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

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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.

Thermally responsive silicon nanowire arrays for native/denatured-protein separation

International Nuclear Information System (INIS)

Wang Hongwei; Wang Yanwei; Yuan Lin; Wang Lei; Yang Weikang; Wu Zhaoqiang; Li Dan; Chen Hong

2013-01-01

We present our findings of the selective adsorption of native and denatured proteins onto thermally responsive, native-protein resistant poly(N-isopropylacrylamide) (PNIPAAm) decorated silicon nanowire arrays (SiNWAs). The PNIPAAm–SiNWAs surface, which shows very low levels of native-protein adsorption, favors the adsorption of denatured proteins. The amount of denatured-protein adsorption is higher at temperatures above the lower critical solution temperature (LCST) of PNIPAAm. Temperature cycling surrounding the LCST, which ensures against thermal denaturation of native proteins, further increases the amount of denatured-protein adsorption. Moreover, the PNIPAAm–SiNWAs surface is able to selectively adsorb denatured protein even from mixtures of different protein species; meanwhile, the amount of native proteins in solution is kept nearly at its original level. It is believed that these results will not only enrich current understanding of protein interactions with PNIPAAm-modified SiNWAs surfaces, but may also stimulate applications of PNIPAAm–SiNWAs surfaces for native/denatured protein separation. (paper)

Native Speakers' Perception of Non-Native English Speech

Science.gov (United States)

Jaber, Maysa; Hussein, Riyad F.

2011-01-01

This study is aimed at investigating the rating and intelligibility of different non-native varieties of English, namely French English, Japanese English and Jordanian English by native English speakers and their attitudes towards these foreign accents. To achieve the goals of this study, the researchers used a web-based questionnaire which…

Biological activity analysis of native and recombinant streptokinase using clot lysis and chromogenic substrate assay.

Science.gov (United States)

Mahboubi, Arash; Sadjady, Seyyed Kazem; Mirzaei Saleh Abadi, Mohammad; Azadi, Saeed; Solaimanian, Roya

2012-01-01

DETERMINATION OF STREPTOKINASE ACTIVITY IS USUALLY ACCOMPLISHED THROUGH TWO ASSAY METHODS: a) Clot lysis, b) Chromogenic substrate assay. In this study the biological activity of two streptokinase products, namely Streptase®, which is a native product and Heberkinasa®, which is a recombinant product, was determined against the third international reference standard using the two forementioned assay methods. The results indicated that whilst the activity of Streptase® was found to be 101 ± 4% and 97 ± 5% of the label claim with Clot lysis and Chromogenic substrate assay respectively, for Heberkinasa® the potency values obtained were 42 ± 5% and 92.5 ± 2% of the label claim respectively. To shed some light on the reason for this finding, the n-terminal sequence of the streptokinase molecules present in the two products was determined. The results showed slight differences in the amino acid sequence of the recombinant product in comparison to the native one at the amino terminus. This finding supports those of other workers who found that n-terminal sequence of the streptokinase molecule can have significant effect on the activity of this protein.

Enhancing trichloroethylene degradation using non-aromatic compounds as growth substrates.

Science.gov (United States)

Kim, Seungjin; Hwang, Jeongmin; Chung, Jinwook; Bae, Wookeun

2014-06-30

The effect of non-aromatic compounds on the trichloroethylene (TCE) degradation of toluene-oxidizing bacteria were evaluated using Burkholderia cepacia G4 that expresses toluene 2-monooxygenase and Pseudomonas putida that expresses toluene dioxygenase. TCE degradation rates for B. cepacia G4 and P. putida with toluene alone as growth substrate were 0.144 and 0.123 μg-TCE/mg-protein h, respectively. When glucose, acetate and ethanol were fed as additional growth substrates, those values increased up to 0.196, 0.418 and 0.530 μg-TCE/mg-protein h, respectively for B. cepacia G4 and 0.319, 0.219 and 0.373 μg-TCE/mg-protein h, respectively for P. putida. In particular, the addition of ethanol resulted in a high TCE degradation rate regardless of the initial concentration. The use of a non-aromatic compound as an additional substrate probably enhanced the TCE degradation because of the additional supply of NADH that is consumed in co-metabolic degradation of TCE. Also, it is expected that the addition of a non-aromatic substrate can reduce the necessary dose of toluene and, subsequently, minimize the potential competitive inhibition upon TCE co-metabolism by toluene. Copyright © 2014 Elsevier B.V. All rights reserved.

Small mammal use of native warm-season and non-native cool-season grass forage fields

Science.gov (United States)

Ryan L Klimstra,; Christopher E Moorman,; Converse, Sarah J.; Royle, J. Andrew; Craig A Harper,

2015-01-01

Recent emphasis has been put on establishing native warm-season grasses for forage production because it is thought native warm-season grasses provide higher quality wildlife habitat than do non-native cool-season grasses. However, it is not clear whether native warm-season grass fields provide better resources for small mammals than currently are available in non-native cool-season grass forage production fields. We developed a hierarchical spatially explicit capture-recapture model to compare abundance of hispid cotton rats (Sigmodon hispidus), white-footed mice (Peromyscus leucopus), and house mice (Mus musculus) among 4 hayed non-native cool-season grass fields, 4 hayed native warm-season grass fields, and 4 native warm-season grass-forb ("wildlife") fields managed for wildlife during 2 summer trapping periods in 2009 and 2010 of the western piedmont of North Carolina, USA. Cotton rat abundance estimates were greater in wildlife fields than in native warm-season grass and non-native cool-season grass fields and greater in native warm-season grass fields than in non-native cool-season grass fields. Abundances of white-footed mouse and house mouse populations were lower in wildlife fields than in native warm-season grass and non-native cool-season grass fields, but the abundances were not different between the native warm-season grass and non-native cool-season grass fields. Lack of cover following haying in non-native cool-season grass and native warm-season grass fields likely was the key factor limiting small mammal abundance, especially cotton rats, in forage fields. Retention of vegetation structure in managed forage production systems, either by alternately resting cool-season and warm-season grass forage fields or by leaving unharvested field borders, should provide refugia for small mammals during haying events.

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

Science.gov (United States)

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.

Determinants of success in native and non-native listening comprehension: an individual differences approach

NARCIS (Netherlands)

Andringa, S.; Olsthoorn, N.; van Beuningen, C.; Schoonen, R.; Hulstijn, J.

2012-01-01

The goal of this study was to explain individual differences in both native and non-native listening comprehension; 121 native and 113 non-native speakers of Dutch were tested on various linguistic and nonlinguistic cognitive skills thought to underlie listening comprehension. Structural equation

GLTP mediated non-vesicular GM1 transport between native membranes.

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Ines Lauria

Full Text Available Lipid transfer proteins (LTPs are emerging as key players in lipid homeostasis by mediating non-vesicular transport steps between two membrane surfaces. Little is known about the driving force that governs the direction of transport in cells. Using the soluble LTP glycolipid transfer protein (GLTP, we examined GM1 (monosialotetrahexosyl-ganglioside transfer to native membrane surfaces. With artificial GM1 donor liposomes, GLTP can be used to increase glycolipid levels over natural levels in either side of the membrane leaflet, i.e., external or cytosolic. In a system with native donor- and acceptor-membranes, we find that GLTP balances highly variable GM1 concentrations in a population of membranes from one cell type, and in addition, transfers lipids between membranes from different cell types. Glycolipid transport is highly efficient, independent of cofactors, solely driven by the chemical potential of GM1 and not discriminating between the extra- and intracellular membrane leaflet. We conclude that GLTP mediated non-vesicular lipid trafficking between native membranes is driven by simple thermodynamic principles and that for intracellular transport less than 1 µM GLTP would be required in the cytosol. Furthermore, the data demonstrates the suitability of GLTP as a tool for artificially increasing glycolipid levels in cellular membranes.

Spot morphology of non-contact printed protein molecules on non-porous substrates with a range of hydrophobicities

NARCIS (Netherlands)

Mujawar, L.H.; Norde, W.; Amerongen, van A.

2013-01-01

Non-contact inkjet printing technology is one of the most promising tools for producing microarrays. The quality of the microarray depends on the type of the substrate used for printing biomolecules. Various porous and non-porous substrates have been used in the past, but due to low production cost

Contrasting xylem vessel constraints on hydraulic conductivity between native and non-native woody understory species

Directory of Open Access Journals (Sweden)

Maria S Smith

2013-11-01

Full Text Available We examined the hydraulic properties of 82 native and non-native woody species common to forests of Eastern North America, including several congeneric groups, representing a range of anatomical wood types. We observed smaller conduit diameters with greater frequency in non-native species, corresponding to lower calculated potential vulnerability to cavitation index. Non-native species exhibited higher vessel-grouping in metaxylem compared with native species, however, solitary vessels were more prevalent in secondary xylem. Higher frequency of solitary vessels in secondary xylem was related to a lower potential vulnerability index. We found no relationship between anatomical characteristics of xylem, origin of species and hydraulic conductivity, indicating that non-native species did not exhibit advantageous hydraulic efficiency over native species. Our results confer anatomical advantages for non-native species under the potential for cavitation due to freezing, perhaps permitting extended growing seasons.

The online application of binding condition B in native and non-native pronoun resolution

Directory of Open Access Journals (Sweden)

Clare ePatterson

2014-02-01

Full Text Available Previous research has shown that anaphor resolution in a non-native language may be more vulnerable to interference from structurally inappropriate antecedents compared to native anaphor resolution. To test whether previous findings on reflexive anaphors generalise to non-reflexive pronouns, we carried out an eye-movement monitoring study investigating the application of binding condition B during native and non-native sentence processing. In two online reading experiments we examined when during processing local and/or non-local antecedents for pronouns were considered in different types of syntactic environment. Our results demonstrate that both native English speakers and native German-speaking learners of English showed online sensitivity to binding condition B in that they did not consider syntactically inappropriate antecedents. For pronouns thought to be exempt from condition B (so-called 'short-distance pronouns', the native readers showed a weak preference for the local antecedent during processing. The non-native readers, on the other hand, showed a preference for the matrix subject even where local coreference was permitted, and despite demonstrating awareness of short-distance pronouns' referential ambiguity in a complementary offline task. This indicates that non-native comprehenders are less sensitive during processing to structural cues that render pronouns exempt from condition B, and prefer to link a pronoun to a salient subject antecedent instead.

Immobilised native plant cysteine proteases: packed-bed reactor for white wine protein stabilisation

OpenAIRE

Benucci, Ilaria; Lombardelli, Claudio; Liburdi, Katia; Acciaro, Giuseppe; Zappino, Matteo; Esti, Marco

2015-01-01

This research presents a feasibility study of using a continuous packed-bed reactor (PBR), containing immobilised native plant cysteine proteases, as a specific and mild alternative technique relative to the usual bentonite fining for white wine protein stabilisation. The operational parameters for a PBR containing immobilised bromelain (PBR-br) or immobilised papain (PBR-pa) were optimised using model wine fortified with synthetic substrate (Bz-Phe-Val-Arg-pNA). The effectiveness of PBR-br, ...

Determinants of Success in Native and Non-Native Listening Comprehension: An Individual Differences Approach

Science.gov (United States)

Andringa, Sible; Olsthoorn, Nomi; van Beuningen, Catherine; Schoonen, Rob; Hulstijn, Jan

2012-01-01

The goal of this study was to explain individual differences in both native and non-native listening comprehension; 121 native and 113 non-native speakers of Dutch were tested on various linguistic and nonlinguistic cognitive skills thought to underlie listening comprehension. Structural equation modeling was used to identify the predictors of…

Chinese College Students' Views on Native English and Non-Native English in EFL Classrooms

Science.gov (United States)

Qian, Yang; Jingxia, Liu

2016-01-01

With the development of globalization, English is clearly spoken by many more non-native than native speakers, which raises the discussion of English varieties and the debate regarding the conformity to Standard English. Although a large number of studies have shown scholars' attitudes towards native English and non-native English, little research…

Whole Protein Native Fitness Potentials

Science.gov (United States)

Faraggi, Eshel; Kloczkowski, Andrzej

2013-03-01

Protein structure prediction can be separated into two tasks: sample the configuration space of the protein chain, and assign a fitness between these hypothetical models and the native structure of the protein. One of the more promising developments in this area is that of knowledge based energy functions. However, standard approaches using pair-wise interactions have shown shortcomings demonstrated by the superiority of multi-body-potentials. These shortcomings are due to residue pair-wise interaction being dependent on other residues along the chain. We developed a method that uses whole protein information filtered through machine learners to score protein models based on their likeness to native structures. For all models we calculated parameters associated with the distance to the solvent and with distances between residues. These parameters, in addition to energy estimates obtained by using a four-body-potential, DFIRE, and RWPlus were used as training for machine learners to predict the fitness of the models. Testing on CASP 9 targets showed that our method is superior to DFIRE, RWPlus, and the four-body potential, which are considered standards in the field.

Activities of native and tyrosine-69 mutant phospholipases A2 on phospholipid analogues. A reevaluation of the minimal substrate requirements.

Science.gov (United States)

Kuipers, O P; Dekker, N; Verheij, H M; de Haas, G H

1990-06-26

The role of Tyr-69 of porcine pancreatic phospholipase A2 in substrate binding was studied with the help of proteins modified by site-directed mutagenesis and phospholipid analogues with a changed head-group geometry. Two mutants were used containing Phe and Lys, respectively, at position 69. Modifications in the phospholipids included introduction of a sulfur at the phosphorus (thionophospholipids), removal of the negative charge at phosphorus (phosphatidic acid dimethyl ester), and reduction (phosphonolipids) or extension (diacylbutanetriol choline phosphate) of the distance between the phosphorus and the acyl ester bond. Replacement of Tyr-69 by Lys reduces enzymatic activity, but the mutant enzyme retains both the stereospecificity and positional specificity of native phospholipase A2. The Phe-69 mutant not only hydrolyzes the Rp isomer of thionophospholipids more efficiently than the wild-type enzyme, but the Sp thiono isomer is hydrolyzed too, although at a low (approximately 4%) rate. Phosphonolipids are hydrolyzed by native phospholipase A2 about 7 times more slowly than natural phospholipids, with retention of positional specificity and a (partial) loss of stereospecificity. The dimethyl ester of phosphatidic acid is degraded efficiently in a calcium-dependent and positional-specific way by native phospholipase A2 and by the mutants, indicating that a negative charge at phosphorus is not an absolute substrate requirement. The activities on the phosphatidic acid dimethyl ester of native enzyme and the Lys-69 mutant are lower than those on the corresponding lecithin, in contrast to the Phe-69 mutant, which has equal activities on both substrates.(ABSTRACT TRUNCATED AT 250 WORDS)

Non-native plant invasions of United States National parks

Science.gov (United States)

Allen, J.A.; Brown, C.S.; Stohlgren, T.J.

2009-01-01

The United States National Park Service was created to protect and make accessible to the public the nation's most precious natural resources and cultural features for present and future generations. However, this heritage is threatened by the invasion of non-native plants, animals, and pathogens. To evaluate the scope of invasions, the USNPS has inventoried non-native plant species in the 216 parks that have significant natural resources, documenting the identity of non-native species. We investigated relationships among non-native plant species richness, the number of threatened and endangered plant species, native species richness, latitude, elevation, park area and park corridors and vectors. Parks with many threatened and endangered plants and high native plant species richness also had high non-native plant species richness. Non-native plant species richness was correlated with number of visitors and kilometers of backcountry trails and rivers. In addition, this work reveals patterns that can be further explored empirically to understand the underlying mechanisms. ?? Springer Science+Business Media B.V. 2008.

Epistemologies in the Text of Children's Books: Native- and non-Native-authored books

Science.gov (United States)

Dehghani, Morteza; Bang, Megan; Medin, Douglas; Marin, Ananda; Leddon, Erin; Waxman, Sandra

2013-09-01

An examination of artifacts provides insights into the goals, practices, and orientations of the persons and cultures who created them. Here, we analyze storybook texts, artifacts that are a part of many children's lives. We examine the stories in books targeted for 4-8-year-old children, contrasting the texts generated by Native American authors versus popular non-Native authors. We focus specifically on the implicit and explicit 'epistemological orientations' associated with relations between human beings and the rest of nature. Native authors were significantly more likely than non-Native authors to describe humans and the rest of nature as psychologically close and embedded in relationships. This pattern converges well with evidence from a behavioral task in which we probed Native (from urban inter-tribal and rural communities) and non-Native children's and adults' attention to ecological relations. We discuss the implications of these differences for environmental cognition and science learning.

Predation by crustaceans on native and non-native Baltic clams

NARCIS (Netherlands)

Ejdung, G.; Flach, E.; Byrén, L.; Hummel, H.

2009-01-01

We studied the effect of crustacean predators on native/non-native Macoma balthica bivalves in aquarium experiments. North Sea M. balthica (NS Macoma) were recently observed in the southern Baltic Sea. They differ genetically and in terms of morphology, behaviour and evolutionary history from Baltic

Growth strategy, phylogeny and stoichiometry determine the allelopathic potential of native and non-native plants

NARCIS (Netherlands)

Grutters, Bart M.C.; Saccomanno, Benedetta; Gross, Elisabeth M.; Van de Waal, Dedmer B.; van Donk, Ellen; Bakker, Elisabeth S.

2017-01-01

Secondary compounds can contribute to the success of non-native plant species if they reduce damage by native herbivores or inhibit the growth of native plant competitors. However, there is opposing evidence on whether the secondary com- pounds of non-native plant species are stronger than those of

Mental health status in pregnancy among native and non-native Swedish-speaking women

DEFF Research Database (Denmark)

Wangel, Anne-Marie; Schei, Berit; Ryding, Elsa Lena

2012-01-01

OBJECTIVES: To describe mental health status in native and non-native Swedish-speaking pregnant women and explore risk factors of depression and posttraumatic stress (PTS) symptoms. DESIGN AND SETTING: A cross-sectional questionnaire study was conducted at midwife-based antenatal clinics in South......OBJECTIVES: To describe mental health status in native and non-native Swedish-speaking pregnant women and explore risk factors of depression and posttraumatic stress (PTS) symptoms. DESIGN AND SETTING: A cross-sectional questionnaire study was conducted at midwife-based antenatal clinics...... in Southern Sweden. SAMPLE: A non-selected group of women in mid-pregnancy. METHODS: Participants completed a questionnaire covering background characteristics, social support, life events, mental health variables and the short Edinburgh Depression Scale. MAIN OUTCOME MEASURES: Depressive symptoms during...... the past week and PTS symptoms during the past year. RESULTS: Out of 1003 women, 21.4% reported another language than Swedish as their mother tongue and were defined as non-native. These women were more likely to be younger, have fewer years of education, potential financial problems, and lack of social...

Probing protein phosphatase substrate binding

DEFF Research Database (Denmark)

Højlys-Larsen, Kim B.; Sørensen, Kasper Kildegaard; Jensen, Knud Jørgen

2012-01-01

Proteomics and high throughput analysis for systems biology can benefit significantly from solid-phase chemical tools for affinity pull-down of proteins from complex mixtures. Here we report the application of solid-phase synthesis of phosphopeptides for pull-down and analysis of the affinity...... profile of the integrin-linked kinase associated phosphatase (ILKAP), a member of the protein phosphatase 2C (PP2C) family. Phosphatases can potentially dephosphorylate these phosphopeptide substrates but, interestingly, performing the binding studies at 4 °C allowed efficient binding to phosphopeptides......, without the need for phosphopeptide mimics or phosphatase inhibitors. As no proven ILKAP substrates were available, we selected phosphopeptide substrates among known PP2Cδ substrates including the protein kinases: p38, ATM, Chk1, Chk2 and RSK2 and synthesized directly on PEGA solid supports through a BAL...

On the radioimmunological determination of native and heat denaturated protein

International Nuclear Information System (INIS)

Menzel, E.J.; Glatz, F.; Technische Univ., Vienna

1981-01-01

Precipitation radioimmunoassay, solid phase radioimmunoassay and passive hemagglutination were examined for their efficiency in the determination of native or denaturated soy proteins. Native as well as autoclaved soy protein could be determined quantitatively in the precipitation radioimmunoassay, using antisera directed against the native product. In the solid phase technique only the autoclaved soy protein could be detected with high sensitivity. In the passive hemagglutination reaction, no agglutination could be observed with erythrocytes coated with autoclaved soy protein. Only antisera against the denaturated (autoclaved) soy protein agglutinated these erythrocytes. (orig.) [de

Growth rate differences between resident native brook trout and non-native brown trout

Science.gov (United States)

Carlson, S.M.; Hendry, A.P.; Letcher, B.H.

2007-01-01

Between species and across season variation in growth was examined by tagging and recapturing individual brook trout Salvelinus fontinalis and brown trout Salmo trutta across seasons in a small stream (West Brook, Massachusetts, U.S.A.). Detailed information on body size and growth are presented to (1) test whether the two species differed in growth within seasons and (2) characterize the seasonal growth patterns for two age classes of each species. Growth differed between species in nearly half of the season- and age-specific comparisons. When growth differed, non-native brown trout grew faster than native brook trout in all but one comparison. Moreover, species differences were most pronounced when overall growth was high during the spring and early summer. These growth differences resulted in size asymmetries that were sustained over the duration of the study. A literature survey also indicated that non-native salmonids typically grow faster than native salmonids when the two occur in sympatry. Taken together, these results suggest that differences in growth are not uncommon for coexisting native and non-native salmonids. ?? 2007 The Authors.

Caged Protein Prenyltransferase Substrates: Tools for Understanding Protein Prenylation

Energy Technology Data Exchange (ETDEWEB)

DeGraw, Amanda J.; Hast, Michael A.; Xu, Juhua; Mullen, Daniel; Beese, Lorena S.; Barany, George; Distefano, Mark D. (Duke); (UMM)

2010-11-15

Originally designed to block the prenylation of oncogenic Ras, inhibitors of protein farnesyltransferase currently in preclinical and clinical trials are showing efficacy in cancers with normal Ras. Blocking protein prenylation has also shown promise in the treatment of malaria, Chagas disease and progeria syndrome. A better understanding of the mechanism, targets and in vivo consequences of protein prenylation are needed to elucidate the mode of action of current PFTase (Protein Farnesyltransferase) inhibitors and to create more potent and selective compounds. Caged enzyme substrates are useful tools for understanding enzyme mechanism and biological function. Reported here is the synthesis and characterization of caged substrates of PFTase. The caged isoprenoid diphosphates are poor substrates prior to photolysis. The caged CAAX peptide is a true catalytically caged substrate of PFTase in that it is to not a substrate, yet is able to bind to the enzyme as established by inhibition studies and X-ray crystallography. Irradiation of the caged molecules with 350 nm light readily releases their cognate substrate and their photolysis products are benign. These properties highlight the utility of those analogs towards a variety of in vitro and in vivo applications.

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

Science.gov (United States)

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,...

Neighbour tolerance, not suppression, provides competitive advantage to non-native plants.

Science.gov (United States)

Golivets, Marina; Wallin, Kimberly F

2018-05-01

High competitive ability has often been invoked as a key determinant of invasion success and ecological impacts of non-native plants. Yet our understanding of the strategies that non-natives use to gain competitive dominance remains limited. Particularly, it remains unknown whether the two non-mutually exclusive competitive strategies, neighbour suppression and neighbour tolerance, are equally important for the competitive advantage of non-native plants. Here, we analyse data from 192 peer-reviewed studies on pairwise plant competition within a Bayesian multilevel meta-analytic framework and show that non-native plants outperform their native counterparts due to high tolerance of competition, as opposed to strong suppressive ability. Competitive tolerance ability of non-native plants was driven by neighbour's origin and was expressed in response to a heterospecific native but not heterospecific non-native neighbour. In contrast to natives, non-native species were not more suppressed by hetero- vs. conspecific neighbours, which was partially due to higher intensity of intraspecific competition among non-natives. Heterogeneity in the data was primarily associated with methodological differences among studies and not with phylogenetic relatedness among species. Altogether, our synthesis demonstrates that non-native plants are competitively distinct from native plants and challenges the common notion that neighbour suppression is the primary strategy for plant invasion success. © 2018 John Wiley & Sons Ltd/CNRS.

Within-category variance and lexical tone discrimination in native and non-native speakers

NARCIS (Netherlands)

Hoffmann, C.W.G.; Sadakata, M.; Chen, A.; Desain, P.W.M.; McQueen, J.M.; Gussenhove, C.; Chen, Y.; Dediu, D.

2014-01-01

In this paper, we show how acoustic variance within lexical tones in disyllabic Mandarin Chinese pseudowords affects discrimination abilities in both native and non-native speakers of Mandarin Chinese. Within-category acoustic variance did not hinder native speakers in discriminating between lexical

Comparison of root-associated communities of native and non-native ectomycorrhizal hosts in an urban landscape.

Science.gov (United States)

Lothamer, K; Brown, S P; Mattox, J D; Jumpponen, A

2014-05-01

Non-native tree species are often used as ornamentals in urban landscapes. However, their root-associated fungal communities remain yet to be examined in detail. Here, we compared richness, diversity and community composition of ectomycorrhizosphere fungi in general and ectomycorrhizal (EcM) fungi in particular between a non-native Pinus nigra and a native Quercus macrocarpa across a growing season in urban parks using 454-pyrosequencing. Our data show that, while the ectomycorrhizosphere community richness and diversity did not differ between the two host, the EcM communities associated with the native host were often more species rich and included more exclusive members than those of the non-native hosts. In contrast, the ectomycorrhizosphere communities of the two hosts were compositionally clearly distinct in nonmetric multidimensional ordination analyses, whereas the EcM communities were only marginally so. Taken together, our data suggest EcM communities with broad host compatibilities and with a limited numbers of taxa with preference to the non-native host. Furthermore, many common fungi in the non-native Pinus were not EcM taxa, suggesting that the fungal communities of the non-native host may be enriched in non-mycorrhizal fungi at the cost of the EcM taxa. Finally, while our colonization estimates did not suggest a shortage in EcM inoculum for either host in urban parks, the differences in the fungi associated with the two hosts emphasize the importance of using native hosts in urban environments as a tool to conserve endemic fungal diversity and richness in man-made systems.

A structural classification of substrate-binding proteins

NARCIS (Netherlands)

Berntsson, Ronnie P. -A.; Smits, Sander H. J.; Schmitt, Lutz; Slotboom, Dirk-Jan; Poolman, Bert

2010-01-01

Substrate-binding proteins (SBP) are associated with a wide variety of protein complexes. The proteins are part of ATP-binding cassette transporters for substrate uptake, ion gradient driven transporters, DNA-binding proteins, as well as channels and receptors from both pro-and eukaryotes. A wealth

Potential population and assemblage influences of non-native trout on native nongame fish in Nebraska headwater streams

Science.gov (United States)

Turek, Kelly C.; Pegg, Mark A.; Pope, Kevin L.; Schainost, Steve

2014-01-01

Non-native trout are currently stocked to support recreational fisheries in headwater streams throughout Nebraska. The influence of non-native trout introductions on native fish populations and their role in structuring fish assemblages in these systems is unknown. The objectives of this study were to determine (i) if the size structure or relative abundance of native fish differs in the presence and absence of non-native trout, (ii) if native fish-assemblage structure differs in the presence and absence of non-native trout and (iii) if native fish-assemblage structure differs across a gradient in abundances of non-native trout. Longnose dace Rhinichthys cataractae were larger in the presence of brown trout Salmo trutta and smaller in the presence of rainbow trout Oncorhynchus mykiss compared to sites without trout. There was also a greater proportion of larger white suckers Catostomus commersonii in the presence of brown trout. Creek chub Semotilus atromaculatus and fathead minnow Pimephales promelas size structures were similar in the presence and absence of trout. Relative abundances of longnose dace, white sucker, creek chub and fathead minnow were similar in the presence and absence of trout, but there was greater distinction in native fish-assemblage structure between sites with trout compared to sites without trout as trout abundances increased. These results suggest increased risk to native fish assemblages in sites with high abundances of trout. However, more research is needed to determine the role of non-native trout in structuring native fish assemblages in streams, and the mechanisms through which introduced trout may influence native fish populations.

Environmental niche separation between native and non-native benthic invertebrate species: Case study of the northern Baltic Sea.

Science.gov (United States)

Jänes, Holger; Herkül, Kristjan; Kotta, Jonne

2017-10-01

Knowledge and understanding of geographic distributions of species is crucial for many aspects in ecology, conservation, policy making and management. In order to reach such an understanding, it is important to know abiotic variables that impact and drive distributions of native and non-native species. We used an existing long-term macrobenthos database for species presence-absence information and biomass estimates at different environmental gradients in the northern Baltic Sea. Region specific abiotic variables (e.g. salinity, depth) were derived from previously constructed bathymetric and hydrodynamic models. Multidimensional ordination techniques were then applied to investigate potential niche space separation between all native and non-native invertebrates in the northern Baltic Sea. Such an approach allowed to obtain data rich and robust estimates of the current native and non-native species distributions and outline important abiotic parameters influencing the observed pattern. The results showed clear niche space separation between native and non-native species. Non-native species were situated in an environmental space characterized by reduced salinity, high temperatures, high proportion of soft seabed and decreased depth and wave exposure whereas native species displayed an opposite pattern. Different placement of native and non-native species along the studied environmental niche space is likely to be explained by the differences in their evolutionary history, human mediated activities and geological youth of the Baltic Sea. The results of this study can provide early warnings and effectively outline coastal areas in the northern Baltic Sea that are prone to further range expansion of non-native species as climate change is expected to significantly reduce salinity and increase temperature in wide coastal areas, both supporting the disappearance of native and appearance of non-native species. Copyright © 2017 Elsevier Ltd. All rights reserved.

Raman molecular fingerprint of non-structural protein 1 in phosphate buffer saline with gold substrate.

Science.gov (United States)

Radzol, A R M; Lee, Khuan Y; Mansor, W

2013-01-01

SERS is a form of Raman spectroscopy that is enhanced with nano-sensing chip as substrate. It can yield distinct biochemical fingerprint for molecule of solids, liquids and gases. Vice versa, it can be used to identify unknown molecule. It has further advantage of being non-invasive, non-contact and cheap, as compared to other existing laboratory based techniques. NS1 has been clinically accepted as an alternative biomarker to IgM in diagnosing viral diseases carried by virus of flaviviridae. Its presence in the blood serum at febrile stage of the flavivirus infection has been proven. Being an antigen, it allows early detection that can help to reduce the mortality rate. This paper proposes SERS as a technique for detection of NS1 from its scattering spectrum. Contribution from our work so far has never been reported. From our experiments, it is found that NS1 protein is Raman active. Its spectrum exhibits five prominent peaks at Raman shift of 548, 1012, 1180, 1540 and 1650 cm(-1). Of these, peak at 1012 cm(-1) scales the highest intensity. It is singled out as the peak to fingerprint the NS1 protein. This is because its presence is verified by the ring breathing vibration of the benzene ring structure side chain molecule. The characteristic peak is found to vary in proportion to concentration. It is found that for a 99% change in concentration, a 96.7% change in intensity is incurred. This yields a high sensitivity of about one a.u. per ppm. Further investigation from the characterization graph shows a correlation coefficient of 0.9978 and a standard error estimation of 0.02782, which strongly suggests a linear relationship between the concentration and characteristic peak intensity of NS1. Our finding produces favorable evidence to the use of SERS technique for detection of NS1 protein for early detection of flavivirus infected diseases with gold substrate.

Non-permeable substrate carrier for electroplating

Science.gov (United States)

Abas, Emmanuel Chua; Chen, Chen-An; Ma, Diana Xiaobing; Ganti, Kalyana Bhargava

2012-11-27

One embodiment relates to a substrate carrier for use in electroplating a plurality of substrates. The substrate carrier comprises a non-conductive carrier body on which the substrates are to be held. Electrically-conductive lines are embedded within the carrier body, and a plurality of contact clips are coupled to the electrically-conductive lines embedded within the carrier body. The contact clips hold the substrates in place and electrically couple the substrates to the electrically-conductive lines. The non-conductive carrier body is continuous so as to be impermeable to flow of electroplating solution through the non-conductive carrier body. Other embodiments, aspects and features are also disclosed.

Phytophagous insects on native and non-native host plants: combining the community approach and the biogeographical approach.

Directory of Open Access Journals (Sweden)

Kim Meijer

Full Text Available During the past centuries, humans have introduced many plant species in areas where they do not naturally occur. Some of these species establish populations and in some cases become invasive, causing economic and ecological damage. Which factors determine the success of non-native plants is still incompletely understood, but the absence of natural enemies in the invaded area (Enemy Release Hypothesis; ERH is one of the most popular explanations. One of the predictions of the ERH, a reduced herbivore load on non-native plants compared with native ones, has been repeatedly tested. However, many studies have either used a community approach (sampling from native and non-native species in the same community or a biogeographical approach (sampling from the same plant species in areas where it is native and where it is non-native. Either method can sometimes lead to inconclusive results. To resolve this, we here add to the small number of studies that combine both approaches. We do so in a single study of insect herbivory on 47 woody plant species (trees, shrubs, and vines in the Netherlands and Japan. We find higher herbivore diversity, higher herbivore load and more herbivory on native plants than on non-native plants, generating support for the enemy release hypothesis.

Seed rain under native and non-native tree species in the Cabo Rojo National Wildlife Refuge, Puerto Rico.

Science.gov (United States)

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.

Higher dropout rate in non-native patients than in native patients in rehabilitation in The Netherlands

NARCIS (Netherlands)

Sloots, Maurits; Scheppers, Emmanuel F.; van de Weg, Frans B.; Bartels, Edien A.; Geertzen, Jan H.; Dekker, Joost; Dekker, Jaap

Dropout from a rehabilitation programme often occurs in patients with chronic nonspecific low back pain of non-native origin. However, the exact dropout rate is not known. The objective of this study was to determine the difference in dropout rate between native and non-native patients with chronic

Engineered, highly reactive substrates of microbial transglutaminase enable protein labeling within various secondary structure elements.

Science.gov (United States)

Rachel, Natalie M; Quaglia, Daniela; Lévesque, Éric; Charette, André B; Pelletier, Joelle N

2017-11-01

Microbial transglutaminase (MTG) is a practical tool to enzymatically form isopeptide bonds between peptide or protein substrates. This natural approach to crosslinking the side-chains of reactive glutamine and lysine residues is solidly rooted in food and textile processing. More recently, MTG's tolerance for various primary amines in lieu of lysine have revealed its potential for site-specific protein labeling with aminated compounds, including fluorophores. Importantly, MTG can label glutamines at accessible positions in the body of a target protein, setting it apart from most labeling enzymes that react exclusively at protein termini. To expand its applicability as a labeling tool, we engineered the B1 domain of Protein G (GB1) to probe the selectivity and enhance the reactivity of MTG toward its glutamine substrate. We built a GB1 library where each variant contained a single glutamine at positions covering all secondary structure elements. The most reactive and selective variants displayed a >100-fold increase in incorporation of a recently developed aminated benzo[a]imidazo[2,1,5-cd]indolizine-type fluorophore, relative to native GB1. None of the variants were destabilized. Our results demonstrate that MTG can react readily with glutamines in α-helical, β-sheet, and unstructured loop elements and does not favor one type of secondary structure. Introducing point mutations within MTG's active site further increased reactivity toward the most reactive substrate variant, I6Q-GB1, enhancing MTG's capacity to fluorescently label an engineered, highly reactive glutamine substrate. This work demonstrates that MTG-reactive glutamines can be readily introduced into a protein domain for fluorescent labeling. © 2017 The Protein Society.

Direct and Indirect Influence of Non-Native Neighbours on Pollination and Fruit Production of a Native Plant.

Directory of Open Access Journals (Sweden)

Ana Montero-Castaño

Full Text Available Entomophilous non-native plants can directly affect the pollination and reproductive success of native plant species and also indirectly, by altering the composition and abundance of floral resources in the invaded community. Separating direct from indirect effects is critical for understanding the mechanisms underlying the impacts of non-native species on recipient communities.Our aims are: (a to explore both the direct effect of the non-native Hedysarum coronarium and its indirect effect, mediated by the alteration of floral diversity, on the pollinator visitation rate and fructification of the native Leopoldia comosa and (b to distinguish whether the effects of the non-native species were due to its floral display or to its vegetative interactions.We conducted field observations within a flower removal experimental setup (i.e. non-native species present, absent and with its inflorescences removed at the neighbourhood scale.Our study illustrates the complexity of mechanisms involved in the impacts of non-native species on native species. Overall, Hedysarum increased pollinator visitation rates to Leopoldia target plants as a result of direct and indirect effects acting in the same direction. Due to its floral display, Hedysarum exerted a direct magnet effect attracting visits to native target plants, especially those made by the honeybee. Indirectly, Hedysarum also increased the visitation rate of native target plants. Due to the competition for resources mediated by its vegetative parts, it decreased floral diversity in the neighbourhoods, which was negatively related to the visitation rate to native target plants. Hedysarum overall also increased the fructification of Leopoldia target plants, even though such an increase was the result of other indirect effects compensating for the observed negative indirect effect mediated by the decrease of floral diversity.

Non-native Listeners’ Recognition of High-Variability Speech Using PRESTO

Science.gov (United States)

Tamati, Terrin N.; Pisoni, David B.

2015-01-01

Background Natural variability in speech is a significant challenge to robust successful spoken word recognition. In everyday listening environments, listeners must quickly adapt and adjust to multiple sources of variability in both the signal and listening environments. High-variability speech may be particularly difficult to understand for non-native listeners, who have less experience with the second language (L2) phonological system and less detailed knowledge of sociolinguistic variation of the L2. Purpose The purpose of this study was to investigate the effects of high-variability sentences on non-native speech recognition and to explore the underlying sources of individual differences in speech recognition abilities of non-native listeners. Research Design Participants completed two sentence recognition tasks involving high-variability and low-variability sentences. They also completed a battery of behavioral tasks and self-report questionnaires designed to assess their indexical processing skills, vocabulary knowledge, and several core neurocognitive abilities. Study Sample Native speakers of Mandarin (n = 25) living in the United States recruited from the Indiana University community participated in the current study. A native comparison group consisted of scores obtained from native speakers of English (n = 21) in the Indiana University community taken from an earlier study. Data Collection and Analysis Speech recognition in high-variability listening conditions was assessed with a sentence recognition task using sentences from PRESTO (Perceptually Robust English Sentence Test Open-Set) mixed in 6-talker multitalker babble. Speech recognition in low-variability listening conditions was assessed using sentences from HINT (Hearing In Noise Test) mixed in 6-talker multitalker babble. Indexical processing skills were measured using a talker discrimination task, a gender discrimination task, and a forced-choice regional dialect categorization task. Vocabulary

Dynamic culture substrate that captures a specific extracellular matrix protein in response to light

International Nuclear Information System (INIS)

Nakanishi, Jun; Nakayama, Hidekazu; Horiike, Yasuhiro; Yamaguchi, Kazuo; Garcia, Andres J

2011-01-01

The development of methods for the off-on switching of immobilization or presentation of cell-adhesive peptides and proteins during cell culture is important because such surfaces are useful for the analysis of the dynamic processes of cell adhesion and migration. This paper describes a chemically functionalized gold substrate that captures a genetically tagged extracellular matrix protein in response to light. The substrate was composed of mixed self-assembled monolayers (SAMs) of three disulfide compounds containing (i) a photocleavable poly(ethylene glycol) (PEG), (ii) nitrilotriacetic acid (NTA) and (iii) hepta(ethylene glycol) (EG 7 ). Although the NTA group has an intrinsic high affinity for oligohistidine tag (His-tag) sequences in its Ni 2+ -ion complex, the interaction was suppressed by the steric hindrance of coexisting PEG on the substrate surface. Upon photoirradiation of the substrate to release the PEG chain from the surface, this interaction became possible and hence the protein was captured at the irradiated regions, while keeping the non-specific adsorption of non-His-tagged proteins blocked by the EG 7 underbrush. In this way, we selectively immobilized a His-tagged fibronectin fragment (FNIII 7-10 ) to the irradiated regions. In contrast, when bovine serum albumin-a major serum protein-was added as a non-His-tagged protein, the surface did not permit its capture, with or without irradiation. In agreement with these results, cells were selectively attached to the irradiated patterns only when a His-tagged FNIII 7-10 was added to the medium. These results indicate that the present method is useful for studying the cellular behavior on the specific extracellular matrix protein in cell-culturing environments.

Dynamic culture substrate that captures a specific extracellular matrix protein in response to light

Energy Technology Data Exchange (ETDEWEB)

Nakanishi, Jun; Nakayama, Hidekazu; Horiike, Yasuhiro [World Premier International (WPI) Research Center Initiative, International Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science - NIMS (Japan); Yamaguchi, Kazuo [Department of Chemistry, Faculty of Science and Research Institute for Photofunctionalized Materials, Kanagawa University (Japan); Garcia, Andres J, E-mail: NAKANISHI.Jun@nims.go.jp [Institute for Bioengineering and Bioscience, Woodruff School of Mechanical Engineering, Georgia Institute of Technology (United States)

2011-08-15

The development of methods for the off-on switching of immobilization or presentation of cell-adhesive peptides and proteins during cell culture is important because such surfaces are useful for the analysis of the dynamic processes of cell adhesion and migration. This paper describes a chemically functionalized gold substrate that captures a genetically tagged extracellular matrix protein in response to light. The substrate was composed of mixed self-assembled monolayers (SAMs) of three disulfide compounds containing (i) a photocleavable poly(ethylene glycol) (PEG), (ii) nitrilotriacetic acid (NTA) and (iii) hepta(ethylene glycol) (EG{sub 7}). Although the NTA group has an intrinsic high affinity for oligohistidine tag (His-tag) sequences in its Ni{sup 2+}-ion complex, the interaction was suppressed by the steric hindrance of coexisting PEG on the substrate surface. Upon photoirradiation of the substrate to release the PEG chain from the surface, this interaction became possible and hence the protein was captured at the irradiated regions, while keeping the non-specific adsorption of non-His-tagged proteins blocked by the EG{sub 7} underbrush. In this way, we selectively immobilized a His-tagged fibronectin fragment (FNIII{sub 7-10}) to the irradiated regions. In contrast, when bovine serum albumin-a major serum protein-was added as a non-His-tagged protein, the surface did not permit its capture, with or without irradiation. In agreement with these results, cells were selectively attached to the irradiated patterns only when a His-tagged FNIII{sub 7-10} was added to the medium. These results indicate that the present method is useful for studying the cellular behavior on the specific extracellular matrix protein in cell-culturing environments.

Student perceptions of native and non-native speaker language instructors: A comparison of ESL and Spanish

Directory of Open Access Journals (Sweden)

Laura Callahan

2006-12-01

Full Text Available The question of the native vs. non-native speaker status of second and foreign language instructors has been investigated chiefly from the perspective of the teacher. Anecdotal evidence suggests that students have strong opinions on the relative qualities of instruction by native and non-native speakers. Most research focuses on students of English as a foreign or second language. This paper reports on data gathered through a questionnaire administered to 55 university students: 31 students of Spanish as FL and 24 students of English as SL. Qualitative results show what strengths students believe each type of instructor has, and quantitative results confirm that any gap students may perceive between the abilities of native and non-native instructors is not so wide as one might expect based on popular notions of the issue. ESL students showed a stronger preference for native-speaker instructors overall, and were at variance with the SFL students' ratings of native-speaker instructors' performance on a number of aspects. There was a significant correlation in both groups between having a family member who is a native speaker of the target language and student preference for and self-identification with a native speaker as instructor. (English text

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

Science.gov (United States)

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-...

Shortening a loop can increase protein native state entropy.

Science.gov (United States)

Gavrilov, Yulian; Dagan, Shlomi; Levy, Yaakov

2015-12-01

Protein loops are essential structural elements that influence not only function but also protein stability and folding rates. It was recently reported that shortening a loop in the AcP protein may increase its native state conformational entropy. This effect on the entropy of the folded state can be much larger than the lower entropic penalty of ordering a shorter loop upon folding, and can therefore result in a more pronounced stabilization than predicted by polymer model for loop closure entropy. In this study, which aims at generalizing the effect of loop length shortening on native state dynamics, we use all-atom molecular dynamics simulations to study how gradual shortening a very long or solvent-exposed loop region in four different proteins can affect their stability. For two proteins, AcP and Ubc7, we show an increase in native state entropy in addition to the known effect of the loop length on the unfolded state entropy. However, for two permutants of SH3 domain, shortening a loop results only with the expected change in the entropy of the unfolded state, which nicely reproduces the observed experimental stabilization. Here, we show that an increase in the native state entropy following loop shortening is not unique to the AcP protein, yet nor is it a general rule that applies to all proteins following the truncation of any loop. This modification of the loop length on the folded state and on the unfolded state may result with a greater effect on protein stability. © 2015 Wiley Periodicals, Inc.

Decoding speech perception by native and non-native speakers using single-trial electrophysiological data.

Directory of Open Access Journals (Sweden)

Alex Brandmeyer

Full Text Available Brain-computer interfaces (BCIs are systems that use real-time analysis of neuroimaging data to determine the mental state of their user for purposes such as providing neurofeedback. Here, we investigate the feasibility of a BCI based on speech perception. Multivariate pattern classification methods were applied to single-trial EEG data collected during speech perception by native and non-native speakers. Two principal questions were asked: 1 Can differences in the perceived categories of pairs of phonemes be decoded at the single-trial level? 2 Can these same categorical differences be decoded across participants, within or between native-language groups? Results indicated that classification performance progressively increased with respect to the categorical status (within, boundary or across of the stimulus contrast, and was also influenced by the native language of individual participants. Classifier performance showed strong relationships with traditional event-related potential measures and behavioral responses. The results of the cross-participant analysis indicated an overall increase in average classifier performance when trained on data from all participants (native and non-native. A second cross-participant classifier trained only on data from native speakers led to an overall improvement in performance for native speakers, but a reduction in performance for non-native speakers. We also found that the native language of a given participant could be decoded on the basis of EEG data with accuracy above 80%. These results indicate that electrophysiological responses underlying speech perception can be decoded at the single-trial level, and that decoding performance systematically reflects graded changes in the responses related to the phonological status of the stimuli. This approach could be used in extensions of the BCI paradigm to support perceptual learning during second language acquisition.

Differences in the Metacognitive Awareness of Reading Strategies among Native and Non-Native Readers.

Science.gov (United States)

Sheorey, R.; Mokhtari, K.

2001-01-01

Examines the differences in the reported use of reading strategies of native and non-native English speakers when reading academic materials. Participants were native English speaking and English-as-a-Second-Language college students who completed a survey of reading strategies aimed at discerning the strategies readers report using when coping…

Dynamic culture substrate that captures a specific extracellular matrix protein in response to light

Directory of Open Access Journals (Sweden)

Jun Nakanishi, Hidekazu Nakayama, Kazuo Yamaguchi, Andres J Garcia and Yasuhiro Horiike

2011-01-01

Full Text Available The development of methods for the off–on switching of immobilization or presentation of cell-adhesive peptides and proteins during cell culture is important because such surfaces are useful for the analysis of the dynamic processes of cell adhesion and migration. This paper describes a chemically functionalized gold substrate that captures a genetically tagged extracellular matrix protein in response to light. The substrate was composed of mixed self-assembled monolayers (SAMs of three disulfide compounds containing (i a photocleavable poly(ethylene glycol (PEG, (ii nitrilotriacetic acid (NTA and (iii hepta(ethylene glycol (EG7. Although the NTA group has an intrinsic high affinity for oligohistidine tag (His-tag sequences in its Ni2+-ion complex, the interaction was suppressed by the steric hindrance of coexisting PEG on the substrate surface. Upon photoirradiation of the substrate to release the PEG chain from the surface, this interaction became possible and hence the protein was captured at the irradiated regions, while keeping the non-specific adsorption of non-His-tagged proteins blocked by the EG7 underbrush. In this way, we selectively immobilized a His-tagged fibronectin fragment (FNIII7–10 to the irradiated regions. In contrast, when bovine serum albumin—a major serum protein—was added as a non-His-tagged protein, the surface did not permit its capture, with or without irradiation. In agreement with these results, cells were selectively attached to the irradiated patterns only when a His-tagged FNIII7-10 was added to the medium. These results indicate that the present method is useful for studying the cellular behavior on the specific extracellular matrix protein in cell-culturing environments.

Ectomycorrhizal fungal communities of native and non-native Pinus and Quercus species in a common garden of 35-year-old trees.

Science.gov (United States)

Trocha, Lidia K; Kałucka, Izabela; Stasińska, Małgorzata; Nowak, Witold; Dabert, Mirosława; Leski, Tomasz; Rudawska, Maria; Oleksyn, Jacek

2012-02-01

Non-native tree species have been widely planted or have become naturalized in most forested landscapes. It is not clear if native trees species collectively differ in ectomycorrhizal fungal (EMF) diversity and communities from that of non-native tree species. Alternatively, EMF species community similarity may be more determined by host plant phylogeny than by whether the plant is native or non-native. We examined these unknowns by comparing two genera, native and non-native Quercus robur and Quercus rubra and native and non-native Pinus sylvestris and Pinus nigra in a 35-year-old common garden in Poland. Using molecular and morphological approaches, we identified EMF species from ectomycorrhizal root tips and sporocarps collected in the monoculture tree plots. A total of 69 EMF species were found, with 38 species collected only as sporocarps, 18 only as ectomycorrhizas, and 13 both as ectomycorrhizas and sporocarps. The EMF species observed were all native and commonly associated with a Holarctic range in distribution. We found that native Q. robur had ca. 120% higher total EMF species richness than the non-native Q. rubra, while native P. sylvestris had ca. 25% lower total EMF species richness than non-native P. nigra. Thus, across genera, there was no evidence that native species have higher EMF species diversity than exotic species. In addition, we found a higher similarity in EMF communities between the two Pinus species than between the two Quercus species. These results support the naturalization of non-native trees by means of mutualistic associations with cosmopolitan and novel fungi.

Relation between native ensembles and experimental structures of proteins

DEFF Research Database (Denmark)

Best, R. B.; Lindorff-Larsen, Kresten; DePristo, M. A.

2006-01-01

Different experimental structures of the same protein or of proteins with high sequence similarity contain many small variations. Here we construct ensembles of "high-sequence similarity Protein Data Bank" (HSP) structures and consider the extent to which such ensembles represent the structural...... Data Bank ensembles; moreover, we show that the effects of uncertainties in structure determination are insufficient to explain the results. These results highlight the importance of accounting for native-state protein dynamics in making comparisons with ensemble-averaged experimental data and suggest...... heterogeneity of the native state in solution. We find that different NMR measurements probing structure and dynamics of given proteins in solution, including order parameters, scalar couplings, and residual dipolar couplings, are remarkably well reproduced by their respective high-sequence similarity Protein...

Intermediate conformation between native β-sheet and non-native α-helix is a precursor of trifluoroethanol-induced aggregation of Human Carbonic Anhydrase-II

International Nuclear Information System (INIS)

Gupta, Preeti; Deep, Shashank

2014-01-01

Highlights: • HCAII forms amyloid-like aggregates at moderate concentration of trifluoroethanol. • Protein adopts a state between β-sheet and α-helix at moderate % of TFE. • Hydrophobic surface(s) of partially structured conformation forms amyloid. • High % of TFE induces stable α-helical state preventing aggregation. - Abstract: In the present work, we examined the correlation between 2,2,2-trifluoroethanol (TFE)-induced conformational transitions of human carbonic anhydrase II (HCAII) and its aggregation propensity. Circular dichroism data indicates that protein undergoes a transition from β-sheet to α-helix on addition of TFE. The protein was found to aggregate maximally at moderate concentration of TFE at which it exists somewhere between β-sheet and α-helix, probably in extended non-native β-sheet conformation. Thioflavin-T (ThT) and Congo-Red (CR) assays along with fluorescence microscopy and transmission electron microscopy (TEM) data suggest that the protein aggregates induced by TFE possess amyloid-like features. Anilino-8-naphthalene sulfonate (ANS) binding studies reveal that the exposure of hydrophobic surface(s) was maximum in intermediate conformation. Our study suggests that the exposed hydrophobic surface and/or the disruption of the structural features protecting a β-sheet protein might be the major reason(s) for the high aggregation propensity of non-native intermediate conformation of HCAII

The biology of non-native proteins

NARCIS (Netherlands)

Herczenik, E.

