native state model: Topics by Science.gov

Sample records for native state model

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

Lammert, Heiko; Noel, Jeffrey K.; Haglund, Ellinor

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 minimalmore » 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.« less
A Hybrid Acoustic and Pronunciation Model Adaptation Approach for Non-native Speech Recognition

NASA Astrophysics Data System (ADS)

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.
Dynamic Folding Pathway Models of the Trp-Cage Protein

PubMed Central

Kim, Seung-Yeon

2013-01-01

Using action-derived molecular dynamics (ADMD), we study the dynamic folding pathway models of the Trp-cage protein by providing its sequential conformational changes from its initial disordered structure to the final native structure at atomic details. We find that the numbers of native contacts and native hydrogen bonds are highly correlated, implying that the native structure of Trp-cage is achieved through the concurrent formations of native contacts and native hydrogen bonds. In early stage, an unfolded state appears with partially formed native contacts (~40%) and native hydrogen bonds (~30%). Afterward, the folding is initiated by the contact of the side chain of Tyr3 with that of Trp6, together with the formation of the N-terminal α-helix. Then, the C-terminal polyproline structure docks onto the Trp6 and Tyr3 rings, resulting in the formations of the hydrophobic core of Trp-cage and its near-native state. Finally, the slow adjustment processes of the near-native states into the native structure are dominant in later stage. The ADMD results are in agreement with those of the experimental folding studies on Trp-cage and consistent with most of other computational studies. PMID:23865078
Fallon, Nevada FORGE Thermal-Hydrological-Mechanical Models

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

Blankenship, Doug; Sonnenthal, Eric

Archive contains thermal-mechanical simulation input/output files. Included are files which fall into the following categories: ( 1 ) Spreadsheets with various input parameter calculations ( 2 ) Final Simulation Inputs ( 3 ) Native-State Thermal-Hydrological Model Input File Folders ( 4 ) Native-State Thermal-Hydrological-Mechanical Model Input Files ( 5 ) THM Model Stimulation Cases See 'File Descriptions.xlsx' resource below for additional information on individual files.
A minimalist model protein with multiple folding funnels

PubMed Central

Locker, C. Rebecca; Hernandez, Rigoberto

2001-01-01

Kinetic and structural studies of wild-type proteins such as prions and amyloidogenic proteins provide suggestive evidence that proteins may adopt multiple long-lived states in addition to the native state. All of these states differ structurally because they lie far apart in configuration space, but their stability is not necessarily caused by cooperative (nucleation) effects. In this study, a minimalist model protein is designed to exhibit multiple long-lived states to explore the dynamics of the corresponding wild-type proteins. The minimalist protein is modeled as a 27-monomer sequence confined to a cubic lattice with three different monomer types. An order parameter—the winding index—is introduced to characterize the extent of folding. The winding index has several advantages over other commonly used order parameters like the number of native contacts. It can distinguish between enantiomers, its calculation requires less computational time than the number of native contacts, and reduced-dimensional landscapes can be developed when the native state structure is not known a priori. The results for the designed model protein prove by existence that the rugged energy landscape picture of protein folding can be generalized to include protein “misfolding” into long-lived states. PMID:11470921
On the role of conformational geometry in protein folding

NASA Astrophysics Data System (ADS)

Du, Rose; Pande, Vijay S.; Grosberg, Alexander Yu.; Tanaka, Toyoichi; Shakhnovich, Eugene

1999-12-01

Using a lattice model of protein folding, we find that once certain native contacts have been formed, folding to the native state is inevitable, even if the only energetic bias in the system is nonspecific, homopolymeric attraction to a collapsed state. These conformations can be quite geometrically unrelated to the native state (with as low as only 53% of the native contacts formed). We demonstrate these results by examining the Monte Carlo kinetics of both heteropolymers under Go interactions and homopolymers, with the folding of both types of polymers to the native state of the heteropolymer. Although we only consider a 48-mer lattice model, our findings shed light on the effects of geometrical restrictions, including those of chain connectivity and steric excluded volume, on protein folding. These effects play a complementary role to that of the rugged energy landscape. In addition, the results of this work can aid in the interpretation of experiments and computer simulations of protein folding performed at elevated temperatures.
A Culturally Responsive Practice Model for Urban Indian Child Welfare Services.

ERIC Educational Resources Information Center

Mindell, Robert; Vidal de Haymes, Maria; Francisco, Dale

2003-01-01

Describes a collaboration among a university, a state child welfare agency, and a Native American community organization to develop a culturally driven practice model for urban, Native American child welfare. Identifies challenges and opportunities in addressing the needs of urban Native American communities. Concludes with principles for…
Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY

DOE PAGES

Shi, Jade; Nobrega, R. Paul; Schwantes, Christian; ...

2017-03-08

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 structuremore » 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.« less
Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY

NASA Astrophysics Data System (ADS)

Shi, Jade; Nobrega, R. Paul; Schwantes, Christian; Kathuria, Sagar V.; Bilsel, Osman; Matthews, C. Robert; Lane, T. J.; Pande, Vijay S.

2017-03-01

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. Here, 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. This 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. Using these results, we then predict incisive single molecule FRET experiments as a means of model validation. This 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.
What determines the spectrum of protein native state structures?

PubMed

Lezon, Timothy R; Banavar, Jayanth R; Lesk, Arthur M; Maritan, Amos

2006-05-01

We present a brief summary of the key factors underlying protein structure, as developed in the investigations of Pauling, Ramachandran, and Rose. We then outline a simplified physical model of proteins that focuses on geometry and symmetry. Although this model superficially appears unrelated to the detailed chemical descriptions commonly applied to proteins, we show that it captures the essential elements of the chemistry and provides a unified framework for understanding the common characteristics of folded proteins. We suggest that the spectrum of protein native state structures is determined by geometry and symmetry and the role of the sequence is to choose its native state structure from this predetermined menu. 2006 Wiley-Liss, Inc.
Elucidating quantitative stability/flexibility relationships within thioredoxin and its fragments using a distance constraint model.

PubMed

Jacobs, Donald J; Livesay, Dennis R; Hules, Jeremy; Tasayco, Maria Luisa

2006-05-05

Numerous quantitative stability/flexibility relationships, within Escherichia coli thioredoxin (Trx) and its fragments are determined using a minimal distance constraint model (DCM). A one-dimensional free energy landscape as a function of global flexibility reveals Trx to fold in a low-barrier two-state process, with a voluminous transition state. Near the folding transition temperature, the native free energy basin is markedly skewed to allow partial unfolded forms. Under native conditions the skewed shape is lost, and the protein forms a compact structure with some flexibility. Predictions on ten Trx fragments are generally consistent with experimental observations that they are disordered, and that complementary fragments reconstitute. A hierarchical unfolding pathway is uncovered using an exhaustive computational procedure of breaking interfacial cross-linking hydrogen bonds that span over a series of fragment dissociations. The unfolding pathway leads to a stable core structure (residues 22-90), predicted to act as a kinetic trap. Direct connection between degree of rigidity within molecular structure and non-additivity of free energy is demonstrated using a thermodynamic cycle involving fragments and their hierarchical unfolding pathway. Additionally, the model provides insight about molecular cooperativity within Trx in its native state, and about intermediate states populating the folding/unfolding pathways. Native state cooperativity correlation plots highlight several flexibly correlated regions, giving insight into the catalytic mechanism that facilitates access to the active site disulfide bond. Residual native cooperativity correlations are present in the core substructure, suggesting that Trx can function when it is partly unfolded. This natively disordered kinetic trap, interpreted as a molten globule, has a wide temperature range of metastability, and it is identified as the "slow intermediate state" observed in kinetic experiments. These computational results are found to be in overall agreement with a large array of experimental data.
Probing the free energy landscape of the FBP28WW domain using multiple techniques.

PubMed

Periole, Xavier; Allen, Lucy R; Tamiola, Kamil; Mark, Alan E; Paci, Emanuele

2009-05-01

The free-energy landscape of a small protein, the FBP 28 WW domain, has been explored using molecular dynamics (MD) simulations with alternative descriptions of the molecule. The molecular models used range from coarse-grained to all-atom with either an implicit or explicit treatment of the solvent. Sampling of conformation space was performed using both conventional and temperature-replica exchange MD simulations. Experimental chemical shifts and NOEs were used to validate the simulations, and experimental phi values both for validation and as restraints. This combination of different approaches has provided insight into the free energy landscape and barriers encountered by the protein during folding and enabled the characterization of native, denatured and transition states which are compatible with the available experimental data. All the molecular models used stabilize well defined native and denatured basins; however, the degree of agreement with the available experimental data varies. While the most detailed, explicit solvent model predicts the data reasonably accurately, it does not fold despite a simulation time 10 times that of the experimental folding time. The less detailed models performed poorly relative to the explicit solvent model: an implicit solvent model stabilizes a ground state which differs from the experimental native state, and a structure-based model underestimates the size of the barrier between the two states. The use of experimental phi values both as restraints, and to extract structures from unfolding simulations, result in conformations which, although not necessarily true transition states, appear to share the geometrical characteristics of transition state structures. In addition to characterizing the native, transition and denatured states of this particular system in this work, the advantages and limitations of using varying levels of representation are discussed. 2008 Wiley Periodicals, Inc.
Show me the numbers: What data currently exist for non-native species in the USA?

USGS Publications Warehouse

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.
A lattice protein with an amyloidogenic latent state: stability and folding kinetics.

PubMed

Palyanov, Andrey Yu; Krivov, Sergei V; Karplus, Martin; Chekmarev, Sergei F

2007-03-15

We have designed a model lattice protein that has two stable folded states, the lower free energy native state and a latent state of somewhat higher energy. The two states have a sizable part of their structures in common (two "alpha-helices") and differ in the content of "alpha-helices" and "beta-strands" in the rest of their structures; i.e. for the native state, this part is alpha-helical, and for the latent state it is composed of beta-strands. Thus, the lattice protein free energy surface mimics that of amyloidogenic proteins that form well organized fibrils under appropriate conditions. A Go-like potential was used and the folding process was simulated with a Monte Carlo method. To gain insight into the equilibrium free energy surface and the folding kinetics, we have combined standard approaches (reduced free energy surfaces, contact maps, time-dependent populations of the characteristic states, and folding time distributions) with a new approach. The latter is based on a principal coordinate analysis of the entire set of contacts, which makes possible the introduction of unbiased reaction coordinates and the construction of a kinetic network for the folding process. The system is found to have four characteristic basins, namely a semicompact globule, an on-pathway intermediate (the bifurcation basin), and the native and latent states. The bifurcation basin is shallow and consists of the structure common to the native and latent states, with the rest disorganized. On the basis of the simulation results, a simple kinetic model describing the transitions between the characteristic states was developed, and the rate constants for the essential transitions were estimated. During the folding process the system dwells in the bifurcation basin for a relatively short time before it proceeds to the native or latent state. We suggest that such a bifurcation may occur generally for proteins in which native and latent states have a sizable part of their structures in common. Moreover, there is the possibility of introducing changes in the system (e.g., mutations), which guide the system toward the native or misfolded state.
Hierarchical folding free energy landscape of HP35 revealed by most probable path clustering.

PubMed

Jain, Abhinav; Stock, Gerhard

2014-07-17

Adopting extensive molecular dynamics simulations of villin headpiece protein (HP35) by Shaw and co-workers, a detailed theoretical analysis of the folding of HP35 is presented. The approach is based on the recently proposed most probable path algorithm which identifies the metastable states of the system, combined with dynamical coring of these states in order to obtain a consistent Markov state model. The method facilitates the construction of a dendrogram associated with the folding free-energy landscape of HP35, which reveals a hierarchical funnel structure and shows that the native state is rather a kinetic trap than a network hub. The energy landscape of HP35 consists of the entropic unfolded basin U, where the prestructuring of the protein takes place, the intermediate basin I, which is connected to U via the rate-limiting U → I transition state reflecting the formation of helix-1, and the native basin N, containing a state close to the NMR structure and a native-like state that exhibits enhanced fluctuations of helix-3. The model is in line with recent experimental observations that the intermediate and native states differ mostly in their dynamics (locked vs unlocked states). Employing dihedral angle principal component analysis, subdiffusive motion on a multidimensional free-energy surface is found.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, Jade; Nobrega, R. Paul; Schwantes, Christian

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

PubMed

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.
Combination of Markov state models and kinetic networks for the analysis of molecular dynamics simulations of peptide folding.

PubMed

Radford, Isolde H; Fersht, Alan R; Settanni, Giovanni

2011-06-09

Atomistic molecular dynamics simulations of the TZ1 beta-hairpin peptide have been carried out using an implicit model for the solvent. The trajectories have been analyzed using a Markov state model defined on the projections along two significant observables and a kinetic network approach. The Markov state model allowed for an unbiased identification of the metastable states of the system, and provided the basis for commitment probability calculations performed on the kinetic network. The kinetic network analysis served to extract the main transition state for folding of the peptide and to validate the results from the Markov state analysis. The combination of the two techniques allowed for a consistent and concise characterization of the dynamics of the peptide. The slowest relaxation process identified is the exchange between variably folded and denatured species, and the second slowest process is the exchange between two different subsets of the denatured state which could not be otherwise identified by simple inspection of the projected trajectory. The third slowest process is the exchange between a fully native and a partially folded intermediate state characterized by a native turn with a proximal backbone H-bond, and frayed side-chain packing and termini. The transition state for the main folding reaction is similar to the intermediate state, although a more native like side-chain packing is observed.
Discrimination of Native-like States of Membrane Proteins with Implicit Membrane-based Scoring Functions.

PubMed

Dutagaci, Bercem; Wittayanarakul, Kitiyaporn; Mori, Takaharu; Feig, Michael

2017-06-13

A scoring protocol based on implicit membrane-based scoring functions and a new protocol for optimizing the positioning of proteins inside the membrane was evaluated for its capacity to discriminate native-like states from misfolded decoys. A decoy set previously established by the Baker lab (Proteins: Struct., Funct., Genet. 2006, 62, 1010-1025) was used along with a second set that was generated to cover higher resolution models. The Implicit Membrane Model 1 (IMM1), IMM1 model with CHARMM 36 parameters (IMM1-p36), generalized Born with simple switching (GBSW), and heterogeneous dielectric generalized Born versions 2 (HDGBv2) and 3 (HDGBv3) were tested along with the new HDGB van der Waals (HDGBvdW) model that adds implicit van der Waals contributions to the solvation free energy. For comparison, scores were also calculated with the distance-scaled finite ideal-gas reference (DFIRE) scoring function. Z-scores for native state discrimination, energy vs root-mean-square deviation (RMSD) correlations, and the ability to select the most native-like structures as top-scoring decoys were evaluated to assess the performance of the scoring functions. Ranking of the decoys in the Baker set that were relatively far from the native state was challenging and dominated largely by packing interactions that were captured best by DFIRE with less benefit of the implicit membrane-based models. Accounting for the membrane environment was much more important in the second decoy set where especially the HDGB-based scoring functions performed very well in ranking decoys and providing significant correlations between scores and RMSD, which shows promise for improving membrane protein structure prediction and refinement applications. The new membrane structure scoring protocol was implemented in the MEMScore web server ( http://feiglab.org/memscore ).
Robustness of atomistic Gō models in predicting native-like folding intermediates

NASA Astrophysics Data System (ADS)

Estácio, S. G.; Fernandes, C. S.; Krobath, H.; Faísca, P. F. N.; Shakhnovich, E. I.

2012-08-01

Gō models are exceedingly popular tools in computer simulations of protein folding. These models are native-centric, i.e., they are directly constructed from the protein's native structure. Therefore, it is important to understand up to which extent the atomistic details of the native structure dictate the folding behavior exhibited by Gō models. Here we address this challenge by performing exhaustive discrete molecular dynamics simulations of a Gō potential combined with a full atomistic protein representation. In particular, we investigate the robustness of this particular type of Gō models in predicting the existence of intermediate states in protein folding. We focus on the N47G mutational form of the Spc-SH3 folding domain (x-ray structure) and compare its folding pathway with that of alternative native structures produced in silico. Our methodological strategy comprises equilibrium folding simulations, structural clustering, and principal component analysis.

Interplay of secondary structures and side-chain contacts in the denatured state of BBA1

NASA Astrophysics Data System (ADS)

Wen, Edward Z.; Luo, Ray

2004-08-01

The denatured state of a miniprotein BBA1 is studied under the native condition with the AMBER/Poisson-Boltzmann energy model and with the self-guided enhanced sampling technique. Forty independent trajectories are collected to sample the highly diversified denatured structures. Our simulation data show that the denatured BBA1 contains high percentage of native helix and native turn, but low percentage of native hairpin. Conditional population analysis indicates that the native helix formation and the native hairpin formation are not cooperative in the denatured state. Side-chain analysis shows that the native hydrophobic contacts are more preferred than the non-native hydrophobic contacts in the denatured BBA1. In contrast, the salt-bridge contacts are more or less nonspecific even if their populations are higher than those of hydrophobic contacts. Analysis of the trajectories shows that the native helix mostly initiates near the N terminus and propagates to the C terminus, and mostly forms from 310-helix/turn to α helix. The same analysis shows that the native turn is important but not necessary in its formation in the denatured BBA1. In addition, the formations of the two strands in the native hairpin are rather asymmetric, demonstrating the likely influence of the protein environment. Energetic analysis shows that the native helix formation is largely driven by electrostatic interactions in denatured BBA1. Further, the native helix formation is associated with the breakup of non-native salt-bridge contacts and the accumulation of native salt-bridge contacts. However, the native hydrophobic contacts only show a small increase upon the native helix formation while the non-native hydrophobic contacts stay essentially the same, different from the evolution of hydrophobic contacts observed in an isolated helix folding.
Native State Volume Fluctuations in Proteins as a Mechanism for Dynamic Allostery.

PubMed

Law, Anthony B; Sapienza, Paul J; Zhang, Jun; Zuo, Xiaobing; Petit, Chad M

2017-03-15

Allostery enables tight regulation of protein function in the cellular environment. Although existing models of allostery are firmly rooted in the current structure-function paradigm, the mechanistic basis for allostery in the absence of structural change remains unclear. In this study, we show that a typical globular protein is able to undergo significant changes in volume under native conditions while exhibiting no additional changes in protein structure. These native state volume fluctuations were found to correlate with changes in internal motions that were previously recognized as a source of allosteric entropy. This finding offers a novel mechanistic basis for allostery in the absence of canonical structural change. The unexpected observation that function can be derived from expanded, low density protein states has broad implications for our understanding of allostery and suggests that the general concept of the native state be expanded to allow for more variable physical dimensions with looser packing.
Using Species Distribution Models to Predict Potential Landscape Restoration Effects on Puma Conservation.

PubMed

Angelieri, Cintia Camila Silva; Adams-Hosking, Christine; Ferraz, Katia Maria Paschoaletto Micchi de Barros; de Souza, Marcelo Pereira; McAlpine, Clive Alexander

2016-01-01

A mosaic of intact native and human-modified vegetation use can provide important habitat for top predators such as the puma (Puma concolor), avoiding negative effects on other species and ecological processes due to cascade trophic interactions. This study investigates the effects of restoration scenarios on the puma's habitat suitability in the most developed Brazilian region (São Paulo State). Species Distribution Models incorporating restoration scenarios were developed using the species' occurrence information to (1) map habitat suitability of pumas in São Paulo State, Southeast, Brazil; (2) test the relative contribution of environmental variables ecologically relevant to the species habitat suitability and (3) project the predicted habitat suitability to future native vegetation restoration scenarios. The Maximum Entropy algorithm was used (Test AUC of 0.84 ± 0.0228) based on seven environmental non-correlated variables and non-autocorrelated presence-only records (n = 342). The percentage of native vegetation (positive influence), elevation (positive influence) and density of roads (negative influence) were considered the most important environmental variables to the model. Model projections to restoration scenarios reflected the high positive relationship between pumas and native vegetation. These projections identified new high suitability areas for pumas (probability of presence >0.5) in highly deforested regions. High suitability areas were increased from 5.3% to 8.5% of the total State extension when the landscapes were restored for ≥ the minimum native vegetation cover rule (20%) established by the Brazilian Forest Code in private lands. This study highlights the importance of a landscape planning approach to improve the conservation outlook for pumas and other species, including not only the establishment and management of protected areas, but also the habitat restoration on private lands. Importantly, the results may inform environmental policies and land use planning in São Paulo State, Brazil.
Native American Indian child welfare system change: implementation of a culturally appropriate practice model across three tribal child welfare systems.

PubMed

Scannapieco, Maria; Iannone, Mary A

2012-01-01

Currently, there are 565 federally recognized tribes in the United States who are independent sovereign nations. These tribes have varying capacities to manage and administer child welfare programs. Most provide some type of child welfare service to the children and families within their tribal land. However, there are no national resources to document the number of children in foster care or the extent of abuse and neglect in the families served by tribal child welfare agencies. Information is only known about those Native American/Alaska Native families and children who are reported to state child protection agencies. Native American children represented 0.9% of all children in the United States in the late 1990s, but they comprised 3.1% of the substitute care population in state-run child welfare systems (Morrison, et al., 2010). Incident rates of child welfare referrals, substantiated referrals, and foster care placement among Native American children and families are relatively high compared to other ethnic groups (Earle & Cross, 2001) but precise interpretation of Native American status is difficult due to variations in child welfare reporting systems (Magruder & Shaw, 2008).
Complete protein-protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling

NASA Astrophysics Data System (ADS)

Plattner, Nuria; Doerr, Stefan; de Fabritiis, Gianni; Noé, Frank

2017-10-01

Protein-protein association is fundamental to many life processes. However, a microscopic model describing the structures and kinetics during association and dissociation is lacking on account of the long lifetimes of associated states, which have prevented efficient sampling by direct molecular dynamics (MD) simulations. Here we demonstrate protein-protein association and dissociation in atomistic resolution for the ribonuclease barnase and its inhibitor barstar by combining adaptive high-throughput MD simulations and hidden Markov modelling. The model reveals experimentally consistent intermediate structures, energetics and kinetics on timescales from microseconds to hours. A variety of flexibly attached intermediates and misbound states funnel down to a transition state and a native basin consisting of the loosely bound near-native state and the tightly bound crystallographic state. These results offer a deeper level of insight into macromolecular recognition and our approach opens the door for understanding and manipulating a wide range of macromolecular association processes.
Revisiting Robinson: The perils of individualistic and ecologic fallacy

PubMed Central

Subramanian, S V; Jones, Kelvyn; Kaddour, Afamia; Krieger, Nancy

2009-01-01

Background W S Robinson made a seminal contribution by demonstrating that correlations for the same two variables can be different at the individual and ecologic level. This study reanalyzes and historically situates Robinson's influential study that laid the foundation for the primacy of analyzing data at only the individual level. Methods We applied a binomial multilevel logistic model to analyse variation in illiteracy as enumerated by the 1930 US. Census (the same data as used by Robinson). The outcome was log odds of being illiterate, while predictors were race/nativity (‘native whites’, ‘foreign-born whites’ and ‘negroes’) at the individual-level, and presence of Jim Crow segregation laws for education at the state-level. We conducted historical research to identify the social and scientific context within which Robinson's study was produced and favourably received. Results Empirically, the substantial state variations in illiteracy could not be accounted by the states' race/nativity composition. Different approaches to modelling state-effects yielded considerably attenuated associations at the individual-level between illiteracy and race/nativity. Furthermore, state variation in illiteracy was different across the race/nativity groups, with state variation being largest for whites and least for foreign-born whites. Strong effects of Jim Crow education laws on illiteracy were observed with the effect being strongest for blacks. Historically, Robinson's study was consonant with the post-World War II ascendancy of methodological individualism. Conclusion Applying a historically informed multilevel perspective to Robinson's profoundly influential study, we demonstrate that meaningful analysis of individual-level relationships requires attention to substantial heterogeneity in state characteristics. The implication is that perils are posed by not only ecological fallacy but also individualistic fallacy. Multilevel thinking, grounded in historical and spatiotemporal context, is thus a necessity, not an option. PMID:19179348
Revisiting Robinson: the perils of individualistic and ecologic fallacy.

PubMed

Subramanian, S V; Jones, Kelvyn; Kaddour, Afamia; Krieger, Nancy

2009-04-01

W S Robinson made a seminal contribution by demonstrating that correlations for the same two variables can be different at the individual and ecologic level. This study reanalyzes and historically situates Robinson's influential study that laid the foundation for the primacy of analyzing data at only the individual level. We applied a binomial multilevel logistic model to analyse variation in illiteracy as enumerated by the 1930 US. Census (the same data as used by Robinson). The outcome was log odds of being illiterate, while predictors were race/nativity ('native whites', 'foreign-born whites' and 'negroes') at the individual-level, and presence of Jim Crow segregation laws for education at the state-level. We conducted historical research to identify the social and scientific context within which Robinson's study was produced and favourably received. Empirically, the substantial state variations in illiteracy could not be accounted by the states' race/nativity composition. Different approaches to modelling state-effects yielded considerably attenuated associations at the individual-level between illiteracy and race/nativity. Furthermore, state variation in illiteracy was different across the race/nativity groups, with state variation being largest for whites and least for foreign-born whites. Strong effects of Jim Crow education laws on illiteracy were observed with the effect being strongest for blacks. Historically, Robinson's study was consonant with the post-World War II ascendancy of methodological individualism. Applying a historically informed multilevel perspective to Robinson's profoundly influential study, we demonstrate that meaningful analysis of individual-level relationships requires attention to substantial heterogeneity in state characteristics. The implication is that perils are posed by not only ecological fallacy but also individualistic fallacy. Multilevel thinking, grounded in historical and spatiotemporal context, is thus a necessity, not an option.
Reading component skills of learners in adult basic education.

PubMed

MacArthur, Charles A; Konold, Timothy R; Glutting, Joseph J; Alamprese, Judith A

2010-01-01

The purposes of this study were to investigate the reliability and construct validity of measures of reading component skills with a sample of adult basic education (ABE) learners, including both native and nonnative English speakers, and to describe the performance of those learners on the measures. Investigation of measures of reading components is needed because available measures were neither developed for nor normed on ABE populations or with nonnative speakers of English. The study included 486 students, 334 born or educated in the United States (native) and 152 not born or educated in the United States (nonnative) but who spoke English well enough to participate in English reading classes. All students had scores on 11 measures covering five constructs: decoding, word recognition, spelling, fluency, and comprehension. Confirmatory factor analysis (CFA) was used to test three models: a two-factor model with print and meaning factors; a three-factor model that separated out a fluency factor; and a five-factor model based on the hypothesized constructs. The five-factor model fit best. In addition, the CFA model fit both native and nonnative populations equally well without modification, showing that the tests measure the same constructs with the same accuracy for both groups. Group comparisons found no difference between the native and nonnative samples on word recognition, but the native sample scored higher on fluency and comprehension and lower on decoding than did the nonnative sample. Students with self-reported learning disabilities scored lower on all reading components. Differences by age and gender were also analyzed.
The impact of kin availability, parental religiosity, and nativity on fertility differentials in the late 19th-century United States

PubMed Central

Hacker, J. David; Roberts, Evan

2017-01-01

METHODS Most quantitative research on fertility decline in the United States ignores the potential impact of cultural and familial factors. We rely on new complete-count data from the 1880 U.S. census to construct couple-level measures of nativity/ethnicity, religiosity, and kin availability. We include these measures with a comprehensive set of demographic, economic, and contextual variables in Poisson regression models of net marital fertility to assess their relative importance. We construct models with and without area fixed effects to control for unobserved heterogeneity. CONTRIBUTION All else being equal, we find a strong impact of nativity on recent net marital fertility. Fertility differentials among second generation couples relative to the native-born white population of native parentage were in most cases less than half of the differential observed among first generation immigrants, suggesting greater assimilation to native-born American childbearing norms. Our measures of parental religiosity and familial propinquity indicated a more modest impact on marital fertility. Couples who chose biblical names for their children had approximately 3% more children than couples relying on secular names while the presence of a potential mother-in-law in a nearby households was associated with 2% more children. Overall, our results demonstrate the need for more inclusive models of fertility behavior that include cultural and familial covariates. PMID:29720893
The impact of kin availability, parental religiosity, and nativity on fertility differentials in the late 19th-century United States.

PubMed

Hacker, J David; Roberts, Evan

2017-12-01

Most quantitative research on fertility decline in the United States ignores the potential impact of cultural and familial factors. We rely on new complete-count data from the 1880 U.S. census to construct couple-level measures of nativity/ethnicity, religiosity, and kin availability. We include these measures with a comprehensive set of demographic, economic, and contextual variables in Poisson regression models of net marital fertility to assess their relative importance. We construct models with and without area fixed effects to control for unobserved heterogeneity. All else being equal, we find a strong impact of nativity on recent net marital fertility. Fertility differentials among second generation couples relative to the native-born white population of native parentage were in most cases less than half of the differential observed among first generation immigrants, suggesting greater assimilation to native-born American childbearing norms. Our measures of parental religiosity and familial propinquity indicated a more modest impact on marital fertility. Couples who chose biblical names for their children had approximately 3% more children than couples relying on secular names while the presence of a potential mother-in-law in a nearby households was associated with 2% more children. Overall, our results demonstrate the need for more inclusive models of fertility behavior that include cultural and familial covariates.
Folding and stability of helical bundle proteins from coarse-grained models.

PubMed

Kapoor, Abhijeet; Travesset, Alex

2013-07-01

We develop a coarse-grained model where solvent is considered implicitly, electrostatics are included as short-range interactions, and side-chains are coarse-grained to a single bead. The model depends on three main parameters: hydrophobic, electrostatic, and side-chain hydrogen bond strength. The parameters are determined by considering three level of approximations and characterizing the folding for three selected proteins (training set). Nine additional proteins (containing up to 126 residues) as well as mutated versions (test set) are folded with the given parameters. In all folding simulations, the initial state is a random coil configuration. Besides the native state, some proteins fold into an additional state differing in the topology (structure of the helical bundle). We discuss the stability of the native states, and compare the dynamics of our model to all atom molecular dynamics simulations as well as some general properties on the interactions governing folding dynamics. Copyright © 2013 Wiley Periodicals, Inc.
Hydrophobic potential of mean force as a solvation function for protein structure prediction.

PubMed

Lin, Matthew S; Fawzi, Nicolas Lux; Head-Gordon, Teresa

2007-06-01

We have developed a solvation function that combines a Generalized Born model for polarization of protein charge by the high dielectric solvent, with a hydrophobic potential of mean force (HPMF) as a model for hydrophobic interaction, to aid in the discrimination of native structures from other misfolded states in protein structure prediction. We find that our energy function outperforms other reported scoring functions in terms of correct native ranking for 91% of proteins and low Z scores for a variety of decoy sets, including the challenging Rosetta decoys. This work shows that the stabilizing effect of hydrophobic exposure to aqueous solvent that defines the HPMF hydration physics is an apparent improvement over solvent-accessible surface area models that penalize hydrophobic exposure. Decoys generated by thermal sampling around the native-state basin reveal a potentially important role for side-chain entropy in the future development of even more accurate free energy surfaces.
Native state volume fluctuations in proteins as a mechanism for dynamic allostery

DOE PAGES

Law, Anthony B.; Sapienza, Paul J.; Zhang, Jun; ...

2017-01-17

Allostery enables tight regulation of protein function in the cellular environment. While existing models of allostery are firmly rooted in the current structure-function paradigm, the mechanistic basis for allostery in the absence of structural change remains unclear. In this study, we show that a typical globular protein is able to undergo significant changes in volume under native conditions while exhibiting no additional changes in protein structure. These native state volume fluctuations were found to correlate with changes in internal motions that were previously recognized as a source of allosteric entropy. This finding offers a novel mechanistic basis for allostery inmore » the absence of canonical structural change. As a result, the unexpected observation that function can be derived from expanded, low density protein states has broad implications for our understanding of allostery and suggests that the general concept of the native state be expanded to allow for more variable physical dimensions with looser packing.« less
Variation in child body mass index patterns by race/ethnicity and maternal nativity status in the United States and England.

PubMed

Martinson, Melissa L; McLanahan, Sara; Brooks-Gunn, Jeanne

2015-02-01

This paper examines body mass index (BMI) trajectories among children from different race/ethnic and maternal nativity backgrounds in the United States and England from early- to middle-childhood. This study is the first to examine race/ethnic and maternal nativity differences in BMI trajectories in both countries. We use two longitudinal birth cohort studies-The Fragile Families and Child Wellbeing Study (n = 3,285) for the United States and the Millennium Cohort Study (n = 6,700) for England to estimate trajectories in child BMI by race/ethnicity and maternal nativity status using multilevel growth models. In the United States our sample includes white, black, and Hispanic children; in England the sample includes white, black, and Asian children. We find significant race/ethnic differences in the initial BMI and BMI trajectories of children in both countries, with all non-white groups having significantly steeper BMI growth trajectories than whites. Nativity differences in BMI trajectories vary by race/ethnic group and are only statistically significantly higher for children of foreign-born blacks in England. Disparities in BMI trajectories are pervasive in the United States and England, despite lower overall BMI among English children. Future studies should consider both race/ethnicity and maternal nativity status subgroups when examining disparities in BMI in the United States and England. Differences in BMI are apparent in early childhood, which suggests that interventions targeting pre-school age children may be most effective at stemming childhood disparities in BMI.
Functional selectivity of G-protein-coupled receptors: from recombinant systems to native human cells.

PubMed

Seifert, Roland

2013-10-01

In the mid 1990s, it was assumed that a two-state model, postulating an inactive (R) state and an active (R*) state provides the molecular basis for GPCR activation. However, it became clear that this model could not accommodate many experimental observations. Accordingly, the two-state model was superseded by a multi-state model according to which any given ligand stabilizes a unique receptor conformation with distinct capabilities of activating down-stream G-proteins and β-arrestin. Much of this research was conducted with the β2-adrenoceptor in recombinant systems. At the molecular level, there is now no doubt anymore that ligand-specific receptor conformations, also referred to as functional selectivity, exist. This concept holds great potential for drug discovery in terms of developing drugs with higher selectivity for specific cells and/or cell functions and fewer side effects. A major challenge is the analysis for functional selectivity in native cells. Here, I discuss our current knowledge on functional selectivity of three representative GPCRs, the β2-adrenoceptor and the histamine H2- and H4-receptors, in recombinant systems and native human cells. Studies with human neutrophils and eosinophils support the concept of functional selectivity. A major strategy for the analysis of functional selectivity in native cells is to generate complete concentration/response curves with a large set of structurally diverse ligands for multiple parameters. Next, correlations of potencies and efficacies are analyzed, and deviations of the correlations from linearity are indicative for functional selectivity. Additionally, pharmacological inhibitors are used to dissect cell functions from each other. Copyright © 2013 Elsevier Inc. All rights reserved.
Catchment-scale determinants of nonindigenous minnow richness in the eastern United States

USGS Publications Warehouse

Peoples, Brandon K.; Midway, Stephen R.; DeWeber, Jefferson T.; Wagner, Tyler

2018-01-01

Understanding the drivers of biological invasions is critical for preserving aquatic biodiversity. Stream fishes make excellent model taxa for examining mechanisms driving species introduction success because their distributions are naturally limited by catchment boundaries. In this study, we compared the relative importance of catchment-scale abiotic and biotic predictors of native and nonindigenous minnow (Cyprinidae) richness in 170 catchments throughout the eastern United States. We compared historic and contemporary cyprinid distributional data to determine catchment-wise native/nonindigenous status for 152 species. Catchment-scale model predictor variables described natural (elevation, precipitation, flow accumulation) and anthropogenic (developed land cover, number of dams) abiotic features, as well as native congener richness. Native congener richness may represent either biotic resistance via interspecific competition, or trait preadaptation according to Darwin's naturalisation hypothesis. We used generalised linear mixed models to examine evidence supporting the relative roles of abiotic and biotic predictors of cyprinid introduction success. Native congener richness was positively correlated with nonindigenous cyprinid richness and was the most important variable predicting nonindigenous cyprinid richness. Mean elevation had a weak positive effect, and effects of other abiotic factors were insignificant and less important. Our results suggest that at this spatial scale, trait preadaptation may be more important than intrageneric competition for determining richness of nonindigenous fishes.
Nebraska NativeGEM (Geospatial Extension Model)

NASA Technical Reports Server (NTRS)

Bowen, Brent

2004-01-01

This proposal, Nebraska NativeGEM (Geospatial Extension Model) features a unique diversity component stemming from the exceptional reputation NNSGC has built by delivering geospatial science experiences to Nebraska s Native Americans. For 7 years, NNSGC has partner4 with the 2 tribal colleges and 4 reservation school districts in Nebraska to form the Nebraska Native American Outreach Program (NNAOP), a partnership among tribal community leaders, academia, tribal schools, and industry reaching close to 1,OOO Native American youth, over 1,200 community members (Lehrer & Zendajas, 2001).NativeGEM addresses all three key components of Cooperative State Research, Education, and Extension Service (CSREES) goals for advancing decision support, education, and workforce development through the GES. The existing long term commitments that the NNSGC and the GES have in these areas allow for the pursuit of a broad range of activities. NativeGEM builds upon these existing successful programs and collaborations. Outcomes and metrics for each proposed project are detailed in the Approach section of this document.
Folding thermodynamics of model four-strand antiparallel beta-sheet proteins.

PubMed Central

Jang, Hyunbum; Hall, Carol K; Zhou, Yaoqi

2002-01-01

The thermodynamic properties for three different types of off-lattice four-strand antiparallel beta-strand protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed for different sizes of the bias gap g, an artificial measure of a model protein's preference for its native state. The thermodynamic transition temperatures are obtained by calculating the squared radius of gyration R(g)(2), the root-mean-squared pair separation fluctuation Delta(B), the specific heat C(v), the internal energy of the system E, and the Lindemann disorder parameter Delta(L). Despite these models' simplicity, they exhibit a complex set of protein transitions, consistent with those observed in experimental studies on real proteins. Starting from high temperature, these transitions include a collapse transition, a disordered-to-ordered globule transition, a folding transition, and a liquid-to-solid transition. The high temperature transitions, i.e., the collapse transition and the disordered-to-ordered globule transition, exist for all three beta-strand proteins, although the native-state geometry of the three model proteins is different. However the low temperature transitions, i.e., the folding transition and the liquid-to-solid transition, strongly depend on the native-state geometry of the model proteins and the size of the bias gap. PMID:11806908
The complex folding pathways of protein A suggest a multiple-funnelled energy landscape

NASA Astrophysics Data System (ADS)

St-Pierre, Jean-Francois; Mousseau, Normand; Derreumaux, Philippe

2008-01-01

Folding proteins into their native states requires the formation of both secondary and tertiary structures. Many questions remain, however, as to whether these form into a precise order, and various pictures have been proposed that place the emphasis on the first or the second level of structure in describing folding. One of the favorite test models for studying this question is the B domain of protein A, which has been characterized by numerous experiments and simulations. Using the activation-relaxation technique coupled with a generic energy model (optimized potential for efficient peptide structure prediction), we generate more than 50 folding trajectories for this 60-residue protein. While the folding pathways to the native state are fully consistent with the funnel-like description of the free energy landscape, we find a wide range of mechanisms in which secondary and tertiary structures form in various orders. Our nonbiased simulations also reveal the presence of a significant number of non-native β and α conformations both on and off pathway, including the visit, for a non-negligible fraction of trajectories, of fully ordered structures resembling the native state of nonhomologous proteins.
Unique structural modulation of a non-native substrate by cochaperone DnaJ.

PubMed

Tiwari, Satyam; Kumar, Vignesh; Jayaraj, Gopal Gunanathan; Maiti, Souvik; Mapa, Koyeli

2013-02-12

The role of bacterial DnaJ protein as a cochaperone of DnaK is strongly appreciated. Although DnaJ unaccompanied by DnaK can bind unfolded as well as native substrate proteins, its role as an individual chaperone remains elusive. In this study, we demonstrate that DnaJ binds a model non-native substrate with a low nanomolar dissociation constant and, more importantly, modulates the structure of its non-native state. The structural modulation achieved by DnaJ is different compared to that achieved by the DnaK-DnaJ complex. The nature of structural modulation exerted by DnaJ is suggestive of a unique unfolding activity on the non-native substrate by the chaperone. Furthermore, we demonstrate that the zinc binding motif along with the C-terminal substrate binding domain of DnaJ is necessary and sufficient for binding and the subsequent binding-induced structural alterations of the non-native substrate. We hypothesize that this hitherto unknown structural alteration of non-native states by DnaJ might be important for its chaperoning activity by removing kinetic traps of the folding intermediates.

Using Species Distribution Models to Predict Potential Landscape Restoration Effects on Puma Conservation

PubMed Central

Angelieri, Cintia Camila Silva; Adams-Hosking, Christine; Ferraz, Katia Maria Paschoaletto Micchi de Barros

2016-01-01

A mosaic of intact native and human-modified vegetation use can provide important habitat for top predators such as the puma (Puma concolor), avoiding negative effects on other species and ecological processes due to cascade trophic interactions. This study investigates the effects of restoration scenarios on the puma’s habitat suitability in the most developed Brazilian region (São Paulo State). Species Distribution Models incorporating restoration scenarios were developed using the species’ occurrence information to (1) map habitat suitability of pumas in São Paulo State, Southeast, Brazil; (2) test the relative contribution of environmental variables ecologically relevant to the species habitat suitability and (3) project the predicted habitat suitability to future native vegetation restoration scenarios. The Maximum Entropy algorithm was used (Test AUC of 0.84 ± 0.0228) based on seven environmental non-correlated variables and non-autocorrelated presence-only records (n = 342). The percentage of native vegetation (positive influence), elevation (positive influence) and density of roads (negative influence) were considered the most important environmental variables to the model. Model projections to restoration scenarios reflected the high positive relationship between pumas and native vegetation. These projections identified new high suitability areas for pumas (probability of presence >0.5) in highly deforested regions. High suitability areas were increased from 5.3% to 8.5% of the total State extension when the landscapes were restored for ≥ the minimum native vegetation cover rule (20%) established by the Brazilian Forest Code in private lands. This study highlights the importance of a landscape planning approach to improve the conservation outlook for pumas and other species, including not only the establishment and management of protected areas, but also the habitat restoration on private lands. Importantly, the results may inform environmental policies and land use planning in São Paulo State, Brazil. PMID:26735128
Chevron Behavior and Isostable Enthalpic Barriers in Protein Folding: Successes and Limitations of Simple Gō-like Modeling

PubMed Central

Kaya, Hüseyin; Liu, Zhirong; Chan, Hue Sun

2005-01-01

It has been demonstrated that a “near-Levinthal” cooperative mechanism, whereby the common Gō interaction scheme is augmented by an extra favorability for the native state as a whole, can lead to apparent two-state folding/unfolding kinetics over a broad range of native stabilities in lattice models of proteins. Here such a mechanism is shown to be generalizable to a simplified continuum (off-lattice) Langevin dynamics model with a Cα protein chain representation, with the resulting chevron plots exhibiting an extended quasilinear regime reminiscent of that of apparent two-state real proteins. Similarly high degrees of cooperativity are possible in Gō-like continuum models with rudimentary pairwise desolvation barriers as well. In these models, cooperativity increases with increasing desolvation barrier height, suggesting strongly that two-state-like folding/unfolding kinetics would be achievable when the pairwise desolvation barrier becomes sufficiently high. Besides cooperativity, another generic folding property of interest that has emerged from published experiments on several apparent two-state proteins is that their folding relaxation under constant native stability (isostability) conditions is essentially Arrhenius, entailing high intrinsic enthalpic folding barriers of ∼17–30 kcal/mol. Based on a new analysis of published data on barnase, here we propose that a similar property should also apply to a certain class of non-two-state proteins that fold with chevron rollovers. However, several continuum Gō-like constructs considered here fail to predict any significant intrinsic enthalpic folding barrier under isostability conditions; thus the physical origin of such barriers in real proteins remains to be elucidated. PMID:15863486
Shortening a loop can increase protein native state entropy.

PubMed

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.
``Sequence space soup'' of proteins and copolymers

NASA Astrophysics Data System (ADS)

Chan, Hue Sun; Dill, Ken A.

1991-09-01

To study the protein folding problem, we use exhaustive computer enumeration to explore ``sequence space soup,'' an imaginary solution containing the ``native'' conformations (i.e., of lowest free energy) under folding conditions, of every possible copolymer sequence. The model is of short self-avoiding chains of hydrophobic (H) and polar (P) monomers configured on the two-dimensional square lattice. By exhaustive enumeration, we identify all native structures for every possible sequence. We find that random sequences of H/P copolymers will bear striking resemblance to known proteins: Most sequences under folding conditions will be approximately as compact as known proteins, will have considerable amounts of secondary structure, and it is most probable that an arbitrary sequence will fold to a number of lowest free energy conformations that is of order one. In these respects, this simple model shows that proteinlike behavior should arise simply in copolymers in which one monomer type is highly solvent averse. It suggests that the structures and uniquenesses of native proteins are not consequences of having 20 different monomer types, or of unique properties of amino acid monomers with regard to special packing or interactions, and thus that simple copolymers might be designable to collapse to proteinlike structures and properties. A good strategy for designing a sequence to have a minimum possible number of native states is to strategically insert many P monomers. Thus known proteins may be marginally stable due to a balance: More H residues stabilize the desired native state, but more P residues prevent simultaneous stabilization of undesired native states.
A Bosque Riparian Community Index Model for the Middle Rio Grande, Albuquerque, New Mexico: Model Documentation

DTIC Science & Technology

2012-09-01

ecological processes involve the invasion of non-native (exotic) species (USEPA 1999). Through direct biotic interactions (predation and competition) and...indirect interactions ( ecological engineering and habitat modification), invasive species can disrupt the natural population dynamics of native...species (USEPA 1999). Invasives can include noxious plants (i.e., plants that are listed by a state because of their unfavorable economic or ecological
Pressure- and heat-induced inactivation of butyrylcholinesterase: evidence for multiple intermediates and the remnant inactivation process.

PubMed Central

Weingand-Ziade, A; Ribes, F; Renault, F; Masson, P

2001-01-01

The inactivation process of native (N) human butyrylcholinesterase (BuChE) by pressure and/or heat was found to be multi-step. It led to irreversible formation of an active intermediate (I) state and a denatured state. This series-inactivation process was described by expanding the Lumry-Eyring [Lumry, R. and Eyring, H. (1954) J. Phys. Chem. 58, 110-120] model. The intermediate state (I) was found to have a K(m) identical with that of the native state and a turnover rate (k(cat)) twofold higher than that of the native state with butyrylthiocholine as the substrate. The increased catalytic efficiency (k(cat)/K(m)) of I can be explained by a conformational change in the active-site gorge and/or restructuring of the water-molecule network in the active-site pocket, making the catalytic steps faster. However, a pressure/heat-induced covalent modification of native BuChE, affecting the catalytic machinery, cannot be ruled out. The inactivation process of BuChE induced by the combined action of pressure and heat was found to continue after interruption of pressure/temperature treatment. This secondary inactivation process was termed 'remnant inactivation'. We hypothesized that N and I were in equilibrium with populated metastable N' and I' states. The N' and I' states can either return to the active forms, N and I, or develop into inactive forms, N(')(in) and I(')(in). Both active N' and I' intermediate states displayed different rates of remnant inactivation depending on the pressure and temperature pretreatments and on the storage temperature. A first-order deactivation model describing the kinetics of the remnant inactivation of BuChE is proposed. PMID:11368776
Predicting patterns of non-native plant invasions in Yosemite National Park, California, USA

USGS Publications Warehouse

Underwood, E.C.; Klinger, R.; Moore, P.E.

2004-01-01

One of the major issues confronting management of parks and reserves is the invasion of non-native plant species. Yosemite National Park is one of the largest and best-known parks in the United States, harbouring significant cultural and ecological resources. Effective management of non-natives would be greatly assisted by information on their potential distribution that can be generated by predictive modelling techniques. Our goal was to identify key environmental factors that were correlated with the percent cover of non-native species and then develop a predictive model using the Genetic Algorithm for Rule-set Production technique. We performed a series of analyses using community-level data on species composition in 236 plots located throughout the park. A total of 41 non-native species were recorded which occurred in 23.7% of the plots. Plots with non-natives occurred most frequently at low- to mid-elevations, in flat areas with other herbaceous species. Based on the community-level results, we selected elevation, slope, and vegetation structure as inputs into the GARP model to predict the environmental niche of non-native species. Verification of results was performed using plot data reserved from the model, which calculated the correct prediction of non-native species occurrence as 76%. The majority of the western, lower-elevation portion of the park was predicted to have relatively low levels of non-native species occurrence, with highest concentrations predicted at the west and south entrances and in the Yosemite Valley. Distribution maps of predicted occurrences will be used by management to: efficiently target monitoring of non-native species, prioritize control efforts according to the likelihood of non-native occurrences, and inform decisions relating to the management of non-native species in postfire environments. Our approach provides a valuable tool for assisting decision makers to better manage non-native species, which can be readily adapted to target non-native species in other locations.
Reassessment of MxiH subunit orientation and fold within native Shigella T3SS needles using surface labelling and solid-state NMR.