2007-01-01

Protein misfolding diseases are linked by common principles of protein aggregation, plaque development and tissue damage. There is no adequate therapy for these highly debilitating diseases. This thesis aims to increase the understanding of protein misfolding diseases, which will hopefully lead to

Kalispel Non-Native Fish Suppression Project 2007 Annual Report.

Energy Technology Data Exchange (ETDEWEB)

Wingert, Michele; Andersen, Todd [Kalispel Natural Resource Department

2008-11-18

Non-native salmonids are impacting native salmonid populations throughout the Pend Oreille Subbasin. Competition, hybridization, and predation by non-native fish have been identified as primary factors in the decline of some native bull trout (Salvelinus confluentus) and westslope cutthroat trout (Oncorhynchus clarki lewisi) populations. In 2007, the Kalispel Natural Resource Department (KNRD) initiated the Kalispel Nonnative Fish Suppression Project. The goal of this project is to implement actions to suppress or eradicate non-native fish in areas where native populations are declining or have been extirpated. These projects have previously been identified as critical to recovering native bull trout and westslope cutthroat trout (WCT). Lower Graham Creek was invaded by non-native rainbow (Oncorhynchus mykiss) and brook trout (Salvelinus fontinalis) after a small dam failed in 1991. By 2003, no genetically pure WCT remained in the lower 700 m of Graham Creek. Further invasion upstream is currently precluded by a relatively short section of steep, cascade-pool stepped channel section that will likely be breached in the near future. In 2008, a fish management structure (barrier) was constructed at the mouth of Graham Creek to preclude further invasion of non-native fish into Graham Creek. The construction of the barrier was preceded by intensive electrofishing in the lower 700 m to remove and relocate all captured fish. Westslope cutthroat trout have recently been extirpated in Cee Cee Ah Creek due to displacement by brook trout. We propose treating Cee Cee Ah Creek with a piscicide to eradicate brook trout. Once eradication is complete, cutthroat trout will be translocated from nearby watersheds. In 2004, the Washington Department of Fish and Wildlife (WDFW) proposed an antimycin treatment within the subbasin; the project encountered significant public opposition and was eventually abandoned. However, over the course of planning this 2004 project, little public

Structural interface parameters are discriminatory in recognising near-native poses of protein-protein interactions.

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Sony Malhotra

Full Text Available Interactions at the molecular level in the cellular environment play a very crucial role in maintaining the physiological functioning of the cell. These molecular interactions exist at varied levels viz. protein-protein interactions, protein-nucleic acid interactions or protein-small molecules interactions. Presently in the field, these interactions and their mechanisms mark intensively studied areas. Molecular interactions can also be studied computationally using the approach named as Molecular Docking. Molecular docking employs search algorithms to predict the possible conformations for interacting partners and then calculates interaction energies. However, docking proposes number of solutions as different docked poses and hence offers a serious challenge to identify the native (or near native structures from the pool of these docked poses. Here, we propose a rigorous scoring scheme called DockScore which can be used to rank the docked poses and identify the best docked pose out of many as proposed by docking algorithm employed. The scoring identifies the optimal interactions between the two protein partners utilising various features of the putative interface like area, short contacts, conservation, spatial clustering and the presence of positively charged and hydrophobic residues. DockScore was first trained on a set of 30 protein-protein complexes to determine the weights for different parameters. Subsequently, we tested the scoring scheme on 30 different protein-protein complexes and native or near-native structure were assigned the top rank from a pool of docked poses in 26 of the tested cases. We tested the ability of DockScore to discriminate likely dimer interactions that differ substantially within a homologous family and also demonstrate that DOCKSCORE can distinguish correct pose for all 10 recent CAPRI targets.

Non-native Speech Learning in Older Adults.

Science.gov (United States)

Ingvalson, Erin M; Nowicki, Casandra; Zong, Audrey; Wong, Patrick C M

2017-01-01

Though there is an extensive literature investigating the ability of younger adults to learn non-native phonology, including investigations into individual differences in younger adults' lexical tone learning, very little is known about older adults' ability to learn non-native phonology, including lexical tone. There are several reasons to suspect that older adults would use different learning mechanisms when learning lexical tone than younger adults, including poorer perception of dynamic pitch, greater reliance on working memory capacity in second language learning, and poorer category learning in older adulthood. The present study examined the relationships among older adults' baseline sensitivity for pitch patterns, working memory capacity, and declarative memory capacity with their ability to learn to associate tone with lexical meaning. In older adults, baseline pitch pattern sensitivity was not associated with generalization performance. Rather, older adults' learning performance was best predicted by declarative memory capacity. These data suggest that training paradigms will need to be modified to optimize older adults' non-native speech sound learning success.

Ecological disequilibrium drives insect pest and pathogen accumulation in non-native trees.

Science.gov (United States)

Crous, Casparus J; Burgess, Treena I; Le Roux, Johannes J; Richardson, David M; Slippers, Bernard; Wingfield, Michael J

2016-12-23

Non-native trees have become dominant components of many landscapes, including urban ecosystems, commercial forestry plantations, fruit orchards, and as invasives in natural ecosystems. Often, these trees have been separated from their natural enemies (i.e. insects and pathogens) leading to ecological disequilibrium, that is, the immediate breakdown of historically co-evolved interactions once introduced into novel environments. Long-established, non-native tree plantations provide useful experiments to explore the dimensions of such ecological disequilibria. We quantify the status quo of non-native insect pests and pathogens catching up with their tree hosts (planted Acacia, Eucalyptus and Pinus species) in South Africa, and examine which native South African enemy species utilise these trees as hosts. Interestingly, pines, with no confamilial relatives in South Africa and the longest residence time (almost two centuries), have acquired only one highly polyphagous native pathogen. This is in contrast to acacias and eucalypts, both with many native and confamilial relatives in South Africa that have acquired more native pathogens. These patterns support the known role of phylogenetic relatedness of non-native and native floras in influencing the likelihood of pathogen shifts between them. This relationship, however, does not seem to hold for native insects. Native insects appear far more likely to expand their feeding habits onto non-native tree hosts than are native pathogens, although they are generally less damaging. The ecological disequilibrium conditions of non-native trees are deeply rooted in the eco-evolutionary experience of the host plant, co-evolved natural enemies, and native organisms from the introduced range. We should expect considerable spatial and temporal variation in ecological disequilibrium conditions among non-native taxa, which can be significantly influenced by biosecurity and management practices. Published by Oxford University Press on

Reliable protein folding on non-funneled energy landscapes: the free energy reaction path

OpenAIRE

Lois, Gregg; Blawzdziewicz, Jerzy; O'Hern, Corey S.

2008-01-01

A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical denaturant or pH, are adjusted to induce folding. A theory based on this insight predicts that (1) proteins with non-funneled energy landscapes can fold reliably to their native state, (2) reliable folding can occur as an equilibrium or out-of-equilibrium pro...

Non-native species impacts on pond occupancy by an anuran

Science.gov (United States)

Adams, Michael J.; Pearl, Christopher A.; Galvan, Stephanie; McCreary, Brome

2011-01-01

Non-native fish and bullfrogs (Lithobates catesbeianus; Rana catesbeiana) are frequently cited as factors contributing to the decline of ranid frogs in the western United States (Bradford 2005). This hypothesis is supported by studies showing competition with or predation by these introduced species (Kupferberg 1997, Kiesecker and Blaustein 1998, Lawler et al. 1999, Knapp et al. 2001) and studies suggesting a deficit of native frogs at sites occupied by bullfrogs or game fish (Hammerson 1982, Schwalbe and Rosen 1988, Fisher and Shaffer 1996, Adams 1999). Conversely, other studies failed to find a negative association between native ranids and bullfrogs and point out that presence of non-native species correlates with habitat alterations that could also contribute to declines of native species (Hayes and Jennings 1986; Adams 1999, 2000; Pearl et al. 2005). A criticism of these studies is that they may not detect an effect of non-native species if the process of displacement is at an early stage. We are not aware of any studies that have monitored a set of native frog populations to determine if non-native species predict population losses. Our objective was to study site occupancy trends in relation to non-native species for northern red-legged frogs (Rana aurora) on federal lands in the southern Willamette Valley, Oregon. We conducted a 5-yr monitoring study to answer the following questions about the status and trends of the northern red-legged frog: 1) What is the rate of local extinction (how often is a site that is occupied in year t unoccupied in year t+1) and what factors predict variation in local extinction? and 2) What is the rate of colonization (how often is a site that is unoccupied in year t occupied in year t+1) and what factors predict variation in colonization? The factors we hypothesized for local extinction were: 1) bullfrog presence, 2) bullfrogs mediated by wetland vegetation, 3) non-native fish (Centrarchidae), 4) non-native fish mediated by

Analysis of protein interactions at native chloroplast membranes by ellipsometry.

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Verena Kriechbaumer

Full Text Available Membrane bound receptors play vital roles in cell signaling, and are the target for many drugs, yet their interactions with ligands are difficult to study by conventional techniques due to the technical difficulty of monitoring these interactions in lipid environments. In particular, the ability to analyse the behaviour of membrane proteins in their native membrane environment is limited. Here, we have developed a quantitative approach to detect specific interactions between low-abundance chaperone receptors within native chloroplast membranes and their soluble chaperone partners. Langmuir-Schaefer film deposition was used to deposit native chloroplasts onto gold-coated glass slides, and interactions between the molecular chaperones Hsp70 and Hsp90 and their receptors in the chloroplast membranes were detected and quantified by total internal reflection ellipsometry (TIRE. We show that native chloroplast membranes deposited on gold-coated glass slides using Langmuir-Schaefer films retain functional receptors capable of binding chaperones with high specificity and affinity. Taking into account the low chaperone receptor abundance in native membranes, these binding properties are consistent with data generated using soluble forms of the chloroplast chaperone receptors, OEP61 and Toc64. Therefore, we conclude that chloroplasts have the capacity to selectively bind chaperones, consistent with the notion that chaperones play an important role in protein targeting to chloroplasts. Importantly, this method of monitoring by TIRE does not require any protein labelling. This novel combination of techniques should be applicable to a wide variety of membranes and membrane protein receptors, thus presenting the opportunity to quantify protein interactions involved in fundamental cellular processes, and to screen for drugs that target membrane proteins.

The effect of polylysine on casein-kinase-2 activity is influenced by both the structure of the protein/peptide substrates and the subunit composition of the enzyme

DEFF Research Database (Denmark)

Meggio, F; Boldyreff, B; Marin, O

1992-01-01

, moreover, is variably accounted for by changes in Vmax and/or Km, depending on the structure of the peptide substrate. Maximum stimulation with all protein/peptide substrates tested requires the presence of the beta subunit, since the recombinant alpha subunit is much less responsive than CK2 holoenzyme......The mechanism by which polybasic peptides stimulate the activity of casein kinase 2 (CK2) has been studied by comparing the effect of polylysine on the phosphorylation of a variety of protein and peptide substrates by the native CK2 holoenzyme and by its recombinant catalytic alpha subunit, either...

Short-Term Response of Native Flora to the Removal of Non-Native Shrubs in Mixed-Hardwood Forests of Indiana, USA

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Joshua M. Shields

2015-05-01

Full Text Available While negative impacts of invasive species on native communities are well documented, less is known about how these communities respond to the removal of established populations of invasive species. With regard to invasive shrubs, studies examining native community response to removal at scales greater than experimental plots are lacking. We examined short-term effects of removing Lonicera maackii (Amur honeysuckle and other non-native shrubs on native plant taxa in six mixed-hardwood forests. Each study site contained two 0.64 ha sample areas—an area where all non-native shrubs were removed and a reference area where no treatment was implemented. We sampled vegetation in the spring and summer before and after non-native shrubs were removed. Cover and diversity of native species, and densities of native woody seedlings, increased after shrub removal. However, we also observed significant increases in L. maackii seedling densities and Alliaria petiolata (garlic mustard cover in removal areas. Changes in reference areas were less pronounced and mostly non-significant. Our results suggest that removing non-native shrubs allows short-term recovery of native communities across a range of invasion intensities. However, successful restoration will likely depend on renewed competition with invasive species that re-colonize treatment areas, the influence of herbivores, and subsequent control efforts.

Non-natives: 141 scientists object

NARCIS (Netherlands)

Simberloff, D.; Van der Putten, W.H.

2011-01-01

Supplementary information to: Non-natives: 141 scientists object Full list of co-signatories to a Correspondence published in Nature 475, 36 (2011); doi: 10.1038/475036a. Daniel Simberloff University of Tennessee, Knoxville, Tennessee, USA. dsimberloff@utk.edu Jake Alexander Institute of Integrative

Non-native Species in Floodplain Secondary Forests in Peninsular Malaysia

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Nor Rasidah Hashim

2010-01-01

Full Text Available There is an increasing concern of alien species invading our tropical ecosystems because anthropogenic land use can create conditions in which non-native species thrive. This study is an assessment of bioinvasion using a quantitative survey of non-native plant species in floodplain secondary forests in Peninsular Malaysia. The study area is known to have a long cultivation and settlement history that provides ample time for non-native species introduction. The survey results showed that introduced species constituted 23% of all the identified species, with seven species unique to riparian forest strips and eleven species unique to abandoned paddy fields and the remaining five species being shared between the two secondary forest types. There existed some habitat preferences amongst the species implying both secondary forests were potentially susceptible to bioinvasion. Fourteen species are also invasive elsewhere (PIER invasives whereas fifteen species have acquired local uses such for traditional medicine and food products. The presence of these non-native species could alter native plant succession trajectory, and eventually leads to native species impoverishment if the exotics managed to outcompete the native species. As such, the findings of this study have a far-reaching application for the national biodiversity conservation efforts because it provides the required information on bioinvasion.

Non-native fishes in Florida freshwaters: a literature review and synthesis

Science.gov (United States)

Schofield, Pamela J.; Loftus, William F.

2015-01-01

Non-native fishes have been known from freshwater ecosystems of Florida since the 1950s, and dozens of species have established self-sustaining populations. Nonetheless, no synthesis of data collected on those species in Florida has been published until now. We searched the literature for peer-reviewed publications reporting original data for 42 species of non-native fishes in Florida that are currently established, were established in the past, or are sustained by human intervention. Since the 1950s, the number of non-native fish species increased steadily at a rate of roughly six new species per decade. Studies documented (in decreasing abundance): geographic location/range expansion, life- and natural-history characteristics (e.g., diet, habitat use), ecophysiology, community composition, population structure, behaviour, aquatic-plant management, and fisheries/aquaculture. Although there is a great deal of taxonomic uncertainty and confusion associated with many taxa, very few studies focused on clarifying taxonomic ambiguities of non-native fishes in the State. Most studies were descriptive; only 15 % were manipulative. Risk assessments, population-control studies and evaluations of effects of non-native fishes were rare topics for research, although they are highly valued by natural-resource managers. Though some authors equated lack of data with lack of effects, research is needed to confirm or deny conclusions. Much more is known regarding the effects of lionfish (Pterois spp.) on native fauna, despite its much shorter establishment time. Natural-resource managers need biological and ecological information to make policy decisions regarding non-native fishes. Given the near-absence of empirical data on effects of Florida non-native fishes, and the lengthy time-frames usually needed to collect such information, we provide suggestions for data collection in a manner that may be useful in the evaluation and prediction of non-native fish effects.

Probabilistic Determination of Native State Ensembles of Proteins

DEFF Research Database (Denmark)

Olsson, Simon; Vögeli, Beat Rolf; Cavalli, Andrea

2014-01-01

ensembles of proteins by the combination of physical force fields and experimental data through modern statistical methodology. As an example, we use NMR residual dipolar couplings to determine a native state ensemble of the extensively studied third immunoglobulin binding domain of protein G (GB3...

Prediction of membrane transport proteins and their substrate specificities using primary sequence information.

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Nitish K Mishra

Full Text Available Membrane transport proteins (transporters move hydrophilic substrates across hydrophobic membranes and play vital roles in most cellular functions. Transporters represent a diverse group of proteins that differ in topology, energy coupling mechanism, and substrate specificity as well as sequence similarity. Among the functional annotations of transporters, information about their transporting substrates is especially important. The experimental identification and characterization of transporters is currently costly and time-consuming. The development of robust bioinformatics-based methods for the prediction of membrane transport proteins and their substrate specificities is therefore an important and urgent task.Support vector machine (SVM-based computational models, which comprehensively utilize integrative protein sequence features such as amino acid composition, dipeptide composition, physico-chemical composition, biochemical composition, and position-specific scoring matrices (PSSM, were developed to predict the substrate specificity of seven transporter classes: amino acid, anion, cation, electron, protein/mRNA, sugar, and other transporters. An additional model to differentiate transporters from non-transporters was also developed. Among the developed models, the biochemical composition and PSSM hybrid model outperformed other models and achieved an overall average prediction accuracy of 76.69% with a Mathews correlation coefficient (MCC of 0.49 and a receiver operating characteristic area under the curve (AUC of 0.833 on our main dataset. This model also achieved an overall average prediction accuracy of 78.88% and MCC of 0.41 on an independent dataset.Our analyses suggest that evolutionary information (i.e., the PSSM and the AAIndex are key features for the substrate specificity prediction of transport proteins. In comparison, similarity-based methods such as BLAST, PSI-BLAST, and hidden Markov models do not provide accurate predictions

Non-native Chinese Foreign Language (CFL) Teachers: Identity and Discourse

DEFF Research Database (Denmark)

Zhang, Chun

2014-01-01

Abstract Native Chinese foreign language (CFL) teacher identity is an emerging subject of research interest in the teacher education. Yet, limited study has been done on the construction of Non-native CFL teachers in their home culture. Guided by a concept of teacher identity-in-discourse, the pa......Abstract Native Chinese foreign language (CFL) teacher identity is an emerging subject of research interest in the teacher education. Yet, limited study has been done on the construction of Non-native CFL teachers in their home culture. Guided by a concept of teacher identity...... teachers face tensions and challenges in constructing their identities as CFL teachers, and the tensions and challenges that arose from Danish teaching culture could influence the Non-native CFL teachers' contributions to CFL teaching in their home cultures. The findings further show that in order to cope...

Positive and Negative Impacts of Non-Native Bee Species around the World.

Science.gov (United States)

Russo, Laura

2016-11-28

Though they are relatively understudied, non-native bees are ubiquitous and have enormous potential economic and environmental impacts. These impacts may be positive or negative, and are often unquantified. In this manuscript, I review literature on the known distribution and environmental and economic impacts of 80 species of introduced bees. The potential negative impacts of non-native bees include competition with native bees for nesting sites or floral resources, pollination of invasive weeds, co-invasion with pathogens and parasites, genetic introgression, damage to buildings, affecting the pollination of native plant species, and changing the structure of native pollination networks. The potential positive impacts of non-native bees include agricultural pollination, availability for scientific research, rescue of native species, and resilience to human-mediated disturbance and climate change. Most non-native bee species are accidentally introduced and nest in stems, twigs, and cavities in wood. In terms of number of species, the best represented families are Megachilidae and Apidae, and the best represented genus is Megachile . The best studied genera are Apis and Bombus , and most of the species in these genera were deliberately introduced for agricultural pollination. Thus, we know little about the majority of non-native bees, accidentally introduced or spreading beyond their native ranges.

Positive and Negative Impacts of Non-Native Bee Species around the World

Directory of Open Access Journals (Sweden)

Laura Russo

2016-11-01

Full Text Available Though they are relatively understudied, non-native bees are ubiquitous and have enormous potential economic and environmental impacts. These impacts may be positive or negative, and are often unquantified. In this manuscript, I review literature on the known distribution and environmental and economic impacts of 80 species of introduced bees. The potential negative impacts of non-native bees include competition with native bees for nesting sites or floral resources, pollination of invasive weeds, co-invasion with pathogens and parasites, genetic introgression, damage to buildings, affecting the pollination of native plant species, and changing the structure of native pollination networks. The potential positive impacts of non-native bees include agricultural pollination, availability for scientific research, rescue of native species, and resilience to human-mediated disturbance and climate change. Most non-native bee species are accidentally introduced and nest in stems, twigs, and cavities in wood. In terms of number of species, the best represented families are Megachilidae and Apidae, and the best represented genus is Megachile. The best studied genera are Apis and Bombus, and most of the species in these genera were deliberately introduced for agricultural pollination. Thus, we know little about the majority of non-native bees, accidentally introduced or spreading beyond their native ranges.

Application of native signal sequences for recombinant proteins secretion in Pichia pastoris

DEFF Research Database (Denmark)

Borodina, Irina; Do, Duy Duc; Eriksen, Jens C.

Background Methylotrophic yeast Pichia pastoris is widely used for recombinant protein production, largely due to its ability to secrete correctly folded heterologous proteins to the fermentation medium. Secretion is usually achieved by cloning the recombinant gene after a leader sequence, where...... alpha‐mating factor (MF) prepropeptide from Saccharomyces cerevisiae is most commonly used. Our aim was to test whether signal peptides from P. pastoris native secreted proteins could be used to direct secretion of recombinant proteins. Results Eleven native signal peptides from P. pastoris were tested...... by optimization of expression of three different proteins in P. pastoris. Conclusions Native signal peptides from P. pastoris can be used to direct secretion of recombinant proteins. A novel USER‐based P. pastoris system allows easy cloning of protein‐coding gene with the promoter and leader sequence of choice....

The Non-Native English Speaker Teachers in TESOL Movement

Science.gov (United States)

Kamhi-Stein, Lía D.

2016-01-01

It has been almost 20 years since what is known as the non-native English-speaking (NNES) professionals' movement--designed to increase the status of NNES professionals--started within the US-based TESOL International Association. However, still missing from the literature is an understanding of what a movement is, and why non-native English…

STUDENTS WRITING EMAILS TO FACULTY: AN EXAMINATION OF E-POLITENESS AMONG NATIVE AND NON-NATIVE SPEAKERS OF ENGLISH

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Sigrun Biesenbach-Lucas

2007-02-01

Full Text Available This study combines interlanguage pragmatics and speech act research with computer-mediated communication and examines how native and non-native speakers of English formulate low- and high-imposition requests to faculty. While some research claims that email, due to absence of non-verbal cues, encourages informal language, other research has claimed the opposite. However, email technology also allows writers to plan and revise messages before sending them, thus affording the opportunity to edit not only for grammar and mechanics, but also for pragmatic clarity and politeness.The study examines email requests sent by native and non-native English speaking graduate students to faculty at a major American university over a period of several semesters and applies Blum-Kulka, House, and Kasper’s (1989 speech act analysis framework – quantitatively to distinguish levels of directness, i.e. pragmatic clarity; and qualitatively to compare syntactic and lexical politeness devices, the request perspectives, and the specific linguistic request realization patterns preferred by native and non-native speakers. Results show that far more requests are realized through direct strategies as well as hints than conventionally indirect strategies typically found in comparative speech act studies. Politeness conventions in email, a text-only medium with little guidance in the academic institutional hierarchy, appear to be a work in progress, and native speakers demonstrate greater resources in creating e-polite messages to their professors than non-native speakers. A possible avenue for pedagogical intervention with regard to instruction in and acquisition of politeness routines in hierarchically upward email communication is presented.

Emotional communication in medical consultations with native and non-native patients applying two different methodological approaches.

Science.gov (United States)

Kale, Emine; Skjeldestad, Kristin; Finset, Arnstein

2013-09-01

To explore the potential agreement between two different methods to investigate emotional communication of native and non-native patients in medical consultations. The data consisted of 12 videotaped hospital consultations with six native and six non-native patients. The consultations were coded according to coding rules of the Verona Coding definitions of Emotional Sequences (VR-CoDES) and afterwards analyzed by discourse analysis (DA) by two co-workers who were blind to the results from VR-CoDES. The agreement between VR-CoDES and DA was high in consultations with many cues and concerns, both with native and non-native patients. In consultations with no (or one cue) according to VR-CoDES criteria the DA still indicated the presence of emotionally salient expressions and themes. In some consultations cues to underlying emotions are communicated so vaguely or veiled by language barriers that standard VR-CoDES coding may miss subtle cues. Many of these sub-threshold cues could potentially be coded as cues according to VR-CoDES main coding categories, if criteria for coding vague or ambiguous cues had been better specified. Combining different analytical frameworks on the same dataset provide us new insights on emotional communication. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Comprehending non-native speakers: theory and evidence for adjustment in manner of processing.

Science.gov (United States)

Lev-Ari, Shiri

2014-01-01

Non-native speakers have lower linguistic competence than native speakers, which renders their language less reliable in conveying their intentions. We suggest that expectations of lower competence lead listeners to adapt their manner of processing when they listen to non-native speakers. We propose that listeners use cognitive resources to adjust by increasing their reliance on top-down processes and extracting less information from the language of the non-native speaker. An eye-tracking study supports our proposal by showing that when following instructions by a non-native speaker, listeners make more contextually-induced interpretations. Those with relatively high working memory also increase their reliance on context to anticipate the speaker's upcoming reference, and are less likely to notice lexical errors in the non-native speech, indicating that they take less information from the speaker's language. These results contribute to our understanding of the flexibility in language processing and have implications for interactions between native and non-native speakers.

Feedback in online course for non-native English-speaking students

CERN Document Server

Olesova, Larisa

2013-01-01

Feedback in Online Course for Non-Native English-Speaking Students is an investigation of the effectiveness of audio and text feedback provided in English in an online course for non-native English-speaking students. The study presents results showing how audio and text feedback can impact on non-native English-speaking students' higher-order learning as they participate in an asynchronous online course. It also discusses the results of how students perceive both types of the feedback provided. In addition, the study examines how the impact and perceptions differ when the instructor giving the

Modulation of legume defense signaling pathways by native and non-native pea aphid clones

Directory of Open Access Journals (Sweden)

Carlos Sanchez-Arcos

2016-12-01

Full Text Available The pea aphid (Acyrthosiphon pisum is a complex of at least 15 genetically different host races that are native to specific legume plants, but can all develop on the universal host plant Vicia faba. Despite much research it is still unclear why pea aphid host races (biotypes are able to colonize their native hosts while other host races are not. All aphids penetrate the plant and salivate into plant cells when they test plant suitability. Thus plants might react differently to the various pea aphid host races. To find out whether legume species vary in their defense responses to different pea aphid host races, we measured the amounts of salicylic acid (SA, the jasmonic acid-isoleucine conjugate (JA-Ile, other jasmonate precursors and derivatives, and abscisic acid (ABA in four different species (Medicago sativa, Trifolium pratense, Pisum sativum, V. faba after infestation by native and non-native pea aphid clones of various host races. Additionally, we assessed the performance of the clones on the four plant species. On M. sativa and T. pratense, non-native clones that were barely able to survive or reproduce, triggered a strong SA and JA-Ile response, whereas infestation with native clones led to lower levels of both phytohormones. On P. sativum, non-native clones, which survived or reproduced to a certain extent, induced fluctuating SA and JA-Ile levels, whereas the native clone triggered only a weak SA and JA-Ile response. On the universal host V. faba all aphid clones triggered only low SA levels initially, but induced clone-specific patterns of SA and JA-Ile later on. The levels of the active JA-Ile conjugate and of the other JA-pathway metabolites measured showed in many cases similar patterns, suggesting that the reduction in JA signaling was due to an effect upstream of OPDA. ABA levels were downregulated in all aphid clone-plant combinations and were therefore probably not decisive factors for aphid-plant compatibility. Our results

Reflecting on the dichotomy native-non native speakers in an EFL context

OpenAIRE

Mariño, Claudia

2011-01-01

This article provides a discussion based on constructs about the dichotomy betweennative and non-native speakers. Several models and examples are displayed about thespreading of the English language with the intention of understanding its developmentin the whole world and in Colombia, specifically. Then, some possible definitions aregiven to the term “native speaker” and its conceptualization is described as both realityand myth. One of the main reasons for writing this article is grounded on...

Impact of Non-Native Birds on Native Ecosystems: A Global Analysis.

Science.gov (United States)

Martin-Albarracin, Valeria L; Amico, Guillermo C; Simberloff, Daniel; Nuñez, Martin A

2015-01-01

Introduction and naturalization of non-native species is one of the most important threats to global biodiversity. Birds have been widely introduced worldwide, but their impacts on populations, communities, and ecosystems have not received as much attention as those of other groups. This work is a global synthesis of the impact of nonnative birds on native ecosystems to determine (1) what groups, impacts, and locations have been best studied; (2) which taxonomic groups and which impacts have greatest effects on ecosystems, (3) how important are bird impacts at the community and ecosystem levels, and (4) what are the known benefits of nonnative birds to natural ecosystems. We conducted an extensive literature search that yielded 148 articles covering 39 species belonging to 18 families -18% of all known naturalized species. Studies were classified according to where they were conducted: Africa, Asia, Australasia, Europe, North America, South America, Islands of the Indian, of the Pacific, and of the Atlantic Ocean. Seven types of impact on native ecosystems were evaluated: competition, disease transmission, chemical, physical, or structural impact on ecosystem, grazing/ herbivory/ browsing, hybridization, predation, and interaction with other non-native species. Hybridization and disease transmission were the most important impacts, affecting the population and community levels. Ecosystem-level impacts, such as structural and chemical impacts were detected. Seven species were found to have positive impacts aside from negative ones. We provide suggestions for future studies focused on mechanisms of impact, regions, and understudied taxonomic groups.

Vulnerability of freshwater native biodiversity to non-native species invasions across the continental United States

Science.gov (United States)

Background/Question/Methods Non-native species pose one of the greatest threats to native biodiversity. The literature provides plentiful empirical and anecdotal evidence of this phenomenon; however, such evidence is limited to local or regional scales. Employing geospatial analy...

Relative Weighting of Semantic and Syntactic Cues in Native and Non-Native Listeners' Recognition of English Sentences.

Science.gov (United States)

Shi, Lu-Feng; Koenig, Laura L

2016-01-01

Non-native listeners do not recognize English sentences as effectively as native listeners, especially in noise. It is not entirely clear to what extent such group differences arise from differences in relative weight of semantic versus syntactic cues. This study quantified the use and weighting of these contextual cues via Boothroyd and Nittrouer's j and k factors. The j represents the probability of recognizing sentences with or without context, whereas the k represents the degree to which context improves recognition performance. Four groups of 13 normal-hearing young adult listeners participated. One group consisted of native English monolingual (EMN) listeners, whereas the other three consisted of non-native listeners contrasting in their language dominance and first language: English-dominant Russian-English, Russian-dominant Russian-English, and Spanish-dominant Spanish-English bilinguals. All listeners were presented three sets of four-word sentences: high-predictability sentences included both semantic and syntactic cues, low-predictability sentences included syntactic cues only, and zero-predictability sentences included neither semantic nor syntactic cues. Sentences were presented at 65 dB SPL binaurally in the presence of speech-spectrum noise at +3 dB SNR. Listeners orally repeated each sentence and recognition was calculated for individual words as well as the sentence as a whole. Comparable j values across groups for high-predictability, low-predictability, and zero-predictability sentences suggested that all listeners, native and non-native, utilized contextual cues to recognize English sentences. Analysis of the k factor indicated that non-native listeners took advantage of syntax as effectively as EMN listeners. However, only English-dominant bilinguals utilized semantics to the same extent as EMN listeners; semantics did not provide a significant benefit for the two non-English-dominant groups. When combined, semantics and syntax benefitted EMN

Immobilised native plant cysteine proteases: packed-bed reactor for white wine protein stabilisation.

Science.gov (United States)

Benucci, Ilaria; Lombardelli, Claudio; Liburdi, Katia; Acciaro, Giuseppe; Zappino, Matteo; Esti, Marco

2016-02-01

This research presents a feasibility study of using a continuous packed-bed reactor (PBR), containing immobilised native plant cysteine proteases, as a specific and mild alternative technique relative to the usual bentonite fining for white wine protein stabilisation. The operational parameters for a PBR containing immobilised bromelain (PBR-br) or immobilised papain (PBR-pa) were optimised using model wine fortified with synthetic substrate (Bz-Phe-Val-Arg-pNA). The effectiveness of PBR-br, both in terms of hazing potential and total protein decrease, was significantly higher than PBR-pa, in all the seven unfined, white wines used. Among the wines tested, Sauvignon Blanc, given its total protein content as well as its very high intrinsic instability, was selected as a control wine to evaluate the effect of the treatment on wine as to its soluble protein profile, phenolic composition, mineral component, and sensory properties. The treatment in a PBR containing immobilised bromelain appeared effective in decreasing both wine hazing potential and total protein amount, while it did not significantly affect the phenol compounds, the mineral component nor the sensory quality of wine. The enzymatic treatment in PBR was shown to be a specific and mild technique for use as an alternative to bentonite fining for white wine protein stabilisation.

Non-native earthworms promote plant invasion by ingesting seeds and modifying soil properties

Science.gov (United States)

Clause, Julia; Forey, Estelle; Lortie, Christopher J.; Lambert, Adam M.; Barot, Sébastien

2015-04-01

Earthworms can have strong direct effects on plant communities through consumption and digestion of seeds, however it is unclear how earthworms may influence the relative abundance and composition of plant communities invaded by non-native species. In this study, earthworms, seed banks, and the standing vegetation were sampled in a grassland of central California. Our objectives were i) to examine whether the abundances of non-native, invasive earthworm species and non-native grassland plant species are correlated, and ii) to test whether seed ingestion by these worms alters the soil seed bank by evaluating the composition of seeds in casts relative to uningested soil. Sampling locations were selected based on historical land-use practices, including presence or absence of tilling, and revegetation by seed using Phalaris aquatica. Only non-native earthworm species were found, dominated by the invasive European species Aporrectodea trapezoides. Earthworm abundance was significantly higher in the grassland blocks dominated by non-native plant species, and these sites had higher carbon and moisture contents. Earthworm abundance was also positively related to increased emergence of non-native seedlings, but had no effect on that of native seedlings. Plant species richness and total seedling emergence were higher in casts than in uningested soils. This study suggests that there is a potential effect of non-native earthworms in promoting non-native and likely invasive plant species within grasslands, due to seed-plant-earthworm interactions via soil modification or to seed ingestion by earthworms and subsequent cast effects on grassland dynamics. This study supports a growing body of literature for earthworms as ecosystem engineers but highlights the relative importance of considering non-native-native interactions with the associated plant community.

Desalting Protein Ions in Native Mass Spectrometry Using Supercharging Reagents

Science.gov (United States)

Cassou, Catherine A.; Williams, Evan R.

2014-01-01

Effects of the supercharging reagents m-NBA and sulfolane on sodium ion adduction to protein ions formed using native mass spectrometry were investigated. There is extensive sodium adduction on protein ions formed by electrospray ionization from aqueous solutions containing millimolar concentrations of NaCl, which can lower sensitivity by distributing the signal of a given charge state over multiple adducted ions and can reduce mass measuring accuracy for large proteins and non-covalent complexes for which individual adducts cannot be resolved. The average number of sodium ions adducted to the most abundant ion formed from ten small (8.6–29 kDa) proteins for which adducts can be resolved is reduced by 58% or 80% on average, respectively, when 1.5% m-NBA or 2.5% sulfolane are added to aqueous solutions containing sodium compared to without the supercharging reagent. Sulfolane is more effective than m-NBA at reducing sodium ion adduction and at preserving non-covalent protein-ligand and protein-protein interactions. Desalting with 2.5% sulfolane enables detection of several glycosylated forms of 79.7 kDa holo-transferrin and NADH bound to the 146 kDa homotetramer LDH, which are otherwise unresolved due to peak broadening from extensive sodium adduction. Although sulfolane is more effective than m-NBA at protein ion desalting, m-NBA reduces salt clusters at high m/z and can increase the signal-to-noise ratios of protein ions by reducing chemical noise. Desalting is likely a result of these supercharging reagents binding sodium ions in solution, thereby reducing the sodium available to adduct to protein ions. PMID:25133273

Long-term trends of native and non-native fish faunas in the American Southwest

Directory of Open Access Journals (Sweden)

Olden, J. D.

2005-06-01

Full Text Available Environmental degradation and the proliferation of non-native fish species threaten the endemic, and highly unique fish faunas of the American Southwest. The present study examines long-term trends (> 160 years of fish species distributions in the Lower Colorado River Basin and identifies those native species (n = 28 exhibiting the greatest rates of decline and those non-native species (n = 48 exhibiting the highest rates of spread. Among the fastest expanding invaders in the basin are red shiner (Cyprinella lutrensis, fathead minnow (Pimephales promelas, green sunfish (Lepomis cyanellus, largemouth bass (Micropterus salmoides, western mosquitofish (Gambussia affinis and channel catfish (Ictalurus punctatus; species considered to be the most invasive in terms of their negative impacts on native fish communities. Interestingly, non-native species that have been recently introduced (1950+ have generally spread at substantially lower rates as compared to species introduced prior to this time (especially from 1920 to 1950, likely reflecting reductions in human-aided spread of species. We found general agreement between patterns of species decline and extant distribution sizes and official listing status under the U.S. Endangered Species Act. ‘Endangered’ species have generally experienced greater declines and have smaller present-day distributions compared to ‘threatened’ species, which in turn have shown greater declines and smaller distributions than those species not currently listed. A number of notable exceptions did exist, however, and these may provide critical information to help guide the future listing of species (i.e., identification of candidates and the upgrading or downgrading of current listed species that are endemic to the Lower Colorado River Basin. The strong correlation between probability estimates of local extirpation and patterns of native species decline and present-day distributions suggest a possible proactive

Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints.

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Nobuyuki Uchikoga

Full Text Available Interaction profile method is a useful method for processing rigid-body docking. After the docking process, the resulting set of docking poses could be classified by calculating similarities among them using these interaction profiles to search for near-native poses. However, there are some cases where the near-native poses are not included in this set of docking poses even when the bound-state structures are used. Therefore, we have developed a method for generating near-native docking poses by introducing a re-docking process. We devised a method for calculating the profile of interaction fingerprints by assembling protein complexes after determining certain core-protein complexes. For our analysis, we used 44 bound-state protein complexes selected from the ZDOCK benchmark dataset ver. 2.0, including some protein pairs none of which generated near-native poses in the docking process. Consequently, after the re-docking process we obtained profiles of interaction fingerprints, some of which yielded near-native poses. The re-docking process involved searching for possible docking poses in a restricted area using the profile of interaction fingerprints. If the profile includes interactions identical to those in the native complex, we obtained near-native docking poses. Accordingly, near-native poses were obtained for all bound-state protein complexes examined here. Application of interaction fingerprints to the re-docking process yielded structures with more native interactions, even when a docking pose, obtained following the initial docking process, contained only a small number of native amino acid interactions. Thus, utilization of the profile of interaction fingerprints in the re-docking process yielded more near-native poses.

Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints.

Science.gov (United States)

Uchikoga, Nobuyuki; Matsuzaki, Yuri; Ohue, Masahito; Hirokawa, Takatsugu; Akiyama, Yutaka

2013-01-01

Interaction profile method is a useful method for processing rigid-body docking. After the docking process, the resulting set of docking poses could be classified by calculating similarities among them using these interaction profiles to search for near-native poses. However, there are some cases where the near-native poses are not included in this set of docking poses even when the bound-state structures are used. Therefore, we have developed a method for generating near-native docking poses by introducing a re-docking process. We devised a method for calculating the profile of interaction fingerprints by assembling protein complexes after determining certain core-protein complexes. For our analysis, we used 44 bound-state protein complexes selected from the ZDOCK benchmark dataset ver. 2.0, including some protein pairs none of which generated near-native poses in the docking process. Consequently, after the re-docking process we obtained profiles of interaction fingerprints, some of which yielded near-native poses. The re-docking process involved searching for possible docking poses in a restricted area using the profile of interaction fingerprints. If the profile includes interactions identical to those in the native complex, we obtained near-native docking poses. Accordingly, near-native poses were obtained for all bound-state protein complexes examined here. Application of interaction fingerprints to the re-docking process yielded structures with more native interactions, even when a docking pose, obtained following the initial docking process, contained only a small number of native amino acid interactions. Thus, utilization of the profile of interaction fingerprints in the re-docking process yielded more near-native poses.

Protein degradation: recognition of ubiquitinylated substrates

DEFF Research Database (Denmark)

Hartmann-Petersen, Rasmus; Gordon, Colin

2004-01-01

A cell-free system has been developed in budding yeast that provides direct evidence that the Dsk2/Dph1, Rad23/Rhp23 and Rpn10/Pus1 multi-ubiquitin-binding proteins, long implicated in substrate recognition and presentation to the 26S proteasome, actually fulfil such a role.......A cell-free system has been developed in budding yeast that provides direct evidence that the Dsk2/Dph1, Rad23/Rhp23 and Rpn10/Pus1 multi-ubiquitin-binding proteins, long implicated in substrate recognition and presentation to the 26S proteasome, actually fulfil such a role....

Are native songbird populations affected by non-native plant invasion?

Science.gov (United States)

Amanda M. Conover; Christopher K. Williams; Vincent. D' Amico

2011-01-01

Development into forested areas is occurring rapidly across the United States, and many of the remnant forests within suburban landscapes are being fragmented into smaller patches, impacting the quality of this habitat for avian species. An ecological effect linked to forest fragmentation is the invasion of non-native plants into the ecosystem.

An Ecosystem-Service Approach to Evaluate the Role of Non-Native Species in Urbanized Wetlands

Directory of Open Access Journals (Sweden)

Rita S. W. Yam

2015-04-01

Full Text Available Natural wetlands have been increasingly transformed into urbanized ecosystems commonly colonized by stress-tolerant non-native species. Although non-native species present numerous threats to natural ecosystems, some could provide important benefits to urbanized ecosystems. This study investigated the extent of colonization by non-native fish and bird species of three urbanized wetlands in subtropical Taiwan. Using literature data the role of each non-native species in the urbanized wetland was evaluated by their effect (benefits/damages on ecosystem services (ES based on their ecological traits. Our sites were seriously colonized by non-native fishes (39%–100%, but <3% by non-native birds. Although most non-native species could damage ES regulation (disease control and wastewater purification, some could be beneficial to the urbanized wetland ES. Our results indicated the importance of non-native fishes in supporting ES by serving as food source to fish-eating waterbirds (native, and migratory species due to their high abundance, particularly for Oreochromis spp. However, all non-native birds are regarded as “harmful” species causing important ecosystem disservices, and thus eradication of these bird-invaders from urban wetlands would be needed. This simple framework for role evaluation of non-native species represents a holistic and transferable approach to facilitate decision making on management priority of non-native species in urbanized wetlands.

Mechanism of Electrochemical Delamination of Two-Dimensional Materials from Their Native Substrates by Bubbling.

Science.gov (United States)

Sun, Jie; Fan, Xing; Guo, Weiling; Liu, Lihui; Liu, Xin; Deng, Jun; Xu, Chen

2015-12-16

A capacitor-based circuit model is proposed to explain the electrochemical delamination of two-dimensional materials from their native substrates where produced gas bubbles squeeze into the interface. The delamination is actually the electric breakdown of the capacitor formed between the solution and substrate. To facilitate the procedure, the backside of the ubstrate has to be shielded so that the capacitor breakdown voltage can be reached. The screening effect can be induced either by nonreactive ions around the electrode or, more effectively, by an undetachable insulator. This mechanism serves as a guideline for the surface science and applications involving the bubbling delamination.

Native protein excited by low doses of γ-radiation serves as a source of secondary biogenic radiation

International Nuclear Information System (INIS)

Kuzin, A.M.; Surkenova, G.N.; Revin, A.F.

1996-01-01

In is demonstrated that native protein of egg-white after being γ-irradiated with law doses is able to stimulate transition of cells of remote biological detector from non-cycling state to proliferation even if irradiated protein is separated from detector by quartz-glass. Animal tissues which have a high protein content (freshly cut hair, insect bodies) reveal the same ability. The role of natural background radiation in the maintenance excitation, state of living tissue proteins is discussed. 13 refs.; 1 figs.; 4 tabs

Kinase Substrate Sensor (KISS), a mammalian in situ protein interaction sensor.

Science.gov (United States)

Lievens, Sam; Gerlo, Sarah; Lemmens, Irma; De Clercq, Dries J H; Risseeuw, Martijn D P; Vanderroost, Nele; De Smet, Anne-Sophie; Ruyssinck, Elien; Chevet, Eric; Van Calenbergh, Serge; Tavernier, Jan

2014-12-01

Probably every cellular process is governed by protein-protein interaction (PPIs), which are often highly dynamic in nature being modulated by in- or external stimuli. Here we present KISS, for KInase Substrate Sensor, a mammalian two-hybrid approach designed to map intracellular PPIs and some of the dynamic features they exhibit. Benchmarking experiments indicate that in terms of sensitivity and specificity KISS is on par with other binary protein interaction technologies while being complementary with regard to the subset of PPIs it is able to detect. We used KISS to evaluate interactions between different types of proteins, including transmembrane proteins, expressed at their native subcellular location. In situ analysis of endoplasmic reticulum stress-induced clustering of the endoplasmic reticulum stress sensor ERN1 and ligand-dependent β-arrestin recruitment to GPCRs illustrated the method's potential to study functional PPI modulation in complex cellular processes. Exploring its use as a tool for in cell evaluation of pharmacological interference with PPIs, we showed that reported effects of known GPCR antagonists and PPI inhibitors are properly recapitulated. In a three-hybrid setup, KISS was able to map interactions between small molecules and proteins. Taken together, we established KISS as a sensitive approach for in situ analysis of protein interactions and their modulation in a changing cellular context or in response to pharmacological challenges. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

NIS occurrence - Non-native species impacts on threatened and endangered salmonids

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The objectives of this project: a) Identify the distribution of non-natives in the Columbia River Basin b) Highlight the impacts of non-natives on salmonids c)...

Substrate type as a selective tool against colonization by non-native sessile invertebrates

Directory of Open Access Journals (Sweden)

Leonardo C Cangussu

2010-09-01

Full Text Available Different substrates of varying composition, color, texture and orientation may selectively influence recruitment of sessile invertebrates and thereby influence the resultant community. Thus substrates may act as a barrier to the establishment of non-indigenous species (NIS. In southern Brazil, granite is the main rock forming natural rocky walls that are available for encrusting organisms. In this study we tested whether granite selectively influences recruitment and impedes colonization by introduced and cryptogenic species that are already established on artificial substrates within the region. Plates of rough cut granite and of polyethylene were made available each month under a pier at a yacht club in Paranaguá Bay. A community is already established on concrete columns and fiber glass floats on the piers. After one, two and twelve months, the faunal composition of the plates was compared between the two treatments and other artificial substrates. Granite was recruited by all the seven introduced species found in the Bay and by 18 of 26 cryptogenic species and therefore is ineffective as a barrier to NIS colonization.Substratos de diferentes materiais, cores, texturas e orientação podem influenciar seletivamente no recrutamento de invertebrados sésseis e, assim, influenciar a comunidade resultante. Deste modo, o substrato pode funcionar como barreira contra o estabelecimento de espécies não nativas (NIS, na sigla em inglês. No sul do Brasil, o granito é a principal rocha formadora de costões rochosos naturais disponíveis para organismos incrustantes. Nesta investigação, nós testamos se o granito seleciona o recrutamento de espécies e se poderia, assim, impedir a colonização de espécies introduzidas ou criptogênicas já estabelecidas em substratos artificiais na região. Placas não polidas de granito e de polietileno foram submersas a cada mês em um píer de um iate clube na Baía de Paranaguá. Há uma comunidade j

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

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Eswen Fava

2014-08-01

Full Text Available 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.

Recombinant proteins incorporating short non-native extensions may display increased aggregation propensity as detected by high resolution NMR spectroscopy

International Nuclear Information System (INIS)

Zanzoni, Serena; D’Onofrio, Mariapina; Molinari, Henriette; Assfalg, Michael

2012-01-01

Highlights: ► Bile acid binding proteins from different constructs retain structural integrity. ► NMR 15 N-T 1 relaxation data of BABPs show differences if LVPR extension is present. ► Deviations from a 15 N-T 1 /molecular-weight calibration curve indicate aggregation. -- Abstract: The use of a recombinant protein to investigate the function of the native molecule requires that the former be obtained with the same amino acid sequence as the template. However, in many cases few additional residues are artificially introduced for cloning or purification purposes, possibly resulting in altered physico-chemical properties that may escape routine characterization. For example, increased aggregation propensity without visible protein precipitation is hardly detected by most analytical techniques but its investigation may be of great importance for optimizing the yield of recombinant protein production in biotechnological and structural biology applications. In this work we show that bile acid binding proteins incorporating the common C-terminal LeuValProArg extension display different hydrodynamic properties from those of the corresponding molecules without such additional amino acids. The proteins were produced enriched in nitrogen-15 for analysis via heteronuclear NMR spectroscopy. Residue-specific spin relaxation rates were measured and related to rotational tumbling time and molecular size. While the native-like recombinant proteins show spin-relaxation rates in agreement with those expected for monomeric globular proteins of their mass, our data indicate the presence of larger adducts for samples of proteins with very short amino acid extensions. The used approach is proposed as a further screening method for the quality assessment of biotechnological protein products.

Recombinant proteins incorporating short non-native extensions may display increased aggregation propensity as detected by high resolution NMR spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Zanzoni, Serena; D' Onofrio, Mariapina; Molinari, Henriette [Department of Biotechnology, University of Verona, 37134 Verona (Italy); Assfalg, Michael, E-mail: michael.assfalg@univr.it [Department of Biotechnology, University of Verona, 37134 Verona (Italy)

2012-10-26

Highlights: Black-Right-Pointing-Pointer Bile acid binding proteins from different constructs retain structural integrity. Black-Right-Pointing-Pointer NMR {sup 15}N-T{sub 1} relaxation data of BABPs show differences if LVPR extension is present. Black-Right-Pointing-Pointer Deviations from a {sup 15}N-T{sub 1}/molecular-weight calibration curve indicate aggregation. -- Abstract: The use of a recombinant protein to investigate the function of the native molecule requires that the former be obtained with the same amino acid sequence as the template. However, in many cases few additional residues are artificially introduced for cloning or purification purposes, possibly resulting in altered physico-chemical properties that may escape routine characterization. For example, increased aggregation propensity without visible protein precipitation is hardly detected by most analytical techniques but its investigation may be of great importance for optimizing the yield of recombinant protein production in biotechnological and structural biology applications. In this work we show that bile acid binding proteins incorporating the common C-terminal LeuValProArg extension display different hydrodynamic properties from those of the corresponding molecules without such additional amino acids. The proteins were produced enriched in nitrogen-15 for analysis via heteronuclear NMR spectroscopy. Residue-specific spin relaxation rates were measured and related to rotational tumbling time and molecular size. While the native-like recombinant proteins show spin-relaxation rates in agreement with those expected for monomeric globular proteins of their mass, our data indicate the presence of larger adducts for samples of proteins with very short amino acid extensions. The used approach is proposed as a further screening method for the quality assessment of biotechnological protein products.

The Impact of Non-Native English Teachers' Linguistic Insecurity on Learners' Productive Skills

Science.gov (United States)

Daftari, Giti Ehtesham; Tavil, Zekiye Müge

2017-01-01

The discrimination between native and non-native English speaking teachers is reported in favor of native speakers in literature. The present study examines the linguistic insecurity of non-native English speaking teachers (NNESTs) and investigates its influence on learners' productive skills by using SPSS software. The eighteen teachers…

Thermal physiology of native cool-climate, and non-native warm-climate Pumpkinseed sunfish raised in a common environment.

Science.gov (United States)

Rooke, Anna C; Burness, Gary; Fox, Michael G

2017-02-01

Contemporary evolution of thermal physiology has the potential to help limit the physiological stress associated with rapidly changing thermal environments; however it is unclear if wild populations can respond quickly enough for such changes to be effective. We used native Canadian Pumpkinseed (Lepomis gibbosus) sunfish, and non-native Pumpkinseed introduced into the milder climate of Spain ~100 years ago, to assess genetic differences in thermal physiology in response to the warmer non-native climate. We compared temperature performance reaction norms of two Canadian and two Spanish Pumpkinseed populations born and raised within a common environment. We found that Canadian Pumpkinseed had higher routine metabolic rates when measured at seasonally high temperatures (15°C in winter, 30°C in summer), and that Spanish Pumpkinseed had higher critical thermal maxima when acclimated to 30°C in the summer. Growth rates were not significantly different among populations, however Canadian Pumpkinseed tended to have faster growth at the warmest temperatures measured (32°C). The observed differences in physiology among Canadian and Spanish populations at the warmest acclimation temperatures are consistent with the introduced populations being better suited to the warmer non-native climate than native populations. The observed differences could be the result of either founder effects, genetic drift, and/or contemporary adaptive evolution in the warmer non-native climate. Copyright © 2016 Elsevier Ltd. All rights reserved.

An Ecosystem-Service Approach to Evaluate the Role of Non-Native Species in Urbanized Wetlands

Science.gov (United States)

Yam, Rita S. W.; Huang, Ko-Pu; Hsieh, Hwey-Lian; Lin, Hsing-Juh; Huang, Shou-Chung

2015-01-01

Natural wetlands have been increasingly transformed into urbanized ecosystems commonly colonized by stress-tolerant non-native species. Although non-native species present numerous threats to natural ecosystems, some could provide important benefits to urbanized ecosystems. This study investigated the extent of colonization by non-native fish and bird species of three urbanized wetlands in subtropical Taiwan. Using literature data the role of each non-native species in the urbanized wetland was evaluated by their effect (benefits/damages) on ecosystem services (ES) based on their ecological traits. Our sites were seriously colonized by non-native fishes (39%–100%), but wetland ES. Our results indicated the importance of non-native fishes in supporting ES by serving as food source to fish-eating waterbirds (native, and migratory species) due to their high abundance, particularly for Oreochromis spp. However, all non-native birds are regarded as “harmful” species causing important ecosystem disservices, and thus eradication of these bird-invaders from urban wetlands would be needed. This simple framework for role evaluation of non-native species represents a holistic and transferable approach to facilitate decision making on management priority of non-native species in urbanized wetlands. PMID:25860870

Students Writing Emails to Faculty: An Examination of E-Politeness among Native and Non-Native Speakers of English

Science.gov (United States)

Biesenbach-Lucas, Sigrun

2007-01-01

This study combines interlanguage pragmatics and speech act research with computer-mediated communication and examines how native and non-native speakers of English formulate low- and high-imposition requests to faculty. While some research claims that email, due to absence of non-verbal cues, encourages informal language, other research has…

DNA metabarcoding of fish larvae for detection of non-native fishes

Science.gov (United States)

Our objective was to evaluate the use of fish larvae for early detection of non-native fishes, comparing traditional and molecular taxonomy approaches to investigate potential efficiencies. Fish larvae present an interesting opportunity for non-native fish early detection because...

Factors influencing non-native tree species distribution in urban landscapes

Science.gov (United States)

Wayne C. Zipperer

2010-01-01

Non-native species are presumed to be pervasive across the urban landscape. Yet, we actually know very little about their actual distribution. For this study, vegetation plot data from Syracuse, NY and Baltimore, MD were used to examine non-native tree species distribution in urban landscapes. Data were collected from remnant and emergent forest patches on upland sites...

Rupturing Giant Plasma Membrane Vesicles to Form Micron-sized Supported Cell Plasma Membranes with Native Transmembrane Proteins.

Science.gov (United States)

Chiang, Po-Chieh; Tanady, Kevin; Huang, Ling-Ting; Chao, Ling

2017-11-09

Being able to directly obtain micron-sized cell blebs, giant plasma membrane vesicles (GPMVs), with native membrane proteins and deposit them on a planar support to form supported plasma membranes could allow the membrane proteins to be studied by various surface analytical tools in native-like bilayer environments. However, GPMVs do not easily rupture on conventional supports because of their high protein and cholesterol contents. Here, we demonstrate the possibility of using compression generated by the air-water interface to efficiently rupture GPMVs to form micron-sized supported membranes with native plasma membrane proteins. We demonstrated that not only lipid but also a native transmembrane protein in HeLa cells, Aquaporin 3 (AQP3), is mobile in the supported membrane platform. This convenient method for generating micron-sized supported membrane patches with mobile native transmembrane proteins could not only facilitate the study of membrane proteins by surface analytical tools, but could also enable us to use native membrane proteins for bio-sensing applications.

Do native parasitic plants cause more damage to exotic invasive hosts than native non-invasive hosts? An implication for biocontrol.

Science.gov (United States)

Li, Junmin; Jin, Zexin; Song, Wenjing

2012-01-01

Field studies have shown that native, parasitic plants grow vigorously on invasive plants and can cause more damage to invasive plants than native plants. However, no empirical test has been conducted and the mechanism is still unknown. We conducted a completely randomized greenhouse experiment using 3 congeneric pairs of exotic, invasive and native, non-invasive herbaceous plant species to quantify the damage caused by parasitic plants to hosts and its correlation with the hosts' growth rate and resource use efficiency. The biomass of the parasitic plants on exotic, invasive hosts was significantly higher than on congeneric native, non-invasive hosts. Parasites caused more damage to exotic, invasive hosts than to congeneric, native, non-invasive hosts. The damage caused by parasites to hosts was significantly positively correlated with the biomass of parasitic plants. The damage of parasites to hosts was significantly positively correlated with the relative growth rate and the resource use efficiency of its host plants. It may be the mechanism by which parasitic plants grow more vigorously on invasive hosts and cause more damage to exotic, invasive hosts than to native, non-invasive hosts. These results suggest a potential biological control effect of native, parasitic plants on invasive species by reducing the dominance of invasive species in the invaded community.

How much does language proficiency by non-native listeners influence speech audiometric tests in noise?

Science.gov (United States)

Warzybok, Anna; Brand, Thomas; Wagener, Kirsten C; Kollmeier, Birger

2015-01-01

The current study investigates the extent to which the linguistic complexity of three commonly employed speech recognition tests and second language proficiency influence speech recognition thresholds (SRTs) in noise in non-native listeners. SRTs were measured for non-natives and natives using three German speech recognition tests: the digit triplet test (DTT), the Oldenburg sentence test (OLSA), and the Göttingen sentence test (GÖSA). Sixty-four non-native and eight native listeners participated. Non-natives can show native-like SRTs in noise only for the linguistically easy speech material (DTT). Furthermore, the limitation of phonemic-acoustical cues in digit triplets affects speech recognition to the same extent in non-natives and natives. For more complex and less familiar speech materials, non-natives, ranging from basic to advanced proficiency in German, require on average 3-dB better signal-to-noise ratio for the OLSA and 6-dB for the GÖSA to obtain 50% speech recognition compared to native listeners. In clinical audiology, SRT measurements with a closed-set speech test (i.e. DTT for screening or OLSA test for clinical purposes) should be used with non-native listeners rather than open-set speech tests (such as the GÖSA or HINT), especially if a closed-set version in the patient's own native language is available.

Mechanism of Electrochemical Delamination of Two-Dimensional Materials from Their Native Substrates by Bubbling

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Jie Sun

2015-12-01

Full Text Available A capacitor-based circuit model is proposed to explain the electrochemical delamination of two-dimensional materials from their native substrates where produced gas bubbles squeeze into the interface. The delamination is actually the electric breakdown of the capacitor formed between the solution and substrate. To facilitate the procedure, the backside of the ubstrate has to be shielded so that the capacitor breakdown voltage can be reached. The screening effect can be induced either by nonreactive ions around the electrode or, more effectively, by an undetachable insulator. This mechanism serves as a guideline for the surface science and applications involving the bubbling delamination.

Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY

International Nuclear Information System (INIS)

Shi, Jade; Schwantes, Christian; Bilsel, Osman

2017-01-01

The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. We report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structure of the excited state ensemble. The resulting prior was then refined against small-angle X-ray scattering (SAXS) data employing an established method (EROS). The most striking feature of the resulting excited state ensemble was an unstructured N-terminus stabilized by non-native contacts in a conformation that is topologically simpler than the native state. We then predict incisive single molecule FRET experiments, using these results, as a means of model validation. Our study demonstrates the paradigm of uniting simulation and experiment in a statistical model to study the structure of protein excited states and rationally design validating experiments.

When the Native Is Also a Non-Native: "Retrodicting" the Complexity of Language Teacher Cognition

Science.gov (United States)

Aslan, Erhan

2015-01-01

The impact of native (NS) and non-native speaker (NNS) identities on second or foreign language teachers' cognition and practices in the classroom has mainly been investigated in ESL/EFL contexts. Using complexity theory as a framework, this case study attempts to fill the gap in the literature by presenting a foreign language teacher in the…

Non-natives: 141 scientists object

OpenAIRE

Simberloff, Daniel; Vilà, Montserrat

2011-01-01

Supplementary information to: Non-natives: 141 scientists object Full list of co-signatories to a Correspondence published in Nature 475, 36 (2011); doi: 10.1038/475036a. Daniel Simberloff University of Tennessee, Knoxville, Tennessee, USA. Jake Alexander Institute of Integrative Biology, Zurich, Switzerland. Fred Allendorf University of Montana, Missoula, Montana, USA. James Aronson CEFE/CNRS, Montpellier, France. Pedro M. Antunes Algoma University, Sault Ste. Marie, Onta...

Managing conflicts arising from fisheries enhancements based on non-native fishes in southern Africa.

Science.gov (United States)

Ellender, B R; Woodford, D J; Weyl, O L F; Cowx, I G

2014-12-01

Southern Africa has a long history of non-native fish introductions for the enhancement of recreational and commercial fisheries, due to a perceived lack of suitable native species. This has resulted in some important inland fisheries being based on non-native fishes. Regionally, these introductions are predominantly not benign, and non-native fishes are considered one of the main threats to aquatic biodiversity because they affect native biota through predation, competition, habitat alteration, disease transfer and hybridization. To achieve national policy objectives of economic development, food security and poverty eradication, countries are increasingly looking towards inland fisheries as vehicles for development. As a result, conflicts have developed between economic and conservation objectives. In South Africa, as is the case for other invasive biota, the control and management of non-native fishes is included in the National Environmental Management: Biodiversity Act. Implementation measures include import and movement controls and, more recently, non-native fish eradication in conservation priority areas. Management actions are, however, complicated because many non-native fishes are important components in recreational and subsistence fisheries that contribute towards regional economies and food security. In other southern African countries, little attention has focussed on issues and management of non-native fishes, and this is cause for concern. This paper provides an overview of introductions, impacts and fisheries in southern Africa with emphasis on existing and evolving legislation, conflicts, implementation strategies and the sometimes innovative approaches that have been used to prioritize conservation areas and manage non-native fishes. © 2014 The Fisheries Society of the British Isles.

Probing the Composition, Assembly and Activity of Protein Molecular Machines using Native Mass Spectrometry

NARCIS (Netherlands)

van de Waterbeemd, M.J.

2017-01-01

Native mass spectrometry and mass spectrometry in general, are powerful analytical tools for studying proteins and protein complexes. Native mass spectrometry may provide accurate mass measurements of large macromolecular assemblies enabling the investigation of their composition and stoichiometry.

The structures of native celluloses, and the origin of their variability

Science.gov (United States)

R. H. Atalla

1999-01-01

The structures of native celluloses have traditionally been presented in terms of two-domain models consisting of crystalline and non-crystalline fractions. Such models have been of little help in advancing understanding of enzyme-substrate interactions. In this report we first address issues that complicate characterization of the structure of native celluloses...

Chaperoning Proteins for Destruction: Diverse Roles of Hsp70 Chaperones and their Co-Chaperones in Targeting Misfolded Proteins to the Proteasome

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Ayala Shiber

2014-07-01

Full Text Available Molecular chaperones were originally discovered as heat shock-induced proteins that facilitate proper folding of proteins with non-native conformations. While the function of chaperones in protein folding has been well documented over the last four decades, more recent studies have shown that chaperones are also necessary for the clearance of terminally misfolded proteins by the Ub-proteasome system. In this capacity, chaperones protect misfolded degradation substrates from spontaneous aggregation, facilitate their recognition by the Ub ligation machinery and finally shuttle the ubiquitylated substrates to the proteasome. The physiological importance of these functions is manifested by inefficient proteasomal degradation and the accumulation of protein aggregates during ageing or in certain neurodegenerative diseases, when chaperone levels decline. In this review, we focus on the diverse roles of stress-induced chaperones in targeting misfolded proteins to the proteasome and the consequences of their compromised activity. We further discuss the implications of these findings to the identification of new therapeutic targets for the treatment of amyloid diseases.

Constructing a folding model for protein S6 guided by native fluctuations deduced from NMR structures

International Nuclear Information System (INIS)

Lammert, Heiko; Noel, Jeffrey K.; Haglund, Ellinor; Onuchic, José N.; Schug, Alexander

2015-01-01

The diversity in a set of protein nuclear magnetic resonance (NMR) structures provides an estimate of native state fluctuations that can be used to refine and enrich structure-based protein models (SBMs). Dynamics are an essential part of a protein’s functional native state. The dynamics in the native state are controlled by the same funneled energy landscape that guides the entire folding process. SBMs apply the principle of minimal frustration, drawn from energy landscape theory, to construct a funneled folding landscape for a given protein using only information from the native structure. On an energy landscape smoothed by evolution towards minimal frustration, geometrical constraints, imposed by the native structure, control the folding mechanism and shape the native dynamics revealed by the model. Native-state fluctuations can alternatively be estimated directly from the diversity in the set of NMR structures for a protein. Based on this information, we identify a highly flexible loop in the ribosomal protein S6 and modify the contact map in a SBM to accommodate the inferred dynamics. By taking into account the probable native state dynamics, the experimental transition state is recovered in the model, and the correct order of folding events is restored. Our study highlights how the shared energy landscape connects folding and function by showing that a better description of the native basin improves the prediction of the folding mechanism

Designing acoustics for linguistically diverse classrooms: Effects of background noise, reverberation and talker foreign accent on speech comprehension by native and non-native English-speaking listeners

Science.gov (United States)

Peng, Zhao Ellen

The current classroom acoustics standard (ANSI S12.60-2010) recommends core learning spaces not to exceed background noise level (BNL) of 35 dBA and reverberation time (RT) of 0.6 second, based on speech intelligibility performance mainly by the native English-speaking population. Existing literature has not correlated these recommended values well with student learning outcomes. With a growing population of non-native English speakers in American classrooms, the special needs for perceiving degraded speech among non-native listeners, either due to realistic room acoustics or talker foreign accent, have not been addressed in the current standard. This research seeks to investigate the effects of BNL and RT on the comprehension of English speech from native English and native Mandarin Chinese talkers as perceived by native and non-native English listeners, and to provide acoustic design guidelines to supplement the existing standard. This dissertation presents two studies on the effects of RT and BNL on more realistic classroom learning experiences. How do native and non-native English-speaking listeners perform on speech comprehension tasks under adverse acoustic conditions, if the English speech is produced by talkers of native English (Study 1) versus native Mandarin Chinese (Study 2)? Speech comprehension materials were played back in a listening chamber to individual listeners: native and non-native English-speaking in Study 1; native English, native Mandarin Chinese, and other non-native English-speaking in Study 2. Each listener was screened for baseline English proficiency level, and completed dual tasks simultaneously involving speech comprehension and adaptive dot-tracing under 15 acoustic conditions, comprised of three BNL conditions (RC-30, 40, and 50) and five RT scenarios (0.4 to 1.2 seconds). The results show that BNL and RT negatively affect both objective performance and subjective perception of speech comprehension, more severely for non-native

LC-MS/MS as an alternative for SDS-PAGE in blue native analysis of protein complexes.

NARCIS (Netherlands)

Wessels, H.C.T.; Vogel, R.O.; Heuvel, L.P.W.J. van den; Smeitink, J.A.M.; Rodenburg, R.J.T.; Nijtmans, L.G.J.; Farhoud, M.H.

2009-01-01

Two-dimensional blue native/SDS-PAGE is widely applied to investigate native protein-protein interactions, particularly those within membrane multi-protein complexes. MS has enabled the application of this approach at the proteome scale, typically by analysis of picked protein spots. Here, we

Linking Native and Invader Traits Explains Native Spider Population Responses to Plant Invasion.

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Jennifer N Smith

Full Text Available Theoretically, the functional traits of native species should determine how natives respond to invader-driven changes. To explore this idea, we simulated a large-scale plant invasion using dead spotted knapweed (Centaurea stoebe stems to determine if native spiders' web-building behaviors could explain differences in spider population responses to structural changes arising from C. stoebe invasion. After two years, irregular web-spiders were >30 times more abundant and orb weavers were >23 times more abundant on simulated invasion plots compared to controls. Additionally, irregular web-spiders on simulated invasion plots built webs that were 4.4 times larger and 5.0 times more likely to capture prey, leading to >2-fold increases in recruitment. Orb-weavers showed no differences in web size or prey captures between treatments. Web-spider responses to simulated invasion mimicked patterns following natural invasions, confirming that C. stoebe's architecture is likely the primary attribute driving native spider responses to these invasions. Differences in spider responses were attributable to differences in web construction behaviors relative to historic web substrate constraints. Orb-weavers in this system constructed webs between multiple plants, so they were limited by the overall quantity of native substrates but not by the architecture of individual native plant species. Irregular web-spiders built their webs within individual plants and were greatly constrained by the diminutive architecture of native plant substrates, so they were limited both by quantity and quality of native substrates. Evaluating native species traits in the context of invader-driven change can explain invasion outcomes and help to identify factors limiting native populations.

FlexAID: Revisiting Docking on Non-Native-Complex Structures.

Science.gov (United States)

Gaudreault, Francis; Najmanovich, Rafael J

2015-07-27

Small-molecule protein docking is an essential tool in drug design and to understand molecular recognition. In the present work we introduce FlexAID, a small-molecule docking algorithm that accounts for target side-chain flexibility and utilizes a soft scoring function, i.e. one that is not highly dependent on specific geometric criteria, based on surface complementarity. The pairwise energy parameters were derived from a large dataset of true positive poses and negative decoys from the PDBbind database through an iterative process using Monte Carlo simulations. The prediction of binding poses is tested using the widely used Astex dataset as well as the HAP2 dataset, while performance in virtual screening is evaluated using a subset of the DUD dataset. We compare FlexAID to AutoDock Vina, FlexX, and rDock in an extensive number of scenarios to understand the strengths and limitations of the different programs as well as to reported results for Glide, GOLD, and DOCK6 where applicable. The most relevant among these scenarios is that of docking on flexible non-native-complex structures where as is the case in reality, the target conformation in the bound form is not known a priori. We demonstrate that FlexAID, unlike other programs, is robust against increasing structural variability. FlexAID obtains equivalent sampling success as GOLD and performs better than AutoDock Vina or FlexX in all scenarios against non-native-complex structures. FlexAID is better than rDock when there is at least one critical side-chain movement required upon ligand binding. In virtual screening, FlexAID results are lower on average than those of AutoDock Vina and rDock. The higher accuracy in flexible targets where critical movements are required, intuitive PyMOL-integrated graphical user interface and free source code as well as precompiled executables for Windows, Linux, and Mac OS make FlexAID a welcome addition to the arsenal of existing small-molecule protein docking methods.

Exploring public perception of non-native species from a visions of nature perspective.

Science.gov (United States)

Verbrugge, Laura N H; Van den Born, Riyan J G; Lenders, H J Rob

2013-12-01

Not much is known about lay public perceptions of non-native species and their underlying values. Public awareness and engagement, however, are important aspects in invasive species management. In this study, we examined the relations between the lay public's visions of nature, their knowledge about non-native species, and their perceptions of non-native species and invasive species management with a survey administered in the Netherlands. Within this framework, we identified three measures for perception of non-native species: perceived risk, control and engagement. In general, respondents scored moderate values for perceived risk and personal engagement. However, in case of potential ecological or human health risks, control measures were supported. Respondents' images of the human-nature relationship proved to be relevant in engagement in problems caused by invasive species and in recognizing the need for control, while images of nature appeared to be most important in perceiving risks to the environment. We also found that eradication of non-native species was predominantly opposed for species with a high cuddliness factor such as mammals and bird species. We conclude that lay public perceptions of non-native species have to be put in a wider context of visions of nature, and we discuss the implications for public support for invasive species management.

Non-native salmonids affect amphibian occupancy at multiple spatial scales

Science.gov (United States)

Pilliod, David S.; Hossack, Blake R.; Bahls, Peter F.; Bull, Evelyn L.; Corn, Paul Stephen; Hokit, Grant; Maxell, Bryce A.; Munger, James C.; Wyrick, Aimee

2010-01-01

Aim The introduction of non-native species into aquatic environments has been linked with local extinctions and altered distributions of native species. We investigated the effect of non-native salmonids on the occupancy of two native amphibians, the long-toed salamander (Ambystoma macrodactylum) and Columbia spotted frog (Rana luteiventris), across three spatial scales: water bodies, small catchments and large catchments. Location Mountain lakes at ≥ 1500 m elevation were surveyed across the northern Rocky Mountains, USA. Methods We surveyed 2267 water bodies for amphibian occupancy (based on evidence of reproduction) and fish presence between 1986 and 2002 and modelled the probability of amphibian occupancy at each spatial scale in relation to habitat availability and quality and fish presence. Results After accounting for habitat features, we estimated that A. macrodactylum was 2.3 times more likely to breed in fishless water bodies than in water bodies with fish. Ambystoma macrodactylum also was more likely to occupy small catchments where none of the water bodies contained fish than in catchments where at least one water body contained fish. However, the probability of salamander occupancy in small catchments was also influenced by habitat availability (i.e. the number of water bodies within a catchment) and suitability of remaining fishless water bodies. We found no relationship between fish presence and salamander occupancy at the large-catchment scale, probably because of increased habitat availability. In contrast to A. macrodactylum, we found no relationship between fish presence and R. luteiventris occupancy at any scale. Main conclusions Our results suggest that the negative effects of non-native salmonids can extend beyond the boundaries of individual water bodies and increase A. macrodactylum extinction risk at landscape scales. We suspect that niche overlap between non-native fish and A. macrodactylum at higher elevations in the northern Rocky

Non-native earthworms promote plant invasion by ingesting seeds and modifying soil properties

OpenAIRE

Clause, J.; Forey, E.; Lortie, C. J.; Lambert, A. M.; Barot, Sébastien

2015-01-01

Earthworms can have strong direct effects on plant communities through consumption and digestion of seeds, however it is unclear how earthworms may influence the relative abundance and composition of plant communities invaded by non-native species. In this study, earthworms, seed banks, and the standing vegetation were sampled in a grassland of central California. Our objectives were i) to examine whether the abundances of non-native, invasive earthworm species and non-native grassland plant ...

Coating extracellular matrix proteins on a (3-aminopropyl)triethoxysilane-treated glass substrate for improved cell culture.

Science.gov (United States)

Masuda, Hiro-taka; Ishihara, Seiichiro; Harada, Ichiro; Mizutani, Takeomi; Ishikawa, Masayori; Kawabata, Kazushige; Haga, Hisashi

2014-01-01

We demonstrate that a (3-aminopropyl)triethoxysilane-treated glass surface is superior to an untreated glass surface for coating with extracellular matrix (ECM) proteins when used as a cell culture substrate to observe cell physiology and behavior. We found that MDCK cells cultured on untreated glass coated with ECM removed the coated ECM protein and secreted different ECM proteins. In contrast, the cells did not remove the coated ECM protein when seeded on (3-aminopropyl)triethoxysilane-treated (i.e., silanized) glass coated with ECM. Furthermore, the morphology and motility of cells grown on silanized glass differed from those grown on non-treated glass, even when both types of glass were initially coated with laminin. We also found that cells on silanized glass coated with laminin had higher motility than those on silanized glass coated with fibronectin. Based on our results, we suggest that silanized glass is a more suitable cell culture substrate than conventional non-treated glass when coated by ECM for observations of ECM effects on cell physiology.

Determining Membrane Protein-Lipid Binding Thermodynamics Using Native Mass Spectrometry.

Science.gov (United States)

Cong, Xiao; Liu, Yang; Liu, Wen; Liang, Xiaowen; Russell, David H; Laganowsky, Arthur

2016-04-06

Membrane proteins are embedded in the biological membrane where the chemically diverse lipid environment can modulate their structure and function. However, the thermodynamics governing the molecular recognition and interaction of lipids with membrane proteins is poorly understood. Here, we report a method using native mass spectrometry (MS), to determine thermodynamics of individual ligand binding events to proteins. Unlike conventional methods, native MS can resolve individual ligand binding events and, coupled with an apparatus to control the temperature, determine binding thermodynamic parameters, such as for protein-lipid interactions. We validated our approach using three soluble protein-ligand systems (maltose binding protein, lysozyme, and nitrogen regulatory protein) and obtained similar results to those using isothermal titration calorimetry and surface plasmon resonance. We also determined for the first time the thermodynamics of individual lipid binding to the ammonia channel (AmtB), an integral membrane protein from Escherichia coli. Remarkably, we observed distinct thermodynamic signatures for the binding of different lipids and entropy-enthalpy compensation for binding lipids of variable chain length. Additionally, using a mutant form of AmtB that abolishes a specific phosphatidylglycerol (PG) binding site, we observed distinct changes in the thermodynamic signatures for binding PG, implying these signatures can identify key residues involved in specific lipid binding and potentially differentiate between specific lipid binding sites.

Calcium-Dependent Protein Kinases from Arabidopsis show substrate specificity differences in an analysis of 103 substrates

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Amy eCurran

2011-08-01

Full Text Available The identification of substrates represents a critical challenge for understanding any protein kinase-based signal transduction pathway. In Arabidopsis, there are more than 1000 different protein kinases, 34 of which belong to a family of Ca2+-dependent protein kinases (CPKs. While CPKs are implicated in regulating diverse aspects of plant biology, from ion transport to transcription, relatively little is known about isoform-specific differences in substrate specificity, or the number of phosphorylation targets. Here, in vitro kinase assays were used to compare phosphorylation targets of four CPKs from Arabidopsis (CPK1, 10, 16 and 34. Significant differences in substrate specificity for each kinase were revealed by assays using 103 different substrates. For example CPK16 phosphorylated Serine 109 in a peptide from the stress-regulated protein, Di19-2 with KM ~70 µM, but this site was not phosphorylated significantly by CPKs 1, 10, or 34. In contrast, CPKs 1, 10, and 34 phosphorylated 93 other peptide substrates not recognized by CPK16. Examples of substrate specificity differences among all four CPKs were verified by kinetic analyses. To test the correlation between in vivo phosphorylation events and in vitro kinase activities, assays were performed with 274 synthetic peptides that contained phosphorylation sites previously mapped in proteins isolated from plants (in vivo-mapped sites. Of these, 74 (27% were found to be phosphorylated by at least one of the four CPKs tested. This 27% success rate validates a robust strategy for linking the activities of specific kinases, such as CPKs, to the thousands of in planta phosphorylation sites that are being uncovered by emerging technologies.

UV Screening in Native and Non-native Plant Species in the Tropical Alpine: Implications for Climate Change-Driven Migration of Species to Higher Elevations

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Paul W. Barnes

2017-08-01

Full Text Available Ongoing changes in Earth’s climate are shifting the elevation ranges of many plant species with non-native species often experiencing greater expansion into higher elevations than native species. These climate change-induced shifts in distributions inevitably expose plants to novel biotic and abiotic environments, including altered solar ultraviolet (UV-B (280–315 nm radiation regimes. Do the greater migration potentials of non-native species into higher elevations imply that they have more effective UV-protective mechanisms than native species? In this study, we surveyed leaf epidermal UV-A transmittance (TUV A in a diversity of plant species representing different growth forms to test whether native and non-native species growing above 2800 m elevation on Mauna Kea, Hawaii differed in their UV screening capabilities. We further compared the degree to which TUV A varied along an elevation gradient in the native shrub Vaccinium reticulatum and the introduced forb Verbascum thapsus to evaluate whether these species differed in their abilities to adjust their levels of UV screening in response to elevation changes in UV-B. For plants growing in the Mauna Kea alpine/upper subalpine, we found that adaxial TUV A, measured with a UVA-PAM fluorometer, varied significantly among species but did not differ between native (mean = 6.0%; n = 8 and non-native (mean = 5.8%; n = 11 species. When data were pooled across native and non-native taxa, we also found no significant effect of growth form on TUV A, though woody plants (shrubs and trees were represented solely by native species whereas herbaceous growth forms (grasses and forbs were dominated by non-native species. Along an elevation gradient spanning 2600–3800 m, TUV A was variable (mean range = 6.0–11.2% and strongly correlated with elevation and relative biologically effective UV-B in the exotic V. thapsus; however, TUV A was consistently low (3% and did not vary with elevation in the native

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

Science.gov (United States)

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…

Non-native species in the vascular flora of highlands and mountains of Iceland

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Pawel Wasowicz

2016-01-01

Full Text Available The highlands and mountains of Iceland are one of the largest remaining wilderness areas in Europe. This study aimed to provide comprehensive and up-to-date data on non-native plant species in these areas and to answer the following questions: (1 How many non-native vascular plant species inhabit highland and mountainous environments in Iceland? (2 Do temporal trends in the immigration of alien species to Iceland differ between highland and lowland areas? (3 Does the incidence of alien species in the disturbed and undisturbed areas within Icelandic highlands differ? (4 Does the spread of non-native species in Iceland proceed from lowlands to highlands? and (5 Can we detect hot-spots in the distribution of non-native taxa within the highlands? Overall, 16 non-native vascular plant species were detected, including 11 casuals and 5 naturalized taxa (1 invasive. Results showed that temporal trends in alien species immigration to highland and lowland areas are similar, but it is clear that the process of colonization of highland areas is still in its initial phase. Non-native plants tended to occur close to man-made infrastructure and buildings including huts, shelters, roads etc. Analysis of spatio-temporal patterns showed that the spread within highland areas is a second step in non-native plant colonization in Iceland. Several statically significant hot spots of alien plant occurrences were identified using the Getis-Ord Gi* statistic and these were linked to human disturbance. This research suggests that human-mediated dispersal is the main driving force increasing the risk of invasion in Iceland’s highlands and mountain areas.

Single-mode optical waveguides on native high-refractive-index substrates

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Richard R. Grote

2016-10-01

Full Text Available High-refractive-index semiconductor optical waveguides form the basis for modern photonic integrated circuits (PICs. However, conventional methods for achieving optical confinement require a thick lower-refractive-index support layer that impedes large-scale co-integration with electronics and limits the materials on which PICs can be fabricated. To address this challenge, we present a general architecture for single-mode waveguides that confine light in a high-refractive-index material on a native substrate. The waveguide consists of a high-aspect-ratio fin of the guiding material surrounded by lower-refractive-index dielectrics and is compatible with standard top-down fabrication techniques. This letter describes a physically intuitive, semi-analytical, effective index model for designing fin waveguides, which is confirmed with fully vectorial numerical simulations. Design examples are presented for diamond and silicon at visible and telecommunications wavelengths, respectively, along with calculations of propagation loss due to bending, scattering, and substrate leakage. Potential methods of fabrication are also discussed. The proposed waveguide geometry allows PICs to be fabricated alongside silicon CMOS electronics on the same wafer, removes the need for heteroepitaxy in III-V PICs, and will enable wafer-scale photonic integration on emerging material platforms such as diamond and SiC.

An Investigation into Native and Non-Native Teachers' Judgments of Oral English Performance: A Mixed Methods Approach

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Kim, Youn-Hee

2009-01-01

This study used a mixed methods research approach to examine how native English-speaking (NS) and non-native English-speaking (NNS) teachers assess students' oral English performance. The evaluation behaviors of two groups of teachers (12 Canadian NS teachers and 12 Korean NNS teachers) were compared with regard to internal consistency, severity,…

Topic Continuity in Informal Conversations between Native and Non-Native Speakers of English

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Morris-Adams, Muna

2013-01-01

Topic management by non-native speakers (NNSs) during informal conversations has received comparatively little attention from researchers, and receives surprisingly little attention in second language learning and teaching. This article reports on one of the topic management strategies employed by international students during informal, social…

Emergence of category-level sensitivities in non-native speech sound learning

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Emily eMyers

2014-08-01

Full Text Available Over the course of development, speech sounds that are contrastive in one’s native language tend to become perceived categorically: that is, listeners are unaware of variation within phonetic categories while showing excellent sensitivity to speech sounds that span linguistically meaningful phonetic category boundaries. The end stage of this developmental process is that the perceptual systems that handle acoustic-phonetic information show special tuning to native language contrasts, and as such, category-level information appears to be present at even fairly low levels of the neural processing stream. Research on adults acquiring non-native speech categories offers an avenue for investigating the interplay of category-level information and perceptual sensitivities to these sounds as speech categories emerge. In particular, one can observe the neural changes that unfold as listeners learn not only to perceive acoustic distinctions that mark non-native speech sound contrasts, but also to map these distinctions onto category-level representations. An emergent literature on the neural basis of novel and non-native speech sound learning offers new insight into this question. In this review, I will examine this literature in order to answer two key questions. First, where in the neural pathway does sensitivity to category-level phonetic information first emerge over the trajectory of speech sound learning? Second, how do frontal and temporal brain areas work in concert over the course of non-native speech sound learning? Finally, in the context of this literature I will describe a model of speech sound learning in which rapidly-adapting access to categorical information in the frontal lobes modulates the sensitivity of stable, slowly-adapting responses in the temporal lobes.

Extensive analysis of native and non-native Centaurea solstitialis L. populations across the world shows no traces of polyploidization

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Ramona-Elena Irimia

2017-08-01

Full Text Available Centaurea solstitialis L. (yellow starthistle, Asteraceae is a Eurasian native plant introduced as an exotic into North and South America, and Australia, where it is regarded as a noxious invasive. Changes in ploidy level have been found to be responsible for numerous plant biological invasions, as they are involved in trait shifts critical to invasive success, like increased growth rate and biomass, longer life-span, or polycarpy. C. solstitialis had been reported to be diploid (2n = 2x = 16 chromosomes, however, actual data are scarce and sometimes contradictory. We determined for the first time the absolute nuclear DNA content by flow cytometry and estimated ploidy level in 52 natural populations of C. solstitialis across its native and non-native ranges, around the world. All the C. solstitialis populations screened were found to be homogeneously diploid (average 2C value of 1.72 pg, SD = ±0.06 pg, with no significant variation in DNA content between invasive and non-invasive genotypes. We did not find any meaningful difference among the extensive number of native and non-native C. solstitialis populations sampled around the globe, indicating that the species invasive success is not due to changes in genome size or ploidy level.

Extensive analysis of native and non-native Centaurea solstitialis L. populations across the world shows no traces of polyploidization.

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Irimia, Ramona-Elena; Montesinos, Daniel; Eren, Özkan; Lortie, Christopher J; French, Kristine; Cavieres, Lohengrin A; Sotes, Gastón J; Hierro, José L; Jorge, Andreia; Loureiro, João

2017-01-01

Centaurea solstitialis L. (yellow starthistle, Asteraceae) is a Eurasian native plant introduced as an exotic into North and South America, and Australia, where it is regarded as a noxious invasive. Changes in ploidy level have been found to be responsible for numerous plant biological invasions, as they are involved in trait shifts critical to invasive success, like increased growth rate and biomass, longer life-span, or polycarpy. C . solstitialis had been reported to be diploid (2 n  = 2 x  = 16 chromosomes), however, actual data are scarce and sometimes contradictory. We determined for the first time the absolute nuclear DNA content by flow cytometry and estimated ploidy level in 52 natural populations of C . solstitialis across its native and non-native ranges, around the world. All the C. solstitialis populations screened were found to be homogeneously diploid (average 2C value of 1.72 pg, SD = ±0.06 pg), with no significant variation in DNA content between invasive and non-invasive genotypes. We did not find any meaningful difference among the extensive number of native and non-native C . solstitialis populations sampled around the globe, indicating that the species invasive success is not due to changes in genome size or ploidy level.

Non-Native Plant Invasion along Elevation and Canopy Closure Gradients in a Middle Rocky Mountain Ecosystem.

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Joshua P Averett

Full Text Available Mountain environments are currently among the ecosystems least invaded by non-native species; however, mountains are increasingly under threat of non-native plant invasion. The slow pace of exotic plant invasions in mountain ecosystems is likely due to a combination of low anthropogenic disturbances, low propagule supply, and extreme/steep environmental gradients. The importance of any one of these factors is debated and likely ecosystem dependent. We evaluated the importance of various correlates of plant invasions in the Wallowa Mountain Range of northeastern Oregon and explored whether non-native species distributions differed from native species along an elevation gradient. Vascular plant communities were sampled in summer 2012 along three mountain roads. Transects (n = 20 were evenly stratified by elevation (~70 m intervals along each road. Vascular plant species abundances and environmental parameters were measured. We used indicator species analysis to identify habitat affinities for non-native species. Plots were ordinated in species space, joint plots and non-parametric multiplicative regression were used to relate species and community variation to environmental variables. Non-native species richness decreased continuously with increasing elevation. In contrast, native species richness displayed a unimodal distribution with maximum richness occurring at mid-elevations. Species composition was strongly related to elevation and canopy openness. Overlays of trait and environmental factors onto non-metric multidimensional ordinations identified the montane-subalpine community transition and over-story canopy closure exceeding 60% as potential barriers to non-native species establishment. Unlike native species, non-native species showed little evidence for high-elevation or closed-canopy specialization. These data suggest that non-native plants currently found in the Wallowa Mountains are dependent on open canopies and disturbance for

Non-Native Plant Invasion along Elevation and Canopy Closure Gradients in a Middle Rocky Mountain Ecosystem.

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Averett, Joshua P; McCune, Bruce; Parks, Catherine G; Naylor, Bridgett J; DelCurto, Tim; Mata-González, Ricardo

2016-01-01

Mountain environments are currently among the ecosystems least invaded by non-native species; however, mountains are increasingly under threat of non-native plant invasion. The slow pace of exotic plant invasions in mountain ecosystems is likely due to a combination of low anthropogenic disturbances, low propagule supply, and extreme/steep environmental gradients. The importance of any one of these factors is debated and likely ecosystem dependent. We evaluated the importance of various correlates of plant invasions in the Wallowa Mountain Range of northeastern Oregon and explored whether non-native species distributions differed from native species along an elevation gradient. Vascular plant communities were sampled in summer 2012 along three mountain roads. Transects (n = 20) were evenly stratified by elevation (~70 m intervals) along each road. Vascular plant species abundances and environmental parameters were measured. We used indicator species analysis to identify habitat affinities for non-native species. Plots were ordinated in species space, joint plots and non-parametric multiplicative regression were used to relate species and community variation to environmental variables. Non-native species richness decreased continuously with increasing elevation. In contrast, native species richness displayed a unimodal distribution with maximum richness occurring at mid-elevations. Species composition was strongly related to elevation and canopy openness. Overlays of trait and environmental factors onto non-metric multidimensional ordinations identified the montane-subalpine community transition and over-story canopy closure exceeding 60% as potential barriers to non-native species establishment. Unlike native species, non-native species showed little evidence for high-elevation or closed-canopy specialization. These data suggest that non-native plants currently found in the Wallowa Mountains are dependent on open canopies and disturbance for establishment in low

Setting Priorities for Monitoring and Managing Non-native Plants: Toward a Practical Approach.

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Koch, Christiane; Jeschke, Jonathan M; Overbeck, Gerhard E; Kollmann, Johannes

2016-09-01

Land managers face the challenge to set priorities in monitoring and managing non-native plant species, as resources are limited and not all non-natives become invasive. Existing frameworks that have been proposed to rank non-native species require extensive information on their distribution, abundance, and impact. This information is difficult to obtain and often not available for many species and regions. National watch or priority lists are helpful, but it is questionable whether they provide sufficient information for environmental management on a regional scale. We therefore propose a decision tree that ranks species based on more simple albeit robust information, but still provides reliable management recommendations. To test the decision tree, we collected and evaluated distribution data from non-native plants in highland grasslands of Southern Brazil. We compared the results with a national list from the Brazilian Invasive Species Database for the state to discuss advantages and disadvantages of the different approaches on a regional scale. Out of 38 non-native species found, only four were also present on the national list. If management would solely rely on this list, many species that were identified as spreading based on the decision tree would go unnoticed. With the suggested scheme, it is possible to assign species to active management, to monitoring, or further evaluation. While national lists are certainly important, management on a regional scale should employ additional tools that adequately consider the actual risk of non-natives to become invasive.

Predicting establishment of non-native fishes in Greece: identifying key features

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Christos Gkenas

2015-11-01

Full Text Available Non-native fishes are known to cause economic damage to human society and are considered a major threat to biodiversity loss in freshwater ecosystems. The growing concern about these impacts has driven to an investigation of the biological traits that facilitate the establishment of non-native fish. However, invalid assessment in choosing the appropriate statistical model can lead researchers to ambiguous conclusions. Here, we present a comprehensive comparison of traditional and alternative statistical methods for predicting fish invasions using logistic regression, classification trees, multicorrespondence analysis and random forest analysis to determine characteristics of successful and failed non-native fishes in Hellenic Peninsula through establishment. We defined fifteen categorical predictor variables with biological relevance and measures of human interest. Our study showed that accuracy differed according to the model and the number of factors considered. Among all the models tested, random forest and logistic regression performed best, although all approaches predicted non-native fish establishment with moderate to excellent results. Detailed evaluation among the models corresponded with differences in variables importance, with three biological variables (parental care, distance from nearest native source and maximum size and two variables of human interest (prior invasion success and propagule pressure being important in predicting establishment. The analyzed statistical methods presented have a high predictive power and can be used as a risk assessment tool to prevent future freshwater fish invasions in this region with an imperiled fish fauna.

Quantitative Photochemical Immobilization of Biomolecules on Planar and Corrugated Substrates: A Versatile Strategy for Creating Functional Biointerfaces

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Martin, Teresa A.; Herman, Christine T.; Limpoco, Francis T.; Michael, Madeline C.; Potts, Gregory K.; Bailey, Ryan C.

2014-01-01

Methods for the generation of substrates presenting biomolecules in a spatially controlled manner are enabling tools for applications in biosensor systems, microarray technologies, fundamental biological studies and biointerface science. We have implemented a method to create biomolecular patterns by using light to control the direct covalent immobilization of biomolecules onto benzophenone-modified glass substrates. We have generated substrates presenting up to three different biomolecules patterned in sequence, and demonstrate biomolecular photopatterning on corrugated substrates. The chemistry of the underlying monolayer was optimized to incorporate poly(ethylene glycol) to enable adhesive cell adhesion onto patterned extracellular matrix proteins. Substrates were characterized with contact angle goniometry, AFM, and immunofluorescence microscopy. Importantly, radioimmunoassays were performed to quantify the site density of immobilized biomolecules on photopatterned substrates. Retention of function of photopatterned proteins was demonstrated both by native ligand recognition and cell adhesion to photopatterned substrates, revealing that substrates generated with this method are suitable for probing specific cell receptor-ligand interactions. This molecularly general photochemical patterning method is an enabling tool that will allow the creation of substrates presenting both biochemical and topographical variation, which is an important feature of many native biointerfaces. PMID:21793535

Analysis of Native-Like Proteins and Protein Complexes Using Cation to Anion Proton Transfer Reactions (CAPTR)

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Laszlo, Kenneth J.; Bush, Matthew F.

2015-12-01

Mass spectra of native-like protein complexes often exhibit narrow charge-state distributions, broad peaks, and contributions from multiple, coexisting species. These factors can make it challenging to interpret those spectra, particularly for mixtures with significant heterogeneity. Here we demonstrate the use of ion/ion proton transfer reactions to reduce the charge states of m/ z-selected, native-like ions of proteins and protein complexes, a technique that we refer to as cation to anion proton transfer reactions (CAPTR). We then demonstrate that CAPTR can increase the accuracy of charge state assignments and the resolution of interfering species in native mass spectrometry. The CAPTR product ion spectra for pyruvate kinase exhibit ~30 peaks and enable unambiguous determination of the charge state of each peak, whereas the corresponding precursor spectra exhibit ~6 peaks and the assigned charge states have an uncertainty of ±3%. 15+ bovine serum albumin and 21+ yeast enolase dimer both appear near m/ z 4450 and are completely unresolved in a mixture. After a single CAPTR event, the resulting product ions are baseline resolved. The separation of the product ions increases dramatically after each subsequent CAPTR event; 12 events resulted in a 3000-fold improvement in separation relative to the precursor ions. Finally, we introduce a framework for interpreting and predicting the figures of merit for CAPTR experiments. More generally, these results suggest that CAPTR strongly complements other mass spectrometry tools for analyzing proteins and protein complexes, particularly those in mixtures.

Economic Impacts of Non-Native Forest Insects in the Continental United States

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Juliann E. Aukema; Brian. Leung; Kent Kovacs; Corey Chivers; Jeffrey Englin; Susan J. Frankel; Robert G. Haight; Thomas P. Holmes; Andrew M. Liebhold; Deborah G. McCullough; Betsy. Von Holle

2011-01-01

Reliable estimates of the impacts and costs of biological invasions are critical to developing credible management, trade and regulatory policies. Worldwide, forests and urban trees provide important ecosystem services as well as economic and social benefits, but are threatened by non-native insects. More than 450 non-native forest insects are established in the United...

Fitness benefits of the fruit fly Rhagoletis alternata on a non-native rose host.

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Meijer, Kim; Smit, Christian; Schilthuizen, Menno; Beukeboom, Leo W

2016-05-01

Many species have been introduced worldwide into areas outside their natural range. Often these non-native species are introduced without their natural enemies, which sometimes leads to uncontrolled population growth. It is rarely reported that an introduced species provides a new resource for a native species. The rose hips of the Japanese rose, Rosa rugosa, which has been introduced in large parts of Europe, are infested by the native monophagous tephritid fruit fly Rhagoletis alternata. We studied differences in fitness benefits between R. alternata larvae using R. rugosa as well as native Rosa species in the Netherlands. R. alternata pupae were larger and heavier when the larvae fed on rose hips of R. rugosa. Larvae feeding on R. rugosa were parasitized less frequently by parasitic wasps than were larvae feeding on native roses. The differences in parasitization are probably due to morphological differences between the native and non-native rose hips: the hypanthium of a R. rugosa hip is thicker and provides the larvae with the possibility to feed deeper into the hip, meaning that the parasitoids cannot reach them with their ovipositor and the larvae escape parasitization. Our study shows that native species switching to a novel non-native host can experience fitness benefits compared to the original native host.

Competitive effects of non-native plants are lowest in native plant communities that are most vulnerable to invasion

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J.Stephen Brewer; W. Chase Bailey

2014-01-01

Despite widespread acknowledgment that disturbance favors invasion, a hypothesis that has received little attention is whether non-native invaders have greater competitive effects on native plants in undisturbed habitats than in disturbed habitats. This hypothesis derives from the assumption that competitive interactions are more persistent in habitats that have not...

Show me the numbers: What data currently exist for non-native species in the USA?

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Crall, Alycia W.; Meyerson, Laura A.; Stohlgren, Thomas J.; Jarnevich, Catherine S.; Newman, Gregory J.; Graham, James

2006-01-01

Non-native species continue to be introduced to the United States from other countries via trade and transportation, creating a growing need for early detection and rapid response to new invaders. It is therefore increasingly important to synthesize existing data on non-native species abundance and distributions. However, no comprehensive analysis of existing data has been undertaken for non-native species, and there have been few efforts to improve collaboration. We therefore conducted a survey to determine what datasets currently exist for non-native species in the US from county, state, multi-state region, national, and global scales. We identified 319 datasets and collected metadata for 79% of these. Through this study, we provide a better understanding of extant non-native species datasets and identify data gaps (ie taxonomic, spatial, and temporal) to help guide future survey, research, and predictive modeling efforts.

COMPARISON OF ANNUAL PRODUCTION ECOLOGY OF NATIVE EELGRASS ZOSTERA MARINA AND THE NON-NATIVE DWARF EELGRASS Z. JAPONICA IN YAQUINA BAY, OREGON

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When non-native plant species invade a system they often change patterns of primary production. I evaluate the contribution of the seagrass Zostera marina and it's non-native congener Z. japonica to primary production in Yaquina Bay. Few measurements of Z. japonica production e...

Non-Native University Students' Perception of Plagiarism

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Ahmad, Ummul Khair; Mansourizadeh, Kobra; Ai, Grace Koh Ming

2012-01-01

Plagiarism is a complex issue especially among non-native students and it has received a lot of attention from researchers and scholars of academic writing. Some scholars attribute this problem to cultural perceptions and different attitudes toward texts. This study evaluates student perception of different aspects of plagiarism. A small group of…

Non-native vascular plants from Canary Islands (Spain): nomenclatural and taxonomical adjustments

OpenAIRE

Verloove, F.

2013-01-01

Se propone correcciones taxonómicas y nomenclaturales respecto a 88 taxones no nativos de la lista de plantas vasculares de las Islas Canarias (España). Non-native vascular plants from Canary Islands (Spain): nomenclatural and taxonomical adjustments. Corrections and other adjustments are proposed for 88 non-native taxa from the checklist of vascular plants from the Canary Islands (Spain).

Promoting Communities of Practice among Non-Native Speakers of English in Online Discussions

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Kim, Hoe Kyeung

2011-01-01

An online discussion involving text-based computer-mediated communication has great potential for promoting equal participation among non-native speakers of English. Several studies claimed that online discussions could enhance the academic participation of non-native speakers of English. However, there is little research around participation…

Analyzing import intermediates of mitochondrial proteins by blue native gel electrophoresis.

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Waizenegger, Thomas; Rapaport, Doron

2007-01-01

Blue native gel electrophoresis (BNGE) is a powerful tool for analyzing native protein complexes from biological membranes as well as water-soluble proteins. It can be used for determining relative molecular masses of protein complexes and their subunit composition and for the detection of subcomplexes. We describe the analysis by BNGE of in vitro import reactions composed of radiolabeled precursor proteins and isolated mitochondria. Such an analysis is a powerful tool to follow import intermediates and to study assembly of protein complexes. Analysis of import reactions by BNGE provides information on the molecular mass of the complex with which the imported precursor is associated. In addition, components of such a complex can be identified by incubating the mitochondrial lysate with either soluble antibodies or antibodies coupled to protein A matrix. The binding of soluble antibodies to specific complexes results in an observed shift in their apparent molecular mass (antibody shift). Alternatively, addition of matrix-bound antibodies followed by removal of the matrix from the mixture will result in depletion of the specific complex from the mitochondrial lysate (antibody depletion). The experimental details of these techniques are described.