PubMed

Verasdonck, Joeri; Shen, Da-Kang; Treadgold, Alexander; Arthur, Christopher; Böckmann, Anja; Meier, Beat H; Blocker, Ariel J

2015-12-01

T3SSs are essential virulence determinants of many Gram-negative bacteria, used to inject bacterial effectors of virulence into eukaryotic host cells. Their major extracellular portion, a ∼50 nm hollow, needle-like structure, is essential to host cell sensing and the conduit for effector secretion. It is formed of a small, conserved subunit arranged as a helical polymer. The structure of the subunit has been studied by electron cryomicroscopy within native polymers and by solid-state NMR in recombinant polymers, yielding two incompatible atomic models. To resolve this controversy, we re-examined the native polymer used for electron cryomicroscopy via surface labelling and solid-state NMR. Our data show the orientation and overall fold of the subunit within this polymer is as established by solid-state NMR for recombinant polymers. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.
Modeling Insights into Haemophilus influenzae Type b Disease, Transmission, and Vaccine Programs

PubMed Central

Rose, Charles E.; Cohn, Amanda; Coronado, Fatima; Clark, Thomas A.; Wenger, Jay D.; Bulkow, Lisa; Bruce, Michael G.; Messonnier, Nancy E.; Hennessy, Thomas W.

2012-01-01

In response to the 2007–2009 Haemophilus influenzae type b (Hib) vaccine shortage in the United States, we developed a flexible model of Hib transmission and disease for optimizing Hib vaccine programs in diverse populations and situations. The model classifies population members by age, colonization/disease status, and antibody levels, with movement across categories defined by differential equations. We implemented the model for the United States as a whole, England and Wales, and the Alaska Native population. This model accurately simulated Hib incidence in all 3 populations, including the increased incidence in England/Wales beginning in 1999 and the change in Hib incidence in Alaska Natives after switching Hib vaccines in 1996. The model suggests that a vaccine shortage requiring deferral of the booster dose could last 3 years in the United States before loss of herd immunity would result in increasing rates of invasive Hib disease in children <5 years of age. PMID:22257582
Native aggregation as a cause of origin of temporary cellular structures needed for all forms of cellular activity, signaling and transformations.

PubMed

Matveev, Vladimir V

2010-06-09

According to the hypothesis explored in this paper, native aggregation is genetically controlled (programmed) reversible aggregation that occurs when interacting proteins form new temporary structures through highly specific interactions. It is assumed that Anfinsen's dogma may be extended to protein aggregation: composition and amino acid sequence determine not only the secondary and tertiary structure of single protein, but also the structure of protein aggregates (associates). Cell function is considered as a transition between two states (two states model), the resting state and state of activity (this applies to the cell as a whole and to its individual structures). In the resting state, the key proteins are found in the following inactive forms: natively unfolded and globular. When the cell is activated, secondary structures appear in natively unfolded proteins (including unfolded regions in other proteins), and globular proteins begin to melt and their secondary structures become available for interaction with the secondary structures of other proteins. These temporary secondary structures provide a means for highly specific interactions between proteins. As a result, native aggregation creates temporary structures necessary for cell activity."One of the principal objects of theoretical research in any department of knowledge is to find the point of view from which the subject appears in its greatest simplicity."Josiah Willard Gibbs (1839-1903).
Reviewing Suicide in Native American Communities: Situating Risk and Protective Factors within a Transactional-Ecological Framework

ERIC Educational Resources Information Center

Alcantara, Carmela; Gone, Joseph P.

2007-01-01

The alarming prevalence of suicidal behaviors in Native American communities remains a major concern in the 21st-century United States. Recent reviews have demonstrated that prevention programs and intervention efforts using transactional-ecological models have effectively reduced suicidal behaviors in the American Indian and Alaska Native…
Cesar Chavez--Grade Five Model Curriculum and Resources.

ERIC Educational Resources Information Center

California State Dept. of Education, Sacramento.

In this California state curriculum model for grade 5, "United States History and Geography: A New Nation," students study the historical developments leading to the discovery and colonization of North America by European countries and the ensuing interactions between Native Americans, Europeans, and enslaved Americans. The curriculum…
Equilibrium Ensembles for Insulin Folding from Bias-Exchange Metadynamics.

PubMed

Singh, Richa; Bansal, Rohit; Rathore, Anurag Singh; Goel, Gaurav

2017-04-25

Earliest events in the aggregation process, such as single molecule reconfiguration, are extremely important and the most difficult to characterize in experiments. To this end, we have used well-tempered bias exchange metadynamics simulations to determine the equilibrium ensembles of an insulin molecule under amyloidogenic conditions of low pH and high temperature. A bin-based clustering method that uses statistics accumulated in bias exchange metadynamics trajectories was employed to construct a detailed thermodynamic and kinetic model of insulin folding. The highest lifetime, lowest free-energy ensemble identified consisted of native conformations adopted by a folded insulin monomer in solution, namely, the R-, the R f -, and the T-states of insulin. The lowest free-energy structure had a root mean square deviation of only 0.15 nm from native x-ray structure. The second longest-lived metastable state was an unfolded, compact monomer with little similarity to the native structure. We have identified three additional long-lived, metastable states from the bin-based model. We then carried out an exhaustive structural characterization of metastable states on the basis of tertiary contact maps and per-residue accessible surface areas. We have also determined the lowest free-energy path between two longest-lived metastable states and confirm earlier findings of non-two-state folding for insulin through a folding intermediate. The ensemble containing the monomeric intermediate retained 58% of native hydrophobic contacts, however, accompanied by a complete loss of native secondary structure. We have discussed the relative importance of nativelike versus nonnative tertiary contacts for the folding transition. We also provide a simple measure to determine the importance of an individual residue for folding transition. Finally, we have compared and contrasted this intermediate with experimental data obtained in spectroscopic, crystallographic, and calorimetric measurements during early stages of insulin aggregation. We have also determined stability of monomeric insulin by incubation at a very low concentration to isolate protein-protein interaction effects. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Culture and Place: A Legacy Darrell Kipp Helped Create

ERIC Educational Resources Information Center

Conti, Gary J.

2013-01-01

Darrell Robes Kipp was a Blackfeet elder who was a national leader in the language immersion movement. He co-founded the Piegan Institute, and its schools have become a model for those seeking to preserve and promote their native language. In addition, he served as a Visiting Native American Scholar at Oklahoma State University. In that role, he…
A Model Comparison for Characterizing Protein Motions from Structure

NASA Astrophysics Data System (ADS)

David, Charles; Jacobs, Donald

2011-10-01

A comparative study is made using three computational models that characterize native state dynamics starting from known protein structures taken from four distinct SCOP classifications. A geometrical simulation is performed, and the results are compared to the elastic network model and molecular dynamics. The essential dynamics is quantified by a direct analysis of a mode subspace constructed from ANM and a principal component analysis on both the FRODA and MD trajectories using root mean square inner product and principal angles. Relative subspace sizes and overlaps are visualized using the projection of displacement vectors on the model modes. Additionally, a mode subspace is constructed from PCA on an exemplar set of X-ray crystal structures in order to determine similarly with respect to the generated ensembles. Quantitative analysis reveals there is significant overlap across the three model subspaces and the model independent subspace. These results indicate that structure is the key determinant for native state dynamics.
Effective Potentials for Folding Proteins

NASA Astrophysics Data System (ADS)

Chen, Nan-Yow; Su, Zheng-Yao; Mou, Chung-Yu

2006-02-01

A coarse-grained off-lattice model that is not biased in any way to the native state is proposed to fold proteins. To predict the native structure in a reasonable time, the model has included the essential effects of water in an effective potential. Two new ingredients, the dipole-dipole interaction and the local hydrophobic interaction, are introduced and are shown to be as crucial as the hydrogen bonding. The model allows successful folding of the wild-type sequence of protein G and may have provided important hints to the study of protein folding.
Assessment of the utility of contact-based restraints in accelerating the prediction of protein structure using molecular dynamics simulations.

PubMed

Raval, Alpan; Piana, Stefano; Eastwood, Michael P; Shaw, David E

2016-01-01

Molecular dynamics (MD) simulation is a well-established tool for the computational study of protein structure and dynamics, but its application to the important problem of protein structure prediction remains challenging, in part because extremely long timescales can be required to reach the native structure. Here, we examine the extent to which the use of low-resolution information in the form of residue-residue contacts, which can often be inferred from bioinformatics or experimental studies, can accelerate the determination of protein structure in simulation. We incorporated sets of 62, 31, or 15 contact-based restraints in MD simulations of ubiquitin, a benchmark system known to fold to the native state on the millisecond timescale in unrestrained simulations. One-third of the restrained simulations folded to the native state within a few tens of microseconds-a speedup of over an order of magnitude compared with unrestrained simulations and a demonstration of the potential for limited amounts of structural information to accelerate structure determination. Almost all of the remaining ubiquitin simulations reached near-native conformations within a few tens of microseconds, but remained trapped there, apparently due to the restraints. We discuss potential methodological improvements that would facilitate escape from these near-native traps and allow more simulations to quickly reach the native state. Finally, using a target from the Critical Assessment of protein Structure Prediction (CASP) experiment, we show that distance restraints can improve simulation accuracy: In our simulations, restraints stabilized the native state of the protein, enabling a reasonable structural model to be inferred. © 2015 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.
Native flexibility of structurally homologous proteins: insights from anisotropic network model.

PubMed

Sarkar, Ranja

2017-01-01

Single-molecule microscopic experiments can measure the mechanical response of proteins to pulling forces applied externally along different directions (inducing different residue pairs in the proteins by uniaxial tension). This response to external forces away from equilibrium should in principle, correlate with the flexibility or stiffness of proteins in their folded states. Here, a simple topology-based atomistic anisotropic network model (ANM) is shown which captures the protein flexibility as a fundamental property that determines the collective dynamics and hence, the protein conformations in native state. An all-atom ANM is used to define two measures of protein flexibility in the native state. One measure quantifies overall stiffness of the protein and the other one quantifies protein stiffness along a particular direction which is effectively the mechanical resistance of the protein towards external pulling force exerted along that direction. These measures are sensitive to the protein sequence and yields reliable values through computations of normal modes of the protein. ANM at an atomistic level (heavy atoms) explains the experimental (atomic force microscopy) observations viz., different mechanical stability of structurally similar but sequentially distinct proteins which, otherwise were implied to possess similar mechanical properties from analytical/theoretical coarse-grained (backbone only) models. The results are exclusively demonstrated for human fibronectin (FN) protein domains. The topology of interatomic contacts in the folded states of proteins essentially determines the native flexibility. The mechanical differences of topologically similar proteins are captured from a high-resolution (atomic level) ANM at a low computational cost. The relative trend in flexibility of such proteins is reflected in their stability differences that they exhibit while unfolding in atomic force microscopic (AFM) experiments.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Law, Anthony B.; Sapienza, Paul J.; Zhang, Jun

Allostery enables tight regulation of protein function in the cellular environment. While existing models of allostery are firmly rooted in the current structure-function paradigm, the mechanistic basis for allostery in the absence of structural change remains unclear. In this study, we show that a typical globular protein is able to undergo significant changes in volume under native conditions while exhibiting no additional changes in protein structure. These native state volume fluctuations were found to correlate with changes in internal motions that were previously recognized as a source of allosteric entropy. This finding offers a novel mechanistic basis for allostery inmore » the absence of canonical structural change. As a result, the unexpected observation that function can be derived from expanded, low density protein states has broad implications for our understanding of allostery and suggests that the general concept of the native state be expanded to allow for more variable physical dimensions with looser packing.« less
Allometric biomass models and applications for branches of Chinese tallow in a Mississippi Bottomland Forest

Treesearch

Allison M. Stoklosa; Nana Tian; Zhaofei Fan

2015-01-01

Chinese tallow [Triadica sebifera (L.) Small, formerly Sapium sebiferum (L.) Roxb.] is a non-native invader moving through the southeastern United States. Tallow can invade a multitude of habitats, from coastal prairies to closed-canopy forests, forming monospecific stands and driving out native flora and fauna (Bruce and others 1997). Tallow has large impacts, both...

1H, 15N and 13C assignments of domain 5 of Dictyostelium discoideum gelation factor (ABP-120) in its native and 8M urea-denatured states.

PubMed

Hsu, Shang-Te Danny; Cabrita, Lisa D; Christodoulou, John; Dobson, Christopher M

2009-06-01

The gelation factor from Dictyostelium discoideum (ABP-120) is an actin binding protein consisting of six immunoglobulin (Ig) domains in the C-terminal rod domain. We have recently used the pair of domains 5 and 6 of ABP-120 as a model system for studying multi-domain nascent chain folding on the ribosome. Here we present the NMR assignments of domain 5 in its native and 8M urea-denatured states.
Native Contact Density and Nonnative Hydrophobic Effects in the Folding of Bacterial Immunity Proteins

PubMed Central

Chen, Tao; Chan, Hue Sun

2015-01-01

The bacterial colicin-immunity proteins Im7 and Im9 fold by different mechanisms. Experimentally, at pH 7.0 and 10°C, Im7 folds in a three-state manner via an intermediate but Im9 folding is two-state-like. Accordingly, Im7 exhibits a chevron rollover, whereas the chevron arm for Im9 folding is linear. Here we address the biophysical basis of their different behaviors by using native-centric models with and without additional transferrable, sequence-dependent energies. The Im7 chevron rollover is not captured by either a pure native-centric model or a model augmented by nonnative hydrophobic interactions with a uniform strength irrespective of residue type. By contrast, a more realistic nonnative interaction scheme that accounts for the difference in hydrophobicity among residues leads simultaneously to a chevron rollover for Im7 and an essentially linear folding chevron arm for Im9. Hydrophobic residues identified by published experiments to be involved in nonnative interactions during Im7 folding are found to participate in the strongest nonnative contacts in this model. Thus our observations support the experimental perspective that the Im7 folding intermediate is largely underpinned by nonnative interactions involving large hydrophobics. Our simulation suggests further that nonnative effects in Im7 are facilitated by a lower local native contact density relative to that of Im9. In a one-dimensional diffusion picture of Im7 folding with a coordinate- and stability-dependent diffusion coefficient, a significant chevron rollover is consistent with a diffusion coefficient that depends strongly on native stability at the conformational position of the folding intermediate. PMID:26016652
Side-chain mobility in the folded state of Myoglobin

NASA Astrophysics Data System (ADS)

Lammert, Heiko; Onuchic, Jose

We study the accessibility of alternative side-chain rotamer configurations in the native state of Myoglobin, using an all-atom structure-based model. From long, unbiased simulation trajectories we determine occupancies of rotameric states and also estimate configurational and vibrational entropies. Direct sampling of the full native-state dynamics, enabled by the simple model, reveals facilitation of side-chain motions by backbone dynamics. Correlations between different dihedral angles are quantified and prove to be weak. We confirm global trends in the mobilities of side-chains, following burial and also the chemical character of residues. Surface residues loose little configurational entropy upon folding; side-chains contribute significantly to the entropy of the folded state. Mobilities of buried side-chains vary strongly with temperature. At ambient temperature, individual side-chains in the core of the protein gain substantial access to alternative rotamers, with occupancies that are likely observable experimentally. Finally, the dynamics of buried side-chains may be linked to the internal pockets, available to ligand gas molecules in Myoglobin.
Reduced native state stability in crowded cellular environment due to protein-protein interactions.

PubMed

Harada, Ryuhei; Tochio, Naoya; Kigawa, Takanori; Sugita, Yuji; Feig, Michael

2013-03-06

The effect of cellular crowding environments on protein structure and stability is a key issue in molecular and cellular biology. The classical view of crowding emphasizes the volume exclusion effect that generally favors compact, native states. Here, results from molecular dynamics simulations and NMR experiments show that protein crowders may destabilize native states via protein-protein interactions. In the model system considered here, mixtures of villin head piece and protein G at high concentrations, villin structures become increasingly destabilized upon increasing crowder concentrations. The denatured states observed in the simulation involve partial unfolding as well as more subtle conformational shifts. The unfolded states remain overall compact and only partially overlap with unfolded ensembles at high temperature and in the presence of urea. NMR measurements on the same systems confirm structural changes upon crowding based on changes of chemical shifts relative to dilute conditions. An analysis of protein-protein interactions and energetic aspects suggests the importance of enthalpic and solvation contributions to the crowding free energies that challenge an entropic-centered view of crowding effects.
Sociocultural Variables That Impact High School Students' Perceptions of Native Fauna: a Study on the Species Component of the Biodiversity Concept

NASA Astrophysics Data System (ADS)

Bermudez, Gonzalo M. A.; Battistón, Luisina V.; García Capocasa, María C.; De Longhi, Ana L.

2017-02-01

This study investigates the influence of school sector (private versus state schools) and student gender on knowledge of native fauna. Our main objectives were (a) to describe the knowledge of high school students from the province of Cordoba, Argentina with respect to native animal species, (b) to determine if any exotic species (introduced or domestic) are considered native, and (c) to analyze the effects of school sector and gender on the students' knowledge of the native fauna. In total, 321 students aged 15-18 from 14 urban schools (8 state and 6 private schools) were asked to write down ten animals native to Córdoba, Argentina, in a free-list questionnaire. Relative frequencies and Generalized Linear Mixed Models (GLMM) were used to analyze the categorized (animal names) and continuous answers (quantity of responses, number of native animals, etc.), with the 25 most frequently mentioned species showing a predominance of native ones, of which "Puma" ( Puma concolor) and "Andean condor" ( Vultur gryphus) were the most prominent. An overrepresentation of mammalian species compared to other classes of chordates was also found, with high school students mentioning native and domestic species higher on the free-list. Using GLMM, we found that school sector had a significant effect on the number of native animals mentioned at both national and local levels, and on domestic and mixed species. Finally, male students mentioned more species and more native animals than their female counterparts. These findings were interpreted and discussed in light of sociocultural and traditional ecological knowledge theories, from which several implications arose related to research and practice.
Substance use among American Indians and Alaska natives: incorporating culture in an "indigenist" stress-coping paradigm.

PubMed Central

Walters, Karina L.; Simoni, Jane M.; Evans-Campbell, Teresa

2002-01-01

OBJECTIVES: This article proposes a new stress-coping model for American Indians and Alaska Natives (AIs) that reflects a paradigmatic shift in the conceptualization of Native health. It reviews sociodemographic information on AIs, rates of substance abuse and related health outcomes, and the research supporting the model's pathways. OBSERVATIONS: Although health outcomes among AIs are improving, large disparities with other racial and ethnic groups in the United States remain. Many health-related problems are directly linked to high rates of substance use and abuse. CONCLUSION: Eurocentric paradigms focus on individual pathology. An "indigenist" perspective of health incorporates the devastating impact of historical trauma and ongoing oppression of AIs. The model emphasizes cultural strengths, such as the family and community, spirituality and traditional healing practices, and group identity attitudes. PMID:12435834
Risk Factors for Obesity at Age 3 in Alaskan Children, Including the Role of Beverage Consumption: Results from Alaska PRAMS 2005-2006 and Its Three-Year Follow-Up Survey, CUBS, 2008-2009

PubMed Central

Wojcicki, Janet M.; Young, Margaret B.; Perham-Hester, Katherine A.; de Schweinitz, Peter; Gessner, Bradford D.

2015-01-01

Background Prenatal and early life risk factors are associated with childhood obesity. Alaska Native children have one of the highest prevalences of childhood obesity of all US racial/ethnic groups. Methods Using the Pregnancy Risk Assessment Monitoring System (PRAMS) and the follow-up survey at 3 years of age (CUBS), we evaluated health, behavioral, lifestyle and nutritional variables in relation to obesity (95th percentile for body mass index (BMI)) at 3 years of age. Multivariate logistic regression modeling was conducted using Stata 12.0 to evaluate independent risk factors for obesity in non-Native and Alaska Native children. Results We found an obesity prevalence of 24.9% in all Alaskan and 42.2% in Alaska Native 3 year olds. Among Alaska Native children, obesity prevalence was highest in the Northern/Southwest part of the state (51.6%, 95%CI (42.6-60.5)). Independent predictive factors for obesity at age 3 years in Alaska non-Native children were low income (<$10,000 in the year before the child was born (OR 3.94, 95%CI 1.22--17.03) and maternal pre-pregnancy obesity (OR 2.01, 95%CI 1.01-4.01) and longer duration of breastfeeding was protective (OR 0.95, 95%CI 0.91-0.995). Among Alaska Native children, predictive factors were witnessing domestic violence/abuse as a 3 year-old (OR 2.28, 95%CI 1.17-7.60). Among obese Alaska Native children, there was an increased daily consumption of energy dense beverages in the Northern/Southwest region of the state, which may explain higher rates of obesity in this part of the state. Conclusions The high prevalence of obesity in Alaska Native children may be explained by differences in lifestyle patterns and food consumption in certain parts of the state, specifically the Northern/Southwest region, which have higher consumption of energy dense beverages. PMID:25793411
Integrated monitoring and information systems for managing aquatic invasive species in a changing climate.

PubMed

Lee, Henry; Reusser, Deborah A; Olden, Julian D; Smith, Scott S; Graham, Jim; Burkett, Virginia; Dukes, Jeffrey S; Piorkowski, Robert J; McPhedran, John

2008-06-01

Changes in temperature, precipitation, and other climatic drivers and sea-level rise will affect populations of existing native and non-native aquatic species and the vulnerability of aquatic environments to new invasions. Monitoring surveys provide the foundation for assessing the combined effects of climate change and invasions by providing baseline biotic and environmental conditions, although the utility of a survey depends on whether the results are quantitative or qualitative, and other design considerations. The results from a variety of monitoring programs in the United States are available in integrated biological information systems, although many include only non-native species, not native species. Besides including natives, we suggest these systems could be improved through the development of standardized methods that capture habitat and physiological requirements and link regional and national biological databases into distributed Web portals that allow drawing information from multiple sources. Combining the outputs from these biological information systems with environmental data would allow the development of ecological-niche models that predict the potential distribution or abundance of native and non-native species on the basis of current environmental conditions. Environmental projections from climate models can be used in these niche models to project changes in species distributions or abundances under altered climatic conditions and to identify potential high-risk invaders. There are, however, a number of challenges, such as uncertainties associated with projections from climate and niche models and difficulty in integrating data with different temporal and spatial granularity. Even with these uncertainties, integration of biological and environmental information systems, niche models, and climate projections would improve management of aquatic ecosystems under the dual threats of biotic invasions and climate change.
Integrated monitoring and information systems for managing aquatic invasive species in a changing climate

USGS Publications Warehouse

Lee, Henry; Reusser, Deborah A.; Olden, Julian D.; Smith, Scott S.; Graham, Jim; Burkett, Virginia; Dukes, Jeffrey S.; Piorkowski, Robert J.; Mcphedran, John

2008-01-01

Changes in temperature, precipitation, and other climatic drivers and sea-level rise will affect populations of existing native and non-native aquatic species and the vulnerability of aquatic environments to new invasions. Monitoring surveys provide the foundation for assessing the combined effects of climate change and invasions by providing baseline biotic and environmental conditions, although the utility of a survey depends on whether the results are quantitative or qualitative, and other design considerations. The results from a variety of monitoring programs in the United States are available in integrated biological information systems, although many include only non-native species, not native species. Besides including natives, we suggest these systems could be improved through the development of standardized methods that capture habitat and physiological requirements and link regional and national biological databases into distributed Web portals that allow drawing information from multiple sources. Combining the outputs from these biological information systems with environmental data would allow the development of ecological-niche models that predict the potential distribution or abundance of native and non-native species on the basis of current environmental conditions. Environmental projections from climate models can be used in these niche models to project changes in species distributions or abundances under altered climatic conditions and to identify potential high-risk invaders. There are, however, a number of challenges, such as uncertainties associated with projections from climate and niche models and difficulty in integrating data with different temporal and spatial granularity. Even with these uncertainties, integration of biological and environmental information systems, niche models, and climate projections would improve management of aquatic ecosystems under the dual threats of biotic invasions and climate change
Plant species invasions along the latitudinal gradient in the United States

USGS Publications Warehouse

Stohlgren, T.J.; Barnett, D.; Flather, C.; Kartesz, J.; Peterjohn, B.

2005-01-01

It has been long established that the richness of vascular plant species and many animal taxa decreases with increasing latitude, a pattern that very generally follows declines in actual and potential evapotranspiration, solar radiation, temperature, and thus, total productivity. Using county-level data on vascular plants from the United States (3000 counties in the conterminous 48 states), we used the Akaike Information Criterion (AIC) to evaluate competing models predicting native and nonnative plant species density (number of species per square kilometer in a county) from various combinations of biotic variables (e.g., native bird species density, vegetation carbon, normalized difference vegetation index), environmental/topographic variables (elevation, variation in elevation, the number of land cover classes in the county; radiation, mean precipitation, actual evapotranspiration, and potential evapotranspiration), and human variables (human population density, crop-land, and percentage of disturbed lands in a county). We found no evidence of a latitudinal gradient for the density of native plant species and a significant, slightly positive latitudinal gradient for the density of nonnative plant species. We found stronger evidence of a significant, positive productivity gradient (vegetation carbon) for the density of native plant species and nonnative plant species. We found much stronger significant relationships when biotic, environmental/topographic, and human variables were used to predict native plant species density and nonnative plant species density. Biotic variables generally had far greater influence in multivariate models than human or environmental/topographic variables. Later, we found that the best, single, positive predictor of the density of nonnative plant species in a county was the density of native plant species in a county. While further study is needed, it may be that, while humans facilitate the initial establishment invasions of nonnative plant species, the spread and subsequent distributions of nonnative species are controlled largely by biotic and environmental factors.
Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework.

PubMed

Zhuravlev, Pavel I; Papoian, Garegin A

2010-08-01

Energy landscape theories have provided a common ground for understanding the protein folding problem, which once seemed to be overwhelmingly complicated. At the same time, the native state was found to be an ensemble of interconverting states with frustration playing a more important role compared to the folding problem. The landscape of the folded protein - the native landscape - is glassier than the folding landscape; hence, a general description analogous to the folding theories is difficult to achieve. On the other hand, the native basin phase volume is much smaller, allowing a protein to fully sample its native energy landscape on the biological timescales. Current computational resources may also be used to perform this sampling for smaller proteins, to build a 'topographical map' of the native landscape that can be used for subsequent analysis. Several major approaches to representing this topographical map are highlighted in this review, including the construction of kinetic networks, hierarchical trees and free energy surfaces with subsequent structural and kinetic analyses. In this review, we extensively discuss the important question of choosing proper collective coordinates characterizing functional motions. In many cases, the substates on the native energy landscape, which represent different functional states, can be used to obtain variables that are well suited for building free energy surfaces and analyzing the protein's functional dynamics. Normal mode analysis can provide such variables in cases where functional motions are dictated by the molecule's architecture. Principal component analysis is a more expensive way of inferring the essential variables from the protein's motions, one that requires a long molecular dynamics simulation. Finally, the two popular models for the allosteric switching mechanism, 'preexisting equilibrium' and 'induced fit', are interpreted within the energy landscape paradigm as extreme points of a continuum of transition mechanisms. Some experimental evidence illustrating each of these two models, as well as intermediate mechanisms, is presented and discussed.
Balancing aggregation and smoothing errors in inverse models

DOE PAGES

Turner, A. J.; Jacob, D. J.

2015-06-30

Inverse models use observations of a system (observation vector) to quantify the variables driving that system (state vector) by statistical optimization. When the observation vector is large, such as with satellite data, selecting a suitable dimension for the state vector is a challenge. A state vector that is too large cannot be effectively constrained by the observations, leading to smoothing error. However, reducing the dimension of the state vector leads to aggregation error as prior relationships between state vector elements are imposed rather than optimized. Here we present a method for quantifying aggregation and smoothing errors as a function ofmore » state vector dimension, so that a suitable dimension can be selected by minimizing the combined error. Reducing the state vector within the aggregation error constraints can have the added advantage of enabling analytical solution to the inverse problem with full error characterization. We compare three methods for reducing the dimension of the state vector from its native resolution: (1) merging adjacent elements (grid coarsening), (2) clustering with principal component analysis (PCA), and (3) applying a Gaussian mixture model (GMM) with Gaussian pdfs as state vector elements on which the native-resolution state vector elements are projected using radial basis functions (RBFs). The GMM method leads to somewhat lower aggregation error than the other methods, but more importantly it retains resolution of major local features in the state vector while smoothing weak and broad features.« less
Balancing aggregation and smoothing errors in inverse models

NASA Astrophysics Data System (ADS)

Turner, A. J.; Jacob, D. J.

2015-01-01

Inverse models use observations of a system (observation vector) to quantify the variables driving that system (state vector) by statistical optimization. When the observation vector is large, such as with satellite data, selecting a suitable dimension for the state vector is a challenge. A state vector that is too large cannot be effectively constrained by the observations, leading to smoothing error. However, reducing the dimension of the state vector leads to aggregation error as prior relationships between state vector elements are imposed rather than optimized. Here we present a method for quantifying aggregation and smoothing errors as a function of state vector dimension, so that a suitable dimension can be selected by minimizing the combined error. Reducing the state vector within the aggregation error constraints can have the added advantage of enabling analytical solution to the inverse problem with full error characterization. We compare three methods for reducing the dimension of the state vector from its native resolution: (1) merging adjacent elements (grid coarsening), (2) clustering with principal component analysis (PCA), and (3) applying a Gaussian mixture model (GMM) with Gaussian pdfs as state vector elements on which the native-resolution state vector elements are projected using radial basis functions (RBFs). The GMM method leads to somewhat lower aggregation error than the other methods, but more importantly it retains resolution of major local features in the state vector while smoothing weak and broad features.
Balancing aggregation and smoothing errors in inverse models

NASA Astrophysics Data System (ADS)

Turner, A. J.; Jacob, D. J.

2015-06-01

Inverse models use observations of a system (observation vector) to quantify the variables driving that system (state vector) by statistical optimization. When the observation vector is large, such as with satellite data, selecting a suitable dimension for the state vector is a challenge. A state vector that is too large cannot be effectively constrained by the observations, leading to smoothing error. However, reducing the dimension of the state vector leads to aggregation error as prior relationships between state vector elements are imposed rather than optimized. Here we present a method for quantifying aggregation and smoothing errors as a function of state vector dimension, so that a suitable dimension can be selected by minimizing the combined error. Reducing the state vector within the aggregation error constraints can have the added advantage of enabling analytical solution to the inverse problem with full error characterization. We compare three methods for reducing the dimension of the state vector from its native resolution: (1) merging adjacent elements (grid coarsening), (2) clustering with principal component analysis (PCA), and (3) applying a Gaussian mixture model (GMM) with Gaussian pdfs as state vector elements on which the native-resolution state vector elements are projected using radial basis functions (RBFs). The GMM method leads to somewhat lower aggregation error than the other methods, but more importantly it retains resolution of major local features in the state vector while smoothing weak and broad features.
The unfolding effects on the protein hydration shell and partial molar volume: a computational study.

PubMed

Del Galdo, Sara; Amadei, Andrea

2016-10-12

In this paper we apply the computational analysis recently proposed by our group to characterize the solvation properties of a native protein in aqueous solution, and to four model aqueous solutions of globular proteins in their unfolded states thus characterizing the protein unfolded state hydration shell and quantitatively evaluating the protein unfolded state partial molar volumes. Moreover, by using both the native and unfolded protein partial molar volumes, we obtain the corresponding variations (unfolding partial molar volumes) to be compared with the available experimental estimates. We also reconstruct the temperature and pressure dependence of the unfolding partial molar volume of Myoglobin dissecting the structural and hydration effects involved in the process.
Structural analysis of kinetic folding intermediates for a TIM barrel protein, indole-3-glycerol phosphate synthase, by hydrogen exchange mass spectrometry and Gō-model simulation

PubMed Central

Gu, Zhenyu; Rao, Maithreyi K.; Forsyth, William R.

2009-01-01

The structures of partially-folded states appearing during the folding of a (βα)8 TIM barrel protein, the indole-3-glycerol phosphate synthase from S. solfataricus (sIGPS), was assessed by hydrogen exchange mass spectrometry (HX-MS) and Gō-model simulations. HX-MS analysis of the peptic peptides derived from the pulse-labeled product of the sub-millisecond folding reaction from the urea-denatured state revealed strong protection in the (βα)4 region, modest protection in the neighboring (βα)1–3 and (βα)5β6 segments and no significant protection in the remaining N- and C-terminal segments. These results demonstrate that this species is not a collapsed form of the unfolded state under native-favoring conditions nor is it the native state formed via fast-track folding. However, the striking contrast of these results with the strong protection observed in the (βα)2–5β6 region after 5 s of folding demonstrates that these species represent kinetically-distinct folding intermediates that are not identical as previously thought. A re-examination of the kinetic folding mechanism by chevron analysis of fluorescence data confirmed distinct roles for these two species: the burst-phase intermediate is predicted to be a misfolded, off-pathway intermediate while the subsequent 5 s intermediate corresponds to an on-pathway equilibrium intermediate. Comparison with the predictions using a Cα Gō-model simulation of the kinetic folding reaction for sIGPS shows good agreement with the core of structure offering protection against exchange in the on-pathway intermediate(s). Because the native-centric Gō-model simulations do not explicitly include sequence-specific information, the simulation results support the hypothesis that the topology of TIM barrel proteins is a primary determinant of the folding free energy surface for the productive folding reaction. The early misfolding reaction must involve aspects of non-native structure not detected by the Gō-model simulation. PMID:17942114
Molecular simulation of surfactant-assisted protein refolding

NASA Astrophysics Data System (ADS)

Lu, Diannan; Liu, Zheng; Liu, Zhixia; Zhang, Minlian; Ouyang, Pingkai

2005-04-01

Protein refolding to its native state in vitro is a challenging problem in biotechnology, i.e., in the biomedical, pharmaceutical, and food industry. Protein aggregation and misfolding usually inhibit the recovery of proteins with their native states. These problems can be partially solved by adding a surfactant into a suitable solution environment. However, the process of this surfactant-assisted protein refolding is not well understood. In this paper, we wish to report on the first-ever simulations of surfactant-assisted protein refolding. For these studies, we defined a simple model for the protein and the surfactant and investigated how a surfactant affected the folding behavior of a two-dimensional lattice protein molecule. The model protein and model surfactant were chosen such that we could capture the important features of the folding process and the interaction between the protein and the surfactant, namely, the hydrophobic interaction. It was shown that, in the absence of surfactants, a protein in an "energy trap" conformation, i.e., a local energy minima, could not fold into the native form, which was characterized by a global energy minimum. The addition of surfactants created folding pathways via the formation of protein-surfactant complexes and thus enabled the conformations that fell into energy trap states to escape from these traps and to form the native proteins. The simulation results also showed that it was necessary to match the hydrophobicity of surfactant to the concentration of denaturant, which was added to control the folding or unfolding of a protein. The surfactants with different hydrophobicity had their own concentration range on assisting protein refolding. All of these simulations agreed well with experimental results reported elsewhere, indicating both the validity of the simulations presented here and the potential application of the simulations for the design of a surfactant on assisting protein refolding.
The role of atomic level steric effects and attractive forces in protein folding.

PubMed

Lammert, Heiko; Wolynes, Peter G; Onuchic, José N

2012-02-01

Protein folding into tertiary structures is controlled by an interplay of attractive contact interactions and steric effects. We investigate the balance between these contributions using structure-based models using an all-atom representation of the structure combined with a coarse-grained contact potential. Tertiary contact interactions between atoms are collected into a single broad attractive well between the C(β) atoms between each residue pair in a native contact. Through the width of these contact potentials we control their tolerance for deviations from the ideal structure and the spatial range of attractive interactions. In the compact native state dominant packing constraints limit the effects of a coarse-grained contact potential. During folding, however, the broad attractive potentials allow an early collapse that starts before the native local structure is completely adopted. As a consequence the folding transition is broadened and the free energy barrier is decreased. Eventually two-state folding behavior is lost completely for systems with very broad attractive potentials. The stabilization of native-like residue interactions in non-perfect geometries early in the folding process frequently leads to structural traps. Global mirror images are a notable example. These traps are penalized by the details of the repulsive interactions only after further collapse. Successful folding to the native state requires simultaneous guidance from both attractive and repulsive interactions. Copyright © 2011 Wiley Periodicals, Inc.
Recovery of native treefrogs after removal of nonindigenous Cuban Treefrogs, Osteopilus septentrionalis

USGS Publications Warehouse

Rice, K.G.; Waddle, J.H.; Miller, M.W.; Crockett, M.E.; Mazzotti, F.J.; Percival, H.F.

2011-01-01

Florida is home to several introduced animal species, especially in the southern portion of the state. Most introduced species are restricted to the urban and suburban areas along the coasts, but some species, like the Cuban Treefrog (Osteopilus septentrionalis), are locally abundant in natural protected areas. Although Cuban Treefrogs are known predators of native treefrog species as both adults and larvae, no study has demonstrated a negative effect of Cuban Treefrogs on native treefrog survival, abundance, or occupancy rate. We monitored survival, capture probability, abundance, and proportion of sites occupied by Cuban Treefrogs and two native species, Green Treefrogs (Hyla cinerea) and Squirrel Treefrogs (Hyla squirella), at four sites in Everglades National Park in southern Florida with the use of capture–mark–recapture techniques. After at least 5 mo of monitoring all species at each site we began removing every Cuban Treefrog captured. We continued to estimate survival, abundance, and occupancy rates of native treefrogs for 1 yr after the commencement of Cuban Treefrog removal. Mark–recapture models that included the effect of Cuban Treefrog removal on native treefrog survival did not have considerable Akaike's Information Criterion (AIC) weight, although capture rates of native species were generally very low prior to Cuban Treefrog removal. Estimated abundance of native treefrogs did increase after commencement of Cuban Treefrog removal, but also varied with the season of the year. The best models of native treefrog occupancy included a Cuban Treefrog removal effect at sites with high initial densities of Cuban Treefrogs. This study demonstrates that an introduced predator can have population-level effects on similar native species.
1994 State Legislation on Native American Issues.

ERIC Educational Resources Information Center

Morin, Kimberly A.

This report includes state-by-state summaries of 1994 legislation pertaining to Native American issues. Of 344 bills introduced in the state legislatures in 1994, 92 were enacted and 20 are still pending. Major issues addressed in 1994 legislation included Native American education; history, language, and culture preservation; sovereignty; law…

Evolutionary Dynamics on Protein Bi-stability Landscapes can Potentially Resolve Adaptive Conflicts

PubMed Central

Sikosek, Tobias; Bornberg-Bauer, Erich; Chan, Hue Sun

2012-01-01

Experimental studies have shown that some proteins exist in two alternative native-state conformations. It has been proposed that such bi-stable proteins can potentially function as evolutionary bridges at the interface between two neutral networks of protein sequences that fold uniquely into the two different native conformations. Under adaptive conflict scenarios, bi-stable proteins may be of particular advantage if they simultaneously provide two beneficial biological functions. However, computational models that simulate protein structure evolution do not yet recognize the importance of bi-stability. Here we use a biophysical model to analyze sequence space to identify bi-stable or multi-stable proteins with two or more equally stable native-state structures. The inclusion of such proteins enhances phenotype connectivity between neutral networks in sequence space. Consideration of the sequence space neighborhood of bridge proteins revealed that bi-stability decreases gradually with each mutation that takes the sequence further away from an exactly bi-stable protein. With relaxed selection pressures, we found that bi-stable proteins in our model are highly successful under simulated adaptive conflict. Inspired by these model predictions, we developed a method to identify real proteins in the PDB with bridge-like properties, and have verified a clear bi-stability gradient for a series of mutants studied by Alexander et al. (Proc Nat Acad Sci USA 2009, 106:21149–21154) that connect two sequences that fold uniquely into two different native structures via a bridge-like intermediate mutant sequence. Based on these findings, new testable predictions for future studies on protein bi-stability and evolution are discussed. PMID:23028272
Cooperative alpha-helix formation of beta-lactoglobulin induced by sodium n-alkyl sulfates.

PubMed

Chamani, J; Moosavi-Movahedi, A A; Rajabi, O; Gharanfoli, M; Momen-Heravi, M; Hakimelahi, G H; Neamati-Baghsiah, A; Varasteh, A R

2006-01-01

It is generally assumed that folding intermediates contain partially formed native-like secondary structures. However, if we consider the fact that the conformational stability of the intermediate state is simpler than that of the native state, it would be expected that the secondary structures in a folding intermediate would not necessarily be similar to those of the native state. beta-Lactoglobulin is a predominantly beta-sheet protein, although it has a markedly high intrinsic preference for alpha-helical structure. The formation of non-native alpha-helical intermediate of beta-lactoglobulin was induced by n-alkyl sulfates including sodium octyl sulfate, SOS; sodium decyl sulfate, SDeS; sodium dodecyl sulfate, SDS; and sodium tetradecyl sulfate, STS at special condition. The effect of n-alkyl sulfates on the structure of native beta-lactoglobulin at pH 2 was utilized to investigate the contribution of hydrophobic interactions to the stability of non-native alpha-helical intermediate. The addition of various concentrations of n-alkyl sulfates to the native state of beta-lactoglobulin (pH 2) appears to support the stabilized form of non-native alpha-helical intermediate at pH 2. The m values of the intermediate state of beta-lactoglobulin by SOS, SDeS, SDS and STS showed substantial variation. The enhancement of m values as the stability criterion of non-native alpha-helical intermediate state corresponded with increasing chain length of the cited n-alkyl sulfates. The present results suggest that the folding reaction of beta-lactoglobulin follows a non-hierarchical mechanism and hydrophobic interactions play important roles in stabilizing the non-native alpha-helical intermediate state.
Validity of Gō models: comparison with a solvent-shielded empirical energy decomposition.

PubMed

Paci, Emanuele; Vendruscolo, Michele; Karplus, Martin

2002-12-01

Do Gō-type model potentials provide a valid approach for studying protein folding? They have been widely used for this purpose because of their simplicity and the speed of simulations based on their use. The essential assumption in such models is that only contact interactions existing in the native state determine the energy surface of a polypeptide chain, even for non-native configurations sampled along folding trajectories. Here we use an all-atom molecular mechanics energy function to investigate the adequacy of Gō-type potentials. We show that, although the contact approximation is accurate, non-native contributions to the energy can be significant. The assumed relation between residue-residue interaction energies and the number of contacts between them is found to be only approximate. By contrast, individual residue energies correlate very well with the number of contacts. The results demonstrate that models based on the latter should give meaningful results (e.g., as used to interpret phi values), whereas those that depend on the former are only qualitative, at best.
Modeling suitable habitat of invasive red lionfish Pterois volitans (Linnaeus, 1758) in North and South America’s coastal waters

USGS Publications Warehouse

Evangelista, Paul H.; Young, Nicholas E.; Schofield, Pamela J.; Jarnevich, Catherine S.

2016-01-01

We used two common correlative species-distribution models to predict suitable habitat of invasive red lionfish Pterois volitans (Linnaeus, 1758) in the western Atlantic and eastern Pacific Oceans. The Generalized Linear Model (GLM) and the Maximum Entropy (Maxent) model were applied using the Software for Assisted Habitat Modeling. We compared models developed using native occurrences, using non-native occurrences, and using both native and non-native occurrences. Models were trained using occurrence data collected before 2010 and evaluated with occurrence data collected from the invaded range during or after 2010. We considered a total of 22 marine environmental variables. Models built with non-native only or both native and non-native occurrence data outperformed those that used only native occurrences. Evaluation metrics based on the independent test data were highest for models that used both native and non-native occurrences. Bathymetry was the strongest environmental predictor for all models and showed increasing suitability as ocean floor depth decreased, with salinity ranking the second strongest predictor for models that used native and both native and non-native occurrences, indicating low habitat suitability for salinities <30. Our model results also suggest that red lionfish could continue to invade southern latitudes in the western Atlantic Ocean and may establish localized populations in the eastern Pacific Ocean. We reiterate the importance in the choice of the training data source (native, non-native, or native/non-native) used to develop correlative species distribution models for invasive species.
Great Basin Native Plant Project: 2015 Progress Report

Treesearch

Francis Kilkenny; Fred Edwards; Alexis Malcomb

2016-01-01

The Interagency Native Plant Materials Development Program outlined in the 2002 United States Department of Agriculture (USDA) and United States Department of Interior (USDI) Report to Congress encouraged use of native plant materials for rangeland rehabilitation and restoration where feasible. The Great Basin Native Plant Project is a cooperative project lead...
An Internship Model for Culturally Relevant Success for Native American High School Students

NASA Astrophysics Data System (ADS)

Nall, J.; Graham, E. M.

2004-12-01

Culturally relevant educational practices can be challenging to implement in the workplace. In an effort to support equity in access to undergraduate internship opportunities for Native American students, NASA Jet Propulsion Laboratory's (JPL) Education Office, Minority Education Initiatives offers a unique approach to supporting students from Native American reservation high schools in Washington State to participate in eight-week technical (Science, Technology, Engineering and Mathematics related) summer internships. This talk will address the Alliance for Learning and Vision for Americans (ALVA) program's twelve years of success based on four programmatic principals, annual review and the critical support of scientists and engineers.
Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling

PubMed Central

Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

2014-01-01

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. PMID:25340714
Great Basin Native Plant Project: 2014 Progress Report

Treesearch

Francis Kilkenny; Anne Halford; Alexis Malcomb

2015-01-01

The Interagency Native Plant Materials Development Program outlined in the 2002 United States Department of Agriculture (USDA) and United States Department of Interior (USDI) Report to Congress encouraged use of native plant materials for rangeland rehabilitation and restoration where feasible. The Great Basin Native Plant Project is a cooperative project lead by the...
Great Basin Native Plant Project: 2013 Progress Report

Treesearch

Francis Kilkenny; Nancy Shaw; Corey Gucker

2014-01-01

The Interagency Native Plant Materials Development Program outlined in the 2002 United States Department of Agriculture (USDA) and United States Department of Interior (USDI) Report to Congress encouraged use of native plant materials for rangeland rehabilitation and restoration where feasible. The Great Basin Native Plant Project is a cooperative project lead by the...
Infant Feeding Practices: Perceptions of Native American Mothers and Health Paraprofessionals

ERIC Educational Resources Information Center

Horodynski, Mildred A; Calcatera, Mary; Carpenter, Amanda

2012-01-01

Objective: To ascertain infant feeding practices and to explore the feasibility of an in-home feeding intervention with Native American Indian (NAI) mothers in six Native American communities in the United States (US). Design: Qualitative focus group study. Setting: Six Native American communities in the Midwest region of the United States.…
Invasive lionfish reduce native fish abundance on a regional scale

NASA Astrophysics Data System (ADS)

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

2016-08-01

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

PubMed

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

2016-08-31

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

PubMed Central

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

2016-01-01

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

PubMed

Vazquez, Diego S; Sánchez, Ignacio E; Garrote, Ana; Sica, Mauricio P; Santos, Javier

2015-02-01

In this work, the unfolding mechanism of oxidized Escherichia coli thioredoxin (EcTRX) was investigated experimentally and computationally. We characterized seven point mutants distributed along the C-terminal α-helix (CTH) and the preceding loop. The mutations destabilized the protein against global unfolding while leaving the native structure unchanged. Global analysis of the unfolding kinetics of all variants revealed a linear unfolding route with a high-energy on-pathway intermediate state flanked by two transition state ensembles TSE1 and TSE2. The experiments show that CTH is mainly unfolded in TSE1 and the intermediate and becomes structured in TSE2. Structure-based molecular dynamics are in agreement with these experiments and provide protein-wide structural information on transient states. In our model, EcTRX folding starts with structure formation in the β-sheet, while the protein helices coalesce later. As a whole, our results indicate that the CTH is a critical module in the folding process, restraining a heterogeneous intermediate ensemble into a biologically active native state and providing the native protein with thermodynamic and kinetic stability. Copyright © 2014 Elsevier B.V. All rights reserved.
Microgravity

NASA Image and Video Library

1996-02-22

Astronaut Franklin R. Chang-Diaz, payload commander, ponders the elements of a model representing the Commercial Protein Crystal Growth (CPCG) experiment. This flight of the experiment marks the first joint United States--Latin America effort in this discipline. The project brings together a small team of investigators from Costa Rica (Chang-Diaz's native land), Chile, and the United States.
Cold hardiness of winter-acclimated Drosophila suzukii (Diptera: Drosophilidae) adults

Treesearch

A.R. Stephens; M.K. Asplen; W.D. Hutchison; Robert C. Venette

2015-01-01

Drosophila suzukii Matsumura, often called spotted wing drosophila, is an exotic vinegar fly that is native to Southeast Asia and was first detected in the continental United States in 2008. Previous modeling studies have suggested that D. suzukii might not survive in portions of the northern United States or southern Canada...
Free energy landscapes for initiation and branching of protein aggregation.

PubMed

Zheng, Weihua; Schafer, Nicholas P; Wolynes, Peter G

2013-12-17

Experiments on artificial multidomain protein constructs have probed the early stages of aggregation processes, but structural details of the species that initiate aggregation remain elusive. Using the associative-memory, water-mediated, structure and energy model known as AWSEM, a transferable coarse-grained protein model, we performed simulations of fused constructs composed of up to four copies of the Titin I27 domain or its mutant I27* (I59E). Free energy calculations enable us to quantify the conditions under which such multidomain constructs will spontaneously misfold. Consistent with experimental results, the dimer of I27 is found to be the smallest spontaneously misfolding construct. Our results show how structurally distinct misfolded states can be stabilized under different thermodynamic conditions, and this result provides a plausible link between the single-molecule misfolding experiments under native conditions and aggregation experiments under denaturing conditions. The conditions for spontaneous misfolding are determined by the interplay among temperature, effective local protein concentration, and the strength of the interdomain interactions. Above the folding temperature, fusing additional domains to the monomer destabilizes the native state, and the entropically stabilized amyloid-like state is favored. Because it is primarily energetically stabilized, the domain-swapped state is more likely to be important under native conditions. Both protofibril-like and branching structures are found in annealing simulations starting from extended structures, and these structures suggest a possible connection between the existence of multiple amyloidogenic segments in each domain and the formation of branched, amorphous aggregates as opposed to linear fibrillar structures.
The individual structures of native celluloses

Treesearch

R. H. Atalla

1999-01-01

Our understanding of the diversity of native celluloses has been limited by the fact that studies of their structures have sought to establish ideal crystal lattice forms for the native state. Departures from ideal structures in the native state are viewed as defects in the ideal lattice. In most instances real celluloses have been regarded as departing from the ideal...
The State of Native American Youth Health.