A highly compliant protein native state with a spontaneous-like mechanical unfolding pathway

DEFF Research Database (Denmark)

Heiðarsson, Pétur Orri; Valpapuram, Immanuel; Camilloni, Carlo

2012-01-01

The mechanical properties of proteins and their force-induced structural changes play key roles in many biological processes. Previous studies have shown that natively folded proteins are brittle under tension, unfolding after small mechanical deformations, while partially folded intermediate...... states, such as molten globules, are compliant and can deform elastically a great amount before crossing the transition state barrier. Moreover, under tension proteins appear to unfold through a different sequence of events than during spontaneous unfolding. Here, we describe the response to force...... of the four-α-helix acyl-CoA binding protein (ACBP) in the low-force regime using optical tweezers and ratcheted molecular dynamics simulations. The results of our studies reveal an unprecedented mechanical behavior of a natively folded protein. ACBP displays an atypical compliance along two nearly orthogonal...

Development of aquatic life criteria for triclosan and comparison of the sensitivity between native and non-native species.

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Wang, Xiao-Nan; Liu, Zheng-Tao; Yan, Zhen-Guang; Zhang, Cong; Wang, Wei-Li; Zhou, Jun-Li; Pei, Shu-Wei

2013-09-15

Triclosan (TCS) is an antimicrobial agent which is used as a broad-spectrum bacteriostatic and found in personal care products, and due to this it is widely spread in the aquatic environment. However, there is no paper dealing with the aquatic life criteria of TCS, mainly result from the shortage of toxicity data of different taxonomic levels. In the present study, toxicity data were obtained from 9 acute toxicity tests and 3 chronic toxicity tests using 9 Chinese native aquatic species from different taxonomic levels, and the aquatic life criteria was derived using 3 methods. Furthermore, differences of species sensitivity distributions (SSD) between native and non-native species were compared. Among the tested species, demersal fish Misgurnus anguillicaudatus was the most sensitive species, and the fishes were more sensitive than the aquatic invertebrates of Annelid and insect, and the insect was the least sensitive species. The comparison showed that there was no significant difference between SSDs constructed from native and non-native taxa. Finally, a criterion maximum concentration of 0.009 mg/L and a criterion continuous concentration of 0.002 mg/L were developed based on different taxa, according to the U.S. Environmental Protection Agency guidelines. Copyright © 2013 Elsevier B.V. All rights reserved.

Minimal effectiveness of native and non-native seeding following three high-severity wildfire

Science.gov (United States)

Ken A. Stella; Carolyn H. Sieg; Pete Z. Fule

2010-01-01

The rationale for seeding following high-severity wildfires is to enhance plant cover and reduce bare ground, thus decreasing the potential for soil erosion and non-native plant invasion. However, experimental tests of the effectiveness of seeding in meeting these objectives in forests are lacking. We conducted three experimental studies of the effectiveness of seeding...

Locking horns with Hawai‘i’s non-native ungulate issues

Science.gov (United States)

Hess, Steve

2014-01-01

Conservation and management interests for sustained-yield hunting of non-native ungulates in Hawai‘i have conflicted with the conservation of native biota for several decades. Hawaiian ecosystems evolved in the absence of large mammals and all currently hunted animals in Hawai‘i are non-native species. The best-studied aspects of Hawai‘i’s ungulates have dealt primarily with direct negative effects on native biota in natural areas, but there has been little research in population dynamics for sustained-yield management. Ungulates have been removed from approximately 750 km2 throughout the Hawaiian Islands to protect these natural areas, thereby reducing the amount of land area available for hunting activities and the maintenance of game populations. At the same time, unauthorized introductions of additional wild ungulate species between Hawaiian Islands have recently increased in frequency. The majority of hunting activities are of feral domestic livestock species for subsistence purposes, which typically do not generate sufficient revenue to offset costs of game management. Moreover, bag limits and seasons are generally not determined from biological criteria because harvest reporting is voluntary and game populations are rarely monitored. Consequently, ungulate populations cannot be managed for any particular level of abundance or other objectives. Research and monitoring which emphasize population dynamics and productivity would enable more precisely regulated sustained-yield game management programs and may reduce potential conflicts with the conservation of native biota.

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

Science.gov (United States)

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.

Application of Native Speaker Models for Identifying Deviations in Rhetorical Moves in Non-Native Speaker Manuscripts

Directory of Open Access Journals (Sweden)

Assef Khalili

2016-06-01

Full Text Available Introduction: Explicit teaching of generic conventions of a text genre, usually extracted from native-speaker (NS manuscripts, has long been emphasized in the teaching of Academic Writing inEnglish for Specific Purposes (henceforthESP classes, both in theory and practice. While consciousness-raising about rhetorical structure can be instrumental to non-native speakers(NNS, it has to be admitted that most works done in the field of ESP have tended to focus almost exclusively on native-speaker (NS productions, giving scant attention to non-native speaker (NNS manuscripts. That is, having outlined established norms for good writing on the basis of NS productions, few have been inclined to provide a descriptive account of NNS attempts at trying to produce a research article (RA in English. That is what we have tried to do in the present research. Methods: We randomly selected 20 RAs in dentistry and used two well-established models for results and discussion sections to try to describe the move structure of these articles and show the points of divergence from the established norms. Results: The results pointed to significant divergences that could seriously compromise the quality of an RA. Conclusion: It is believed that the insights gained on the deviations in NNS manuscripts could prove very useful in designing syllabi for ESP classes.

Genome-scale metabolic model of Pichia pastoris with native and humanized glycosylation of recombinant proteins.

Science.gov (United States)

Irani, Zahra Azimzadeh; Kerkhoven, Eduard J; Shojaosadati, Seyed Abbas; Nielsen, Jens

2016-05-01

Pichia pastoris is used for commercial production of human therapeutic proteins, and genome-scale models of P. pastoris metabolism have been generated in the past to study the metabolism and associated protein production by this yeast. A major challenge with clinical usage of recombinant proteins produced by P. pastoris is the difference in N-glycosylation of proteins produced by humans and this yeast. However, through metabolic engineering, a P. pastoris strain capable of producing humanized N-glycosylated proteins was constructed. The current genome-scale models of P. pastoris do not address native nor humanized N-glycosylation, and we therefore developed ihGlycopastoris, an extension to the iLC915 model with both native and humanized N-glycosylation for recombinant protein production, but also an estimation of N-glycosylation of P. pastoris native proteins. This new model gives a better prediction of protein yield, demonstrates the effect of the different types of N-glycosylation of protein yield, and can be used to predict potential targets for strain improvement. The model represents a step towards a more complete description of protein production in P. pastoris, which is required for using these models to understand and optimize protein production processes. © 2015 Wiley Periodicals, Inc.

Can Natural Proteins Designed with ‘Inverted’ Peptide Sequences Adopt Native-Like Protein Folds?

Science.gov (United States)

Sridhar, Settu; Guruprasad, Kunchur

2014-01-01

We have carried out a systematic computational analysis on a representative dataset of proteins of known three-dimensional structure, in order to evaluate whether it would possible to ‘swap’ certain short peptide sequences in naturally occurring proteins with their corresponding ‘inverted’ peptides and generate ‘artificial’ proteins that are predicted to retain native-like protein fold. The analysis of 3,967 representative proteins from the Protein Data Bank revealed 102,677 unique identical inverted peptide sequence pairs that vary in sequence length between 5–12 and 18 amino acid residues. Our analysis illustrates with examples that such ‘artificial’ proteins may be generated by identifying peptides with ‘similar structural environment’ and by using comparative protein modeling and validation studies. Our analysis suggests that natural proteins may be tolerant to accommodating such peptides. PMID:25210740

A cDNA Immunization Strategy to Generate Nanobodies against Membrane Proteins in Native Conformation

Science.gov (United States)

Eden, Thomas; Menzel, Stephan; Wesolowski, Janusz; Bergmann, Philine; Nissen, Marion; Dubberke, Gudrun; Seyfried, Fabienne; Albrecht, Birte; Haag, Friedrich; Koch-Nolte, Friedrich

2018-01-01

Nanobodies (Nbs) are soluble, versatile, single-domain binding modules derived from the VHH variable domain of heavy-chain antibodies naturally occurring in camelids. Nbs hold huge promise as novel therapeutic biologics. Membrane proteins are among the most interesting targets for therapeutic Nbs because they are accessible to systemically injected biologics. In order to be effective, therapeutic Nbs must recognize their target membrane protein in native conformation. However, raising Nbs against membrane proteins in native conformation can pose a formidable challenge since membrane proteins typically contain one or more hydrophobic transmembrane regions and, therefore, are difficult to purify in native conformation. Here, we describe a highly efficient genetic immunization strategy that circumvents these difficulties by driving expression of the target membrane protein in native conformation by cells of the immunized camelid. The strategy encompasses ballistic transfection of skin cells with cDNA expression plasmids encoding one or more orthologs of the membrane protein of interest and, optionally, other costimulatory proteins. The plasmid is coated onto 1 µm gold particles that are then injected into the shaved and depilated skin of the camelid. A gene gun delivers a helium pulse that accelerates the DNA-coated particles to a velocity sufficient to penetrate through multiple layers of cells in the skin. This results in the exposure of the extracellular domains of the membrane protein on the cell surface of transfected cells. Repeated immunization drives somatic hypermutation and affinity maturation of target-specific heavy-chain antibodies. The VHH/Nb coding region is PCR-amplified from B cells obtained from peripheral blood or a lymph node biopsy. Specific Nbs are selected by phage display or by screening of Nb-based heavy-chain antibodies expressed as secretory proteins in transfected HEK cells. Using this strategy, we have successfully generated agonistic

Hsc66 substrate specificity is directed toward a discrete region of the iron-sulfur cluster template protein IscU.

Science.gov (United States)

Hoff, Kevin G; Ta, Dennis T; Tapley, Tim L; Silberg, Jonathan J; Vickery, Larry E

2002-07-26

Hsc66 and Hsc20 comprise a specialized chaperone system important for the assembly of iron-sulfur clusters in Escherchia coli. Only a single substrate, the Fe/S template protein IscU, has been identified for the Hsc66/Hsc20 system, but the mechanism by which Hsc66 selectively binds IscU is unknown. We have investigated Hsc66 substrate specificity using phage display and a peptide array of IscU. Screening of a heptameric peptide phage display library revealed that Hsc66 prefers peptides with a centrally located Pro-Pro motif. Using a cellulose-bound peptide array of IscU we determined that Hsc66 interacts specifically with a region (residues 99-103, LPPVK) that is invariant among all IscU family members. A synthetic peptide (ELPPVKIHC) corresponding to IscU residues 98-106 behaves in a similar manner to native IscU, stimulating the ATPase activity of Hsc66 with similar affinity as IscU, preventing Hsc66 suppression of bovine rhodanese aggregation, and interacting with the peptide-binding domain of Hsc66. Unlike native IscU, however, the synthetic peptide is not bound by Hsc20 and does not synergistically stimulate Hsc66 ATPase activity with Hsc20. Our results indicate that Hsc66 and Hsc20 recognize distinct regions of IscU and further suggest that Hsc66 will not bind LPPVK motifs with high affinity in vivo unless they are in the context of native IscU and can be directed to Hsc66 by Hsc20.

Presence and abundance of non-native plant species associated with recent energy development in the Williston Basin

Science.gov (United States)

Preston, Todd M.

2015-01-01

The Williston Basin, located in the Northern Great Plains, is experiencing rapid energy development with North Dakota and Montana being the epicenter of current and projected development in the USA. The average single-bore well pad is 5 acres with an estimated 58,485 wells in North Dakota alone. This landscape-level disturbance may provide a pathway for the establishment of non-native plants. To evaluate potential influences of energy development on the presence and abundance of non-native species, vegetation surveys were conducted at 30 oil well sites (14 ten-year-old and 16 five-year-old wells) and 14 control sites in native prairie environments across the Williston Basin. Non-native species richness and cover were recorded in four quadrats, located at equal distances, along four transects for a total of 16 quadrats per site. Non-natives were recorded at all 44 sites and ranged from 5 to 13 species, 7 to 15 species, and 2 to 8 species at the 10-year, 5-year, and control sites, respectively. Respective non-native cover ranged from 1 to 69, 16 to 76, and 2 to 82 %. Total, forb, and graminoid non-native species richness and non-native forb cover were significantly greater at oil well sites compared to control sites. At oil well sites, non-native species richness and forb cover were significantly greater adjacent to the well pads and decreased with distance to values similar to control sites. Finally, non-native species whose presence and/or abundance were significantly greater at oil well sites relative to control sites were identified to aid management efforts.

Native whey protein with high levels of leucine results in similar post-exercise muscular anabolic responses as regular whey protein: a randomized controlled trial.

Science.gov (United States)

Hamarsland, Håvard; Nordengen, Anne Lene; Nyvik Aas, Sigve; Holte, Kristin; Garthe, Ina; Paulsen, Gøran; Cotter, Matthew; Børsheim, Elisabet; Benestad, Haakon B; Raastad, Truls

2017-01-01

Protein intake is essential to maximally stimulate muscle protein synthesis, and the amino acid leucine seems to possess a superior effect on muscle protein synthesis compared to other amino acids. Native whey has higher leucine content and thus a potentially greater anabolic effect on muscle than regular whey (WPC-80). This study compared the acute anabolic effects of ingesting 2 × 20 g of native whey protein, WPC-80 or milk protein after a resistance exercise session. A total of 24 young resistance trained men and women took part in this double blind, randomized, partial crossover, controlled study. Participants received either WPC-80 and native whey ( n  = 10), in a crossover design, or milk ( n  = 12). Supplements were ingested immediately (20 g) and two hours after (20 g) a bout of heavy-load lower body resistance exercise. Blood samples and muscle biopsies were collected to measure plasma concentrations of amino acids by gas-chromatography mass spectrometry, muscle phosphorylation of p70S6K, 4E-BP1 and eEF-2 by immunoblotting, and mixed muscle protein synthesis by use of [ 2 H 5 ]phenylalanine-infusion, gas-chromatography mass spectrometry and isotope-ratio mass spectrometry. Being the main comparison, differences between native whey and WPC-80 were analysed by a one-way ANOVA and comparisons between the whey supplements and milk were analysed by a two-way ANOVA. Native whey increased blood leucine concentrations more than WPC-80 and milk ( P  whey ingestion induced a greater phosphorylation of p70S6K than milk 180 min after exercise ( P  = 0.03). Muscle protein synthesis rates increased 1-3 h hours after exercise with WPC-80 (0.119%), and 1-5 h after exercise with native whey (0.112%). Muscle protein synthesis rates were higher 1-5 h after exercise with native whey than with milk (0.112% vs. 0.064, P  = 0.023). Despite higher-magnitude increases in blood leucine concentrations with native whey, it was not superior to WPC-80

Functional NifD-K fusion protein in Azotobacter vinelandii is a homodimeric complex equivalent to the native heterotetrameric MoFe protein

International Nuclear Information System (INIS)

Lahiri, Surobhi; Pulakat, Lakshmi; Gavini, Nara

2005-01-01

The MoFe protein of the complex metalloenzyme nitrogenase folds as a heterotetramer containing two copies each of the homologous α and β subunits, encoded by the nifD and the nifK genes respectively. Recently, the functional expression of a fusion NifD-K protein of nitrogenase was demonstrated in Azotobacter vinelandii, strongly implying that the MoFe protein is flexible as it could accommodate major structural changes, yet remain functional [M.H. Suh, L. Pulakat, N. Gavini, J. Biol. Chem. 278 (2003) 5353-5360]. This finding led us to further explore the type of interaction between the fused MoFe protein units. We aimed to determine whether an interaction exists between the two fusion MoFe proteins to form a homodimer that is equivalent to native heterotetrameric MoFe protein. Using the Bacteriomatch Two-Hybrid System, translationally fused constructs of NifD-K (fusion) with the full-length λCI of the pBT bait vector and also NifD-K (fusion) with the N-terminal α-RNAP of the pTRG target vector were made. To compare the extent of interaction between the fused NifD-K proteins to that of the β-β interactions in the native MoFe protein, we proceeded to generate translationally fused constructs of NifK with the α-RNAP of the pTRG vector and λCI protein of the pBT vector. The strength of the interaction between the proteins in study was determined by measuring the β-galactosidase activity and extent of ampicillin resistance of the colonies expressing these proteins. This analysis demonstrated that direct protein-protein interaction exists between NifD-K fusion proteins, suggesting that they exist as homodimers. As the interaction takes place at the β-interfaces of the NifD-K fusion proteins, we propose that these homodimers of NifD-K fusion protein may function in a similar manner as that of the heterotetrameric native MoFe protein. The observation that the extent of protein-protein interaction between the β-subunits of the native MoFe protein in Bacterio

A proteomic approach for comprehensively screening substrates of protein kinases such as Rho-kinase.

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Mutsuki Amano

Full Text Available BACKGROUND: Protein kinases are major components of signal transduction pathways in multiple cellular processes. Kinases directly interact with and phosphorylate downstream substrates, thus modulating their functions. Despite the importance of identifying substrates in order to more fully understand the signaling network of respective kinases, efficient methods to search for substrates remain poorly explored. METHODOLOGY/PRINCIPAL FINDINGS: We combined mass spectrometry and affinity column chromatography of the catalytic domain of protein kinases to screen potential substrates. Using the active catalytic fragment of Rho-kinase/ROCK/ROK as the model bait, we obtained about 300 interacting proteins from the rat brain cytosol fraction, which included the proteins previously reported as Rho-kinase substrates. Several novel interacting proteins, including doublecortin, were phosphorylated by Rho-kinase both in vitro and in vivo. CONCLUSIONS/SIGNIFICANCE: This method would enable identification of novel specific substrates for kinases such as Rho-kinase with high sensitivity.

Folding 19 proteins to their native state and stability of large proteins from a coarse-grained model.

Science.gov (United States)

Kapoor, Abhijeet; Travesset, Alex

2014-03-01

We develop an intermediate resolution model, where the backbone is modeled with atomic resolution but the side chain with a single bead, by extending our previous model (Proteins (2013) DOI: 10.1002/prot.24269) to properly include proline, preproline residues and backbone rigidity. Starting from random configurations, the model properly folds 19 proteins (including a mutant 2A3D sequence) into native states containing β sheet, α helix, and mixed α/β. As a further test, the stability of H-RAS (a 169 residue protein, critical in many signaling pathways) is investigated: The protein is stable, with excellent agreement with experimental B-factors. Despite that proteins containing only α helices fold to their native state at lower backbone rigidity, and other limitations, which we discuss thoroughly, the model provides a reliable description of the dynamics as compared with all atom simulations, but does not constrain secondary structures as it is typically the case in more coarse-grained models. Further implications are described. Copyright © 2013 Wiley Periodicals, Inc.

Substrate-Bound Protein Gradients to Study Haptotaxis

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Sebastien G. Ricoult

2015-03-01

Full Text Available Cells navigate in response to inhomogeneous distributions of extracellular guidance cues. The cellular and molecular mechanisms underlying migration in response to gradients of chemical cues have been investigated for over a century. Following the introduction of micropipettes and more recently microfluidics for gradient generation, much attention and effort was devoted to study cellular chemotaxis, which is defined as guidance by gradients of chemical cues in solution. Haptotaxis, directional migration in response to gradients of substrate-bound cues, has received comparatively less attention; however it is increasingly clear that in vivo many physiologically relevant guidance proteins – including many secreted cues – are bound to cellular surfaces or incorporated into extracellular matrix and likely function via a haptotactic mechanism. Here, we review the history of haptotaxis. We examine the importance of the reference surface, the surface in contact with the cell that is not covered by the cue, which forms a gradient opposing the gradient of the protein cue and must be considered in experimental designs and interpretation of results. We review and compare microfluidics, contact-printing, light patterning and 3D fabrication to pattern substrate-bound protein gradients in vitro, and focus on their application to study axon guidance. The range of methods to create substrate-bound gradients discussed herein make possible systematic analyses of haptotactic mechanisms. Furthermore, understanding the fundamental mechanisms underlying cell motility will inform bioengineering approaches to program cell navigation and recover lost function.

Unpacking Race, Culture, and Class in Rural Alaska: Native and Non-Native Multidisciplinary Professionals' Perceptions of Child Sexual Abuse

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Bubar, Roe; Bundy-Fazioli, Kimberly

2011-01-01

The purpose of this study was to unpack notions of class, culture, and race as they relate to multidisciplinary team (MDT) professionals and their perceptions of prevalence in child sexual abuse cases in Native and non-Native rural Alaska communities. Power and privilege within professional settings is significant for all social work professionals…

Non-Native English Speakers and Nonstandard English: An In-Depth Investigation

Science.gov (United States)

Polat, Brittany

2012-01-01

Given the rising prominence of nonstandard varieties of English around the world (Jenkins 2007), learners of English as a second language are increasingly called on to communicate with speakers of both native and non-native nonstandard English varieties. In many classrooms around the world, however, learners continue to be exposed only to…

Structure based protein engineering of Bacillus stearothermophilus {alpha}-amylase: toward a new substrate specificity

Energy Technology Data Exchange (ETDEWEB)

Rasera, Ana Claudia [Sao Paulo Univ., SP (Brazil). Inst. de Ciencias Biomedicas; Iulek, Jorge [Universidade Estadual de Ponta Grossa, PR (Brazil). Inst. de Quimica; Delboni, Luis Fernando; Barbosa, Valma Martins Barbosa [Parana Univ., Curitiba, PR (Brazil). Dept. de Bioquimica

1997-12-31

Full text. Structural similarity is observed in all members of {alpha}-amylase family but different products are generated during hydrolysis of starch due to different affinities for intermediate dextrins. In order to understand the structural determinants for this property and to introduce different specificity to {alpha}-amylase of Bacillus stearothermophilus we intend to solve the three dimensional structure by X-ray crystallography of the native protein by using synchrotron radiation at Brazilian National Synchrotron Light Laboratory (LNLS). Protein was over expressed in E. coli, purified and crystallization experiments were carried out by using sparse matrix Crystal Screen and Crystal Screen II from Hampton Research (Laguna Hills, CA, USA). Several condition have produced crystals with some defined characteristic: MDP seems to be important to the crystallization: the preferential pH is around 7.5 with organic buffer (HEPES); organic solvent as 2-propanol seems to be also important for the crystallization. On those condition crystals appeared as cluster of needles or small crystals with high number of nucleation. New conditions are being prepared to improve the site and quality of crystals. Data collection of native of Bacillus stearothermophilus {alpha}-amylase will e done at Protein Crystallography Station at LNLS. Crystal structure of mutated {alpha}-amylase bu site direct mutagenesis of residues suggested by the native crystal structure will be obtained. Co-crystallization of Bacillus stearothermophilus {alpha}-amylase and oligosaccharide will be carried out to identify residues involved in the binding site to plan new mutation. In another series of mutation the putative binding site residues, once identified, will be mutated to residues observed in TAKA amylase to confer different specificity to {alpha}-amylase. Based on the available TAKA amylase structure, in the primary sequence homology and in the three dimensional model of Bacillus stearothermophilus

Structure based protein engineering of Bacillus stearothermophilus α-amylase: toward a new substrate specificity

International Nuclear Information System (INIS)

Rasera, Ana Claudia; Iulek, Jorge; Delboni, Luis Fernando; Barbosa, Valma Martins Barbosa

1997-01-01

Full text. Structural similarity is observed in all members of α-amylase family but different products are generated during hydrolysis of starch due to different affinities for intermediate dextrins. In order to understand the structural determinants for this property and to introduce different specificity to α-amylase of Bacillus stearothermophilus we intend to solve the three dimensional structure by X-ray crystallography of the native protein by using synchrotron radiation at Brazilian National Synchrotron Light Laboratory (LNLS). Protein was over expressed in E. coli, purified and crystallization experiments were carried out by using sparse matrix Crystal Screen and Crystal Screen II from Hampton Research (Laguna Hills, CA, USA). Several condition have produced crystals with some defined characteristic: MDP seems to be important to the crystallization: the preferential pH is around 7.5 with organic buffer (HEPES); organic solvent as 2-propanol seems to be also important for the crystallization. On those condition crystals appeared as cluster of needles or small crystals with high number of nucleation. New conditions are being prepared to improve the site and quality of crystals. Data collection of native of Bacillus stearothermophilus α-amylase will e done at Protein Crystallography Station at LNLS. Crystal structure of mutated α-amylase bu site direct mutagenesis of residues suggested by the native crystal structure will be obtained. Co-crystallization of Bacillus stearothermophilus α-amylase and oligosaccharide will be carried out to identify residues involved in the binding site to plan new mutation. In another series of mutation the putative binding site residues, once identified, will be mutated to residues observed in TAKA amylase to confer different specificity to α-amylase. Based on the available TAKA amylase structure, in the primary sequence homology and in the three dimensional model of Bacillus stearothermophilus α-amylase (using Bacillus

Prey utilisation and trophic overlap between the non native mosquitofish and a native fish in two Mediterranean rivers

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E. KALOGIANNI

2014-04-01

Full Text Available Non native freshwater fish species have been long implicated in the decline of native Mediterranean ichthyofauna, through hybridization, disease transmission, competition for food and habitat, predation and/or ecosystem alteration; our knowledge, however, on the underlying mechanisms of these ecological impacts remains very limited. To explore the potential for trophic competition between the widespread Eastern mosquitofish Gambusia holbrooki and its co-occurring native toothcarp Valencia letourneuxi we compared resource use, feeding strategies, trophic selectivities and diet niche overlap. For this purpose, we studied two populations of the two species from a freshwater and a brackish habitat respectively, characterized by different food resource availabilities. In both habitats, the mosquitofish consumed a greater diversity of invertebrates and preyed on terrestrial invertebrates more frequently than the native toothcarp. Furthermore, in the less diverse and less rich brackish habitat, the non native relied heavily on plant material to balance a decrease in animal prey consumption and modified its individual feeding strategy, whereas these adaptive changes were not apparent in the native species. Their diet overlapped, indicating trophic competition, but this overlap was affected by resource availability variation; in the freshwater habitat, there was limited overlap in their diet, whereas in the brackish habitat, their diets and prey selectivities converged and there was high overlap in resource use, indicative of intense interspecific trophic competition. Overall, it appears that the underlying mechanism of the putative negative impacts of the mosquitofish on the declining Corfu toothcarp is mainly trophic competition, regulated by resource variability, though there is also evidence of larvae predation by the mosquitofish.

Multistage unfolding of an SH3 domain: an initial urea-filled dry molten globule precedes a wet molten globule with non-native structure.

Science.gov (United States)

Dasgupta, Amrita; Udgaonkar, Jayant B; Das, Payel

2014-06-19

The unfolding of the SH3 domain of the PI3 kinase in aqueous urea has been studied using a synergistic experiment-simulation approach. The experimental observation of a transient wet molten globule intermediate, IU, with an unusual non-native burial of the sole Trp residue, W53, provides the benchmark for the unfolding simulations performed (eight in total, each at least 0.5 μs long). The simulations reveal that the partially unfolded IU ensemble is preceded by an early native-like molten globule intermediate ensemble I*. In the very initial stage of unfolding, dry globule conformations with the protein core filled with urea instead of water are transiently observed within the I* ensemble. Water penetration into the urea-filled core of dry globule conformations is frequently accompanied by very transient burial of W53. Later during gradual unfolding, W53 is seen to again become transiently buried in the IU ensemble for a much longer time. In the structurally heterogeneous IU ensemble, conformational flexibility of the C-terminal β-strands enables W53 burial by the formation of non-native, tertiary contacts with hydrophobic residues, which could serve to protect the protein from aggregation during unfolding.

Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes.

Science.gov (United States)

Lu, Jonathan; Trnka, Michael J; Roh, Soung-Hun; Robinson, Philip J J; Shiau, Carrie; Fujimori, Danica Galonic; Chiu, Wah; Burlingame, Alma L; Guan, Shenheng

2015-12-01

Native electrospray-ionization mass spectrometry (native MS) measures biomolecules under conditions that preserve most aspects of protein tertiary and quaternary structure, enabling direct characterization of large intact protein assemblies. However, native spectra derived from these assemblies are often partially obscured by low signal-to-noise as well as broad peak shapes because of residual solvation and adduction after the electrospray process. The wide peak widths together with the fact that sequential charge state series from highly charged ions are closely spaced means that native spectra containing multiple species often suffer from high degrees of peak overlap or else contain highly interleaved charge envelopes. This situation presents a challenge for peak detection, correct charge state and charge envelope assignment, and ultimately extraction of the relevant underlying mass values of the noncovalent assemblages being investigated. In this report, we describe a comprehensive algorithm developed for addressing peak detection, peak overlap, and charge state assignment in native mass spectra, called PeakSeeker. Overlapped peaks are detected by examination of the second derivative of the raw mass spectrum. Charge state distributions of the molecular species are determined by fitting linear combinations of charge envelopes to the overall experimental mass spectrum. This software is capable of deconvoluting heterogeneous, complex, and noisy native mass spectra of large protein assemblies as demonstrated by analysis of (1) synthetic mononucleosomes containing severely overlapping peaks, (2) an RNA polymerase II/α-amanitin complex with many closely interleaved ion signals, and (3) human TriC complex containing high levels of background noise. Graphical Abstract ᅟ.

Supplementing with non-glycoside hydrolase proteins enhances enzymatic deconstruction of plant biomass.

Science.gov (United States)

Su, Xiaoyun; Zhang, Jing; Mackie, Roderick I; Cann, Isaac K O

2012-01-01

The glycoside hydrolases (GH) of Caldicellulosiruptor bescii are thermophilic enzymes, and therefore they can hydrolyze plant cell wall polysaccharides at high temperatures. Analyses of two C. bescii glycoside hydrolases, CbCelA-TM1 and CbXyn10A with cellulase and endoxylanase activity, respectively, demonstrated that each enzyme is highly thermostable under static incubation at 70°C. Both enzymes, however, rapidly lost their enzymatic activities when incubated at 70°C with end-over-end shaking. Since crowding conditions, even at low protein concentrations, seem to influence enzymatic properties, three non-glycoside hydrolase proteins were tested for their capacity to stabilize the thermophilic proteins at high temperatures. The three proteins investigated were a small heat shock protein CbHsp18 from C. bescii, a histone MkHistone1 from Methanopyrus kandleri, and bovine RNase A, from a commercial source. Fascinatingly, each of these proteins increased the thermostability of the glycoside hydrolases at 70°C during end-over-end shaking incubation, and this property translated into increases in hydrolysis of several substrates including the bioenergy feedstock Miscanthus. Furthermore, MkHistone1 and RNase A also altered the initial products released from the cello-oligosaccharide cellopentaose during hydrolysis with the cellodextrinase CbCdx1A, which further demonstrated the capacity of the three non-GH proteins to influence hydrolysis of substrates by the thermophilic glycoside hydrolases. The non-GH proteins used in the present report were small proteins derived from each of the three lineages of life, and therefore expand the space from which different polypeptides can be tested for their influence on plant cell wall hydrolysis, a critical step in the emerging biofuel industry.

Supplementing with non-glycoside hydrolase proteins enhances enzymatic deconstruction of plant biomass.

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Xiaoyun Su

Full Text Available The glycoside hydrolases (GH of Caldicellulosiruptor bescii are thermophilic enzymes, and therefore they can hydrolyze plant cell wall polysaccharides at high temperatures. Analyses of two C. bescii glycoside hydrolases, CbCelA-TM1 and CbXyn10A with cellulase and endoxylanase activity, respectively, demonstrated that each enzyme is highly thermostable under static incubation at 70°C. Both enzymes, however, rapidly lost their enzymatic activities when incubated at 70°C with end-over-end shaking. Since crowding conditions, even at low protein concentrations, seem to influence enzymatic properties, three non-glycoside hydrolase proteins were tested for their capacity to stabilize the thermophilic proteins at high temperatures. The three proteins investigated were a small heat shock protein CbHsp18 from C. bescii, a histone MkHistone1 from Methanopyrus kandleri, and bovine RNase A, from a commercial source. Fascinatingly, each of these proteins increased the thermostability of the glycoside hydrolases at 70°C during end-over-end shaking incubation, and this property translated into increases in hydrolysis of several substrates including the bioenergy feedstock Miscanthus. Furthermore, MkHistone1 and RNase A also altered the initial products released from the cello-oligosaccharide cellopentaose during hydrolysis with the cellodextrinase CbCdx1A, which further demonstrated the capacity of the three non-GH proteins to influence hydrolysis of substrates by the thermophilic glycoside hydrolases. The non-GH proteins used in the present report were small proteins derived from each of the three lineages of life, and therefore expand the space from which different polypeptides can be tested for their influence on plant cell wall hydrolysis, a critical step in the emerging biofuel industry.

Cross-modal Association between Auditory and Visuospatial Information in Mandarin Tone Perception in Noise by Native and Non-native Perceivers

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Beverly Hannah

2017-12-01

Full Text Available Speech perception involves multiple input modalities. Research has indicated that perceivers establish cross-modal associations between auditory and visuospatial events to aid perception. Such intermodal relations can be particularly beneficial for speech development and learning, where infants and non-native perceivers need additional resources to acquire and process new sounds. This study examines how facial articulatory cues and co-speech hand gestures mimicking pitch contours in space affect non-native Mandarin tone perception. Native English as well as Mandarin perceivers identified tones embedded in noise with either congruent or incongruent Auditory-Facial (AF and Auditory-FacialGestural (AFG inputs. Native Mandarin results showed the expected ceiling-level performance in the congruent AF and AFG conditions. In the incongruent conditions, while AF identification was primarily auditory-based, AFG identification was partially based on gestures, demonstrating the use of gestures as valid cues in tone identification. The English perceivers’ performance was poor in the congruent AF condition, but improved significantly in AFG. While the incongruent AF identification showed some reliance on facial information, incongruent AFG identification relied more on gestural than auditory-facial information. These results indicate positive effects of facial and especially gestural input on non-native tone perception, suggesting that cross-modal (visuospatial resources can be recruited to aid auditory perception when phonetic demands are high. The current findings may inform patterns of tone acquisition and development, suggesting how multi-modal speech enhancement principles may be applied to facilitate speech learning.

A chemical genetic approach to engineer phototropin kinases for substrate labeling.

Science.gov (United States)

Schnabel, Jonathan; Hombach, Peter; Waksman, Thomas; Giuriani, Giovanni; Petersen, Jan; Christie, John M

2018-04-13

Protein kinases (PKs) control many aspects of plant physiology by regulating signaling networks through protein phosphorylation. Phototropins (phots) are plasma membrane-associated serine/threonine PKs that control a range of physiological processes that collectively serve to optimize photosynthetic efficiency in plants. These include phototropism, leaf positioning and flattening, chloroplast movement, and stomatal opening. Despite their identification over two decades ago, only a handful of substrates have been identified for these PKs. Progress in this area has been hampered by the lack of a convenient means to confirm the identity of potential substrate candidates. Here we demonstrate that the kinase domain of Arabidopsis phot1 and phot2 can be successfully engineered to accommodate non-natural ATP analogues by substituting the bulky gatekeeper residue threonine for glycine. This approach circumvents the need for radioactivity to track phot kinase activity and follow light-induced receptor autophosphorylation in vitro by incorporating thiophosphate from N 6 -benzyl-ATPγS. Consequently, thiophosphorylation of phot substrate candidates can be readily monitored when added or co-expressed with phots in vitro Furthermore, gatekeeper-modified phot1 retained its functionality and its ability to accommodate N 6 -benzyl-ATPγS as a phosphodonor when expressed in Arabidopsis We therefore anticipate that this chemical genetic approach will provide new opportunities for labeling and identifying substrates for phots and other related AGC kinases under in vitro and near-native in vivo conditions. © 2018 Schnabel et al.

Non-Native (Exotic) Snake Envenomations in the U.S., 2005–2011

OpenAIRE

Warrick, Brandon J.; Boyer, Leslie V.; Seifert, Steven A.

2014-01-01

Non-native (exotic) snakes are a problematic source of envenomation worldwide. This manuscript describes the current demographics, outcomes and challenges of non-native snakebites in the United States (U.S.). We performed a retrospective case series of the National Poison Data System (NPDS) database between 2005 and 2011. There were 258 human exposures involving at least 61 unique exotic venomous species (average = 37 per year; range = 33–40). Males comprised 79% and females 21%. The averag...

Can a native rodent species limit the invasive potential of a non-native rodent species in tropical agroforest habitats?

Science.gov (United States)

Stuart, Alexander M; Prescott, Colin V; Singleton, Grant R

2016-06-01

Little is known about native and non-native rodent species interactions in complex tropical agroecosystems. We hypothesised that the native non-pest rodent Rattus everetti may be competitively dominant over the invasive pest rodent Rattus tanezumi within agroforests. We tested this experimentally by using pulse removal for three consecutive months to reduce populations of R. everetti in agroforest habitat, and assessed over 6 months the response of R. tanezumi and other rodent species. Following removal, R. everetti individuals rapidly immigrated into removal sites. At the end of the study period, R. tanezumi were larger and there was a significant shift in their microhabitat use with respect to the use of ground vegetation cover following the perturbation of R. everetti. Irrespective of treatment, R. tanezumi selected microhabitat with less tree canopy cover, indicative of severely disturbed habitat, whereas R. everetti selected microhabitat with a dense canopy. Our results suggest that sustained habitat disturbance in agroforests favours R. tanezumi, while the regeneration of agroforests towards a more natural state would favour native species and may reduce pest pressure in adjacent crops. In addition, the rapid recolonisation of R. everetti suggests this species would be able to recover from non-target impacts of short-term rodent pest control. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

Aggregation of natively folded proteins: a theoretical approach

International Nuclear Information System (INIS)

Trovato, Antonio; Maritan, Amos; Seno, Flavio

2007-01-01

The reliable identification of β-aggregating stretches in protein sequences is essential for the development of therapeutic agents for Alzheimer's and Parkinson's diseases, as well as other pathological conditions associated with protein deposition. While the list of aggregation related diseases is growing, it has also been shown that many proteins that are normally well behaved can be induced to aggregate in vitro. This fact suggests the existence of a unified framework that could explain both folding and aggregation. By assuming this universal behaviour, we have recently introduced an algorithm (PASTA: prediction of amyloid structure aggregation), which is based on a sequence-specific energy function derived from the propensity of two residue types to be found paired in neighbouring strands within β-sheets in globular proteins. The algorithm is able to predict the most aggregation-prone portions of several proteins initially unfolded, in excellent agreement with experimental results. Here, we apply the method to a set of proteins which are known to aggregate, but which are natively folded. The quality of the prediction is again very high, corroborating the hypothesis that the amyloid structure is stabilized by the same physico-chemical determinants as those operating in folded proteins

Effects of the Differences between Native and Non-Native English-Speaking Teachers on Students' Attitudes and Motivation toward Learning English

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Pae, Tae-Il

2017-01-01

This study presents findings on three research agendas: (1) the difference between native English-speaking teachers (NESTs) and non-native English-speaking teachers (NNESTs) in students' attitudes toward and motivation for learning English, (2) the moderating effect of the type of class (i.e., English Conversation vs. Practical English) on the…

A cDNA Immunization Strategy to Generate Nanobodies against Membrane Proteins in Native Conformation

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Thomas Eden

2018-01-01

Full Text Available Nanobodies (Nbs are soluble, versatile, single-domain binding modules derived from the VHH variable domain of heavy-chain antibodies naturally occurring in camelids. Nbs hold huge promise as novel therapeutic biologics. Membrane proteins are among the most interesting targets for therapeutic Nbs because they are accessible to systemically injected biologics. In order to be effective, therapeutic Nbs must recognize their target membrane protein in native conformation. However, raising Nbs against membrane proteins in native conformation can pose a formidable challenge since membrane proteins typically contain one or more hydrophobic transmembrane regions and, therefore, are difficult to purify in native conformation. Here, we describe a highly efficient genetic immunization strategy that circumvents these difficulties by driving expression of the target membrane protein in native conformation by cells of the immunized camelid. The strategy encompasses ballistic transfection of skin cells with cDNA expression plasmids encoding one or more orthologs of the membrane protein of interest and, optionally, other costimulatory proteins. The plasmid is coated onto 1 µm gold particles that are then injected into the shaved and depilated skin of the camelid. A gene gun delivers a helium pulse that accelerates the DNA-coated particles to a velocity sufficient to penetrate through multiple layers of cells in the skin. This results in the exposure of the extracellular domains of the membrane protein on the cell surface of transfected cells. Repeated immunization drives somatic hypermutation and affinity maturation of target-specific heavy-chain antibodies. The VHH/Nb coding region is PCR-amplified from B cells obtained from peripheral blood or a lymph node biopsy. Specific Nbs are selected by phage display or by screening of Nb-based heavy-chain antibodies expressed as secretory proteins in transfected HEK cells. Using this strategy, we have successfully

What determines the structures of native folds of proteins?

International Nuclear Information System (INIS)

Trovato, Antonio; Hoang, Trinh X; Banavar, Jayanth R; Maritan, Amos; Seno, Flavio

2005-01-01

We review a simple physical model (Hoang et al 2004 Proc. Natl Acad. Sci. USA 101 7960, Banavar et al 2004 Phys. Rev. E at press) which captures the essential physico-chemical ingredients that determine protein structure, such as the inherent anisotropy of a chain molecule, the geometrical and energetic constraints placed by hydrogen bonds, sterics, and hydrophobicity. Within this framework, marginally compact conformations resembling the native state folds of proteins emerge as competing minima in the free energy landscape. Here we demonstrate that a hydrophobic-polar (HP) sequence composed of regularly repeated patterns has as its ground state a β-helical structure remarkably similar to a known architecture in the Protein Data Bank

Serum biochemistry and native protein electrophoresis in diarrheic calves with arthritis

Directory of Open Access Journals (Sweden)

Pekcan M.

2012-01-01

Full Text Available In this study, serum biochemistry and native protein electrophoresis in newborn calves with diarrhea and arthritis, were performed in order to evaluate the changes along with clinical findings for their possible application in the diagnosis and prognosis of disease. Based on clinical examination, animals were allotied into two groups comprising either diseased or healthy animals. Urea, creatinine, ALT, AST, LDH, albumin, total protein, glucose, total cholesterol, uric acid and iron levels were determined in the sera. Serum protein native polyacrilamide gel electrophoresis (nPAGE was performed followed by protein band ratio estimation supported with densitometry at 596 nm. Differences between the average mean of healthy and diseased animals were compared statistically (Kruskal-Walley test. In this study a decrease in serum glucose and cholesterol values (p<0.001, increase in urea, LDH levels and α1-and α2-globulin levels (p<0.01 and p<0.05 respectively were found to be associated with the disease. As a result, the observed significant changes in biochemical parameters and clinical investigation in calves, suggesting acute inflammation causing the decrease in glucose and increase in α-globulins, may be of prognostic value.

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

Science.gov (United States)

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.

Protein design and engineering of a de novo pathway for microbial production of 1,3-propanediol from glucose.

Science.gov (United States)

Chen, Zhen; Geng, Feng; Zeng, An-Ping

2015-02-01

Protein engineering to expand the substrate spectrum of native enzymes opens new possibilities for bioproduction of valuable chemicals from non-natural pathways. No natural microorganism can directly use sugars to produce 1,3-propanediol (PDO). Here, we present a de novo route for the biosynthesis of PDO from sugar, which may overcome the mentioned limitations by expanding the homoserine synthesis pathway. The accomplishment of pathway from homoserine to PDO is achieved by protein engineering of glutamate dehydrogenase (GDH) and pyruvate decarboxylase to sequentially convert homoserine to 4-hydroxy-2-ketobutyrate and 3-hydroxypropionaldehyde. The latter is finally converted to PDO by using a native alcohol dehydrogenase. In this work, we report on experimental accomplishment of this non-natural pathway, especially by protein engineering of GDH for the key step of converting homoserine to 4-hydroxy-2-ketobutyrate. These results show the feasibility and significance of protein engineering for de novo pathway design and overproduction of desired industrial products. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

During Threaded Discussions Are Non-Native English Speakers Always at a Disadvantage?

Science.gov (United States)

Shafer Willner, Lynn

2014-01-01

When participating in threaded discussions, under what conditions might non¬native speakers of English (NNSE) be at a comparative disadvantage to their classmates who are native speakers of English (NSE)? This study compares the threaded discussion perspectives of closely-matched NNSE and NSE adult students having different levels of threaded…

A non-native prey mediates the effects of a shared predator on an ecosystem service.

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James E Byers

Full Text Available Non-native species can alter ecosystem functions performed by native species often by displacing influential native species. However, little is known about how ecosystem functions may be modified by trait-mediated indirect effects of non-native species. Oysters and other reef-associated filter feeders enhance water quality by controlling nutrients and contaminants in many estuarine environments. However, this ecosystem service may be mitigated by predation, competition, or other species interactions, especially when such interactions involve non-native species that share little evolutionary history. We assessed trophic and other interference effects on the critical ecosystem service of water filtration in mesocosm experiments. In single-species trials, typical field densities of oysters (Crassostrea virginica reduced water-column chlorophyll a more strongly than clams (Mercenaria mercenaria. The non-native filter-feeding reef crab Petrolisthes armatus did not draw down chlorophyll a. In multi-species treatments, oysters and clams combined additively to influence chlorophyll a drawdown. Petrolisthes did not affect net filtration when added to the bivalve-only treatments. Addition of the predatory mud crab Panopeus herbstii did not influence oyster feeding rates, but it did stop chlorophyll a drawdown by clams. However, when Petrolisthes was also added in with the clams, the clams filtered at their previously unadulterated rates, possibly because Petrolisthes drew the focus of predators or habituated the clams to crab stimuli. In sum, oysters were the most influential filter feeder, and neither predators nor competitors interfered with their net effect on water-column chlorophyll. In contrast, clams filtered less, but were more sensitive to predators as well as a facilitative buffering effect of Petrolisthes, illustrating that non-native species can indirectly affect an ecosystem service by aiding the performance of a native species.

Miniaturized protein separation using a liquid chromatography column on a flexible substrate

International Nuclear Information System (INIS)

Yang Yongmo; Chae, Junseok

2008-01-01

We report a prototype protein separator that successfully miniaturizes existing technology for potential use in biocompatible health monitoring implants. The prototype is a liquid chromatography (LC) column (LC mini-column) fabricated on an inexpensive, flexible, biocompatible polydimethylsiloxane (PDMS) enclosure. The LC mini-column separates a mixture of proteins using size exclusion chromatography (SEC) with polydivinylbenzene beads (5–20 µm in diameter with 10 nm pore size). The LC mini-column is smaller than any commercially available LC column by a factor of ∼11 000 and successfully separates denatured and native protein mixtures at ∼71 psi of the applied fluidic pressure. Separated proteins are analyzed using NuPAGE-gel electrophoresis, high-performance liquid chromatography (HPLC) and an automated electrophoresis system. Quantitative HPLC results demonstrate successful separation based on intensity change: within 12 min, the intensity between large and small protein peaks changed by a factor of ∼20. In further evaluation using the automated electrophoresis system, the plate height of the LC mini-column is between 36 µm and 100 µm. The prototype LC mini-column shows the potential for real-time health monitoring in applications that require inexpensive, flexible implant technology that can function effectively under non-laboratory conditions

Making the Transition from Non-Native Speaker to Near-Native Speaker Teachers of English: Facing Globalization Challenges in Teaching English

Science.gov (United States)

Bin Mohamed Ali, Haja Mohideen

2009-01-01

Many job advertisements seeking teachers of English to work in Japan, China, South Korea and Thailand, for instance, specify that they are looking for native speaking teachers from USA, UK, Australia and New Zealand. They do not seem to be interested even in trained non-native speaking teachers from their own countries. This situation also exists…

Using Audiovisual TV Interviews to Create Visible Authors that Reduce the Learning Gap between Native and Non-Native Language Speakers

Science.gov (United States)

Inglese, Terry; Mayer, Richard E.; Rigotti, Francesca

2007-01-01

Can archives of audiovisual TV interviews be used to make authors more visible to students, and thereby reduce the learning gap between native and non-native language speakers in college classes? We examined students in a college course who learned about one scholar's ideas through watching an audiovisual TV interview (i.e., visible author format)…

Electrophoretic mobility shift in native gels indicates calcium-dependent structural changes of neuronal calcium sensor proteins.

Science.gov (United States)

Viviano, Jeffrey; Krishnan, Anuradha; Wu, Hao; Venkataraman, Venkat

2016-02-01

In proteins of the neuronal calcium sensor (NCS) family, changes in structure as well as function are brought about by the binding of calcium. In this article, we demonstrate that these structural changes, solely due to calcium binding, can be assessed through electrophoresis in native gels. The results demonstrate that the NCS proteins undergo ligand-dependent conformational changes that are detectable in native gels as a gradual decrease in mobility with increasing calcium but not other tested divalent cations such as magnesium, strontium, and barium. Surprisingly, such a gradual change over the entire tested range is exhibited only by the NCS proteins but not by other tested calcium-binding proteins such as calmodulin and S100B, indicating that the change in mobility may be linked to a unique NCS family feature--the calcium-myristoyl switch. Even within the NCS family, the changes in mobility are characteristic of the protein, indicating that the technique is sensitive to the individual features of the protein. Thus, electrophoretic mobility on native gels provides a simple and elegant method to investigate calcium (small ligand)-induced structural changes at least in the superfamily of NCS proteins. Copyright © 2015 Elsevier Inc. All rights reserved.

Residue-specific description of non-native transient structures in the ensemble of acid-denatured structures of the all-beta protein c-src SH3

DEFF Research Database (Denmark)

Rösner, Heike I; Poulsen, Flemming Martin

2010-01-01

-src loop to the third beta-strand, exhibited an apparent helicity of nearly 45%. Furthermore, the RT loop and the diverging turn appeared to adopt non-native-like helical conformations. Interestingly, none of the residues found in transient helical conformations exhibited significant varphi-values [Riddle......Secondary chemical shift analysis has been used to characterize the unfolded state of acid-denatured c-src SH3. Even though native c-src SH3 adopts an all-beta fold, we found evidence of transient helicity in regions corresponding to native loops. In particular, residues 40-46, connecting the n...

Evidence of native α-synuclein conformers in the human brain.

Science.gov (United States)

Gould, Neal; Mor, Danielle E; Lightfoot, Richard; Malkus, Kristen; Giasson, Benoit; Ischiropoulos, Harry

2014-03-14

α-Synuclein aggregation is central to the pathogenesis of several brain disorders. However, the native conformations and functions of this protein in the human brain are not precisely known. The native state of α-synuclein was probed by gel filtration coupled with native gradient gel separation, an array of antibodies with non-overlapping epitopes, and mass spectrometry. The existence of metastable conformers and stable monomer was revealed in the human brain.

Why Not Non-Native Varieties of English as Listening Comprehension Test Input?

Science.gov (United States)

Abeywickrama, Priyanvada

2013-01-01

The existence of different varieties of English in target language use (TLU) domains calls into question the usefulness of listening comprehension tests whose input is limited only to a native speaker variety. This study investigated the impact of non-native varieties or accented English speech on test takers from three different English use…

The Role of Conformational Flexibility on Protein Supercharging in Native Electrospray Ionization

Science.gov (United States)

Sterling, Harry J.; Cassou, Catherine A.; Trnka, Michael J.; Burlingame, A. L.; Krantz, Bryan A.; Williams, Evan R.