ERIC Educational Resources Information Center

Minnesota Univ., Minneapolis. Div. of General Pediatrics and Adolescent Health.

This survey on the health status of Native American adolescents living on or near reservations was completed by 14,000 American Indian and Alaska Native youths from 50 tribes attending 200 schools in 12 states. Results indicate that most Native teenagers felt their family cared about them a great deal, and many would go to a family member first…
Use of an Improved Matching Algorithm to Select Scaffolds for Enzyme Design Based on a Complex Active Site Model.

PubMed

Huang, Xiaoqiang; Xue, Jing; Lin, Min; Zhu, Yushan

2016-01-01

Active site preorganization helps native enzymes electrostatically stabilize the transition state better than the ground state for their primary substrates and achieve significant rate enhancement. In this report, we hypothesize that a complex active site model for active site preorganization modeling should help to create preorganized active site design and afford higher starting activities towards target reactions. Our matching algorithm ProdaMatch was improved by invoking effective pruning strategies and the native active sites for ten scaffolds in a benchmark test set were reproduced. The root-mean squared deviations between the matched transition states and those in the crystal structures were < 1.0 Å for the ten scaffolds, and the repacking calculation results showed that 91% of the hydrogen bonds within the active sites are recovered, indicating that the active sites can be preorganized based on the predicted positions of transition states. The application of the complex active site model for de novo enzyme design was evaluated by scaffold selection using a classic catalytic triad motif for the hydrolysis of p-nitrophenyl acetate. Eighty scaffolds were identified from a scaffold library with 1,491 proteins and four scaffolds were native esterase. Furthermore, enzyme design for complicated substrates was investigated for the hydrolysis of cephalexin using scaffold selection based on two different catalytic motifs. Only three scaffolds were identified from the scaffold library by virtue of the classic catalytic triad-based motif. In contrast, 40 scaffolds were identified using a more flexible, but still preorganized catalytic motif, where one scaffold corresponded to the α-amino acid ester hydrolase that catalyzes the hydrolysis and synthesis of cephalexin. Thus, the complex active site modeling approach for de novo enzyme design with the aid of the improved ProdaMatch program is a promising approach for the creation of active sites with high catalytic efficiencies towards target reactions.

Use of an Improved Matching Algorithm to Select Scaffolds for Enzyme Design Based on a Complex Active Site Model

PubMed Central

Huang, Xiaoqiang; Xue, Jing; Lin, Min; Zhu, Yushan

2016-01-01

Active site preorganization helps native enzymes electrostatically stabilize the transition state better than the ground state for their primary substrates and achieve significant rate enhancement. In this report, we hypothesize that a complex active site model for active site preorganization modeling should help to create preorganized active site design and afford higher starting activities towards target reactions. Our matching algorithm ProdaMatch was improved by invoking effective pruning strategies and the native active sites for ten scaffolds in a benchmark test set were reproduced. The root-mean squared deviations between the matched transition states and those in the crystal structures were < 1.0 Å for the ten scaffolds, and the repacking calculation results showed that 91% of the hydrogen bonds within the active sites are recovered, indicating that the active sites can be preorganized based on the predicted positions of transition states. The application of the complex active site model for de novo enzyme design was evaluated by scaffold selection using a classic catalytic triad motif for the hydrolysis of p-nitrophenyl acetate. Eighty scaffolds were identified from a scaffold library with 1,491 proteins and four scaffolds were native esterase. Furthermore, enzyme design for complicated substrates was investigated for the hydrolysis of cephalexin using scaffold selection based on two different catalytic motifs. Only three scaffolds were identified from the scaffold library by virtue of the classic catalytic triad-based motif. In contrast, 40 scaffolds were identified using a more flexible, but still preorganized catalytic motif, where one scaffold corresponded to the α-amino acid ester hydrolase that catalyzes the hydrolysis and synthesis of cephalexin. Thus, the complex active site modeling approach for de novo enzyme design with the aid of the improved ProdaMatch program is a promising approach for the creation of active sites with high catalytic efficiencies towards target reactions. PMID:27243223
Conformation Types of Ubiquitin [M+8H]8+ Ions from Water:Methanol Solutions: Evidence for the N and A States in Aqueous Solution

PubMed Central

Shi, Huilin; Pierson, Nicholas A.; Valentine, Stephen J.; Clemmer, David E.

2012-01-01

Ion mobility and mass spectrometry measurements are used to examine the gas-phase populations of [M+8H]8+ ubiquitin ions formed upon electrospraying 20 different solutions: from 100:0 to 5:95 water:methanol that are maintained at pH = 2.0. Over this range of solution conditions, mobility distributions for the +8 charge state show substantial variations. Here we develop a model that treats the combined measurements as one data set. By varying the relative abundances of a discrete set of conformation types, it is possible to represent distributions obtained from any solution. For solutions that favor the well-known A-state ubiquitin, it is possible to represent the gas-phase distributions with seven conformation types. Aqueous conditions that favor the native structure require four more structural types to represent the distribution. This analysis provides the first direct evidence for trace amounts of the A state under native conditions. The method of analysis presented here should help illuminate how solution populations evolve into new gas-phase structures as solvent is removed. Evidence for trace quantities of previously unknown states under native solution conditions may provide insight about the relationship of dynamics to protein function as well as misfolding and aggregation phenomena. PMID:22315998
Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations.

PubMed

Lei, Hongxing; Wu, Chun; Liu, Haiguang; Duan, Yong

2007-03-20

High-accuracy ab initio folding has remained an elusive objective despite decades of effort. To explore the folding landscape of villin headpiece subdomain HP35, we conducted two sets of replica exchange molecular dynamics for 200 ns each and three sets of conventional microsecond-long molecular dynamics simulations, using AMBER FF03 force field and a generalized-Born solvation model. The protein folded consistently to the native state; the lowest C(alpha)-rmsd from the x-ray structure was 0.46 A, and the C(alpha)- rmsd of the center of the most populated cluster was 1.78 A at 300 K. ab initio simulations have previously not reached this level. The folding landscape of HP35 can be partitioned into the native, denatured, and two intermediate-state regions. The native state is separated from the major folding intermediate state by a small barrier, whereas a large barrier exists between the major folding intermediate and the denatured states. The melting temperature T(m) = 339 K extracted from the heat-capacity profile was in close agreement with the experimentally derived T(m) = 342 K. A comprehensive picture of the kinetics and thermodynamics of HP35 folding emerges when the results from replica exchange and conventional molecular dynamics simulations are combined.
Biophysical and structural considerations for protein sequence evolution

PubMed Central

2011-01-01

Background Protein sequence evolution is constrained by the biophysics of folding and function, causing interdependence between interacting sites in the sequence. However, current site-independent models of sequence evolutions do not take this into account. Recent attempts to integrate the influence of structure and biophysics into phylogenetic models via statistical/informational approaches have not resulted in expected improvements in model performance. This suggests that further innovations are needed for progress in this field. Results Here we develop a coarse-grained physics-based model of protein folding and binding function, and compare it to a popular informational model. We find that both models violate the assumption of the native sequence being close to a thermodynamic optimum, causing directional selection away from the native state. Sampling and simulation show that the physics-based model is more specific for fold-defining interactions that vary less among residue type. The informational model diffuses further in sequence space with fewer barriers and tends to provide less support for an invariant sites model, although amino acid substitutions are generally conservative. Both approaches produce sequences with natural features like dN/dS < 1 and gamma-distributed rates across sites. Conclusions Simple coarse-grained models of protein folding can describe some natural features of evolving proteins but are currently not accurate enough to use in evolutionary inference. This is partly due to improper packing of the hydrophobic core. We suggest possible improvements on the representation of structure, folding energy, and binding function, as regards both native and non-native conformations, and describe a large number of possible applications for such a model. PMID:22171550
Ab initio folding of proteins using all-atom discrete molecular dynamics

PubMed Central

Ding, Feng; Tsao, Douglas; Nie, Huifen; Dokholyan, Nikolay V.

2008-01-01

Summary Discrete molecular dynamics (DMD) is a rapid sampling method used in protein folding and aggregation studies. Until now, DMD was used to perform simulations of simplified protein models in conjunction with structure-based force fields. Here, we develop an all-atom protein model and a transferable force field featuring packing, solvation, and environment-dependent hydrogen bond interactions. Using the replica exchange method, we perform folding simulations of six small proteins (20–60 residues) with distinct native structures. In all cases, native or near-native states are reached in simulations. For three small proteins, multiple folding transitions are observed and the computationally-characterized thermodynamics are in quantitative agreement with experiments. The predictive power of all-atom DMD highlights the importance of environment-dependent hydrogen bond interactions in modeling protein folding. The developed approach can be used for accurate and rapid sampling of conformational spaces of proteins and protein-protein complexes, and applied to protein engineering and design of protein-protein interactions. PMID:18611374
Stabilization of a metastable state of Torpedo californica acetylcholinesterase by chemical chaperones

PubMed Central

Millard, Charles B.; Shnyrov, Valery L.; Newstead, Simon; Shin, Irina; Roth, Esther; Silman, Israel; Weiner, Lev

2003-01-01

Chemical modification of Torpedo californica acetylcholinesterase by the natural thiosulfinate allicin produces an inactive enzyme through reaction with the buried cysteine Cys 231. Optical spectroscopy shows that the modified enzyme is “native-like,” and inactivation can be reversed by exposure to reduced glutathione. The allicin-modified enzyme is, however, metastable, and is converted spontaneously and irreversibly, at room temperature, with t1/2 ≃ 100 min, to a stable, partially unfolded state with the physicochemical characteristics of a molten globule. Osmolytes, including trimethylamine-N-oxide, glycerol, and sucrose, and the divalent cations, Ca2+, Mg2+, and Mn2+ can prevent this transition of the native-like state for >24 h at room temperature. Trimethylamine-N-oxide and Mg2+ can also stabilize the native enzyme, with only slight inactivation being observed over several hours at 39°C, whereas in their absence it is totally inactivated within 5 min. The stabilizing effects of the osmolytes can be explained by their differential interaction with the native and native-like states, resulting in a shift of equilibrium toward the native state. The stabilizing effects of the divalent cations can be ascribed to direct stabilization of the native state, as supported by differential scanning calorimetry. PMID:14500892
78 FR 40696 - Honey From the People's Republic of China: Notice of Court Decision Not in Harmony With Final...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-08

... Zhejiang Native Produce & Animal By-Products Import & Export Corp. v. United States, Court No. 02-00057... Court Remand Zhejiang Native Produce & Animal By-Products Import & Export Corp., et al. v. United States... Zhejiang Native Produce & Animal By-Products Import & Export Corp., et al., v. United States, Results of...
Native Transformations in the Pacific Northwest: A strength-based model of protection against substance use disorder.

PubMed

Rasmus, Stacy; Allen, James; Connor, William; Freeman, William; Skewes, Monica

2016-01-01

This paper presents findings from the Native Transformations Project, an exploratory community-based participatory research study that aims to identify sources of strength and protection against substance use disorder in three tribal communities in the coastal Pacific Northwest. Preliminary results from the study describe the specific settings, acts, and behaviors that build strengths and provide protection at the family, community, individual, and spiritual levels within coastal Pacific Northwest local tribal cultures. Findings from this study give voice to stated community preferences for grassroots Native intervention programs based in local cultural knowledge, worldviews, values, and theories of change, that operate at the local level on their own terms.
NATIVE TRANSFORMATIONS IN THE PACIFIC NORTHWEST: A STRENGTH-BASED MODEL OF PROTECTION AGAINST SUBSTANCE USE DISORDER

PubMed Central

Rasmus, Stacy; Allen, James; Connor, William; Freeman, William; Skewes, Monica

2016-01-01

This paper presents findings from the Native Transformations Project, an exploratory community-based participatory research study that aims to identify sources of strength and protection against substance use disorder in three tribal communities in the coastal Pacific Northwest. Preliminary results from the study describe the specific settings, acts, and behaviors that build strengths and provide protection at the family, community, individual, and spiritual levels within coastal Pacific Northwest local tribal cultures. Findings from this study give voice to stated community preferences for grassroots Native intervention programs based in local cultural knowledge, worldviews, values, and theories of change, that operate at the local level on their own terms. PMID:27383091
High resolution approach to the native state ensemble kinetics and thermodynamics.

PubMed

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

2008-12-15

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

PubMed

Kuznetsov, Vyacheslav I; Haws, Spencer A; Fox, Catherine A; Denu, John M

2018-05-24

Biochemical, proteomic and epigenetic studies of chromatin rely on the efficient ability to isolate native nucleosomes in high yield and purity. However, isolation of native chromatin suitable for many downstream experiments remains a challenging task. This is especially true for the budding yeast Saccharomyces cerevisiae, which continues to serve as an important model organism for the study of chromatin structure and function. Here, we developed a time- and cost-efficient universal protocol for isolation of native chromatin fragments from yeast, insect, and mammalian cells. The resulting protocol preserves histone posttranslational modification in the native chromatin state, and is applicable for both parallel multi-sample spin-column purification and large scale isolation. This protocol is based on the efficient and stable purification of polynucleosomes, features a combination of optimized cell lysis and purification conditions, three options for chromatin fragmentation, and a novel ion-exchange chromatographic purification strategy. The procedure will aid chromatin researchers interested in isolating native chromatin material for biochemical studies, and as a mild, acid- and detergent-free sample preparation method for mass-spectrometry analysis. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.
Predicting invasiveness of species in trade: Climate match, trophic guild and fecundity influence establishment and impact of non-native freshwater fishes

USGS Publications Warehouse

Howeth, Jennifer G.; Gantz, Crysta A.; Angermeier, Paul; Frimpong, Emmanuel A.; Hoff, Michael H.; Keller, Reuben P.; Mandrak, Nicholas E.; Marchetti, Michael P.; Olden, Julian D.; Romagosa, Christina M.; Lodge, David M.

2016-01-01

AimImpacts of non-native species have motivated development of risk assessment tools for identifying introduced species likely to become invasive. Here, we develop trait-based models for the establishment and impact stages of freshwater fish invasion, and use them to screen non-native species common in international trade. We also determine which species in the aquarium, biological supply, live bait, live food and water garden trades are likely to become invasive. Results are compared to historical patterns of non-native fish establishment to assess the relative importance over time of pathways in causing invasions.LocationLaurentian Great Lakes region.MethodsTrait-based classification trees for the establishment and impact stages of invasion were developed from data on freshwater fish species that established or failed to establish in the Great Lakes. Fishes in trade were determined from import data from Canadian and United States regulatory agencies, assigned to specific trades and screened through the developed models.ResultsClimate match between a species’ native range and the Great Lakes region predicted establishment success with 75–81% accuracy. Trophic guild and fecundity predicted potential harmful impacts of established non-native fishes with 75–83% accuracy. Screening outcomes suggest the water garden trade poses the greatest risk of introducing new invasive species, followed by the live food and aquarium trades. Analysis of historical patterns of introduction pathways demonstrates the increasing importance of these trades relative to other pathways. Comparisons among trades reveal that model predictions parallel historical patterns; all fishes previously introduced from the water garden trade have established. The live bait, biological supply, aquarium and live food trades have also contributed established non-native fishes.Main conclusionsOur models predict invasion risk of potential fish invaders to the Great Lakes region and could help managers prioritize efforts among species and pathways to minimize such risk. Similar approaches could be applied to other taxonomic groups and geographic regions.
A macro-level fetal alcohol syndrome prevention program for Native Americans and Alaska Natives: description and evaluation.

PubMed

May, P A; Hymbaugh, K J

1989-11-01

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

PubMed Central

Uversky, Vladimir N.

2009-01-01

Aggregation and subsequent development of protein deposition diseases originate from conformational changes in corresponding amyloidogenic proteins. The accumulated data support the model where protein fibrillogenesis proceeds via the formation of a relatively unfolded amyloidogenic conformation, which shares many structural properties with the pre-molten globule state, a partially folded intermediate first found during the equilibrium and kinetic (un)folding studies of several globular proteins and later described as one of the structural forms of natively unfolded proteins. The flexibility of this structural form is essential for the conformational rearrangements driving the formation of the core cross-beta structure of the amyloid fibril. Obviously, molecular mechanisms describing amyloidogenesis of ordered and natively unfolded proteins are different. For ordered protein to fibrillate, its unique and rigid structure has to be destabilized and partially unfolded. On the other hand, fibrillogenesis of a natively unfolded protein involves the formation of partially folded conformation; i.e., partial folding rather than unfolding. In this review recent findings are surveyed to illustrate some unique features of the natively unfolded proteins amyloidogenesis. PMID:18537543
Unfolding pathway of CotA-laccase and the role of copper on the prevention of refolding through aggregation of the unfolded state

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

Fernandes, Andre T.; Lopes, Carlos; Martins, Ligia O.

2012-06-08

Highlights: Black-Right-Pointing-Pointer CotA-laccase unfolds with an intermediate state. Black-Right-Pointing-Pointer Copper stabilizes the native and the intermediate state. Black-Right-Pointing-Pointer Copper binding to the unfolded state prevents refolding through protein aggregation. Black-Right-Pointing-Pointer Copper incorporation in CotA-laccase occurs as a later step during folding. -- Abstract: Copper is a redox-active metal and the main player in electron transfer reactions occurring in multicopper oxidases. The role of copper in the unfolding pathway and refolding of the multicopper oxidase CotA laccase in vitro was solved using double-jump stopped-flow experiments. Unfolding of apo- and holo-CotA was described as a three-state process with accumulation of an intermediatemore » in between the native and unfolded state. Copper stabilizes the native holo-CotA but also the intermediate state showing that copper is still bound to this state. Also, copper binds to unfolded holo-CotA in a non-native coordination promoting CotA aggregation and preventing refolding to the native structure. These results gather information on unfolding/folding pathways of multicopper oxidases and show that copper incorporation in vivo should be a tight controlled process as copper binding to the unfolded state under native conditions promotes protein aggregation.« less
Native Prairie Adaptive Management: a multi region adaptive approach to invasive plant management on Fish and Wildlife Service owned native prairies

USGS Publications Warehouse

Gannon, Jill J.; Shaffer, Terry L.; Moore, Clinton T.

2013-01-01

Much of the native prairie managed by the U.S. Fish and Wildlife Service (FWS) in the Prairie Pothole Region (PPR) of the northern Great Plains is extensively invaded by the introduced cool-season grasses, smooth brome (Bromus inermis) and Kentucky bluegrass (Poa pratensis). Management to suppress these invasive plants has had poor to inconsistent success. The central challenge to managers is selecting appropriate management actions in the face of biological and environmental uncertainties. In partnership with the FWS, the U.S. Geological Survey (USGS) developed an adaptive decision support framework to assist managers in selecting management actions under uncertainty and maximizing learning from management outcomes. This joint partnership is known as the Native Prairie Adaptive Management (NPAM) initiative. The NPAM decision framework is built around practical constraints faced by FWS refuge managers and includes identification of the management objective and strategies, analysis of uncertainty and construction of competing decision models, monitoring, and mechanisms for model feedback and decision selection. Nineteen FWS field stations, spanning four states of the PPR, have participated in the initiative. These FWS cooperators share a common management objective, available management strategies, and biological uncertainties. Though the scope is broad, the initiative interfaces with individual land managers who provide site-specific information and receive updated decision guidance that incorporates understanding gained from the collective experience of all cooperators. We describe the technical components of this approach, how the components integrate and inform each other, how data feedback from individual cooperators serves to reduce uncertainty across the whole region, and how a successful adaptive management project is coordinated and maintained on a large scale. During an initial scoping workshop, FWS cooperators developed a consensus management objective: increase the composition of native grasses and forbs on native sod while minimizing cost. Cooperators agreed that decision guidance should be provided annually and should account for local, real-time vegetation conditions observed on the ground. Over the course of development, two prototypes of the decision framework were considered. The final framework recognized four alternative actions that managers could take in any given year: (1) Graze—targeted use of grazing ungulates to achieve defoliation, (2) Burn—application of prescribed fire as the single form of defoliation, (3) Burn/Graze—a combination treatment, and (4) Rest—no action. The study area included northern mixed-grass and tallgrass prairie. Native vegetation in mixed–grass prairie has a strong cool-season component and thus the dominant native species have a phenology similar to that of smooth brome and Kentucky bluegrass, making management of those species challenging. In contrast, tallgrass prairie has a strong warm-season native component, leading to an existence of cool-season windows, periods of time in the fall and spring when cool‐season invasive grass species are actively growing and vulnerable to damage via select management actions, but warm‐season grass species are not active and are thus less susceptible to damage via the same actions. This dichotomy between prairie types necessitated the development of separate but parallel decision support systems for mixed-grass and tallgrass biomes. Management units are parcels of native prairie that receive a single management treatment at any one time over their entire extent. At any particular time, the vegetation state of each management unit is characterized by the amount of cover of native grasses and forbs and the type of invasive grass that is dominant. In addition, each unit has a defoliation state which reflects the number of years since the last defoliation event and an index to how intensively the unit was managed during the previous 7 years. State-transition models are used to predict the state of a management unit in year t+1 from its state in year t and a prescribed management action that was applied between the two monitoring events. Alternative models are built around key uncertainties that make choice of a management action difficult. Three uncertainties revolve around whether the effect of management actions depends on (1) type of dominant invader, (2) past defoliation history, and (3) level of invasion. Two additional uncertainties are considered when choosing a management action for tallgrass units: (4) the effectiveness of grazing within the cool-season window as a surrogate for burning when smooth brome is the dominant invader, and (5) the differential effect of active management outside the window as compared to rest. Because data on the probability of transitioning from one state to another under the various models were lacking, expert opinion and elicitation were used to parameterize the models. In addition, cooperators participated in elicitation exercises to extract their beliefs regarding the value of having native prairie compared to the cost of achieving it. Quantifying the subjective expression of utility in this way allowed for mathematical representation of the management objective into an objective function. By maximizing the objective function, cumulative utility is maximized, leading to the identification of a sequence of decisions that will achieve the management objective. The NPAM system adopted a vegetation monitoring protocol that was rapid, inexpensive, and familiar to many of the cooperators. The monitoring protocol served three purposes: (1) determining current vegetation and defoliation states of each unit, (2) evaluating progress toward the management objective, and (3) assessing predictive performance of the alternative models. The management year runs from September 1 to August 31. Management can be applied anytime during that period and monitoring takes places from late June to mid-August. Cooperators enter vegetation data and management information into a centralized database by August 25 of each year. Given the current state of the system (vegetation and defoliation states) and the current understanding of the system (or the belief state), identifying the current best management decision is a matter of looking up the combination (that is, system state and belief state) in the appropriate (mixed-grass or tallgrass) optimal decision table. Given complete uncertainty at the outset of decision-making, initial assignment of equal belief weights to each model was believed reasonable. The decisions in the optimal decision table that correspond to the current belief state constitute the current optimal decision policy. By August 31 of each year, individual cooperators are provided with a recommended management action for each of their management units for the upcoming management year. Upon receiving the management recommendations for their units, managers consider the recommendation, along with other relevant information, and at some point during the year one of the management alternatives is carried out. This iterative cycle of making and implementing a management decision, predicting the response, monitoring the outcome, comparing predicted and observed outcomes, updating model weights, and recommending a management action for the next cycle is expected to result in an accumulation of weight on a representative model of system dynamics, thereby increasing understanding needed to effectively manage native prairies. The NPAM system is now entering its second full year of complete operation, and represents one of only a few fully implemented applications of adaptive management within the U.S. Fish and Wildlife Service. NPAM is truly unique in that it originated from the ground up as a result of the leadership and steadfastness of several refuge biologists and managers confronted with a common problem. These biologists recognized that working together across a large landscape presented perhaps the best opportunity for halting and reversing the invasion of native grasslands by non-native cool-season grasses. Importantly, the NPAM system encapsulates the collective thinking and experience of tens if not hundreds of individuals who have battled this vexing problem for much of their careers. The NPAM initiative is rooted in principles of adaptive management, thereby affording the opportunity for grassland managers to pursue management objectives while acquiring information to reduce uncertainty and improve future management. The project introduced a number of technical innovations that will serve as templates for conservation efforts throughout and beyond the U.S. Fish and Wildlife Service. First, NPAM is an on-the-ground implementation of active adaptive management—possibly the first of its kind in conservation management—in which recommended management actions result from a prospective analysis of future learning (Williams, 1996). Second, by the use of dynamic optimization, NPAM demonstrates how decisions can be made that take into account possible future transitions of the system. Third, NPAM demonstrates how models of partial controllability are an effective means of accommodating unpredictable circumstances that cause a manager to follow a different course than was intended. Finally, the database developed for NPAM is an unparalleled system that enables the rapid integration of data from the field for the generation of ‘just-in-time’ management recommendations. In all, NPAM provides an example of how a science-management partnership can be forged to achieve large-scale conservation objectives.
A study of the native cell wall structures of the marine alga Ventricaria ventricosa (Siphonocladales, Chlorophyceae) using atomic force microscopy.

PubMed

Eslick, Enid M; Beilby, Mary J; Moon, Anthony R

2014-04-01

A substantial proportion of the architecture of the plant cell wall remains unknown with a few cell wall models being proposed. Moreover, even less is known about the green algal cell wall. Techniques that allow direct visualization of the cell wall in as near to its native state are of importance in unravelling the spatial arrangement of cell wall structures and hence in the development of cell wall models. Atomic force microscopy (AFM) was used to image the native cell wall of living cells of Ventricaria ventricosa (V. ventricosa) at high resolution under physiological conditions. The cell wall polymers were identified mainly qualitatively via their structural appearance. The cellulose microfibrils (CMFs) were easily recognizable and the imaging results indicate that the V. ventricosa cell wall has a cross-fibrillar structure throughout. We found the native wall to be abundant in matrix polysaccharides existing in different curing states. The soft phase matrix polysaccharides susceptible by the AFM scanning tip existed as a glutinous fibrillar meshwork, possibly incorporating both the pectic- and hemicellulosic-type substances. The hard phase matrix producing clearer images, revealed coiled fibrillar structures associated with CMFs, sometimes being resolved as globular structures by the AFM tip. The coiling fibrillar structures were also seen in the images of isolated cell wall fragments. The mucilaginous component of the wall was discernible from the gelatinous cell wall matrix as it formed microstructural domains over the surface. AFM has been successful in imaging the native cell wall and revealing novel findings such as the 'coiling fibrillar structures' and cell wall components which have previously not been seen, that is, the gelatinous matrix phase.
Diversity, distribution, and conservation status of the native freshwater fishes of the Southern United States

Treesearch

Melvin L. Warren; Brooks M. Burr; Stephen J. Walsh; Henry L. Bart; Robert C. Cashner; David A. Etnier; Byron J. Freeman; Bernard R. Kuhajda; Richard L. Mayden; Henry W. Robison; Stephen T. Ross; Wayne C. Starnes

2000-01-01

The Southeastern Fishes Council Technical Advisory Committee reviewed the diversity, distribution, and status of all native freshwater and diadromous fishes across 51 major drainage units of the Southern United States. The Southern United States supports more native fishes than any area of comparable size on the North American continent north of Mexico, but also has a...
Kinetic Aspects of Surfactant-Induced Structural Changes of Proteins - Unsolved Problems of Two-State Model for Protein Denaturation -.

PubMed

Takeda, Kunio; Moriyama, Yoshiko

2015-01-01

The kinetic mechanism of surfactant-induced protein denaturation is discussed on the basis of not only stopped-flow kinetic data but also the changes of protein helicities caused by the surfactants and the discontinuous mobility changes of surfactant-protein complexes. For example, the α-helical structures of bovine serum albumin (BSA) are partially disrupted due to the addition of sodium dodecyl sulfate (SDS). Formation of SDS-BSA complex can lead to only four complex types with specific mobilities depending on the surfactant concentration. On the other hand, the apparent rate constant of the structural change of BSA increases with an increase of SDS concentration, indicating that the rate of the structural change becomes fast as the degree of the change increases. When a certain amount of surfactant ions bind to proteins, their native structures transform directly to particular structures without passing through intermediate stages that might be induced due to the binding of fewer amounts of the surfactant ions. Furthermore, this review brings up a question about two-state and three-state models, N⇌D and N⇌D'⇌D (N: native state, D: denatured sate, D': intermediate between N and D), which have been often adopted without hesitation in discussion on general denaturations of proteins. First of all, doubtful is whether any equilibrium relationship exists in such denaturation reactions. It cannot be disregarded that the D states in these models differ depending on the changes of intensities of the denaturing factors. The authors emphasize that the denaturations or the structural changes of proteins should be discussed assuming one-way reaction models with no backward processes rather than assuming the reversible two-state reaction models or similar modified reaction models.
Free energy landscape of protein folding in water: explicit vs. implicit solvent.

PubMed

Zhou, Ruhong

2003-11-01

The Generalized Born (GB) continuum solvent model is arguably the most widely used implicit solvent model in protein folding and protein structure prediction simulations; however, it still remains an open question on how well the model behaves in these large-scale simulations. The current study uses the beta-hairpin from C-terminus of protein G as an example to explore the folding free energy landscape with various GB models, and the results are compared to the explicit solvent simulations and experiments. All free energy landscapes are obtained from extensive conformation space sampling with a highly parallel replica exchange method. Because solvation model parameters are strongly coupled with force fields, five different force field/solvation model combinations are examined and compared in this study, namely the explicit solvent model: OPLSAA/SPC model, and the implicit solvent models: OPLSAA/SGB (Surface GB), AMBER94/GBSA (GB with Solvent Accessible Surface Area), AMBER96/GBSA, and AMBER99/GBSA. Surprisingly, we find that the free energy landscapes from implicit solvent models are quite different from that of the explicit solvent model. Except for AMBER96/GBSA, all other implicit solvent models find the lowest free energy state not the native state. All implicit solvent models show erroneous salt-bridge effects between charged residues, particularly in OPLSAA/SGB model, where the overly strong salt-bridge effect results in an overweighting of a non-native structure with one hydrophobic residue F52 expelled from the hydrophobic core in order to make better salt bridges. On the other hand, both AMBER94/GBSA and AMBER99/GBSA models turn the beta-hairpin in to an alpha-helix, and the alpha-helical content is much higher than the previously reported alpha-helices in an explicit solvent simulation with AMBER94 (AMBER94/TIP3P). Only AMBER96/GBSA shows a reasonable free energy landscape with the lowest free energy structure the native one despite an erroneous salt-bridge between D47 and K50. Detailed results on free energy contour maps, lowest free energy structures, distribution of native contacts, alpha-helical content during the folding process, NOE comparison with NMR, and temperature dependences are reported and discussed for all five models. Copyright 2003 Wiley-Liss, Inc.

Membrane protein stability can be compromised by detergent interactions with the extramembranous soluble domains

PubMed Central

Yang, Zhengrong; Wang, Chi; Zhou, Qingxian; An, Jianli; Hildebrandt, Ellen; Aleksandrov, Luba A; Kappes, John C; DeLucas, Lawrence J; Riordan, John R; Urbatsch, Ina L; Hunt, John F; Brouillette, Christie G

2014-01-01

Detergent interaction with extramembranous soluble domains (ESDs) is not commonly considered an important determinant of integral membrane protein (IMP) behavior during purification and crystallization, even though ESDs contribute to the stability of many IMPs. Here we demonstrate that some generally nondenaturing detergents critically destabilize a model ESD, the first nucleotide-binding domain (NBD1) from the human cystic fibrosis transmembrane conductance regulator (CFTR), a model IMP. Notably, the detergents show equivalent trends in their influence on the stability of isolated NBD1 and full-length CFTR. We used differential scanning calorimetry (DSC) and circular dichroism (CD) spectroscopy to monitor changes in NBD1 stability and secondary structure, respectively, during titration with a series of detergents. Their effective harshness in these assays mirrors that widely accepted for their interaction with IMPs, i.e., anionic > zwitterionic > nonionic. It is noteworthy that including lipids or nonionic detergents is shown to mitigate detergent harshness, as will limiting contact time. We infer three thermodynamic mechanisms from the observed thermal destabilization by monomer or micelle: (i) binding to the unfolded state with no change in the native structure (all detergent classes); (ii) native state binding that alters thermodynamic properties and perhaps conformation (nonionic detergents); and (iii) detergent binding that directly leads to denaturation of the native state (anionic and zwitterionic). These results demonstrate that the accepted model for the harshness of detergents applies to their interaction with an ESD. It is concluded that destabilization of extramembranous soluble domains by specific detergents will influence the stability of some IMPs during purification. PMID:24652590
Economic Impacts of Non-Native Forest Insects in the Continental United States

PubMed Central

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

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 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. PMID:21931766
Clonal dynamics of native haematopoiesis

PubMed Central

Sun, Jianlong; Ramos, Azucena; Chapman, Brad; Johnnidis, Jonathan B.; Le, Linda; Ho, Yu-Jui; Klein, Allon; Hofmann, Oliver; Camargo, Fernando D.

2015-01-01

It is currently thought that life-long blood cell production is driven by the action of a small number of multipotent haematopoietic stem cells. Evidence supporting this view has been largely acquired through the use of functional assays involving transplantation. However, whether these mechanisms also govern native non-transplant haematopoiesis is entirely unclear. Here we have established a novel experimental model in mice where cells can be uniquely and genetically labelled in situ to address this question. Using this approach, we have performed longitudinal analyses of clonal dynamics in adult mice that reveal unprecedented features of native haematopoiesis. In contrast to what occurs following transplantation, steady-state blood production is maintained by the successive recruitment of thousands of clones, each with a minimal contribution to mature progeny. Our results demonstrate that a large number of long-lived progenitors, rather than classically defined haematopoietic stem cells, are the main drivers of steady-state haematopoiesis during most of adulthood. Our results also have implications for understanding the cellular origin of haematopoietic disease. PMID:25296256
Clonal dynamics of native haematopoiesis.

PubMed

Sun, Jianlong; Ramos, Azucena; Chapman, Brad; Johnnidis, Jonathan B; Le, Linda; Ho, Yu-Jui; Klein, Allon; Hofmann, Oliver; Camargo, Fernando D

2014-10-16

It is currently thought that life-long blood cell production is driven by the action of a small number of multipotent haematopoietic stem cells. Evidence supporting this view has been largely acquired through the use of functional assays involving transplantation. However, whether these mechanisms also govern native non-transplant haematopoiesis is entirely unclear. Here we have established a novel experimental model in mice where cells can be uniquely and genetically labelled in situ to address this question. Using this approach, we have performed longitudinal analyses of clonal dynamics in adult mice that reveal unprecedented features of native haematopoiesis. In contrast to what occurs following transplantation, steady-state blood production is maintained by the successive recruitment of thousands of clones, each with a minimal contribution to mature progeny. Our results demonstrate that a large number of long-lived progenitors, rather than classically defined haematopoietic stem cells, are the main drivers of steady-state haematopoiesis during most of adulthood. Our results also have implications for understanding the cellular origin of haematopoietic disease.
Rebuilding TRUST: A Community, Multi-Agency, State, and University Partnership to Improve Behavioral Health Care for American Indian Youth, their Families, and Communities

PubMed Central

Goodkind, Jessica R.; Ross-Toledo, Kimberly; John, Susie; Lee Hall, Janie; Ross, Lucille; Freeland, Lance; Colleta, Ernest; Becenti-Fundark, Twila

2014-01-01

American Indian/Alaska Native youth represent the strength and survival of many Nations and Tribes. However, the aftermath of colonialism has resulted in numerous health disparities and challenges for Native youth, including the highest rate of suicide in the United States. With the aims of elucidating the causes of behavioral health disparities, eliminating them, and improving behavioral health care for Native youth, a partnership of providers, community members, and university faculty and staff completed a comprehensive literature review; conducted advisory meetings with 71 American Indian youth, parents, and elders; surveyed 25 service providers; and engaged in ongoing consultation with traditional practitioners. Results from the multiple sources were synthesized and are reported with 20 policy, provider, and research recommendations that recognize the importance of moving beyond exclusive reliance on western models of care and that seek to foster transformation of individuals, families, communities, behavioral health service systems of care, and social structures. PMID:25076801
A flexible Bayesian hierarchical model of preterm birth risk among US Hispanic subgroups in relation to maternal nativity and education

PubMed Central

2011-01-01

Background Previous research has documented heterogeneity in the effects of maternal education on adverse birth outcomes by nativity and Hispanic subgroup in the United States. In this article, we considered the risk of preterm birth (PTB) using 9 years of vital statistics birth data from New York City. We employed finer categorizations of exposure than used previously and estimated the risk dose-response across the range of education by nativity and ethnicity. Methods Using Bayesian random effects logistic regression models with restricted quadratic spline terms for years of completed maternal education, we calculated and plotted the estimated posterior probabilities of PTB (gestational age < 37 weeks) for each year of education by ethnic and nativity subgroups adjusted for only maternal age, as well as with more extensive covariate adjustments. We then estimated the posterior risk difference between native and foreign born mothers by ethnicity over the continuous range of education exposures. Results The risk of PTB varied substantially by education, nativity and ethnicity. Native born groups showed higher absolute risk of PTB and declining risk associated with higher levels of education beyond about 10 years, as did foreign-born Puerto Ricans. For most other foreign born groups, however, risk of PTB was flatter across the education range. For Mexicans, Central Americans, Dominicans, South Americans and "Others", the protective effect of foreign birth diminished progressively across the educational range. Only for Puerto Ricans was there no nativity advantage for the foreign born, although small numbers of foreign born Cubans limited precision of estimates for that group. Conclusions Using flexible Bayesian regression models with random effects allowed us to estimate absolute risks without strong modeling assumptions. Risk comparisons for any sub-groups at any exposure level were simple to calculate. Shrinkage of posterior estimates through the use of random effects allowed for finer categorization of exposures without restricting joint effects to follow a fixed parametric scale. Although foreign born Hispanic women with the least education appeared to generally have low risk, this seems likely to be a marker for unmeasured environmental and behavioral factors, rather than a causally protective effect of low education itself. PMID:21504612
A flexible Bayesian hierarchical model of preterm birth risk among US Hispanic subgroups in relation to maternal nativity and education.

PubMed

Kaufman, Jay S; MacLehose, Richard F; Torrone, Elizabeth A; Savitz, David A

2011-04-19

Previous research has documented heterogeneity in the effects of maternal education on adverse birth outcomes by nativity and Hispanic subgroup in the United States. In this article, we considered the risk of preterm birth (PTB) using 9 years of vital statistics birth data from New York City. We employed finer categorizations of exposure than used previously and estimated the risk dose-response across the range of education by nativity and ethnicity. Using Bayesian random effects logistic regression models with restricted quadratic spline terms for years of completed maternal education, we calculated and plotted the estimated posterior probabilities of PTB (gestational age < 37 weeks) for each year of education by ethnic and nativity subgroups adjusted for only maternal age, as well as with more extensive covariate adjustments. We then estimated the posterior risk difference between native and foreign born mothers by ethnicity over the continuous range of education exposures. The risk of PTB varied substantially by education, nativity and ethnicity. Native born groups showed higher absolute risk of PTB and declining risk associated with higher levels of education beyond about 10 years, as did foreign-born Puerto Ricans. For most other foreign born groups, however, risk of PTB was flatter across the education range. For Mexicans, Central Americans, Dominicans, South Americans and "Others", the protective effect of foreign birth diminished progressively across the educational range. Only for Puerto Ricans was there no nativity advantage for the foreign born, although small numbers of foreign born Cubans limited precision of estimates for that group. Using flexible Bayesian regression models with random effects allowed us to estimate absolute risks without strong modeling assumptions. Risk comparisons for any sub-groups at any exposure level were simple to calculate. Shrinkage of posterior estimates through the use of random effects allowed for finer categorization of exposures without restricting joint effects to follow a fixed parametric scale. Although foreign born Hispanic women with the least education appeared to generally have low risk, this seems likely to be a marker for unmeasured environmental and behavioral factors, rather than a causally protective effect of low education itself.
Controlling protein molecular dynamics: How to accelerate folding while preserving the native state

NASA Astrophysics Data System (ADS)

Jensen, Christian H.; Nerukh, Dmitry; Glen, Robert C.

2008-12-01

The dynamics of peptides and proteins generated by classical molecular dynamics (MD) is described by using a Markov model. The model is built by clustering the trajectory into conformational states and estimating transition probabilities between the states. Assuming that it is possible to influence the dynamics of the system by varying simulation parameters, we show how to use the Markov model to determine the parameter values that preserve the folded state of the protein and at the same time, reduce the folding time in the simulation. We investigate this by applying the method to two systems. The first system is an imaginary peptide described by given transition probabilities with a total folding time of 1μs. We find that only small changes in the transition probabilities are needed to accelerate (or decelerate) the folding. This implies that folding times for slowly folding peptides and proteins calculated using MD cannot be meaningfully compared to experimental results. The second system is a four residue peptide valine-proline-alanine-leucine in water. We control the dynamics of the transitions by varying the temperature and the atom masses. The simulation results show that it is possible to find the combinations of parameter values that accelerate the dynamics and at the same time preserve the native state of the peptide. A method for accelerating larger systems without performing simulations for the whole folding process is outlined.
An Exotic Species Is the Favorite Prey of a Native Enemy

PubMed Central

Li, Yiming; Ke, Zunwei; Wang, Supen; Smith, Geoffrey R.; Liu, Xuan

2011-01-01

Although native enemies in an exotic species' new range are considered to affect its ability to invade, few studies have evaluated predation pressures from native enemies on exotic species in their new range. The exotic prey naiveté hypothesis (EPNH) states that exotic species may be at a disadvantage because of its naïveté towards native enemies and, therefore, may suffer higher predation pressures from the enemy than native prey species. Corollaries of this hypothesis include the native enemy preferring exotic species over native species and the diet of the enemy being influenced by the abundance of the exotic species. We comprehensively tested this hypothesis using introduced North American bullfrogs (Lithobates catesbeianus, referred to as bullfrog), a native red-banded snake (Dinodon rufozonatum, the enemy) and four native anuran species in permanent still water bodies as a model system in Daishan, China. We investigated reciprocal recognition between snakes and anuran species (bullfrogs and three common native species) and the diet preference of the snakes for bullfrogs and the three species in laboratory experiments, and the diet preference and bullfrog density in the wild. Bullfrogs are naive to the snakes, but the native anurans are not. However, the snakes can identify bullfrogs as prey, and in fact, prefer bullfrogs over the native anurans in manipulative experiments with and without a control for body size and in the wild, indicating that bullfrogs are subjected to higher predation pressures from the snakes than the native species. The proportion of bullfrogs in the snakes' diet is positively correlated with the abundance of bullfrogs in the wild. Our results provide strong evidence for the EPNH. The results highlight the biological resistance of native enemies to naïve exotic species. PMID:21915306
An exotic species is the favorite prey of a native enemy.

PubMed

Li, Yiming; Ke, Zunwei; Wang, Supen; Smith, Geoffrey R; Liu, Xuan

2011-01-01

Although native enemies in an exotic species' new range are considered to affect its ability to invade, few studies have evaluated predation pressures from native enemies on exotic species in their new range. The exotic prey naiveté hypothesis (EPNH) states that exotic species may be at a disadvantage because of its naïveté towards native enemies and, therefore, may suffer higher predation pressures from the enemy than native prey species. Corollaries of this hypothesis include the native enemy preferring exotic species over native species and the diet of the enemy being influenced by the abundance of the exotic species. We comprehensively tested this hypothesis using introduced North American bullfrogs (Lithobates catesbeianus, referred to as bullfrog), a native red-banded snake (Dinodon rufozonatum, the enemy) and four native anuran species in permanent still water bodies as a model system in Daishan, China. We investigated reciprocal recognition between snakes and anuran species (bullfrogs and three common native species) and the diet preference of the snakes for bullfrogs and the three species in laboratory experiments, and the diet preference and bullfrog density in the wild. Bullfrogs are naive to the snakes, but the native anurans are not. However, the snakes can identify bullfrogs as prey, and in fact, prefer bullfrogs over the native anurans in manipulative experiments with and without a control for body size and in the wild, indicating that bullfrogs are subjected to higher predation pressures from the snakes than the native species. The proportion of bullfrogs in the snakes' diet is positively correlated with the abundance of bullfrogs in the wild. Our results provide strong evidence for the EPNH. The results highlight the biological resistance of native enemies to naïve exotic species.
Feature-based respiratory motion tracking in native fluoroscopic sequences for dynamic roadmaps during minimally invasive procedures in the thorax and abdomen

NASA Astrophysics Data System (ADS)

Wagner, Martin G.; Laeseke, Paul F.; Schubert, Tilman; Slagowski, Jordan M.; Speidel, Michael A.; Mistretta, Charles A.

2017-03-01

Fluoroscopic image guidance for minimally invasive procedures in the thorax and abdomen suffers from respiratory and cardiac motion, which can cause severe subtraction artifacts and inaccurate image guidance. This work proposes novel techniques for respiratory motion tracking in native fluoroscopic images as well as a model based estimation of vessel deformation. This would allow compensation for respiratory motion during the procedure and therefore simplify the workflow for minimally invasive procedures such as liver embolization. The method first establishes dynamic motion models for both the contrast-enhanced vasculature and curvilinear background features based on a native (non-contrast) and a contrast-enhanced image sequence acquired prior to device manipulation, under free breathing conditions. The model of vascular motion is generated by applying the diffeomorphic demons algorithm to an automatic segmentation of the subtraction sequence. The model of curvilinear background features is based on feature tracking in the native sequence. The two models establish the relationship between the respiratory state, which is inferred from curvilinear background features, and the vascular morphology during that same respiratory state. During subsequent fluoroscopy, curvilinear feature detection is applied to determine the appropriate vessel mask to display. The result is a dynamic motioncompensated vessel mask superimposed on the fluoroscopic image. Quantitative evaluation of the proposed methods was performed using a digital 4D CT-phantom (XCAT), which provides realistic human anatomy including sophisticated respiratory and cardiac motion models. Four groups of datasets were generated, where different parameters (cycle length, maximum diaphragm motion and maximum chest expansion) were modified within each image sequence. Each group contains 4 datasets consisting of the initial native and contrast enhanced sequences as well as a sequence, where the respiratory motion is tracked. The respiratory motion tracking error was between 1.00 % and 1.09 %. The estimated dynamic vessel masks yielded a Sørensen-Dice coefficient between 0.94 and 0.96. Finally, the accuracy of the vessel contours was measured in terms of the 99th percentile of the error, which ranged between 0.64 and 0.96 mm. The presented results show that the approach is feasible for respiratory motion tracking and compensation and could therefore considerably improve the workflow of minimally invasive procedures in the thorax and abdomen
The origin of consistent protein structure refinement from structural averaging.

PubMed

Park, Hahnbeom; DiMaio, Frank; Baker, David

2015-06-02

Recent studies have shown that explicit solvent molecular dynamics (MD) simulation followed by structural averaging can consistently improve protein structure models. We find that improvement upon averaging is not limited to explicit water MD simulation, as consistent improvements are also observed for more efficient implicit solvent MD or Monte Carlo minimization simulations. To determine the origin of these improvements, we examine the changes in model accuracy brought about by averaging at the individual residue level. We find that the improvement in model quality from averaging results from the superposition of two effects: a dampening of deviations from the correct structure in the least well modeled regions, and a reinforcement of consistent movements towards the correct structure in better modeled regions. These observations are consistent with an energy landscape model in which the magnitude of the energy gradient toward the native structure decreases with increasing distance from the native state. Copyright © 2015 Elsevier Ltd. All rights reserved.
78 FR 50103 - Notice of Inventory Completion: Colorado State University, Fort Collins, CO

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-16

... remains, in consultation with the appropriate Indian tribes or Native Hawaiian organizations, and has... or Native Hawaiian organizations. Representatives of any Indian tribe or Native Hawaiian organization... submit a written request to Colorado State University, Department of Anthropology. If no additional...
78 FR 59960 - Notice of Inventory Completion: Colorado State University, Fort Collins, CO

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-30

... remains, in consultation with the appropriate Indian tribes or Native Hawaiian organizations, and has... or Native Hawaiian organizations. Representatives of any Indian tribe or Native Hawaiian organization... submit a written request to Colorado State University, Department of Anthropology. If no additional...
The Dropout/Graduation Crisis among American Indian and Alaska Native Students: Failure to Respond Places the Future of Native Peoples at Risk

ERIC Educational Resources Information Center

Faircloth, Susan C.; Tippeconnic, John W., III

2010-01-01

This paper examines the graduation/dropout crisis among American Indian and Alaska Native students using data from the National Center for Education Statistics. Data from 2005 is drawn from the seven states with the highest percentage of American Indian and Alaska Native students as well as five states in the Pacific and Northwestern regions of…
Competition between protein folding and aggregation: A three-dimensional lattice-model simulation

NASA Astrophysics Data System (ADS)

Bratko, D.; Blanch, H. W.

2001-01-01

Aggregation of protein molecules resulting in the loss of biological activity and the formation of insoluble deposits represents a serious problem for the biotechnology and pharmaceutical industries and in medicine. Considerable experimental and theoretical efforts are being made in order to improve our understanding of, and ability to control, the process. In the present work, we describe a Monte Carlo study of a multichain system of coarse-grained model proteins akin to lattice models developed for simulations of protein folding. The model is designed to examine the competition between intramolecular interactions leading to the native protein structure, and intermolecular association, resulting in the formation of aggregates of misfolded chains. Interactions between the segments are described by a variation of the Go potential [N. Go and H. Abe, Biopolymers 20, 1013 (1981)] that extends the recognition between attracting types of segments to pairs on distinct chains. For the particular model we adopt, the global free energy minimum of a pair of protein molecules corresponds to a dimer of native proteins. When three or more molecules interact, clusters of misfolded chains can be more stable than aggregates of native folds. A considerable fraction of native structure, however, is preserved in these cases. Rates of conformational changes rapidly decrease with the size of the protein cluster. Within the timescale accessible to computer simulations, the folding-aggregation balance is strongly affected by kinetic considerations. Both the native form and aggregates can persist in metastable states, even if conditions such as temperature or concentration favor a transition to an alternative form. Refolding yield can be affected by the presence of an additional polymer species mimicking the function of a molecular chaperone.
Drivers of Non-Native Aquatic Species Invasions across the ...

EPA Pesticide Factsheets

Background/Question/Methods 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 a single taxa, missing the opportunity to observe and understand the drivers of macroscale invasion patterns at sub-continental or continental scales. Here we map the distribution of exotic freshwater species richness across the continental United States using publicly accessible species occurrence data (e.g GBIF) and investigate the role of human activity in driving macroscale patterns of aquatic invasion. Using a dasymetric model of human population density and a spatially explicit model of recreational freshwater fishing demand, we analyzed the effect of these metrics of human influence on non-native aquatic species richness at the watershed scale, while controlling for spatial and sampling bias. We also assessed the effects that a temporal mismatch between occurrence data (collected since 1815) and cross-sectional predictors (developed using 2010 data) may have on model fit. Results/Conclusions Our results indicated that non-native aquatic species richness exhibits a highly patchy distribution, with hotspots in the Northeast, Great Lakes, Florida, and human population centers on the Pacific coast. These richness patterns are correlated with population density, but are m
Using Local States To Drive the Sampling of Global Conformations in Proteins

PubMed Central

2016-01-01

Conformational changes associated with protein function often occur beyond the time scale currently accessible to unbiased molecular dynamics (MD) simulations, so that different approaches have been developed to accelerate their sampling. Here we investigate how the knowledge of backbone conformations preferentially adopted by protein fragments, as contained in precalculated libraries known as structural alphabets (SA), can be used to explore the landscape of protein conformations in MD simulations. We find that (a) enhancing the sampling of native local states in both metadynamics and steered MD simulations allows the recovery of global folded states in small proteins; (b) folded states can still be recovered when the amount of information on the native local states is reduced by using a low-resolution version of the SA, where states are clustered into macrostates; and (c) sequences of SA states derived from collections of structural motifs can be used to sample alternative conformations of preselected protein regions. The present findings have potential impact on several applications, ranging from protein model refinement to protein folding and design. PMID:26808351
Using Local States To Drive the Sampling of Global Conformations in Proteins.

PubMed

Pandini, Alessandro; Fornili, Arianna

2016-03-08

Conformational changes associated with protein function often occur beyond the time scale currently accessible to unbiased molecular dynamics (MD) simulations, so that different approaches have been developed to accelerate their sampling. Here we investigate how the knowledge of backbone conformations preferentially adopted by protein fragments, as contained in precalculated libraries known as structural alphabets (SA), can be used to explore the landscape of protein conformations in MD simulations. We find that (a) enhancing the sampling of native local states in both metadynamics and steered MD simulations allows the recovery of global folded states in small proteins; (b) folded states can still be recovered when the amount of information on the native local states is reduced by using a low-resolution version of the SA, where states are clustered into macrostates; and (c) sequences of SA states derived from collections of structural motifs can be used to sample alternative conformations of preselected protein regions. The present findings have potential impact on several applications, ranging from protein model refinement to protein folding and design.
Gifted Education for Native American Students: A State of Affairs.

ERIC Educational Resources Information Center

Knutson, Kari A.; McCarthy-Tucker, Sherri N.

Although Native American children are theoretically eligible for gifted programming, equality of opportunity does not exist. Arizona state data show that Native American students are underrepresented statewide and in 13 of 14 counties examined. Two issues related to this underrepresentation are the definition of "gifted" used for…

To express the policy of the United States regarding the United States relationship with Native Hawaiians, to provide a process for the reorganization of a Native Hawaiian government and the recognition by the United States of the Native Hawaiian government, and for other purposes.

THOMAS, 111th Congress

Rep. Abercrombie, Neil [D-HI-1

2009-02-04

House - 07/23/2009 Referred to the Subcommittee on the Constitution, Civil Rights, and Civil Liberties. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:
The Effect of Intensified Language Exposure on Accommodating Talker Variability.

PubMed

Antoniou, Mark; Wong, Patrick C M; Wang, Suiping

2015-06-01

This study systematically examined the role of intensified exposure to a second language on accommodating talker variability. English native listeners (n = 37) were compared with Mandarin listeners who had either lived in the United States for an extended period of time (n = 33) or had lived only in China (n = 44). Listeners responded to target words in an English word-monitoring task in which sequences of words were randomized. Half of the sequences were spoken by a single talker and the other half by multiple talkers. Mandarin listeners living in China were slower and less accurate than both English listeners and Mandarin listeners living in the United States. Mandarin listeners living in the United States were less accurate than English natives only in the more cognitively demanding mixed-talker condition. Mixed-talker speech affects processing in native and nonnative listeners alike, although the decrement is larger in nonnatives and further exaggerated in less proficient listeners. Language immersion improves listeners' ability to resolve talker variability, and this suggests that immersion may automatize nonnative processing, freeing cognitive resources that may play a crucial role in speech perception. These results lend support to the active control model of speech perception.
A virtual-system coupled multicanonical molecular dynamics simulation: Principles and applications to free-energy landscape of protein-protein interaction with an all-atom model in explicit solvent

NASA Astrophysics Data System (ADS)

Higo, Junichi; Umezawa, Koji; Nakamura, Haruki

2013-05-01

We propose a novel generalized ensemble method, a virtual-system coupled multicanonical molecular dynamics (V-McMD), to enhance conformational sampling of biomolecules expressed by an all-atom model in an explicit solvent. In this method, a virtual system, of which physical quantities can be set arbitrarily, is coupled with the biomolecular system, which is the target to be studied. This method was applied to a system of an Endothelin-1 derivative, KR-CSH-ET1, known to form an antisymmetric homodimer at room temperature. V-McMD was performed starting from a configuration in which two KR-CSH-ET1 molecules were mutually distant in an explicit solvent. The lowest free-energy state (the most thermally stable state) at room temperature coincides with the experimentally determined native complex structure. This state was separated to other non-native minor clusters by a free-energy barrier, although the barrier disappeared with elevated temperature. V-McMD produced a canonical ensemble faster than a conventional McMD method.
American Indian/Alaska Native Voices in the Model of Institutional Adaptation to Student Diversity

ERIC Educational Resources Information Center

Guillory, Raphael; Wolverton, Mimi; Appleton, Valerie

2008-01-01

Richardson and Skinner (1991) in their Model of Institutional Adaptation to Student Diversity (MIASD) assert that state higher education boards have significant influence on the degree to which institutions respond to student diversity. The purpose of the study (conducted in the 2001-2002 school year) reported in this article was to determine…
A New Paradigm for Diagnosing Contributions to Model Aerosol Forcing Error

NASA Astrophysics Data System (ADS)

Jones, A. L.; Feldman, D. R.; Freidenreich, S.; Paynter, D.; Ramaswamy, V.; Collins, W. D.; Pincus, R.

2017-12-01

A new paradigm in benchmark absorption-scattering radiative transfer is presented that enables both the globally averaged and spatially resolved testing of climate model radiation parameterizations in order to uncover persistent sources of biases in the aerosol instantaneous radiative effect (IRE). A proof of concept is demonstrated with the Geophysical Fluid Dynamics Laboratory AM4 and Community Earth System Model 1.2.2 climate models. Instead of prescribing atmospheric conditions and aerosols, as in prior intercomparisons, native snapshots of the atmospheric state and aerosol optical properties from the participating models are used as inputs to an accurate radiation solver to uncover model-relevant biases. These diagnostic results show that the models' aerosol IRE bias is of the same magnitude as the persistent range cited ( 1 W/m2) and also varies spatially and with intrinsic aerosol optical properties. The findings underscore the significance of native model error analysis and its dispositive ability to diagnose global biases, confirming its fundamental value for the Radiative Forcing Model Intercomparison Project.
A Comprehensive Look at Native American College Students in New York State for Academic Year 1990-91. Second Annual Report.

ERIC Educational Resources Information Center

New York State Education Dept., Albany. Native American Indian Education Unit.

This report describes a study of 451 Native American college students who received New York State Indian Aid for the academic year 1990-91. Data were collected from the New York State Native American Postsecondary Grant-in-Aid Program, which awarded about $430,000 in 1990-91 (compared to $493,000 in 1989-90). Participants came from all 10 of New…
Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations

NASA Astrophysics Data System (ADS)

Lei, Hongxing; Wu, Chun; Wang, Zhi-Xiang; Zhou, Yaoqi; Duan, Yong

2008-06-01

Reaching the native states of small proteins, a necessary step towards a comprehensive understanding of the folding mechanisms, has remained a tremendous challenge to ab initio protein folding simulations despite the extensive effort. In this work, the folding process of the B domain of protein A (BdpA) has been simulated by both conventional and replica exchange molecular dynamics using AMBER FF03 all-atom force field. Started from an extended chain, a total of 40 conventional (each to 1.0 μs) and two sets of replica exchange (each to 200.0 ns per replica) molecular dynamics simulations were performed with different generalized-Born solvation models and temperature control schemes. The improvements in both the force field and solvent model allowed successful simulations of the folding process to the native state as demonstrated by the 0.80 A˚ Cα root mean square deviation (RMSD) of the best folded structure. The most populated conformation was the native folded structure with a high population. This was a significant improvement over the 2.8 A˚ Cα RMSD of the best nativelike structures from previous ab initio folding studies on BdpA. To the best of our knowledge, our results demonstrate, for the first time, that ab initio simulations can reach the native state of BdpA. Consistent with experimental observations, including Φ-value analyses, formation of helix II/III hairpin was a crucial step that provides a template upon which helix I could form and the folding process could complete. Early formation of helix III was observed which is consistent with the experimental results of higher residual helical content of isolated helix III among the three helices. The calculated temperature-dependent profile and the melting temperature were in close agreement with the experimental results. The simulations further revealed that phenylalanine 31 may play critical to achieve the correct packing of the three helices which is consistent with the experimental observation. In addition to the mechanistic studies, an ab initio structure prediction was also conducted based on both the physical energy and a statistical potential. Based on the lowest physical energy, the predicted structure was 2.0 A˚ Cα RMSD away from the experimentally determined structure.
Evolutionary dynamics of nationalism and migration

NASA Astrophysics Data System (ADS)

Barreira da Silva Rocha, André

2013-08-01

I present a dynamic evolutionary game model to address the relation between nationalism against immigrants and assimilation of the latter into the host country culture. I assume a country composed of two different large polymorphic populations, one of native citizens and the other of immigrants. A native citizen may behave nationalistically or may welcome immigrants. Immigrants may have an interest in learning the host country language or not. Evolution is modeled using replicator dynamics (RD). I also account for the presence of an enclave of immigrants in the host country. In the RD, the latter represents the immigrants’ own population effect, which contribution to fitness is controlled using a parameter ρ, 0≤ρ≤1, that represents the enclave size. In line with the empirical literature on migration, the existence of an enclave of immigrants makes assimilation less likely to occur. For large values of ρ, complete assimilation may not occur even if immigrants and natives share very close cultures and norms. Government policy regarding nationalism is modeled both exogenously and endogenously. A single or multiple asymptotically stable states exist for all cases studied but one in which the dynamics is similar to that found in the predator-prey model of Lotka-Volterra for competing species.
76 FR 12742 - Proposed Information Collection Activity; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-08

... Services: Grants to State; Native American Tribes and Alaskan Native Villages, and State Domestic Violence..., Tribes--and Tribal Organizations, and State Domestic Violence Coalitions for family violence prevention... Grant Application 53 1 10 530 Tribal Grant Application 200 1 5 1,000 State Domestic Violence Coalition...
Listen! Native Radio Can Save Languages.

ERIC Educational Resources Information Center

Martin, Kallen

1996-01-01

In the United States and Canada, the number of radio stations operated by Native Americans has greatly increased in recent years, as have the amount of programming in native languages and the number of native language instructional programs. Such programming can play a role in maintaining vigorous native languages and revitalizing endangered…
Pilot test of a cervical cancer prevention video developed for Alaska Native women.

PubMed Central

Stillwater, B; Echavarria, V A; Lanier, A P

1995-01-01

Cancer of the cervix is twice as likely to occur among Alaska Native women than among Caucasian women in the United State. To understand some of the factors associated with this high incidence, a random sample of 528 Alaska Native women were surveyed about their knowledge, attitudes, and behavior regarding cervical cancer and its risk factors. From the results of the Alaska Native Women's Health Project study, the need for more public education related to cervical cancer prevention was identified. A review of existing educational resources revealed that no culturally appropriate materials related to cervical cancer had been developed for Alaska Native women. To increase Native women's knowledge about cervical cancer and to motivate them to obtain annual Papanicolaou tests, a 12-minute videotape presentation was developed specifically for this population. The videotape portrayed Alaska Native women as role models from the community discussing cervical cancer and Papanicolaou tests and engaging in healthy lifestyles. The videotape was pilot tested with several groups of Alaska Native women. The women were surveyed before and after watching the video and were asked to rate the tape and make comments about it. The results of the posttest demonstrated a significant increase in the knowledge level of the participants. The videotape was well received because of its cultural sensitivity and appropriateness. On the basis of this study, the development of additional culturally appropriate educational materials related to cancer prevention of Alaska Native women is recommended. Images p213-a PMID:7631000
Systematic optimization model and algorithm for binding sequence selection in computational enzyme design

PubMed Central

Huang, Xiaoqiang; Han, Kehang; Zhu, Yushan

2013-01-01

A systematic optimization model for binding sequence selection in computational enzyme design was developed based on the transition state theory of enzyme catalysis and graph-theoretical modeling. The saddle point on the free energy surface of the reaction system was represented by catalytic geometrical constraints, and the binding energy between the active site and transition state was minimized to reduce the activation energy barrier. The resulting hyperscale combinatorial optimization problem was tackled using a novel heuristic global optimization algorithm, which was inspired and tested by the protein core sequence selection problem. The sequence recapitulation tests on native active sites for two enzyme catalyzed hydrolytic reactions were applied to evaluate the predictive power of the design methodology. The results of the calculation show that most of the native binding sites can be successfully identified if the catalytic geometrical constraints and the structural motifs of the substrate are taken into account. Reliably predicting active site sequences may have significant implications for the creation of novel enzymes that are capable of catalyzing targeted chemical reactions. PMID:23649589
Mapping the potential distribution of the invasive Red Shiner, Cyprinella lutrensis (Teleostei: Cyprinidae) across waterways of the conterminous United States

USGS Publications Warehouse

Poulos, Helen M.; Chernoff, Barry; Fuller, Pam L.; Butman, David

2012-01-01

Predicting the future spread of non-native aquatic species continues to be a high priority for natural resource managers striving to maintain biodiversity and ecosystem function. Modeling the potential distributions of alien aquatic species through spatially explicit mapping is an increasingly important tool for risk assessment and prediction. Habitat modeling also facilitates the identification of key environmental variables influencing species distributions. We modeled the potential distribution of an aggressive invasive minnow, the red shiner (Cyprinella lutrensis), in waterways of the conterminous United States using maximum entropy (Maxent). We used inventory records from the USGS Nonindigenous Aquatic Species Database, native records for C. lutrensis from museum collections, and a geographic information system of 20 raster climatic and environmental variables to produce a map of potential red shiner habitat. Summer climatic variables were the most important environmental predictors of C. lutrensis distribution, which was consistent with the high temperature tolerance of this species. Results from this study provide insights into the locations and environmental conditions in the US that are susceptible to red shiner invasion.
Direct and mediated effects of nativity and other indicators of acculturation on Hispanic mothers' use of physical aggression.

PubMed

Altschul, Inna; Lee, Shawna J

2011-11-01

This study used data from 845 foreign-born (n = 328) and native-U.S. born (n = 517) Hispanic mothers who participated in the Fragile Families and Child Wellbeing Study (FFCWS) to examine four indicators of acculturation--nativity, years lived in the United States, religious attendance, and endorsement of traditional gender norms--as predictors of maternal physical aggression directed toward young children. The authors also examined whether psychosocial risk factors associated with child maltreatment and acculturation--maternal alcohol use, depression, parenting stress, and intimate partner aggression and violence--mediate relationships between acculturation and maternal aggression. Foreign-born Hispanic mothers had significantly lower rates of physical aggression than native-born Hispanic mothers. In path modeling results, U.S. nativity, along with maternal alcohol use, parenting stress, and child aggressive behavior, emerged as the strongest risk factors for maternal physical aggression. Among the four acculturation indicators, only foreign birth was directly associated with lower maternal aggression. Study findings suggest immigrant status is a unique protective factor that contributes to lower levels of physical aggression among Hispanic mothers.
The Folding Energy Landscape and Free Energy Excitations of Cytochrome c

PubMed Central

Weinkam, Patrick; Zimmermann, Jörg; Romesberg, Floyd E.

2014-01-01

The covalently bound heme cofactor plays a dominant role in the folding of cytochrome c. Due to the complicated inorganic chemistry of the heme, some might consider the folding of cytochrome c to be a special case that follows different principles than those used to describe folding of proteins without cofactors. Recent investigations, however, demonstrate that models which are commonly used to describe folding for many proteins work well for cytochrome c when heme is explicitly introduced and generally provide results that agree with experimental observations. We will first discuss results from simple native structure-based models. These models include attractive interactions between nonadjacent residues only if they are present in the crystal structure at pH 7. Since attractive nonnative contacts are not included in native structure-based models, their energy landscapes can be described as “perfectly funneled.” In other words, native structure-based models are energetically guided towards the native state and contain no energetic traps that would hinder folding. Energetic traps are sources of frustration which cause specific transient intermediates to be populated. Native structure-based models do include repulsion between residues due to excluded volume. Nonenergetic traps can therefore exist if the chain, which cannot cross over itself, must partially unfold in order for folding to proceed. The ability of native structure-based models to capture these type of motions is in part responsible for their successful predictions of folding pathways for many types of proteins. Models without frustration describe well the sequence of folding events for cytochrome c inferred from hydrogen exchange experiments thereby justifying their use as a starting point. At low pH, the folding sequence of cytochrome c deviates from that at pH 7 and from those predicted from models with perfectly funneled energy landscapes. Alternate folding pathways are a result of “chemical frustration.” This frustration arises because some regions of the protein are destabilized more than others due to the heterogeneous distribution of titratable residues that are protonated at low pH. We construct more complex models that include chemical frustration, in addition to the native structure-based terms. These more complex models only modestly perturb the energy landscape which remains overall well funneled. These perturbed models can accurately describe how alternative folding pathways are used at low pH. At alkaline pH, cytochrome c populates distinctly different structural ensembles. For instance, lysine residues are deprotonated and compete for the heme ligation site. The same models that can describe folding at low pH also predict well the structures and relative stabilities of intermediates populated at alkaline pH. PMID:20143816
Release of Native-like Gaseous Proteins from Electrospray Droplets via the Charged Residue Mechanism: Insights from Molecular Dynamics Simulations.

PubMed

McAllister, Robert G; Metwally, Haidy; Sun, Yu; Konermann, Lars

2015-10-07

The mechanism whereby gaseous protein ions are released from charged solvent droplets during electrospray ionization (ESI) remains a matter of debate. Also, it is unclear to what extent electrosprayed proteins retain their solution structure. Molecular dynamics (MD) simulations offer insights into the temporal evolution of protein systems. Surprisingly, there have been no all-atom simulations of the protein ESI process to date. The current work closes this gap by investigating the behavior of protein-containing aqueous nanodroplets that carry excess positive charge. We focus on "native ESI", where proteins initially adopt their biologically active solution structures. ESI proceeds while the protein remains entrapped within the droplet. Protein release into the gas phase occurs upon solvent evaporation to dryness. Droplet shrinkage is accompanied by ejection of charge carriers (Na(+) for the conditions chosen here), keeping the droplet at ∼85% of the Rayleigh limit throughout its life cycle. Any remaining charge carriers bind to the protein as the final solvent molecules evaporate. The outcome of these events is largely independent of the initial protein charge and the mode of charge carrier binding. ESI charge states and collision cross sections of the MD structures agree with experimental data. Our results confirm the Rayleigh/charged residue model (CRM). Field emission of excess Na(+) plays an ancillary role by governing the net charge of the shrinking droplet. Models that envision protein ejection from the droplet are not supported. Most nascent CRM ions retain native-like conformations. For unfolded proteins ESI likely proceeds along routes that are different from the native state mechanism explored here.
Black Immigrants and Black Natives Attending Selective Colleges and Universities in the United States

ERIC Educational Resources Information Center

Massey, Douglas S.; Mooney, Margarita; Torres, Kimberly C.; Charles, Camille Z.

2007-01-01

This analysis uses data from the National Longitudinal Survey of Freshmen (NLSF) to study black immigrants and natives attending selective colleges and universities in the United States. In the NLSF, 747 black students were of native origin, and 281 were of immigrant origin, yielding an overall immigrant percentage of 27 percent. The…
Creating Official Language Policy from Local Practice: The Example of the Native American Languages Act 1990/1992

ERIC Educational Resources Information Center

Warhol, Larisa

2012-01-01

This research explores the development of landmark federal language policy in the United States: the Native American Languages Act of 1990/1992 (NALA). Overturning more than two centuries of United States American Indian policy, NALA established the federal role in preserving and protecting Native American languages. Indigenous languages in the…
Non-native plant invasions of United States National parks

USGS Publications Warehouse

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.
Anomalous droughts, not invasion, decrease persistence of native fishes in a desert river.

PubMed

Ruhí, Albert; Holmes, Elizabeth E; Rinne, John N; Sabo, John L

2015-04-01

Changing climate extremes and invasion by non-native species are two of the most prominent threats to native faunas. Predicting the relationships between global change and native faunas requires a quantitative toolkit that effectively links the timing and magnitude of extreme events to variation in species abundances. Here, we examine how discharge anomalies--unexpected floods and droughts--determine covariation in abundance of native and non-native fish species in a highly variable desert river in Arizona. We quantified stochastic variation in discharge using Fourier analyses on >15,000 daily observations. We subsequently coupled maximum annual spectral anomalies with a 15-year time series of fish abundances (1994-2008), using Multivariate Autoregressive State-Space (MARSS) models. Abiotic drivers (discharge anomalies) were paramount in determining long-term fish abundances, whereas biotic drivers (species interactions) played only a secondary role. As predicted, anomalous droughts reduced the abundances of native species, while floods increased them. However, in contrast to previous studies, we observed that the non-native assemblage was surprisingly unresponsive to extreme events. Biological trait analyses showed that functional uniqueness was higher in native than in non-native fishes. We also found that discharge anomalies influenced diversity patterns at the meta-community level, with nestedness increasing after anomalous droughts due to the differential impairment of native species. Overall, our results advance the notion that discharge variation is key in determining community trajectories in the long term, predicting the persistence of native fauna even in the face of invasion. We suggest this variation, rather than biotic interactions, may commonly underlie covariation between native and non-native faunas, especially in highly variable environments. If droughts become increasingly severe due to climate change, and floods increasingly muted due to regulation, fish assemblages in desert rivers may become taxonomically and functionally impoverished and dominated by non-native taxa. © 2014 John Wiley & Sons Ltd.

Electronic polarization stabilizes tertiary structure prediction of HP-36.

PubMed

Duan, Li L; Zhu, Tong; Zhang, Qing G; Tang, Bo; Zhang, John Z H

2014-04-01

Molecular dynamic (MD) simulations with both implicit and explicit solvent models have been carried out to study the folding dynamics of HP-36 protein. Starting from the extended conformation, the secondary structure of all three helices in HP-36 was formed in about 50 ns and remained stable in the remaining simulation. However, the formation of the tertiary structure was difficult. Although some intermediates were close to the native structure, the overall conformation was not stable. Further analysis revealed that the large structure fluctuation of loop and hydrophobic core regions was devoted mostly to the instability of the structure during MD simulation. The backbone root-mean-square deviation (RMSD) of the loop and hydrophobic core regions showed strong correlation with the backbone RMSD of the whole protein. The free energy landscape indicated that the distribution of main chain torsions in loop and turn regions was far away from the native state. Starting from an intermediate structure extracted from the initial AMBER simulation, HP-36 was found to generally fold to the native state under the dynamically adjusted polarized protein-specific charge (DPPC) simulation, while the peptide did not fold into the native structure when AMBER force filed was used. The two best folded structures were extracted and taken into further simulations in water employing AMBER03 charge and DPPC for 25 ns. Result showed that introducing polarization effect into interacting potential could stabilize the near-native protein structure.
Immigration and Status Exchange in Australia and the United States

PubMed Central

Choi, Kate H.; Tienda, Marta; Cobb-Clark, Deborah; Sinning, Mathias

2012-01-01

This paper evaluates the status exchange hypothesis for Australia and the United States, two Anglophone nations with long immigration traditions whose admission regimes place different emphases on skills. Using log-linear methods, we demonstrate that foreign-born spouses trade educational credentials via marriage with natives in both Australian and U.S. marriage markets and, moreover, that nativity is a more salient marriage barrier for men than for women. With some exceptions, immigrant spouses in mixed nativity couples are better educated than native spouses in same nativity couples, but status exchange is more prevalent among the less-educated spouses in both countries. Support for the status exchange hypothesis is somewhat weaker in Australia partly because of lower average levels of education compared with the United States and partly because of less sharply defined educational hierarchy at the postsecondary level. PMID:23226914
Native American Healing Traditions

ERIC Educational Resources Information Center

Portman, Tarrell A. A.; Garrett, Michael T.

2006-01-01

Indigenous healing practices among Native Americans have been documented in the United States since colonisation. Cultural encapsulation has deterred the acknowledgement of Native American medicinal practices as a precursor to folk medicine and many herbal remedies, which have greatly influenced modern medicine. Understanding Native American…
College Persistence of Alaska Native Students: An Assessment of the Rural Alaska Honors Institute, 1983-88.

ERIC Educational Resources Information Center

Gaylord, Thomas A.; Kaul, Gitanjali

Despite efforts by educators, full participation by Alaska native students in the state's colleges and universities has not yet been achieved. Alaska Natives are the state's only racial group that is underrepresented in enrollments at the University of Alaska (UA). This report examines the contribution of the Rural Alaska Honors Institute (RAHI)…
The State of Higher Education in California: Asian Americans, Native Hawaiians, Pacific Islanders

ERIC Educational Resources Information Center

Valliani, Nadia; Byrd, Daniel

2015-01-01

Approximately, 6.3 million Asian Americans and 347,501 Native Hawaiian and Pacific Islander (NHPIs) live in California. The Asian American, Native Hawaiian, and Pacific Islander community is one that is both significant in size and in diversity. It also represents the fastest growing racial/ethnic group in the state. Ensuring their access to and…
Sharing Tails®: A State-Wide Public Outreach Program Teaching Children about Native Arizona Fish

ERIC Educational Resources Information Center

Pacey, Carol A.; Marsh, Paul C.

2013-01-01

Limited public outreach programs about Arizona native fish exist and those that do are passive, fee-based, or Web-oriented, while others limit their geographic range. The program this article addresses sought to improve this situation with development of a state-wide outreach program with a goal to educate Arizona's children about native fish with…
The role of solid state 13 C NMR spectroscopy in studies of the nature of native celluloses

Treesearch

R.H. Atalla; D.L. VanderHart

1999-01-01

Published spectroscopic observations pertaining to the crystal structure of native celluloses are reviewed for the purpose of defining our current level of understanding about crystalline polymorphism in these materials. Emphasis is placed on observations from solid state 13 C nuclear magnetic resonance (NMR), which first led to the postulate that most native,...
A residue in helical conformation in the native state adopts a β-strand conformation in the folding transition state despite its high and canonical Φ-value.

PubMed

Zarrine-Afsar, Arash; Dahesh, Samira; Davidson, Alan R

2012-05-01

Delineating structures of the transition states in protein folding reactions has provided great insight into the mechanisms by which proteins fold. The most common method for obtaining this information is Φ-value analysis, which is carried out by measuring the changes in the folding and unfolding rates caused by single amino acid substitutions at various positions within a given protein. Canonical Φ-values range between 0 and 1, and residues displaying high values within this range are interpreted to be important in stabilizing the transition state structure, and to elicit this stabilization through native-like interactions. Although very successful in defining the general features of transition state structures, Φ-value analysis can be confounded when non-native interactions stabilize this state. In addition, direct information on backbone conformation within the transition state is not provided. In the work described here, we have investigated structure formation at a conserved β-bulge (with helical conformation) in the Fyn SH3 domain by characterizing the effects of substituting all natural amino acids at one position within this structural motif. By comparing the effects on folding rates of these substitutions with database-derived local structure propensity values, we have determined that this position adopts a non-native backbone conformation in the folding transition state. This result is surprising because this position displays a high and canonical Φ-value of 0.7. This work emphasizes the potential role of non-native conformations in folding pathways and demonstrates that even positions displaying high and canonical Φ-values may, nevertheless, adopt a non-native conformation in the transition state. Copyright © 2012 Wiley Periodicals, Inc.
Aromatic residues engineered into the beta-turn nucleation site of ubiquitin lead to a complex folding landscape, non-native side-chain interactions, and kinetic traps.

PubMed

Rea, Anita M; Simpson, Emma R; Meldrum, Jill K; Williams, Huw E L; Searle, Mark S

2008-12-02

The fast folding of small proteins is likely to be the product of evolutionary pressures that balance the search for native-like contacts in the transition state with the minimum number of stable non-native interactions that could lead to partially folded states prone to aggregation and amyloid formation. We have investigated the effects of non-native interactions on the folding landscape of yeast ubiquitin by introducing aromatic substitutions into the beta-turn region of the N-terminal beta-hairpin, using both the native G-bulged type I turn sequence (TXTGK) as well as an engineered 2:2 XNGK type I' turn sequence. The N-terminal beta-hairpin is a recognized folding nucleation site in ubiquitin. The folding kinetics for wt-Ub (TLTGK) and the type I' turn mutant (TNGK) reveal only a weakly populated intermediate, however, substitution with X = Phe or Trp in either context results in a high propensity to form a stable compact intermediate where the initial U-->I collapse is visible as a distinct kinetic phase. The introduction of Trp into either of the two host turn sequences results in either complex multiphase kinetics with the possibility of parallel folding pathways, or formation of a highly compact I-state stabilized by non-native interactions that must unfold before refolding. Sequence substitutions with aromatic residues within a localized beta-turn capable of forming non-native hydrophobic contacts in both the native state and partially folded states has the undesirable consequence that folding is frustrated by the formation of stable compact intermediates that evolutionary pressures at the sequence level may have largely eliminated.
State Legislation Relating to Native Americans, 1991.

ERIC Educational Resources Information Center

Reed, James B.

1991-01-01

This report summarizes legislative activities in states that enacted bills and resolutions relating to Native Americans in 1991. Conflicts between states and the Indian tribes within their borders were the subject of significant legislation in 1991. In all, 220 bills and resolutions were introduced in state legislatures; 77 passed and 20 are still…
Three key residues form a critical contact network in a protein folding transition state

NASA Astrophysics Data System (ADS)

Vendruscolo, Michele; Paci, Emanuele; Dobson, Christopher M.; Karplus, Martin

2001-02-01

Determining how a protein folds is a central problem in structural biology. The rate of folding of many proteins is determined by the transition state, so that a knowledge of its structure is essential for understanding the protein folding reaction. Here we use mutation measurements-which determine the role of individual residues in stabilizing the transition state-as restraints in a Monte Carlo sampling procedure to determine the ensemble of structures that make up the transition state. We apply this approach to the experimental data for the 98-residue protein acylphosphatase, and obtain a transition-state ensemble with the native-state topology and an average root-mean-square deviation of 6Å from the native structure. Although about 20 residues with small positional fluctuations form the structural core of this transition state, the native-like contact network of only three of these residues is sufficient to determine the overall fold of the protein. This result reveals how a nucleation mechanism involving a small number of key residues can lead to folding of a polypeptide chain to its unique native-state structure.
Unraveling energy conversion modeling in the intrinsic persistent upconverted luminescence of solids: a study of native point defects in antiferromagnetic Er2O3.

PubMed

Huang, Bolong

2016-05-11

We investigated the mechanism of the intrinsic persistent luminescence of Er2O3 in the A-type lattice based on first-principles calculations. We found that the native point defects were engaged in mutual subtle interactions in the form of chemical reactions between different charge states. The release of energy related to lattice distortion facilitates the conversion of energy for electrons to be transported between the valence band and the trap levels or even between the deep trap levels so as to generate persistent luminescence. The defect transitions that take place along the zero-phonon line release energy to enable optical transitions, with the exact amount of negative effective correlation energy determined by the lattice distortions. Our calculations on the thermodynamic transition levels confirm that both the visible and NIR experimentally observed intrinsic persistent luminescence (phosphor or afterglow) are related to the thermodynamic transition levels of oxygen-related defects, and the thermodynamic transition levels within different charge states for these defects are independent of the chemical potentials of the given species. Lattice distortion defects such as anion Frenkel (a-Fr) pair defects play an important role in transporting O-related defects between different lattice sites. To obtain red persistent luminescence that matches the biological therapeutic window, it is suggested to increase the electron transition levels between high-coordinated O vacancies and related metastable a-Fr defects; a close-packed core-shell structure is required to quench low-coordinated O-related defects so as to reduce the green band luminescence. We further established a conversed chain reaction (CCR) model to interpret the energy conversion process of persistent luminescence in terms of the inter-reactions of native point defects between different charge states. It is advantageous to use the study of defect levels combined with formation energies to suggest limits to doping energy and explain photostimulated luminescence in terms of native point defects.
Transient intermediates are populated in the folding pathways of single-domain two-state folding protein L

NASA Astrophysics Data System (ADS)

Maity, Hiranmay; Reddy, Govardhan

2018-04-01

Small single-domain globular proteins, which are believed to be dominantly two-state folders, played an important role in elucidating various aspects of the protein folding mechanism. However, recent single molecule fluorescence resonance energy transfer experiments [H. Y. Aviram et al. J. Chem. Phys. 148, 123303 (2018)] on a single-domain two-state folding protein L showed evidence for the population of an intermediate state and it was suggested that in this state, a β-hairpin present near the C-terminal of the native protein state is unfolded. We performed molecular dynamics simulations using a coarse-grained self-organized-polymer model with side chains to study the folding pathways of protein L. In agreement with the experiments, an intermediate is populated in the simulation folding pathways where the C-terminal β-hairpin detaches from the rest of the protein structure. The lifetime of this intermediate structure increased with the decrease in temperature. In low temperature conditions, we also observed a second intermediate state, which is globular with a significant fraction of the native-like tertiary contacts satisfying the features of a dry molten globule.
The folding energy landscape and free energy excitations of cytochrome c.

PubMed

Weinkam, Patrick; Zimmermann, Jörg; Romesberg, Floyd E; Wolynes, Peter G

2010-05-18

The covalently bound heme cofactor plays a dominant role in the folding of cytochrome c. Because of the complicated inorganic chemistry of the heme, some might consider the folding of cytochrome c to be a special case, following principles different from those used to describe the folding of proteins without cofactors. Recent investigations, however, demonstrate that common models describing folding for many proteins work well for cytochrome c when heme is explicitly introduced, generally providing results that agree with experimental observations. In this Account, we first discuss results from simple native structure-based models. These models include attractive interactions between nonadjacent residues only if they are present in the crystal structure at pH 7. Because attractive nonnative contacts are not included in native structure-based models, their energy landscapes can be described as "perfectly funneled". In other words, native structure-based models are energetically guided towards the native state and contain no energetic traps that would hinder folding. Energetic traps are denoted sources of "frustration", which cause specific transient intermediates to be populated. Native structure-based models do, however, include repulsion between residues due to excluded volume. Nonenergetic traps can therefore exist if the chain, which cannot cross over itself, must partially unfold so that folding can proceed. The ability of native structure-based models to capture this kind of motion is partly responsible for their successful predictions of folding pathways for many types of proteins. Models without frustration describe the sequence of folding events for cytochrome c well (as inferred from hydrogen-exchange experiments), thereby justifying their use as a starting point. At low pH, the experimentally observed folding sequence of cytochrome c deviates from that at pH 7 and from models with perfectly funneled energy landscapes. Here, alternate folding pathways are a result of "chemical frustration". This frustration arises because some regions of the protein are destabilized more than others due to the heterogeneous distribution of titratable residues that are protonated at low pH. Beginning with native structure-based terms, we construct more complex models by adding chemical frustration. These more complex models only modestly perturb the energy landscape, which remains, overall, well funneled. These perturbed models can accurately describe how alternative folding pathways are used at low pH. At alkaline pH, cytochrome c populates distinctly different structural ensembles. For instance, lysine residues are deprotonated and compete for the heme ligation site. The same models that can describe folding at low pH also predict well the structures and relative stabilities of intermediates populated at alkaline pH. The success of models based on funneled energy landscapes suggest that cytochrome c folding is driven primarily by native contacts. The presence of heme appears to add chemical complexity to the folding process, but it does not require fundamental modification of the general principles used to describe folding. Moreover, its added complexity provides a valuable means of probing the folding energy landscape in greater detail than is possible with simpler systems.
Native-Language Education: Addressing the Interests of Special Populations within U.S. Federal Policy

ERIC Educational Resources Information Center

Best, Jane; Dunlap, Allison

2012-01-01

This brief provides an overview of three federal laws that address native-language education and illustrates how these federal laws produce different results when coupled with state laws and other regional circumstances. For the purposes of this brief, native-language education refers to American Indians, Alaska Natives, and Native Hawaiians and…
Resilience and resistance of sagebrush ecosystems: implications for state and transition models and management treatments

USGS Publications Warehouse

Chambers, Jeanne C.; Miller, Richard F.; Board, David I.; Pyke, David A.; Roundy, Bruce A.; Grace, James B.; Schupp, Eugene W.; Tausch, Robin J.

2014-01-01

In sagebrush ecosystems invasion of annual exotics and expansion of piñon (Pinus monophylla Torr. and Frem.) and juniper (Juniperus occidentalis Hook., J. osteosperma [Torr.] Little) are altering fire regimes and resulting in large-scale ecosystem transformations. Management treatments aim to increase resilience to disturbance and enhance resistance to invasive species by reducing woody fuels and increasing native perennial herbaceous species. We used Sagebrush Steppe Treatment Evaluation Project data to test predictions on effects of fire vs. mechanical treatments on resilience and resistance for three site types exhibiting cheatgrass (Bromus tectorum L.) invasion and/or piñon and juniper expansion: 1) warm and dry Wyoming big sagebrush (WY shrub); 2) warm and moist Wyoming big sagebrush (WY PJ); and 3) cool and moist mountain big sagebrush (Mtn PJ). Warm and dry (mesic/aridic) WY shrub sites had lower resilience to fire (less shrub recruitment and native perennial herbaceous response) than cooler and moister (frigid/xeric) WY PJ and Mtn PJ sites. Warm (mesic) WY Shrub and WY PJ sites had lower resistance to annual exotics than cool (frigid to cool frigid) Mtn PJ sites. In WY shrub, fire and sagebrush mowing had similar effects on shrub cover and, thus, on perennial native herbaceous and exotic cover. In WY PJ and Mtn PJ, effects were greater for fire than cut-and-leave treatments and with high tree cover in general because most woody vegetation was removed increasing resources for other functional groups. In WY shrub, about 20% pretreatment perennial native herb cover was necessary to prevent increases in exotics after treatment. Cooler and moister WY PJ and especially Mtn PJ were more resistant to annual exotics, but perennial native herb cover was still required for site recovery. We use our results to develop state and transition models that illustrate how resilience and resistance influence vegetation dynamics and management options.
ROTAS: a rotamer-dependent, atomic statistical potential for assessment and prediction of protein structures.

PubMed

Park, Jungkap; Saitou, Kazuhiro

2014-09-18

Multibody potentials accounting for cooperative effects of molecular interactions have shown better accuracy than typical pairwise potentials. The main challenge in the development of such potentials is to find relevant structural features that characterize the tightly folded proteins. Also, the side-chains of residues adopt several specific, staggered conformations, known as rotamers within protein structures. Different molecular conformations result in different dipole moments and induce charge reorientations. However, until now modeling of the rotameric state of residues had not been incorporated into the development of multibody potentials for modeling non-bonded interactions in protein structures. In this study, we develop a new multibody statistical potential which can account for the influence of rotameric states on the specificity of atomic interactions. In this potential, named "rotamer-dependent atomic statistical potential" (ROTAS), the interaction between two atoms is specified by not only the distance and relative orientation but also by two state parameters concerning the rotameric state of the residues to which the interacting atoms belong. It was clearly found that the rotameric state is correlated to the specificity of atomic interactions. Such rotamer-dependencies are not limited to specific type or certain range of interactions. The performance of ROTAS was tested using 13 sets of decoys and was compared to those of existing atomic-level statistical potentials which incorporate orientation-dependent energy terms. The results show that ROTAS performs better than other competing potentials not only in native structure recognition, but also in best model selection and correlation coefficients between energy and model quality. A new multibody statistical potential, ROTAS accounting for the influence of rotameric states on the specificity of atomic interactions was developed and tested on decoy sets. The results show that ROTAS has improved ability to recognize native structure from decoy models compared to other potentials. The effectiveness of ROTAS may provide insightful information for the development of many applications which require accurate side-chain modeling such as protein design, mutation analysis, and docking simulation.
Significant Literature by and about Native Americans.

ERIC Educational Resources Information Center

Willis, Cecilia A., Comp.; Travis, M. Eunice, Comp.

Significant literature about Native Americans, some written by Native Americans, comprises this bibliography. Materials relevant to Native Americans found at Kansas State University are listed. Over 850 books, articles on microfiche, studies, documents, and publications arranged by subject categories are contained in this bibliography. The subject…
Oligomeric State of Lipocalin-1 (LCN1) by Multiangle Laser Light Scattering and Fluorescence Anisotropy Decay

PubMed Central

Gasymov, Oktay K.; Abduragimov, Adil R.; Merschak, Petra; Redl, Bernhard; Glasgow, Ben J.

2007-01-01

Multiangle laser light scattering and fluorescence anisotropy decay measurements clarified the oligomeric states of native and recombinant tear lipocalin (lipocalin-1, TL). Native TL is monomeric. Recombinant TL (5-68 μM) with or without the histidine tag shows less than 7% dimer formation that is not in equilibrium with the monomeric form. Fluorescence anisotropy decay showed a correlation time of 9-10 ns for TL (10 μM- 1mM). Hydrodynamic calculations based on the crystallographic structure of a monomeric TL mutant closely concur with the observed correlation time. The solution properties calculated with HYDROPRO and SOLPRO programs from the available crystallographic structure of a monomeric TL mutant concur closely with the observed fluorescence anisotropy decay. The resulting model shows that protein topology is the major determinant of rotational correlation time and accounts for deviation from the Stokes-Einstein relation. The data challenge previous gel filtration studies to show that native TL exists predominantly as a monomer in solution rather than as a dimer. Delipidation of TL results in a formation of a complex oligomeric state (up to 25%). These findings are important as the dynamic processes in the tear film are limited by diffusional, translational as well as rotational, properties of the protein. PMID:17869594
State of the science and challenges of breeding landscape plants with ecological function

PubMed Central

Wilde, H Dayton; Gandhi, Kamal J K; Colson, Gregory

2015-01-01

Exotic plants dominate esthetically-managed landscapes, which cover 30–40 million hectares in the United States alone. Recent ecological studies have found that landscaping with exotic plant species can reduce biodiversity on multiple trophic levels. To support biodiversity in urbanized areas, the increased use of native landscaping plants has been advocated by conservation groups and US federal and state agencies. A major challenge to scaling up the use of native species in landscaping is providing ornamental plants that are both ecologically functional and economically viable. Depending on ecological and economic constraints, accelerated breeding approaches could be applied to ornamental trait development in native plants. This review examines the impact of landscaping choices on biodiversity, the current status of breeding and selection of native ornamental plants, and the interdisciplinary research needed to scale up landscaping plants that can support native biodiversity. PMID:26504560

The topomer-sampling model of protein folding

PubMed Central

Debe, Derek A.; Carlson, Matt J.; Goddard, William A.

1999-01-01

Clearly, a protein cannot sample all of its conformations (e.g., ≈3100 ≈ 1048 for a 100 residue protein) on an in vivo folding timescale (<1 s). To investigate how the conformational dynamics of a protein can accommodate subsecond folding time scales, we introduce the concept of the native topomer, which is the set of all structures similar to the native structure (obtainable from the native structure through local backbone coordinate transformations that do not disrupt the covalent bonding of the peptide backbone). We have developed a computational procedure for estimating the number of distinct topomers required to span all conformations (compact and semicompact) for a polypeptide of a given length. For 100 residues, we find ≈3 × 107 distinct topomers. Based on the distance calculated between different topomers, we estimate that a 100-residue polypeptide diffusively samples one topomer every ≈3 ns. Hence, a 100-residue protein can find its native topomer by random sampling in just ≈100 ms. These results suggest that subsecond folding of modest-sized, single-domain proteins can be accomplished by a two-stage process of (i) topomer diffusion: random, diffusive sampling of the 3 × 107 distinct topomers to find the native topomer (≈0.1 s), followed by (ii) intratopomer ordering: nonrandom, local conformational rearrangements within the native topomer to settle into the precise native state. PMID:10077555
Species richness and patterns of invasion in plants, birds, and fishes in the United States

USGS Publications Warehouse

Stohlgren, Thomas J.; Barnett, David; Flather, Curtis; Fuller, Pamela L.; Peterjohn, Bruce G.; Kartesz, John; Master, Lawrence L.

2006-01-01

We quantified broad-scale patterns of species richness and species density (mean # species/km2) for native and non-indigenous plants, birds, and fishes in the continental USA and Hawaii. We hypothesized that the species density of native and non-indigenous taxa would generally decrease in northern latitudes and higher elevations following declines in potential evapotranspiration, mean temperature, and precipitation. County data on plants (n = 3004 counties) and birds (n=3074 counties), and drainage (6 HUC) data on fishes (n = 328 drainages) showed that the densities of native and non-indigenous species were strongly positively correlated for plant species (r = 0.86, P < 0.0001), bird species (r = 0.93, P<0.0001), and fish species (r = 0.41, P<0.0001). Multiple regression models showed that the densities of native plant and bird species could be strongly predicted (adj. R2 = 0.66 in both models) at county levels, but fish species densities were less predictable at drainage levels (adj. R2 = 0.31,P<0.0001). Similarly, non-indigenous plant and bird species densities were strongly predictable (adj. R2 = 0.84 and 0.91 respectively), but non-indigenous fish species density was less predictable (adj. R2 = 0.38). County level hotspots of native and non-indigenous plants, birds, and fishes were located in low elevation areas close to the coast with high precipitation and productivity (vegetation carbon). We show that (1) native species richness can be moderately well predicted with abiotic factors; (2) human populations have tended to settle in areas rich in native species; and (3) the richness and density of non-indigenous plant, bird, and fish species can be accurately predicted from biotic and abiotic factors largely because they are positively correlated to native species densities. We conclude that while humans facilitate the initial establishment, invasions of non-indigenous species, the spread and subsequent distributions of non-indigenous species may be controlled largely by environmental factors.
Status of native fishes in the western United States and issues for fire and fuels management

Treesearch

Bruce Rieman; Danny Lee; Dave Burns; Robert Gresswell; Michael Young; Rick Stowell; John Rinne; Philip Howell

2003-01-01

Conservation of native fishes and changing patterns in wildfire and fuels are defining challenges for managers of forested landscapes in the western United States. Many species and populations of native fishes have declined in recorded history and some now occur as isolated remnants of what once were larger more complex systems. Land management activities have been...
Developing native grass seed industries for revegetation in Australia and the western United States: A contrast in production and adoption

Treesearch

C. M. Waters; N. L. Shaw

2003-01-01

Globally, an increased desire to restore, rehabilitate or revegetate with native plants represents a shift toward more ecologically focused restoration goals. In the Australian rangelands, an increasing need to address revegetation is not being matched by an availability of seed material. This contrasts with the United States where a well-structured native seed...
Water-Rights Settlements and Reclamation in Central Arizona as a Cross-Cultural Experience: A Reexamination of Native Water Policy

ERIC Educational Resources Information Center

Matsui, Kenichi

2011-01-01

As of December 2010, the US Congress had enacted more than twenty major community-specific Native water-rights settlements, and the state of Arizona had more of these settlements (eight) than any other US state. This unique situation has invited voluminous studies on Arizona's Native water-rights settlements. Although these studies have clarified…
The effect of charge mutations on the stability and aggregation of a human single chain Fv fragment.