2012-01-01

Effects of covalent intramolecular bonds, either native disulfide bridges or chemical crosslinks, on ESI supercharging of proteins from aqueous solutions were investigated. Chemically modifying cytochrome c with up to seven crosslinks or ubiquitin with up to two crosslinks did not affect the average or maximum charge states of these proteins in the absence of m-nitrobenzyl alcohol (m-NBA), but the extent of supercharging induced by m-NBA increased with decreasing numbers of crosslinks. For the model random coil polypeptide reduced/alkylated RNase A, a decrease in charging with increasing m-NBA concentration attributable to reduced surface tension of the ESI droplet was observed, whereas native RNase A electrosprayed from these same solutions exhibited enhanced charging. The inverse relationship between the extent of supercharging and the number of intramolecular crosslinks for folded proteins, as well as the absence of supercharging for proteins that are random coils in aqueous solution, indicate that conformational restrictions induced by the crosslinks reduce the extent of supercharging. These results provide additional evidence that protein and protein complex supercharging from aqueous solution is primarily due to partial or significant unfolding that occurs as a result of chemical and/or thermal denaturation induced by the supercharging reagent late in the ESI droplet lifetime. PMID:21399817

Is 30 years enough time to niche segregation between a non-native and a native congeneric fish species? Evidences from stable isotopes

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Gustavo Henrique Zaia Alves

2015-12-01

Full Text Available The invasion of non-native species that are phylogenetically similar to native species was observed in the Upper Paraná River following the construction of the Itaipu hydroelectric plant and subsequent removal of a natural geographic barrier (Sete Quedas Falls. Endemic fish species from the Lower Paraná River, such as the piranha Serrasalmus marginatus, successfully colonized the new environment. A few years later, S. marginatus had become the dominant species, while the prevalence of the congeneric species, Serrasalmus maculatus, had declined. Considering that the two piranha species naturally coexist in the Pantanal and that S. marginatus is a non-native species in the Upper Paraná River floodplain, we hypothesized that trophic niche overlap between Serrasalmus species only occurred in the Upper Paraná River floodplain due to short-term co-existence. The study area in which the isotopic niche overlap between S. maculatus and S. marginatus was evaluated consisted of two ponds located in different floodplains, the Pantanal and the Upper Paraná River. We used carbon and nitrogen stable isotope analysis to elucidate the differences in the energy intake by the native and non-native species. We used mixing models and calculated the isotopic niche area and niche overlap to infer the nature of the trophic interactions between the species in both habitats. According to the mixing model, the predominant source of carbon for both species was terrestrial. Nevertheless, in Upper Paraná River, the δ13C signature of the two species differed significantly and the non-native species had a greater niche width than the native species. In the Pantanal, there were no differences in δ13C, but the species differed with respect to δ 15N, and the niche widths were narrow for both species.Based on these results, it can be inferred that the species depend on different food sources. Piranhas obtain energy from distinct prey species, which probably consume

Impact of non-native terrestrial mammals on the structure of the terrestrial mammal food web of Newfoundland, Canada.

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Justin S Strong

Full Text Available The island of Newfoundland is unique because it has as many non-native terrestrial mammals as native ones. The impacts of non-native species on native flora and fauna can be profound and invasive species have been identified as one of the primary drivers of species extinction. Few studies, however, have investigated the effects of a non-native species assemblage on community and ecosystem properties. We reviewed the literature to build the first terrestrial mammal food web for the island of Newfoundland and then used network analyses to investigate how the timing of introductions and trophic position of non-native species has affected the structure of the terrestrial mammal food web in Newfoundland. The first non-native mammals (house mouse and brown rat became established in Newfoundland with human settlement in the late 15th and early 16th centuries. Coyotes and southern red-backed voles are the most recent mammals to establish themselves on the island in 1985 and 1998, respectively. The fraction of intermediate species increased with the addition of non-native mammals over time whereas the fraction of basal and top species declined over time. This increase in intermediate species mediated by non-native species arrivals led to an overall increase in the terrestrial mammal food web connectance and generality (i.e. mean number of prey per predator. This diverse prey base and sources of carrion may have facilitated the natural establishment of coyotes on the island. Also, there is some evidence that the introduction of non-native prey species such as the southern red-backed vole has contributed to the recovery of the threatened American marten. Long-term monitoring of the food web is required to understand and predict the impacts of the diverse novel interactions that are developing in the terrestrial mammal food web of Newfoundland.

Levels of protein hydroperoxides and carbonyl groups in guinea pigs native of high altitudes (Huancavelica, 3660 m)

OpenAIRE

Huayta, Roxana; Zúñiga, Haydée; Esquerre, Cynthia; Hernández, Luz; Carranza, Elizabeth

2014-01-01

The influence of hypobaric hypoxia on protein oxidation in lungs, heart, liver, kidneys and testicles of high altitude native guinea pigs (Huancavelica, 3660 m) in comparison to sea level (Lima, 150 m) native guinea pigs was evaluated. The concentration of protein hydroperoxides (POOH) and carbonyl groups (GC) as markers of protein oxidation, as well as total thiols (TT) concentration, powerful reducing agents that act as live antioxidants were determined. The results showed low concentration...

Native and non-native plants provide similar refuge to invertebrate prey, but less than artificial plants

NARCIS (Netherlands)

Grutters, Bart; Pollux, B.J.A.; Verberk, W.C.E.P.; Bakker, E.S.

2015-01-01

Non-native species introductions are widespread and can affect ecosystem functioning by altering the structure of food webs. Invading plants often modify habitat structure, which may affect the suitability of vegetation as refuge and could thus impact predator-prey dynamics. Yet little is known

An improved method to unravel phosphoacceptors in Ser/Thr protein kinase-phosphorylated substrates.

Science.gov (United States)

Molle, Virginie; Leiba, Jade; Zanella-Cléon, Isabelle; Becchi, Michel; Kremer, Laurent

2010-11-01

Identification of the phosphorylated residues of bacterial Ser/Thr protein kinase (STPK) substrates still represents a challenging task. Herein, we present a new strategy allowing the rapid determination of phosphoacceptors in kinase substrates, essentially based on the dual expression of the kinase with its substrate in the surrogate E. coli, followed by MS analysis in a single-step procedure. The performance of this strategy is illustrated using two distinct proteins from Mycobacterium tuberculosis as model substrates, the GroEL2 and HspX chaperones. A comparative analysis with a standard method that includes mass spectrometry analysis of in vitro phosphorylated substrates is also addressed.

Status and management of non-native plant invasion in three of the largest national parks in the United States

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Scott Abella

2015-06-01

Full Text Available Globally, invasion by non-native plants threatens resources that nature reserves are designated to protect. We assessed the status of non-native plant invasion on 1,662, 0.1-ha plots in Death Valley National Park, Mojave National Preserve, and Lake Mead National Recreation Area. These parks comprise 2.5 million ha, 23% of the national park land in the contiguous USA. At least one non-native species inhabited 82% of plots. Thirty-one percent of plots contained one non-native species, 30% two, 17% three, and 4% four to ten non-native species. Red brome (Bromus rubens, an ‘ecosystem engineer’ that alters fire regimes, was most widespread, infesting 60% of plots. By identifying frequency of species through this assessment, early detection and treatment can target infrequent species or minimally invaded sites, while containment strategies could focus on established invaders. We further compared two existing systems for prioritizing species for management and found that a third of species on plots had no rankings available. Moreover, rankings did not always agree between ranking systems for species that were ranked. Presence of multiple non-native species complicates treatment, and while we found that 40% of plots contained both forb and grass invaders, exploiting accelerated phenology of non-natives (compared to native annuals might help manage multi-species invasions. Large sizes of these parks and scale of invasion are formidable challenges for management. Yet, precisely because of their size, these reserves represent opportunities to conserve large landscapes of native species by managing non-native plant invasions.

Antipredator responses by native mosquitofish to non-native cichlids: An examination of the role of prey naiveté

Science.gov (United States)

Rehage, Jennifer S.; Dunlop, Katherine L.; Loftus, William F.

2009-01-01

The strong impact of non-native predators in aquatic systems is thought to relate to the evolutionary naiveté of prey. Due to isolation and limited dispersal, this naiveté may be relatively high in freshwater systems. In this study, we tested this notion by examining the antipredator response of native mosquitofish, Gambusia holbrooki, to two non-native predators found in the Everglades, the African jewelfish,Hemichromis letourneuxi, and the Mayan cichlid, Cichlasoma urophthalmus. We manipulated prey naiveté by using two mosquitofish populations that varied in their experience with the recent invader, the African jewelfish, but had similar levels of experience with the longer-established Mayan cichlid. Specifically, we tested these predictions: (1) predator hunting modes differed between the two predators, (2) predation rates would be higher by the novel jewelfish predator, (3) particularly on the naive population living where jewelfish have not invaded yet, (4) antipredator responses would be stronger to Mayan cichlids due to greater experience and weaker and/or ineffective to jewelfish, and (5) especially weakest by the naive population. We assayed prey and predator behavior, and prey mortality in lab aquaria where both predators and prey were free-ranging. Predator hunting modes and habitat domains differed, with jewelfish being more active search predators that used slightly higher parts of the water column and less of the habitat structure relative to Mayan cichlids. In disagreement with our predictions, predation rates were similar between the two predators, antipredator responses were stronger to African jewelfish (except for predator inspections), and there was no difference in response between jewelfish-savvy and jewelfish-naive populations. These results suggest that despite the novelty of introduced predators, prey may be able to respond appropriately if non-native predator archetypes are similar enough to those of native predators, if prey rely

Beyond Histones: New Substrate Proteins of Lysine Deacetylases in Arabidopsis Nuclei

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Magdalena Füßl

2018-04-01

Full Text Available The reversible acetylation of lysine residues is catalyzed by the antagonistic action of lysine acetyltransferases and deacetylases, which can be considered as master regulators of their substrate proteins. Lysine deacetylases, historically referred to as histone deacetylases, have profound functions in regulating stress defenses and development in plants. Lysine acetylation of the N-terminal histone tails promotes gene transcription and decondensation of chromatin, rendering the DNA more accessible to the transcription machinery. In plants, the classical lysine deacetylases from the RPD3/HDA1-family have thus far mainly been studied in the context of their deacetylating activities on histones, and their versatility in molecular activities is still largely unexplored. Here we discuss the potential impact of lysine acetylation on the recently identified nuclear substrate proteins of lysine deacetylases from the Arabidopsis RPD3/HDA1-family. Among the deacetylase substrate proteins, many interesting candidates involved in nuclear protein import, transcriptional regulation, and chromatin remodeling have been identified. These candidate proteins represent key starting points for unraveling new molecular functions of the Arabidopsis lysine deacetylases. Site-directed engineering of lysine acetylation sites on these target proteins might even represent a new approach for optimizing plant growth under climate change conditions.

Exploring Native and Non-Native Intuitions of Word Frequency.

Science.gov (United States)

Schmitt, Norbert; Dunham, Bruce

1999-01-01

Asked native and nonnative speakers to give judgments of frequency for near synonyms in second-language lexical sets and compared those responses to modern corpus word counts. Native speakers were able to discern the core word in lexical sets either 77% or 85%, and nonnative speakers at 71% or 79%. (Author/VWL)

Two-step purification of His-tagged Nef protein in native condition using heparin and immobilized metal ion affinity chromatographies.

Science.gov (United States)

Finzi, Andrés; Cloutier, Jonathan; Cohen, Eric A

2003-07-01

The Nef protein encoded by human immunodeficiency virus type 1 (HIV-1) has been shown to be an important factor of progression of viral growth and pathogenesis in both in vitro and in vivo. The lack of a simple procedure to purify Nef in its native conformation has limited molecular studies on Nef function. A two-step procedure that includes heparin and immobilized metal ion affinity chromatographies (IMACs) was developed to purify His-tagged Nef (His(6)-Nef) expressed in bacteria in native condition. During the elaboration of this purification procedure, we identified two closely SDS-PAGE-migrating contaminating bacterial proteins, SlyD and GCHI, that co-eluted with His(6)-Nef in IMAC in denaturing condition and developed purification steps to eliminate these contaminants in native condition. Overall, this study describes a protocol that allows rapid purification of His(6)-Nef protein expressed in bacteria in native condition and that removes metal affinity resin-binding bacterial proteins that can contaminate recombinant His-tagged protein preparation.

An evaluation of behavioural and personality differences between native and non-native male adolescents in the Netherlands ordered into treatment in a forensic psychiatric outpatient clinic, and their non-violent peers.

NARCIS (Netherlands)

Hornsveld, R.H.J.; Cuperus, H.; Vries, E.T. de; Kraaimaat, F.W.

2008-01-01

BACKGROUND: In a previous study of the dynamic criminogenic needs of violent outpatients we did not differentiate between native and non-native adolescents, but differences between personality traits and problem behaviours may require adaptations to any treatment programme. AIM: To compare, in the

Synthetic study on prion protein fragments using a SPPS and native chemical ligation

Czech Academy of Sciences Publication Activity Database

Zawada, Z.; Šebestík, Jaroslav; Bednárová, Lucie; Bouř, Petr; Hlaváček, Jan; Stibor, Ivan

2009-01-01

Roč. 37, Suppl. 1 (2009), s. 44-44 ISSN 0939-4451. [International Congress on Amino Acids, Peptides and Proteins /11./. 03.08.2009-07.08.2009, Vienna] Institutional research plan: CEZ:AV0Z40550506 Keywords : prion protein * SPPS * native chemical ligation * fragments Subject RIV: CC - Organic Chemistry

An essential nonredundant role for mycobacterial DnaK in native protein folding.

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Allison Fay

2014-07-01

Full Text Available Protein chaperones are essential in all domains of life to prevent and resolve protein misfolding during translation and proteotoxic stress. HSP70 family chaperones, including E. coli DnaK, function in stress induced protein refolding and degradation, but are dispensable for cellular viability due to redundant chaperone systems that prevent global nascent peptide insolubility. However, the function of HSP70 chaperones in mycobacteria, a genus that includes multiple human pathogens, has not been examined. We find that mycobacterial DnaK is essential for cell growth and required for native protein folding in Mycobacterium smegmatis. Loss of DnaK is accompanied by proteotoxic collapse characterized by the accumulation of insoluble newly synthesized proteins. DnaK is required for solubility of large multimodular lipid synthases, including the essential lipid synthase FASI, and DnaK loss is accompanied by disruption of membrane structure and increased cell permeability. Trigger Factor is nonessential and has a minor role in native protein folding that is only evident in the absence of DnaK. In unstressed cells, DnaK localizes to multiple, dynamic foci, but relocalizes to focal protein aggregates during stationary phase or upon expression of aggregating peptides. Mycobacterial cells restart cell growth after proteotoxic stress by isolating persistent DnaK containing protein aggregates away from daughter cells. These results reveal unanticipated essential nonredunant roles for mycobacterial DnaK in mycobacteria and indicate that DnaK defines a unique susceptibility point in the mycobacterial proteostasis network.

Non-native grass removal and shade increase soil moisture and seedling performance during Hawaiian dry forest restoration

Science.gov (United States)

Jared M. Thaxton; Susan Cordell; Robert J. Cabin; Darren R. Sandquist

2012-01-01

Invasive non-native species can create especially problematic restoration barriers in subtropical and tropical dry forests. Native dry forests in Hawaii presently cover less than 10% of their original area. Many sites that historically supported dry forest are now completely dominated by non-native species, particularly grasses. Within a grass-dominated site in leeward...

Professional Development in Japanese Non-Native English Speaking Teachers' Identity and Efficacy

Science.gov (United States)

Takayama, Hiromi

2015-01-01

This mixed methods study investigates how Japanese non-native English speaking teachers' (NNESTs) efficacy and identity are developed and differentiated from those of native English speaking teachers (NESTs). To explore NNESTs' efficacy, this study focuses on the contributing factors, such as student engagement, classroom management, instructional…

An invasion risk map for non-native aquatic macrophytes of the Iberian Peninsula

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Argantonio Rodríguez-Merino

2017-05-01

Full Text Available Freshwater systems are particularly susceptible to non-native organisms, owing to their high sensitivity to the impacts that are caused by these organisms. Species distribution models, which are based on both environmental and socio-economic variables, facilitate the identification of the most vulnerable areas for the spread of non-native species. We used MaxEnt to predict the potential distribution of 20 non-native aquatic macrophytes in the Iberian Peninsula. Some selected variables, such as the temperature seasonality and the precipitation in the driest quarter, highlight the importance of the climate on their distribution. Notably, the human influence in the territory appears as a key variable in the distribution of studied species. The model discriminated between favorable and unfavorable areas with high accuracy. We used the model to build an invasion risk map of aquatic macrophytes for the Iberian Peninsula that included results from 20 individual models. It showed that the most vulnerable areas are located near to the sea, the major rivers basins, and the high population density areas. These facts suggest the importance of the human impact on the colonization and distribution of non-native aquatic macrophytes in the Iberian Peninsula, and more precisely agricultural development during the Green Revolution at the end of the 70’s. Our work also emphasizes the utility of species distribution models for the prevention and management of biological invasions.

Coupling ligand recognition to protein folding in an engineered variant of rabbit ileal lipid binding protein.

Science.gov (United States)

Kouvatsos, Nikolaos; Meldrum, Jill K; Searle, Mark S; Thomas, Neil R

2006-11-28

We have engineered a variant of the beta-clam shell protein ILBP which lacks the alpha-helical motif that caps the central binding cavity; the mutant protein is sufficiently destabilised that it is unfolded under physiological conditions, however, it unexpectedly binds its natural bile acid substrates with high affinity forming a native-like beta-sheet rich structure and demonstrating strong thermodynamic coupling between ligand binding and protein folding.

Lack of detectable allergenicity in genetically modified maize containing "Cry" proteins as compared to native maize based on in silico & in vitro analysis.

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Chandni Mathur

Full Text Available Genetically modified, (GM crops with potential allergens must be evaluated for safety and endogenous IgE binding pattern compared to native variety, prior to market release.To compare endogenous IgE binding proteins of three GM maize seeds containing Cry 1Ab,1Ac,1C transgenic proteins with non GM maize.An integrated approach of in silico & in vitro methods was employed. Cry proteins were tested for presence of allergen sequence by FASTA in allergen databases. Biochemical assays for maize extracts were performed. Specific IgE (sIgE and Immunoblot using food sensitized patients sera (n = 39 to non GM and GM maize antigens was performed.In silico approaches, confirmed for non sequence similarity of stated transgenic proteins in allergen databases. An insignificant (p> 0.05 variation in protein content between GM and non GM maize was observed. Simulated Gastric Fluid (SGF revealed reduced number of stable protein fractions in GM then non GM maize which might be due to shift of constituent protein expression. Specific IgE values from patients showed insignificant difference in non GM and GM maize extracts. Five maize sensitized cases, recognized same 7 protein fractions of 88-28 kD as IgE bindng in both GM and non-GM maize, signifying absence of variation. Four of the reported IgE binding proteins were also found to be stable by SGF.Cry proteins did not indicate any significant similarity of >35% in allergen databases. Immunoassays also did not identify appreciable differences in endogenous IgE binding in GM and non GM maize.

Studies on voltammetric determination of cadmium in samples containing native and digested proteins

Energy Technology Data Exchange (ETDEWEB)

Drozd, Marcin; Pietrzak, Mariusz, E-mail: mariusz@ch.pw.edu.pl; Malinowska, Elżbieta

2014-03-01

Highlights: • Proteins exhibit diverse impact on the DPASV cadmium signals. • Proteins subjected to HNO{sub 3} introduce less interference, than the native ones. • Optimal amount of SDS depends on the kind of protein. • Presence of thiolated coating agents of QDs do not influence the analysis. - Abstract: This work focuses on determination of cadmium ions using anodic stripping voltammetry (ASV) on thin film mercury electrode in conditions corresponding to those obtained after digestion of cadmium-based quantum dots and their conjugates. It presents the impact of selected proteins, including potential receptors and surface blocking agents on the voltammetric determination of cadmium. Experiments regarding elimination of interferences related to proteins presence using sodium dodecyl sulfate (SDS) are also shown. Effect of SDS on selected analytical parameters and simplicity of analyses carried out was investigated in the framework of current studies. The significant differences of influence among tested proteins on ASV cadmium determination, as well as the variability in SDS effectiveness as the antifouling agent were observed and explained. This work is especially important for those, who design new bioassays and biosensors with a use of quantum dots as electrochemical labels, as it shows what problems may arise from presence of native and digested proteins in tested samples.

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

Science.gov (United States)

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.

A global organism detection and monitoring system for non-native species

Science.gov (United States)

Graham, J.; Newman, G.; Jarnevich, C.; Shory, R.; Stohlgren, T.J.

2007-01-01

Harmful invasive non-native species are a significant threat to native species and ecosystems, and the costs associated with non-native species in the United States is estimated at over $120 Billion/year. While some local or regional databases exist for some taxonomic groups, there are no effective geographic databases designed to detect and monitor all species of non-native plants, animals, and pathogens. We developed a web-based solution called the Global Organism Detection and Monitoring (GODM) system to provide real-time data from a broad spectrum of users on the distribution and abundance of non-native species, including attributes of their habitats for predictive spatial modeling of current and potential distributions. The four major subsystems of GODM provide dynamic links between the organism data, web pages, spatial data, and modeling capabilities. The core survey database tables for recording invasive species survey data are organized into three categories: "Where, Who & When, and What." Organisms are identified with Taxonomic Serial Numbers from the Integrated Taxonomic Information System. To allow users to immediately see a map of their data combined with other user's data, a custom geographic information system (GIS) Internet solution was required. The GIS solution provides an unprecedented level of flexibility in database access, allowing users to display maps of invasive species distributions or abundances based on various criteria including taxonomic classification (i.e., phylum or division, order, class, family, genus, species, subspecies, and variety), a specific project, a range of dates, and a range of attributes (percent cover, age, height, sex, weight). This is a significant paradigm shift from "map servers" to true Internet-based GIS solutions. The remainder of the system was created with a mix of commercial products, open source software, and custom software. Custom GIS libraries were created where required for processing large datasets

Hydroxyapatite coating on the titanium substrate modulated by a recombinant collagen-like protein

International Nuclear Information System (INIS)

Pan Mingli; Kong Xiangdong; Cai Yurong; Yao Juming

2011-01-01

Research highlights: → Hydroxyapatite was deposited on alkali-heat treated Ti substrate by immersing in 1.5 x SBF solution containing the recombinant collagen-like protein. → The recombinant collagen-like protein accelerated the preferential nucleation and growth of hydroxyapatite along c axis on the Ti substrate. → Hydroxyapatite-collagen composite on the Ti substrate promoted the attachment, subsequently proliferation and differentiation of MG-63 cells. - Abstract: Plenty of techniques have been developed to modify the surface character of titanium (Ti) and its alloys in order to realize their biological bond to natural bone. In this work, a biomimetic process was employed to form a hydroxyapatite (HAp) coating on the alkali-heat treated Ti substrate in 1.5 times simulated body fluid (1.5 x SBF) with the addition of a recombinant collagen-like protein. The coating was characterized using SEM-EDX, FESEM, and XRD. Results showed that the recombinant collagen-like protein could accelerate the preferential nucleation and directional growth along c axis of HAp on the pretreated Ti substrates. The investigation of in vitro cell cultivation showed that the existence of recombinant collagen-like protein in coating could improve the initial cell adhesion, proliferation and differentiation of MG-63 cells, which implied the materials possessed excellent biocompatibility and had a wide potential in biomedical application.

Hydroxyapatite coating on the titanium substrate modulated by a recombinant collagen-like protein

Energy Technology Data Exchange (ETDEWEB)

Pan Mingli [Key Laboratory of Advanced Textile Materials and Manufacturing Technology of Ministry of Education, College of Materials and Textile, Zhejiang Sci-Tech University, Hangzhou 310018 (China); Kong Xiangdong [College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018 (China); Cai Yurong [Key Laboratory of Advanced Textile Materials and Manufacturing Technology of Ministry of Education, College of Materials and Textile, Zhejiang Sci-Tech University, Hangzhou 310018 (China); Yao Juming, E-mail: yaoj@zstu.edu.cn [Key Laboratory of Advanced Textile Materials and Manufacturing Technology of Ministry of Education, College of Materials and Textile, Zhejiang Sci-Tech University, Hangzhou 310018 (China)

2011-04-15

Research highlights: {yields} Hydroxyapatite was deposited on alkali-heat treated Ti substrate by immersing in 1.5 x SBF solution containing the recombinant collagen-like protein. {yields} The recombinant collagen-like protein accelerated the preferential nucleation and growth of hydroxyapatite along c axis on the Ti substrate. {yields} Hydroxyapatite-collagen composite on the Ti substrate promoted the attachment, subsequently proliferation and differentiation of MG-63 cells. - Abstract: Plenty of techniques have been developed to modify the surface character of titanium (Ti) and its alloys in order to realize their biological bond to natural bone. In this work, a biomimetic process was employed to form a hydroxyapatite (HAp) coating on the alkali-heat treated Ti substrate in 1.5 times simulated body fluid (1.5 x SBF) with the addition of a recombinant collagen-like protein. The coating was characterized using SEM-EDX, FESEM, and XRD. Results showed that the recombinant collagen-like protein could accelerate the preferential nucleation and directional growth along c axis of HAp on the pretreated Ti substrates. The investigation of in vitro cell cultivation showed that the existence of recombinant collagen-like protein in coating could improve the initial cell adhesion, proliferation and differentiation of MG-63 cells, which implied the materials possessed excellent biocompatibility and had a wide potential in biomedical application.

Evolution under changing climates: climatic niche stasis despite rapid evolution in a non-native plant.

Science.gov (United States)

Alexander, Jake M

2013-09-22

A topic of great current interest is the capacity of populations to adapt genetically to rapidly changing climates, for example by evolving the timing of life-history events, but this is challenging to address experimentally. I use a plant invasion as a model system to tackle this question by combining molecular markers, a common garden experiment and climatic niche modelling. This approach reveals that non-native Lactuca serriola originates primarily from Europe, a climatic subset of its native range, with low rates of admixture from Asia. It has rapidly refilled its climatic niche in the new range, associated with the evolution of flowering phenology to produce clines along climate gradients that mirror those across the native range. Consequently, some non-native plants have evolved development times and grow under climates more extreme than those found in Europe, but not among populations from the native range as a whole. This suggests that many plant populations can adapt rapidly to changed climatic conditions that are already within the climatic niche space occupied by the species elsewhere in its range, but that evolution to conditions outside of this range is more difficult. These findings can also help to explain the prevalence of niche conservatism among non-native species.

Estimating the non-market costs and benefits of native woodland restoration using the contingent valuation method.

OpenAIRE

MacMillan, Douglas C.; Duff, Elizabeth I.

1998-01-01

The restoration of native forests is an important priority for forestry and conservation organizations in the United Kingdom. The economic case for public sector support for native woodland restoration in the United Kingdom rests almost entirely on the provision of non-market benefits related to wildlife, landscape and recreational opportunities. This paper describes a discrete choice contingent valuation (CV) to estimate the value of the non-market benefits of restoring two native pinewood f...

Combining native MS approaches to decipher archaeal box H/ACA ribonucleoprotein particle structure and activity.

Science.gov (United States)

Saliou, Jean-Michel; Manival, Xavier; Tillault, Anne-Sophie; Atmanene, Cédric; Bobo, Claude; Branlant, Christiane; Van Dorsselaer, Alain; Charpentier, Bruno; Cianférani, Sarah

2015-08-01

Site-specific isomerization of uridines into pseudouridines in RNAs is catalyzed either by stand-alone enzymes or by box H/ACA ribonucleoprotein particles (sno/sRNPs). The archaeal box H/ACA sRNPs are five-component complexes that consist of a guide RNA and the aCBF5, aNOP10, L7Ae, and aGAR1 proteins. In this study, we performed pairwise incubations of individual constituents of archaeal box H/ACA sRNPs and analyzed their interactions by native MS to build a 2D-connectivity map of direct binders. We describe the use of native MS in combination with ion mobility-MS to monitor the in vitro assembly of the active H/ACA sRNP particle. Real-time native MS was used to monitor how box H/ACA particle functions in multiple-turnover conditions. Native MS also unambiguously revealed that a substrate RNA containing 5-fluorouridine (f(5) U) was hydrolyzed into 5-fluoro-6-hydroxy-pseudouridine (f(5) ho(6) Ψ). In terms of enzymatic mechanism, box H/ACA sRNP was shown to catalyze the pseudouridylation of a first RNA substrate, then to release the RNA product (S22 f(5) ho(6) ψ) from the RNP enzyme and reload a new substrate RNA molecule. Altogether, our native MS-based approaches provide relevant new information about the potential assembly process and catalytic mechanism of box H/ACA RNPs. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Protein adsorption on tailored substrates: long-range forces and conformational changes

Energy Technology Data Exchange (ETDEWEB)

Bellion, M; Santen, L [Department of Theoretical Physics, Saarland University, 66041 Saarbruecken (Germany); Mantz, H; Haehl, H; Quinn, A; Nagel, A; Gilow, C; Weitenberg, C; Schmitt, Y; Jacobs, K [Department of Experimental Physics, Saarland University, 66041 Saarbruecken (Germany)], E-mail: k.jacobs@physik.uni-saarland.de

2008-10-08

Adsorption of proteins onto solid surfaces is an everyday phenomenon that is not yet fully understood. To further the current understanding, we have performed in situ ellipsometry studies to reveal the adsorption kinetics of three different proteins, lysozyme, {alpha}-amylase and bovine serum albumin. As substrates we offer Si wafers with a controlled Si oxide layer thickness and a hydrophilic or hydrophobic surface functionalization, allowing the tailoring of the influence of short- and long-range interactions. Our studies show that not only the surface chemistry determines the properties of an adsorbed protein layer but also the van der Waals contributions of a composite substrate. We compare the experimental findings to results of a colloidal Monte Carlo approach that includes conformational changes of the adsorbed proteins induced by density fluctuations.

Introduction of non-native marine fish species to the Canary Islands waters through oil platforms as vectors

Science.gov (United States)

Pajuelo, José G.; González, José A.; Triay-Portella, Raül; Martín, José A.; Ruiz-Díaz, Raquel; Lorenzo, José M.; Luque, Ángel

2016-11-01

This work documents the introduction of non-native fish species to the Canary Islands (central-eastern Atlantic) through oil rigs. Methodological approaches have included surveys by underwater visual censuses around and under oil platforms and along the docking area of rigs at the Port of Las Palmas. Eleven non-native fish species were registered. Paranthias furcifer, Abudefduf hoefleri, Acanthurus bahianus, Acanthurus chirurgus, and Acanthurus coeruleus are first recorded from the Canaries herein. Other three species could not be identified, although they have never been observed in the Canaries. Cephalopholis taeniops, Abudefduf saxatilis, and Acanthurus monroviae had been previously recorded. Native areas of these species coincide with the areas of origin and the scale of oil rigs with destination the Port of Las Palmas. The absence of native species in the censuses at rigs and their presence at rigs docking area, together with the observation of non-native species after the departure of platforms, reject the possibility that these non-native species were already present in the area introduced by another vector. C. taeniops, A. hoefleri, A. saxatilis, A. chirurgus, A. coeruleus and A. monroviae are clearly seafarer species. A. bahianus seems to be a potential seafarer species. P. furcifer is a castaway species. For the moment, the number of individuals of the non-native species in marine ecosystems of the Canaries seems to be low, and more investigation is needed for controlling these translocations.

Brownian dynamic study of an enzyme metabolon in the TCA cycle: Substrate kinetics and channeling.

Science.gov (United States)

Huang, Yu-Ming M; Huber, Gary A; Wang, Nuo; Minteer, Shelley D; McCammon, J Andrew

2018-02-01

Malate dehydrogenase (MDH) and citrate synthase (CS) are two pacemaking enzymes involved in the tricarboxylic acid (TCA) cycle. Oxaloacetate (OAA) molecules are the intermediate substrates that are transferred from the MDH to CS to carry out sequential catalysis. It is known that, to achieve a high flux of intermediate transport and reduce the probability of substrate leaking, a MDH-CS metabolon forms to enhance the OAA substrate channeling. In this study, we aim to understand the OAA channeling within possible MDH-CS metabolons that have different structural orientations in their complexes. Three MDH-CS metabolons from native bovine, wild-type porcine, and recombinant sources, published in recent work, were selected to calculate OAA transfer efficiency by Brownian dynamics (BD) simulations and to study, through electrostatic potential calculations, a possible role of charges that drive the substrate channeling. Our results show that an electrostatic channel is formed in the metabolons of native bovine and recombinant porcine enzymes, which guides the oppositely charged OAA molecules passing through the channel and enhances the transfer efficiency. However, the channeling probability in a suggested wild-type porcine metabolon conformation is reduced due to an extended diffusion length between the MDH and CS active sites, implying that the corresponding arrangements of MDH and CS result in the decrease of electrostatic steering between substrates and protein surface and then reduce the substrate transfer efficiency from one active site to another. © 2017 The Protein Society.

Non-Native English Teachers' Beliefs on Grammar Instruction

Science.gov (United States)

Önalan, Okan

2018-01-01

Research on teacher cognition, which mainly focuses on identifying what teachers think, know and believe, is essential to understanding teachers' cognitive framework as it relates to the instructional choices they make. The aim of this study is to find out the beliefs of non-native speaker teachers of English on grammar instruction and to explain…

A Hybrid Acoustic and Pronunciation Model Adaptation Approach for Non-native Speech Recognition

Science.gov (United States)

Oh, Yoo Rhee; Kim, Hong Kook

In this paper, we propose a hybrid model adaptation approach in which pronunciation and acoustic models are adapted by incorporating the pronunciation and acoustic variabilities of non-native speech in order to improve the performance of non-native automatic speech recognition (ASR). Specifically, the proposed hybrid model adaptation can be performed at either the state-tying or triphone-modeling level, depending at which acoustic model adaptation is performed. In both methods, we first analyze the pronunciation variant rules of non-native speakers and then classify each rule as either a pronunciation variant or an acoustic variant. The state-tying level hybrid method then adapts pronunciation models and acoustic models by accommodating the pronunciation variants in the pronunciation dictionary and by clustering the states of triphone acoustic models using the acoustic variants, respectively. On the other hand, the triphone-modeling level hybrid method initially adapts pronunciation models in the same way as in the state-tying level hybrid method; however, for the acoustic model adaptation, the triphone acoustic models are then re-estimated based on the adapted pronunciation models and the states of the re-estimated triphone acoustic models are clustered using the acoustic variants. From the Korean-spoken English speech recognition experiments, it is shown that ASR systems employing the state-tying and triphone-modeling level adaptation methods can relatively reduce the average word error rates (WERs) by 17.1% and 22.1% for non-native speech, respectively, when compared to a baseline ASR system.

A recombinant fusion protein-based, fluorescent protease assay for high throughput-compatible substrate screening.

Science.gov (United States)

Bozóki, Beáta; Gazda, Lívia; Tóth, Ferenc; Miczi, Márió; Mótyán, János András; Tőzsér, József

2018-01-01

In connection with the intensive investigation of proteases, several methods have been developed for analysis of the substrate specificity. Due to the great number of proteases and the expected target molecules to be analyzed, time- and cost-efficient high-throughput screening (HTS) methods are preferred. Here we describe the development and application of a separation-based HTS-compatible fluorescent protease assay, which is based on the use of recombinant fusion proteins as substrates of proteases. The protein substrates used in this assay consists of N-terminal (hexahistidine and maltose binding protein) fusion tags, cleavage sequences of the tobacco etch virus (TEV) and HIV-1 proteases, and a C-terminal fluorescent protein (mApple or mTurquoise2). The assay is based on the fluorimetric detection of the fluorescent proteins, which are released from the magnetic bead-attached substrates by the proteolytic cleavage. The protease assay has been applied for activity measurements of TEV and HIV-1 proteases to test the suitability of the system for enzyme kinetic measurements, inhibition studies, and determination of pH optimum. We also found that denatured fluorescent proteins can be renatured after SDS-PAGE of denaturing conditions, but showed differences in their renaturation abilities. After in-gel renaturation both substrates and cleavage products can be identified by in-gel UV detection. Copyright © 2017 Elsevier Inc. All rights reserved.

Facilitation of a native pest of rice, Stenotus rubrovittatus (Hemiptera: Miridae), by the non-native Lolium multiflorum (Cyperales: Poaceae) in an agricultural landscape.

Science.gov (United States)

Yoshioka, Akira; Takada, Mayura; Washitani, Izumi

2011-10-01

Source populations of polyphagous pests often occur on host plants other than the economically damaged crop. We evaluated the contribution of patches of a non-native meadow grass, Lolium multiflorum Lam. (Poaceae), and other weeds growing in fallow fields or meadows as source hosts of an important native pest of rice, Stenotus rubrovittatus (Matsumura) (Hemiptera: Miridae), in an agricultural landscape of northern Japan. Periodical censuses of this mirid bug by using the sweeping method, vegetation surveys, and statistical analysis revealed that L. multiflorum was the only plant species that was positively correlated with the density of adult S. rubrovittatus through two generations and thus may be the most stable and important host of the mirid bug early in the season before the colonization of rice paddies. The risk and cost of such an indirect negative effect on a crop plant through facilitation of a native pest by a non-native plant in the agricultural landscape should not be overlooked.

Energy landscape of all-atom protein-protein interactions revealed by multiscale enhanced sampling.

Directory of Open Access Journals (Sweden)

Kei Moritsugu

2014-10-01

Full Text Available Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface. To understand such an elusive phenomenon, it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using the all-atom model in explicit solvent and to delineate the energy landscape of protein-protein interactions. In this study, we carried out a multiscale enhanced sampling (MSES simulation of the formation of a barnase-barstar complex, which is a protein complex characterized by an extraordinary tight and fast binding, to determine the energy landscape of atomistic protein-protein interactions. The MSES adopts a multicopy and multiscale scheme to enable for the enhanced sampling of the all-atom model of large proteins including explicit solvent. During the 100-ns MSES simulation of the barnase-barstar system, we observed the association-dissociation processes of the atomistic protein complex in solution several times, which contained not only the native complex structure but also fully non-native configurations. The sampled distributions suggest that a large variety of non-native states went downhill to the stable complex structure, like a fast folding on a funnel-like potential. This funnel landscape is attributed to dominant configurations in the early stage of the association process characterized by near-native orientations, which will accelerate the native inter-molecular interactions. These configurations are guided mostly by the shape complementarity between barnase and barstar, and lead to the fast formation of the final complex structure along the downhill energy landscape.

The Power of Protection: A Population-Based Comparison of Native and Non-Native Youth Suicide Attempters

Science.gov (United States)

Mackin, Juliette; Perkins, Tamara; Furrer, Carrie

2012-01-01

This study provides actionable information about intervening with American Indian/Alaska Native (AI/AN) youth to prevent suicide. Statewide school survey data were used to model the impact of risk and protective factors on self-reported suicide attempts (both AI/AN and non-AI/AN). The cumulative risk and protective model worked similarly for both…

High-level secretion of native recombinant human calreticulin in yeast

DEFF Research Database (Denmark)

Čiplys, Evaldas; Žitkus, Eimantas; Gold, Leslie I.

2015-01-01

, Saccharomyces cerevisiae and Pichia pastoris. RESULTS: Expression of a full-length human CRT precursor including its native signal sequence resulted in high-level secretion of mature recombinant protein into the culture medium by both S. cerevisiae and P. pastoris. To ensure the structural and functional...... by non-denaturing PAGE. Moreover, limited trypsin digestion yielded identical fragment patterns of calcium-binding recombinant and native CRT suggesting that the yeast-derived CRT was correctly folded. Furthermore, both native and recombinant CRT induced cellular proliferation (MTS assay) and migration...... recombinant CRT protein with yields reaching 75 % of total secreted protein and with production levels of 60 and 200 mg/l from S. cerevisiae and P. pastoris, respectively. Finally, cultivation of P. pastoris in a bioreactor yielded CRT secretion titer to exceed 1.5 g/l of culture medium. CONCLUSIONS: Yeasts...

Comprehensive identification of protein substrates of the Dot/Icm type IV transporter of Legionella pneumophila.

Directory of Open Access Journals (Sweden)

Wenhan Zhu

2011-03-01

Full Text Available A large number of proteins transferred by the Legionella pneumophila Dot/Icm system have been identified by various strategies. With no exceptions, these strategies are based on one or more characteristics associated with the tested proteins. Given the high level of diversity exhibited by the identified proteins, it is possible that some substrates have been missed in these screenings. In this study, we took a systematic method to survey the L. pneumophila genome by testing hypothetical orfs larger than 300 base pairs for Dot/Icm-dependent translocation. 798 of the 832 analyzed orfs were successfully fused to the carboxyl end of β-lactamase. The transfer of the fusions into mammalian cells was determined using the β-lactamase reporter substrate CCF4-AM. These efforts led to the identification of 164 proteins positive in translocation. Among these, 70 proteins are novel substrates of the Dot/Icm system. These results brought the total number of experimentally confirmed Dot/Icm substrates to 275. Sequence analysis of the C-termini of these identified proteins revealed that Lpg2844, which contains few features known to be important for Dot/Icm-dependent protein transfer can be translocated at a high efficiency. Thus, our efforts have identified a large number of novel substrates of the Dot/Icm system and have revealed the diverse features recognizable by this protein transporter.

Evaluating ecosystem services provided by non-native species: an experimental test in California grasslands.

Science.gov (United States)

Stein, Claudia; Hallett, Lauren M; Harpole, W Stanley; Suding, Katharine N

2014-01-01

The concept of ecosystem services--the benefits that nature provides to human's society--has gained increasing attention over the past decade. Increasing global abiotic and biotic change, including species invasions, is threatening the secure delivery of these ecosystem services. Efficient evaluation methods of ecosystem services are urgently needed to improve our ability to determine management strategies and restoration goals in face of these new emerging ecosystems. Considering a range of multiple ecosystem functions may be a useful way to determine such strategies. We tested this framework experimentally in California grasslands, where large shifts in species composition have occurred since the late 1700's. We compared a suite of ecosystem functions within one historic native and two non-native species assemblages under different grazing intensities to address how different species assemblages vary in provisioning, regulatory and supporting ecosystem services. Forage production was reduced in one non-native assemblage (medusahead). Cultural ecosystem services, such as native species diversity, were inherently lower in both non-native assemblages, whereas most other services were maintained across grazing intensities. All systems provided similar ecosystem services under the highest grazing intensity treatment, which simulated unsustainable grazing intensity. We suggest that applying a more comprehensive ecosystem framework that considers multiple ecosystem services to evaluate new emerging ecosystems is a valuable tool to determine management goals and how to intervene in a changing ecosystem.

Identifying protein phosphorylation sites with kinase substrate specificity on human viruses.

Directory of Open Access Journals (Sweden)

Neil Arvin Bretaña

Full Text Available Viruses infect humans and progress inside the body leading to various diseases and complications. The phosphorylation of viral proteins catalyzed by host kinases plays crucial regulatory roles in enhancing replication and inhibition of normal host-cell functions. Due to its biological importance, there is a desire to identify the protein phosphorylation sites on human viruses. However, the use of mass spectrometry-based experiments is proven to be expensive and labor-intensive. Furthermore, previous studies which have identified phosphorylation sites in human viruses do not include the investigation of the responsible kinases. Thus, we are motivated to propose a new method to identify protein phosphorylation sites with its kinase substrate specificity on human viruses. The experimentally verified phosphorylation data were extracted from virPTM--a database containing 301 experimentally verified phosphorylation data on 104 human kinase-phosphorylated virus proteins. In an attempt to investigate kinase substrate specificities in viral protein phosphorylation sites, maximal dependence decomposition (MDD is employed to cluster a large set of phosphorylation data into subgroups containing significantly conserved motifs. The experimental human phosphorylation sites are collected from Phospho.ELM, grouped according to its kinase annotation, and compared with the virus MDD clusters. This investigation identifies human kinases such as CK2, PKB, CDK, and MAPK as potential kinases for catalyzing virus protein substrates as confirmed by published literature. Profile hidden Markov model is then applied to learn a predictive model for each subgroup. A five-fold cross validation evaluation on the MDD-clustered HMMs yields an average accuracy of 84.93% for Serine, and 78.05% for Threonine. Furthermore, an independent testing data collected from UniProtKB and Phospho.ELM is used to make a comparison of predictive performance on three popular kinase

Identifying protein phosphorylation sites with kinase substrate specificity on human viruses.

Science.gov (United States)

Bretaña, Neil Arvin; Lu, Cheng-Tsung; Chiang, Chiu-Yun; Su, Min-Gang; Huang, Kai-Yao; Lee, Tzong-Yi; Weng, Shun-Long

2012-01-01

Viruses infect humans and progress inside the body leading to various diseases and complications. The phosphorylation of viral proteins catalyzed by host kinases plays crucial regulatory roles in enhancing replication and inhibition of normal host-cell functions. Due to its biological importance, there is a desire to identify the protein phosphorylation sites on human viruses. However, the use of mass spectrometry-based experiments is proven to be expensive and labor-intensive. Furthermore, previous studies which have identified phosphorylation sites in human viruses do not include the investigation of the responsible kinases. Thus, we are motivated to propose a new method to identify protein phosphorylation sites with its kinase substrate specificity on human viruses. The experimentally verified phosphorylation data were extracted from virPTM--a database containing 301 experimentally verified phosphorylation data on 104 human kinase-phosphorylated virus proteins. In an attempt to investigate kinase substrate specificities in viral protein phosphorylation sites, maximal dependence decomposition (MDD) is employed to cluster a large set of phosphorylation data into subgroups containing significantly conserved motifs. The experimental human phosphorylation sites are collected from Phospho.ELM, grouped according to its kinase annotation, and compared with the virus MDD clusters. This investigation identifies human kinases such as CK2, PKB, CDK, and MAPK as potential kinases for catalyzing virus protein substrates as confirmed by published literature. Profile hidden Markov model is then applied to learn a predictive model for each subgroup. A five-fold cross validation evaluation on the MDD-clustered HMMs yields an average accuracy of 84.93% for Serine, and 78.05% for Threonine. Furthermore, an independent testing data collected from UniProtKB and Phospho.ELM is used to make a comparison of predictive performance on three popular kinase-specific phosphorylation site

Syntactic constraints and individual differences in native and non-native processing of wh-movement

Directory of Open Access Journals (Sweden)

Adrienne eJohnson

2016-04-01

Full Text Available 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

Assessing the impact of non-native freshwater fishes on native species using relative weight

Directory of Open Access Journals (Sweden)

Giannetto D.

2012-01-01

Full Text Available The aim of the research was to test relative weight (Wr, a condition index which allows evaluation of fish well-being, as a tool to investigate the impact of the presence of non native species (NNS on the condition of the key native species (NS of the Tiber River basin (Italy: Barbustyberinus Bonaparte, Leuciscus cephalus (Linnaeus, Leuciscus lucumonis Bianco, Rutilus rubilio (Bonaparte and Telestes muticellus (Bonaparte. By means of Canonical Correlation Analysis, data from 130 sampling sites, distributed throughout Tiber River basin, were examined. Wr of NS was related to densities of NNS and to environmental variables. Moreover, the correlation between Wr of NS and density of NNS was investigated through linear regression analysis and covariance analysis. Preliminary results encourage the use of Wr as a tool to assess the relationship between NS and ecological factors (such as the presence of NNS and to explain the changes that occur along the longitudinal gradient of a river.

Native and Non-native English Teachers' Perceptions of their Professional Identity: Convergent or Divergent?

Directory of Open Access Journals (Sweden)

Zia Tajeddin

2016-10-01

Full Text Available There is still a preference for native speaker teachers in the language teaching profession, which is supposed to influence the self-perceptions of native and nonnative teachers. However, the status of English as a globalized language is changing the legitimacy of native/nonnative teacher dichotomy. This study sought to investigate native and nonnative English-speaking teachers’ perceptions about native and nonnative teachers’ status and the advantages and disadvantages of being a native or nonnative teacher. Data were collected by means of a questionnaire and a semi-structured interview. A total of 200 native and nonnative teachers of English from the UK and the US, i.e. the inner circle, and Turkey and Iran, the expanding circle, participated in this study. A significant majority of nonnative teachers believed that native speaker teachers have better speaking proficiency, better pronunciation, and greater self-confidence. The findings also showed nonnative teachers’ lack of self-confidence and awareness of their role and status compared with native-speaker teachers, which could be the result of existing inequities between native and nonnative English-speaking teachers in ELT. The findings also revealed that native teachers disagreed more strongly with the concept of native teachers’ superiority over nonnative teachers. Native teachers argued that nonnative teachers have a good understanding of teaching methodology whereas native teachers are more competent in correct language. It can be concluded that teacher education programs in the expanding-circle countries should include materials for teachers to raise their awareness of their own professional status and role and to remove their misconception about native speaker fallacy.

The Spread of Non-native Plant Species Collection of Cibodas Botanical Garden into Mt. Gede Pangrango National Park

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Musyarofah Zuhri

2013-05-01

Full Text Available The role of botanic garden in spread of non-native plant species has concerned of international worldwide. This study aimed to study the extent of non-native plant species from Cibodas Botanical Garden (CBG which invades into natural rainforest. A line transect was made edge-to-interior with 1,600 m in distance from CBG boundary. Result showed that distance from CBG was not significant in correlation with non-native tree and treelet density. Furthermore, presence of existing CBG’s plant collection was not a single aspect which influenced presence and abundance. Three invasive species possibly was escape from CBG and it showed edge-to-interior in stems density, i.e. Cinchona pubescens, Calliandra calothyrsus and Cestrum aurantiacum. The patterns of non-native species were influenced by presence of ditch across transect, existence of human trail, and the other non-native species did not have general pattern of spread distribution. Overall, botanical gardens should minimize the risk of unintentional introduced plant by perform site-specific risk assessment.

Optimizing Automatic Speech Recognition for Low-Proficient Non-Native Speakers

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Catia Cucchiarini

2010-01-01

Full Text Available Computer-Assisted Language Learning (CALL applications for improving the oral skills of low-proficient learners have to cope with non-native speech that is particularly challenging. Since unconstrained non-native ASR is still problematic, a possible solution is to elicit constrained responses from the learners. In this paper, we describe experiments aimed at selecting utterances from lists of responses. The first experiment on utterance selection indicates that the decoding process can be improved by optimizing the language model and the acoustic models, thus reducing the utterance error rate from 29–26% to 10–8%. Since giving feedback on incorrectly recognized utterances is confusing, we verify the correctness of the utterance before providing feedback. The results of the second experiment on utterance verification indicate that combining duration-related features with a likelihood ratio (LR yield an equal error rate (EER of 10.3%, which is significantly better than the EER for the other measures in isolation.

Non-native tree species in urban areas of the city of Nitra

International Nuclear Information System (INIS)

Galis, M

2014-01-01

Non-native plant species are part of our environment. The introduction of these species is huge conditioned by anthropogenic activities, such as the urban environment is characterized by. During the field surveys of selected town Nitra (Chrenova, Mikova Ves, Zobor), we studied the frequency of non-native tree species in the contact zone. Overall, we found out the presence of 10 alien species, observed in this area. Our results show dominant presence of the species Rhus typhina, followed by the Robinia pseudoacacia and Ailanthus altissima. Individual plants were tied largely to the surrounding of built-up areas, often growns directly in front of houses, or as a part of urban green. (author)

Prefoldin Promotes Proteasomal Degradation of Cytosolic Proteins with Missense Mutations by Maintaining Substrate Solubility.