PubMed

Austerberry, James I; Dajani, Rana; Panova, Stanislava; Roberts, Dorota; Golovanov, Alexander P; Pluen, Alain; van der Walle, Christopher F; Uddin, Shahid; Warwicker, Jim; Derrick, Jeremy P; Curtis, Robin

2017-06-01

The aggregation propensities for a series of single-chain variable fragment (scFv) mutant proteins containing supercharged sequences, salt bridges and lysine/arginine-enriched motifs were characterised as a function of pH and ionic strength to isolate the electrostatic contributions. Recent improvements in aggregation predictors rely on using knowledge of native-state protein-protein interactions. Consistent with previous findings, electrostatic contributions to native protein-protein interactions correlate with aggregate growth pathway and rates. However, strong reversible self-association observed for selected mutants under native conditions did not correlate with aggregate growth, indicating 'sticky' surfaces that are exposed in the native monomeric state are inaccessible when aggregates grow. We find that even though similar native-state protein-protein interactions occur for the arginine and lysine-enriched mutants, aggregation propensity is increased for the former and decreased for the latter, providing evidence that lysine suppresses interactions between partially folded states under these conditions. The supercharged mutants follow the behaviour observed for basic proteins under acidic conditions; where excess net charge decreases conformational stability and increases nucleation rates, but conversely reduces aggregate growth rates due to increased intermolecular electrostatic repulsion. The results highlight the limitations of using conformational stability and native-state protein-protein interactions as predictors for aggregation propensity and provide guidance on how to engineer stabilizing charged mutations. Copyright © 2017. Published by Elsevier B.V.
Differential population responses of native and alien rodents to an invasive predator, habitat alteration and plant masting.

PubMed

Fukasawa, Keita; Miyashita, Tadashi; Hashimoto, Takuma; Tatara, Masaya; Abe, Shintaro

2013-12-22

Invasive species and anthropogenic habitat alteration are major drivers of biodiversity loss. When multiple invasive species occupy different trophic levels, removing an invasive predator might cause unexpected outcomes owing to complex interactions among native and non-native prey. Moreover, external factors such as habitat alteration and resource availability can affect such dynamics. We hypothesized that native and non-native prey respond differently to an invasive predator, habitat alteration and bottom-up effects. To test the hypothesis, we used Bayesian state-space modelling to analyse 8-year data on the spatio-temporal patterns of two endemic rat species and the non-native black rat in response to the continual removal of the invasive small Indian mongoose on Amami Island, Japan. Despite low reproductive potentials, the endemic rats recovered better after mongoose removal than did the black rat. The endemic species appeared to be vulnerable to predation by mongooses, whose eradication increased the abundances of the endemic rats, but not of the black rat. Habitat alteration increased the black rat's carrying capacity, but decreased those of the endemic species. We propose that spatio-temporal monitoring data from eradication programmes will clarify the underlying ecological impacts of land-use change and invasive species, and will be useful for future habitat management.
A New Paradigm for Diagnosing Contributions to Model Aerosol Forcing Error: Diagnosing Model Aerosol Forcing Error

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

Jones, A. L.; Feldman, D. R.; Freidenreich, S.

A new paradigm in benchmark absorption-scattering radiative transfer is presented that enables both the globally averaged and spatially resolved testing of climate model radiation parameterizations in order to uncover persistent sources of biases in the aerosol instantaneous radiative effect (IRE). A proof of concept is demonstrated with the Geophysical Fluid Dynamics Laboratory AM4 and Community Earth System Model 1.2.2 climate models. Instead of prescribing atmospheric conditions and aerosols, as in prior intercomparisons, native snapshots of the atmospheric state and aerosol optical properties from the participating models are used as inputs to an accurate radiation solver to uncover model-relevant biases. Thesemore » diagnostic results show that the models' aerosol IRE bias is of the same magnitude as the persistent range cited (~1 W/m 2) and also varies spatially and with intrinsic aerosol optical properties. The findings presented here underscore the significance of native model error analysis and its dispositive ability to diagnose global biases, confirming its fundamental value for the Radiative Forcing Model Intercomparison Project.« less
A New Paradigm for Diagnosing Contributions to Model Aerosol Forcing Error: Diagnosing Model Aerosol Forcing Error

DOE PAGES

Jones, A. L.; Feldman, D. R.; Freidenreich, S.; ...

2017-12-07

A new paradigm in benchmark absorption-scattering radiative transfer is presented that enables both the globally averaged and spatially resolved testing of climate model radiation parameterizations in order to uncover persistent sources of biases in the aerosol instantaneous radiative effect (IRE). A proof of concept is demonstrated with the Geophysical Fluid Dynamics Laboratory AM4 and Community Earth System Model 1.2.2 climate models. Instead of prescribing atmospheric conditions and aerosols, as in prior intercomparisons, native snapshots of the atmospheric state and aerosol optical properties from the participating models are used as inputs to an accurate radiation solver to uncover model-relevant biases. Thesemore » diagnostic results show that the models' aerosol IRE bias is of the same magnitude as the persistent range cited (~1 W/m 2) and also varies spatially and with intrinsic aerosol optical properties. The findings presented here underscore the significance of native model error analysis and its dispositive ability to diagnose global biases, confirming its fundamental value for the Radiative Forcing Model Intercomparison Project.« less
Oregon American Indian/Alaska Native Education State Plan.

ERIC Educational Resources Information Center

Oregon State Dept. of Education, Salem.

The Oregon State Plan for American Indian and Alaska Native (AI/AN) education was developed by AI/AN communities and educators, the State Board of Education, and the State Department of Education. The plan includes 11 major educational goals: (1) the Oregon Department of Education (ODE) should promote effective education for AI/AN children; (2)…
Statistical Record of Native North Americans. Second Edition.

ERIC Educational Resources Information Center

Reddy, Marlita A., Ed.

This book compiles statistical data on Native North American populations, including Alaska and Canada Natives. Data sources include federal and state agencies, census records, tribal governments, associations, and other organizations. The book includes statistics on Native North Americans as compared with other racial and ethnic groups under…
Native American Children in Michigan. [Executive Summary

ERIC Educational Resources Information Center

W. K. Kellogg Foundation, 2012

2012-01-01

"Native American Children in Michigan," provides a historical context for the tenuous relationship between Michigan's 12 federally recognized tribes and the state government, paying particular attention to the erosion of Native American education programs and the disproportionate number of Native children who find themselves in both the…
Vulnerability of freshwater native biodiversity to non-native species invasions across the continental United States

EPA Science Inventory

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...
The folding transition state of Protein L is extensive with non-native interactions (and not small and polarized)

PubMed Central

Yoo, Tae Yeon; Adhikari, Aashish; Xia, Zhen; Huynh, Tien; Freed, Karl F.; Zhou, Ruhong; Sosnick, Tobin R.

2012-01-01

Progress in understanding protein folding relies heavily upon an interplay between experiment and theory. In particular, readily interpretable experimental data are required that can be meaningfully compared to simulations. According to standard mutational φ analysis, the transition state for Protein L contains only a single hairpin. However, we demonstrate here using ψ analysis with engineered metal ion binding sites that the transition state is extensive, containing the entire four-stranded β sheet. Underreporting of the structural content of the transition state by φ analysis also occurs for acyl phosphatase1, ubiquitin2 and BdpA3. The carboxy terminal hairpin in the transition state of Protein L is found to be non-native, a significant result that agrees with our PDB-based backbone sampling and all-atom simulations. The non-native character partially explains the failure of accepted experimental and native-centric computational approaches to adequately describe the transition state. Hence, caution is required even when an apparent agreement exists between experiment and theory, thus highlighting the importance of having alternative methods for characterizing transition states. PMID:22522126
Hexafluoroisopropanol-induced helix-sheet transition of stem bromelain: correlation to function.

PubMed

Dave, Sandeep; Dkhar, H Kitdorlang; Singh, Manvendra Pratap; Gupta, Garima; Chandra, Vemika; Mahajan, Sahil; Gupta, Pawan

2010-06-01

Stem bromelain is a proteolytic phytoprotein with a variety of therapeutic effects. Understanding its structural properties could provide insight into the mechanisms underlying its clinical utility. Stem bromelain was evaluated for its conformational and folding properties at the pH conditions it encounters when administered orally. It exists as a partially folded intermediate at pH 2.0. The conformational changes to this intermediate state were evaluated using fluorinated alcohols known to induce changes similar to those seen in vivo. Studies using circular dichroism, fluorescence emission spectroscopy, binding of the hydrophobic dye 1-anilino-8-naphthalene sulfonic acid and mass spectrometry indicate that treatment with 10-30% hexafluoroisopropanol induces the partially folded intermediate to adopt much of the native protein's secondary structure, but only a rudimentary tertiary structure, characteristic of the molten globule state. Addition of slightly higher concentrations of hexafluoroisopropanol caused transformation from an alpha-helix to a beta-sheet and induced formation of a compact nonnative structure. This nonnative form was more inhibitory of cell survival than either the native or the partially folded intermediate forms, as measured by enhanced suppression of proliferative cues (e.g., extracellular-signal-regulated kinase) and initiation of apoptotic events. The nonnative form also showed better antitumorigenic properties, as evaluated using an induced two-stage mouse skin papilloma model. In contrast, the nonnative state showed only a fraction of the proteolytic activity of the native form. This study demonstrates that hexafluoroisopropanol can induce a conformational change in stem bromelain to a form with potentially useful therapeutic properties different from those of the native protein. Copyright 2010 Elsevier Ltd. All rights reserved.
Competent Communities: A Critical Analysis of Theories and Public Policy.

ERIC Educational Resources Information Center

Padilla, Amado M.

Blacks, Native Americans, Mexicans, Asians, Hispanics, and other minority groups have managed to survive many consequences of racial/ethnic bias and discrimination in the United States. However, certain theoretical models that social scientists apply to studies of social problems reflect majority group biases that tend to perpetuate discrimination…
Encountering Complexity: Native Musics in the Curriculum.

ERIC Educational Resources Information Center

Boyea, Andrea

1999-01-01

Describes Native American musics, focusing on issues such as music and the experience of time, metaphor and metaphorical aspects, and spirituality and sounds from nature. Discusses Native American metaphysics and its reflection in the musics. States that an effective curriculum would provide a new receptivity to Native American musics. (CMK)
78 FR 65366 - Notice of Inventory Completion: University of Michigan, Ann Arbor, MI

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-31

... remains, in consultation with the appropriate Indian tribes or Native Hawaiian organizations, and has... or Native Hawaiian organizations. Representatives of any Indian tribe or Native Hawaiian organization..., transfer of control of the human remains to the Indian tribes or Native Hawaiian organizations stated in...
78 FR 65369 - Notice of Inventory Completion: University of Michigan, Ann Arbor, MI

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-31

... remains, in consultation with the appropriate Indian tribes or Native Hawaiian organizations, and has... or Native Hawaiian organizations. Representatives of any Indian tribe or Native Hawaiian organization..., transfer of control of the human remains to the Indian tribes or Native Hawaiian organizations stated in...
50 CFR 18.3 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-10-01

...), Eskimo, or Aleut blood, or combination thereof. The term includes any Native, as so defined, either or... blood quantum, any citizen of the United States who is regarded as an Alaska Native by the Native... formation of traditional native groups, such as cooperatives, is permitted so long as no large-scale mass...

PCR diagnosis of tick-borne pathogens in Maharashtra state, India indicates fitness cost associated with carrier infections is greater for crossbreed than native cattle breeds

PubMed Central

Kolte, Sunil W.; Larcombe, Stephen D.; Jadhao, Suresh G.; Magar, Swapnil P.; Warthi, Ganesh; Kurkure, Nitin V.; Glass, Elizabeth J.; Shiels, Brian R.

2017-01-01

Tick-borne pathogens (TBP) are responsible for significant economic losses to cattle production, globally. This is particularly true in countries like India where TBP constrain rearing of high yielding Bos taurus, as they show susceptibility to acute tick borne disease (TBD), most notably tropical theileriosis caused by Theileria annulata. This has led to a programme of cross breeding Bos taurus (Holstein-Friesian or Jersey) with native Bos indicus (numerous) breeds to generate cattle that are more resistant to disease. However, the cost to fitness of subclinical carrier infection in crossbreeds relative to native breeds is unknown, but could represent a significant hidden economic cost. In this study, a total of 1052 bovine blood samples, together with associated data on host type, sex and body score, were collected from apparently healthy animals in four different agro-climatic zones of Maharashtra state. Samples were screened by PCR for detection of five major TBPs: T. annulata, T. orientalis, B. bigemina, B. bovis and Anaplasma spp.. The results demonstrated that single and co-infection with TBP are common, and although differences in pathogen spp. prevalence across the climatic zones were detected, simplistic regression models predicted that host type, sex and location are all likely to impact on prevalence of TBP. In order to remove issues with autocorrelation between variables, a subset of the dataset was modelled to assess any impact of TBP infection on body score of crossbreed versus native breed cattle (breed type). The model showed significant association between infection with TBP (particularly apicomplexan parasites) and poorer body condition for crossbreed animals. These findings indicate potential cost of TBP carrier infection on crossbreed productivity. Thus, there is a case for development of strategies for targeted breeding to combine productivity traits with disease resistance, or to prevent transmission of TBP in India for economic benefit. PMID:28358861
PCR diagnosis of tick-borne pathogens in Maharashtra state, India indicates fitness cost associated with carrier infections is greater for crossbreed than native cattle breeds.

PubMed

Kolte, Sunil W; Larcombe, Stephen D; Jadhao, Suresh G; Magar, Swapnil P; Warthi, Ganesh; Kurkure, Nitin V; Glass, Elizabeth J; Shiels, Brian R

2017-01-01

Tick-borne pathogens (TBP) are responsible for significant economic losses to cattle production, globally. This is particularly true in countries like India where TBP constrain rearing of high yielding Bos taurus, as they show susceptibility to acute tick borne disease (TBD), most notably tropical theileriosis caused by Theileria annulata. This has led to a programme of cross breeding Bos taurus (Holstein-Friesian or Jersey) with native Bos indicus (numerous) breeds to generate cattle that are more resistant to disease. However, the cost to fitness of subclinical carrier infection in crossbreeds relative to native breeds is unknown, but could represent a significant hidden economic cost. In this study, a total of 1052 bovine blood samples, together with associated data on host type, sex and body score, were collected from apparently healthy animals in four different agro-climatic zones of Maharashtra state. Samples were screened by PCR for detection of five major TBPs: T. annulata, T. orientalis, B. bigemina, B. bovis and Anaplasma spp.. The results demonstrated that single and co-infection with TBP are common, and although differences in pathogen spp. prevalence across the climatic zones were detected, simplistic regression models predicted that host type, sex and location are all likely to impact on prevalence of TBP. In order to remove issues with autocorrelation between variables, a subset of the dataset was modelled to assess any impact of TBP infection on body score of crossbreed versus native breed cattle (breed type). The model showed significant association between infection with TBP (particularly apicomplexan parasites) and poorer body condition for crossbreed animals. These findings indicate potential cost of TBP carrier infection on crossbreed productivity. Thus, there is a case for development of strategies for targeted breeding to combine productivity traits with disease resistance, or to prevent transmission of TBP in India for economic benefit.
Reconceptualizing Native Women's Health: An “Indigenist” Stress-Coping Model

PubMed Central

Walters, Karina L.; Simoni, Jane M.

2002-01-01

This commentary presents an “indigenist” model of Native women's health, a stress-coping paradigm that situates Native women's health within the larger context of their status as a colonized people. The model is grounded in empirical evidence that traumas such as the “soul wound” of historical and contemporary discrimination among Native women influence health and mental health outcomes. The preliminary model also incorporates cultural resilience, including as moderators identity, enculturation, spiritual coping, and traditional healing practices. Current epidemiological data on Native women's general health and mental health are reconsidered within the framework of this model. PMID:11919043
RACER a Coarse-Grained RNA Model for Capturing Folding Free Energy in Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Cheng, Sara; Bell, David; Ren, Pengyu

RACER is a coarse-grained RNA model that can be used in molecular dynamics simulations to predict native structures and sequence-specific variation of free energy of various RNA structures. RACER is capable of accurate prediction of native structures of duplexes and hairpins (average RMSD of 4.15 angstroms), and RACER can capture sequence-specific variation of free energy in excellent agreement with experimentally measured stabilities (r-squared =0.98). The RACER model implements a new effective non-bonded potential and re-parameterization of hydrogen bond and Debye-Huckel potentials. Insights from the RACER model include the importance of treating pairing and stacking interactions separately in order to distinguish folded an unfolded states and identification of hydrogen-bonding, base stacking, and electrostatic interactions as essential driving forces for RNA folding. Future applications of the RACER model include predicting free energy landscapes of more complex RNA structures and use of RACER for multiscale simulations.
Role of non-native electrostatic interactions in the coupled folding and binding of PUMA with Mcl-1

PubMed Central

Chu, Wen-Ting; Clarke, Jane; Shammas, Sarah L.; Wang, Jin

2017-01-01

PUMA, which belongs to the BH3-only protein family, is an intrinsically disordered protein (IDP). It binds to its cellular partner Mcl-1 through its BH3 motif, which folds upon binding into an α helix. We have applied a structure-based coarse-grained model, with an explicit Debye—Hückel charge model, to probe the importance of electrostatic interactions both in the early and the later stages of this model coupled folding and binding process. This model was carefully calibrated with the experimental data on helical content and affinity, and shown to be consistent with previously published experimental data on binding rate changes with respect to ionic strength. We find that intramolecular electrostatic interactions influence the unbound states of PUMA only marginally. Our results further suggest that intermolecular electrostatic interactions, and in particular non-native electrostatic interactions, are involved in formation of the initial encounter complex. We are able to reveal the binding mechanism in more detail than is possible using experimental data alone however, and in particular we uncover the role of non-native electrostatic interactions. We highlight the potential importance of such electrostatic interactions for describing the binding reactions of IDPs. Such approaches could be used to provide predictions for the results of mutational studies. PMID:28369057
Environmental exposures to metals in Native communities and implications for child development: basis for the Navajo birth cohort study.

PubMed

Lewis, Johnnye; Gonzales, Melissa; Burnette, Courtney; Benally, Malcolm; Seanez, Paula; Shuey, Christopher; Nez, Helen; Nez, Christopher; Nez, Seraphina

2015-01-01

Two disparate statistics often cited for the Western United States raise concern about risks for developmental disabilities in Native American children. First, 13 of the states with the highest percentage of Native American population are located in the Western United States (U.S. Census Bureau, 2012 ). Second, more than 161,000 abandoned hard-rock mines are located in 12 Western states (General Accounting Office, 2014 ). Moreover, numerous studies have linked low-level metals exposure with birth defects and developmental delays. Concern has emerged among tribal populations that metals exposure from abandoned mines might threaten development of future generations.
Optimizing physical energy functions for protein folding.

PubMed

Fujitsuka, Yoshimi; Takada, Shoji; Luthey-Schulten, Zaida A; Wolynes, Peter G

2004-01-01

We optimize a physical energy function for proteins with the use of the available structural database and perform three benchmark tests of the performance: (1) recognition of native structures in the background of predefined decoy sets of Levitt, (2) de novo structure prediction using fragment assembly sampling, and (3) molecular dynamics simulations. The energy parameter optimization is based on the energy landscape theory and uses a Monte Carlo search to find a set of parameters that seeks the largest ratio deltaE(s)/DeltaE for all proteins in a training set simultaneously. Here, deltaE(s) is the stability gap between the native and the average in the denatured states and DeltaE is the energy fluctuation among these states. Some of the energy parameters optimized are found to show significant correlation with experimentally observed quantities: (1) In the recognition test, the optimized function assigns the lowest energy to either the native or a near-native structure among many decoy structures for all the proteins studied. (2) Structure prediction with the fragment assembly sampling gives structure models with root mean square deviation less than 6 A in one of the top five cluster centers for five of six proteins studied. (3) Structure prediction using molecular dynamics simulation gives poorer performance, implying the importance of having a more precise description of local structures. The physical energy function solely inferred from a structural database neither utilizes sequence information from the family of the target nor the outcome of the secondary structure prediction but can produce the correct native fold for many small proteins. Copyright 2003 Wiley-Liss, Inc.
Native American casino gambling in Arizona: A case study of the Fort McDowell reservation.

PubMed

Anders, G C

1996-09-01

Since Congress passed the American Indian Gambling Regulatory Act (IGRA) in 1988, there has been an explosion in the number of gambling casinos located on Native American reservations. It is estimated that in 1994 the total net revenue from 81 Native American casinos exceeded $2.3 billion dollars. As the number of Native American casinos grows along with the volume of gambling activity, opposition increases from states, the established gambling industry hurt by lost revenues, and groups with moral objections to gambling. This article reports on an effort to measure the economic impact of the Fort McDowell casino located near Phoenix, Arizona. The article discusses the casino's history and current operations. Next, it explains the use of an input-output model to compute the impact of casino's income and employment effects on the economy of Maricopa County. It is estimated that the casino is responsible for 2,483 new jobs, and an increase of approximately $80.35 million in regional output. Additional information is necessary to more accurately assess both the benefits and costs of the casino. Unfortunately, subsequent efforts to collect additional data have been unsuccessful. The conclusion discusses why, and raises questions regarding Native American gaming.
Ensemble-based evaluation for protein structure models.

PubMed

Jamroz, Michal; Kolinski, Andrzej; Kihara, Daisuke

2016-06-15

Comparing protein tertiary structures is a fundamental procedure in structural biology and protein bioinformatics. Structure comparison is important particularly for evaluating computational protein structure models. Most of the model structure evaluation methods perform rigid body superimposition of a structure model to its crystal structure and measure the difference of the corresponding residue or atom positions between them. However, these methods neglect intrinsic flexibility of proteins by treating the native structure as a rigid molecule. Because different parts of proteins have different levels of flexibility, for example, exposed loop regions are usually more flexible than the core region of a protein structure, disagreement of a model to the native needs to be evaluated differently depending on the flexibility of residues in a protein. We propose a score named FlexScore for comparing protein structures that consider flexibility of each residue in the native state of proteins. Flexibility information may be extracted from experiments such as NMR or molecular dynamics simulation. FlexScore considers an ensemble of conformations of a protein described as a multivariate Gaussian distribution of atomic displacements and compares a query computational model with the ensemble. We compare FlexScore with other commonly used structure similarity scores over various examples. FlexScore agrees with experts' intuitive assessment of computational models and provides information of practical usefulness of models. https://bitbucket.org/mjamroz/flexscore dkihara@purdue.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.
Ensemble-based evaluation for protein structure models

PubMed Central

Jamroz, Michal; Kolinski, Andrzej; Kihara, Daisuke

2016-01-01

Motivation: Comparing protein tertiary structures is a fundamental procedure in structural biology and protein bioinformatics. Structure comparison is important particularly for evaluating computational protein structure models. Most of the model structure evaluation methods perform rigid body superimposition of a structure model to its crystal structure and measure the difference of the corresponding residue or atom positions between them. However, these methods neglect intrinsic flexibility of proteins by treating the native structure as a rigid molecule. Because different parts of proteins have different levels of flexibility, for example, exposed loop regions are usually more flexible than the core region of a protein structure, disagreement of a model to the native needs to be evaluated differently depending on the flexibility of residues in a protein. Results: We propose a score named FlexScore for comparing protein structures that consider flexibility of each residue in the native state of proteins. Flexibility information may be extracted from experiments such as NMR or molecular dynamics simulation. FlexScore considers an ensemble of conformations of a protein described as a multivariate Gaussian distribution of atomic displacements and compares a query computational model with the ensemble. We compare FlexScore with other commonly used structure similarity scores over various examples. FlexScore agrees with experts’ intuitive assessment of computational models and provides information of practical usefulness of models. Availability and implementation: https://bitbucket.org/mjamroz/flexscore Contact: dkihara@purdue.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307633
Kinetically trapped metastable intermediate of a disulfide-deficient mutant of the starch-binding domain of glucoamylase.

PubMed

Sugimoto, Hayuki; Nakaura, Miho; Nishimura, Shigenori; Karita, Shuichi; Miyake, Hideo; Tanaka, Akiyoshi

2009-08-01

Refolding of a thermally unfolded disulfide-deficient mutant of the starch-binding domain of glucoamylase was investigated using differential scanning calorimetry, isothermal titration calorimetry, CD, and (1)H NMR. When the protein solution was rapidly cooled from a higher temperature, a kinetic intermediate was formed during refolding. The intermediate was unexpectedly stable compared with typical folding intermediates that have short half-lives. It was shown that this intermediate contained substantial secondary structure and tertiary packing and had the same binding ability with beta-cyclodextrin as the native state, suggesting that the intermediate is highly-ordered and native-like on the whole. These characteristics differ from those of partially folded intermediates such as molten globule states. Far-UV CD spectra showed that the secondary structure was once disrupted during the transition from the intermediate to the native state. These results suggest that the intermediate could be an off-pathway type, possibly a misfolded state, that has to undergo unfolding on its way to the native state.
Improvement on a simplified model for protein folding simulation.

PubMed

Zhang, Ming; Chen, Changjun; He, Yi; Xiao, Yi

2005-11-01

Improvements were made on a simplified protein model--the Ramachandran model-to achieve better computer simulation of protein folding. To check the validity of such improvements, we chose the ultrafast folding protein Engrailed Homeodomain as an example and explored several aspects of its folding. The engrailed homeodomain is a mainly alpha-helical protein of 61 residues from Drosophila melanogaster. We found that the simplified model of Engrailed Homeodomain can fold into a global minimum state with a tertiary structure in good agreement with its native structure.
Address to Yukon-Kuskokwim Delta Regional Summit on Native Education (Bethel, Alaska, April 24, 2002).

ERIC Educational Resources Information Center

Ongtooguk, Paul

Remarks of Alaska Native researcher and educator Paul Ongtooguk are presented. Alaska Native students perform worse on exit exams than any other population in the state. In the past, formal education was offered to Alaska Natives only if they gave up being Alaska Natives. The current system is not designed to solve the problems of Alaska Native…
The protein structure prediction problem could be solved using the current PDB library

PubMed Central

Zhang, Yang; Skolnick, Jeffrey

2005-01-01

For single-domain proteins, we examine the completeness of the structures in the current Protein Data Bank (PDB) library for use in full-length model construction of unknown sequences. To address this issue, we employ a comprehensive benchmark set of 1,489 medium-size proteins that cover the PDB at the level of 35% sequence identity and identify templates by structure alignment. With homologous proteins excluded, we can always find similar folds to native with an average rms deviation (RMSD) from native of 2.5 Å with ≈82% alignment coverage. These template structures often contain a significant number of insertions/deletions. The tasser algorithm was applied to build full-length models, where continuous fragments are excised from the top-scoring templates and reassembled under the guide of an optimized force field, which includes consensus restraints taken from the templates and knowledge-based statistical potentials. For almost all targets (except for 2/1,489), the resultant full-length models have an RMSD to native below 6 Å (97% of them below 4 Å). On average, the RMSD of full-length models is 2.25 Å, with aligned regions improved from 2.5 Å to 1.88 Å, comparable with the accuracy of low-resolution experimental structures. Furthermore, starting from state-of-the-art structural alignments, we demonstrate a methodology that can consistently bring template-based alignments closer to native. These results are highly suggestive that the protein-folding problem can in principle be solved based on the current PDB library by developing efficient fold recognition algorithms that can recover such initial alignments. PMID:15653774
A Study of the Diffusion, Electrochemical Mobility and Removal of Dissolved Copper in a Saturated Porous Medium.

DTIC Science & Technology

1980-11-01

aqueous solutions : use of activity coefficients in transition-state models: Geochimica et Cosmochimica Acta, v...native state at 25°C at any activity level below 10+46.0 in an aqueous solution . Because such an activity level is impossible, sodium cannot be reduced...stoichiometric coefficients . It is necessary to calculqte the activity coefficients of dissolved copper in the test solutions in order to render an
Landscape-scale evaluation of asymmetric interactions between Brown Trout and Brook Trout using two-species occupancy models

USGS Publications Warehouse

Wagner, Tyler; Jefferson T. Deweber,; Jason Detar,; John A. Sweka,

2013-01-01

Predicting the distribution of native stream fishes is fundamental to the management and conservation of many species. Modeling species distributions often consists of quantifying relationships between species occurrence and abundance data at known locations with environmental data at those locations. However, it is well documented that native stream fish distributions can be altered as a result of asymmetric interactions between dominant exotic and subordinate native species. For example, the naturalized exotic Brown Trout Salmo trutta has been identified as a threat to native Brook Trout Salvelinus fontinalis in the eastern United States. To evaluate large-scale patterns of co-occurrence and to quantify the potential effects of Brown Trout presence on Brook Trout occupancy, we used data from 624 stream sites to fit two-species occupancy models. These models assumed that asymmetric interactions occurred between the two species. In addition, we examined natural and anthropogenic landscape characteristics we hypothesized would be important predictors of occurrence of both species. Estimated occupancy for Brook Trout, from a co-occurrence model with no landscape covariates, at sites with Brown Trout present was substantially lower than sites where Brown Trout were absent. We also observed opposing patterns for Brook and Brown Trout occurrence in relation to percentage forest, impervious surface, and agriculture within the network catchment. Our results are consistent with other studies and suggest that alterations to the landscape, and specifically the transition from a forested catchment to one that contains impervious surface or agriculture, reduces the occurrence probability of wild Brook Trout. Our results, however, also suggest that the presence of Brown Trout results in lower occurrence probability of Brook Trout over a range of anthropogenic landscape characteristics, compared with streams where Brown Trout were absent.
Comparison of potentially preventable hospitalizations related to diabetes among Native Hawaiian, Chinese, Filipino, and Japanese elderly compared with whites, Hawai'i, December 2006-December 2010.

PubMed

Sentell, Tetine L; Ahn, Hyeong Jun; Juarez, Deborah T; Tseng, Chien-Wen; Chen, John J; Salvail, Florentina R; Miyamura, Jill; Mau, Marjorie L M

2013-07-25

Approximately 25% of individuals aged 65 years or older in the United States have diabetes mellitus. Diabetes rates in this age group are higher for Asian American and Pacific Islanders (AA/PI) than for whites. We examined racial/ethnic differences in diabetes-related potentially preventable hospitalizations (DRPH) among people aged 65 years or older for Japanese, Chinese, Filipinos, Native Hawaiians, and whites. Discharge data for hospitalizations in Hawai'i for people aged 65 years or older from December 2006 through December 2010 were compared. Annual rates of DRPH by patient were calculated for each racial/ethnic group by sex. Rate ratios (RRs) were calculated relative to whites. Multivariable models controlling for insurer, comorbidity, diabetes prevalence, age, and residence location provided final adjusted rates and RRs. A total of 1,815 DRPH were seen from 1,515 unique individuals. Unadjusted RRs for DRPH by patient were greater than 1 in all AA/PI study groups compared with whites, but were highest among Native Hawaiians and Filipinos [corrected]. In fully adjusted models accounting for higher diabetes prevalence in AA/PI groups, Native Hawaiian (adjusted rate ratio [aRR] = 1.59), Filipino (aRR = 2.26), and Japanese (aRR = 1.86) men retained significantly higher rates of diabetes-related potentially preventable hospitalizations than whites, as did Filipino women (aRR = 1.61). Native Hawaiian, Filipino, and Japanese men and Filipino women aged 65 years or older have a higher risk than whites for DRPH. Health care providers and public health programs for elderly patients should consider effective programs to reduce potentially preventable hospitalizations among Native Hawaiian, Filipino, and Japanese men and Filipino women aged 65 years or older.
A Model of Mandarin Tone Categories--A Study of Perception and Production

ERIC Educational Resources Information Center

Yang, Bei

2010-01-01

The current study lays the groundwork for a model of Mandarin tones based on both native speakers' and non-native speakers' perception and production. It demonstrates that there is variability in non-native speakers' tone productions and that there are differences in the perceptual boundaries in native speakers and non-native speakers. There…
North Dakota Native American Essential Understandings

ERIC Educational Resources Information Center

North Dakota Department of Public Instruction, 2015

2015-01-01

In the spring of 2015, the North Dakota Department of Public Instruction brought together tribal Elders from across North Dakota to share stories, memories, songs, and wisdom in order to develop the North Dakota Native American Essential Understandings (NDNAEU) to guide the learning of both Native and non-Native students across the state. They…
Tamarisk coalition - native riparian plant materials program

Treesearch

Stacy Kolegas

2012-01-01

The Tamarisk Coalition (TC), a nonprofit organization dedicated to riparian restoration in the western United States, has created a Native Plant Materials Program to address the identified need for native riparian plant species for use in revegetation efforts on the Colorado Plateau. The specific components of the Native Plant Materials Program include: 1) provide seed...

36 CFR 51.83 - Sale of Native Handicrafts.

Code of Federal Regulations, 2010 CFR

2010-07-01

... in the Metalakatla Indian Community), Eskimo, or Aleut blood, or combination thereof. The term... includes, in the absence of a minimum blood quantum, any citizen of the United States who is regarded as an Alaska Native by the Alaska native village or native groups of which he or she claims to be a member and...
Population Structure, Diversity and Reproductive Mode of the Grape Phylloxera (Daktulosphaira vitifoliae) across Its Native Range

PubMed Central

Walker, M. Andrew

2017-01-01

Grape Phylloxera, Daktulosphaira vitifoliae, is a gall-forming insect that feeds on the leaves and roots of many Vitis species. The roots of the cultivated V. vinifera cultivars and hybrids are highly susceptible to grape phylloxera feeding damage. The native range of this insect covers most of North America, and it is particularly abundant in the eastern and central United States. Phylloxera was introduced from North America to almost all grape-growing regions across five of the temperate zone continents. It devastated vineyards in each of these regions causing large-scale disruptions to grape growers, wine makers and national economies. In order to understand the population diversity of grape phylloxera in its native range, more than 500 samples from 19 States and 34 samples from the introduced range (northern California, Europe and South America) were genotyped with 32 simple sequence repeat markers. STRUCTURE, a model based clustering method identified five populations within these samples. The five populations were confirmed by a neighbor-joining tree and principal coordinate analysis (PCoA). These populations were distinguished by their Vitis species hosts and their geographic locations. Samples collected from California, Europe and South America traced back to phylloxera sampled in the northeastern United States on V. riparia, with some influence from phylloxera collected along the Atlantic Coast and Central Plains on V. vulpina. Reproductive statistics conclusively confirmed that sexual reproduction is common in the native range and is combined with cyclical parthenogenesis. Native grape phylloxera populations were identified to be under Hardy-Weinberg equilibrium. The identification of admixed samples between many of these populations indicates that shared environments facilitate sexual reproduction between different host associated populations to create new genotypes of phylloxera. This study also found that assortative mating might occur across the sympatric range of the V. vulpina west and V. cinerea populations. PMID:28125736
Distribution and abundance of saltcedar and Russian olive in the western United States

USGS Publications Warehouse

Nagler, Pamela L.; Glenn, Edward P.; Jarnevich, Catherine S.; Shafroth, Patrick B.

2011-01-01

Over the past century, two introduced Eurasian trees, saltcedar (Tamarix spp.) and Russian olive (Elaeagnus angustifolia) have become wide spread on western United States of American (U.S.) rivers. This paper reviews the literature on the following five key areas related to their distribution and abundance in the western United States: (1) the history of introduction, planting, and spread of saltcedar and Russian olive; (2) their current distribution; (3) their current abundance; (4) factors controlling their current distribution and abundance; and (5) models that have been developed to predict their future distribution and abundance. Saltcedar and Russian olive are now the third and fourth most frequently occurring woody riparian plants and the second and fifth most abundant species (out of 42 native and non-native species) along rivers in the western United States. Currently there is not a precise estimate of the areas that these species occupy in the entire West. Climatic variables are important determinants of their distribution and abundance. For example, saltcedar is limited by its sensitivity to hard freezes, whereas Russian olive appears to have a chilling requirement for bud break and seed germination, and can presumably survive colder winter temperatures. Either species can be dominant, co-dominant or sub-dominant relative to native species on a given river system. A number of environmental factors such as water availability, soil salinity, degree of stream flow regulation, and fire frequency can influence the abundance of these species relative to native species. Numerous studies suggest that both species have spread on western rivers primarily through a replacement process, whereby stress-tolerant species have moved into expanded niches that are no longer suitable for mesic native pioneer species. Better maps of current distribution and rigorous monitoring of distributional changes though time can help to resolve differences in predictions of potential future spread. An adequate understanding does not yet exist of what fraction of western riparian zones is resistant to dominance by either of these species, what fraction is at risk and could benefit from intervention, and what fraction has been altered to the point that saltcedar or Russian olive are most likely to thrive.
Protection policy for Hawaii's native wildlife during geothermal energy development

NASA Astrophysics Data System (ADS)

Hannah, Lee

1986-09-01

Hawaii possesses abundant geothermal resources and rare native wildlife. Geothermal energy development has not posed a threat to native wildlife in the past, but development potential has recently reached a level at which concern for native wildlife is warranted. Potential geothermal resource areas in Hawaii intersect important native forest and endangered species habitat. The ability of existing laws to constrain development in these areas is in question. State and federal endangered species and environmental reporting laws have little ability to constrain geothermal development on private land. Hawaii's Land Use Law had been viewed by conservationists as protecting natural areas important to native wildlife, but recent decisions of the state Land Board sharply challenge this view. While this dispute was being resolved in the courts, the state legislature passed the Geothermal Subzone Act of 1983. Wildlife value was assessed in the geothermal subzone designation process mandated by this act, but the subzones designated primarily reflected inappropriate developer influence. All areas in which there was developer interest received subzone designation, and no area in which there was no developer interest was subzoned. This overriding emphasis on developer interest violated the intent of the sub-zone act, and trivialized the importance of other assessment criteria, among them native wildlife values.
Wind Power on Native American Lands: Opportunities, Challenges, and Status (Poster)

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

Jimenez, A.; Johnson, P. B.; Gough, R.

2007-06-01

The United States is home to more than 700 American Indian tribes and Native Alaska villages and corporations located on 96 million acres. Many of these tribes and villages have excellent wind resources that could be commercially developed to meet their electricity needs or for electricity export. This conference poster for Windpower 2007 describes the opportunities, challenges, and status of wind energy projects on Native American lands in the United States.
Achievement Gap Patterns of Grade 8 American Indian and Alaska Native Students in Reading and Math. Issues & Answers. REL 2009-No. 073

ERIC Educational Resources Information Center

Nelson, Steven; Greenough, Richard; Sage, Nicole

2009-01-01

Focusing on student proficiency in reading and math from 2003-04 to 2006-07, this report compares gaps in performance on state achievement tests between grade 8 American Indian and Alaska Native students and all other grade 8 students in 26 states serving large populations of American Indian and Alaska Native students. In response to a request by…
Direct folding simulation of a long helix in explicit water

NASA Astrophysics Data System (ADS)

Gao, Ya; Lu, Xiaoliang; Duan, Lili; Zhang, Dawei; Mei, Ye; Zhang, John Z. H.

2013-05-01

A recently proposed Polarizable Hydrogen Bond (PHB) method has been employed to simulate the folding of a 53 amino acid helix (PDB ID 2KHK) in explicit water. Under PHB simulation, starting from a fully extended structure, the peptide folds into the native state as confirmed by measured time evolutions of radius of gyration, root mean square deviation (RMSD), and native hydrogen bond. Free energy and cluster analysis show that the folded helix is thermally stable under the PHB model. Comparison of simulation results under, respectively, PHB and standard nonpolarizable force field demonstrates that polarization is critical for stable folding of this long α-helix.
Natural succession impeded by smooth brome (Bromus inermis) and intermediate wheatgrass (Agropyron intermedium) in an abandoned agricultural field

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

Nelson, J.K.

1997-11-01

In 1975, an abandoned agricultural field at Rocky Flats Environmental Technology Site (Site) that had been cultivated for more than 38 years, was seeded with smooth brome (Bromus inermis) and intermediate wheatgrass (Agropyron intermedium). Although these species are commonly planted in reclamation and roadside seed mixtures, few studies have documented their impact on the re-establishment of native plant communities. In 1994, species richness, cover, and biomass were sampled in the agricultural field and compared to the surrounding mixed-grass prairie at the Site. The agricultural field contained only 61 plant species (62% native), compared to 143 species (81% native) in themore » surrounding mixed-grass prairie. Community similarity based on species presence/absence was 0.47 (Sorensen coefficient of similarity). Basal vegetative cover was 11.2% in the agricultural field and 29.1% in the mixed-grass prairie. Smooth brome and intermediate wheatgrass accounted for 93% of the relative foliar cover and 96% of the biomass in the agricultural field. The aggressive nature of these two planted species has impeded the natural succession of the agricultural field to a more native prairie community. Studies of natural succession on abandoned fields and roads in northeastern Colorado have indicated that if left alone, fields would return to their native climax state in approximately 50 years and would be approaching their native state after 20--25 years. Based on the results of this study, this agricultural field may take more than 100 years to return to a native mixed-grass prairie state and it may never achieve a native state without human intervention.« less
A Prescription for Success.

ERIC Educational Resources Information Center

Oros, Tia

1993-01-01

Describes the Native American Pharmacy Program at North Dakota State University (Fargo), which recruits Native American students into the field of pharmacy, offers summer enrichment programs for Native American secondary and college students and provides scholarships and student support services. (LP)
Assessing state-wide biodiversity in the Florida Gap analysis project

USGS Publications Warehouse

Pearlstine, L.G.; Smith, S.E.; Brandt, L.A.; Allen, Craig R.; Kitchens, W.M.; Stenberg, J.

2002-01-01

The Florida Gap (FI-Gap) project provides an assessment of the degree to which native animal species and natural communities are or are not represented in existing conservation lands. Those species and communities not adequately represented in areas being managed for native species constitute 'gaps' in the existing network of conservation lands. The United States Geological Survey Gap Analysis Program is a national effort and so, eventually, all 50 states will have completed it. The objective of FI-Gap was to provide broad geographic information on the status of terrestrial vertebrates, butterflies, skippers and ants and their respective habitats to address the loss of biological diversity. To model the distributions and potential habitat of all terrestrial species of mammals, breeding birds, reptiles, amphibians, butterflies, skippers and ants in Florida, natural land cover was mapped to the level of dominant or co-dominant plant species. Land cover was classified from Landsat Thematic Mapper (TM) satellite imagery and auxiliary data such as the national wetlands inventory (NWI), soils maps, aerial imagery, existing land use/land cover maps, and on-the-ground surveys, Wildlife distribution models were produced by identifying suitable habitat for each species within that species' range, Mammalian models also assessed a minimum critical area required for sustainability of the species' population. Wildlife species richness was summarized against land stewardship ranked by an area's mandates for conservation protection. ?? 2002 Elsevier Science Ltd. All rights reserved.
Effects of desolvation barriers and sidechains on local-nonlocal coupling and chevron behaviors in coarse-grained models of protein folding.

PubMed

Chen, Tao; Chan, Hue Sun

2014-04-14

Local-nonlocal coupling is an organizational principle in protein folding. It envisions a cooperative energetic interplay between local conformational preferences and favorable nonlocal contacts. Previous theoretical studies by our group showed that two classes of native-centric coarse-grained models can capture the experimentally observed high degrees of protein folding cooperativity and diversity in folding rates. These models either embody an explicit local-nonlocal coupling mechanism or incorporate desolvation barriers in the models' pairwise interactions. Here a conceptual connection is made between these two paradigmatic coarse-grained interaction schemes by showing that desolvation barriers enhance local-nonlocal coupling. Furthermore, we find that a class of coarse-grained protein models with a single-site representation of sidechains also increases local-nonlocal coupling relative to mainchain models without sidechains. Enhanced local-nonlocal coupling generally leads to higher folding cooperativity and chevron plots with more linear folding arms. For the sidechain models studied, the chevron plot simulated with entirely native-centric intrachain interactions behaves very similarly to the corresponding chevron plots simulated with interactions that are partly modulated by sequence- and denaturant-dependent transfer free energies. In these essentially native-centric models, the mild chevron rollovers in the simulated folding arm are caused by occasionally populated intermediates as well as the movement of the unfolded and putative folding transition states. The strength and limitation of the models are analyzed by comparison with experiment. New formulations of sidechain models that may provide a physical account for nonnative interactions are also explored.
Evidence for a Shared Mechanism in the Formation of Urea-Induced Kinetic and Equilibrium Intermediates of Horse Apomyoglobin from Ultrarapid Mixing Experiments.

PubMed

Mizukami, Takuya; Abe, Yukiko; Maki, Kosuke

2015-01-01

In this study, the equivalence of the kinetic mechanisms of the formation of urea-induced kinetic folding intermediates and non-native equilibrium states was investigated in apomyoglobin. Despite having similar structural properties, equilibrium and kinetic intermediates accumulate under different conditions and via different mechanisms, and it remains unknown whether their formation involves shared or distinct kinetic mechanisms. To investigate the potential mechanisms of formation, the refolding and unfolding kinetics of horse apomyoglobin were measured by continuous- and stopped-flow fluorescence over a time range from approximately 100 μs to 10 s, along with equilibrium unfolding transitions, as a function of urea concentration at pH 6.0 and 8°C. The formation of a kinetic intermediate was observed over a wider range of urea concentrations (0-2.2 M) than the formation of the native state (0-1.6 M). Additionally, the kinetic intermediate remained populated as the predominant equilibrium state under conditions where the native and unfolded states were unstable (at ~0.7-2 M urea). A continuous shift from the kinetic to the equilibrium intermediate was observed as urea concentrations increased from 0 M to ~2 M, which indicates that these states share a common kinetic folding mechanism. This finding supports the conclusion that these intermediates are equivalent. Our results in turn suggest that the regions of the protein that resist denaturant perturbations form during the earlier stages of folding, which further supports the structural equivalence of transient and equilibrium intermediates. An additional folding intermediate accumulated within ~140 μs of refolding and an unfolding intermediate accumulated in <1 ms of unfolding. Finally, by using quantitative modeling, we showed that a five-state sequential scheme appropriately describes the folding mechanism of horse apomyoglobin.
Using state-and-transition models to project cheatgrass and juniper invasion in Southeastern Oregon sagebrush steppe

Treesearch

Megan K. Creutzburg; Joshua S. Halofsky; Miles A. Hemstrom

2012-01-01

Many threats are jeopardizing the sagebrush steppe of the Columbia Basin, including the spread of invasive species such as cheatgrass (Bromus tectorum L.) and the expansion of western juniper (Juniperus occidentalis Hook.) into historic shrub steppe. Native sagebrush steppe provides productive grazing lands and important...
A prototype application of state and transition simulation modeling in support of grassland management

Treesearch

Matt Reeves; Paulette Ford; Leonardo Frid; David Augustine; Justin Derner

2016-01-01

The Great Plains grasslands of North America provide a multitude of ecosystem services including clean water, forage, habitat, recreation, and pollination of native and agricultural plants. A general lack of quantitative information regarding the effects of varied management strategies on these spatially heterogeneous landscapes complicates our understanding...
Challenges in Applying Indigenous Evaluation Practices in Mainstream Grant Programs to Indigenous Communities

ERIC Educational Resources Information Center

Grover, Jane Gray

2008-01-01

How can indigenous evaluators implement culturally competent models in First Nations communities while ensuring that government grant evaluation requirements are met? Through describing the challenges in one tribal community in the United States, this article will discuss how American Indian/Alaska Native substance abuse prevention programs are…
Taming Malaria: A New Health Model for the Indigenous Populations in Brazil.

ERIC Educational Resources Information Center

Martins, Leda Leitao

1999-01-01

In the late 1980s, a gold rush in Roraima state, Brazil, had devastating effects on the health of indigenous populations. Since then, a new health system emerged combining the assets of nongovernmental organizations, government agencies, and Native peoples such as the Macuxi. Community-chosen indigenous health workers and microscope technicians…
Community-level plant-soil feedbacks explain landscape distribution of native and non-native plants.

PubMed

Kulmatiski, Andrew

2018-02-01

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

PubMed Central

Bahar, Ivet; Lezon, Timothy R.; Yang, Lee-Wei; Eyal, Eran

2010-01-01

Biomolecular systems possess unique, structure-encoded dynamic properties that underlie their biological functions. Recent studies indicate that these dynamic properties are determined to a large extent by the topology of native contacts. In recent years, elastic network models used in conjunction with normal mode analyses have proven to be useful for elucidating the collective dynamics intrinsically accessible under native state conditions, including in particular the global modes of motions that are robustly defined by the overall architecture. With increasing availability of structural data for well-studied proteins in different forms (liganded, complexed, or free), there is increasing evidence in support of the correspondence between functional changes in structures observed in experiments and the global motions predicted by these coarse-grained analyses. These observed correlations suggest that computational methods may be advantageously employed for assessing functional changes in structure and allosteric mechanisms intrinsically favored by the native fold. PMID:20192781
Global dynamics of proteins: bridging between structure and function.

PubMed

Bahar, Ivet; Lezon, Timothy R; Yang, Lee-Wei; Eyal, Eran

2010-01-01

Biomolecular systems possess unique, structure-encoded dynamic properties that underlie their biological functions. Recent studies indicate that these dynamic properties are determined to a large extent by the topology of native contacts. In recent years, elastic network models used in conjunction with normal mode analyses have proven to be useful for elucidating the collective dynamics intrinsically accessible under native state conditions, including in particular the global modes of motions that are robustly defined by the overall architecture. With increasing availability of structural data for well-studied proteins in different forms (liganded, complexed, or free), there is increasing evidence in support of the correspondence between functional changes in structures observed in experiments and the global motions predicted by these coarse-grained analyses. These observed correlations suggest that computational methods may be advantageously employed for assessing functional changes in structure and allosteric mechanisms intrinsically favored by the native fold.
Alaska Native Villages and Rural Communities Water Grant Program

EPA Pesticide Factsheets

Significant human health and water quality problems exist in Alaska Native Village and other rural communities in the state due to lack of sanitation. To address these issues, EPA created the Alaska Rural and Native Villages Grant Program.

Salish Kootenai College Project for Recruitment and Retention of Native Americans in Associate Degree Nursing. Final Report.

ERIC Educational Resources Information Center

Dolberry, Jacque

The purpose of the Salish Koontenai College (SKC) Project for Recruitment and Retention of Native Americans in Associate Degree Nursing was to increase the numbers of Native American registered nurses providing health care to the Native American population of Montana and the northwest mountain states. Recruitment and retention efforts targeted…
Adversity and Resiliency in the Lives of Native Hawaiian Elders

ERIC Educational Resources Information Center

Browne, Colette V.; Mokuau, Noreen; Braun, Kathryn L.

2009-01-01

Native Hawaiians constitute 401,000 or 0.1 percent of the total U.S. population, with approximately 60 percent residing in the state of Hawai'i. In Hawai'i, Native Hawaiian elders ("na kupuna") face a number of social and health disparities when compared with their non-Native Hawaiian counterparts: higher rates of poverty, greater…
Integrating subsistence practice and species distribution modeling: assessing invasive elodea’s potential impact on Native Alaskan subsistence of Chinook salmon and whitefish

USGS Publications Warehouse

Luizza, Matthew; Evangelista, Paul; Jarnevich, Catherine S.; West, Amanda; Stewart, Heather

2016-01-01

Alaska has one of the most rapidly changing climates on earth and is experiencing an accelerated rate of human disturbance, including resource extraction and transportation infrastructure development. Combined, these factors increase the state’s vulnerability to biological invasion, which can have acute negative impacts on ecological integrity and subsistence practices. Of growing concern is the spread of Alaska’s first documented freshwater aquatic invasive plant Elodea spp. (elodea). In this study, we modeled the suitable habitat of elodea using global and state-specific species occurrence records and environmental variables, in concert with an ensemble of model algorithms. Furthermore, we sought to incorporate local subsistence concerns by using Native Alaskan knowledge and available statewide subsistence harvest data to assess the potential threat posed by elodea to Chinook salmon (Oncorhynchus tshawytscha) and whitefish (Coregonus nelsonii) subsistence. State models were applied to future climate (2040–2059) using five general circulation models best suited for Alaska. Model evaluations indicated that our results had moderate to strong predictability, with area under the receiver-operating characteristic curve values above 0.80 and classification accuracies ranging from 66 to 89 %. State models provided a more robust assessment of elodea habitat suitability. These ensembles revealed different levels of management concern statewide, based on the interaction of fish subsistence patterns, known spawning and rearing sites, and elodea habitat suitability, thus highlighting regions with additional need for targeted monitoring. Our results suggest that this approach can hold great utility for invasion risk assessments and better facilitate the inclusion of local stakeholder concerns in conservation planning and management.
Activities commemorating John B. Herrington as first Native American astronaut

NASA Technical Reports Server (NTRS)

2002-01-01

KENNEDY SPACE CENTER, FLA. -- Seminole Native American Veterans serve as color guard during a pre-launch Native American ceremony at the Rocket Garden in the KSC Visitor Complex. David Nunez, U.S. Navy, carries the State of Florida Flag; David Stephen Bowers, U.S. Army, carries the Flag of the United States of America; Charles Billie Hiers, U.S. Marine Corps., carries the Seminole Tribe of Florida Flag. The ceremony was part of several days' activities commemorating John B. Herrington as the first tribally enrolled Native American astronaut to fly on a Shuttle mission. Herrington is a Mission Specialist on STS-113.
Supercharging with Trivalent Metal Ions in Native Mass Spectrometry

PubMed Central

Flick, Tawnya G.; Williams, Evan R.

2012-01-01

Addition of 1.0 mM LaCl3 to aqueous ammonium acetate solutions containing proteins in their folded native forms can result in a significant increase in the molecular ion charging obtained with electrospray ionization as a result of cation adduction. In combination with m-nitrobenzyl alcohol, molecular ion charge states that are greater than the number of basic sites in the protein can be produced from these native solutions, even for lysozyme, which is conformationally constrained by four intramolecular disulfide bonds. Circular dichroism spectroscopy indicates that the conformation of ubiquitin is not measurably affected with up to 1.0 M LaCl3, but ion mobility data indicate that the high charge states that are formed when 1.0 mM LaCl3 is present are more unfolded than the low charge states formed without this reagent. These and other results indicate that the increased charging is a result of La3+ preferentially adducting onto compact or more native-like conformers during ESI and the gas-phase ions subsequently unfolding as a result of increased Coulomb repulsion. Electron capture dissociation of these high charge-state ions formed from these native solutions results in comparable sequence coverage to that obtained for ions formed from denaturing solutions without supercharging reagents, making this method a potentially powerful tool for obtaining structural information in native mass spectrometry. PMID:22948901
Foreign nurse importation and the supply of native nurses.

PubMed

Cortés, Patricia; Pan, Jessica

2014-09-01

The importation of foreign registered nurses has been used as a strategy to ease nursing shortages in the United States. The effectiveness of this policy depends critically on the long-run response of native nurses. We examine the effects of immigration of foreign-born registered nurses on the long-run employment and occupational choice of native nurses. Using a variety of empirical strategies that exploit the geographical distribution of immigrant nurses across US cities, we find evidence of large displacement effects - over a ten-year period, for every foreign nurse that migrates to a city, between 1 and 2 fewer native nurses are employed in the city. We find similar results using data on nursing board exam-takers at the state level - an increase in the flow of foreign nurses significantly reduces the number of natives sitting for licensure exams in more dependent states relative to less dependent states. Using data on self-reported workplace satisfaction among a sample of California nurses, we find suggestive evidence that part of the displacement effects could be driven by a decline in the perceived quality of the workplace environment. Copyright © 2014 Elsevier B.V. All rights reserved.
Thermal fluctuations of immature SOD1 lead to separate folding and misfolding pathways

PubMed Central

Sekhar, Ashok; Rumfeldt, Jessica AO; Broom, Helen R; Doyle, Colleen M; Bouvignies, Guillaume; Meiering, Elizabeth M; Kay, Lewis E

2015-01-01

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease involving cytotoxic conformations of Cu, Zn superoxide dismutase (SOD1). A major challenge in understanding ALS disease pathology has been the identification and atomic-level characterization of these conformers. Here, we use a combination of NMR methods to detect four distinct sparsely populated and transiently formed thermally accessible conformers in equilibrium with the native state of immature SOD1 (apoSOD12SH). Structural models of two of these establish that they possess features present in the mature dimeric protein. In contrast, the other two are non-native oligomers in which the native dimer interface and the electrostatic loop mediate the formation of aberrant intermolecular interactions. Our results show that apoSOD12SH has a rugged free energy landscape that codes for distinct kinetic pathways leading to either maturation or non-native association and provide a starting point for a detailed atomic-level understanding of the mechanisms of SOD1 oligomerization. DOI: http://dx.doi.org/10.7554/eLife.07296.001 PMID:26099300
Resolution of the unfolded state.

NASA Astrophysics Data System (ADS)

Beaucage, Gregory

2008-03-01

The unfolded states in proteins and nucleic acids remain weakly understood despite their importance to protein folding; misfolding diseases (Parkinson's & Alzheimer's); natively unfolded proteins (˜ 30% of eukaryotic proteins); and to understanding ribozymes. Research has been hindered by the inability to quantify the residual (native) structure present in an unfolded protein or nucleic acid. Here, a scaling model is proposed to quantify the degree of folding and the unfolded state (Beaucage, 2004, 2007). The model takes a global view of protein structure and can be applied to a number of analytic methods and to simulations. Three examples are given of application to small-angle scattering from pressure induced unfolding of SNase (Panick, 1998), from acid unfolded Cyt c (Kataoka, 1993) and from folding of Azoarcus ribozyme (Perez-Salas, 2004). These examples quantitatively show 3 characteristic unfolded states for proteins, the statistical nature of a folding pathway and the relationship between extent of folding and chain size during folding for charge driven folding in RNA. Beaucage, G., Biophys. J., in press (2007). Beaucage, G., Phys. Rev. E. 70, 031401 (2004). Kataoka, M., Y. Hagihara, K. Mihara, Y. Goto J. Mol. Biol. 229, 591 (1993). Panick, G., R. Malessa, R. Winter, G. Rapp, K. J. Frye, C. A. Royer J. Mol. Biol. 275, 389 (1998). Perez-Salas U. A., P. Rangan, S. Krueger, R. M. Briber, D. Thirumalai, S. A. Woodson, Biochemistry 43 1746 (2004).
Modeling-independent elucidation of inactivation pathways in recombinant and native A-type Kv channels.

PubMed

Fineberg, Jeffrey D; Ritter, David M; Covarrubias, Manuel

2012-11-01

A-type voltage-gated K(+) (Kv) channels self-regulate their activity by inactivating directly from the open state (open-state inactivation [OSI]) or by inactivating before they open (closed-state inactivation [CSI]). To determine the inactivation pathways, it is often necessary to apply several pulse protocols, pore blockers, single-channel recording, and kinetic modeling. However, intrinsic hurdles may preclude the standardized application of these methods. Here, we implemented a simple method inspired by earlier studies of Na(+) channels to analyze macroscopic inactivation and conclusively deduce the pathways of inactivation of recombinant and native A-type Kv channels. We investigated two distinct A-type Kv channels expressed heterologously (Kv3.4 and Kv4.2 with accessory subunits) and their native counterparts in dorsal root ganglion and cerebellar granule neurons. This approach applies two conventional pulse protocols to examine inactivation induced by (a) a simple step (single-pulse inactivation) and (b) a conditioning step (double-pulse inactivation). Consistent with OSI, the rate of Kv3.4 inactivation (i.e., the negative first derivative of double-pulse inactivation) precisely superimposes on the profile of the Kv3.4 current evoked by a single pulse because the channels must open to inactivate. In contrast, the rate of Kv4.2 inactivation is asynchronous, already changing at earlier times relative to the profile of the Kv4.2 current evoked by a single pulse. Thus, Kv4.2 inactivation occurs uncoupled from channel opening, indicating CSI. Furthermore, the inactivation time constant versus voltage relation of Kv3.4 decreases monotonically with depolarization and levels off, whereas that of Kv4.2 exhibits a J-shape profile. We also manipulated the inactivation phenotype by changing the subunit composition and show how CSI and CSI combined with OSI might affect spiking properties in a full computational model of the hippocampal CA1 neuron. This work unambiguously elucidates contrasting inactivation pathways in neuronal A-type Kv channels and demonstrates how distinct pathways might impact neurophysiological activity.
Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes.

PubMed

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.
Non-Native α-Helices in the Initial Folding Intermediate Facilitate the Ordered Assembly of the β-Barrel in β-Lactoglobulin.

PubMed

Sakurai, Kazumasa; Yagi, Masanori; Konuma, Tsuyoshi; Takahashi, Satoshi; Nishimura, Chiaki; Goto, Yuji

2017-09-12

The roles of non-native α-helices frequently observed in the initial folding stage of β-sheet proteins have been examined for many years. We herein investigated the residue-level structures of several mutants of bovine β-lactoglobulin (βLG) in quenched-flow pH-pulse labeling experiments. βLG assumes a collapsed intermediate with a non-native α-helical structure (I 0 ) in the early stage of folding, although its native form is predominantly composed of β-structures. The protection profile in I 0 of pseudo-wild type (WT*) βLG was found to deviate from the pattern of the "average area buried upon folding" (AABUF). In particular, the level of protection at the region of strand A, at which non-native α-helices form in the I 0 state, was significantly low compared to AABUF. G17E, the mutant with an increased helical propensity, showed a similar protection pattern. In contrast, the protection pattern for I 0 of E44L, the mutant with an increased β-sheet propensity, was distinct from that of WT* and resembled the AABUF pattern. Transverse relaxation measurements demonstrated that the positions of the residual structures in the unfolded states of these mutants were consistent with those of the protected residues in the respective I 0 states. On the basis of the slower conversion of I 0 to the native state for E44L to that for WT*, non-native α-helices facilitate the ordered assembly of the β-barrel by preventing interactions that trap folding.
Native Hydrophobic Binding Interactions at the Transition State for Association between the TAZ1 Domain of CBP and the Disordered TAD-STAT2 Are Not a Requirement.

PubMed

Lindström, Ida; Dogan, Jakob

2017-08-15

A significant fraction of the eukaryotic proteome consists of proteins that are either partially or completely disordered under native-like conditions. Intrinsically disordered proteins (IDPs) are common in protein-protein interactions and are involved in numerous cellular processes. Although many proteins have been identified as disordered, much less is known about the binding mechanisms of the coupled binding and folding reactions involving IDPs. Here we have analyzed the rate-limiting transition state for binding between the TAZ1 domain of CREB binding protein and the intrinsically disordered transactivation domain of STAT2 (TAD-STAT2) by site-directed mutagenesis and kinetic experiments (Φ-value analysis) and found that the native protein-protein binding interface is not formed at the transition state for binding. Instead, native hydrophobic binding interactions form late, after the rate-limiting barrier has been crossed. The association rate constant in the absence of electrostatic enhancement was determined to be rather high. This is consistent with the Φ-value analysis, which showed that there are few or no obligatory native contacts. Also, linear free energy relationships clearly demonstrate that native interactions are cooperatively formed, a scenario that has usually been observed for proteins that fold according to the so-called nucleation-condensation mechanism. Thus, native hydrophobic binding interactions at the rate-limiting transition state for association between TAD-STAT2 and TAZ1 are not a requirement, which is generally in agreement with previous findings on other IDP systems and might be a common mechanism for IDPs.
75 FR 65611 - Native American Tribal Insignia Database

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-26

... DEPARTMENT OF COMMERCE Patent and Trademark Office Native American Tribal Insignia Database ACTION... comprehensive database containing the official insignia of all federally- and State- recognized Native American... to create this database. The USPTO database of official tribal insignias assists trademark attorneys...
Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions.

PubMed

Materese, Christopher Kroboth; Goldmon, Christa Charisse; Papoian, Garegin A

2008-08-05

The native state dynamics of the small globular serine protease inhibitor eglin c has been studied in a long 336 ns computer simulation in explicit solvent. We have elucidated the energy landscape explored during the course of the simulation by using Principal Component Analysis. We observe several basins in the energy landscape in which the system lingers for extended periods. Through an iterative process we have generated a tree-like hierarchy of states describing the observed dynamics. We observe a range of divergent contact types including salt bridges, hydrogen bonds, hydrophilic interactions, and hydrophobic interactions, pointing to the frustration between competing interactions. Additionally, we find evidence of competing water-mediated interactions. Divergence in water-mediated interactions may be found to supplement existing direct contacts, but they are also found to be independent of such changes. Water-mediated contacts facilitate interactions between residues of like charge as observed in the simulation. Our results provide insight into the complexity of the dynamic native state of a globular protein and directly probe the residual frustration in the native state.
Creating Pathways toward Geoscience Education for Native American Youth: The Importance of Cultural Relevance and Self-Concept

ERIC Educational Resources Information Center

Unsworth, Sara; Riggs, Eric M.; Chavez, Marc

2012-01-01

Native American nations in the United States have a unique legal status that is rooted in a complex relationship between the United States federal government, individual state and local governments and tribal authorities. Although geosciences are often at the center of these relationships, especially as they pertain to the development of natural…
Role of macromolecular crowding and salt ions on the structural-fluctuation of a highly compact configuration of carbonmonoxycytochrome c.

PubMed

Kumar, Rajesh; Sharma, Deepak; Jain, Rishu; Kumar, Sandeep; Kumar, Rajesh

2015-12-01

Carbonmonoxycytochrome c refolds to a native-like compact state (NCO-state), where the non-native Fe(2+)-CO interaction persists. Structural and molecular properties extracted from CD, fluorescence and NMR experiments reveal that the NCO-state shows the generic properties of molten globules. Slow thermal-dissociation of CO transforms the NCO-state to native-state (N-state), where the native Fe(2+)-M80 bond recovers. To determine the role of crowding agents and salt ions on the structural-fluctuation of NCO, the kinetic and thermodynamic parameters for CO-dissociation from NCO (NCO→N+CO) were measured at varying concentrations of crowding agents (dextran 70, dextran 40, ficoll 70) and salt ions (anion: ClO4(-), I(-), Br(-), NO3(-), Cl(-); cation: NH4(+), K(+), Na(+)). As [crowding agent] or [ion] is increased, the rate coefficient of CO-dissociation (kdiss) decreases exponentially. Furthermore, the extent of decrease in kdiss is found to be dependent on (i) size, charge density and charge dispersion of the ion, and (ii) size, shape, and viscosity of the crowding agent. Copyright © 2015 Elsevier B.V. All rights reserved.
Selective herbicide applications for low impact vegetation management of exotic species and enhancement of native plant communities

Treesearch

Max Williamson

1998-01-01

Selective and specific management for the control of exotic (non-native) plants is necessary for preservation of native plant communities. Managers of federal, state, or county land holdings and parks, wildlife areas, recreation areas, and historic sites are frequently charged with selectively managing the enhancement of desirable or native plant communities. In...
Modeling the response of native steelhead to hatchery supplementation programs in an Idaho River

USGS Publications Warehouse

Byrne, Alan; Bjornn, T.C.; McIntyre, J.D.

1993-01-01

A life history model was used to predict the response of native steelhead Oncorhynchus mykiss in the Lochsa River, Idaho, to long-term supplementation with hatchery fry and smolts. The four key factors affecting the response of the native fish to a stocking program were (1) the number of native spawners, (2) the number of stocked fish, (3) the number and fitness of progeny from stocked fish, and (4) the amount of mating between hatchery and native fish. Long-term stocking of fry or smolts led to the extinction of native fish in some scenarios. The model can be used to help assess the risks and benefits of proposed stocking programs.
The Organizational Model for the Saskatchewan Urban Native Teacher Education Program (SUNTEP).

ERIC Educational Resources Information Center

Whyte, Kenn

Designed to train Canadian Natives as professional educators and models for Native students in urban schools, the Saskatchewan Urban Native Teacher Education Program (SUNTEP), initiated by the Association of Metis and Non-status Indians of Saskatchewan and offered by the Gabriel Dumont Institute, incorporates two basic objectives: to assist Native…
TESOL Teachers' Engagement with the Native Speaker Model: How Does Teacher Education Impact on Their Beliefs?

ERIC Educational Resources Information Center

Nguyen, Mai Xuan Nhat Chi

2017-01-01

This research investigates non-native English teachers' engagement with the native speaker model, i.e. whether they agree/disagree with measuring English teaching and learning performance against native speaker standards. More importantly, it aims to unearth the impact of teacher education on teachers' attitudes and beliefs about…

Role of Tryptophan Side Chain Dynamics on the Trp-Cage Mini-Protein Folding Studied by Molecular Dynamics Simulations

PubMed Central

Kannan, Srinivasaraghavan; Zacharias, Martin

2014-01-01

The 20 residue Trp-cage mini-protein is one of smallest proteins that adopt a stable folded structure containing also well-defined secondary structure elements. The hydrophobic core is arranged around a single central Trp residue. Despite several experimental and simulation studies the detailed folding mechanism of the Trp-cage protein is still not completely understood. Starting from fully extended as well as from partially folded Trp-cage structures a series of molecular dynamics simulations in explicit solvent and using four different force fields was performed. All simulations resulted in rapid collapse of the protein to on average relatively compact states. The simulations indicate a significant dependence of the speed of folding to near-native states on the side chain rotamer state of the central Trp residue. Whereas the majority of intermediate start structures with the central Trp side chain in a near-native rotameric state folded successfully within less than 100 ns only a fraction of start structures reached near-native folded states with an initially non-native Trp side chain rotamer state. Weak restraining of the Trp side chain dihedral angles to the state in the folded protein resulted in significant acceleration of the folding both starting from fully extended or intermediate conformations. The results indicate that the side chain conformation of the central Trp residue can create a significant barrier for controlling transitions to a near native folded structure. Similar mechanisms might be of importance for the folding of other protein structures. PMID:24563686
A Model for Recruiting and Retaining Teachers in Alaska's Rural K-12 Schools

ERIC Educational Resources Information Center

Adams, Barbara L.; Woods, Ashley

2015-01-01

The Alaska Statewide Mentor Project (ASMP) is a joint effort of the University of Alaska and the Alaska Department of Education & Early Development to address the persistently low teacher retention rates in the state, especially in rural districts that predominantly serve Alaska Native (AN) students. Over six years, teacher retention in rural…
Effects of Steady-State Noise on Verbal Working Memory in Young Adults

ERIC Educational Resources Information Center

Marrone, Nicole; Alt, Mary; DeDe, Gayle; Olson, Sarah; Shehorn, James

2015-01-01

Purpose: We set out to examine the impact of perceptual, linguistic, and capacity demands on performance of verbal working-memory tasks. The Ease of Language Understanding model (Rönnberg et al., 2013) provides a framework for testing the dynamics of these interactions within the auditory-cognitive system. Methods: Adult native speakers of English…
Learning to Do Diversity Work: A Model for Continued Education of Program Organizers

ERIC Educational Resources Information Center

Dounas-Frazer, Dimitri R.; Hyater-Adams, Simone A.; Reinholz, Daniel L.

2017-01-01

Physics and physics education in the United States suffer from severe (and, in some cases, worsening) underrepresentation of Black, Latinx, and Native American people of all genders and women of all races and ethnicities. In this paper, we describe an approach to facilitating physics students' collective and continued education about such…
Group Counseling with United States Racial Minority Groups: A 25-Year Content Analysis

ERIC Educational Resources Information Center

Stark-Rose, Rose M.; Livingston-Sacin, Tina M.; Merchant, Niloufer; Finley, Amanda C.

2012-01-01

A 25-year content analysis was conducted of published group work articles that focused on 5 racial groups (African American, Asian American/Pacific Islander, Latino/a, Native American, and Intercultural group). Articles were included if they described an intervention or conceptual model with 1 of the racial groups. The analysis revealed 15 content…
Percutaneous Transcatheter One-Step Mechanical Aortic Disc Valve Prosthesis Implantation: A Preliminary Feasibility Study in Swine

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

Sochman, Jan; Peregrin, Jan H.; Rocek, Miloslav

Purpose. To evaluate the feasibility of one-step implantation of a new type of stent-based mechanical aortic disc valve prosthesis (MADVP) above and across the native aortic valve and its short-term function in swine with both functional and dysfunctional native valves. Methods. The MADVP consisted of a folding disc valve made of silicone elastomer attached to either a nitinol Z-stent (Z model) or a nitinol cross-braided stent (SX model). Implantation of 10 MADVPs (6 Z and 4 SX models) was attempted in 10 swine: 4 (2 Z and 2 SX models) with a functional native valve and 6 (4 Z andmore » 2 SX models) with aortic regurgitation induced either by intentional valve injury or by MADVP placement across the native valve. MADVP function was observed for up to 3 hr after implantation. Results. MADVP implantation was successful in 9 swine. One animal died of induced massive regurgitation prior to implantation. Four MADVPs implanted above functioning native valves exhibited good function. In 5 swine with regurgitation, MADVP implantation corrected the induced native valve dysfunction and the device's continuous good function was observed in 4 animals. One MADVP (SX model) placed across native valve gradually migrated into the left ventricle. Conclusion. The tested MADVP can be implanted above and across the native valve in a one-step procedure and can replace the function of the regurgitating native valve. Further technical development and testing are warranted, preferably with a manufactured MADVP.« less
Multiple-probe analysis of folding and unfolding pathways of human serum albumin. Evidence for a framework mechanism of folding.

PubMed

Santra, Manas Kumar; Banerjee, Abhijit; Krishnakumar, Shyam Sundar; Rahaman, Obaidur; Panda, Dulal

2004-05-01

The changes in the far-UV CD signal, intrinsic tryptophan fluorescence and bilirubin absorbance showed that the guanidine hydrochloride (GdnHCl)-induced unfolding of a multidomain protein, human serum albumin (HSA), followed a two-state process. However, using environment sensitive Nile red fluorescence, the unfolding and folding pathways of HSA were found to follow a three-state process and an intermediate was detected in the range 0.25-1.5 m GdnHCl. The intermediate state displayed 45% higher fluorescence intensity than that of the native state. The increase in the Nile red fluorescence was found to be due to an increase in the quantum yield of the HSA-bound Nile red. Low concentrations of GdnHCl neither altered the binding affinity of Nile red to HSA nor induced the aggregation of HSA. In addition, the secondary structure of HSA was not perturbed during the first unfolding transition (<1.5 m GdnHCl); however, the secondary structure was completely lost during the second transition. The data together showed that the half maximal loss of the tertiary structure occurred at a lower GdnHCl concentration than the loss of the secondary structure. Further kinetic studies of the refolding process of HSA using multiple spectroscopic techniques showed that the folding occurred in two phases, a burst phase followed by a slow phase. An intermediate with native-like secondary structure but only a partial tertiary structure was found to form in the burst phase of refolding. Then, the intermediate slowly folded into the native state. An analysis of the refolding data suggested that the folding of HSA could be best explained by the framework model.
Migrant children and migrants’ children: Nativity differences in school enrollment in Mexico and the United States

PubMed Central

Glick, Jennifer E.; Yabiku, Scott T.

2016-01-01

BACKGROUND The growing prevalence of migrant children in diverse contexts requires a reconsideration of the intergenerational consequences of migration. To understand how migration and duration of residence are associated with children’s schooling, we need more comparative work that can point to the similarities and differences in outcomes for children across contexts. OBJECTIVE This paper addresses the importance of nativity and duration of residence for children’s school enrollment on both sides of a binational migration system: The United States and Mexico. The analyses are designed to determine whether duration of residence has a similar association with school enrollment across these different settings. METHODS The analyses are based on nationally representative household data from the 2010 Mexican Census and the 2006–2010 American Community Survey. Logistic regression models compare school enrollment patterns of Mexican and U.S.-born children of Mexican origin in the United States and those of Mexican and U.S.-born children in Mexico. Interactions for nativity/duration of residence and age are also included. RESULTS The results demonstrate that, adjusting for household resources and household-level migration experience, Mexican-born children in the United States and U.S.-born children in Mexico, particularly those who arrived recently, lag behind in school enrollment. These differences are most pronounced at older ages. CONCLUSIONS The comparisons across migration contexts point to greater school attrition and non-enrollment among older, recent migrant youth, regardless of the context. The interactions suggest that recent migration is associated with lower schooling for youth who engage in migration at older ages in both the United States and Mexico. PMID:28077926
Short communication: Assessing antihypertensive activity in native and model Queso Fresco cheeses.

PubMed

Paul, M; Van Hekken, D L

2011-05-01

Hispanic-style cheeses are one of the fastest growing varieties in the United States, making up approximately 2% of the total cheese production in this country. Queso Fresco is one of most popular Hispanic-style cheeses. Protein extracts from several varieties of Mexican Queso Fresco and model Queso Fresco were analyzed for potential antihypertensive activity. Many Quesos Frescos obtained from Mexico are made from raw milk and therefore the native microflora is included in the cheese-making process. Model Queso Fresco samples were made from pasteurized milk and did not utilize starter cultures. Water-soluble protein extracts from 6 Mexican Quesos Frescos and 12 model cheeses were obtained and assayed for their ability to inhibit angiotensin-converting enzyme, implying potential as foods that can help to lower blood pressure. All model cheeses displayed antihypertensive activity, but mainly after 8 wk of aging when they were no longer consumable, whereas the Mexican samples did display some angiotensin-converting enzyme inhibitory action after minimal aging. Copyright © 2011 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.
Political Status of Native Indian Women: Contradictory Implications of Canadian State Policy.

ERIC Educational Resources Information Center

Fiske, Jo-Anne

1995-01-01

Explores the ambiguous nature of Canadian Native women's political status in relation to men within the internal political processes of Indian reserve communities. Examines linkages among economic factors, domestic organization, and political process, and the disruption of Indian women's lives by state intervention (particularly federal laws…
ASSESSING OZONE EFFECTS ON PLANTS NATIVE TO THE SOUTHEASTERN UNITED STATES

EPA Science Inventory

For the last six years, the U.S. National Park Service, U.S. Environmental Protection Agency, and University researchers have been documenting the effects of ozone on a large number of woody and herbaceous species native to the southeastern United States. n Great Smoky Mountains ...
Institutional innovation in less than ideal conditions: management of commons by an Alaska Native village corporation

Treesearch

Dixie Dayo; Gary Kofinas

2010-01-01

Alaska Natives have experienced less than ideal conditions for engaging in management of their homeland commons. During the first 100 years after the Treaty of Cession of 1867, Alaska Natives received limited recognition by the United States. The Alaska Native Claims Settlement Act of 1971 (ANCSA) was signed into law by President Richard Nixon after tedious...
Parameterization of the InVEST Crop Pollination Model to spatially predict abundance of wild blueberry (Vaccinium angustifolium Aiton) native bee pollinators in Maine, USA

USGS Publications Warehouse

Groff, Shannon C.; Loftin, Cynthia S.; Drummond, Frank; Bushmann, Sara; McGill, Brian J.

2016-01-01

Non-native honeybees historically have been managed for crop pollination, however, recent population declines draw attention to pollination services provided by native bees. We applied the InVEST Crop Pollination model, developed to predict native bee abundance from habitat resources, in Maine's wild blueberry crop landscape. We evaluated model performance with parameters informed by four approaches: 1) expert opinion; 2) sensitivity analysis; 3) sensitivity analysis informed model optimization; and, 4) simulated annealing (uninformed) model optimization. Uninformed optimization improved model performance by 29% compared to expert opinion-informed model, while sensitivity-analysis informed optimization improved model performance by 54%. This suggests that expert opinion may not result in the best parameter values for the InVEST model. The proportion of deciduous/mixed forest within 2000 m of a blueberry field also reliably predicted native bee abundance in blueberry fields, however, the InVEST model provides an efficient tool to estimate bee abundance beyond the field perimeter.
Survival Differences among Native-Born and Foreign-Born Older Adults in the United States

PubMed Central

Dupre, Matthew E.; Gu, Danan; Vaupel, James W.

2012-01-01

Background Studies show that the U.S. foreign-born population has lower mortality than the native-born population before age 65. Until recently, the lack of data prohibited reliable comparisons of U.S. mortality by nativity at older ages. This study provides reliable estimates of U.S. foreign-born and native-born mortality at ages 65 and older at the end of the 20th century. Life expectancies of the U.S. foreign born are compared to other developed nations and the foreign-born contribution to total life expectancy (TLE) in the United States is assessed. Methods Newly available data from Medicare Part B records linked with Social Security Administration files are used to estimate period life tables for nearly all U.S. adults aged 65 and older in 1995. Age-specific survival differences and life expectancies are examined in 1995 by sex, race, and place of birth. Results Foreign-born men and women had lower mortality at almost every age from 65 to 100 compared to native-born men and women. Survival differences by nativity were substantially greater for blacks than whites. Foreign-born blacks had the longest life expectancy of all population groups (18.73 [95% confidence interval {CI}, 18.15–19.30] years at age 65 for men and 22.76 [95% CI, 22.28–23.23] years at age 65 for women). The foreign-born population increased TLE in the United States at older ages, and by international comparison, the U.S. foreign born were among the longest-lived persons in the world. Conclusion Survival estimates based on reliable Medicare data confirm that foreign-born adults have longer life expectancy at older ages than native-born adults in the United States. PMID:22615929
Potential impacts of projected climate change on vegetation management in Hawai`i Volcanoes National Park

USGS Publications Warehouse

Camp, Richard J.; Loh, Rhonda; Berkowitz, S. Paul; Brinck, Kevin W.; Jacobi, James D.; Price, Jonathan; McDaniel, Sierra; Fortini, Lucas B.

2018-01-01

Climate change will likely alter the seasonal and annual patterns of rainfall and temperature in Hawai`i. This is a major concern for resource managers at Hawai`i Volcanoes National Park where intensely managed Special Ecological Areas (SEAs), focal sites for managing rare and endangered plants, may no longer provide suitable habitat under future climate. Expanding invasive species’ distributions also may pose a threat to areas where native plants currently predominate. We combine recent climate modeling efforts for the state of Hawai`i with plant species distribution models to forecast changes in biodiversity in SEAs under future climate conditions. Based on this bioclimatic envelope model, we generated projected species range maps for four snapshots in time (2000, 2040, 2070, and 2090) to assess whether the range of 39 native and invasive species of management interest are expected to contract, expand, or remain the same under a moderately warmer and more variable precipitation scenario. Approximately two-thirds of the modeled native species were projected to contract in range, while one-third were shown to increase. Most of the park’s SEAs were projected to lose a majority of the native species modeled. Nine of the 10 modeled invasive species were projected to contract within the park; this trend occurred in most SEAs, including those at low, middle, and high elevations. There was good congruence in the current (2000) distribution of species richness and SEA configuration; however, the congruence between species richness hotspots and SEAs diminished by the end of this century. Over time the projected species-rich hotspots increasingly occurred outside of current SEA boundaries. Our research brought together managers and scientists to increase understanding of potential climate change impacts, and provide needed information to address how plants may respond under future conditions relative to current managed areas.
Native Music in College Curricula?

ERIC Educational Resources Information Center

Olsen, Loran

1986-01-01

Culminating a 10-year effort to include the study of Native Americans and their music as it reflects cultural realities, life, thought, religion, and history as a choice in requirements for graduation, the elective course, "Native Music of North America," is now recognized at Washington State University as meeting both…
50 CFR 18.23 - Native exemptions.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 8 2011-10-01 2011-10-01 false Native exemptions. 18.23 Section 18.23 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE INTERIOR (CONTINUED... PLANTS (CONTINUED) MARINE MAMMALS General Exceptions § 18.23 Native exemptions. (a) Taking. Except as...
50 CFR 18.23 - Native exemptions.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 50 Wildlife and Fisheries 9 2012-10-01 2012-10-01 false Native exemptions. 18.23 Section 18.23 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE INTERIOR (CONTINUED... PLANTS (CONTINUED) MARINE MAMMALS General Exceptions § 18.23 Native exemptions. (a) Taking. Except as...
50 CFR 18.23 - Native exemptions.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 50 Wildlife and Fisheries 9 2013-10-01 2013-10-01 false Native exemptions. 18.23 Section 18.23 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE INTERIOR (CONTINUED... PLANTS (CONTINUED) MARINE MAMMALS General Exceptions § 18.23 Native exemptions. (a) Taking. Except as...
50 CFR 18.23 - Native exemptions.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 50 Wildlife and Fisheries 9 2014-10-01 2014-10-01 false Native exemptions. 18.23 Section 18.23 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE INTERIOR (CONTINUED... PLANTS (CONTINUED) MARINE MAMMALS General Exceptions § 18.23 Native exemptions. (a) Taking. Except as...

A knowledge-based potential with an accurate description of local interactions improves discrimination between native and near-native protein conformations.

PubMed

Ferrada, Evandro; Vergara, Ismael A; Melo, Francisco

2007-01-01

The correct discrimination between native and near-native protein conformations is essential for achieving accurate computer-based protein structure prediction. However, this has proven to be a difficult task, since currently available physical energy functions, empirical potentials and statistical scoring functions are still limited in achieving this goal consistently. In this work, we assess and compare the ability of different full atom knowledge-based potentials to discriminate between native protein structures and near-native protein conformations generated by comparative modeling. Using a benchmark of 152 near-native protein models and their corresponding native structures that encompass several different folds, we demonstrate that the incorporation of close non-bonded pairwise atom terms improves the discriminating power of the empirical potentials. Since the direct and unbiased derivation of close non-bonded terms from current experimental data is not possible, we obtained and used those terms from the corresponding pseudo-energy functions of a non-local knowledge-based potential. It is shown that this methodology significantly improves the discrimination between native and near-native protein conformations, suggesting that a proper description of close non-bonded terms is important to achieve a more complete and accurate description of native protein conformations. Some external knowledge-based energy functions that are widely used in model assessment performed poorly, indicating that the benchmark of models and the specific discrimination task tested in this work constitutes a difficult challenge.
Directed transport as a mechanism for protein folding in vivo.

PubMed

González-Candela, Ernesto; Romero-Rochín, Víctor

2010-01-21

We propose a model for protein folding in vivo based on a Brownian ratchet mechanism in the multidimensional energy landscape space. The device is able to produce directed transport taking advantage of the assumed intrinsic asymmetric properties of the proteins and employing the consumption of energy provided by an external source. Through such a directed transport phenomenon, the polypeptide finds the native state starting from any initial state in the energy landscape with great efficacy and robustness, even in the presence of different types of obstacles. This model solves Levinthal's paradox without requiring biased transition probabilities but at the expense of opening the system to an external field.
Application of Time-Resolved Tryptophan Phosphorescence Spectroscopy to Protein Folding Studies.

NASA Astrophysics Data System (ADS)

Subramaniam, Vinod

This thesis presents studies of the protein folding problem, one of the most significant questions in contemporary biophysics. Sensitive biophysical techniques, including room temperature tryptophan phosphorescence, which reports on the local environment of the residue, and the lability of proteins to denaturation, a global parameter, were used to assess the validity of the traditional assumption that the biologically active state of a protein is the 'native' state, and to determine whether the pathways of folding in vitro lead to the folded state achieved in vivo. Phosphorescence techniques have also been extended to study, for the first time, emission from tryptophan residues engineered into specific positions as reporters of protein structure. During in vitro refolding of E. coli alkaline phosphatase and bovine 13-lactoglobulin, significant differences were found between the refolded proteins and the native conformations, which have no apparent effect on the biological functions. Slow conformational transitions, termed 'annealing,' that occur long after the return of enzyme activity of alkaline phosphatase are manifested in the retarded recovery of phosphorescence intensity, lifetime, and protein lability. While 'annealing' is not observed for beta -lactoglobulin, both phosphorescence and lability experiments reveal changes in the structure of the refolded protein, even though its biological activity, retinol binding, is fully recovered. This result suggests that the pathways of folding in vitro need not lead to the structure formed in vivo. We have used phosphorescence techniques to study the refolding of ribonuclease T1, which exhibits slow kinetics characteristic of proline isomerization. Furthermore, the ability to extract structural information from phosphorescent tryptophan probes engineered into selected regions represents an important advance in studying protein structure; we have reported the first such results from a mutant staphylococcal nuclease. The refolding data have been interpreted in the context of recent theoretical work on rugged energy landscape models of protein folding. Our results suggest that the barriers to folding can be as large as ~ 20 kcal-mol^{-1}, and imply that the conventional definition of the 'native' state as the biologically active conformation may need revision to acknowledge that the active state may represent a long-lived intermediate on the pathway to the native structure.
NMR based solvent exchange experiments to understand the conformational preference of intrinsically disordered proteins using FG-nucleoporin peptide as a model

PubMed Central

Heisel, Kurt A.; Krishnan, V. V.

2014-01-01

The conformational preference of a peptide with three phenylalanine-glycine (FG) repeats from the intrinsically disordered domain of nucleoporin 159 (nup159) from the yeast nucleopore complex (NPC) is studied. Conformational states of this FG-peptide in dimethyl sulfoxide (DMSO), a non-native solvent are first studied. A solvent exchange scheme is designed and performed to understand how the conformational preferences of the peptide are altered as the solvent shifts from DMSO to water. An ensemble of structures of a 19-residue peptide is determined based on 13Cα, 1Hα, and 1HN chemical shifts and with inter-proton distances. An experimental model is then presented where chemical shifts and amide-proton temperature dependence is probed at changing DMSO to water ratios. These co-solvent experiments provide evidence of a conformational change as the fraction of water increases by the stark change in the behavior of amide protons under varied temperature. This investigation provides a NMR based experimental method in the field of intrinsically disordered proteins to realize conformational transitions from a non-native set of structures (in DMSO) to a native set of disordered conformers (in water). PMID:24037535
Cooperative Tertiary Interaction Network Guides RNA Folding

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

Behrouzi, Reza; Roh, Joon Ho; Kilburn, Duncan

2013-04-08

Noncoding RNAs form unique 3D structures, which perform many regulatory functions. To understand how RNAs fold uniquely despite a small number of tertiary interaction motifs, we mutated the major tertiary interactions in a group I ribozyme by single-base substitutions. The resulting perturbations to the folding energy landscape were measured using SAXS, ribozyme activity, hydroxyl radical footprinting, and native PAGE. Double- and triple-mutant cycles show that most tertiary interactions have a small effect on the stability of the native state. Instead, the formation of core and peripheral structural motifs is cooperatively linked in near-native folding intermediates, and this cooperativity depends onmore » the native helix orientation. The emergence of a cooperative interaction network at an early stage of folding suppresses nonnative structures and guides the search for the native state. We suggest that cooperativity in noncoding RNAs arose from natural selection of architectures conducive to forming a unique, stable fold.« less
78 FR 72711 - Notice of Intent To Repatriate Cultural Items: U.S. Department of the Interior, Bureau of Land...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-03

...The U.S. Department of the Interior, Bureau of Land Management (BLM), Alaska State Office, in consultation with the appropriate Indian tribes or Native Hawaiian organizations, has determined that the items listed in this notice meet the definition of unassociated funerary objects. Lineal descendants or representatives of any Indian tribe or Native Hawaiian organization not identified in this notice that wish to claim these items should submit a written request to the BLM Alaska State Office. If no additional claimants come forward, transfer of control of the items to the lineal descendants, Indian tribes, or Native Hawaiian organizations stated in this notice may proceed.
Prologue to a Vision of Aboriginal Education.

ERIC Educational Resources Information Center

Medicine, Beatrice

1995-01-01

Beatrice Medicine, Professor Emerita from California State University, suggests that a higher education program for Native Americans should integrate the knowledge and wisdom of elders as well as address the different cultural values and spirituality of Native American students. The challenge is to prepare Native students to live and work in the…
BEHAVIORAL RESPONSES OF ANURAN LARVAE TO CHEMICAL CUES OF NATIVE AND INTRODUCED PREDATORS IN THE PACIFIC NORTHWESTERN UNITED STATES

EPA Science Inventory

We compared behavioral responses of larvae of three Pacific Northwest anurans from different hydroperiods to water borne cues of native and introduced predators. Two native anurans (Pacific Treefrog, Pseudacris regilla, and Northern Red-Legged Frog, Rana aurora aurora) and intro...
Teaching Native American Music with Story for Multicultural Ends.

ERIC Educational Resources Information Center

Boyea, Andrea

2000-01-01

States that the alliance between story and music within Native American culture can be carried over into the curriculum. Provides a rationale for utilizing story while teaching Native American music, specifically related to the multicultural curriculum. Discusses the value of cultural music to the multicultural curriculum. (CMK)
78 FR 44593 - Notice of Inventory Completion: Washington State Parks and Recreation Commission, Olympia, WA

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-24

... tribes or Native Hawaiian organizations, and has determined that there is a cultural affiliation between the human remains and present-day Indian tribes or Native Hawaiian organizations. Lineal descendants or representatives of any Indian tribe or Native Hawaiian organization not identified in this notice...
Cultivating Native American scientists: an application of an Indigenous model to an undergraduate research experience

NASA Astrophysics Data System (ADS)

McMahon, Tracey R.; Griese, Emily R.; Kenyon, DenYelle Baete

2018-03-01

With growing evidence demonstrating the impact of undergraduate research experiences on educational persistence, efforts are currently being made to expand these opportunities within universities and research institutions throughout the United States. Recruiting underrepresented students into these programs has become an increasingly popular method of promoting diversity in science. Given the low matriculation into postsecondary education and completion rates among Native Americans, there is a great need for Native American undergraduate research internships. Although research has shown that Western education models tend to be less effective with Native populations, the implementation of indigenous epistemologies and pedagogies within higher education, including research experiences, is rare. This study explores the applicability of a cognitive apprenticeship merged with an indigenous approach, the Circle of Courage, to build a scientific learning environment and enhance the academic and professional development of Native students engaged in an undergraduate research experience in the health sciences. Data were drawn from focus groups with 20 students who participated in this program in 2012-2014. Questions explored the extent to which relational bonds between students and mentors were cultivated as well as the impact of this experience on the development of research skills, intellectual growth, academic and professional self-determination, and the attachment of meaning to their research experiences. Data were analyzed via deductive content analysis, allowing for an assessment of how the theoretical constructs inherent to this model (belonging, mastery, independence, and generosity) impacted students. Findings suggest that engaging Native students in research experiences that prioritize the needs of belonging, mastery, independence, and generosity can be a successful means of fostering a positive learning environment, in which students felt like significant members of a research team, developed a greater understanding and appreciation for the role of science in education and its various applications to socially relevant health issues, made more informed decisions about a career in research and the health sciences, and worked toward improving the health and well-being of others while also inspiring hope among their people back home. This study represents an extension of the application of the Circle of Courage to an undergraduate research experience and provides evidence of its ability to be used as a framework for cultivating Native scientists.
Bioinvasive species and the preservation of cutthroat trout in the western United States: Ecological, social, and economic issues

USGS Publications Warehouse

Quist, M.C.; Hubert, W.A.

2004-01-01

The cutthroat trout (Oncorhynchus clarki) was the only endemic salmonid species across most of the western United States, and it has severely declined largely due to introduction and bioinvasion by non-native salmonid species. However, the ecological, social, and economic consequences of cutthroat trout declines and replacement by non-native salmonid species are relatively minor, and measurable affects on ecosystem function are rare. Restoration efforts for cutthroat trout involve removal or control of bioinvasive salmonid species, but such efforts are costly, ongoing, and resisted frequently by segments of society. Cutthroat trout declines are of little concern to much of the public because they are valued similarly to non-native salmonids, and non-native salmonid species frequently have higher recreational values. Due to the low values placed on cutthroat trout relative to non-native salmonid species, net economic benefits of preserving cutthroat trout are equal to or less than those for non-native salmonids. Cutthroat trout provide a classic case of the consequences of biological invasion; however, other native species are faced with similar issues. We suggest that management agencies establish realistic goals to preserve native species within the context of ecological, social, and economic issues. ?? 2004 Elsevier Ltd. All rights reserved.
Cross-Cultural Service Learning with Native Americans: Pedagogy for Building Cultural Competence

ERIC Educational Resources Information Center

Bolea, Patricia S.

2012-01-01

This paper articulates a curricular approach that centers on a Native American service learning course. Social work students engaged in cross-cultural immersion on a reservation in the United States. By examination of historical United States policy impacting Indian tribes and contemporary experiences that challenge basic instruction in public…
THE APPLICABILITY OF EMAP'S WESTERN PILOT TO STATE AND REGIONAL QUESTIONS OF FISH ASSEMBLAGE STRUCTURE

EPA Science Inventory

What percentage of the West's 209,381 kilometers of streams and rivers contain fish? What proportion contains only native fish? Do aliens dominate the fish fauna of streams in any region or state? What are the ranges and relative densities of the most common fish, native and al...
A State Response to Indian Vocational Education.

ERIC Educational Resources Information Center

McConnell, Bruce

In 1977 more than 500 Native Americans attended Wisconsin's vocational, technical and adult schools located in the state's 16 vocational-technical districts. While many problems still lack a clear identification and many new programs are needed to meet the needs of Native Americans, a great deal of progress has been made. A group of four Indians…
Report on State's Role in Native American Higher Education. House Memorial 28 Public Hearing.

ERIC Educational Resources Information Center

New Mexico State Board of Educational Finance, Santa Fe.

These hearing transcripts and recommendations were in response to requests from the New Mexico Legislature for investigation of the state's role in Native American higher education. Section I contains abbreviated transcripts of testimony on 10 study committees covering needs and recommendations in curriculum/academic issues, off-campus training,…
77 FR 59659 - Notice of Inventory Completion for Native American Human Remains and Associated Funerary Objects...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-28

... the Department of Anthropology, San Francisco State University, San Francisco, CA; Correction AGENCY... Department of Anthropology, San Francisco State University have determined that, pursuant to 25 U.S.C. 3001(9), the human remains listed above represent the physical remains of 55 individuals of Native American...
Bill of Rights in Tribal Constitutions. [First Draft].

ERIC Educational Resources Information Center

Rusco, Elmer R.

Because Native American societies are held by United States courts to possess rights of self-government where these rights have not been explicitly withdrawn, the constitutions of 280 Native American governments in the United States (exclusive of 219 in Alaska) were examined as they existed in September 1981 to determine the extent and character…
Oregon American Indian Alaska Native Education State Plan.

ERIC Educational Resources Information Center

Castillo, Susan

This state plan presents Oregon's 11 educational goals for American Indian/Alaska Native (AI/AN) education, which have been revised and detailed by the statewide Indian Education Council. The goals support the policy of the Oregon Department of Education (ODE), the educational philosophy of the AI/AN community, and the Indian Student Bill of…
Native Americans of Washington State (A Curriculum Guide for Elementary Grades). First Edition.