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Sophie A Comyn

2016-07-01

Full Text Available Misfolded proteins challenge the ability of cells to maintain protein homeostasis and can accumulate into toxic protein aggregates. As a consequence, cells have adopted a number of protein quality control pathways to prevent protein aggregation, promote protein folding, and target terminally misfolded proteins for degradation. In this study, we employed a thermosensitive allele of the yeast Guk1 guanylate kinase as a model misfolded protein to investigate degradative protein quality control pathways. We performed a flow cytometry based screen to identify factors that promote proteasomal degradation of proteins misfolded as the result of missense mutations. In addition to the E3 ubiquitin ligase Ubr1, we identified the prefoldin chaperone subunit Gim3 as an important quality control factor. Whereas the absence of GIM3 did not impair proteasomal function or the ubiquitination of the model substrate, it led to the accumulation of the poorly soluble model substrate in cellular inclusions that was accompanied by delayed degradation. We found that Gim3 interacted with the Guk1 mutant allele and propose that prefoldin promotes the degradation of the unstable model substrate by maintaining the solubility of the misfolded protein. We also demonstrated that in addition to the Guk1 mutant, prefoldin can stabilize other misfolded cytosolic proteins containing missense mutations.

Which English? Whose English? An Investigation of "Non-Native" Teachers' Beliefs about Target Varieties

Science.gov (United States)

Young, Tony Johnstone; Walsh, Steve

2010-01-01

This study explored the beliefs of "non-native English speaking" teachers about the usefulness and appropriacy of varieties such as English as an International Language (EIL) and English as a Lingua Franca (ELF), compared with native speaker varieties. The study therefore addresses the current theoretical debate concerning "appropriate" target…

Proteolytic Activity of Prostate-Specific Antigen (PSA) towards Protein Substrates and Effect of Peptides Stimulating PSA Activity

Science.gov (United States)

Mattsson, Johanna M.; Ravela, Suvi; Hekim, Can; Jonsson, Magnus; Malm, Johan; Närvänen, Ale; Stenman, Ulf-Håkan; Koistinen, Hannu

2014-01-01

Prostate-specific antigen (PSA or kallikrein-related peptidase-3, KLK3) exerts chymotrypsin-like proteolytic activity. The main biological function of PSA is the liquefaction of the clot formed after ejaculation by cleavage of semenogelins I and II in seminal fluid. PSA also cleaves several other substrates, which may explain its putative functions in prostate cancer and its antiangiogenic activity. We compared the proteolytic efficiency of PSA towards several protein and peptide substrates and studied the effect of peptides stimulating the activity of PSA with these substrates. An endothelial cell tube formation model was used to analyze the effect of PSA-degraded protein fragments on angiogenesis. We showed that PSA degrades semenogelins I and II much more efficiently than other previously identified protein substrates, e.g., fibronectin, galectin-3 and IGFBP-3. We identified nidogen-1 as a new substrate for PSA. Peptides B2 and C4 that stimulate the activity of PSA towards small peptide substrates also enhanced the proteolytic activity of PSA towards protein substrates. Nidogen-1, galectin-3 or their fragments produced by PSA did not have any effect on endothelial cell tube formation. Although PSA cleaves several other protein substrates, in addition to semenogelins, the physiological importance of this activity remains speculative. The PSA levels in prostate are very high, but several other highly active proteases, such as hK2 and trypsin, are also expressed in the prostate and may cleave protein substrates that are weakly cleaved by PSA. PMID:25237904

Molecular dynamics simulations of protein-tyrosine phosphatase 1B: II. Substrate-enzyme interactions and dynamics

DEFF Research Database (Denmark)

Peters, Günther H.j.; Frimurer, T. M.; Andersen, J. N.

2000-01-01

Molecular dynamics simulations of protein tyrosine phosphatase 1B (PTP1B) complexed with the phosphorylated peptide substrate DADEpYL and the free substrate have been conducted to investigate 1) the physical forces involved in substrate-protein interactions, 2) the importance of enzyme...... to substrate binding. Based on essential dynamics analysis of the PTP1B/DADEpYL trajectory, it is shown that internal motions in the binding pocket occur in a subspace of only a few degrees of freedom. in particular, relatively large flexibilities are observed along several eigenvectors in the segments: Arg(24...... for catalysis. Analysis of the individual enzyme-substrate interaction energies revealed that mainly electrostatic forces contribute to binding. Indeed, calculation of the electrostatic field of the enzyme reveals that only the field surrounding the binding pocket is positive, while the remaining protein...

Projecting invasion risk of non-native watersnakes (Nerodia fasciata and Nerodia sipedon in the western United States.

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Jonathan P Rose

Full Text Available Species distribution models (SDMs are increasingly used to project the potential distribution of introduced species outside their native range. Such studies rarely explicitly evaluate potential conflicts with native species should the range of introduced species expand. Two snake species native to eastern North America, Nerodia fasciata and Nerodia sipedon, have been introduced to California where they represent a new stressor to declining native amphibians, fish, and reptiles. To project the potential distributions of these non-native watersnakes in western North America, we built ensemble SDMs using MaxEnt, Boosted Regression Trees, and Random Forests and habitat and climatic variables. We then compared the overlap between the projected distribution of invasive watersnakes and the distributions of imperiled native amphibians, fish, and reptiles that can serve as prey or competitors for the invaders, to estimate the risk to native species posed by non-native watersnakes. Large areas of western North America were projected to be climatically suitable for both species of Nerodia according to our ensemble SDMs, including much of central California. The potential distributions of both N. fasciata and N. sipedon overlap extensively with the federally threatened Giant Gartersnake, Thamnophis gigas, which inhabits a similar ecological niche. N. fasciata also poses risk to the federally threatened California Tiger Salamander, Ambystoma californiense, whereas N. sipedon poses risk to some amphibians of conservation concern, including the Foothill Yellow-legged Frog, Rana boylii. We conclude that non-native watersnakes in California can likely inhabit ranges of several native species of conservation concern that are expected to suffer as prey or competing species for these invaders. Action should be taken now to eradicate or control these invasions before detrimental impacts on native species are widespread. Our methods can be applied broadly to quantify

Why and how does native topology dictate the folding speed of a protein?

Science.gov (United States)

Rustad, Mark; Ghosh, Kingshuk

2012-11-01

Since the pioneering work of Plaxco, Simons, and Baker, it is now well known that the rates of protein folding strongly correlate with the average sequence separation (absolute contact order (ACO)) of native contacts. In spite of multitude of papers, our understanding to the basis of the relation between folding speed and ACO is still lacking. We model the transition state as a Gaussian polymer chain decorated with weak springs between native contacts while the unfolded state is modeled as a Gaussian chain only. Using these hamiltonians, our perturbative calculation explicitly shows folding speed and ACO are linearly related when only the first order term in the series is considered. However, to the second order, we notice the existence of two new topological metrics, termed COC1 and COC2 (COC stands for contact order correction). These additional correction terms are needed to properly account for the entropy loss due to overlapping (nested or linked) loops that are not well described by simple addition of entropies in ACO. COC1 and COC2 are related to fluctuations and correlations among different sequence separations. The new metric combining ACO, COC1, and COC2 improves folding speed dependence on native topology when applied to three different databases: (i) two-state proteins with only α/β and β proteins, (ii) two-state proteins (α/β, β and purely helical proteins all combined), and (iii) master set (multi-state and two-state) folding proteins. Furthermore, the first principle calculation provides us direct physical insights to the meaning of the fit parameters. The coefficient of ACO, for example, is related to the average strength of the contacts, while the constant term is related to the protein folding speed limit. With the new scaling law, our estimate of the folding speed limit is in close agreement with the widely accepted value of 1 μs observed in proteins and RNA. Analyzing an exhaustive set (7367) of monomeric proteins from protein data bank

Identification of a Degradation Signal Sequence within Substrates of the Mitochondrial i-AAA Protease.

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Rampello, Anthony J; Glynn, Steven E

2017-03-24

The i-AAA protease is a component of the mitochondrial quality control machinery that regulates respiration, mitochondrial dynamics, and protein import. The protease is required to select specific substrates for degradation from among the diverse complement of proteins present in mitochondria, yet the rules that govern this selection are unclear. Here, we reconstruct the yeast i-AAA protease, Yme1p, to examine the in vitro degradation of two intermembrane space chaperone subunits, Tim9 and Tim10. Yme1p degrades Tim10 more rapidly than Tim9 despite high sequence and structural similarity, and loss of Tim10 is accelerated by the disruption of conserved disulfide bonds within the substrate. An unstructured N-terminal region of Tim10 is necessary and sufficient to target the substrate to the protease through recognition of a short phenylalanine-rich motif, and the presence of similar motifs in other small Tim proteins predicts robust degradation by the protease. Together, these results identify the first specific degron sequence within a native i-AAA protease substrate. Copyright © 2017 Elsevier Ltd. All rights reserved.

Lack of Detectable Allergenicity in Genetically Modified Maize Containing “Cry” Proteins as Compared to Native Maize Based on In Silico & In Vitro Analysis

Science.gov (United States)

Mathur, Chandni; Kathuria, Pooran C.; Dahiya, Pushpa; Singh, Anand B.

2015-01-01

Background Genetically modified, (GM) crops with potential allergens must be evaluated for safety and endogenous IgE binding pattern compared to native variety, prior to market release. Objective To compare endogenous IgE binding proteins of three GM maize seeds containing Cry 1Ab,1Ac,1C transgenic proteins with non GM maize. Methods An integrated approach of in silico & in vitro methods was employed. Cry proteins were tested for presence of allergen sequence by FASTA in allergen databases. Biochemical assays for maize extracts were performed. Specific IgE (sIgE) and Immunoblot using food sensitized patients sera (n = 39) to non GM and GM maize antigens was performed. Results In silico approaches, confirmed for non sequence similarity of stated transgenic proteins in allergen databases. An insignificant (p> 0.05) variation in protein content between GM and non GM maize was observed. Simulated Gastric Fluid (SGF) revealed reduced number of stable protein fractions in GM then non GM maize which might be due to shift of constituent protein expression. Specific IgE values from patients showed insignificant difference in non GM and GM maize extracts. Five maize sensitized cases, recognized same 7 protein fractions of 88-28 kD as IgE bindng in both GM and non-GM maize, signifying absence of variation. Four of the reported IgE binding proteins were also found to be stable by SGF. Conclusion Cry proteins did not indicate any significant similarity of >35% in allergen databases. Immunoassays also did not identify appreciable differences in endogenous IgE binding in GM and non GM maize. PMID:25706412

Contrasting Pollinators and Pollination in Native and Non-Native Regions of Highbush Blueberry Production.

Science.gov (United States)

Gibbs, Jason; Elle, Elizabeth; Bobiwash, Kyle; Haapalainen, Tiia; Isaacs, Rufus

2016-01-01

Highbush blueberry yields are dependent on pollination by bees, and introduction of managed honey bees is the primary strategy used for pollination of this crop. Complementary pollination services are also provided by wild bees, yet highbush blueberry is increasingly grown in regions outside its native range where wild bee communities may be less adapted to the crop and growers may still be testing appropriate honey bee stocking densities. To contrast crop pollination in native and non-native production regions, we sampled commercial 'Bluecrop' blueberry fields in British Columbia and Michigan with grower-selected honey bee stocking rates (0-39.5 hives per ha) to compare bee visitors to blueberry flowers, pollination and yield deficits, and how those vary with local- and landscape-scale factors. Observed and Chao-1 estimated species richness, as well as Shannon diversity of wild bees visiting blueberries were significantly higher in Michigan where the crop is within its native range. The regional bee communities were also significantly different, with Michigan farms having greater dissimilarity than British Columbia. Blueberry fields in British Columbia had fewer visits by honey bees than those in Michigan, irrespective of stocking rate, and they also had lower berry weights and a significant pollination deficit. In British Columbia, pollination service increased with abundance of wild bumble bees, whereas in Michigan the abundance of honey bees was the primary predictor of pollination. The proportion of semi-natural habitat at local and landscape scales was positively correlated with wild bee abundance in both regions. Wild bee abundance declined significantly with distance from natural borders in Michigan, but not in British Columbia where large-bodied bumble bees dominated the wild bee community. Our results highlight the varying dependence of crop production on different types of bees and reveal that strategies for pollination improvement in the same crop can

Contrasting Pollinators and Pollination in Native and Non-Native Regions of Highbush Blueberry Production.

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Jason Gibbs

Full Text Available Highbush blueberry yields are dependent on pollination by bees, and introduction of managed honey bees is the primary strategy used for pollination of this crop. Complementary pollination services are also provided by wild bees, yet highbush blueberry is increasingly grown in regions outside its native range where wild bee communities may be less adapted to the crop and growers may still be testing appropriate honey bee stocking densities. To contrast crop pollination in native and non-native production regions, we sampled commercial 'Bluecrop' blueberry fields in British Columbia and Michigan with grower-selected honey bee stocking rates (0-39.5 hives per ha to compare bee visitors to blueberry flowers, pollination and yield deficits, and how those vary with local- and landscape-scale factors. Observed and Chao-1 estimated species richness, as well as Shannon diversity of wild bees visiting blueberries were significantly higher in Michigan where the crop is within its native range. The regional bee communities were also significantly different, with Michigan farms having greater dissimilarity than British Columbia. Blueberry fields in British Columbia had fewer visits by honey bees than those in Michigan, irrespective of stocking rate, and they also had lower berry weights and a significant pollination deficit. In British Columbia, pollination service increased with abundance of wild bumble bees, whereas in Michigan the abundance of honey bees was the primary predictor of pollination. The proportion of semi-natural habitat at local and landscape scales was positively correlated with wild bee abundance in both regions. Wild bee abundance declined significantly with distance from natural borders in Michigan, but not in British Columbia where large-bodied bumble bees dominated the wild bee community. Our results highlight the varying dependence of crop production on different types of bees and reveal that strategies for pollination improvement in

Decarboxylative alkylation for site-selective bioconjugation of native proteins via oxidation potentials

Science.gov (United States)

Bloom, Steven; Liu, Chun; Kölmel, Dominik K.; Qiao, Jennifer X.; Zhang, Yong; Poss, Michael A.; Ewing, William R.; MacMillan, David W. C.

2018-02-01

The advent of antibody-drug conjugates as pharmaceuticals has fuelled a need for reliable methods of site-selective protein modification that furnish homogeneous adducts. Although bioorthogonal methods that use engineered amino acids often provide an elegant solution to the question of selective functionalization, achieving homogeneity using native amino acids remains a challenge. Here, we explore visible-light-mediated single-electron transfer as a mechanism towards enabling site- and chemoselective bioconjugation. Specifically, we demonstrate the use of photoredox catalysis as a platform to selectivity wherein the discrepancy in oxidation potentials between internal versus C-terminal carboxylates can be exploited towards obtaining C-terminal functionalization exclusively. This oxidation potential-gated technology is amenable to endogenous peptides and has been successfully demonstrated on the protein insulin. As a fundamentally new approach to bioconjugation this methodology provides a blueprint toward the development of photoredox catalysis as a generic platform to target other redox-active side chains for native conjugation.

Decarboxylative alkylation for site-selective bioconjugation of native proteins via oxidation potentials.

Science.gov (United States)

Bloom, Steven; Liu, Chun; Kölmel, Dominik K; Qiao, Jennifer X; Zhang, Yong; Poss, Michael A; Ewing, William R; MacMillan, David W C

2018-02-01

The advent of antibody-drug conjugates as pharmaceuticals has fuelled a need for reliable methods of site-selective protein modification that furnish homogeneous adducts. Although bioorthogonal methods that use engineered amino acids often provide an elegant solution to the question of selective functionalization, achieving homogeneity using native amino acids remains a challenge. Here, we explore visible-light-mediated single-electron transfer as a mechanism towards enabling site- and chemoselective bioconjugation. Specifically, we demonstrate the use of photoredox catalysis as a platform to selectivity wherein the discrepancy in oxidation potentials between internal versus C-terminal carboxylates can be exploited towards obtaining C-terminal functionalization exclusively. This oxidation potential-gated technology is amenable to endogenous peptides and has been successfully demonstrated on the protein insulin. As a fundamentally new approach to bioconjugation this methodology provides a blueprint toward the development of photoredox catalysis as a generic platform to target other redox-active side chains for native conjugation.

A pairwise residue contact area-based mean force potential for discrimination of native protein structure

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Pezeshk Hamid

2010-01-01

Full Text Available Abstract Background Considering energy function to detect a correct protein fold from incorrect ones is very important for protein structure prediction and protein folding. Knowledge-based mean force potentials are certainly the most popular type of interaction function for protein threading. They are derived from statistical analyses of interacting groups in experimentally determined protein structures. These potentials are developed at the atom or the amino acid level. Based on orientation dependent contact area, a new type of knowledge-based mean force potential has been developed. Results We developed a new approach to calculate a knowledge-based potential of mean-force, using pairwise residue contact area. To test the performance of our approach, we performed it on several decoy sets to measure its ability to discriminate native structure from decoys. This potential has been able to distinguish native structures from the decoys in the most cases. Further, the calculated Z-scores were quite high for all protein datasets. Conclusions This knowledge-based potential of mean force can be used in protein structure prediction, fold recognition, comparative modelling and molecular recognition. The program is available at http://www.bioinf.cs.ipm.ac.ir/softwares/surfield

A Novel Semi-biosynthetic Route for Artemisinin Production Using Engineered Substrate-Promiscuous P450BM3

Energy Technology Data Exchange (ETDEWEB)

Dietrich, Jeffrey; Yoshikuni, Yasuo; Fisher, Karl; Woolard, Frank; Ockey, Denise; McPhee, Derek; Renninger, Neil; Chang, Michelle; Baker, David; Keasling, Jay

2009-11-30

Production of fine heterologus pathways in microbial hosts is frequently hindered by insufficient knowledge of the native metabolic pathway and its cognate enzymes; often the pathway is unresolved and enzymes lack detailed characterization. An alternative paradigm to using native pathways is de novo pathway design using well-characterized, substrate-promiscuous enzymes. We demonstrate this concept using P450BM3 from Bacillus megaterium. Using a computer model, we illustrate how key P450BM3 activ site mutations enable binding of non-native substrate amorphadiene, incorporating these mutations into P450BM3 enabled the selective oxidation of amorphadiene arteminsinic-11s,12-epoxide, at titers of 250 mg L"1 in E. coli. We also demonstrate high-yeilding, selective transformations to dihydroartemisinic acid, the immediate precursor to the high value anti-malarial drug artemisinin.

Non-native gobies facilitate the transmission of Bucephalus polymorphus (Trematoda)

Czech Academy of Sciences Publication Activity Database

Ondračková, Markéta; Hudcová, Iveta; Dávidová, Martina; Adámek, Zdeněk; Kašný, M.; Jurajda, Pavel

2015-01-01

Roč. 8, č. 1 (2015), s. 382 ISSN 1756-3305 R&D Projects: GA ČR(CZ) GAP505/12/2569 Institutional support: RVO:68081766 Keywords : Bucephalus polymorphus * Complex life cycle * Goby * Infectivity * Intermediate host * Non-native species * Trematode Subject RIV: EH - Ecology, Behaviour Impact factor: 3.234, year: 2015

Broad substrate tolerance of tubulin tyrosine ligase enables one-step site-specific enzymatic protein labeling.

Science.gov (United States)

Schumacher, Dominik; Lemke, Oliver; Helma, Jonas; Gerszonowicz, Lena; Waller, Verena; Stoschek, Tina; Durkin, Patrick M; Budisa, Nediljko; Leonhardt, Heinrich; Keller, Bettina G; Hackenberger, Christian P R

2017-05-01

The broad substrate tolerance of tubulin tyrosine ligase is the basic rationale behind its wide applicability for chemoenzymatic protein functionalization. In this context, we report that the wild-type enzyme enables ligation of various unnatural amino acids that are substantially bigger than and structurally unrelated to the natural substrate, tyrosine, without the need for extensive protein engineering. This unusual substrate flexibility is due to the fact that the enzyme's catalytic pocket forms an extended cavity during ligation, as confirmed by docking experiments and all-atom molecular dynamics simulations. This feature enabled one-step C-terminal biotinylation and fluorescent coumarin labeling of various functional proteins as demonstrated with ubiquitin, an antigen binding nanobody, and the apoptosis marker Annexin V. Its broad substrate tolerance establishes tubulin tyrosine ligase as a powerful tool for in vitro enzyme-mediated protein modification with single functional amino acids in a specific structural context.

Growing Periandra mediterranea on post-mining substrate: native Fabaceae with potential for revegetation of degraded rupestrian grasslands in Brazil

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Maurilio Assis Figueiredo

2018-01-01

Full Text Available ABSTRACT Recovery of degraded areas of rupestrian grasslands is hampered mainly by the limited knowledge regarding substrate management and the biology of native species suitable for revegetation of these areas. The aim of our study was to examine the establishment and growth of Periandra mediterranea in different textures of lateritic substrate from a mining-degraded area. The growth of P. mediterranea was evaluated using fine and coarse laterite, both with and without the addition of topsoil. Survival, dry biomass, content of chemical elements and nodulation were evaluated in ten individuals per treatment sixteen months after planting. Although the substrate has low nutrient content, yet high metal concentrations, all plants survived. Plants growing on coarse laterite had 140 % greater biomass than those growing on fine laterite. The addition of topsoil increased biomass in coarse and fine laterite by 46 and 151 %, respectively, and doubled the number of nodulated plants, regardless of grain size. The biomass accumulation of P. mediterranea to a dystrophic substrate revealed its potential for use in the revegetation of degraded areas of rupestrian grasslands. Furthermore, the addition of topsoil facilitated the association of P. mediterranea with nitrogen-fixing bacteria, and increased its growth and capacity to improve substrate fertility.

Non-Native Japanese Listeners' Perception of Vowel Length Contrasts in Japanese and Modern Standard Arabic (MSA)

Science.gov (United States)

Tsukada, Kimiko

2012-01-01

This study aimed to compare the perception of short vs. long vowel contrasts in Japanese and Modern Standard Arabic (MSA) by four groups of listeners differing in their linguistic backgrounds: native Arabic (NA), native Japanese (NJ), non-native Japanese (NNJ) and Australian English (OZ) speakers. The NNJ and OZ groups shared the first language…

Proteolytic activity of prostate-specific antigen (PSA towards protein substrates and effect of peptides stimulating PSA activity.

Directory of Open Access Journals (Sweden)

Johanna M Mattsson

Full Text Available Prostate-specific antigen (PSA or kallikrein-related peptidase-3, KLK3 exerts chymotrypsin-like proteolytic activity. The main biological function of PSA is the liquefaction of the clot formed after ejaculation by cleavage of semenogelins I and II in seminal fluid. PSA also cleaves several other substrates, which may explain its putative functions in prostate cancer and its antiangiogenic activity. We compared the proteolytic efficiency of PSA towards several protein and peptide substrates and studied the effect of peptides stimulating the activity of PSA with these substrates. An endothelial cell tube formation model was used to analyze the effect of PSA-degraded protein fragments on angiogenesis. We showed that PSA degrades semenogelins I and II much more efficiently than other previously identified protein substrates, e.g., fibronectin, galectin-3 and IGFBP-3. We identified nidogen-1 as a new substrate for PSA. Peptides B2 and C4 that stimulate the activity of PSA towards small peptide substrates also enhanced the proteolytic activity of PSA towards protein substrates. Nidogen-1, galectin-3 or their fragments produced by PSA did not have any effect on endothelial cell tube formation. Although PSA cleaves several other protein substrates, in addition to semenogelins, the physiological importance of this activity remains speculative. The PSA levels in prostate are very high, but several other highly active proteases, such as hK2 and trypsin, are also expressed in the prostate and may cleave protein substrates that are weakly cleaved by PSA.

PROSPER: an integrated feature-based tool for predicting protease substrate cleavage sites.

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Jiangning Song

Full Text Available The ability to catalytically cleave protein substrates after synthesis is fundamental for all forms of life. Accordingly, site-specific proteolysis is one of the most important post-translational modifications. The key to understanding the physiological role of a protease is to identify its natural substrate(s. Knowledge of the substrate specificity of a protease can dramatically improve our ability to predict its target protein substrates, but this information must be utilized in an effective manner in order to efficiently identify protein substrates by in silico approaches. To address this problem, we present PROSPER, an integrated feature-based server for in silico identification of protease substrates and their cleavage sites for twenty-four different proteases. PROSPER utilizes established specificity information for these proteases (derived from the MEROPS database with a machine learning approach to predict protease cleavage sites by using different, but complementary sequence and structure characteristics. Features used by PROSPER include local amino acid sequence profile, predicted secondary structure, solvent accessibility and predicted native disorder. Thus, for proteases with known amino acid specificity, PROSPER provides a convenient, pre-prepared tool for use in identifying protein substrates for the enzymes. Systematic prediction analysis for the twenty-four proteases thus far included in the database revealed that the features we have included in the tool strongly improve performance in terms of cleavage site prediction, as evidenced by their contribution to performance improvement in terms of identifying known cleavage sites in substrates for these enzymes. In comparison with two state-of-the-art prediction tools, PoPS and SitePrediction, PROSPER achieves greater accuracy and coverage. To our knowledge, PROSPER is the first comprehensive server capable of predicting cleavage sites of multiple proteases within a single substrate

Identification of secreted proteins of Aspergillus oryzae associated with growth on solid cereal substrates

NARCIS (Netherlands)

Biesebeke, R. te; Boussier, A.; Biezen, N. van; Hondel, C.A.M.J.J. van den; Punt, P.J.

2006-01-01

Filamentous growth of Aspergillus oryzae on solid cereal substrates involves secretion of substrate converting enzymes and a solid substrate specific polarised hyphal growth phenotype. To identify proteins produced under these specific conditions, the extracts of A. oryzae grown on wheat-based media

Atypical lateralization of ERP response to native and non-native speech in infants at risk for autism spectrum disorder.

Science.gov (United States)

Seery, Anne M; Vogel-Farley, Vanessa; Tager-Flusberg, Helen; Nelson, Charles A

2013-07-01

Language impairment is common in autism spectrum disorders (ASD) and is often accompanied by atypical neural lateralization. However, it is unclear when in development language impairment or atypical lateralization first emerges. To address these questions, we recorded event-related-potentials (ERPs) to native and non-native speech contrasts longitudinally in infants at risk for ASD (HRA) over the first year of life to determine whether atypical lateralization is present as an endophenotype early in development and whether these infants show delay in a very basic precursor of language acquisition: phonemic perceptual narrowing. ERP response for the HRA group to a non-native speech contrast revealed a trajectory of perceptual narrowing similar to a group of low-risk controls (LRC), suggesting that phonemic perceptual narrowing does not appear to be delayed in these high-risk infants. In contrast there were significant group differences in the development of lateralized ERP response to speech: between 6 and 12 months the LRC group displayed a lateralized response to the speech sounds, while the HRA group failed to display this pattern. We suggest the possibility that atypical lateralization to speech may be an ASD endophenotype over the first year of life. Copyright © 2012 Elsevier Ltd. All rights reserved.

Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading?

Science.gov (United States)

Vendruscolo, M; Najmanovich, R; Domany, E

2000-02-01

We present a method to derive contact energy parameters from large sets of proteins. The basic requirement on which our method is based is that for each protein in the database the native contact map has lower energy than all its decoy conformations that are obtained by threading. Only when this condition is satisfied one can use the proposed energy function for fold identification. Such a set of parameters can be found (by perceptron learning) if Mp, the number of proteins in the database, is not too large. Other aspects that influence the existence of such a solution are the exact definition of contact and the value of the critical distance Rc, below which two residues are considered to be in contact. Another important novel feature of our approach is its ability to determine whether an energy function of some suitable proposed form can or cannot be parameterized in a way that satisfies our basic requirement. As a demonstration of this, we determine the region in the (Rc, Mp) plane in which the problem is solvable, i.e., we can find a set of contact parameters that stabilize simultaneously all the native conformations. We show that for large enough databases the contact approximation to the energy cannot stabilize all the native folds even against the decoys obtained by gapless threading.

Using the Speech Transmission Index for predicting non-native speech intelligibility

NARCIS (Netherlands)

Wijngaarden, S.J. van; Bronkhorst, A.W.; Houtgast, T.; Steeneken, H.J.M.

2004-01-01

While the Speech Transmission Index ~STI! is widely applied for prediction of speech intelligibility in room acoustics and telecommunication engineering, it is unclear how to interpret STI values when non-native talkers or listeners are involved. Based on subjectively measured psychometric functions

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

Science.gov (United States)

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.

Understanding the threats posed by non-native species: public vs. conservation managers.

Directory of Open Access Journals (Sweden)

Rodolphe E Gozlan

Full Text Available Public perception is a key factor influencing current conservation policy. Therefore, it is important to determine the influence of the public, end-users and scientists on the prioritisation of conservation issues and the direct implications for policy makers. Here, we assessed public attitudes and the perception of conservation managers to five non-native species in the UK, with these supplemented by those of an ecosystem user, freshwater anglers. We found that threat perception was not influenced by the volume of scientific research or by the actual threats posed by the specific non-native species. Media interest also reflected public perception and vice versa. Anglers were most concerned with perceived threats to their recreational activities but their concerns did not correspond to the greatest demonstrated ecological threat. The perception of conservation managers was an amalgamation of public and angler opinions but was mismatched to quantified ecological risks of the species. As this suggests that invasive species management in the UK is vulnerable to a knowledge gap, researchers must consider the intrinsic characteristics of their study species to determine whether raising public perception will be effective. The case study of the topmouth gudgeon Pseudorasbora parva reveals that media pressure and political debate has greater capacity to ignite policy changes and impact studies on non-native species than scientific evidence alone.

Precise determination of protein extinction coefficients under native and denaturing conditions using SV-AUC.

Science.gov (United States)

Hoffmann, Andreas; Grassl, Kerstin; Gommert, Janine; Schlesak, Christian; Bepperling, Alexander

2018-04-17

The accurate determination of protein concentration is an important though non-trivial task during the development of a biopharmaceutical. The fundamental prerequisite for this is the availability of an accurate extinction coefficient. Common approaches for the determination of an extinction coefficient for a given protein are either based on the theoretical prediction utilizing the amino acid sequence or the photometric determination combined with a measurement of absolute protein concentration. Here, we report on an improved SV-AUC based method utilizing an analytical ultracentrifuge equipped with absorbance and Rayleigh interference optics. Global fitting of datasets helped to overcome some of the obstacles encountered with the traditional method employing synthetic boundary cells. Careful calculation of dn/dc values taking glycosylation and solvent composition into account allowed the determination of the extinction coefficients of monoclonal antibodies and an Fc-fusion protein under native as well as under denaturing conditions. An intra-assay precision of 0.9% and an accuracy of 1.8% compared to the theoretical value was achieved for monoclonal antibodies. Due to the large number of data points of a single dataset, no meaningful difference between the ProteomeLab XL-I and the new Optima AUC platform could be observed. Thus, the AUC-based approach offers a precise, convenient and versatile alternative to conventional methods like total amino acid analysis (AAA).

Predictors of natively unfolded proteins: unanimous consensus score to detect a twilight zone between order and disorder in generic datasets

Directory of Open Access Journals (Sweden)

Deiana Antonio

2010-04-01

Full Text Available Abstract Background Natively unfolded proteins lack a well defined three dimensional structure but have important biological functions, suggesting a re-assignment of the structure-function paradigm. To assess that a given protein is natively unfolded requires laborious experimental investigations, then reliable sequence-only methods for predicting whether a sequence corresponds to a folded or to an unfolded protein are of interest in fundamental and applicative studies. Many proteins have amino acidic compositions compatible both with the folded and unfolded status, and belong to a twilight zone between order and disorder. This makes difficult a dichotomic classification of protein sequences into folded and natively unfolded ones. In this work we propose an operational method to identify proteins belonging to the twilight zone by combining into a consensus score good performing single predictors of folding. Results In this methodological paper dichotomic folding indexes are considered: hydrophobicity-charge, mean packing, mean pairwise energy, Poodle-W and a new global index, that is called here gVSL2, based on the local disorder predictor VSL2. The performance of these indexes is evaluated on different datasets, in particular on a new dataset composed by 2369 folded and 81 natively unfolded proteins. Poodle-W, gVSL2 and mean pairwise energy have good performance and stability in all the datasets considered and are combined into a strictly unanimous combination score SSU, that leaves proteins unclassified when the consensus of all combined indexes is not reached. The unclassified proteins: i belong to an overlap region in the vector space of amino acidic compositions occupied by both folded and unfolded proteins; ii are composed by approximately the same number of order-promoting and disorder-promoting amino acids; iii have a mean flexibility intermediate between that of folded and that of unfolded proteins. Conclusions Our results show that

How amide hydrogens exchange in native proteins.

Science.gov (United States)

Persson, Filip; Halle, Bertil

2015-08-18

Amide hydrogen exchange (HX) is widely used in protein biophysics even though our ignorance about the HX mechanism makes data interpretation imprecise. Notably, the open exchange-competent conformational state has not been identified. Based on analysis of an ultralong molecular dynamics trajectory of the protein BPTI, we propose that the open (O) states for amides that exchange by subglobal fluctuations are locally distorted conformations with two water molecules directly coordinated to the N-H group. The HX protection factors computed from the relative O-state populations agree well with experiment. The O states of different amides show little or no temporal correlation, even if adjacent residues unfold cooperatively. The mean residence time of the O state is ∼100 ps for all examined amides, so the large variation in measured HX rate must be attributed to the opening frequency. A few amides gain solvent access via tunnels or pores penetrated by water chains including native internal water molecules, but most amides access solvent by more local structural distortions. In either case, we argue that an overcoordinated N-H group is necessary for efficient proton transfer by Grotthuss-type structural diffusion.

How amide hydrogens exchange in native proteins

Science.gov (United States)

Persson, Filip; Halle, Bertil

2015-01-01

Amide hydrogen exchange (HX) is widely used in protein biophysics even though our ignorance about the HX mechanism makes data interpretation imprecise. Notably, the open exchange-competent conformational state has not been identified. Based on analysis of an ultralong molecular dynamics trajectory of the protein BPTI, we propose that the open (O) states for amides that exchange by subglobal fluctuations are locally distorted conformations with two water molecules directly coordinated to the N–H group. The HX protection factors computed from the relative O-state populations agree well with experiment. The O states of different amides show little or no temporal correlation, even if adjacent residues unfold cooperatively. The mean residence time of the O state is ∼100 ps for all examined amides, so the large variation in measured HX rate must be attributed to the opening frequency. A few amides gain solvent access via tunnels or pores penetrated by water chains including native internal water molecules, but most amides access solvent by more local structural distortions. In either case, we argue that an overcoordinated N–H group is necessary for efficient proton transfer by Grotthuss-type structural diffusion. PMID:26195754

Listening to a non-native speaker: Adaptation and generalization

Science.gov (United States)

Clarke, Constance M.

2004-05-01

Non-native speech can cause perceptual difficulty for the native listener, but experience can moderate this difficulty. This study explored the perceptual benefit of a brief (approximately 1 min) exposure to foreign-accented speech using a cross-modal word matching paradigm. Processing speed was tracked by recording reaction times (RTs) to visual probe words following English sentences produced by a Spanish-accented speaker. In experiment 1, RTs decreased significantly over 16 accented utterances and by the end were equal to RTs to a native voice. In experiment 2, adaptation to one Spanish-accented voice improved perceptual efficiency for a new Spanish-accented voice, indicating that abstract properties of accented speech are learned during adaptation. The control group in Experiment 2 also adapted to the accented voice during the test block, suggesting adaptation can occur within two to four sentences. The results emphasize the flexibility of the human speech processing system and the need for a mechanism to explain this adaptation in models of spoken word recognition. [Research supported by an NSF Graduate Research Fellowship and the University of Arizona Cognitive Science Program.] a)Currently at SUNY at Buffalo, Dept. of Psych., Park Hall, Buffalo, NY 14260, cclarke2@buffalo.edu

Exploring the role of wood waste landfills in early detection of non-native alien wood-boring beetles

Science.gov (United States)

Davide Rassati; Massimo Faccoli; Lorenzo Marini; Robert A. Haack; Andrea Battisti; Edoardo. Petrucco Toffolo

2015-01-01

Non-native wood-boring beetles (Coleoptera) represent one of the most commonly intercepted groups of insects at ports worldwide. The development of early detection methods is a crucial step when implementing rapid response programs so that non-native wood-boring beetles can be quickly detected and a timely action plan can be produced. However, due to the limited...

Bacillus subtilis BY-kinase PtkA controls enzyme activity and localization of its protein substrates

DEFF Research Database (Denmark)

Jers, Carsten; Pedersen, Malene Mejer; Paspaliari, Dafni Katerina

2010-01-01

-phosphorylated proteins in B. subtilis. We found that the majority of these proteins could be phosphorylated by PtkA in vitro. Among these new substrates, single-stranded DNA exonuclease YorK, and aspartate semialdehyde dehydrogenase Asd were activated by PtkA-dependent phosphorylation. Because enzyme activity......A was dramatically altered in Delta ptkA background. Our results confirm that PtkA can control enzyme activity of its substrates in some cases, but also reveal a new mode of action for PtkA, namely ensuring correct cellular localization of its targets.......P>Bacillus subtilis BY-kinase PtkA was previously shown to phosphorylate, and thereby regulate the activity of two classes of protein substrates: UDP-glucose dehydrogenases and single-stranded DNA-binding proteins. Our recent phosphoproteome study identified nine new tyrosine...

Agarose gel shift assay reveals that calreticulin favors substrates with a quaternary structure in solution

DEFF Research Database (Denmark)

Boelt, Sanne Grundvad; Houen, Gunnar; Højrup, Peter

2015-01-01

Here we present an agarose gel shift assay that, in contrast to other electrophoresis approaches, is loaded in the center of the gel. This allows proteins to migrate in either direction according to their isoelectric points. Therefore, the presented assay enables a direct visualization, separation...... structure. It is also demonstrated that the agarose gel shift assay is useful in the study of other protein interactions and can be used as an alternative method to native polyacrylamide gel electrophoresis....... measure of interactions. Therefore, no interaction studies between calreticulin and substrates in solution have been investigated previously. The results presented here indicate that calreticulin has a preference for substrates with a quaternary structure and primarily β-sheets in their secondary...

Integration of conducting polymer network in non-conductive polymer substrates

DEFF Research Database (Denmark)

Hansen, Thomas Steen; West, Keld; Hassager, Ole

2006-01-01

Anew method for integration ofconjugated, inherently conducting polymers into non-conductive polymer substrates has been developed. Alayer of the conducting polymer is polymerised by chemical oxidation, e.g. using Fe(ID) p-toluene sulfonate (ferri tosylate) followed by washing with a solvent which...... simultaneously removes residual and spent oxidant and at the same time dissolves the top layer of the polymer substrate. This results in an integration of the conducting polymer into the surface layers of the polymer substrate. Several combinations of conducting polymers and substrates have been tested...... absorption during sequential reactive ion etching has allowed for analysis of the PEDOT distribution within the surface layer of thePMMA substrate. The surface resistance ofthe conducting polymer layer remains low while the surface layer at the same time adapts some of the mechanical properties...

Invasion of non-native grasses causes a drop in soil carbon storage in California grasslands

Energy Technology Data Exchange (ETDEWEB)

Koteen, Laura E; Harte, John [Energy and Resources Group, 310 Barrows Hall, University of California, Berkeley, CA 94720 (United States); Baldocchi, Dennis D, E-mail: lkoteen@berkeley.edu [Department of Environmental Science, Policy and Management, 137 Mulford Hall, University of California, Berkeley, CA 94720 (United States)

2011-10-15

Vegetation change can affect the magnitude and direction of global climate change via its effect on carbon cycling among plants, the soil and the atmosphere. The invasion of non-native plants is a major cause of land cover change, of biodiversity loss, and of other changes in ecosystem structure and function. In California, annual grasses from Mediterranean Europe have nearly displaced native perennial grasses across the coastal hillsides and terraces of the state. Our study examines the impact of this invasion on carbon cycling and storage at two sites in northern coastal California. The results suggest that annual grass invasion has caused an average drop in soil carbon storage of 40 Mg/ha in the top half meter of soil, although additional mechanisms may also contribute to soil carbon losses. We attribute the reduction in soil carbon storage to low rates of net primary production in non-native annuals relative to perennial grasses, a shift in rooting depth and water use to primarily shallow sources, and soil respiratory losses in non-native grass soils that exceed production rates. These results indicate that even seemingly subtle land cover changes can significantly impact ecosystem functions in general, and carbon storage in particular.

Invasion of non-native grasses causes a drop in soil carbon storage in California grasslands

International Nuclear Information System (INIS)

Koteen, Laura E; Harte, John; Baldocchi, Dennis D

2011-01-01

Vegetation change can affect the magnitude and direction of global climate change via its effect on carbon cycling among plants, the soil and the atmosphere. The invasion of non-native plants is a major cause of land cover change, of biodiversity loss, and of other changes in ecosystem structure and function. In California, annual grasses from Mediterranean Europe have nearly displaced native perennial grasses across the coastal hillsides and terraces of the state. Our study examines the impact of this invasion on carbon cycling and storage at two sites in northern coastal California. The results suggest that annual grass invasion has caused an average drop in soil carbon storage of 40 Mg/ha in the top half meter of soil, although additional mechanisms may also contribute to soil carbon losses. We attribute the reduction in soil carbon storage to low rates of net primary production in non-native annuals relative to perennial grasses, a shift in rooting depth and water use to primarily shallow sources, and soil respiratory losses in non-native grass soils that exceed production rates. These results indicate that even seemingly subtle land cover changes can significantly impact ecosystem functions in general, and carbon storage in particular.

Invasion of non-native grasses causes a drop in soil carbon storage in California grasslands

Science.gov (United States)

Koteen, Laura E.; Baldocchi, Dennis D.; Harte, John

2011-10-01

Vegetation change can affect the magnitude and direction of global climate change via its effect on carbon cycling among plants, the soil and the atmosphere. The invasion of non-native plants is a major cause of land cover change, of biodiversity loss, and of other changes in ecosystem structure and function. In California, annual grasses from Mediterranean Europe have nearly displaced native perennial grasses across the coastal hillsides and terraces of the state. Our study examines the impact of this invasion on carbon cycling and storage at two sites in northern coastal California. The results suggest that annual grass invasion has caused an average drop in soil carbon storage of 40 Mg/ha in the top half meter of soil, although additional mechanisms may also contribute to soil carbon losses. We attribute the reduction in soil carbon storage to low rates of net primary production in non-native annuals relative to perennial grasses, a shift in rooting depth and water use to primarily shallow sources, and soil respiratory losses in non-native grass soils that exceed production rates. These results indicate that even seemingly subtle land cover changes can significantly impact ecosystem functions in general, and carbon storage in particular.

Non-Protein Coding RNAs

CERN Document Server

Walter, Nils G; Batey, Robert T

2009-01-01

This book assembles chapters from experts in the Biophysics of RNA to provide a broadly accessible snapshot of the current status of this rapidly expanding field. The 2006 Nobel Prize in Physiology or Medicine was awarded to the discoverers of RNA interference, highlighting just one example of a large number of non-protein coding RNAs. Because non-protein coding RNAs outnumber protein coding genes in mammals and other higher eukaryotes, it is now thought that the complexity of organisms is correlated with the fraction of their genome that encodes non-protein coding RNAs. Essential biological processes as diverse as cell differentiation, suppression of infecting viruses and parasitic transposons, higher-level organization of eukaryotic chromosomes, and gene expression itself are found to largely be directed by non-protein coding RNAs. The biophysical study of these RNAs employs X-ray crystallography, NMR, ensemble and single molecule fluorescence spectroscopy, optical tweezers, cryo-electron microscopy, and ot...

The influence of substrate material on ascidian larval settlement.

Science.gov (United States)

Chase, Anna L; Dijkstra, Jennifer A; Harris, Larry G

2016-05-15

Submerged man-made structures present novel habitat for marine organisms and often host communities that differ from those on natural substrates. Although many factors are known to contribute to these differences, few studies have directly examined the influence of substrate material on organism settlement. We quantified larval substrate preferences of two species of ascidians, Ciona intestinalis (cryptogenic, formerly C. intestinalis type B) and Botrylloides violaceus (non-native), on commonly occurring natural (granite) and man-made (concrete, high-density polyethylene, PVC) marine materials in laboratory trials. Larvae exhibited species-specific settlement preferences, but generally settled more often than expected by chance on concrete and HDPE. Variation in settlement between materials may reflect preferences for rougher substrates, or may result from the influence of leached chemicals on ascidian settlement. These findings indicate that an experimental plate material can influence larval behavior and may help us understand how substrate features may contribute to differences in settlement in the field. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Acquisition of English Focus Marking by Non-Native Speakers

Science.gov (United States)

Baker, Rachel Elizabeth

This dissertation examines Mandarin and Korean speakers' acquisition of English focus marking, which is realized by accenting particular words within a focused constituent. It is important for non-native speakers to learn how accent placement relates to focus in English because appropriate accent placement and realization makes a learner's English more native-like and easier to understand. Such knowledge may also improve their English comprehension skills. In this study, 20 native English speakers, 20 native Mandarin speakers, and 20 native Korean speakers participated in four experiments: (1) a production experiment, in which they were recorded reading the answers to questions, (2) a perception experiment, in which they were asked to determine which word in a recording was the last prominent word, (3) an understanding experiment, in which they were asked whether the answers in recorded question-answer pairs had context-appropriate prosody, and (4) an accent placement experiment, in which they were asked which word they would make prominent in a particular context. Finally, a new group of native English speakers listened to utterances produced in the production experiment, and determined whether the prosody of each utterance was appropriate for its context. The results of the five experiments support a novel predictive model for second language prosodic focus marking acquisition. This model holds that both transfer of linguistic features from a learner's native language (L1) and features of their second language (L2) affect learners' acquisition of prosodic focus marking. As a result, the model includes two complementary components: the Transfer Component and the L2 Challenge Component. The Transfer Component predicts that prosodic structures in the L2 will be more easily acquired by language learners that have similar structures in their L1 than those who do not, even if there are differences between the L1 and L2 in how the structures are realized. The L2

Ethical Considerations in Conducting Research with Non-Native Speakers of English

Science.gov (United States)

Koulouriotis, Joanna

2011-01-01

The ethical considerations of three education researchers working with non-native English-speaking participants were examined from a critical theory stand-point in the light of the literature on research ethics in various disciplines. Qualitative inquiry and data analysis were used to identify key themes, which centered around honor and respect…

Versatility of non-native forms of human cytochrome c: pH and micellar concentration dependence.

Science.gov (United States)

Simon, Matthieu; Metzinger-Le Meuth, Valérie; Chevance, Soizic; Delalande, Olivier; Bondon, Arnaud

2013-01-01

In addition to its electron transfer activity, cytochrome c is now known to trigger apoptosis via peroxidase activity. This new function is related to a structural modification of the cytochrome upon association with anionic lipids, particularly cardiolipin present in the mitochondrial membrane. However, the exact nature of the non-native state induced by this interaction remains an active subject of debate. In this work, using human cytochromes c (native and two single-histidine mutants and the corresponding double mutant) and micelles as a hydrophobic medium, we succeeded, through UV-visible spectroscopy, circular dichroism spectroscopy and NMR spectroscopy, in fully characterizing the nature of the sixth ligand replacing the native methionine. Furthermore, careful pH titrations permitted the identification of the amino acids involved in the iron binding over a range of pH values. Replacement of the methionine by lysine was only observed at pH above 8.5, whereas histidine binding is dependent on both pH and micelle concentration. The pH variation range for histidine protonation is relatively narrow and is consistent with the mitochondrial intermembrane pH changes occurring during apoptosis. These results allow us to rule out lysine as the sixth ligand at pH values close to neutrality and reinforce the role of histidines (preferentially His33 vs. His26) as the main candidate to replace methionine in the non-native cytochrome c. Finally, on the basis of these results and molecular dynamics simulations, we propose a 3D model for non-native cytochrome c in a micellar environment.

Pengaruh Nisbah Energi-Protein, Nitrogen-Sulfur dan Kalsium-Fosfor Terhadap Produk Metabolisme Rumen dan Kecernaan Substrat

Directory of Open Access Journals (Sweden)

S.N.O. Suwandyastuti

2013-10-01

Full Text Available Influence of the ratio of energy-protein, nitrogen-sulphur, and calsium-phosphor upon rumen metabolism product and digestibility of substrat ABSTRACT. The Rumen microbes are capable to digest the glucosa polymer of plant waste for energy source and can used the Non Protein Nitrogen (NPN for body protein synthesis, if the other precussor (Sulphur, Phospor and Branch Chain of Carbon are available.  To know the effectivity of the utilization of plant waste for energy, an experiment have been conducted by in vitro method, used the Randomized Black Design, four replication, factorial 33.  The factors tested are : (1 three levels of energy : protein (E/P ratio : 4, 5 and 6; (2 three levels of Nitrogen : Sulphur (N/Sratio: 7.5, 10 and 12.5; (3 three levels of Calsium : Phospor (Ca/P ratio : 0.5, 1 and 2. The variables measured are : synthesis of protein microbes (SPM ; production of Volatile Fatty Acid (VFA and Nitrogen Ammonia (N-NH3; the digestibility of substrat. Based on the all variable measured, the experiment can be concluded : (1 the effectivity of the utilization of rice straw will be increased if it used is fortified with 50 percent TDN as energy source (E/P=4, 0.20 percent dry matter of sulphur (N/S=10 and 0.0625 - 0.125 percent dry matter (DM of phospor (Ca/P=1.0 – 2.0; (2 To stimulate the activity of cellulolytic microbes, its need the fortification of sulphur until reach the optimum level (must be investigated.

RanBP3 influences interactions between CRM1 and its nuclear protein export substrates

OpenAIRE

Englmeier, Ludwig; Fornerod, Maarten; Bischoff, F. Ralf; Petosa, Carlo; Mattaj, Iain W.; Kutay, Ulrike

2001-01-01

We investigated the role of RanBP3, a nuclear member of the Ran-binding protein 1 family, in CRM1-mediated protein export in higher eukaryotes. RanBP3 interacts directly with CRM1 and also forms a trimeric complex with CRM1 and RanGTP. However, RanBP3 does not bind to CRM1 like an export substrate. Instead, it can stabilize CRM1–export substrate interaction. Nuclear RanBP3 stimulates CRM1-dependent protein export in permeabilized cells. These data indicate that RanBP3 functions by a novel mec...

Ecohydrological consequences of non-native riparian vegetation in the southwestern United States: A review from an ecophysiological perspective

Science.gov (United States)

Hultine, K. R.; Bush, S. E.

2011-07-01

Protecting water resources for expanding human enterprise while conserving valued natural habitat is among the greatest challenges of the 21st century. Global change processes such as climate change and intensive land use pose significant threats to water resources, particularly in arid regions where potential evapotranspiration far exceeds annual rainfall. Potentially compounding these shortages is the progressive expansion of non-native plant species in riparian areas along streams, canals and rivers in geographically arid regions. This paper sets out to identify when and where non-native riparian plant species are likely to have the highest potential impact on hydrologic fluxes of arid and semiarid river systems. We develop an ecophysiological framework that focuses on two main criteria: (1) examination of the physiological traits that promote non-native species establishment and persistence across environmental gradients, and (2) assessment of where and to what extent hydrologic fluxes are potentially altered by the establishment of introduced species at varying scales from individual plants, to small river reaches, to entire river basins. We highlight three non-native plant species that currently dominate southwestern United States riparian forests. These include tamarisk (Tamarix spp.), Russian olive (Eleagnus angustifolia), and Russian knapweed (Acroptilon repens). As with other recent reviews, we suspect that in many cases the removal of these, and other non-native species will have little or no impact on either streamflow volume or groundwater levels. However, we identify potential exceptions where the expansion of non-native plant species could have significant impact on ecohydrologic processes associated with southwestern United States river systems. Future research needs are outlined that will ultimately assist land managers and policy makers with restoration and conservation priorities to preserve water resources and valued riparian habitat given

Functional diversity measures revealed impacts of non-native species and habitat degradation on species-poor freshwater fish assemblages.

Science.gov (United States)

Colin, Nicole; Villéger, Sébastien; Wilkes, Martin; de Sostoa, Adolfo; Maceda-Veiga, Alberto

2018-06-01

Trait-based ecology has been developed for decades to infer ecosystem responses to stressors based on the functional structure of communities, yet its value in species-poor systems is largely unknown. Here, we used an extensive dataset in a Spanish region highly prone to non-native fish invasions (15 catchments, N=389 sites) to assess for the first time how species-poor communities respond to large-scale environmental gradients using a taxonomic and functional trait-based approach in riverine fish. We examined total species richness and three functional trait-based indices available when many sites have ≤3 species (specialization, FSpe; originality, FOri and entropy, FEnt). We assessed the responses of these taxonomic and functional indices along gradients of altitude, water pollution, physical habitat degradation and non-native fish biomass. Whilst species richness was relatively sensitive to spatial effects, functional diversity indices were responsive across natural and anthropogenic gradients. All four diversity measures declined with altitude but this decline was modulated by physical habitat degradation (richness, FSpe and FEnt) and the non-native:total fish biomass ratio (FSpe and FOri) in ways that varied between indices. Furthermore, FSpe and FOri were significantly correlated with Total Nitrogen. Non-native fish were a major component of the taxonomic and functional structure of fish communities, raising concerns about potential misdiagnosis between invaded and environmentally-degraded river reaches. Such misdiagnosis was evident in a regional fish index widely used in official monitoring programs. We recommend the application of FSpe and FOri to extensive datasets from monitoring programs in order to generate valuable cross-system information about the impacts of non-native species and habitat degradation, even in species-poor systems. Scoring non-native species apart from habitat degradation in the indices used to determine ecosystem health is

Identification of protein tyrosine phosphatase 1B and casein as substrates for 124-v-Mos

Directory of Open Access Journals (Sweden)

Stabel Silvia

2002-04-01

Full Text Available Abstract Background The mos proto-oncogene encodes a cytoplasmic serine/threonine-specific protein kinase with crucial function during meiotic cell division in vertebrates. Based on oncogenic amino acid substitutions the viral derivative, 124-v-Mos, displays constitutive protein kinase activity and functions independent of unknown upstream effectors of mos protein kinase. We have utilized this property of 124-v-Mos and screened for novel mos substrates in immunocomplex kinase assays in vitro. Results We generated recombinant 124-v-Mos using the baculovirus expression system in Spodoptera frugiperda cells and demonstrated constitutive kinase activity by the ability of 124-v-Mos to auto-phosphorylate and to phosphorylate vimentin, a known substrate of c-Mos. Using this approach we analyzed a panel of acidic and basic substrates in immunocomplex protein kinase assays and identified novel in vitro substrates for 124-v-Mos, the protein tyrosine phosphatase 1B (PTP1B, alpha-casein and beta-casein. We controlled mos-specific phosphorylation of PTP1B and casein in comparative assays using a synthetic kinase-inactive 124-v-Mos mutant and further, tryptic digests of mos-phosphorylated beta-casein identified a phosphopeptide specifically targeted by wild-type 124-v-Mos. Two-dimensional phosphoamino acid analyses showed that 124-v-mos targets serine and threonine residues for phosphorylation in casein at a 1:1 ratio but auto-phosphorylation occurs predominantly on serine residues. Conclusion The mos substrates identified in this study represent a basis to approach the identification of the mos-consensus phosphorylation motif, important for the development of specific inhibitors of the Mos protein kinase.

An assessment of a proposal to eradicate non-native fish from ...

African Journals Online (AJOL)

African Journal of Aquatic Science ... A pilot project to evaluate the use of the piscicide rotenone to eradicate non-native fish from selected reaches in four rivers has been proposed by CapeNature, the conservation ... It is expected that the project will be successful while having minimal impact on other aquatic fauna.

Sensitive Electrochemical Detection of Native and Aggregated x-Synuclein Protein Involved in Parkinson's Disease

NARCIS (Netherlands)

Masarik, Michal; Stobiecka, Agata; Kizek, René; Jelen, Frantisek; Pechan, Zdenk; Hoyer, Wolfgang; Subramaniam, Vinod; Palecek, Emil

2004-01-01

The aggregation of α-synuclein, a 14 kDa protein, is involved in several human neurodegenerative disorders, including Parkinson's disease. We studied native and in vitro aggregated α-synuclein by circular dichroism (CD), atomic force microscopy (AFM) and electrochemical methods. We used constant

Analysis of oligomeric transition of silkworm small heat shock protein sHSP20.8 using high hydrostatic pressure native PAGE

Science.gov (United States)

Fujisawa, Tetsuro; Ueda, Toshifumi; Kameyama, Keiichi; Aso, Yoichi; Ishiguro, Ryo

2013-06-01

The small heat shock proteins (sHSPs) solubilize thermo-denatured proteins without adenosine triphosphate energy consumption to facilitate protein refolding. sHSP20.8 is one of the silkworm (Bombyx mori) sHSPs having only one cystein in the N-terminal domain: Cys43. We report a simple measurement of oligomeric transition of sHSP20.8 using high hydrostatic pressure native polyacrylamide gel electrophoresis (high hydrostatic pressure (HP) native polyacrylamide gel electrophoresis (PAGE)). At ambient pressure under oxydative condition, the native PAGE of thermal transition of sHSP20.8 oligomer displayed a cooperative association. In contrast, HP native PAGE clearly demonstrated that sHSP20.8 dissociated at 80 MPa and 25°C, and the resultant molecular species gradually reassociated with time under that condition. In addition, the reassociation process was suppressed in the presence of the reductant. These results are consistent with the idea that sHSP20.8 oligomer temporally dissociates at the first thermo-sensing step and reassociates with the oxidation of Cys43.

Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies

Science.gov (United States)

2018-01-01

Membrane proteins perform a host of vital cellular functions. Deciphering the molecular mechanisms whereby they fulfill these functions requires detailed biophysical and structural investigations. Detergents have proven pivotal to extract the protein from its native surroundings. Yet, they provide a milieu that departs significantly from that of the biological membrane, to the extent that the structure, the dynamics, and the interactions of membrane proteins in detergents may considerably vary, as compared to the native environment. Understanding the impact of detergents on membrane proteins is, therefore, crucial to assess the biological relevance of results obtained in detergents. Here, we review the strengths and weaknesses of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR studies of membrane proteins. While this class of detergents is often successful for membrane protein solubilization, a growing list of examples points to destabilizing and denaturing properties, in particular for α-helical membrane proteins. Our comprehensive analysis stresses the importance of stringent controls when working with this class of detergents and when analyzing the structure and dynamics of membrane proteins in alkyl phosphocholine detergents. PMID:29488756

Ligand-directed tosyl chemistry for in situ native protein labeling and engineering in living systems: from basic properties to applications.

Science.gov (United States)

Tsukiji, Shinya; Hamachi, Itaru

2014-08-01

The ability to introduce any chemical probe to any endogenous target protein in its native environment, that is in cells and in vivo, is anticipated to provide various new exciting tools for biological and biomedical research. Although still at the prototype stage, the ligand-directed tosyl (LDT) chemistry is a novel type of affinity labeling technique that we developed for such a dream. This chemistry allows for modifying native proteins by various chemical probes with high specificity in various biological settings ranging from in vitro (in test tubes) to in living cells and in vivo. Since the first report, the list of proteins that are successfully labeled by the LDT chemistry has been increasing. A growing number of studies have demonstrated its utility to create semisynthetic proteins directly in cellular contexts. The in situ generated semisynthetic proteins are applicable for various types of analysis and imaging of intracellular biological processes. In this review, we summarize the basic properties of the LDT chemistry and its applications toward in situ engineering and analysis of native proteins in living systems. Current limitations and future challenges of this area are also described. Copyright © 2014 Elsevier Ltd. All rights reserved.

(Non)native Speakered: Rethinking (Non)nativeness and Teacher Identity in TESOL Teacher Education

Science.gov (United States)

Aneja, Geeta A.

2016-01-01

Despite its imprecision, the native-nonnative dichotomy has become the dominant paradigm for examining language teacher identity development. The nonnative English speaking teacher (NNEST) movement in particular has considered the impact of deficit framings of nonnativeness on "NNEST" preservice teachers. Although these efforts have…

Economic impacts of non-native forest insects in the continental United States.

Directory of Open Access Journals (Sweden)

Juliann E Aukema

Full Text Available Reliable estimates of the impacts and costs of biological invasions are critical to developing credible management, trade and regulatory policies. Worldwide, forests and urban trees provide important ecosystem services as well as economic and social benefits, but are threatened by non-native insects. More than 450 non-native forest insects are established in the United States but estimates of broad-scale economic impacts associated with these species are largely unavailable. We developed a novel modeling approach that maximizes the use of available data, accounts for multiple sources of uncertainty, and provides cost estimates for three major feeding guilds of non-native forest insects. For each guild, we calculated the economic damages for five cost categories and we estimated the probability of future introductions of damaging pests. We found that costs are largely borne by homeowners and municipal governments. Wood- and phloem-boring insects are anticipated to cause the largest economic impacts by annually inducing nearly $1.7 billion in local government expenditures and approximately $830 million in lost residential property values. Given observations of new species, there is a 32% chance that another highly destructive borer species will invade the U.S. in the next 10 years. Our damage estimates provide a crucial but previously missing component of cost-benefit analyses to evaluate policies and management options intended to reduce species introductions. The modeling approach we developed is highly flexible and could be similarly employed to estimate damages in other countries or natural resource sectors.

Metalorganic chemical vapor deposition growth of high-mobility AlGaN/AlN/GaN heterostructures on GaN templates and native GaN substrates

Energy Technology Data Exchange (ETDEWEB)

Chen, Jr-Tai, E-mail: jrche@ifm.liu.se; Hsu, Chih-Wei; Forsberg, Urban; Janzén, Erik [Department of Physics, Chemistry, and Biology (IFM), Linköping University, SE 581 83 Linköping (Sweden)

2015-02-28

Severe surface decomposition of semi-insulating (SI) GaN templates occurred in high-temperature H{sub 2} atmosphere prior to epitaxial growth in a metalorganic chemical vapor deposition system. A two-step heating process with a surface stabilization technique was developed to preserve the GaN template surface. Utilizing the optimized heating process, a high two-dimensional electron gas mobility ∼2000 cm{sup 2}/V·s was obtained in a thin AlGaN/AlN/GaN heterostructure with an only 100-nm-thick GaN spacer layer homoepitaxially grown on the GaN template. This technique was also demonstrated viable for native GaN substrates to stabilize the surface facilitating two-dimensional growth of GaN layers. Very high residual silicon and oxygen concentrations were found up to ∼1 × 10{sup 20 }cm{sup −3} at the interface between the GaN epilayer and the native GaN substrate. Capacitance-voltage measurements confirmed that the residual carbon doping controlled by growth conditions of the GaN epilayer can be used to successfully compensate the donor-like impurities. State-of-the-art structural properties of a high-mobility AlGaN/AlN/GaN heterostructure was then realized on a 1 × 1 cm{sup 2} SI native GaN substrate; the full width at half maximum of the X-ray rocking curves of the GaN (002) and (102) peaks are only 21 and 14 arc sec, respectively. The surface morphology of the heterostructure shows uniform parallel bilayer steps, and no morphological defects were noticeable over the entire epi-wafer.

Non-native (exotic) snake envenomations in the U.S., 2005-2011.

Science.gov (United States)

Warrick, Brandon J; Boyer, Leslie V; Seifert, Steven A

2014-09-29

Non-native (exotic) snakes are a problematic source of envenomation worldwide. This manuscript describes the current demographics, outcomes and challenges of non-native snakebites in the United States (U.S.). We performed a retrospective case series of the National Poison Data System (NPDS) database between 2005 and 2011. There were 258 human exposures involving at least 61 unique exotic venomous species (average = 37 per year; range = 33-40). Males comprised 79% and females 21%. The average age was 33 years with 16% less than 20 years old. 70% of bites occurred in a private residence and 86% were treated at a healthcare facility. 35% of cases received antivenom and 10% were given antibiotics. This study is compared to our previous study (1994-2004) in which there was a substantial coding error rate. Software modifications significantly reduced coding errors. Identification and acquisition of appropriate antivenoms pose a number of logistical difficulties in the management of these envenomations. In the U.S., poison centers have valuable systems and clinical roles in the provision of expert consultation and in the management of these cases.

High water-use efficiency and growth contribute to success of non-native Erodium cicutarium in a Sonoran Desert winter annual community.

Science.gov (United States)

Kimball, Sarah; Gremer, Jennifer R; Barron-Gafford, Greg A; Angert, Amy L; Huxman, Travis E; Venable, D Lawrence

2014-01-01

The success of non-native, invasive species may be due to release from natural enemies, superior competitive abilities, or both. In the Sonoran Desert, Erodium cicutarium has increased in abundance over the last 30 years. While native species in this flora exhibit a strong among-species trade-off between relative growth rate and water-use efficiency, E. cicutarium seems to have a higher relative growth rate for its water-use efficiency value relative to the pattern across native species. This novel trait combination could provide the non-native species with a competitive advantage in this water-limited environment. To test the hypothesis that E. cicutarium is able to achieve high growth rates due to release from native herbivores, we compared the effects of herbivory on E. cicutarium and its native congener, Erodium texanum. We also compared these two species across a range of environmental conditions, both in a common garden and in two distinct seasons in the field, using growth analysis, isotopic compositions and leaf-level gas exchange. Additionally, we compared the competitive abilities of the two Erodium species in a greenhouse experiment. We found no evidence of herbivory to either species. Physiological measurements in a common environment revealed that E. cicutarium was able to achieve high growth rates while simultaneously controlling leaf-level water loss. Non-native E. cicutarium responded to favourable conditions in the field with greater specific leaf area and leaf area ratio than native E. texanum. The non-native Erodium was a stronger competitor than its native congener in a greenhouse competition experiment. The ability to maintain relatively higher values of water-use efficiency:relative growth rate in comparison to the native flora may be what enables E. cictarium to outcompete native species in both wet and dry years, resulting in an increase in abundance in the highly variable Sonoran Desert.

Examining the Heterogeneous Genome Content of Multipartite Viruses BMV and CCMV by Native Mass Spectrometry

NARCIS (Netherlands)

van de Waterbeemd, Michiel; Snijder, Joost; Tsvetkova, Irina B.; Dragnea, Bogdan G.; Cornelissen, Jeroen J.; Heck, Albert J.R.

2016-01-01

Since the concept was first introduced by Brian Chait and co-workers in 1991, mass spectrometry of proteins and protein complexes under non-denaturing conditions (native MS) has strongly developed, through parallel advances in instrumentation, sample preparation, and data analysis tools. However,

Protein as chemical cue: non-nutritional growth enhancement by exogenous protein in Pseudomonas putida KT2440.

Directory of Open Access Journals (Sweden)

Hiren Joshi

Full Text Available Research pertaining to microbe-microbe and microbe-plant interactions has been largely limited to small molecules like quorum sensing chemicals. However, a few recent reports have indicated the role of complex molecules like proteins and polysaccharides in microbial communication. Here we demonstrate that exogenous proteins present in culture media can considerably accelerate the growth of Pseudomonas putida KT2440, even when such proteins are not internalized by the cells. The growth enhancement is observed when the exogenous protein is not used as a source of carbon or nitrogen. The data show non-specific nature of the protein inducing growth; growth enhancement was observed irrespective of the protein type. It is shown that growth enhancement is mediated via increased siderophore secretion in response to the exogenous protein, leading to better iron uptake. We highlight the ecological significance of the observation and hypothesize that exogenous proteins serve as chemical cues in the case of P.putida and are perceived as indicator of the presence of competitors in the environment. It is argued that enhanced siderophore secretion in response to exogenous protein helps P.putida establish numerical superiority over competitors by way of enhanced iron assimilation and quicker utilization of aromatic substrates.

BIOCHEMICAL CHARACTERIZATION OF NATIVE USHER PROTEIN COMPLEXES FROM A VESICULAR SUBFRACTION OF TRACHEAL EPITHELIAL CELLS†

Science.gov (United States)

Zallocchi, Marisa; Sisson, Joseph H.; Cosgrove, Dominic

2010-01-01

Usher syndrome is the major cause of deaf/blindness in the world. It is a genetic heterogeneous disorder, with nine genes already identified as causative for the disease. We noted expression of all known Usher proteins in bovine tracheal epithelial cells, and exploited this system for large-scale biochemical analysis of Usher protein complexes. The dissected epithelia were homogenized in non-detergent buffer, and sedimented on sucrose gradients. At least two complexes were evident after the first gradient: one formed by specific isoforms of CDH23, PCDH15 and VLGR-1, and a different one at the top of the gradient that included all the Usher proteins and rab5, a transport vesicle marker. TEM analysis of these top fractions found them enriched in 100–200 nm vesicles, confirming a vesicular association of the Usher complex(es). Immunoisolation of these vesicles confirmed some of the associations already predicted and identified novel interactions. When the vesicles are lysed in the presence of phenylbutyrate, most of the Usher proteins co-sediment into the gradient at a sedimentation coefficient of approximately 50S, correlating with a predicted molecular mass of 2 × 106 Daltons. Although it is still unclear whether there is only one complex or several independent complexes that are trafficked within distinct vesicular pools, this work shows for the first time that native Usher proteins complexes occur in vivo. This complex(es) is present primarily in transport vesicles at the apical pole of tracheal epithelial cells, predicting that Usher proteins may be directionally transported as complexes in hair cells and photoreceptors. PMID:20058854

Alignment of non-covalent interactions at protein-protein interfaces.

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Hongbo Zhu

Full Text Available BACKGROUND: The study and comparison of protein-protein interfaces is essential for the understanding of the mechanisms of interaction between proteins. While there are many methods for comparing protein structures and protein binding sites, so far no methods have been reported for comparing the geometry of non-covalent interactions occurring at protein-protein interfaces. METHODOLOGY/PRINCIPAL FINDINGS: Here we present a method for aligning non-covalent interactions between different protein-protein interfaces. The method aligns the vector representations of van der Waals interactions and hydrogen bonds based on their geometry. The method has been applied to a dataset which comprises a variety of protein-protein interfaces. The alignments are consistent to a large extent with the results obtained using two other complementary approaches. In addition, we apply the method to three examples of protein mimicry. The method successfully aligns respective interfaces and allows for recognizing conserved interface regions. CONCLUSIONS/SIGNIFICANCE: The Galinter method has been validated in the comparison of interfaces in which homologous subunits are involved, including cases of mimicry. The method is also applicable to comparing interfaces involving non-peptidic compounds. Galinter assists users in identifying local interface regions with similar patterns of non-covalent interactions. This is particularly relevant to the investigation of the molecular basis of interaction mimicry.

Fabrication of non-hexagonal close packed colloidal array on a substrate by transfer

Science.gov (United States)

Banik, Meneka; Mukherjee, Rabibrata

Self-organized colloidal arrays find application in fabrication of solar cells with advanced light management strategies. We report a simple spincoating based approach for fabricating two dimensional colloidal crystals with hexagonal and non-hexagonal close packed assembly on flat and nanopatterned substrates. The non-HCP arrays were fabricated by spin coating the particles onto soft lithographically fabricated substrates. The substrate patterns impose directionality to the particles by confining them within the grooves. We have developed a technique by which the HCP and non-HCP arrays can be transferred to any surface. For this purpose the colloidal arrays were fabricated on a UV degradable PMMA layer, resulting in transfer of the particles on UV exposure. This allows the colloidal structures to be transported across substrates irrespective of their surface energy, wettability or morphology. Since the particles are transferred without exposing it to any kind of chemical or thermal environment, it can be utilized for placing particles on top of thin film solar cells for improving their absorption efficiency.

Improving decoy databases for protein folding algorithms

KAUST Repository

Lindsey, Aaron

2014-01-01

Copyright © 2014 ACM. Predicting protein structures and simulating protein folding are two of the most important problems in computational biology today. Simulation methods rely on a scoring function to distinguish the native structure (the most energetically stable) from non-native structures. Decoy databases are collections of non-native structures used to test and verify these functions. We present a method to evaluate and improve the quality of decoy databases by adding novel structures and removing redundant structures. We test our approach on 17 different decoy databases of varying size and type and show significant improvement across a variety of metrics. We also test our improved databases on a popular modern scoring function and show that they contain a greater number of native-like structures than the original databases, thereby producing a more rigorous database for testing scoring functions.

Mapping Proteoforms and Protein Complexes From King Cobra Venom Using Both Denaturing and Native Top-down Proteomics.

Science.gov (United States)

Melani, Rafael D; Skinner, Owen S; Fornelli, Luca; Domont, Gilberto B; Compton, Philip D; Kelleher, Neil L

2016-07-01

Characterizing whole proteins by top-down proteomics avoids a step of inference encountered in the dominant bottom-up methodology when peptides are assembled computationally into proteins for identification. The direct interrogation of whole proteins and protein complexes from the venom of Ophiophagus hannah (king cobra) provides a sharply clarified view of toxin sequence variation, transit peptide cleavage sites and post-translational modifications (PTMs) likely critical for venom lethality. A tube-gel format for electrophoresis (called GELFrEE) and solution isoelectric focusing were used for protein fractionation prior to LC-MS/MS analysis resulting in 131 protein identifications (18 more than bottom-up) and a total of 184 proteoforms characterized from 14 protein toxin families. Operating both GELFrEE and mass spectrometry to preserve non-covalent interactions generated detailed information about two of the largest venom glycoprotein complexes: the homodimeric l-amino acid oxidase (∼130 kDa) and the multichain toxin cobra venom factor (∼147 kDa). The l-amino acid oxidase complex exhibited two clusters of multiproteoform complexes corresponding to the presence of 5 or 6 N-glycans moieties, each consistent with a distribution of N-acetyl hexosamines. Employing top-down proteomics in both native and denaturing modes provides unprecedented characterization of venom proteoforms and their complexes. A precise molecular inventory of venom proteins will propel the study of snake toxin variation and the targeted development of new antivenoms or other biotherapeutics. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Recreational freshwater fishing drives non-native aquatic species richness patterns at a continental scale

Data.gov (United States)

U.S. Environmental Protection Agency — Aim. Mapping the geographic distribution of non-native aquatic species is a critically important precursor to understanding the anthropogenic and environmental...

Application of virus-like particles (VLP) to NMR characterization of viral membrane protein interactions

Energy Technology Data Exchange (ETDEWEB)

Antanasijevic, Aleksandar; Kingsley, Carolyn [University of Illinois at Chicago, Department of Biochemistry and Molecular Genetics (United States); Basu, Arnab; Bowlin, Terry L. [Microbiotix Inc. (United States); Rong, Lijun [University of Illinois at Chicago, Department of Microbiology and Immunology (United States); Caffrey, Michael, E-mail: caffrey@uic.edu [University of Illinois at Chicago, Department of Biochemistry and Molecular Genetics (United States)

2016-03-15

The membrane proteins of viruses play critical roles in the virus life cycle and are attractive targets for therapeutic intervention. Virus-like particles (VLP) present the possibility to study the biochemical and biophysical properties of viral membrane proteins in their native environment. Specifically, the VLP constructs contain the entire protein sequence and are comprised of native membrane components including lipids, cholesterol, carbohydrates and cellular proteins. In this study we prepare VLP containing full-length hemagglutinin (HA) or neuraminidase (NA) from influenza and characterize their interactions with small molecule inhibitors. Using HA-VLP, we first show that VLP samples prepared using the standard sucrose gradient purification scheme contain significant amounts of serum proteins, which exhibit high potential for non-specific interactions, thereby complicating NMR studies of ligand-target interactions. We then show that the serum contaminants may be largely removed with the addition of a gel filtration chromatography step. Next, using HA-VLP we demonstrate that WaterLOGSY NMR is significantly more sensitive than Saturation Transfer Difference (STD) NMR for the study of ligand interactions with membrane bound targets. In addition, we compare the ligand orientation to HA embedded in VLP with that of recombinant HA by STD NMR. In a subsequent step, using NA-VLP we characterize the kinetic and binding properties of substrate analogs and inhibitors of NA, including study of the H274Y-NA mutant, which leads to wide spread resistance to current influenza antivirals. In summary, our work suggests that VLP have high potential to become standard tools in biochemical and biophysical studies of viral membrane proteins, particularly when VLP are highly purified and combined with control VLP containing native membrane proteins.

Near-native protein loop sampling using nonparametric density estimation accommodating sparcity.

Science.gov (United States)

Joo, Hyun; Chavan, Archana G; Day, Ryan; Lennox, Kristin P; Sukhanov, Paul; Dahl, David B; Vannucci, Marina; Tsai, Jerry

2011-10-01

Unlike the core structural elements of a protein like regular secondary structure, template based modeling (TBM) has difficulty with loop regions due to their variability in sequence and structure as well as the sparse sampling from a limited number of homologous templates. We present a novel, knowledge-based method for loop sampling that leverages homologous torsion angle information to estimate a continuous joint backbone dihedral angle density at each loop position. The φ,ψ distributions are estimated via a Dirichlet process mixture of hidden Markov models (DPM-HMM). Models are quickly generated based on samples from these distributions and were enriched using an end-to-end distance filter. The performance of the DPM-HMM method was evaluated against a diverse test set in a leave-one-out approach. Candidates as low as 0.45 Å RMSD and with a worst case of 3.66 Å were produced. For the canonical loops like the immunoglobulin complementarity-determining regions (mean RMSD 7.0 Å), this sampling method produces a population of loop structures to around 3.66 Å for loops up to 17 residues. In a direct test of sampling to the Loopy algorithm, our method demonstrates the ability to sample nearer native structures for both the canonical CDRH1 and non-canonical CDRH3 loops. Lastly, in the realistic test conditions of the CASP9 experiment, successful application of DPM-HMM for 90 loops from 45 TBM targets shows the general applicability of our sampling method in loop modeling problem. These results demonstrate that our DPM-HMM produces an advantage by consistently sampling near native loop structure. The software used in this analysis is available for download at http://www.stat.tamu.edu/~dahl/software/cortorgles/.

Near-native protein loop sampling using nonparametric density estimation accommodating sparcity.

Directory of Open Access Journals (Sweden)

Hyun Joo

2011-10-01

Full Text Available Unlike the core structural elements of a protein like regular secondary structure, template based modeling (TBM has difficulty with loop regions due to their variability in sequence and structure as well as the sparse sampling from a limited number of homologous templates. We present a novel, knowledge-based method for loop sampling that leverages homologous torsion angle information to estimate a continuous joint backbone dihedral angle density at each loop position. The φ,ψ distributions are estimated via a Dirichlet process mixture of hidden Markov models (DPM-HMM. Models are quickly generated based on samples from these distributions and were enriched using an end-to-end distance filter. The performance of the DPM-HMM method was evaluated against a diverse test set in a leave-one-out approach. Candidates as low as 0.45 Å RMSD and with a worst case of 3.66 Å were produced. For the canonical loops like the immunoglobulin complementarity-determining regions (mean RMSD 7.0 Å, this sampling method produces a population of loop structures to around 3.66 Å for loops up to 17 residues. In a direct test of sampling to the Loopy algorithm, our method demonstrates the ability to sample nearer native structures for both the canonical CDRH1 and non-canonical CDRH3 loops. Lastly, in the realistic test conditions of the CASP9 experiment, successful application of DPM-HMM for 90 loops from 45 TBM targets shows the general applicability of our sampling method in loop modeling problem. These results demonstrate that our DPM-HMM produces an advantage by consistently sampling near native loop structure. The software used in this analysis is available for download at http://www.stat.tamu.edu/~dahl/software/cortorgles/.

Near-Native Protein Loop Sampling Using Nonparametric Density Estimation Accommodating Sparcity

Science.gov (United States)

Day, Ryan; Lennox, Kristin P.; Sukhanov, Paul; Dahl, David B.; Vannucci, Marina; Tsai, Jerry

2011-01-01

Unlike the core structural elements of a protein like regular secondary structure, template based modeling (TBM) has difficulty with loop regions due to their variability in sequence and structure as well as the sparse sampling from a limited number of homologous templates. We present a novel, knowledge-based method for loop sampling that leverages homologous torsion angle information to estimate a continuous joint backbone dihedral angle density at each loop position. The φ,ψ distributions are estimated via a Dirichlet process mixture of hidden Markov models (DPM-HMM). Models are quickly generated based on samples from these distributions and were enriched using an end-to-end distance filter. The performance of the DPM-HMM method was evaluated against a diverse test set in a leave-one-out approach. Candidates as low as 0.45 Å RMSD and with a worst case of 3.66 Å were produced. For the canonical loops like the immunoglobulin complementarity-determining regions (mean RMSD 7.0 Å), this sampling method produces a population of loop structures to around 3.66 Å for loops up to 17 residues. In a direct test of sampling to the Loopy algorithm, our method demonstrates the ability to sample nearer native structures for both the canonical CDRH1 and non-canonical CDRH3 loops. Lastly, in the realistic test conditions of the CASP9 experiment, successful application of DPM-HMM for 90 loops from 45 TBM targets shows the general applicability of our sampling method in loop modeling problem. These results demonstrate that our DPM-HMM produces an advantage by consistently sampling near native loop structure. The software used in this analysis is available for download at http://www.stat.tamu.edu/~dahl/software/cortorgles/. PMID:22028638

Molecular dynamics investigations of BioH protein substrate specificity for biotin synthesis.

Science.gov (United States)

Xue, Qiao; Cui, Ying-Lu; Zheng, Qing-Chuan; Zhang, Hong-Xing

2016-05-01

BioH, an enzyme of biotin synthesis, plays an important role in fatty acid synthesis which assembles the pimelate moiety. Pimeloyl-acyl carrier protein (ACP) methyl ester, which is long known to be a biotin precursor, is the physiological substrate of BioH. Azelayl methyl ester, which has a longer chain than pimeloyl methyl ester, conjugated to ACP is also indeed accepted by BioH with very low rate of hydrolysis. To date, the substrate specificity for BioH and the molecular origin for the experimentally observed rate changes of hydrolysis by the chain elongation have remained elusive. To this end, we have investigated chain elongation effects on the structures by using the fully atomistic molecular dynamics simulations combined with binding free energy calculations. The results indicate that the substrate specificity is determined by BioH together with ACP. The added two methylenes would increase the structural flexibility by protein motions at the interface of ACP and BioH, instead of making steric clashes with the side chains of the BioH hydrophobic cavity. On the other hand, the slower hydrolysis of azelayl substrate is suggested to be associated with the loose of contacts between BioH and ACP, and with the lost electrostatic interactions of two ionic/hydrogen bonding networks at the interface of the two proteins. The present study provides important insights into the structure-function relationships of the complex of BioH with pimeloyl-ACP methyl ester, which could contribute to further understanding about the mechanism of the biotin synthetic pathway, including the catalytic role of BioH.

Na+/substrate Coupling in the Multidrug Antiporter NorM Probed with a Spin-labeled Substrate

Science.gov (United States)

Steed, P. Ryan; Stein, Richard A.; Mishra, Smriti; Goodman, Michael C.; Mchaourab, Hassane S.

2013-01-01

NorM of the multidrug and toxic compound extrusion (MATE) family of transporters couples the efflux of a broad range of hydrophobic molecules to an inward Na+ gradient across the cell membrane. Several crystal structures of MATE transporters revealed distinct substrate binding sites leading to differing models of the mechanism of ion-coupled substrate extrusion. In the experiments reported here, we observed that a spin-labeled derivative of daunorubicin, Ruboxyl, is transported by NorM from Vibrio cholerae. It is therefore ideal to characterize mechanistically relevant binding interactions with NorM and to directly address the coupling of ion and drug binding. Fluorescence and EPR experiments revealed that Ruboxyl binds to NorM with micromolar affinity and becomes immobilized upon binding, even in the presence of Na+. Using double electron-electron resonance (DEER) spectroscopy, we determined that Ruboxyl binds to a single site on the periplasmic side of the protein. The presence of Na+ did not translocate the substrate to a second site as previously proposed. These experiments surprisingly show that Na+ does not affect the affinity or location of the substrate binding site on detergent-solubilized NorM, thus suggesting that additional factors beyond simple mutual exclusivity of binding, such as the presence of a Na+ gradient across the native membrane, govern Na+/drug coupling during antiport. PMID:23902581

In Situ Blotting : A Novel Method for Direct Transfer of Native Proteins from Sectioned Tissue to Blotting Membrane

NARCIS (Netherlands)

Okabe, Masashi; Nyakas, Csaba; Buwalda, Bauke; Luiten, Paul G.M.

1993-01-01

We describe a novel technique for direct transfer of native proteins from unfixed frozen tissue sections to an immobilizing matrix, e.g., nitrocellulose, polyvinyliden difluoride, or positively charged nylon membranes. Proteins are directly blotted onto the membrane, providing optimal accessibility

 Invasibility of three major non-native invasive shrubs and associated factors in Upper Midwest U.S. forest lands

Science.gov (United States)

W. Keith Moser; Zhaofei Fan; Mark H. Hansen; Michael K. Crosby; Shirley X. Fan

2016-01-01

We used non-native invasive plant data from the US Forest Service’s Forest Inventory and Analysis (FIA) program, spatial statistical methods, and the space (cover class)-for-time approach to quantify the invasion potential and success ("invasibility") of three major invasive shrubs (multiflora rose, non-native bush honeysuckles, and common buckthorn...

Invasive Acer negundo outperforms native species in non-limiting resource environments due to its higher phenotypic plasticity.

Science.gov (United States)

Porté, Annabel J; Lamarque, Laurent J; Lortie, Christopher J; Michalet, Richard; Delzon, Sylvain

2011-11-24

To identify the determinants of invasiveness, comparisons of traits of invasive and native species are commonly performed. Invasiveness is generally linked to higher values of reproductive, physiological and growth-related traits of the invasives relative to the natives in the introduced range. Phenotypic plasticity of these traits has also been cited to increase the success of invasive species but has been little studied in invasive tree species. In a greenhouse experiment, we compared ecophysiological traits between an invasive species to Europe, Acer negundo, and early- and late-successional co-occurring native species, under different light, nutrient availability and disturbance regimes. We also compared species of the same species groups in situ, in riparian forests. Under non-limiting resources, A. negundo seedlings showed higher growth rates than the native species. However, A. negundo displayed equivalent or lower photosynthetic capacities and nitrogen content per unit leaf area compared to the native species; these findings were observed both on the seedlings in the greenhouse experiment and on adult trees in situ. These physiological traits were mostly conservative along the different light, nutrient and disturbance environments. Overall, under non-limiting light and nutrient conditions, specific leaf area and total leaf area of A. negundo were substantially larger. The invasive species presented a higher plasticity in allocation to foliage and therefore in growth with increasing nutrient and light availability relative to the native species. The higher level of plasticity of the invasive species in foliage allocation in response to light and nutrient availability induced a better growth in non-limiting resource environments. These results give us more elements on the invasiveness of A. negundo and suggest that such behaviour could explain the ability of A. negundo to outperform native tree species, contributes to its spread in European resource

Biologically Complex Planar Cell Plasma Membranes Supported on Polyelectrolyte Cushions Enhance Transmembrane Protein Mobility and Retain Native Orientation.

Science.gov (United States)

Liu, Han-Yuan; Chen, Wei-Liang; Ober, Christopher K; Daniel, Susan

2018-01-23

Reconstituted supported lipid bilayers (SLB) are widely used as in vitro cell-surface models because they are compatible with a variety of surface-based analytical techniques. However, one of the challenges of using SLBs as a model of the cell surface is the limited complexity in membrane composition, including the incorporation of transmembrane proteins and lipid diversity that may impact the activity of those proteins. Additionally, it is challenging to preserve the transmembrane protein native orientation, function, and mobility in SLBs. Here, we leverage the interaction between cell plasma membrane vesicles and polyelectrolyte brushes to create planar bilayers from cell plasma membrane vesicles that have budded from the cell surface. This approach promotes the direct incorporation of membrane proteins and other species into the planar bilayer without using detergent or reconstitution and preserves membrane constituents. Furthermore, the structure of the polyelectrolyte brush serves as a cushion between the planar bilayer and rigid supporting surface, limiting the interaction of the cytosolic domains of membrane proteins with this surface. Single particle tracking was used to analyze the motion of GPI-linked yellow fluorescent proteins (GPI-YFP) and neon-green fused transmembrane P2X2 receptors (P2X2-neon) and shows that this platform retains over 75% mobility of multipass transmembrane proteins in its native membrane environment. An enzyme accessibility assay confirmed that the protein orientation is preserved and results in the extracellular domain facing toward the bulk phase and the cytosolic side facing the support. Because the platform presented here retains the complexity of the cell plasma membrane and preserves protein orientation and mobility, it is a better representative mimic of native cell surfaces, which may find many applications in biological assays aimed at understanding cell membrane phenomena.

Effects of thermally induced denaturation on technological-functional properties of whey protein isolate-based films.

Science.gov (United States)

Schmid, M; Krimmel, B; Grupa, U; Noller, K

2014-09-01

This study examined how and to what extent the degree of denaturation affected the technological-functional properties of whey protein isolate (WPI)-based coatings. It was observed that denaturation affected the material properties of WPI-coated films significantly. Surface energy decreased by approximately 20% compared with native coatings. Because the surface energy of a coating should be lower than that of the substrate, this might result in enhanced wettability characteristics between WPI-based solution and substrate surface. Water vapor barrier properties increased by about 35% and oxygen barrier properties increased by approximately 33%. However, significant differences were mainly observed between coatings made of fully native WPI and ones with a degree of denaturation of 25%. Higher degrees of denaturation did not lead to further improvement of material properties. This observation offers cost-saving potential: a major share of denatured whey proteins may be replaced by fully native ones that are not exposed to energy-intensive heat treatment. Furthermore, native WPI solutions can be produced with higher dry matter content without gelatinizing. Hence, less moisture has to be removed through drying, resulting in reduced energy consumption. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Gopherus agassizii (Desert Tortoise). Non-native seed dispersal

Science.gov (United States)

Ennen, J.R.; Loughran, Caleb L.; Lovich, Jeffrey E.

2011-01-01

Sahara Mustard (Brassica tournefortii) is a non-native, highly invasive weed species of southwestern U.S. deserts. Sahara Mustard is a hardy species, which flourishes under many conditions including drought and in both disturbed and undisturbed habitats (West and Nabhan 2002. In B. Tellman [ed.], Invasive Plants: Their Occurrence and Possible Impact on the Central Gulf Coast of Sonora and the Midriff Islands in the Sea of Cortes, pp. 91–111. University of Arizona Press, Tucson). Because of this species’ ability to thrive in these habitats, B. tournefortii has been able to propagate throughout the southwestern United States establishing itself in the Mojave and Sonoran Deserts in Arizona, California, Nevada, and Utah. Unfortunately, naturally disturbed areas created by native species, such as the Desert Tortoise (Gopherus agassizii), within these deserts could have facilitated the propagation of B. tournefortii. (Lovich 1998. In R. G. Westbrooks [ed.], Invasive Plants, Changing the Landscape of America: Fact Book, p. 77. Federal Interagency Committee for the Management of Noxious and Exotic Weeds [FICMNEW], Washington, DC). However, Desert Tortoises have never been directly observed dispersing Sahara Mustard seeds. Here we present observations of two Desert Tortoises dispersing Sahara Mustard seeds at the interface between the Mojave and Sonoran deserts in California.

Toxic Exposure Surveillance System (TESS)-based characterization of U.S. non-native venomous snake exposures, 1995-2004.

Science.gov (United States)

Seifert, Steven A; Oakes, Jennifer A; Boyer, Leslie V

2007-01-01

Non-native (exotic) snake exposures in the United States have not been systematically characterized. The Toxic Exposure Surveillance System (TESS) database of the American Association of Poison Control Centers was analyzed to quantify the number and types, demographic associations, clinical presentations, managements and outcomes, and the health resource utilization of non-native snake exposures. From 1995 through 2004, there were 399 non-native exposures in the TESS database. Of these, 350 snakes (87%) were identified by genus and species, comprising at least 77 different varieties. Roughly equal percentages of snakes originated in Asia, Africa and Latin America, with a smaller number from the Middle-East, Australia, and Europe. Nearly half were viperids and a little more than a third were elapids. The vast majority of exposed individuals were adults. However, almost 15% were aged 17 years or less, and almost 7% were children aged 5 years or younger. Eighty-four percent were males. The vast majority of exposures occurred at the victim's own residence. Over 50% were evaluated at a healthcare facility, with 28.7% admitted to an ICU. Overall, 26% of patients were coded as receiving antivenom treatment. Coded outcomes were similar between viperid and elapid envenomations. There were three deaths, two involving viperid snakes and one elapid. Enhancements to the TESS database are required for better precision in and more complete characterization of non-native snake envenomations.

Interactions between non-native armored suckermouth catfish (Loricariidae: Pterygoplichthys) and native Florida manatee (Trichechus manatus latirostris) in artesian springs

Science.gov (United States)

Nico, Leo G.; Loftus, William F.; Reid, James P.

2009-01-01

Non-native suckermouth armored catfishes (Loricariidae) of the genus Pterygoplichthys are now common throughout much of peninsular Florida. In this paper, we present preliminary observations on interactions between a Pterygoplichthys species, tentatively identified as P. disjunctivus (Weber, 1991), and endangered native Florida manatees, Trichechus manatus latirostris (Harlan, 1824), in artesian spring systems in Florida's St. Johns River drainage. The introduced catfish have become abundant in spring habitats, sites used by manatees as winter thermal refuges. In the spring runs, Pterygoplichthys regularly attaches to manatees and grazes the epibiota on their skin. On occasion, dozens of Pterygoplichthys congregate on individual manatees. Manatee responses varied widely; some did not react visibly to attached catfish whereas others appeared agitated and attempted to dislodge the fish. The costs and/or benefits of this interaction to manatees remain unclear.

Activation of the DnaK-ClpB Complex is Regulated by the Properties of the Bound Substrate.

Science.gov (United States)

Fernández-Higuero, Jose Angel; Aguado, Alejandra; Perales-Calvo, Judit; Moro, Fernando; Muga, Arturo

2018-04-11

The chaperone ClpB in bacteria is responsible for the reactivation of aggregated proteins in collaboration with the DnaK system. Association of these chaperones at the aggregate surface stimulates ATP hydrolysis, which mediates substrate remodeling. However, a question that remains unanswered is whether the bichaperone complex can be selectively activated by substrates that require remodeling. We find that large aggregates or bulky, native-like substrates activates the complex, whereas a smaller, permanently unfolded protein or extended, short peptides fail to stimulate it. Our data also indicate that ClpB interacts differently with DnaK in the presence of aggregates or small peptides, displaying a higher affinity for aggregate-bound DnaK, and that DnaK-ClpB collaboration requires the coupled ATPase-dependent remodeling activities of both chaperones. Complex stimulation is mediated by residues at the β subdomain of DnaK substrate binding domain, which become accessible to the disaggregase when the lid is allosterically detached from the β subdomain. Complex activation also requires an active NBD2 and the integrity of the M domain-ring of ClpB. Disruption of the M-domain ring allows the unproductive stimulation of the DnaK-ClpB complex in solution. The ability of the DnaK-ClpB complex to discrimínate different substrate proteins might allow its activation when client proteins require remodeling.

Urban American Indian/Alaskan Natives Compared to Non-Indians in Out-of-Home Care

Science.gov (United States)

Carter, Vernon B.

2011-01-01

Historically, American Indian/Alaskan Native (AI/AN) children have been disproportionately represented in the foster care system. In this study, nationally representative child welfare data from October 1999 was used to compare urban AI/AN children to non-Indian children placed into out-of-home care. Compared to non-Indian children, urban AI/AN…

Potential for water salvage by removal of non-native woody vegetation from dryland river systems

Science.gov (United States)

Doody, T.M.; Nagler, P.L.; Glenn, E.P.; Moore, G.W.; Morino, K.; Hultine, K.R.; Benyon, R.G.

2011-01-01

Globally, expansion of non-native woody vegetation across floodplains has raised concern of increased evapotranspiration (ET) water loss with consequent reduced river flows and groundwater supplies. Water salvage programs, established to meet water supply demands by removing introduced species, show little documented evidence of program effectiveness. We use two case studies in the USA and Australia to illustrate factors that contribute to water salvage feasibility for a given ecological setting. In the USA, saltcedar (Tamarix spp.) has become widespread on western rivers, with water salvage programs attempted over a 50-year period. Some studies document riparian transpiration or ET reduction after saltcedar removal, but detectable increases in river base flow are not conclusively shown. Furthermore, measurements of riparian vegetation ET in natural settings show saltcedar ET overlaps the range measured for native riparian species, thereby constraining the possibility of water salvage by replacing saltcedar with native vegetation. In Australia, introduced willows (Salix spp.) have become widespread in riparian systems in the Murray-Darling Basin. Although large-scale removal projects have been undertaken, no attempts have been made to quantify increases in base flows. Recent studies of ET indicate that willows growing in permanently inundated stream beds have high transpiration rates, indicating water savings could be achieved from removal. In contrast, native Eucalyptus trees and willows growing on stream banks show similar ET rates with no net water salvage from replacing willows with native trees. We conclude that water salvage feasibility is highly dependent on the ecohydrological setting in which the non-native trees occur. We provide an overview of conditions favorable to water salvage. Copyright ?? 2011 John Wiley & Sons, Ltd.

SPRED: A machine learning approach for the identification of classical and non-classical secretory proteins in mammalian genomes

Energy Technology Data Exchange (ETDEWEB)

Kandaswamy, Krishna Kumar [Institute for Neuro- and Bioinformatics, University of Luebeck, 23538 Luebeck (Germany); Graduate School for Computing in Medicine and Life Sciences, University of Luebeck, 23538 Luebeck (Germany); Pugalenthi, Ganesan [School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798 (Singapore); Hartmann, Enno; Kalies, Kai-Uwe [Centre for Structural and Cell Biology in Medicine, Institute of Biology, University of Luebeck, 23538 Luebeck (Germany); Moeller, Steffen [Institute for Neuro- and Bioinformatics, University of Luebeck, 23538 Luebeck (Germany); Suganthan, P.N. [School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798 (Singapore); Martinetz, Thomas, E-mail: martinetz@inb.uni-luebeck.de [Institute for Neuro- and Bioinformatics, University of Luebeck, 23538 Luebeck (Germany)

2010-01-15

Eukaryotic protein secretion generally occurs via the classical secretory pathway that traverses the ER and Golgi apparatus. Secreted proteins usually contain a signal sequence with all the essential information required to target them for secretion. However, some proteins like fibroblast growth factors (FGF-1, FGF-2), interleukins (IL-1 alpha, IL-1 beta), galectins and thioredoxin are exported by an alternative pathway. This is known as leaderless or non-classical secretion and works without a signal sequence. Most computational methods for the identification of secretory proteins use the signal peptide as indicator and are therefore not able to identify substrates of non-classical secretion. In this work, we report a random forest method, SPRED, to identify secretory proteins from protein sequences irrespective of N-terminal signal peptides, thus allowing also correct classification of non-classical secretory proteins. Training was performed on a dataset containing 600 extracellular proteins and 600 cytoplasmic and/or nuclear proteins. The algorithm was tested on 180 extracellular proteins and 1380 cytoplasmic and/or nuclear proteins. We obtained 85.92% accuracy from training and 82.18% accuracy from testing. Since SPRED does not use N-terminal signals, it can detect non-classical secreted proteins by filtering those secreted proteins with an N-terminal signal by using SignalP. SPRED predicted 15 out of 19 experimentally verified non-classical secretory proteins. By scanning the entire human proteome we identified 566 protein sequences potentially undergoing non-classical secretion. The dataset and standalone version of the SPRED software is available at (http://www.inb.uni-luebeck.de/tools-demos/spred/spred).

SPRED: A machine learning approach for the identification of classical and non-classical secretory proteins in mammalian genomes

International Nuclear Information System (INIS)

Kandaswamy, Krishna Kumar; Pugalenthi, Ganesan; Hartmann, Enno; Kalies, Kai-Uwe; Moeller, Steffen; Suganthan, P.N.; Martinetz, Thomas

2010-01-01

Eukaryotic protein secretion generally occurs via the classical secretory pathway that traverses the ER and Golgi apparatus. Secreted proteins usually contain a signal sequence with all the essential information required to target them for secretion. However, some proteins like fibroblast growth factors (FGF-1, FGF-2), interleukins (IL-1 alpha, IL-1 beta), galectins and thioredoxin are exported by an alternative pathway. This is known as leaderless or non-classical secretion and works without a signal sequence. Most computational methods for the identification of secretory proteins use the signal peptide as indicator and are therefore not able to identify substrates of non-classical secretion. In this work, we report a random forest method, SPRED, to identify secretory proteins from protein sequences irrespective of N-terminal signal peptides, thus allowing also correct classification of non-classical secretory proteins. Training was performed on a dataset containing 600 extracellular proteins and 600 cytoplasmic and/or nuclear proteins. The algorithm was tested on 180 extracellular proteins and 1380 cytoplasmic and/or nuclear proteins. We obtained 85.92% accuracy from training and 82.18% accuracy from testing. Since SPRED does not use N-terminal signals, it can detect non-classical secreted proteins by filtering those secreted proteins with an N-terminal signal by using SignalP. SPRED predicted 15 out of 19 experimentally verified non-classical secretory proteins. By scanning the entire human proteome we identified 566 protein sequences potentially undergoing non-classical secretion. The dataset and standalone version of the SPRED software is available at (http://www.inb.uni-luebeck.de/tools-demos/spred/spred).

Learning foreign sounds in an alien world: videogame training improves non-native speech categorization.

Science.gov (United States)

Lim, Sung-joo; Holt, Lori L

2011-01-01

Although speech categories are defined by multiple acoustic dimensions, some are perceptually weighted more than others and there are residual effects of native-language weightings in non-native speech perception. Recent research on nonlinguistic sound category learning suggests that the distribution characteristics of experienced sounds influence perceptual cue weights: Increasing variability across a dimension leads listeners to rely upon it less in subsequent category learning (Holt & Lotto, 2006). The present experiment investigated the implications of this among native Japanese learning English /r/-/l/ categories. Training was accomplished using a videogame paradigm that emphasizes associations among sound categories, visual information, and players' responses to videogame characters rather than overt categorization or explicit feedback. Subjects who played the game for 2.5h across 5 days exhibited improvements in /r/-/l/ perception on par with 2-4 weeks of explicit categorization training in previous research and exhibited a shift toward more native-like perceptual cue weights. Copyright © 2011 Cognitive Science Society, Inc.

Growth form and distribution of introduced plants in their native and non-native ranges in Eastern Asia and North America

Science.gov (United States)

Robert E. Ricklefs; Qinfeng Guo; Hong Qian

2008-01-01

There is a growing interest in understanding the influence of plant traits on their ability to spread in non-native regions. Many studies addressing this issue have been based on relatively small areas or restricted taxonomic groups. Here, we analyse a large data base involving 1567 plant species introduced between Eastern Asia and North America or from elsewhere to...

Long-distance dispersal of non-native pine bark beetles from host resources

Science.gov (United States)

Kevin Chase; Dave Kelly; Andrew M. Liebhold; Martin K.-F. Bader; Eckehard G. Brockerhoff

2017-01-01

Dispersal and host detection are behaviours promoting the spread of invading populations in a landscape matrix. In fragmented landscapes, the spatial arrangement of habitat structure affects the dispersal success of organisms. The aim of the present study was to determine the long distance dispersal capabilities of two non-native pine bark beetles (Hylurgus...

Chemical protein synthesis: Inventing synthetic methods to decipher how proteins work.