ERIC Educational Resources Information Center

Forsyth, Karen Williams; Neal, Colleen

Developed as a supplemental curriculum guide for elementary teachers, the guide assists in implementing Native American activities to classroom curriculum to make students aware of the numerous tribes within the state of Washington. Divided in three geographic, cultural areas (Northwest Coast region, Puget Sound Lowlands region, and Plateau…

Linguistic Support for Non-Native English Speakers: Higher Education Practices in the United States

ERIC Educational Resources Information Center

Snow Andrade, Maureen; Evans, Norman W.; Hartshorn, K. James

2014-01-01

Higher education institutions in English-speaking nations host significant populations of non-native English speakers (NNES), both international and resident. English language proficiency is a critical factor to their success. This study reviews higher education practices in the United States related to this population. Findings indicate…
77 FR 11583 - Notice of Inventory Completion for Native American Human Remains and Associated Funerary Objects...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-27

... Native American Human Remains and Associated Funerary Objects From Arizona in the Possession of San Diego State University, San Diego, CA; Correction AGENCY: National Park Service, Interior. ACTION: Notice... funerary objects in the possession of San Diego State University, San Diego, CA. The human remains and...
Impact of non-native plant removal on lizards in riparian habitats in the southwestern United States

Treesearch

Heather L. Bateman; Alice Chung-MacCoubrey; Howard L. Snell

2008-01-01

Many natural processes in the riparian cottonwood (Populus deltoides) forest of the Middle Rio Grande (MRG) in the southwestern United States have been disrupted or altered, allowing non-native plants such as saltcedar (Tamarix spp.) and Russian olive (Elaeagnus angustifolia) to establish. We investigated...
Restoration efforts in the Rio Grande Valley State Park

Treesearch

Ondrea C. Linderoth

1999-01-01

Restoration techniques for riparian habitats in the Southwest are being widely studied. Efforts for natural regrowth of native species are a high priority. Techniques for native cottonwood (Populus fremontii) regeneration are being investigated in the Rio Grande Valley State Park. Experimentation with flooding of riparian zones using different techniques is beginning...
Realized niche shift associated with the Eurasian charophyte Nitellopsis obtusa becoming invasive in North America

PubMed Central

Escobar, Luis E.; Qiao, Huijie; Phelps, Nicholas B. D.; Wagner, Carli K.; Larkin, Daniel J.

2016-01-01

Nitellopsis obtusa (starry stonewort) is a dioecious green alga native to Europe and Asia that has emerged as an aquatic invasive species in North America. Nitellopsis obtusa is rare across large portions of its native range, but has spread rapidly in northern-tier lakes in the United States, where it can interfere with recreation and may displace native species. Little is known about the invasion ecology of N. obtusa, making it difficult to forecast future expansion. Using ecological niche modeling we investigated environmental variables associated with invasion risk. We used species records, climate data, and remotely sensed environmental variables to characterize the species’ multidimensional distribution. We found that N. obtusa is exploiting novel ecological niche space in its introduced range, which may help explain its invasiveness. While the fundamental niche of N. obtusa may be stable, there appears to have been a shift in its realized niche associated with invasion in North America. Large portions of the United States are predicted to constitute highly suitable habitat for N. obtusa. Our results can inform early detection and rapid response efforts targeting N. obtusa and provide testable estimates of the physiological tolerances of this species as a baseline for future empirical research. PMID:27363541
Hydrophobic interactions of sucralose with protein structures.

PubMed

Shukla, Nimesh; Pomarico, Enrico; Hecht, Cody J S; Taylor, Erika A; Chergui, Majed; Othon, Christina M

2018-02-01

Sucralose is a commonly employed artificial sweetener that appears to destabilize protein native structures. This is in direct contrast to the bio-preservative nature of its natural counterpart, sucrose, which enhances the stability of biomolecules against environmental stress. We have further explored the molecular interactions of sucralose as compared to sucrose to illuminate the origin of the differences in their bio-preservative efficacy. We show that the mode of interactions of sucralose and sucrose in bulk solution differ subtly through the use of hydration dynamics measurement and computational simulation. Sucralose does not appear to disturb the native state of proteins for moderate concentrations (<0.2 M) at room temperature. However, as the concentration increases, or in the thermally stressed state, sucralose appears to differ in its interactions with protein leading to the reduction of native state stability. This difference in interaction appears weak. We explored the difference in the preferential exclusion model using time-resolved spectroscopic techniques and observed that both molecules appear to be effective reducers of bulk hydration dynamics. However, the chlorination of sucralose appears to slightly enhance the hydrophobicity of the molecule, which reduces the preferential exclusion of sucralose from the protein-water interface. The weak interaction of sucralose with hydrophobic pockets on the protein surface differs from the behavior of sucrose. We experimentally followed up upon the extent of this weak interaction using isothermal titration calorimetry (ITC) measurements. We propose this as a possible origin for the difference in their bio-preservative properties. Copyright © 2017 Elsevier Inc. All rights reserved.
Structural plasticity of 4-α-helical bundles exemplified by the puzzle-like molecular assembly of the Rop protein

PubMed Central

Amprazi, Maria; Kotsifaki, Dina; Providaki, Mary; Kapetaniou, Evangelia G.; Fellas, Georgios; Kyriazidis, Ioannis; Pérez, Javier; Kokkinidis, Michael

2014-01-01

The dimeric Repressor of Primer (Rop) protein, a widely used model system for the study of coiled-coil 4-α-helical bundles, is characterized by a remarkable structural plasticity. Loop region mutations lead to a wide range of topologies, folding states, and altered physicochemical properties. A protein-folding study of Rop and several loop variants has identified specific residues and sequences that are linked to the observed structural plasticity. Apart from the native state, native-like and molten-globule states have been identified; these states are sensitive to reducing agents due to the formation of nonnative disulfide bridges. Pro residues in the loop are critical for the establishment of new topologies and molten globule states; their effects, however, can be in part compensated by Gly residues. The extreme plasticity in the assembly of 4-α-helical bundles reflects the capacity of the Rop sequence to combine a specific set of hydrophobic residues into strikingly different hydrophobic cores. These cores include highly hydrated ones that are consistent with the formation of interchain, nonnative disulfide bridges and the establishment of molten globules. Potential applications of this structural plasticity are among others in the engineering of bio-inspired materials. PMID:25024213
An Exploratory Factor Analysis of the Sheltered Instruction Observation Protocol as an Evaluation Tool to Measure Teaching Effectiveness

ERIC Educational Resources Information Center

Polat, Nihat; Cepik, Saban

2016-01-01

To narrow the achievement gap between English language learners (ELLs) and their native-speaking peers in K-12 settings in the United States, effective instructional models must be identified. However, identifying valid observation protocols that can measure the effectiveness of specially designed instructional practices is not an easy task. This…
Behavioral evidence for fruit odor discrimination and sympatric host races of Rhagoletis pomonella flies in the western United States

USDA-ARS?s Scientific Manuscript database

The recent shift of Rhagoletis pomonella (Diptera: Tephritidae) from its native host downy hawthorn, Crataegus mollis, to introduced domesticated apple, Malus domestica, in the eastern U.S. is a model for sympatric host race formation. However, the fly is also present in the western U.S. where it ma...
Implementing Two-Way Dual-Language Immersion Programs: Classroom Insights from an Urban District. Research Brief. RB-9921

ERIC Educational Resources Information Center

Li, Jennifer J.; Steele, Jennifer L.; Slater, Robert; Bacon, Michael; Miller, Trey

2016-01-01

Dual-language immersion programs--in which students learn core subjects (language arts, math, science, and social studies) in both English and a "partner" language--have been gaining in popularity across the United States. Such programs may use a "two-way model," in which roughly half the students are native speakers of the…
Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy

PubMed Central

Snow, Christopher D.; Qiu, Linlin; Du, Deguo; Gai, Feng; Hagen, Stephen J.; Pande, Vijay S.

2004-01-01

We studied the microsecond folding dynamics of three β hairpins (Trp zippers 1–3, TZ1–TZ3) by using temperature-jump fluorescence and atomistic molecular dynamics in implicit solvent. In addition, we studied TZ2 by using time-resolved IR spectroscopy. By using distributed computing, we obtained an aggregate simulation time of 22 ms. The simulations included 150, 212, and 48 folding events at room temperature for TZ1, TZ2, and TZ3, respectively. The all-atom optimized potentials for liquid simulations (OPLSaa) potential set predicted TZ1 and TZ2 properties well; the estimated folding rates agreed with the experimentally determined folding rates and native conformations were the global potential-energy minimum. The simulations also predicted reasonable unfolding activation enthalpies. This work, directly comparing large simulated folding ensembles with multiple spectroscopic probes, revealed both the surprising predictive ability of current models as well as their shortcomings. Specifically, for TZ1–TZ3, OPLS for united atom models had a nonnative free-energy minimum, and the folding rate for OPLSaa TZ3 was sensitive to the initial conformation. Finally, we characterized the transition state; all TZs fold by means of similar, native-like transition-state conformations. PMID:15020773
Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy

NASA Astrophysics Data System (ADS)

Snow, Christopher D.; Qiu, Linlin; Du, Deguo; Gai, Feng; Hagen, Stephen J.; Pande, Vijay S.

2004-03-01

We studied the microsecond folding dynamics of three hairpins (Trp zippers 1-3, TZ1-TZ3) by using temperature-jump fluorescence and atomistic molecular dynamics in implicit solvent. In addition, we studied TZ2 by using time-resolved IR spectroscopy. By using distributed computing, we obtained an aggregate simulation time of 22 ms. The simulations included 150, 212, and 48 folding events at room temperature for TZ1, TZ2, and TZ3, respectively. The all-atom optimized potentials for liquid simulations (OPLSaa) potential set predicted TZ1 and TZ2 properties well; the estimated folding rates agreed with the experimentally determined folding rates and native conformations were the global potential-energy minimum. The simulations also predicted reasonable unfolding activation enthalpies. This work, directly comparing large simulated folding ensembles with multiple spectroscopic probes, revealed both the surprising predictive ability of current models as well as their shortcomings. Specifically, for TZ1-TZ3, OPLS for united atom models had a nonnative free-energy minimum, and the folding rate for OPLSaa TZ3 was sensitive to the initial conformation. Finally, we characterized the transition state; all TZs fold by means of similar, native-like transition-state conformations.
Markov state models of protein misfolding

NASA Astrophysics Data System (ADS)

Sirur, Anshul; De Sancho, David; Best, Robert B.

2016-02-01

Markov state models (MSMs) are an extremely useful tool for understanding the conformational dynamics of macromolecules and for analyzing MD simulations in a quantitative fashion. They have been extensively used for peptide and protein folding, for small molecule binding, and for the study of native ensemble dynamics. Here, we adapt the MSM methodology to gain insight into the dynamics of misfolded states. To overcome possible flaws in root-mean-square deviation (RMSD)-based metrics, we introduce a novel discretization approach, based on coarse-grained contact maps. In addition, we extend the MSM methodology to include "sink" states in order to account for the irreversibility (on simulation time scales) of processes like protein misfolding. We apply this method to analyze the mechanism of misfolding of tandem repeats of titin domains, and how it is influenced by confinement in a chaperonin-like cavity.
Estimating conformation content of a protein using citrate-stabilized Au nanoparticles

NASA Astrophysics Data System (ADS)

Deka, Jashmini; Paul, Anumita; Chattopadhyay, Arun

2010-08-01

Herein we report the use of the optical properties of citrate-stabilized gold nanoparticles (Au NPs) for estimation of native or denatured conformation content in a mixture of a protein in solution. The UV-vis extinction spectrum of citrate-stabilized Au NPs is known to broaden differently in the presence of native and denatured states of α-amylase, bovine serum albumin (BSA) or amyloglucosidase (AMG). On the other hand, herein we show that when a mixture of native and denatured protein was present in the medium, the broadening of the spectrum differed for different fractional content of the conformations. Also, the total area under the extinction spectrum varied linearly with the change in the mole fraction content of a state and for a constant total protein concentration. Transmission electron microscopy (TEM) measurements revealed different levels of agglomeration for different fractional contents of the native or denatured state of a protein. In addition, time-dependent denaturation of a protein could be followed using the present method. The rate constants calculated for denaturation indicated a possible fast change in conformation of a protein before complete thermal denaturation. The observations have been explained based on the changes in extinction coefficient (thereby oscillator strength) upon interaction of citrate-stabilized NPs with proteins being in different states and levels of agglomeration.Herein we report the use of the optical properties of citrate-stabilized gold nanoparticles (Au NPs) for estimation of native or denatured conformation content in a mixture of a protein in solution. The UV-vis extinction spectrum of citrate-stabilized Au NPs is known to broaden differently in the presence of native and denatured states of α-amylase, bovine serum albumin (BSA) or amyloglucosidase (AMG). On the other hand, herein we show that when a mixture of native and denatured protein was present in the medium, the broadening of the spectrum differed for different fractional content of the conformations. Also, the total area under the extinction spectrum varied linearly with the change in the mole fraction content of a state and for a constant total protein concentration. Transmission electron microscopy (TEM) measurements revealed different levels of agglomeration for different fractional contents of the native or denatured state of a protein. In addition, time-dependent denaturation of a protein could be followed using the present method. The rate constants calculated for denaturation indicated a possible fast change in conformation of a protein before complete thermal denaturation. The observations have been explained based on the changes in extinction coefficient (thereby oscillator strength) upon interaction of citrate-stabilized NPs with proteins being in different states and levels of agglomeration. Electronic supplementary information (ESI) available: Additional UV-vis and fluorescence spectra and graphs based on UV-vis studies. See DOI: 10.1039/c0nr00154f
Interdomain Contacts Control Native State Switching of RfaH on a Dual-Funneled Landscape

PubMed Central

Ramírez-Sarmiento, César A.; Noel, Jeffrey K.; Valenzuela, Sandro L.; Artsimovitch, Irina

2015-01-01

RfaH is a virulence factor from Escherichia coli whose C-terminal domain (CTD) undergoes a dramatic α-to-β conformational transformation. The CTD in its α-helical fold is stabilized by interactions with the N-terminal domain (NTD), masking an RNA polymerase binding site until a specific recruitment site is encountered. Domain dissociation is triggered upon binding to DNA, allowing the NTD to interact with RNA polymerase to facilitate transcription while the CTD refolds into the β-barrel conformation that interacts with the ribosome to activate translation. However, structural details of this transformation process in the context of the full protein remain to be elucidated. Here, we explore the mechanism of the α-to-β conformational transition of RfaH in the full-length protein using a dual-basin structure-based model. Our simulations capture several features described experimentally, such as the requirement of disruption of interdomain contacts to trigger the α-to-β transformation, confirms the roles of previously indicated residues E48 and R138, and suggests a new important role for F130, in the stability of the interdomain interaction. These native basins are connected through an intermediate state that builds up upon binding to the NTD and shares features from both folds, in agreement with previous in silico studies of the isolated CTD. We also examine the effect of RNA polymerase binding on the stabilization of the β fold. Our study shows that native-biased models are appropriate for interrogating the detailed mechanisms of structural rearrangements during the dramatic transformation process of RfaH. PMID:26230837
Metabolic syndrome: prevalence among American Indian and Alaska native people living in the southwestern United States and in Alaska.

PubMed

Schumacher, Catherine; Ferucci, Elizabeth D; Lanier, Anne P; Slattery, Martha L; Schraer, Cynthia D; Raymer, Terry W; Dillard, Denise; Murtaugh, Maureen A; Tom-Orme, Lillian

2008-12-01

Metabolic syndrome occurs commonly in the United States. The purpose of this study was to measure the prevalence of metabolic syndrome among American Indian and Alaska Native people. We measured the prevalence rates of metabolic syndrome, as defined by the National Cholesterol Education Program, among four groups of American Indian and Alaska Native people aged 20 years and older. One group was from the southwestern United States (Navajo Nation), and three groups resided within Alaska. Prevalence rates were age-adjusted to the U.S. adult 2000 population and compared to rates for U.S. whites (National Health and Nutrition Examination Survey [NHANES] 1988-1994). Among participants from the southwestern United States, metabolic syndrome was found among 43.2% of men and 47.3% of women. Among Alaska Native people, metabolic syndrome was found among 26.5% of men and 31.2% of women. In Alaska, the prevalence rate varied by region, ranging among men from 18.9% (western Alaska) to 35.1% (southeast), and among women from 22.0% (western Alaska) to 38.4 % (southeast). Compared to U.S. whites, American Indian/Alaska Native men and women from all regions except western Alaska were more likely to have metabolic syndrome; men in western Alaska were less likely to have metabolic syndrome than U.S. whites, and the prevalence among women in western Alaska was similar to that of U.S. whites. The prevalence rate of metabolic syndrome varies widely among different American Indian and Alaska Native populations. Differences paralleled differences in the prevalence rates of diabetes.
Asymmetric hybridization between non-native winter moth, Operophtera brumata (Lepidoptera: Geometridae), and native Bruce spanworm, Operophtera bruceata, in the Northeastern United States, assessed with novel microsatellites and SNPs

Treesearch

N.P. Havill; J. Elkinton; J.C. Andersen; S.B. Hagen; Hannah J. Broadley; G.J. Boettner; A. Caccone

2017-01-01

The European winter moth, Operophtera brumata, is a non-native pest in the Northeastern USA causing defoliation of forest trees and crops such as apples and blueberries. This species is known to hybridize with O. bruceata, the Bruce spanworm, a native species across North America, although it is not known if there are hybrid...
Assisting Native Americans in Assuring the Survival and Continuing Vitality of Their Languages. Report To Accompany S. 2044. Senate, 102d Congress, 2d Session.

ERIC Educational Resources Information Center

Congress of the U.S., Washington, DC. Senate Select Committee on Indian Affairs.

Past U.S. policies toward Indian and other Native American languages have attempted to suppress the use of the languages in government-operated Indian schools for assimilating Indian children. About 155 Native languages are spoken today in the United States, but only 20 are spoken by people of all ages. The Native American Languages Act of 1990…
Evidence of native α-synuclein conformers in the human brain.

PubMed

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.
Engineering hydrogels as extracellular matrix mimics

PubMed Central

Geckil, Hikmet; Xu, Feng; Zhang, Xiaohui; Moon, SangJun

2010-01-01

Extracellular matrix (ECM) is a complex cellular environment consisting of proteins, proteoglycans, and other soluble molecules. ECM provides structural support to mammalian cells and a regulatory milieu with a variety of important cell functions, including assembling cells into various tissues and organs, regulating growth and cell–cell communication. Developing a tailored in vitro cell culture environment that mimics the intricate and organized nanoscale meshwork of native ECM is desirable. Recent studies have shown the potential of hydrogels to mimic native ECM. Such an engineered native-like ECM is more likely to provide cells with rational cues for diagnostic and therapeutic studies. The research for novel biomaterials has led to an extension of the scope and techniques used to fabricate biomimetic hydrogel scaffolds for tissue engineering and regenerative medicine applications. In this article, we detail the progress of the current state-of-the-art engineering methods to create cell-encapsulating hydrogel tissue constructs as well as their applications in in vitro models in biomedicine. PMID:20394538

The Internal Colonialism Model: What the Model Has Done to the Education of Native Americans.

ERIC Educational Resources Information Center

Oliver, Christopher

This paper explores the shortcomings of the internal colonialism model of education that has persisted in North America throughout the history of Native American education. Since the arrival of Europeans in North America, their colonizing societies have attempted to repress the values and ways of life of Native Americans. Internal colonialism…
Solid-State NMR Studies Reveal Native-like β-Sheet Structures in Transthyretin Amyloid

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

Lim, Kwang Hun; Dasari, Anvesh K. R.; Hung, Ivan

Structural characterization of amyloid rich in cross-β structures is crucial for unraveling the molecular basis of protein misfolding and amyloid formation associated with a wide range of human disorders. Elucidation of the β-sheet structure in noncrystalline amyloid has, however, remained an enormous challenge. Here we report structural analyses of the β-sheet structure in a full-length transthyretin amyloid using solid-state NMR spectroscopy. Magic-angle-spinning (MAS) solid-state NMR was employed to investigate native-like β-sheet structures in the amyloid state using selective labeling schemes for more efficient solid-state NMR studies. Analyses of extensive long-range 13 C- 13 C correlation MAS spectra obtained with selectivelymore » 13 CO- and 13 Cα-labeled TTR reveal that the two main β-structures in the native state, the CBEF and DAGH β-sheets, remain intact after amyloid formation. The tertiary structural information would be of great use for examining the quaternary structure of TTR amyloid.« less
Solid-State NMR Studies Reveal Native-like β-Sheet Structures in Transthyretin Amyloid

DOE PAGES

Lim, Kwang Hun; Dasari, Anvesh K. R.; Hung, Ivan; ...

2016-09-02

Structural characterization of amyloid rich in cross-β structures is crucial for unraveling the molecular basis of protein misfolding and amyloid formation associated with a wide range of human disorders. Elucidation of the β-sheet structure in noncrystalline amyloid has, however, remained an enormous challenge. Here we report structural analyses of the β-sheet structure in a full-length transthyretin amyloid using solid-state NMR spectroscopy. Magic-angle-spinning (MAS) solid-state NMR was employed to investigate native-like β-sheet structures in the amyloid state using selective labeling schemes for more efficient solid-state NMR studies. Analyses of extensive long-range 13 C- 13 C correlation MAS spectra obtained with selectivelymore » 13 CO- and 13 Cα-labeled TTR reveal that the two main β-structures in the native state, the CBEF and DAGH β-sheets, remain intact after amyloid formation. The tertiary structural information would be of great use for examining the quaternary structure of TTR amyloid.« less
Following Their Dreams: Native American Students Pursuing Medical School.

ERIC Educational Resources Information Center

Boswell, Evelyn

1997-01-01

Four Native American first-year medical school students from Montana discuss their career choice and their goals for establishing medical practices in Native American communities. A regional program has enabled the students to take their first year of classes at Montana State University-Bozeman and to complete their studies at the University of…
BEHAVIORAL RESPONSES OF ANURAN LARVAE TO CHEMICAL CUES OF NATIVE AND INTRODUCED PREDATORS IN THE PACIFIC - NORTHWESTERN UNITED STATES - 2003

EPA Science Inventory

We compared behavioral responses of larvae of three Pacific Northwest anurans from different hydroperiods to water borne cues of native and introduced predators. Two native anurans (Pacific Treefrog, Pseudacris regilla, and Northern Red-Legged Frog, Rana aurora aurora) and introd...
Adolescent Pregnancy Prevention in a Rural Native American Community

ERIC Educational Resources Information Center

Hagen, Janet W.; Skenandore, Alice H.; Scow, Beverly M.; Schanen, Jennifer G.; Clary, Frieda Hugo

2012-01-01

Nationally, the United States has a higher rate of teen pregnancy than any other industrialized nation. Native American youth have a higher birth rate than the national rate. A full-year healthy relationship program, based on Native American teachings, traditions, and cultural norms, was delivered to all eighth-grade students at a rural tribal…
Botrytis and native grape yeasts – not all interactions are created equal

USDA-ARS?s Scientific Manuscript database

Native yeasts are of increasing interest to grape growers and winemakers in Washington State because of their potential to contribute to vineyard health and wine quality. In this pilot project, we used eleven strains of native yeasts and nine isolates of the Botrytis bunch rot pathogen, all obtained...
Are native songbird populations affected by non-native plant invasion?

Treesearch

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.
78 FR 21403 - Notice of Inventory Completion: San Francisco State University NAGPRA Program, San Francisco, CA

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-10

... consultation with the appropriate Indian tribes or Native Hawaiian organizations, and has determined that there... Indian tribes or Native Hawaiian organizations. Lineal descendants or representatives of any Indian tribe or Native Hawaiian organization not identified in this notice that wish to request transfer of...
78 FR 59966 - Notice of Inventory Completion: Michigan State Police, Jackson Post, Jackson, MI

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-30

... Indian tribes or Native Hawaiian organizations, and has determined that there is no cultural affiliation between the human remains and any present-day Indian tribes or Native Hawaiian organizations. Representatives of any Indian tribe or Native Hawaiian organization not identified in this notice that wish to...
78 FR 59954 - Notice of Inventory Completion: Michigan State Police, Mount Pleasant Post, Mount Pleasant, MI

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-30

... tribes or Native Hawaiian organizations, and has determined that there is a cultural affiliation between the human remains and present- day Indian tribes or Native Hawaiian organizations. Lineal descendants or representatives of any Indian tribe or Native Hawaiian organization not identified in this notice...
The State of Native American Youth Health.

ERIC Educational Resources Information Center

Minnesota Univ., Minneapolis. Div. of General Pediatrics and Adolescent Health.

Between 1988 and 1990, nearly 14,000 American Indian and Alaska Native adolescents living in rural areas and on reservations participated in the Adolescent Health Survey of health and risk behaviors. Although the findings may not be representative of Native adolescents, as a convenience sample was used, some findings of the survey were: (1) less…
Farming for restoration: Building bridges for native seeds

Treesearch

Sabine Tishew; Berta Youtie; Anita Kirmer; Nancy Shaw

2011-01-01

In both Europe and the United States, a shortage of native plant material frequently precludes successful restoration. Native plant materials are needed to restore ecosystem functioning and services, provide for in situ conservation of biodiversity (e.g., Hobbs and Cramer 2008), maintain genetic diversity (Bischoff et al. 2010), and afford resistance to invasive...
78 FR 10636 - Task Force on Research on Violence Against American Indian and Alaska Native Women; Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-14

... DEPARTMENT OF JUSTICE Task Force on Research on Violence Against American Indian and Alaska Native Women; Meeting AGENCY: Office on Violence Against Women, United States Department of Justice. ACTION... public meeting of the Task Force on Research on Violence Against American Indian and Alaska Native Women...
Reflections of Native American Teacher Education on Bear Ridge

ERIC Educational Resources Information Center

Locke, Steven

2004-01-01

This study examines an elementary teacher education certification program delivered by a state university to Native American teacher aides on the reservation. Data were collected over two semesters using a Freirean critical theory framework to analyze the data and to explicate the problematic nature of Native American education. Analysis of the…
"South of the Border" at the NMAI

ERIC Educational Resources Information Center

Delugan, Robin Maria

2006-01-01

This essay specifically examines how the NMAI engages Native peoples from Latin America. In this article, the author argues that more than showcasing the diversity of Native cultures the museum is an important platform for reporting Indian and nation-state tensions and other struggles and victories. By situating the realities of Native peoples…
3 CFR 13647 - Executive Order 13647 of June 26, 2013. Establishing the White House Council on Native American...

Code of Federal Regulations, 2014 CFR

2014-01-01

... Science and Technology Policy; (xxvi) the Council on Environmental Quality; (xxvii) the White House Office... life for Native Americans, and shall coordinate the United States Government's engagement with tribal... of Federal resources and create greater opportunities to help improve the quality of life for Native...
Native Alaska's Floating Factoryship--She Plies the Pacific Ocean for Native Alaska.

ERIC Educational Resources Information Center

Wassaja, The Indian Historian, 1980

1980-01-01

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

ERIC Educational Resources Information Center

Casey, James; Ross, Randy; Warren, Marcia

This report on the status of telecommunications and information technology in Indian Country was created as a tool for reference, training, planning, and general educational purposes to be used by Native Americans, government policy makers, and others. A background section discusses policy and the current state of Native communities with regard to…
Spontaneous hybrids between native and exotic Rubus in the Western United States produce offspring both by apomixis and by sexual recombination

PubMed Central

Clark, L V; Jasieniuk, M

2012-01-01

Facultative asexual reproduction is a trait commonly found in invasive species. With a combination of sexual and asexual reproductive modes, such species may adapt to new environments via sexual recombination during range expansion, while at the same time having the benefits of asexuality such as the maintenance of fitness effects that depend upon heterozygosity. In the Western United States, native species of Rubus (Rosaceae) reproduce sexually whereas exotic naturalized Rubus species reproduce by pseudogamous apomixis. We hypothesized that new asexual lineages of Rubus could arise from hybridization in this range. To detect hybridization between native and exotic Rubus, we genotyped 579 individuals collected across California, Oregon and Washington with eight nuclear microsatellites and two chloroplast markers. Principal Coordinate Analysis and Bayesian clustering revealed a limited amount of hybridization of the native R. ursinus with the exotic R. armeniacus and R. pensilvanicus, as well as cultivated varieties. Genetic distances between these hybrids and their offspring indicated that both R. ursinus × R. armeniacus and R. ursinus × R. pensilvanicus produced a mix of apomictic and sexual seeds, with sexual seeds being more viable. Although neither of these hybrid types is currently considered invasive, they model the early stages of evolution of new invasive lineages, given the potential for fixed heterosis and the generation of novel genotypes. The hybrids also retain the ability to increase their fitness via sexual recombination and natural selection. Mixed reproductive systems such as those described here may be an important step in the evolution of asexual invasive species. PMID:22850699

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

ERIC Educational Resources Information Center

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…
National Project: Increasing Participation of Native Americans in Vocational Education. 1976-1977 Final Report.

ERIC Educational Resources Information Center

Stufflebean, Tana; And Others

The overall objective of the 1977 national project was to assist participating states in increasing the number and participation of Native American students, teachers, and teacher educators in vocational and technical education. Participants in the major training activity (a 3-day workshop) were 15 3-member state teams and about 30 tribal and…
78 FR 64327 - Endangered and Threatened Wildlife and Plants; Designation of Critical Habitat for the Bi-State...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-28

... 2001 (Pub. L. 106-554; H.R. 5658)), and our associated Information Quality Guidelines, provide criteria..., agricultural lands, and steppe dominated by native grasses and forbs. However, the Bi-State DPS of greater sage... sagebrush vegetation as well as a vegetative understory composed of native grasses and forbs are essential...
Diversity and antifungal activity of the endophytic fungi associated with the native medicinal cactus Opuntia humifusa (Cactaceae) from the United States

USDA-ARS?s Scientific Manuscript database

The endophytic fungal community associated with the native cactus Opuntia humifusa in the United States was investigated and its potential for providing antifungal compounds. A total of 108 endophytic fungal isolates were obtained and identified by molecular methods into 17 different taxa of the gen...
Information encoded in non-native states drives substrate-chaperone pairing.

PubMed

Mapa, Koyeli; Tiwari, Satyam; Kumar, Vignesh; Jayaraj, Gopal Gunanathan; Maiti, Souvik

2012-09-05

Many proteins refold in vitro through kinetic folding intermediates that are believed to be by-products of native-state centric evolution. These intermediates are postulated to play only minor roles, if any, in vivo because they lack any information related to translation-associated vectorial folding. We demonstrate that refolding intermediate of a test protein, generated in vitro, is able to find its cognate chaperone, from the whole complement of Escherichia coli soluble chaperones. Cognate chaperone-binding uniquely alters the conformation of non-native substrate. Importantly, precise chaperone targeting of substrates are maintained as long as physiological molar ratios of chaperones remain unaltered. Using a library of different chaperone substrates, we demonstrate that kinetically trapped refolding intermediates contain sufficient structural features for precise targeting to cognate chaperones. We posit that evolution favors sequences that, in addition to coding for a functional native state, encode folding intermediates with higher affinity for cognate chaperones than noncognate ones. Copyright © 2012 Elsevier Ltd. All rights reserved.
Pharmacological chaperone reshapes the energy landscape for folding and aggregation of the prion protein

NASA Astrophysics Data System (ADS)

Gupta, Amar Nath; Neupane, Krishna; Rezajooei, Negar; Cortez, Leonardo M.; Sim, Valerie L.; Woodside, Michael T.

2016-06-01

The development of small-molecule pharmacological chaperones as therapeutics for protein misfolding diseases has proven challenging, partly because their mechanism of action remains unclear. Here we study Fe-TMPyP, a tetrapyrrole that binds to the prion protein PrP and inhibits misfolding, examining its effects on PrP folding at the single-molecule level with force spectroscopy. Single PrP molecules are unfolded with and without Fe-TMPyP present using optical tweezers. Ligand binding to the native structure increases the unfolding force significantly and alters the transition state for unfolding, making it more brittle and raising the barrier height. Fe-TMPyP also binds the unfolded state, delaying native refolding. Furthermore, Fe-TMPyP binding blocks the formation of a stable misfolded dimer by interfering with intermolecular interactions, acting in a similar manner to some molecular chaperones. The ligand thus promotes native folding by stabilizing the native state while also suppressing interactions driving aggregation.
Relation between native ensembles and experimental structures of proteins

PubMed Central

Best, Robert B.; Lindorff-Larsen, Kresten; DePristo, Mark A.; Vendruscolo, Michele

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 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 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 that even a modest number of structures of a protein determined under different conditions, or with small variations in sequence, capture a representative subset of the true native-state ensemble. PMID:16829580
Soil Quality of Bauxite Mining Areas

NASA Astrophysics Data System (ADS)

Terezinha Gonçalves Bizuti, Denise; Dinarowski, Marcela; Casagrande, José Carlos; Silva, Luiz Gabriel; Soares, Marcio Roberto; Henrique Santin Brancalion, Pedro

2015-04-01

The study on soil quality index (SQI) aims to assess the current state of the soil after use and estimating its recovery through sustainable management practices This type of study is being used in this work in order to check the efficiency of forest recovery techniques in areas that have been deeply degraded by bauxite mining process, and compare them with the area of native forest, through the determination of SQI. Treatments were newly mined areas, areas undergoing restoration (topsoil use with planting of native forest species), areas in rehabilitation (employment of the green carpet with topsoil and planting of native forest species) and areas of native forests, with six repetitions, in areas of ALCOA, in the municipality of Poços de Caldas/MG. To this end, we used the additive pondered model, establishing three functions: Fertility, water movement and root development, based on chemical parameters (organic matter, base saturation, aluminum saturation and calcium content); physical (macroporosity, soil density and clay content); and microbiological testing (basal respiration by the emission of CO2 ). The SQIs obtained for each treatment was 41%, 56%, 63% and 71% for newly mined areas, native forest, areas in restoration and rehabilitation, respectively. The recovering technique that most approximates the degraded soil to the soil of reference is the restoration, where there was no statistically significant difference of areas restored with native forest. It was found that for the comparison of the studied areas must take into account the nutrient cycling, that disappear with plant removal in mining areas, once the soil of native forest features low fertility and high saturation by aluminum, also taking in account recovering time.
Native-likeness in second language lexical categorization reflects individual language history and linguistic community norms.

PubMed

Zinszer, Benjamin D; Malt, Barbara C; Ameel, Eef; Li, Ping

2014-01-01

SECOND LANGUAGE LEARNERS FACE A DUAL CHALLENGE IN VOCABULARY LEARNING: First, they must learn new names for the 100s of common objects that they encounter every day. Second, after some time, they discover that these names do not generalize according to the same rules used in their first language. Lexical categories frequently differ between languages (Malt et al., 1999), and successful language learning requires that bilinguals learn not just new words but new patterns for labeling objects. In the present study, Chinese learners of English with varying language histories and resident in two different language settings (Beijing, China and State College, PA, USA) named 67 photographs of common serving dishes (e.g., cups, plates, and bowls) in both Chinese and English. Participants' response patterns were quantified in terms of similarity to the responses of functionally monolingual native speakers of Chinese and English and showed the cross-language convergence previously observed in simultaneous bilinguals (Ameel et al., 2005). For English, bilinguals' names for each individual stimulus were also compared to the dominant name generated by the native speakers for the object. Using two statistical models, we disentangle the effects of several highly interactive variables from bilinguals' language histories and the naming norms of the native speaker community to predict inter-personal and inter-item variation in L2 (English) native-likeness. We find only a modest age of earliest exposure effect on L2 category native-likeness, but importantly, we find that classroom instruction in L2 negatively impacts L2 category native-likeness, even after significant immersion experience. We also identify a significant role of both L1 and L2 norms in bilinguals' L2 picture naming responses.
Native-likeness in second language lexical categorization reflects individual language history and linguistic community norms

PubMed Central

Zinszer, Benjamin D.; Malt, Barbara C.; Ameel, Eef; Li, Ping

2014-01-01

Second language learners face a dual challenge in vocabulary learning: First, they must learn new names for the 100s of common objects that they encounter every day. Second, after some time, they discover that these names do not generalize according to the same rules used in their first language. Lexical categories frequently differ between languages (Malt et al., 1999), and successful language learning requires that bilinguals learn not just new words but new patterns for labeling objects. In the present study, Chinese learners of English with varying language histories and resident in two different language settings (Beijing, China and State College, PA, USA) named 67 photographs of common serving dishes (e.g., cups, plates, and bowls) in both Chinese and English. Participants’ response patterns were quantified in terms of similarity to the responses of functionally monolingual native speakers of Chinese and English and showed the cross-language convergence previously observed in simultaneous bilinguals (Ameel et al., 2005). For English, bilinguals’ names for each individual stimulus were also compared to the dominant name generated by the native speakers for the object. Using two statistical models, we disentangle the effects of several highly interactive variables from bilinguals’ language histories and the naming norms of the native speaker community to predict inter-personal and inter-item variation in L2 (English) native-likeness. We find only a modest age of earliest exposure effect on L2 category native-likeness, but importantly, we find that classroom instruction in L2 negatively impacts L2 category native-likeness, even after significant immersion experience. We also identify a significant role of both L1 and L2 norms in bilinguals’ L2 picture naming responses. PMID:25386149
Conformational dynamics of a protein in the folded and the unfolded state

NASA Astrophysics Data System (ADS)

Fitter, Jörg

2003-08-01

In a quasielastic neutron scattering experiment, the picosecond dynamics of α-amylase was investigated for the folded and the unfolded state of the protein. In order to ensure a reasonable interpretation of the internal protein dynamics, the protein was measured in D 2O-buffer solution. The much higher structural flexibility of the pH induced unfolded state as compared to the native folded state was quantified using a simple analytical model, describing a local diffusion inside a sphere. In terms of this model the conformational volume, which is explored mainly by confined protein side-chain movements, is parameterized by the radius of a sphere (folded state, r=1.2 Å; unfolded state, 1.8 Å). Differences in conformational dynamics between the folded and the unfolded state of a protein are of fundamental interest in the field of protein science, because they are assumed to play an important role for the thermodynamics of folding/unfolding transition and for protein stability.
Enhancing Accuracy in Molecular Weight Determination of Highly Heterogeneously Glycosylated Proteins by Native Tandem Mass Spectrometry.

PubMed

Wang, Guanbo; de Jong, Rob N; van den Bremer, Ewald T J; Parren, Paul W H I; Heck, Albert J R

2017-05-02

The determination of molecular weights (MWs) of heavily glycosylated proteins is seriously hampered by the physicochemical characteristics and heterogeneity of the attached carbohydrates. Glycosylation impacts protein migration during sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE) and size-exclusion chromatography (SEC) analysis. Standard electrospray ionization (ESI)-mass spectrometry does not provide a direct solution as this approach is hindered by extensive interference of ion signals caused by closely spaced charge states of broadly distributed glycoforms. Here, we introduce a native tandem MS-based approach, enabling charge-state resolution and charge assignment of protein ions including those that escape mass analysis under standard MS conditions. Using this method, we determined the MW of two model glycoproteins, the extra-cellular domains of the highly and heterogeneously glycosylated proteins CD38 and epidermal growth factor receptor (EGFR), as well as the overall MW and binding stoichiometries of these proteins in complex with a specific antibody.
Tobacco Industry Promotional Strategies Targeting American Indians/Alaska Natives and Exploiting Tribal Sovereignty.

PubMed

Lempert, Lauren K; Glantz, Stanton A

2018-03-12

American Indians/Alaska Natives have the highest commercial tobacco use in the United States, resulting in higher tobacco-caused deaths and diseases than the general population. Some American Indians/Alaska Natives use commercial tobacco for ceremonial as well as recreational uses. Because federally-recognized Tribal lands are sovereign, they are not subject to state cigarette taxes and smokefree laws. This study analyzes tobacco industry promotional efforts specifically targeting American Indians/Alaska Natives and exploiting Tribal lands to understand appropriate policy responses in light of American Indians'/Alaska Natives' unique sovereign status and culture. We analyzed previously secret tobacco industry documents available at the Truth Tobacco Documents Library (https://industrydocuments.library.ucsf.edu/tobacco/). Tobacco companies used promotional strategies targeting American Indians/Alaska Natives and exploiting Tribal lands that leveraged the federally-recognized Tribes' unique sovereign status exempting them from state cigarette taxes and smokefree laws, and exploited some Tribes' existing traditional uses of ceremonial tobacco and poverty. Tactics included price reductions, coupons, giveaways, gaming promotions, charitable contributions and sponsorships. Additionally, tobacco companies built alliances with Tribal leaders to help improve their corporate image, advance ineffective "youth smoking prevention" programs, and defeat tobacco control policies. The industry's promotional tactics likely contribute to disparities in smoking prevalence and smoking-related diseases among American Indians//Alaska Natives. Proven policy interventions to address these disparities including tobacco price increases, cigarette taxes, comprehensive smokefree laws, and industry denormalization campaigns to reduce smoking prevalence and smoking-related disease could be considered by Tribal communities. The sovereign status of federally-recognized Tribes does not prevent them from adopting these measures.
KSC-02pp1743

NASA Image and Video Library

2002-11-10

KENNEDY SPACE CENTER, FLA. -- Seminole Native American Veterans serve as color guard during a pre-launch Native American ceremony at the Rocket Garden in the KSC Visitor Complex. David Nunez, U.S. Navy, carries the State of Florida Flag; David Stephen Bowers, U.S. Army, carries the Flag of the United States of America; Charles Billie Hiers, U.S. Marine Corps., carries the Seminole Tribe of Florida Flag. The ceremony was part of several days' activities commemorating John B. Herrington as the first tribally enrolled Native American astronaut to fly on a Shuttle mission. Herrington is a Mission Specialist on STS-113.
Evidence for a Shared Mechanism in the Formation of Urea-Induced Kinetic and Equilibrium Intermediates of Horse Apomyoglobin from Ultrarapid Mixing Experiments

PubMed Central

Mizukami, Takuya; Abe, Yukiko; Maki, Kosuke

2015-01-01

In this study, the equivalence of the kinetic mechanisms of the formation of urea-induced kinetic folding intermediates and non-native equilibrium states was investigated in apomyoglobin. Despite having similar structural properties, equilibrium and kinetic intermediates accumulate under different conditions and via different mechanisms, and it remains unknown whether their formation involves shared or distinct kinetic mechanisms. To investigate the potential mechanisms of formation, the refolding and unfolding kinetics of horse apomyoglobin were measured by continuous- and stopped-flow fluorescence over a time range from approximately 100 μs to 10 s, along with equilibrium unfolding transitions, as a function of urea concentration at pH 6.0 and 8°C. The formation of a kinetic intermediate was observed over a wider range of urea concentrations (0–2.2 M) than the formation of the native state (0–1.6 M). Additionally, the kinetic intermediate remained populated as the predominant equilibrium state under conditions where the native and unfolded states were unstable (at ~0.7–2 M urea). A continuous shift from the kinetic to the equilibrium intermediate was observed as urea concentrations increased from 0 M to ~2 M, which indicates that these states share a common kinetic folding mechanism. This finding supports the conclusion that these intermediates are equivalent. Our results in turn suggest that the regions of the protein that resist denaturant perturbations form during the earlier stages of folding, which further supports the structural equivalence of transient and equilibrium intermediates. An additional folding intermediate accumulated within ~140 μs of refolding and an unfolding intermediate accumulated in <1 ms of unfolding. Finally, by using quantitative modeling, we showed that a five-state sequential scheme appropriately describes the folding mechanism of horse apomyoglobin. PMID:26244984
A culturally appropriate program that works: Native Americans in Marine and Space Sciences

NASA Astrophysics Data System (ADS)

Vergun, J. R.

2001-05-01

For more than ten years, the College of Oceanic and Atmospheric Sciences at Oregon State University has carried out the Native Americans in Marine and Space Sciences (NAMSS) Program. Its long-term goal is to increase the number of American Indian and Native Alaskan undergraduates in science who complete degrees, continue to graduate school and enter the professional scientific work force. Ninety-eight percent of NAMSS students have earned BS degrees and almost forty percent have continued in graduate school. These are impressive results considering the high national drop-out rate for Native American studentsaround 70% according to the Chronicle of Higher Education (26 May 1993, page A29). Most often, Native students wishing to earn degrees in science find few programs that fit with their traditional sense of place and community. Most programs are narrowly focused and do not support or nurture Native views of interrelationship of all things. While Western science's recent ecological systems thinking approach more closely resembles the traditional Native view, Traditional Ecological Knowledge is often perceived as anecdotal or storytelling and not real science. This is a problem for Native students who are strongly underrepresented in the U.S. scientific community as a whole and nearly absent from the marine sciences. Undergraduates from this group are without scientific career models or mentors from their ethnic group and experience difficulty establishing contacts with majority scientists. They have limited access to opportunities to explore career possibilities in the sciences through research participation. Once on campus they have difficulty establishing a sense of belonging in the University community and do not have an organized way to enter into the scientific activities that initially attracted them. Representation of Native Americans in the ranks of U.S. scientists will not be increased without special efforts to retain them as undergraduates and to recruit them into graduate programs. In this presentation, we will discuss how our program and expansive outreach activities is successful in overcoming many of these difficulties. We provide opportunities to our students by helping them earn the financial support needed to remain in the University and by facilitating the career choices of these undergraduates through meaningful and active participation in ongoing research projects at OSU. In addition, we have formed alliances with Federal and State agencies, private industry and tribal organizations to provide internships for NAMSS students. These experiences educate them in science and help them to overcome cultural barriers to career possibilities. NAMSS provides these students with: 1) Direct contact with career models who help them to learn about the nature of scientific research and application of knowledge; 2) encouragement and stimulation of their interest to sustain them in their determination to remain in school and to complete their degrees; 3) a sense of legitimate place and worth in the University community through a mentoring relation with an established scientist and NAMS staff and counselors, and by association with other students involved in scientific careers; 4) entry into the network of professional contacts in science; and, 5) the financial support they need to remain in college.
Effects of two solvent conditions on the free energy landscape of the BBL peripheral subunit binding domain.

PubMed

Liu, Hanzhong; Huo, Shuanghong

2012-01-12

BBL is a small independently folding domain with two main parallel helices. The experiment of C(α) secondary shifts has shown that changing the pH from ~7 to ~5 results in the reduced helicity at the C-terminus of helix 2. Combining constant pH molecular dynamics with replica exchange, we sampled the protein conformation space and protonation states extensively under a neutral pH condition and an acidic condition. Our results reveal that the solvent conditions influence the free energy landscape. Under the neutral pH condition, the denatured state and the native state are well separated. The condition of the acidic pH reshapes the free energy surface, leading to a broadly populated denatured-state basin and a low free energy barrier between the denatured state and the native state. The acidic pH shifts the equilibrium between the denatured state and the native state in favor of the denatured state. Caution must be used to interpret experimental data under the acidic condition because the contribution of the denatured state is significant. Our simulation results are supported by the fact that the calculated chemical shifts are in good agreement with the experiment data.
Can a continuum solvent model reproduce the free energy landscape of a -hairpin folding in water?

NASA Astrophysics Data System (ADS)

Zhou, Ruhong; Berne, Bruce J.

2002-10-01

The folding free energy landscape of the C-terminal -hairpin of protein G is explored using the surface-generalized Born (SGB) implicit solvent model, and the results are compared with the landscape from an earlier study with explicit solvent model. The OPLSAA force field is used for the -hairpin in both implicit and explicit solvent simulations, and the conformational space sampling is carried out with a highly parallel replica-exchange method. Surprisingly, we find from exhaustive conformation space sampling that the free energy landscape from the implicit solvent model is quite different from that of the explicit solvent model. In the implicit solvent model some nonnative states are heavily overweighted, and more importantly, the lowest free energy state is no longer the native -strand structure. An overly strong salt-bridge effect between charged residues (E42, D46, D47, E56, and K50) is found to be responsible for this behavior in the implicit solvent model. Despite this, we find that the OPLSAA/SGB energies of all the nonnative structures are higher than that of the native structure; thus the OPLSAA/SGB energy is still a good scoring function for structure prediction for this -hairpin. Furthermore, the -hairpin population at 282 K is found to be less than 40% from the implicit solvent model, which is much smaller than the 72% from the explicit solvent model and 80% from experiment. On the other hand, both implicit and explicit solvent simulations with the OPLSAA force field exhibit no meaningful helical content during the folding process, which is in contrast to some very recent studies using other force fields.
Can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water?

PubMed Central

Zhou, Ruhong; Berne, Bruce J.

2002-01-01

The folding free energy landscape of the C-terminal β-hairpin of protein G is explored using the surface-generalized Born (SGB) implicit solvent model, and the results are compared with the landscape from an earlier study with explicit solvent model. The OPLSAA force field is used for the β-hairpin in both implicit and explicit solvent simulations, and the conformational space sampling is carried out with a highly parallel replica-exchange method. Surprisingly, we find from exhaustive conformation space sampling that the free energy landscape from the implicit solvent model is quite different from that of the explicit solvent model. In the implicit solvent model some nonnative states are heavily overweighted, and more importantly, the lowest free energy state is no longer the native β-strand structure. An overly strong salt-bridge effect between charged residues (E42, D46, D47, E56, and K50) is found to be responsible for this behavior in the implicit solvent model. Despite this, we find that the OPLSAA/SGB energies of all the nonnative structures are higher than that of the native structure; thus the OPLSAA/SGB energy is still a good scoring function for structure prediction for this β-hairpin. Furthermore, the β-hairpin population at 282 K is found to be less than 40% from the implicit solvent model, which is much smaller than the 72% from the explicit solvent model and ≈80% from experiment. On the other hand, both implicit and explicit solvent simulations with the OPLSAA force field exhibit no meaningful helical content during the folding process, which is in contrast to some very recent studies using other force fields. PMID:12242327
Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water?