Science.gov (United States)

Kent, Stephen

2017-09-15

Total chemical synthesis of proteins has been rendered practical by the chemical ligation principle: chemoselective condensation of unprotected peptide segments equipped with unique, mutually reactive functional groups, enabled by formation of a non-native replacement for the peptide bond. Ligation chemistries are briefly described, including native chemical ligation - thioester-mediated, amide-forming reaction at Xaa-Cys sites - and its extensions. Case studies from the author's own works are used to illustrate the utility and applications of chemical protein synthesis. Selected recent developments in the field are briefly discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbial proteins produced from cannery wastes. II. Different cellulosic wastes used as substrate

Energy Technology Data Exchange (ETDEWEB)

Lee, H.C.; Chen, S.H.; Chang, J.S.; Lee, S.C.

1980-01-01

The production of protein by the cultivation of Cellulomonas species 34 on cellulosic wastes was studied. Maximum protein production on bamboo shoot husks was 4.77 g/L in 48 h when aeration was 1 vol./min, stirring rate was 1000 rpm, and substrate concentration was 3%. The chemical compounds of asparagus peel and pineapple peel and the conditions for their treatment with NaOH for protein fermentation are given.

Structure of the JmjC domain-containing protein NO66 complexed with ribosomal protein Rpl8

Energy Technology Data Exchange (ETDEWEB)

Wang, Chengliang [University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People’s Republic of (China); Chinese Academy of Sciences, Hefei, Anhui 230026, People’s Republic of (China); Zhang, Qiongdi [University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People’s Republic of (China); Hang, Tianrong [University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People’s Republic of (China); Chinese Academy of Sciences, Hefei, Anhui 230026, People’s Republic of (China); Tao, Yue [Shanghai Children’s Medical Center, 1678 Dongfang Road, Pudong, Shanghai 200120, People’s Republic of (China); Ma, Xukai [University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People’s Republic of (China); Wu, Minhao; Zhang, Xuan, E-mail: xuanzbin@ustc.edu.cn; Zang, Jianye, E-mail: xuanzbin@ustc.edu.cn [University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People’s Republic of (China); Chinese Academy of Sciences, Hefei, Anhui 230026, People’s Republic of (China)

2015-08-28

The structure of the complex of NO66 and Rpl8 was solved in the native state and NO66 recognizes the consensus motif NHXH . Tetramerization is required for efficient substrate binding and catalysis by NO66. The JmjC domain-containing proteins belong to a large family of oxygenases possessing distinct substrate specificities which are involved in the regulation of different biological processes, such as gene transcription, RNA processing and translation. Nucleolar protein 66 (NO66) is a JmjC domain-containing protein which has been reported to be a histone demethylase and a ribosome protein 8 (Rpl8) hydroxylase. The present biochemical study confirmed the hydroxylase activity of NO66 and showed that oligomerization is required for NO66 to efficiently catalyze the hydroxylation of Rpl8. The structures of NO66{sup 176–C} complexed with Rpl8{sup 204–224} in a tetrameric form and of the mutant protein M2 in a dimeric form were solved. Based on the results of structural and biochemical analyses, the consensus sequence motif NHXH recognized by NO66 was confirmed. Several potential substrates of NO66 were found by a BLAST search according to the consensus sequence motif. When binding to substrate, the relative positions of each subunit in the NO66 tetramer shift. Oligomerization may facilitate the motion of each subunit in the NO66 tetramer and affect the catalytic activity.

Native chemical ligation at Asx-Cys, Glx-Cys: chemical synthesis and high-resolution X-ray structure of ShK toxin by racemic protein crystallography.

Science.gov (United States)

Dang, Bobo; Kubota, Tomoya; Mandal, Kalyaneswar; Bezanilla, Francisco; Kent, Stephen B H

2013-08-14

We have re-examined the utility of native chemical ligation at -Gln/Glu-Cys- [Glx-Cys] and -Asn/Asp-Cys- [Asx-Cys] sites. Using the improved thioaryl catalyst 4-mercaptophenylacetic acid (MPAA), native chemical ligation could be performed at -Gln-Cys- and Asn-Cys- sites without side reactions. After optimization, ligation at a -Glu-Cys- site could also be used as a ligation site, with minimal levels of byproduct formation. However, -Asp-Cys- is not appropriate for use as a site for native chemical ligation because of formation of significant amounts of β-linked byproduct. The feasibility of native chemical ligation at -Gln-Cys- enabled a convergent total chemical synthesis of the enantiomeric forms of the ShK toxin protein molecule. The D-ShK protein molecule was ~50,000-fold less active in blocking the Kv1.3 channel than the L-ShK protein molecule. Racemic protein crystallography was used to obtain high-resolution X-ray diffraction data for ShK toxin. The structure was solved by direct methods and showed significant differences from the previously reported NMR structures in some regions of the ShK protein molecule.

Effects of different substrates on the yield and protein content of ...

African Journals Online (AJOL)

The effects of seven substrates for the cultivation, yield and protein content of the mushroom, Pleurotus tuberregium (Fries) Singer were investigated. The experimental design used was completely randomized design (CRD) of 7 treatments and 10 replicates. The highest fresh weight yield was obtained from mushrooms ...

Substrate-Triggered Formation and Remarkable Stability of the C-H-Cleaving Chloroferryl Intermediate in the Aliphatic Halogenase, SyrB2†

Science.gov (United States)

Matthews, Megan L.; Krest, Courtney M.; Barr, Eric W.; Vaillancourt, Frédéric H.; Walsh, Christopher T.; Green, Michael T.; Krebs, Carsten; Bollinger, J. Martin

2009-01-01

Aliphatic halogenases activate O2, cleave α-ketoglutarate (αKG) to CO2 and succinate, and form haloferryl [X-Fe(IV)=O; X = Cl, Br] complexes that cleave aliphatic C-H bonds to install halogens during the biosynthesis of natural products by non-ribosomal peptide synthetases (NRPSs). For the related αKG-dependent dioxygenases, it has been shown that reaction of the Fe(II) cofactor with O2 to form the C-H-cleaving ferryl complex is “triggered” by binding of the target substrate. In this study, we have tested for and defined structural determinants of substrate triggering (ST) in the halogenase, SyrB2, from the syringomycin E biosynthetic NRPS of Pseudomonas syringae B301D. As for other halogen ases, the substrate of SyrB2 is complex, consisting of l-Thr tethered via thioester linkage to a covalently bound phosphopantetheine (PPant) cofactor of a carrier protein, SyrB1. Without an appended amino acid, SyrB1 does not trigger formation of the chloroferryl intermediate state in SyrB2, even in the presence of free l-Thr or its analogues, but SyrB1 charged either by l-Thr or by any of several non-native amino acids does trigger the reaction by as much as 8,000-fold (for l-Thr-S-SyrB1). Triggering efficacy is sensitive to the structures of both the amino acid and the carrier protein, being diminished by 5–20-fold when the native l-Thr is replaced by another amino acid and by ∼ 40-fold when SyrB1 is replaced by a heterologous carrier protein, CytC2. The directing effect of the carrier protein and consequent tolerance for profound modifications to the target amino acid allow the chloroferryl state to be formed in the presence of substrates that perturb the ratio of its two putative coordination isomers, lack the target C-H bond (l-Ala-S-SyrB1), or contain a C-H bond of enhanced strength (l-cyclopropylglycyl-S-SyrB1). For the latter two cases, the SyrB2 chloroferryl state so formed exhibits unprecedented stability (t1/2 = 30 – 110 min at 0 °C), can be trapped in

Comparing differential tolerance of native and non-indigenous marine species to metal pollution using novel assay techniques

International Nuclear Information System (INIS)

Piola, Richard F.; Johnston, Emma L.

2009-01-01

Recent research suggests anthropogenic disturbance may disproportionately advantage non-indigenous species (NIS), aiding their establishment within impacted environments. This study used novel laboratory- and field-based toxicity testing to determine whether non-indigenous and native bryozoans (common within marine epibenthic communities worldwide) displayed differential tolerance to the common marine pollutant copper (Cu). In laboratory assays on adult colonies, NIS showed remarkable tolerance to Cu, with strong post-exposure recovery and growth. In contrast, native species displayed negative growth and reduced feeding efficiency across most exposure levels. Field transplant experiments supported laboratory findings, with NIS growing faster under Cu conditions. In field-based larval assays, NIS showed strong recruitment and growth in the presence of Cu relative to the native species. We suggest that strong selective pressures exerted by the toxic antifouling paints used on transport vectors (vessels), combined with metal contamination in estuarine environments, may result in metal tolerant NIS advantaged by anthropogenically modified selection regimes. - Greater tolerance to pollutants in marine NIS may increase the risk of invasion in port and harbours worldwide by providing a competitive advantage over native taxa.

DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications.

Science.gov (United States)

Lu, Cheng-Tsung; Huang, Kai-Yao; Su, Min-Gang; Lee, Tzong-Yi; Bretaña, Neil Arvin; Chang, Wen-Chi; Chen, Yi-Ju; Chen, Yu-Ju; Huang, Hsien-Da

2013-01-01

Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability and activity of a protein; thus altering protein function. Due to the high throughput of mass spectrometry (MS)-based methods in identifying site-specific post-translational modifications (PTMs), dbPTM (http://dbPTM.mbc.nctu.edu.tw/) is updated to integrate experimental PTMs obtained from public resources as well as manually curated MS/MS peptides associated with PTMs from research articles. Version 3.0 of dbPTM aims to be an informative resource for investigating the substrate specificity of PTM sites and functional association of PTMs between substrates and their interacting proteins. In order to investigate the substrate specificity for modification sites, a newly developed statistical method has been applied to identify the significant substrate motifs for each type of PTMs containing sufficient experimental data. According to the data statistics in dbPTM, >60% of PTM sites are located in the functional domains of proteins. It is known that most PTMs can create binding sites for specific protein-interaction domains that work together for cellular function. Thus, this update integrates protein-protein interaction and domain-domain interaction to determine the functional association of PTM sites located in protein-interacting domains. Additionally, the information of structural topologies on transmembrane (TM) proteins is integrated in dbPTM in order to delineate the structural correlation between the reported PTM sites and TM topologies. To facilitate the investigation of PTMs on TM proteins, the PTM substrate sites and the structural topology are graphically represented. Also, literature information related to PTMs, orthologous conservations and substrate motifs of PTMs are also provided in the resource. Finally, this version features an improved web interface to facilitate convenient access to the resource.

Genetically based differentiation in growth of multiple non-native plant species along a steep environmental gradient.

Science.gov (United States)

Haider, Sylvia; Kueffer, Christoph; Edwards, Peter J; Alexander, Jake M

2012-09-01

A non-native plant species spreading along an environmental gradient may need to adjust its growth to the prevailing conditions that it encounters by a combination of phenotypic plasticity and genetic adaptation. There have been several studies of how non-native species respond to changing environmental conditions along latitudinal gradients, but much less is known about elevational gradients. We conducted a climate chamber experiment to investigate plastic and genetically based growth responses of 13 herbaceous non-native plants along an elevational gradient from 100 to 2,000 m a.s.l. in Tenerife. Conditions in the field ranged from high anthropogenic disturbance but generally favourable temperatures for plant growth in the lower half of the gradient, to low disturbance but much cooler conditions in the upper half. We collected seed from low, mid and high elevations and grew them in climate chambers under the characteristic temperatures at these three elevations. Growth of all species was reduced under lower temperatures along both halves of the gradient. We found consistent genetically based differences in growth over the upper elevational gradient, with plants from high-elevation sites growing more slowly than those from mid-elevation ones, while the pattern in the lower part of the gradient was more mixed. Our data suggest that many non-native plants might respond to climate along elevational gradients by genetically based changes in key traits, especially at higher elevations where low temperatures probably impose a stronger selection pressure. At lower elevations, where anthropogenic influences are greater, higher gene flow and frequent disturbance might favour genotypes with broad ecological amplitudes. Thus the importance of evolutionary processes for invasion success is likely to be context-dependent.

Revealing Abrupt and Spontaneous Ruptures of Protein Native Structure under picoNewton Compressive Force Manipulation.

Science.gov (United States)

Chowdhury, S Roy; Cao, Jin; He, Yufan; Lu, H Peter

2018-03-27

Manipulating protein conformations for exploring protein structure-function relationship has shown great promise. Although protein conformational changes under pulling force manipulation have been extensively studied, protein conformation changes under a compressive force have not been explored quantitatively. The latter is even more biologically significant and relevant in revealing protein functions in living cells associated with protein crowdedness, distribution fluctuations, and cell osmotic stress. Here we report our experimental observations on abrupt ruptures of protein native structures under compressive force, demonstrated and studied by single-molecule AFM-FRET spectroscopic nanoscopy. Our results show that the protein ruptures are abrupt and spontaneous events occurred when the compressive force reaches a threshold of 12-75 pN, a force amplitude accessible from thermal fluctuations in a living cell. The abrupt ruptures are sensitive to local environment, likely a general and important pathway of protein unfolding in living cells.

Common neural substrates support speech and non-speech vocal tract gestures

OpenAIRE

Chang, Soo-Eun; Kenney, Mary Kay; Loucks, Torrey M.J.; Poletto, Christopher J.; Ludlow, Christy L.

2009-01-01

The issue of whether speech is supported by the same neural substrates as non-speech vocal-tract gestures has been contentious. In this fMRI study we tested whether producing non-speech vocal tract gestures in humans shares the same functional neuroanatomy as non-sense speech syllables. Production of non-speech vocal tract gestures, devoid of phonological content but similar to speech in that they had familiar acoustic and somatosensory targets, were compared to the production of speech sylla...

Distribution and status of five non-native fish species in the Tampa Bay drainage (USA), a hot spot for fish introductions

Science.gov (United States)

Lawson, Katelyn M.; Tuckett, Quenton M.; Ritch, Jared L.; Nico, Leo; Fuller, Pam; Matheson, Richard E.; Hill, Jeffrey E.

2017-01-01

The Tampa Bay region of Florida (USA) is a hot spot for non-native freshwater fishes. However, published information on most non-native fishes in the basin is not current. Systematic sampling efforts targeting non-native fishes in the region were conducted from 2013–2015 by the University of Florida Tropical Aquaculture Laboratory. Data from these recent surveys were analyzed, along with historic and new data from published and unpublished sources, to assess current fish distributions and determine status. We focus on five of the non-native species sampled: pike killifish Belonesox belizanus Kner, 1860, green swordtail Xiphophorus hellerii Heckel, 1848, southern platyfish Xiphophorus maculatus (Günther, 1866), Mayan cichlid Mayaheros urophthalmus (Günther, 1862), and Jack Dempsey Rocio octofasciata (Regan, 1903). All five were found to have reproducing populations in the basin, each showing broader distributions than previously indicated. Non-native populations of four of the species have persisted in the Tampa Bay region since at least the 1990s. In contrast, the presence of Mayan cichlid in the basin was not confirmed until 2004. Based on numbers, distributions, and years of persistence, these five species all maintain established populations. Pike killifish and Mayan cichlid are established and spreading throughout multiple habitat types, while green swordtail, southern platyfish, and Jack Dempsey are localized and found primarily in more marginal habitats (e.g., small ditches and first order tributary streams). Factors affecting continued existence and distributions likely include aquaculture, biotic resistance, and thermal and salinity tolerances. We also clarify non-native species status determination using a multi-agency collaborative approach, and reconcile differences in terminology usage and interpretation.

Impacts of non-native Norway spruce plantation on abundance and species richness of ground beetles (Coleoptera: Carabidae

Directory of Open Access Journals (Sweden)

Z. Elek

2001-06-01

Full Text Available The impacts of non-native Norway spruce plantation on the abundance and species richness of carabids were studied in the Bükk National Park in Hungary, central Europe. Pitfall catches from recently established (5 yr old, young (15 yr after planting, middle-aged (30 yr after planting, old Norway spruce Picea abies plantation (50 yr after planting, and a native submontane beech forest (Fagetum sylvaticae as a control stand were compared.

Our results showed that deciduous forest species decreased significantly in abundance in the plantations, and appeared in high abundance only in the native beech forest. Furthermore, open habitat species increased remarkably in abundance in the recently established plantation. Carabids were significantly more abundant and species rich in the native forest than in the plantations, while differences were not significant among the plantations. Multiple regression between the abundance and species richness of carabids and twelve environmental measurements showed that pH of the soil, herb cover and density of the carabids’ prey had a significant effect in determining abundance and species richness.

Our results showed that plantation of non-native Norway spruce species had a detrimental effect on the composition of carabid communities and no regeneration could be observed during the growth of plantations even 50 yr after the establishment. This emphasises the importance of an active nature management practice to facilitate the recolonization of the native species.

Leaf gas exchange and water status responses of a native and non-native grass to precipitation across contrasting soil surfaces in the Sonoran Desert.

Science.gov (United States)

Ignace, Danielle D; Huxman, Travis E; Weltzin, Jake F; Williams, David G

2007-06-01

Arid and semi-arid ecosystems of the southwestern US are undergoing changes in vegetation composition and are predicted to experience shifts in climate. To understand implications of these current and predicted changes, we conducted a precipitation manipulation experiment on the Santa Rita Experimental Range in southeastern Arizona. The objectives of our study were to determine how soil surface and seasonal timing of rainfall events mediate the dynamics of leaf-level photosynthesis and plant water status of a native and non-native grass species in response to precipitation pulse events. We followed a simulated precipitation event (pulse) that occurred prior to the onset of the North American monsoon (in June) and at the peak of the monsoon (in August) for 2002 and 2003. We measured responses of pre-dawn water potential, photosynthetic rate, and stomatal conductance of native (Heteropogon contortus) and non-native (Eragrostis lehmanniana) C(4) bunchgrasses on sandy and clay-rich soil surfaces. Soil surface did not always amplify differences in plant response to a pulse event. A June pulse event lead to an increase in plant water status and photosynthesis. Whereas the August pulse did not lead to an increase in plant water status and photosynthesis, due to favorable soil moisture conditions facilitating high plant performance during this period. E. lehmanniana did not demonstrate heightened photosynthetic performance over the native species in response to pulses across both soil surfaces. Overall accumulated leaf-level CO(2) response to a pulse event was dependent on antecedent soil moisture during the August pulse event, but not during the June pulse event. This work highlights the need to understand how desert species respond to pulse events across contrasting soil surfaces in water-limited systems that are predicted to experience changes in climate.

Non-Native Speakers of the Language of Instruction: Self-Perceptions of Teaching Ability

Science.gov (United States)

Samuel, Carolyn

2017-01-01

Given the linguistically diverse instructor and student populations at Canadian universities, mutually comprehensible oral language may not be a given. Indeed, both instructors who are non-native speakers of the language of instruction (NNSLIs) and students have acknowledged oral communication challenges. Little is known, though, about how the…

Recreational freshwater fishing drives non-native aquatic species richness patterns at a continental scale.

Science.gov (United States)

Mapping the geographic distribution of non-native aquatic species is a critically important precursor to understanding the anthropogenic and environmental factors that drive freshwater biological invasions. Such efforts are often limited to local scales and/or to single species, ...

Oxysterol-binding protein-related protein (ORP) 9 is a PDK-2 substrate and regulates Akt phosphorylation.

Science.gov (United States)

Lessmann, Eva; Ngo, Mike; Leitges, Michael; Minguet, Susana; Ridgway, Neale D; Huber, Michael

2007-02-01

The oxysterol-binding protein and oxysterol-binding protein-related protein family has been implicated in lipid transport and metabolism, vesicle trafficking and cell signaling. While investigating the phosphorylation of Akt/protein kinase B in stimulated bone marrow-derived mast cells, we observed that a monoclonal antibody directed against phospho-S473 Akt cross-reacted with oxysterol-binding protein-related protein 9 (ORP9). Further analysis revealed that mast cells exclusively express ORP9S, an N-terminal truncated version of full-length ORP9L. A PDK-2 consensus phosphorylation site in ORP9L and OPR9S at S287 (VPEFS(287)Y) was confirmed by site-directed mutagenesis. In contrast to Akt, increased phosphorylation of ORP9S S287 in stimulated mast cells was independent of phosphatidylinositol 3-kinase but sensitive to inhibition of conventional PKC isotypes. PKC-beta dependence was confirmed by lack of ORP9S phosphorylation at S287 in PKC-beta-deficient, but not PKC-alpha-deficient, mast cells. Moreover, co-immunoprecipitation of PKC-beta and ORP9S, and in vitro phosphorylation of ORP9S in this complex, argued for direct phosphorylation of ORP9S by PKC-beta, introducing ORP9S as a novel PKC-beta substrate. Akt was also detected in a PKC-beta/ORP9S immune complex and phosphorylation of Akt on S473 was delayed in PKC-deficient mast cells. In HEK293 cells, RNAi experiments showed that depletion of ORP9L increased Akt S473 phosphorylation 3-fold without affecting T308 phosphorylation in the activation loop. Furthermore, mammalian target of rapamycin was implicated in ORP9L phosphorylation in HEK293 cells. These studies identify ORP9 as a PDK-2 substrate and negative regulator of Akt phosphorylation at the PDK-2 site.

Loss of proteostatic control as a substrate for Atrial Fibrillation; a novel target for upstream therapy by Heat Shock Proteins

Directory of Open Access Journals (Sweden)

Roelien Amanda Marjolein Meijering

2012-02-01

Full Text Available Atrial Fibrillation (AF is the most common, sustained clinical tachyarrhythmia associated with significant morbidity and mortality. AF is a persistent condition with progressive structural remodeling of the atrial cardiomyocytes due to the AF itself, resulting in cellular changes commonly observed in ageing and in other heart diseases. While rhythm control by electrocardioversion or drug treatment is the treatment of choice in symptomatic AF patients, its effectiveness is still limited. Current research is directed at preventing new-onset AF by limiting the development of substrates underlying AF promotion and resembles mechanism-based therapy. Upstream therapy refers to the use of non-ion channel anti-arrhythmic drugs that modify the atrial substrate- or target-specific mechanisms of AF, with the ultimate aim to prevent the occurrence (primary prevention or recurrence of the arrhythmia following (spontaneous conversion (secondary prevention.Heat shock proteins (HSPs are molecular chaperones and comprise a large family of proteins involved in the protection against various forms of cellular stress. Their classical function is the conservation of proteostasis via prevention of toxic protein aggregation by binding to (partially unfolded proteins. Our recent data reveal that HSPs prevent electrical, contractile and structural remodeling of cardiomyocytes, thus attenuating the AF substrate in cellular, Drosophila melanogaster and animal experimental models. Furthermore, studies in humans suggest a protective role for HSPs against the progression from paroxysmal AF to persistent AF and in recurrence of AF. In this review, we discuss upregulation of the heat shock response system as a novel target for upstream therapy to prevent derailment of proteostasis and consequently promotion and recurrence of AF.

Production of carbon-13-labeled cadaverine by engineered Corynebacterium glutamicum using carbon-13-labeled methanol as co-substrate.

Science.gov (United States)

Leßmeier, Lennart; Pfeifenschneider, Johannes; Carnicer, Marc; Heux, Stephanie; Portais, Jean-Charles; Wendisch, Volker F

2015-12-01

Methanol, a one-carbon compound, can be utilized by a variety of bacteria and other organisms as carbon and energy source and is regarded as a promising substrate for biotechnological production. In this study, a strain of non-methylotrophic Corynebacterium glutamicum, which was able to produce the polyamide building block cadaverine as non-native product, was engineered for co-utilization of methanol. Expression of the gene encoding NAD+-dependent methanol dehydrogenase (Mdh) from the natural methylotroph Bacillus methanolicus increased methanol oxidation. Deletion of the endogenous aldehyde dehydrogenase genes ald and fadH prevented methanol oxidation to carbon dioxide and formaldehyde detoxification via the linear formaldehyde dissimilation pathway. Heterologous expression of genes for the key enzymes hexulose-6-phosphate synthase and 6-phospho-3-hexuloisomerase of the ribulose monophosphate (RuMP) pathway in this strain restored growth in the presence of methanol or formaldehyde, which suggested efficient formaldehyde detoxification involving RuMP key enzymes. While growth with methanol as sole carbon source was not observed, the fate of 13C-methanol added as co-substrate to sugars was followed and the isotopologue distribution indicated incorporation into central metabolites and in vivo activity of the RuMP pathway. In addition, 13C-label from methanol was traced to the secreted product cadaverine. Thus, this synthetic biology approach led to a C. glutamicum strain that converted the non-natural carbon substrate methanol at least partially to the non-native product cadaverine.

Biological activity of egg-yolk protein by-product hydrolysates obtained with the use of non-commercial plant protease

Directory of Open Access Journals (Sweden)

A. Zambrowicz

2015-12-01

Full Text Available Enzymatic hydrolysis leads to improved functional and biological properties of protein by-products, which can be further used as nutraceuticals and protein ingredients for food applications.The present study evaluated ACE-inhibitory, antioxidant and immunostimulating activities in hydrolysates of egg-yolk protein by-product (YP, generated during industrial process of delipidation of yolk. The protein substrate was hydrolyzed using non-commercial protease from Asian pumpkin (Cucurbita ficifolia. The reaction was conducted in 0.1 M Tris-HCl buffer (pH 8.0 at temperature of 37°C for 4 hours using different enzyme doses (100-1000 U/mg of substrate. The protein degradation was monitored by the determination of the degree of hydrolysis (DH, release of free amino groups (FAG and by RP-HPLC. In the obtained hydrolysates we also evaluated biological activities. It was shown that the highest DH of substrate (46.6% was obtained after 4h of reaction at the highest amount of enzyme. This hydrolysate exhibited antioxidant activity, including ferricion reducing (FRAP (56.41 μg Fe2+/mg, ferric ion chelating (695.76 μg Fe2+/mg and DPPH free radical scavenging (0.89 μmol troloxeq/mg as well as ACE-inhibitory (IC50=837.75 μg/mL activities.The research showed improved biological properties of enzymatically modified YP by-product.

User requirement analysis of social conventions learning applications for Non-natives and low-literates

NARCIS (Netherlands)

Schouten, D.; Smets, N.; Driessen, M.; Hanekamp, M.; Cremers, A.H.M.; Neerincx, M.A.

2013-01-01

Learning and acting on social conventions is problematic for low-literates and non-natives, causing problems with societal participation and citizenship. Using the Situated Cognitive Engineering method, requirements for the design of social conventions learning software are derived from demographic

Electrophoretic deposition of thin film zirconia electrolyte on non-conducting NiO-YSZ substrate

International Nuclear Information System (INIS)

Das, Debasish; Basu, Rajendra N.

2014-01-01

Eight (8) mol% yttria stabilized zirconia (YSZ), an electrolyte material for solid oxide fuel cell (SOFC), has been deposited onto porous non-conducting NiO-YSZ substrate using electrophoretic deposition technique (EPD) from a stable non-aqueous suspension of YSZ. Normally, EPD cannot be performed on a non-conducting substrate, but, in this present study, YSZ particulate film has been successfully deposited on a non-conducting NiO-YSZ substrate following two different EPD approaches:(a) using a conducting metallic plate on the reverse side of the porous NiO-YSZ anode substrate and (b) using a conducting polymer coated NiO-YSZ substrate. The deposited films are then formed dense coatings of 5-15 μm after sintering at 1400℃ for 6 h in air. Surface and cross-sectional morphologies of green and sintered films deposited by different EPD approaches are investigated using SEM. La 0.65 Sr 0.3 MnO 3 (LSM), a cathode for SOFC, is then screen-printed onto the electrolyte layer of such sintered half cells (anode+electrolyte) prepared by both the above approaches to construct SOFC single cells. A maximum output power density of 0.37 W.cm -2 is obtained using single cells prepared by conducting metallic plate assisted EPD compared to that of 0.73 W.cm -2 for polymer coated at 800℃ using H 2 as fuel and O 2 as oxidant. (author)

Hydrolysis of protein and model dipeptide substrated by attached and nonattached marine Pseudomonas sp. strain NCIMB 2021

International Nuclear Information System (INIS)

Griffith, P.C.; Fletcher, M.

1991-01-01

Rates of substrate hydrolysis by nonattached bacteria and by bacteria attached to particles derived from marine diatom frustules were estimated by using two substrates, a dipeptide analog and a protein. Adsorption of the two substrates onto the particles was also evaluated. Methyl-coumarinyl-amide-leucine (MCA-leucine) was used to estimate hydrolysis of dipeptides by measuring an increase in fluorescence as MCA-leucine was hydrolyzed to leucine and the fluorochrome methylcoumarin. To examine hydrolysis of a larger molecule, was prepared a radiolabeled protein by 14 C-methylation of bovine serum albumin. The rate of protein hydrolysis in samples of particle-attached or nonattached bacteria was estimated by precipitating all nonhydrolyzed protein with cold trichloroacetic acid and then determining the trichloroacetic acid-soluble radiolabeled material, which represented methyl- 14 C-peptides and -amino acids. About 25% of the MCA-leucine adsorbed to the particles. MCA-leucine was hydrolyzed faster by nonattached than attached bacteria, which was probably related to its tendency to remain dissolved in the liquid phase. In contrast, almost 100% of the labeled protein adsorbed to the particles. Accordingly, protein was much less available to nonattached bacteria but was rapidly hydrolyzed by attached bacteria

Teaching a Growing a Population of Non-Native English-Speaking Students in American Universities: Cultural and Linguistic Challenges

OpenAIRE

Maria Cristina Fava

2016-01-01

The increasing number of non-native English speaking students in American universities, mostly from Asian countries, presents unprecedented challenges and calls for an in-depth study on how we teach western art music history. This essay challenges some aspects of liberal multiculturalism and proposes the creation of channels of communication that allow non-native English speaking students to understand the premises of a Eurocentric system of knowledge without undermining their own cultural ba...

Enzymatic cross-linking of soy proteins within non-fat set yogurt gel.

Science.gov (United States)

Soleymanpuori, Rana; Madadlou, Ashkan; Zeynali, Fariba; Khosrowshahi, Asghar

2014-08-01

Soy proteins as the health-promoting ingredients and candidate fat substitutes in dairy products are good substrates for the cross-linking action of the enzyme transglutaminase. Non-fat set yogurt samples were prepared from the milks enriched with soy protein isolate (SPI) and/or treated with the enzyme transglutaminase. The highest titrable acidity was recorded for the yogurt enriched with SPI and treated with the enzyme throughout the cold storage for 21 d. SPI-enrichment of yogurt milk increased the water holding capacity. Although enrichment with SPI did not influence the count of Streptococcus themophilus, increased that of Lactobacillus bulgaricus ∼3 log cycles. The enzymatic treatment of SPI-enriched milk however, suppressed the bacteria growth-promoting influence of SPI due probably to making the soy proteins inaccessible for Lactobacillus. SPI-enrichment and enzymatic treatment of milk decreased the various organic acids content in yoghurt samples; influence of the former was more significant. The cross-linking of milk proteins to soy proteins was confirmed with the gel electrophoresis results.

The Big Four Skills: Teachers’ Assumptions on Measurement of Cognition and Academic Skills for Non-Native Students.

OpenAIRE

Figueiredo, Sandra; Silva, Carlos Fernandes da; Nunes, Odete; Martins, Maria Margarida Alves d'Orey

2016-01-01

The four-skills on tests for young native speakers commonly do not generate correlation incongruency concerning the cognitive strategies frequently reported. Considering the non-native speakers there are parse evidence to determine which tasks are important to assess properly the cognitive and academic language proficiency (Cummins, 1980; 2012). Research questions: It is of high probability that young students with origin in immigration ...

Non-Native Ambrosia Beetles as Opportunistic Exploiters of Living but Weakened Trees.

Science.gov (United States)

Ranger, Christopher M; Schultz, Peter B; Frank, Steven D; Chong, Juang H; Reding, Michael E

2015-01-01

Exotic Xylosandrus spp. ambrosia beetles established in non-native habitats have been associated with sudden and extensive attacks on a diverse range of living trees, but factors driving their shift from dying/dead hosts to living and healthy ones are not well understood. We sought to characterize the role of host physiological condition on preference and colonization by two invaders, Xylosandrus germanus and Xylosandrus crassiusculus. When given free-choice under field conditions among flooded and non-flooded deciduous tree species of varying intolerance to flooding, beetles attacked flood-intolerant tree species over more tolerant species within 3 days of initiating flood stress. In particular, flood-intolerant flowering dogwood (Cornus florida) sustained more attacks than flood-tolerant species, including silver maple (Acer saccharinum) and swamp white oak (Quercus bicolor). Ethanol, a key host-derived attractant, was detected at higher concentrations 3 days after initiating flooding within stems of flood intolerant species compared to tolerant and non-flooded species. A positive correlation was also detected between ethanol concentrations in stem tissue and cumulative ambrosia beetle attacks. When adult X. germanus and X. crassiusculus were confined with no-choice to stems of flood-stressed and non-flooded C. florida, more ejected sawdust resulting from tunneling activity was associated with the flood-stressed trees. Furthermore, living foundresses, eggs, larvae, and pupae were only detected within galleries created in stems of flood-stressed trees. Despite a capability to attack diverse tree genera, X. germanus and X. crassiusculus efficiently distinguished among varying host qualities and preferentially targeted trees based on their intolerance of flood stress. Non-flooded trees were not preferred or successfully colonized. This study demonstrates the host-selection strategy exhibited by X. germanus and X. crassiusculus in non-native habitats involves

Non-Native Ambrosia Beetles as Opportunistic Exploiters of Living but Weakened Trees.

Directory of Open Access Journals (Sweden)

Christopher M Ranger

Full Text Available Exotic Xylosandrus spp. ambrosia beetles established in non-native habitats have been associated with sudden and extensive attacks on a diverse range of living trees, but factors driving their shift from dying/dead hosts to living and healthy ones are not well understood. We sought to characterize the role of host physiological condition on preference and colonization by two invaders, Xylosandrus germanus and Xylosandrus crassiusculus. When given free-choice under field conditions among flooded and non-flooded deciduous tree species of varying intolerance to flooding, beetles attacked flood-intolerant tree species over more tolerant species within 3 days of initiating flood stress. In particular, flood-intolerant flowering dogwood (Cornus florida sustained more attacks than flood-tolerant species, including silver maple (Acer saccharinum and swamp white oak (Quercus bicolor. Ethanol, a key host-derived attractant, was detected at higher concentrations 3 days after initiating flooding within stems of flood intolerant species compared to tolerant and non-flooded species. A positive correlation was also detected between ethanol concentrations in stem tissue and cumulative ambrosia beetle attacks. When adult X. germanus and X. crassiusculus were confined with no-choice to stems of flood-stressed and non-flooded C. florida, more ejected sawdust resulting from tunneling activity was associated with the flood-stressed trees. Furthermore, living foundresses, eggs, larvae, and pupae were only detected within galleries created in stems of flood-stressed trees. Despite a capability to attack diverse tree genera, X. germanus and X. crassiusculus efficiently distinguished among varying host qualities and preferentially targeted trees based on their intolerance of flood stress. Non-flooded trees were not preferred or successfully colonized. This study demonstrates the host-selection strategy exhibited by X. germanus and X. crassiusculus in non-native habitats

THE ROLE OF NON-NATIVE ENGLISH SPEAKER TEACHERS IN ENGLISH LANGUAGE LEARNING

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Lutfi Ashar Mauludin

2017-04-01

Full Text Available Native-English Speaker Teachers (NESTs and Non-Native English Speaker Teachers (NNESTs have their own advantages and disadvantages. However, for English Language Learners (ELLs, NNESTs have more advantages in helping students to acquire English skills. At least there are three factors that can only be performed by NNESTs in English Language Learning. The factors are knowledge of the subject, effective communication, and understanding students‘ difficulties/needs. The NNESTs can effectively provide the clear explanation of knowledge of the language because they are supported by the same background and culture. NNESTs also can communicate with the students with all levels effectively. The use of L1 is effective to help students building their knowledge. Finally, NNESTs can provide the objectives and materials that are suitable with the needs of the students.

Identification of unknown protein complex members by radiolocalization and analysis of low-abundance complexes resolved using native polyacrylamide gel electrophoresis.

Science.gov (United States)

Bose, Mahuya; Adams, Brian P; Whittal, Randy M; Bose, Himangshu S

2008-02-01

Identification of unknown binding partners of a protein of interest can be a difficult process. Current strategies to determine protein binding partners result in a high amount of false-positives, requiring use of several different methods to confirm the accuracy of the apparent association. We have developed and utilized a method that is reliable and easily substantiated. Complexes are isolated from cell extract after exposure to the radiolabeled protein of interest, followed by resolution on a native polyacrylamide gel. Native conformations are preserved, allowing the complex members to maintain associations. By radiolabeling the protein of interest, the complex can be easily identified at detection levels below the threshold of Serva Blue, Coomassie, and silver stains. The visualized radioactive band is analyzed by MS to identify binding partners, which can be subsequently verified by antibody shift and immunoprecipitation of the complex. By using this method we have successfully identified binding partners of two proteins that reside in different locations of a cellular organelle.

Genome and metabolic engineering in non-conventional yeasts: Current advances and applications.

Science.gov (United States)

Löbs, Ann-Kathrin; Schwartz, Cory; Wheeldon, Ian

2017-09-01

Microbial production of chemicals and proteins from biomass-derived and waste sugar streams is a rapidly growing area of research and development. While the model yeast Saccharomyces cerevisia e is an excellent host for the conversion of glucose to ethanol, production of other chemicals from alternative substrates often requires extensive strain engineering. To avoid complex and intensive engineering of S. cerevisiae, other yeasts are often selected as hosts for bioprocessing based on their natural capacity to produce a desired product: for example, the efficient production and secretion of proteins, lipids, and primary metabolites that have value as commodity chemicals. Even when using yeasts with beneficial native phenotypes, metabolic engineering to increase yield, titer, and production rate is essential. The non-conventional yeasts Kluyveromyces lactis, K. marxianus, Scheffersomyces stipitis, Yarrowia lipolytica, Hansenula polymorpha and Pichia pastoris have been developed as eukaryotic hosts because of their desirable phenotypes, including thermotolerance, assimilation of diverse carbon sources, and high protein secretion. However, advanced metabolic engineering in these yeasts has been limited. This review outlines the challenges of using non-conventional yeasts for strain and pathway engineering, and discusses the developed solutions to these problems and the resulting applications in industrial biotechnology.

Combinations of SPR and MS for Characterizations of Native and Recombinant Proteins in Cell Lysates

DEFF Research Database (Denmark)

Borch, Jonas; Roepstorff, Peter

2006-01-01

Surface plasmon resonance and mass spectrometry (SPR-MS) has been combined for quality check of recombinant 6xHis-tagged 14-3-3 proteins expressed in Escherichia coli. Lysates were injected over an SPR sensorchip with immobilized Ni2+ for SPR analysis of the specific Ni2+ binding response...... and stability. To validate the identity, intactness and homogeneity of the captured proteins were eluted for mass spectrometric analysis of intact molecular weight and peptide mass mapping. Additionally, the captured recombinant proteins were investigated for specific binding to known phosphorylated ligands...... of 14-3-3 proteins in order to test their activity. Specific binding of recombinant and native 14-3-3 proteins in complex mixtures to immobilized phosphopeptides and subsequent elution was also tested by SPR-MS. Ammonium sulfate precipitate fractions from lysates of E. coli expressing 14-3-3 protein...

Characterization and evaluation of whey protein-based biofilms as substrates for in vitro cell cultures.

Science.gov (United States)

Gilbert, Vanessa; Rouabhia, Mahmoud; Wang, Hongxum; Arnould, Anne-Lise; Remondetto, Gabriel; Subirade, Muriel

2005-12-01

Whey proteins-based biofilms were prepared using different plasticizers in order to obtain a biomaterial for the human keratinocytes and fibroblasts in vitro culture. The film properties were evaluated by Fourier Transform Infrared Spectroscopy (FTIR) technique and mechanical tests. A relationship was found between the decrease of intermolecular hydrogen bond strength and film mechanical behavior changes, expressed by a breaking stress and Young modulus values diminishing. These results allow stating that the film molecular configuration could induce dissimilarities in its mechanical properties. The films toxicity was assessed by evaluating the cutaneous cells adherence, growth, proliferation and structural stratification. Microscopic observation demonstrated that both keratinocytes and fibroblasts adhered to the biofilms. The trypan blue exclusion test showed that keratinocytes grew at a significantly high rate on all the biofilms. Structural analysis demonstrated that keratinocytes stratified when cultured on the whey protein-based biofilms and gave rise to multi-layered epidermal structures. The most organized epidermis was obtained with whey protein isolate/DEG biofilm. This structure had a well-organized basal layer under supra-basal and corneous layers. This study demonstrated that whey proteins, an inexpensive renewable resource which can be obtained readily, were non-toxic to cutaneous cells and thus they could be useful substrates for a variety of biomedical applications, including tissue engineering.

Positive feedback loop between introductions of non-native marine species and cultivation of oysters in Europe.

Science.gov (United States)

Mineur, Frederic; Le Roux, Auguste; Maggs, Christine A; Verlaque, Marc

2014-12-01

With globalization, agriculture and aquaculture activities are increasingly affected by diseases that are spread through movement of crops and stock. Such movements are also associated with the introduction of non-native species via hitchhiking individual organisms. The oyster industry, one of the most important forms of marine aquaculture, embodies these issues. In Europe disease outbreaks affecting cultivated populations of the naturalized oyster Crassostrea gigas caused a major disruption of production in the late 1960s and early 1970s. Mitigation procedures involved massive imports of stock from the species' native range in the northwestern Pacific from 1971 to 1977. We assessed the role stock imports played in the introduction of non-native marine species (including pathogens) from the northwestern Pacific to Europe through a methodological and critical appraisal of record data. The discovery rate of non-native species (a proxy for the introduction rate) from 1966 to 2012 suggests a continuous vector activity over the entire period. Disease outbreaks that have been affecting oyster production since 2008 may be a result of imports from the northwestern Pacific, and such imports are again being considered as an answer to the crisis. Although successful as a remedy in the short and medium terms, such translocations may bring new diseases that may trigger yet more imports (self-reinforcing or positive feedback loop) and lead to the introduction of more hitchhikers. Although there is a legal framework to prevent or reduce these introductions, existing procedures should be improved. © 2014 Society for Conservation Biology.

Non-Native (Exotic) Snake Envenomations in the U.S., 2005–2011

Science.gov (United States)

Warrick, Brandon J.; Boyer, Leslie V.; Seifert, Steven A.

2014-01-01

Non-native (exotic) snakes are a problematic source of envenomation worldwide. This manuscript describes the current demographics, outcomes and challenges of non-native snakebites in the United States (U.S.). We performed a retrospective case series of the National Poison Data System (NPDS) database between 2005 and 2011. There were 258 human exposures involving at least 61 unique exotic venomous species (average = 37 per year; range = 33–40). Males comprised 79% and females 21%. The average age was 33 years with 16% less than 20 years old. 70% of bites occurred in a private residence and 86% were treated at a healthcare facility. 35% of cases received antivenom and 10% were given antibiotics. This study is compared to our previous study (1994–2004) in which there was a substantial coding error rate. Software modifications significantly reduced coding errors. Identification and acquisition of appropriate antivenoms pose a number of logistical difficulties in the management of these envenomations. In the U.S., poison centers have valuable systems and clinical roles in the provision of expert consultation and in the management of these cases. PMID:25268980

Non-Native (Exotic Snake Envenomations in the U.S., 2005–2011

Directory of Open Access Journals (Sweden)

Brandon J. Warrick

2014-09-01

Full Text Available Non-native (exotic snakes are a problematic source of envenomation worldwide. This manuscript describes the current demographics, outcomes and challenges of non-native snakebites in the United States (U.S.. We performed a retrospective case series of the National Poison Data System (NPDS database between 2005 and 2011. There were 258 human exposures involving at least 61 unique exotic venomous species (average = 37 per year; range = 33–40. Males comprised 79% and females 21%. The average age was 33 years with 16% less than 20 years old. 70% of bites occurred in a private residence and 86% were treated at a healthcare facility. 35% of cases received antivenom and 10% were given antibiotics. This study is compared to our previous study (1994–2004 in which there was a substantial coding error rate. Software modifications significantly reduced coding errors. Identification and acquisition of appropriate antivenoms pose a number of logistical difficulties in the management of these envenomations. In the U.S., poison centers have valuable systems and clinical roles in the provision of expert consultation and in the management of these cases.

Investigation of thin oxide layer removal from Si substrates using an SiO2 atomic layer etching approach: the importance of the reactivity of the substrate

International Nuclear Information System (INIS)

Metzler, Dominik; Oehrlein, Gottlieb S; Li, Chen; Lai, C Steven; Hudson, Eric A

2017-01-01

The evaluation of a plasma-based atomic layer etching (ALE) approach for native oxide surface removal from Si substrates is described. Objectives include removal of the native oxide while minimizing substrate damage, surface residues and substrate loss. Oxide thicknesses were measured using in situ ellipsometry and surface chemistry was analyzed by x-ray photoelectron spectroscopy. The cyclic ALE approach when used for removal of native oxide SiO 2 from a Si substrate did not remove native oxide to the extent required. This is due to the high reactivity of the silicon substrate during the low-energy (<40 eV) ion bombardment phase of the cyclic ALE approach which leads to reoxidation of the silicon surface. A modified process, which used continuously biased Ar plasma with periodic CF 4 injection, achieved significant oxygen removal from the Si surface, with some residual carbon and fluorine. A subsequent H 2 /Ar plasma exposure successfully removed residual carbon and fluorine while passivating the silicon surface. The combined treatment reduced oxygen and carbon levels to about half compared to as received silicon surfaces. The downside of this process sequence is a net loss of about 40 Å of Si. A generic insight of this work is the importance of the substrate and final surface chemistry in addition to precise etch control of the target film for ALE processes. By a fluorocarbon-based ALE technique, thin SiO 2 layer removal at the Ångstrom level can be precisely performed from an inert substrate, e.g. a thick SiO 2 layer. However, from a reactive substrate, like Si, complete removal of the thin SiO 2 layer is prevented by the high reactivity of low energy Ar + ion bombarded Si. The Si surfaces are reoxidized during the ALE ion bombardment etch step, even for very clean and ultra-low O 2 process conditions. (paper)

Can misfolded proteins be beneficial? The HAMLET case.

Science.gov (United States)

Pettersson-Kastberg, Jenny; Aits, Sonja; Gustafsson, Lotta; Mossberg, Anki; Storm, Petter; Trulsson, Maria; Persson, Filip; Mok, K Hun; Svanborg, Catharina

2009-01-01

By changing the three-dimensional structure, a protein can attain new functions, distinct from those of the native protein. Amyloid-forming proteins are one example, in which conformational change may lead to fibril formation and, in many cases, neurodegenerative disease. We have proposed that partial unfolding provides a mechanism to generate new and useful functional variants from a given polypeptide chain. Here we present HAMLET (Human Alpha-lactalbumin Made LEthal to Tumor cells) as an example where partial unfolding and the incorporation of cofactor create a complex with new, beneficial properties. Native alpha-lactalbumin functions as a substrate specifier in lactose synthesis, but when partially unfolded the protein binds oleic acid and forms the tumoricidal HAMLET complex. When the properties of HAMLET were first described they were surprising, as protein folding intermediates and especially amyloid-forming protein intermediates had been regarded as toxic conformations, but since then structural studies have supported functional diversity arising from a change in fold. The properties of HAMLET suggest a mechanism of structure-function variation, which might help the limited number of human protein genes to generate sufficient structural diversity to meet the diverse functional demands of complex organisms.

Teaching a Growing a Population of Non-Native English-Speaking Students in American Universities: Cultural and Linguistic Challenges

Directory of Open Access Journals (Sweden)

Maria Cristina Fava

2016-12-01

Full Text Available The increasing number of non-native English speaking students in American universities, mostly from Asian countries, presents unprecedented challenges and calls for an in-depth study on how we teach western art music history. This essay challenges some aspects of liberal multiculturalism and proposes the creation of channels of communication that allow non-native English speaking students to understand the premises of a Eurocentric system of knowledge without undermining their own cultural backgrounds.

Proteins in Soy Might Have a Higher Role in Cancer Prevention than Previously Expected: Soybean Protein Fractions Are More Effective MMP-9 Inhibitors Than Non-Protein Fractions, Even in Cooked Seeds

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Ana Lima

2017-02-01

Full Text Available The search for anticancer MMP-9 inhibitors (MMPIs in food products has become a major goal for research. MMPIs in soy have been related only to saponins and isoflavones, but recently, low specific protein fractions in soybeans were shown to reduce MMP-9 activity as well. The present work aimed at comparing the MMPI potential of protein fractions (P and non-protein fractions (NP isolated from soybean seeds, before and after soaking and cooking, mimicking dietary exposures. Reverse and substrate zymography, as well as a fluoregenic DQ gelatin assay were used to evaluate MMP-9 activities. Colon cancer cell migration and proliferation was also tested in HT29 cells. Regarding MMP-9 inhibition, proteins in soy presented IC50 values 100 times lower than non-protein extracts, and remained active after cooking, suggesting that proteins may be more effective MMP-9 inhibitors than non-protein compounds. Using the determined IC50 concentrations, NP fractions were able to induce higher inhibitions of HT29 cell migration and proliferation, but not through MMP-9 inhibition, whilst protein fractions were shown to specifically inhibit MMP-9 activity. Overall, our results show that protein fractions in soybeans might have a higher role in soy-related cancer prevention as MMPIs than previously expected. Being nontoxic and active at lower concentrations, the discovery of these heat-resistant specific MMPI proteins in soy can be of significant importance for cancer preventive diets, particularly considering the increasing use of soy proteins in food products and the controversy around isoflavones amongst consumers.

Native Mass Spectrometry in Fragment-Based Drug Discovery.

Science.gov (United States)

Pedro, Liliana; Quinn, Ronald J

2016-07-28

The advent of native mass spectrometry (MS) in 1990 led to the development of new mass spectrometry instrumentation and methodologies for the analysis of noncovalent protein-ligand complexes. Native MS has matured to become a fast, simple, highly sensitive and automatable technique with well-established utility for fragment-based drug discovery (FBDD). Native MS has the capability to directly detect weak ligand binding to proteins, to determine stoichiometry, relative or absolute binding affinities and specificities. Native MS can be used to delineate ligand-binding sites, to elucidate mechanisms of cooperativity and to study the thermodynamics of binding. This review highlights key attributes of native MS for FBDD campaigns.

Application of native agarose gel electrophoresis of serum proteins in veterinary diagnostics

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Jania Bartosz

2016-12-01

Full Text Available Electrophoretic techniques, used to separate mixtures of electrically charged particles, are widely used in science. One of these techniques, native protein electrophoresis in an agarose gel, is applied in human and veterinary medicine. Changes in the proportions of individual protein fractions correspond to significant changes in the physiology of the body. Although the pattern obtained by electrophoretic separation rarely indicates a specific disease, it provides valuable information for the differential diagnosis. Decades of research on the types of patterns obtained in the case of particular diseases have led to the accumulation of substantial knowledge. The paper presents the available information on this topic. Serum protein electrophoresis is recommended in cases of increased levels of total protein in order to reveal the nature of the process. The basic information which can be obtained from electrophoretic separation includes the immune status of the organism. Both increased antigenic stimulation and immunodeficiency are clearly visible in electropherograms. Moreover, the level of heterogeneity of the corresponding protein fractions can help to distinguish between infectious diseases and cancer - multiple myeloma - the latter producing a homogeneous immunoglobulin fraction. Analysis of other protein fractions helps to detect or confirm an ongoing inflammatory process and provides information regarding liver function. Even when the concentration of total protein is within the reference range, this analysis can be recommended as a basic laboratory test.

Optimization of photoactive protein Z for fast and efficient site-specific conjugation of native IgG.