PubMed

Zhou, Ruhong; Berne, Bruce J

2002-10-01

The folding free energy landscape of the C-terminal beta-hairpin of protein G is explored using the surface-generalized Born (SGB) implicit solvent model, and the results are compared with the landscape from an earlier study with explicit solvent model. The OPLSAA force field is used for the beta-hairpin in both implicit and explicit solvent simulations, and the conformational space sampling is carried out with a highly parallel replica-exchange method. Surprisingly, we find from exhaustive conformation space sampling that the free energy landscape from the implicit solvent model is quite different from that of the explicit solvent model. In the implicit solvent model some nonnative states are heavily overweighted, and more importantly, the lowest free energy state is no longer the native beta-strand structure. An overly strong salt-bridge effect between charged residues (E42, D46, D47, E56, and K50) is found to be responsible for this behavior in the implicit solvent model. Despite this, we find that the OPLSAA/SGB energies of all the nonnative structures are higher than that of the native structure; thus the OPLSAA/SGB energy is still a good scoring function for structure prediction for this beta-hairpin. Furthermore, the beta-hairpin population at 282 K is found to be less than 40% from the implicit solvent model, which is much smaller than the 72% from the explicit solvent model and approximately equal 80% from experiment. On the other hand, both implicit and explicit solvent simulations with the OPLSAA force field exhibit no meaningful helical content during the folding process, which is in contrast to some very recent studies using other force fields.

Native American Historic Context for the United States Military Academy, West Point, New York

DTIC Science & Technology

2006-04-01

Native Americans in the Hudson Highlands Pre-Contact Period A number of American Indian nations have over time either occupied the Hudson Valley...inability of Western legal institutions to grasp American Indian and Alaska Native claims that some places on the planet possess a degree of...archeological sites near the USMA. It contains a brief history of various Native American nations that may have been living in or using the West Point
Models of Experimentally Derived Competitive Effects Predict Biogeographical Differences in the Abundance of Invasive and Native Plant Species

PubMed Central

Xiao, Sa; Ni, Guangyan; Callaway, Ragan M.

2013-01-01

Mono-dominance by invasive species provides opportunities to explore determinants of plant distributions and abundance; however, linking mechanistic results from small scale experiments to patterns in nature is difficult. We used experimentally derived competitive effects of an invader in North America, Acroptilon repens, on species with which it co-occurs in its native range of Uzbekistan and on species with which it occurs in its non-native ranges in North America, in individual-based models. We found that competitive effects yielded relative abundances of Acroptilon and other species in models that were qualitatively similar to those observed in the field in the two ranges. In its non-native range, Acroptilon can occur in nearly pure monocultures at local scales, whereas such nearly pure stands of Acroptilon appear to be much less common in its native range. Experimentally derived competitive effects of Acroptilon on other species predicted Acroptilon to be 4–9 times more proportionally abundant than natives in the North American models, but proportionally equal to or less than the abundance of natives in the Eurasian models. Our results suggest a novel way to integrate complex combinations of interactions simultaneously, and that biogeographical differences in the competitive effects of an invader correspond well with biogeographical differences in abundance and impact. PMID:24265701
The Box and the Circle--Two Systems of Life: A Model for Understanding Native-Non-Native Issues.

ERIC Educational Resources Information Center

Derrick, Jann

Working as a family systems therapist with Native and non-Native families, the author observed two opposing social systems. Non-native families systems typify "The Box System," whereas native family systems portray "The Circle System." A few characteristics of the Circle System are: (1) a focus on life and peacefulness; (2) females and children…
Cancer Control Research Training for Native Researchers: A Model for Development of Additional Native Researcher Training Programs

ERIC Educational Resources Information Center

Becker, Thomas M.; Dunn, Esther; Tom-Orme, Lillian; Joe, Jennie

2005-01-01

Several social and biological scientists who have Native status are engaged in productive research careers, but the encouragement that has been offered to Native students to formulate career goals devoted to cancer etiology or cancer control in Native peoples has had limited success. Hence, the Native Researchers' Cancer Control Training Program…
Proceedings of a USGS Workshop on Facing Tomorrow's Challenges Along the U.S.-Mexico Border - Monitoring, Modeling, and Forecasting Change Within the Arizona-Sonora Transboundary Watersheds

USGS Publications Warehouse

Norman, Laura M.; Hirsch, Derrick D.; Ward, A. Wesley

2008-01-01

INTRODUCTION TO THE WORKSHOP PROCEEDINGS Competition for water resources, habitats, and urban areas in the Borderlands has become an international concern. In the United States, Department of Interior Bureaus, Native American Tribes, and other State and Federal partners rely on the U.S. Geological Survey (USGS) to provide unbiased science and leadership in the Borderlands region. Consequently, the USGS hosted a workshop, ?Facing Tomorrow?s Challenges along the U.S.-Mexico Border,? on March 20?22, 2007, in Tucson, Ariz., focused specifically on monitoring, modeling, and forecasting change within the Arizona-Sonora Transboundary Watersheds
Transition of vegetation states positively affects harvester ants in the Great Basin, United States

USGS Publications Warehouse

Holbrook, Joseph D.; Pilliod, David S.; Arkle, Robert; Rachlow, Janet L.; Vierling, Kerri T.; Wiest, Michelle M.

2016-01-01

Invasions by non-native plants can alter ecosystems such that new ecological states are reached, but less is known about how these transitions influence animal populations. Sagebrush (Artemisia tridentata) ecosystems are experiencing state changes because of fire and invasion by exotic annual grasses. Our goal was to study the effects of these state changes on the Owyhee and western harvester ants (Pogonomyrmex salinusOlsen and P. occidentalis Cresson, respectively). We sampled 358 1-ha plots across the northern Great Basin, which captured unburned and burned conditions across 1 −≥31 years postfire. Our results indicated an immediate and consistent change in vegetation states from shrubland to grassland between 1 and 31 years postfire. Harvester ant occupancy was unrelated to time since fire, whereas we observed a positive effect of fire on nest density. Similarly, we discovered that fire and invasion by exotic annuals were weak predictors of harvester ant occupancy but strong predictors of nest density. Occupancy of harvester ants was more likely in areas with finer-textured soils, low precipitation, abundant native forbs, and low shrub cover. Nest density was higher in arid locations that recently burned and exhibited abundant exotic annual and perennial (exotic and native) grasses. Finally, we discovered that burned areas that received postfire restoration had minimal influence on harvester ant occupancy or nest density compared with burned and untreated areas. These results suggest that fire-induced state changes from native shrublands to grasslands dominated by non-native grasses have a positive effect on density of harvester ants (but not occupancy), and that postfire restoration does not appear to positively or negatively affect harvester ants. Although wildfire and invasion by exotic annual grasses may negatively affect other species, harvester ants may indeed be one of the few winners among a myriad of losers linked to vegetation state changes within sagebrush ecosystems.
Propagating native plants at the National Tropical Botanical Garden

Treesearch

Diane Ragone

2002-01-01

Hawaii has the dubious distinction of being the extinction capital of the United States with close to 30 percent of native plant species listed as endangered. The National Tropical Botanical Garden has been a leader in efforts to propagate and conserve native Hawaiian plants with close to 800 species collected for ex situ conservation since 1990....
Survival, Growth and Reproduction of Non-Native Nile Tilapia II: Fundamental Niche Projections and Invasion Potential in the Northern Gulf of Mexico

DTIC Science & Technology

2012-07-27

Cambridge University Press. 47. Gritti ESB, Smith B, Sykes MT (2006) Vulnerability of Mediterranean Basin ecosystems to climate change and invasion by...2011) Monitoring diets and growth rates of native predatory fish stocked to suppress non-native tilapia. MS Thesis, Nicholls State University
Embracing Intercultural Diversification: Teaching Young Adult Literature with Native American Themes

ERIC Educational Resources Information Center

Metzger, Kenan; Box, Andrea; Blasingame, James

2013-01-01

According to the most recent census, there are five million Native Americans in the United States. Of these, there are at least 500,000 Native Americans attending public schools. However, the educational system does not fully serve this population and in fact often ignores them. More importantly, each tribe and clan has its own distinct cultural…
Biological Control of Introduced Weeds of Native Hawaiian Forests

Treesearch

George P. Markin; Roddy F. Nagata; Donald E. Gardner

1992-01-01

Among the many threats to the continued existence of the remaining native forests and other native ecosystems of the Hawaiian Islands, the most severe and the most difficult to control are the invasion and replacement by induced species of plants. Because conventional methods of plant management have faild to control this invasion, a multiagency, state and federal...
Economic Impacts of Non-Native Forest Insects in the Continental United States

Treesearch

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...
MANAGEMENT OF SMALL MAMMALS IN A RELICT GRASSLAND IN CALIFORNIA'S CENTRAL VALLEY

Treesearch

ANNE POOPATANAPONG; DOUGLAS A. KELT

1999-01-01

land-use patterns over the past century. In California's Central Valley these changes have resulted in replacement of native grassland vegetation by non-native annual grasses. Jepson Prairie is a natural reserve that has been set aside to preserve native vernal pool and bunchgrass habitats. Jepson Prairie also provides habitat for several state and federally...
The Nativization of the Tribal Workforce: A Vision for the Future

ERIC Educational Resources Information Center

Ahmed Al-Asfour

2018-01-01

Perhaps the most challenging issue facing many Native nations is employment--or rather, the lack of employment opportunity--on or near the reservation. How to best foster economic development for Native American communities has long been discussed at the local, state, and federal levels. Agencies such as the Bureau of Indian Affairs (BIA) have…
First report of downy mildew disease caused by Plasmopara halstedii on the native Rudbeckia fulgida Aiton var. speciosa (Wender.)

USDA-ARS?s Scientific Manuscript database

The showy black-eyed Susan Rudbeckia fulgida Aiton var. speciosa (Wender.) is an important perennial wildflower native to the Northeast and Midwest regions of the United States. Besides its aesthetic value in the landscape, this native plant attracts pollinators and provides seeds for birds during t...
Work of the Bureau of Education for the Natives of Alaska. Bulletin, 1929, No. 12

ERIC Educational Resources Information Center

Hamilton, William

1929-01-01

In addition to maintaining schools for the native children of Alaska, the United States Bureau of Education aids entire communities by extending medical aid, by relieving destitution, by fostering commercial enterprises, by supervising the reindeer industry, and by promoting generally the interests of the natives. The organization of the Alaska…
A resolution recognizing National Native American Heritage Month and celebrating the heritages and cultures of Native Americans and the contributions of Native Americans to the United States.

THOMAS, 112th Congress

Sen. Akaka, Daniel K. [D-HI

2012-09-19

Senate - 09/22/2012 Resolution agreed to in Senate without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:
Holistic System of Care: a ten-year perspective.

PubMed

Nebelkopf, Ethan; Wright, Serena

2011-01-01

The Holistic System of Care for Native Americans in an Urban Environment is a community-focused intervention that provides behavioral health care, promotes health, and prevents disease. This approach is based on a community strategic planning process that honored Native American culture and relationships. Substance abuse, mental illness, homelessness, poverty, crime, physical illness, and violence are symptoms of historical trauma, family dysfunction, and spiritual imbalance. The holistic model links treatment, prevention, and recovery. The link between prevention and treatment is early intervention. Peer support is the link between treatment and recovery. Recovering individuals serve as role models linking recovery to prevention. Culture and spirituality build a strong and resilient foundation for recovery. This article documents the effectiveness of the holistic model over a ten-year period that it has been implemented at the Family & Child Guidance Clinic of the Native American Health Center in the San Francisco Bay Area. The holistic model has produced statistically significant reductions in substance abuse among adult Native American women, men, reentry, and homeless populations; reductions in substance abuse among Native American adolescents; reductions in HIV/AIDS high-risk behavior among Native American men, women, and adolescents; and decreases in acting out behavior among Native American severely emotionally disturbed children.
Incorporating hemlock woolly adelgid impacts into the Forest Vegetation Simulator model

Treesearch

R. Talbot III Trotter; Anthony W. Courter; Richard M. Turcotte; Brad. Onken

2008-01-01

The hemlock woolly adelgid (HWA), Adelges tsugae, is a small aphid-like insect that feeds on the xylem ray parenchyma cells near the base of hemlock needles. This insect, a native of Asia and western North America, was first noted in eastern North America in 1951 and has now spread to infest hemlock in at least 17 states. The increased hemlock...
Modeling-independent elucidation of inactivation pathways in recombinant and native A-type Kv channels

PubMed Central

Fineberg, Jeffrey D.; Ritter, David M.

2012-01-01

A-type voltage-gated K+ (Kv) channels self-regulate their activity by inactivating directly from the open state (open-state inactivation [OSI]) or by inactivating before they open (closed-state inactivation [CSI]). To determine the inactivation pathways, it is often necessary to apply several pulse protocols, pore blockers, single-channel recording, and kinetic modeling. However, intrinsic hurdles may preclude the standardized application of these methods. Here, we implemented a simple method inspired by earlier studies of Na+ channels to analyze macroscopic inactivation and conclusively deduce the pathways of inactivation of recombinant and native A-type Kv channels. We investigated two distinct A-type Kv channels expressed heterologously (Kv3.4 and Kv4.2 with accessory subunits) and their native counterparts in dorsal root ganglion and cerebellar granule neurons. This approach applies two conventional pulse protocols to examine inactivation induced by (a) a simple step (single-pulse inactivation) and (b) a conditioning step (double-pulse inactivation). Consistent with OSI, the rate of Kv3.4 inactivation (i.e., the negative first derivative of double-pulse inactivation) precisely superimposes on the profile of the Kv3.4 current evoked by a single pulse because the channels must open to inactivate. In contrast, the rate of Kv4.2 inactivation is asynchronous, already changing at earlier times relative to the profile of the Kv4.2 current evoked by a single pulse. Thus, Kv4.2 inactivation occurs uncoupled from channel opening, indicating CSI. Furthermore, the inactivation time constant versus voltage relation of Kv3.4 decreases monotonically with depolarization and levels off, whereas that of Kv4.2 exhibits a J-shape profile. We also manipulated the inactivation phenotype by changing the subunit composition and show how CSI and CSI combined with OSI might affect spiking properties in a full computational model of the hippocampal CA1 neuron. This work unambiguously elucidates contrasting inactivation pathways in neuronal A-type Kv channels and demonstrates how distinct pathways might impact neurophysiological activity. PMID:23109714
Internet cigarette sales and Native American sovereignty: political and public health contexts.

PubMed

Samuel, Kari A; Ribisl, Kurt M; Williams, Rebecca S

2012-05-01

Internet cigarette vendors (ICVs) advertise low prices for tobacco products, subverting public health policy efforts to curtail smoking by raising prices. Many online retailers in the United States claim affiliation with Native American tribes and share in tribal tax-free status. Sales of discounted cigarettes from both online vendors and brick-and-mortar stores have angered non-Native retailers and triggered enforcement actions by state and federal governments in the United States concerned over lost cigarette excise tax revenue. Examination of the history and politics of cigarette sales on reservations and attempts to regulate Internet cigarette sales highlights the potential role for greater use of negotiated intergovernmental agreements to address reservation-based tobacco sales. Our review notes global parallels and explicates history and politics of such regulation in the United States, and offers background for collaborative efforts to regulate tobacco sales and decrease tobacco use.

New records and range extensions of several species of native bees (Hymenoptera: Apoidea) from Mississippi

PubMed Central

Griswold, Terry; Ikerd, Harold W; Orr, Michael Christopher

2018-01-01

Abstract Background The native bee fauna of Mississippi, USA has been historically poorly sampled, but is of particular relevance to determine range limits for species that occur in the southern United States. Currently published literature includes 184 species of bees that occur within the state of Mississippi. Additions to the list of native bees known for Mississippi are reported with notes on range, ecology and resources for identification. New information The geographic ranges of seven additional species are extended into the state of Mississippi: Andrena (Melandrena) obscuripennis Smith, 1853, Anthemurgus passiflorae Robertson, 1902, Dieunomia bolliana (Cockerell 1910), Diadasia (Diadasia) enavata (Cresson 1872), Peponapis crassidentata (Cockerell 1949), Triepeolus subnitens Cockerell and Timberlake, 1929 and Brachynomada nimia (Snelling and Rozen 1987). These records raise the total number of published species known from the state to 191. Anthemurgus and Brachynomada are also genera new to Mississippi. PMID:29853776
New records and range extensions of several species of native bees (Hymenoptera: Apoidea) from Mississippi.

PubMed

Parys, Katherine; Griswold, Terry; Ikerd, Harold W; Orr, Michael Christopher

2018-01-01

The native bee fauna of Mississippi, USA has been historically poorly sampled, but is of particular relevance to determine range limits for species that occur in the southern United States. Currently published literature includes 184 species of bees that occur within the state of Mississippi. Additions to the list of native bees known for Mississippi are reported with notes on range, ecology and resources for identification. The geographic ranges of seven additional species are extended into the state of Mississippi: Andrena (Melandrena) obscuripennis Smith, 1853, Anthemurgus passiflorae Robertson, 1902, Dieunomia bolliana (Cockerell 1910), Diadasia (Diadasia) enavata (Cresson 1872), Peponapis crassidentata (Cockerell 1949), Triepeolus subnitens Cockerell and Timberlake, 1929 and Brachynomada nimia (Snelling and Rozen 1987). These records raise the total number of published species known from the state to 191. Anthemurgus and Brachynomada are also genera new to Mississippi.
Comparison of successive transition states for folding reveals alternative early folding pathways of two homologous proteins

PubMed Central

Calosci, Nicoletta; Chi, Celestine N.; Richter, Barbara; Camilloni, Carlo; Engström, Åke; Eklund, Lars; Travaglini-Allocatelli, Carlo; Gianni, Stefano; Vendruscolo, Michele; Jemth, Per

2008-01-01

The energy landscape theory provides a general framework for describing protein folding reactions. Because a large number of studies, however, have focused on two-state proteins with single well-defined folding pathways and without detectable intermediates, the extent to which free energy landscapes are shaped up by the native topology at the early stages of the folding process has not been fully characterized experimentally. To this end, we have investigated the folding mechanisms of two homologous three-state proteins, PTP-BL PDZ2 and PSD-95 PDZ3, and compared the early and late transition states on their folding pathways. Through a combination of Φ value analysis and molecular dynamics simulations we obtained atomic-level structures of the transition states of these homologous three-state proteins and found that the late transition states are much more structurally similar than the early ones. Our findings thus reveal that, while the native state topology defines essentially in a unique way the late stages of folding, it leaves significant freedom to the early events, a result that reflects the funneling of the free energy landscape toward the native state. PMID:19033470
Analyses on hydrophobicity and attractiveness of all-atom distance-dependent potentials

PubMed Central

Shirota, Matsuyuki; Ishida, Takashi; Kinoshita, Kengo

2009-01-01

Accurate model evaluation is a crucial step in protein structure prediction. For this purpose, statistical potentials, which evaluate a model structure based on the observed atomic distance frequencies in comparison with those in reference states, have been widely used. The reference state is a virtual state where all of the atomic interactions are turned off, and it provides a standard to measure the observed frequencies. In this study, we examined seven all-atom distance-dependent potentials with different reference states. As results, we observed that the variations of atom pair composition and those of distance distributions in the reference states produced systematic changes in the hydrophobic and attractive characteristics of the potentials. The performance evaluations with the CASP7 structures indicated that the preference of hydrophobic interactions improved the correlation between the energy and the GDT-TS score, but decreased the Z-score of the native structure. The attractiveness of potential improved both the correlation and Z-score for template-based modeling targets, but the benefit was smaller in free modeling targets. These results indicated that the performances of the potentials were more strongly influenced by their characteristics than by the accuracy of the definitions of the reference states. PMID:19588493
The extent of selected non-native invasive plants on Missouri forestland

Treesearch

W. Keith Moser; Mark H. Hansen; Mark D. Nelson

2008-01-01

The Northern Research Station's Forest Inventory and Analysis Program (NRSFIA) collects forest-related data throughout a 24-state region in the northeastern United States, ranging from North Dakota to Maine and Kansas to Maryland. Based on discussions with stakeholders and others, NRS-FIA found that the impact of non-native invasive plants (NNIPs) may be known at...
Native shrub seed industries in the western United States and Australia: Status and outlook

Treesearch

N. L. Shaw; C. M. Waters

2003-01-01

Attempts to improve habitat for wildlife and increase forage for livestock contributed to development of native shrub seed industries in the western United States and in Australia. Shrub seedings and plantings in both countries are concentrated in areas with low and unpredictable precipitation and high probability for planting failures. In addition, both countries have...
Immigrant and Native-Born Adolescents' Civic Knowledge and Attitudes in Sweden and the United States: Emergent Citizenship within Developmental Niches

ERIC Educational Resources Information Center

Barber, Carolyn; Torney-Purta, Judith; Wilkenfeld, Britt; Ross, Jessica

2015-01-01

Using the Developmental Niche for Emergent Participatory Citizenship (Torney-Purta and Amadeo, 2011) as a framework, we examined differences between immigrant and native-born youth's civic knowledge and support for women's rights in Sweden and the United States, and explored whether experiences with peers and parents, and in formal and informal…
Biology of the European oak borer in Michigan, United States of America, with comparisons to the native twolined chestnut borer

Treesearch

Toby R. Petrice; Robert A. Haack

2014-01-01

In 2010-2011, we studied the European oak borer (EOB), Agrilus sulcicollis Lacordaire (Coleoptera: Buprestidae), in Michigan, United States of America, and made comparisons with the native twolined chestnut borer (TLCB), Agrilus bilineatus (Weber). EOB adult flight began and peaked before TLCB. More EOB females were captured on...
Acquisition of English Grammatical Morphology by Native Mandarin-Speaking Children and Adolescents: Age-Related Differences

ERIC Educational Resources Information Center

Jia, Gisela; Fuse, Akiko

2007-01-01

Purpose: This 5-year longitudinal study investigated the acquisition of 6 English grammatical morphemes (i.e., regular and irregular past tense, 3rd person singular, progressive aspect-"ing", copula BE, and auxiliary DO) by 10 native Mandarin-speaking children and adolescents in the United States (arrived in the United States between 5…
Effect of Geography on the Analysis of Coccidioidomycosis-Associated Deaths, United States.

PubMed

Noble, Jason A; Nelson, Robert G; Fufaa, Gudeta D; Kang, Paul; Shafir, Shira Chani; Galgiani, John N

2016-10-01

Because coccidioidomycosis death rates vary by region, we reanalyzed coccidioidomycosis-associated mortality in the United States by race/ethnicity, then limited analysis to Arizona and California. Coccidioidomycosis-associated deaths were shown to increase among African-Americans but decrease among Native Americans and Hispanics. Separately, in a Native American cohort, diabetes co-varied with coccidioidomycosis-associated death.
Versatility of non-native forms of human cytochrome c: pH and micellar concentration dependence.

PubMed

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.
Success Models for Gifted Native Students.

ERIC Educational Resources Information Center

Sing, David K.

The Center for Gifted and Talented Native Hawaiian Children at the University of Hawaii at Hilo aims to develop culturally appropriate gifted and talented programs and identification procedures for Native Hawaiian children. Every Center program incorporates four elements of the Na Pua No'eau model: talent enhancement, self-esteem development,…
Introduced brown trout alter native acanthocephalan infections in native fish.

PubMed

Paterson, Rachel A; Townsend, Colin R; Poulin, Robert; Tompkins, Daniel M

2011-09-01

1. Native parasite acquisition provides introduced species with the potential to modify native host-parasite dynamics by acting as parasite reservoirs (with the 'spillback' of infection increasing the parasite burdens of native hosts) or sinks (with the 'dilution' of infection decreasing the parasite burdens of native hosts) of infection. 2. In New Zealand, negative correlations between the presence of introduced brown trout (Salmo trutta) and native parasite burdens of the native roundhead galaxias (Galaxias anomalus) have been observed, suggesting that parasite dilution is occurring. 3. We used a multiple-scale approach combining field observations, experimental infections and dynamic population modelling to investigate whether native Acanthocephalus galaxii acquisition by brown trout alters host-parasite dynamics in native roundhead galaxias. 4. Field observations demonstrated higher infection intensity in introduced trout than in native galaxias, but only small, immature A. galaxii were present in trout. Experimental infections also demonstrated that A. galaxii does not mature in trout, although parasite establishment and initial growth were similar in the two hosts. Taken together, these results support the hypothesis that trout may serve as an infection sink for the native parasite. 5. However, dynamic population modelling predicts that A. galaxii infections in native galaxias should at most only be slightly reduced by dilution in the presence of trout. Rather, model exploration indicates parasite densities in galaxias are highly sensitive to galaxias predation on infected amphipods, and to relative abundances of galaxias and trout. Hence, trout presence may instead reduce parasite burdens in galaxias by either reducing galaxias density or by altering galaxias foraging behaviour. © 2011 The Authors. Journal of Animal Ecology © 2011 British Ecological Society.
Modulation of dimerization by residues distant from the interface in bovine neurophysin-II.

PubMed

Zheng, C; Peyton, D; Breslow, E

1997-09-01

The crystal structure of bovine neurophysin-II in its liganded state (Chen et al. [1991] Proc. Natl. Acad. Sci. USA 88, 4240-4244) indicates that the 1-6 sequence has a disordered conformation, lacks noncovalent contacts to other regions of the protein and is distant from the monomer-monomer interface. Cleavage of the 1-6 sequence by Staphylococcus protease V8 yielded a protein that, for the first time, crystallized in both liganded and unliganded states. Insights into the role of the 1-6 sequence in the unliganded state were obtained by NMR and related biophysical comparisons of the native and des-1-6 proteins. NMR spectra demonstrated that the environment and/or conformation of residues in the 1-6 sequence differed in liganded and unliganded states. Additionally, the unliganded des-1-6 protein exhibited a dimerization constant four to five times that of the native protein, potentially accounting for the observation that its peptide affinity was also increased. NMR studies further indicated that the increased dimerization constant of the des-1-6 protein correlated with the presence in the native protein of two isoenergetic forms of the monomer, in contrast to only a single form in the des-1-6 protein, as evidenced by signals from an internal dimerization-sensitive alpha-proton. Thus, the 1-6 sequence reduces the dimerization constant by stabilization of an alternative monomer conformation. A second product of Staphylococcus protease V8 digestion of the native protein was identified as the des-1-6 protein with an internal clip after binding site residue Glu-47, the clip presumably breaking the short 3,10 helix that most directly connects the interface to the interface to the binding site. This product, although unable to bind peptide, retained the dimerization constant of the des-1-6 protein, suggesting a lack of importance of the helix in dimerization and contrasting with the effects of the 1-6 sequence. A model is proposed in which the 1-6 sequence stabilizes the second conformation of the unliganded monomer via interactions affecting the loop region that separates the two neurophysin domains and which has been shown to influence neurophysin self-association.
Model Adaptation in Parametric Space for POD-Galerkin Models

NASA Astrophysics Data System (ADS)

Gao, Haotian; Wei, Mingjun

2017-11-01

The development of low-order POD-Galerkin models is largely motivated by the expectation to use the model developed with a set of parameters at their native values to predict the dynamic behaviors of the same system under different parametric values, in other words, a successful model adaptation in parametric space. However, most of time, even small deviation of parameters from their original value may lead to large deviation or unstable results. It has been shown that adding more information (e.g. a steady state, mean value of a different unsteady state, or an entire different set of POD modes) may improve the prediction of flow with other parametric states. For a simple case of the flow passing a fixed cylinder, an orthogonal mean mode at a different Reynolds number may stabilize the POD-Galerkin model when Reynolds number is changed. For a more complicated case of the flow passing an oscillatory cylinder, a global POD-Galerkin model is first applied to handle the moving boundaries, then more information (e.g. more POD modes) is required to predicate the flow under different oscillatory frequencies. Supported by ARL.
The molten globule state is unusually deformable under mechanical force

PubMed Central

Elms, Phillip J.; Chodera, John D.; Bustamante, Carlos; Marqusee, Susan

2012-01-01

Recently, the role of force in cellular processes has become more evident, and now with advances in force spectroscopy, the response of proteins to force can be directly studied. Such studies have found that native proteins are brittle, and thus not very deformable. Here, we examine the mechanical properties of a class of intermediates referred to as the molten globule state. Using optical trap force spectroscopy, we investigated the response to force of the native and molten globule states of apomyoglobin along different pulling axes. Unlike natively folded proteins, the molten globule state of apomyoglobin is compliant (large distance to the transition state); this large compliance means that the molten globule is more deformable and the unfolding rate is more sensitive to force (the application of force or tension will have a more dramatic effect on the unfolding rate). Our studies suggest that these are general properties of molten globules and could have important implications for mechanical processes in the cell. PMID:22355138
NAWIG News: The Quarterly Newsletter of the Native American Wind Interest Group; Summer 2006

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

Not Available

2006-06-01

The United States is home to more than 700 American Indian tribes and Native Alaska villages and corporations located on 96 million acres. Many of these tribes and villages have excellent wind resources that could be commercially developed to meet their electricity needs or for electricity export. The Wind Powering America program engages Native Americans in wind energy development, and as part of that effort, the NAWIG newsletter informs readers of events in the Native American/wind energy community.
NAWIG News: The Quarterly Newsletter of the Native American Wind Interest Group; Summer 2005

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

Not Available

2005-09-01

The United States is home to more than 700 American Indian tribes and Native Alaska villages and corporations located on 96 million acres. Many of these tribes and villages have excellent wind resources that could be commercially developed to meet their electricity needs or for electricity export. The Wind Powering America program engages Native Americans in wind energy development, and as part of that effort, the NAWIG newsletter informs readers of events in the Native American/wind energy community.
Native American Commercial Driving Training and Technical Assistance Act. Hearing before the Committee on Indian Affairs, United States Senate, One Hundred Seventh Congress, Second Session, on S. 1344, To Provide Training and Technical Assistance to Native Americans Who Are Interested in Commercial Vehicle Driving Careers (July 24, 2002).

ERIC Educational Resources Information Center

Congress of the U.S., Washington, DC. Senate Committee on Indian Affairs.

A Senate committe hearing received testimony on the proposed "Native American Commercial Driving Training and Technical Assistance Act" (Senate Bill 1344). The Act cites the high unemployment and economic distress among Native Americans, the federal government's obligation to assist Indian tribes with economic development, the high…
Multiple ecosystem services in a working landscape

PubMed Central

Eastburn, Danny J.; O’Geen, Anthony T.; Tate, Kenneth W.; Roche, Leslie M.

2017-01-01

Policy makers and practitioners are in need of useful tools and models for assessing ecosystem service outcomes and the potential risks and opportunities of ecosystem management options. We utilize a state-and-transition model framework integrating dynamic soil and vegetation properties to examine multiple ecosystem services—specifically agricultural production, biodiversity and habitat, and soil health—across human created vegetation states in a managed oak woodland landscape in a Mediterranean climate. We found clear tradeoffs and synergies in management outcomes. Grassland states maximized agricultural productivity at a loss of soil health, biodiversity, and other ecosystem services. Synergies existed among multiple ecosystem services in savanna and woodland states with significantly larger nutrient pools, more diversity and native plant richness, and less invasive species. This integrative approach can be adapted to a diversity of working landscapes to provide useful information for science-based ecosystem service valuations, conservation decision making, and management effectiveness assessments. PMID:28301475

Multiple ecosystem services in a working landscape.

PubMed

Eastburn, Danny J; O'Geen, Anthony T; Tate, Kenneth W; Roche, Leslie M

2017-01-01

Policy makers and practitioners are in need of useful tools and models for assessing ecosystem service outcomes and the potential risks and opportunities of ecosystem management options. We utilize a state-and-transition model framework integrating dynamic soil and vegetation properties to examine multiple ecosystem services-specifically agricultural production, biodiversity and habitat, and soil health-across human created vegetation states in a managed oak woodland landscape in a Mediterranean climate. We found clear tradeoffs and synergies in management outcomes. Grassland states maximized agricultural productivity at a loss of soil health, biodiversity, and other ecosystem services. Synergies existed among multiple ecosystem services in savanna and woodland states with significantly larger nutrient pools, more diversity and native plant richness, and less invasive species. This integrative approach can be adapted to a diversity of working landscapes to provide useful information for science-based ecosystem service valuations, conservation decision making, and management effectiveness assessments.
Urea-Induced Unfolding of the Immunity Protein Im9 Monitored by spFRET

PubMed Central

Tezuka-Kawakami, Tomoko; Gell, Chris; Brockwell, David J.; Radford, Sheena E.; Smith, D. Alastair

2006-01-01

We have studied the urea-induced unfolding of the E colicin immunity protein Im9 using diffusion single-pair fluorescence resonance energy transfer. Detailed examination of the proximity ratio of the native and denatured molecules over a wide range of urea concentrations suggests that the conformational properties of both species are denaturant-dependent. Whereas native molecules become gradually more expanded as urea concentration increases, denatured molecules show a dramatic dependence of the relationship between proximity ratio and denaturant concentration, consistent with substantial compaction of the denatured ensemble at low denaturant concentrations. Analysis of the widths of the proximity ratio distributions for each state suggests that whereas the native state ensemble is relatively narrow and homogeneous, the denatured state may possess heterogeneity in mildly denaturing conditions. PMID:16798813
Roles of water molecules in bacteria and viruses

NASA Astrophysics Data System (ADS)

Cox, C. S.

1993-02-01

In addition to water, microbes mainly comprise lipids, carbohydrates, proteins and nucleic acids. Their structure and function singularly and conjointly is affected by water activity. Desiccation leads to dramatic lipid phase changes whereas carbohydrates, proteins and nucleic acids initially suffer spontaneous, reversible low activation energy Maillard reactions forming products that more slowly re-arrange, cross-link etc. to give non-native states. While initial products spontaneously may reverse to native states by raising water activity, later products only do so through energy consumption and enzymatic activity eg. repair. Yet, native states of lipid membranes and associated enzymes are required to generate energy. Consequently, good reserves of high energy compounds (e.g. ATP) and of membrane stabilisers (e.g. trehalose) may be expected to enhance survival following drying and rehydration (e.g. anhydrobiotic organisms).
Behavioral evidence for fruit odor discrimination and sympatric host races of Rhagoletis pomonella flies in the Western United States.

PubMed

Linn, Charles E; Yee, Wee L; Sim, Sheina B; Cha, Dong H; Powell, Thomas H Q; Goughnour, Robert B; Feder, Jeffrey L

2012-11-01

The recent shift of Rhagoletis pomonella (Diptera: Tephritidae) from its native host downy hawthorn, Crataegus mollis, to introduced domesticated apple, Malus domestica, in the eastern United States is a model for sympatric host race formation. However, the fly is also present in the western United States, where it may have been introduced via infested apples within the last 60 years. In addition to apple, R. pomonella also infests two hawthorns in the West, one the native black hawthorn, C. douglasii, and the other the introduced English ornamental hawthorn, C. monogyna. Here, we test for behavioral evidence of host races in the western United States. through flight tunnel assays of western R. pomonella flies to host fruit volatile blends. We report that western apple, black hawthorn, and ornamental hawthorn flies showed significantly increased levels of upwind-directed flight to their respective natal compared to nonnatal fruit volatile blends, consistent with host race status. We discuss the implications of the behavioral results for the origin(s) of western R. pomonella, including the possibility that western apple flies were not introduced, but may represent a recent shift from local hawthorn fly populations. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.
Consistent free energy landscapes and thermodynamic properties of small proteins based on a single all-atom force field employing an implicit solvation.

PubMed

Kim, Eunae; Jang, Soonmin; Pak, Youngshang

2007-10-14

We have attempted to improve the PARAM99 force field in conjunction with the generalized Born (GB) solvation model with a surface area correction for more consistent protein folding simulations. For this purpose, using an extended alphabeta training set of five well-studied molecules with various folds (alpha, beta, and betabetaalpha), a previously modified version of PARAM99/GBSA is further refined, such that all native states of the five training species correspond to their lowest free energy minimum states. The resulting modified force field (PARAM99MOD5/GBSA) clearly produces reasonably acceptable conformational free energy surfaces of the training set with correct identifications of their native states in the free energy minimum states. Moreover, due to its well-balanced nature, this new force field is expected to describe secondary structure propensities of diverse folds in a more consistent manner. Remarkably, temperature dependent behaviors simulated with the current force field are in good agreement with the experiment. This agreement is a significant improvement over the existing standard all-atom force fields. In addition, fundamentally important thermodynamic quantities, such as folding enthalpy (DeltaH) and entropy (DeltaS), agree reasonably well with the experimental data.
ACHP | ACHP Native American Program: Guidance for Federal Agencies

Science.gov Websites

Working with Section 106 Federal, State, & Tribal Programs Training & Education Publications Search skip specific nav links Home arrow Working with Section 106 arrow ACHP Native American Program
Thermodynamic study of the native and phosphorylated regulatory domain of the CFTR

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

Marasini, Carlotta, E-mail: marasini@ge.ibf.cnr.it; Galeno, Lauretta; Moran, Oscar

2012-07-06

Highlights: Black-Right-Pointing-Pointer CFTR mutations produce cystic fibrosis. Black-Right-Pointing-Pointer Chloride transport depends on the regulatory domain phosphorylation. Black-Right-Pointing-Pointer Regulatory domain is intrinsically disordered. Black-Right-Pointing-Pointer Secondary structure and protein stability change upon phosphorylation. -- Abstract: The regulatory domain (RD) of the cystic fibrosis transmembrane conductance regulator (CFTR), the defective protein in cystic fibrosis, is the region of the channel that regulates the CFTR activity with multiple phosphorylation sites. This domain is an intrinsically disordered protein, characterized by lack of stable or unique tertiary structure. The disordered character of a protein is directly correlated with its function. The flexibility of RD may bemore » important for its regulatory role: the continuous conformational change may be necessary for the progressive phosphorylation, and thus activation, of the channel. However, the lack of a defined and stable structure results in a considerable limitation when trying to in build a unique molecular model for the RD. Moreover, several evidences indicate significant structural differences between the native, non-phosphorylated state, and the multiple phosphorylated state of the protein. The aim of our work is to provide data to describe the conformations and the thermodynamic properties in these two functional states of RD. We have done the circular dichroism (CD) spectra in samples with a different degree of phosphorylation, from the non-phosphorylated state to a bona fide completely phosphorylated state. Analysis of CD spectra showed that the random coil and {beta}-sheets secondary structure decreased with the polypeptide phosphorylation, at expenses of an increase of {alpha}-helix. This observation lead to interpret phosphorylation as a mechanism favoring a more structured state. We also studied the thermal denaturation curves of the protein in the two conditions, monitoring the changes of the mean residue ellipticity measured at 222 nm as a function of temperature, between 20 and 95 Degree-Sign C. The thermodynamic analysis of the denaturation curves shows that phosphorylation of the protein induces a state of lower stability of R domain, characterized by a lower transition temperature, and by a smaller Gibbs free energy difference between the native and the unfolded states.« less
Bidirectional Transformation of a Metamorphic Protein between the Water-Soluble and Transmembrane Native States.

PubMed

Tanaka, Koji; Caaveiro, Jose M M; Tsumoto, Kouhei

2015-11-24

The bidirectional transformation of a protein between its native water-soluble and integral transmembrane conformations is demonstrated for FraC, a hemolytic protein of the family of pore-forming toxins. In the presence of biological membranes, the water-soluble conformation of FraC undergoes a remarkable structural reorganization generating cytolytic transmembrane nanopores conducive to cell death. So far, the reverse transformation from the native transmembrane conformation to the native water-soluble conformation has not been reported. We describe the use of detergents with different physicochemical properties to achieve the spontaneous conversion of transmembrane pores of FraC back into the initial water-soluble state. Thermodynamic and kinetic stability data suggest that specific detergents cause an asymmetric change in the energy landscape of the protein, allowing the bidirectional transformation of a membrane protein.
Forest Bird Distribution, Density and Trends in the Ka'u Region of Hawai'i Island

USGS Publications Warehouse

Gorresen, P. Marcos; Camp, Richard J.; Pratt, Thane K.

2007-01-01

An accurate and current measure of population status and trend is necessary for conservation and management efforts. Scott and Kepler (1985) provided a comprehensive review of the status of native Hawaiian birds based on the extensive Hawaii Forest Bird Survey (HFBS) of the main islands (Scott et al. 1986). At that time, they documented declining populations and decreasing ranges for most species, and the extinction of several species over the previous 50 years. Many native bird species continue to decline throughout Hawai`i (Camp et al. In review, Gorresen et al. In prep.). The focus of this study is the mid-to-high elevation rainforest on the southeast windward slopes of Mauna Loa Volcano (Figure 1). Known as Ka`u, the region encompasses forest lands protected by Kamehameha Schools, The Nature Conservancy, Hawai`i Volcanoes National Park (HVNP), and the State of Hawai'i's Ka`u Forest Reserve, Kapapala Forest Reserve and Kapapala Cooperative Game Management Area,. Together these lands support one of three main concentrations of native forest birds on the Hawai`i Island (the other two being centered on the Hakalau Forest National Wildlife Refuge and Kulani-Keauhou area in the north and central windward part of the island, respectively.) Because this region harbors important populations of native and endangered forest birds in some of the best remaining forest habitat on the island, it has been a focus of forest bird surveys since the 1970s. The Ka`u region was first quantitatively surveyed in 1976 by the Hawaii Forest Bird Survey (Scott et al. 1986). Surveys were conducted by State of Hawai`i Division of Forestry and Wildlife in 1993 and 2002 and by the U.S. National Park Service and the U.S. Geological Survey in 2004 and 2005. In this report, we present analyses of the density, distribution and trends of native and introduced forest bird within the Ka`u region of Hawai`i Island. The analyses cover only those species with sufficient detections to model detection probability and calculate density. These include three endangered native passerines: `Akiapola`au (Hemignathus munroi), Hawai`i Creeper (Oreomystis mana), and Hawai`i `Akepa (Loxops coccineus); five more common native passerines: the Hawai`i `Elepaio (Chasiempis sandwichensis), `Oma`o (Myadestes obscurus), Hawai`i `Amakihi (Hemignathus virens), `I`iwi (Vestiaria coccinea) and `Apapane (Himatione sanguinea); and three non-native species: Red-billed Leiothrix (Leiothrix lutea), Japanese White-eye (Zosterops japonicus), and Northern Cardinal (Cardinalis cardinalis).
DOE Office of Scientific and Technical Information (OSTI.GOV)

Krishnan, Venkat; Cole, Wesley

Power sector capacity expansion models (CEMs) have a broad range of spatial resolutions. This paper uses the Regional Energy Deployment System (ReEDS) model, a long-term national scale electric sector CEM, to evaluate the value of high spatial resolution for CEMs. ReEDS models the United States with 134 load balancing areas (BAs) and captures the variability in existing generation parameters, future technology costs, performance, and resource availability using very high spatial resolution data, especially for wind and solar modeled at 356 resource regions. In this paper we perform planning studies at three different spatial resolutions--native resolution (134 BAs), state-level, and NERCmore » region level--and evaluate how results change under different levels of spatial aggregation in terms of renewable capacity deployment and location, associated transmission builds, and system costs. The results are used to ascertain the value of high geographically resolved models in terms of their impact on relative competitiveness among renewable energy resources.« less
High-pressure NMR reveals close similarity between cold and alcohol protein denaturation in ubiquitin.

PubMed

Vajpai, Navratna; Nisius, Lydia; Wiktor, Maciej; Grzesiek, Stephan

2013-01-29

Proteins denature not only at high, but also at low temperature as well as high pressure. These denatured states are not easily accessible for experiment, because usually heat denaturation causes aggregation, whereas cold or pressure denaturation occurs at temperatures well below the freezing point of water or pressures above 5 kbar, respectively. Here we have obtained atomic details of the pressure-assisted, cold-denatured state of ubiquitin at 2,500 bar and 258 K by high-resolution NMR techniques. Under these conditions, a folded, native-like and a disordered state exist in slow exchange. Secondary chemical shifts show that the disordered state has structural propensities for a native-like N-terminal β-hairpin and α-helix and a nonnative C-terminal α-helix. These propensities are very similar to the previously described alcohol-denatured (A-)state. Similar to the A-state, (15)N relaxation data indicate that the secondary structure elements move as independent segments. The close similarity of pressure-assisted, cold-denatured, and alcohol-denatured states with native and nonnative secondary elements supports a hierarchical mechanism of folding and supports the notion that similar to alcohol, pressure and cold reduce the hydrophobic effect. Indeed, at nondenaturing concentrations of methanol, a complete transition from the native to the A-state can be achieved at ambient temperature by varying the pressure from 1 to 2,500 bar. The methanol-assisted pressure transition is completely reversible and can also be induced in protein G. This method should allow highly detailed studies of protein-folding transitions in a continuous and reversible manner.
Study of protein folding under native conditions by rapidly switching the hydrostatic pressure inside an NMR sample cell

PubMed Central

Charlier, Cyril; Alderson, T. Reid; Courtney, Joseph M.; Ying, Jinfa; Anfinrud, Philip

2018-01-01

In general, small proteins rapidly fold on the timescale of milliseconds or less. For proteins with a substantial volume difference between the folded and unfolded states, their thermodynamic equilibrium can be altered by varying the hydrostatic pressure. Using a pressure-sensitized mutant of ubiquitin, we demonstrate that rapidly switching the pressure within an NMR sample cell enables study of the unfolded protein under native conditions and, vice versa, study of the native protein under denaturing conditions. This approach makes it possible to record 2D and 3D NMR spectra of the unfolded protein at atmospheric pressure, providing residue-specific information on the folding process. 15N and 13C chemical shifts measured immediately after dropping the pressure from 2.5 kbar (favoring unfolding) to 1 bar (native) are close to the random-coil chemical shifts observed for a large, disordered peptide fragment of the protein. However, 15N relaxation data show evidence for rapid exchange, on a ∼100-μs timescale, between the unfolded state and unstable, structured states that can be considered as failed folding events. The NMR data also provide direct evidence for parallel folding pathways, with approximately one-half of the protein molecules efficiently folding through an on-pathway kinetic intermediate, whereas the other half fold in a single step. At protein concentrations above ∼300 μM, oligomeric off-pathway intermediates compete with folding of the native state. PMID:29666248
A Civilising Mission? Perceptions and Representations of the New Zealand Native Schools System

ERIC Educational Resources Information Center

Simon, Judith, Ed.; Smith, Linda Tuhiwai, Ed.

The Native Schools system was a system of village primary schools for Maori children operated by the New Zealand state from 1867 to 1969. The official purpose of the system was assimilation. Virtually all previous historical accounts of the Native Schools have been written by Pakeha (non-Maori, usually of European descent) and based on material…
Cultural plant harvests on federal lands: perspectives from members of the Northwest Native American Basketweavers Association

Treesearch

Rebecca Dobkins; Ceara Lewis; Susan Hummel; Emily. Dickey

2016-01-01

Native Americans who wish to harvest forest plants for traditional uses report difficulties gaining access to federal lands in the northwestern United States. To learn more about this issue, we reviewed the published literature on site access and resource harvests by tribal members and discussed it with Native American traditional users of plant resources. Specifically...
Running the "Medicine Line": Images of the Border in Contemporary Native American Art

ERIC Educational Resources Information Center

Morris, Kate

2011-01-01

In this article the author is concerned with the intersection of two congruent phenomena: (1) an increasing number of references to borders in contemporary Native American art; and (2) an increasing occurrence of border-rights conflicts between Native nations and the governments of the United States and Canada. Focusing on the period roughly 1990…
The American Indian and Alaska Native Higher Education Funding Guide. A Financial Guide to Undergraduate and Graduate Sources of Funding for American Indians and Alaska Natives.

ERIC Educational Resources Information Center

Frazier, Gregory W.

This book provides American Indian and Alaska Native students with sources for securing financial aid for higher education. The first section covers sources of funding and grants for individuals who are pursuing undergraduate degrees. This financial support includes scholarships with state residency requirements, general undergraduate…
Native American Kids: American Indian Children's Well-Being Indicators for the Nation and Two States

ERIC Educational Resources Information Center

Willeto, Angela A. A.

2007-01-01

American Indian/Alaska Native well-being, survival-based data are rare. This study explores the question of whether or not it is possible to produce such well-being information using secondary data sources. The answer is yes, with some limitations. Hence, Native American data for 10 well-being indicators nationally and for New Mexico and South…
Significant Impact of Environment Regarding Eligibility of Native American and Alaskan Native Students for ESEA Title VII Regulations.

ERIC Educational Resources Information Center

Travis, Michael

Early Russian religious and educational influences on the 20 various Alaskan Native languages are described, followed by those of American origin in schools and religious groups after the American purchase in 1867, all of which show the development of diglossia and language shifts. The present dual educational system, which includes state schools…
Association of Contextual Factors with Drug Use and Binge Drinking among White, Native American, and Mixed-Race Adolescents in the General Population

ERIC Educational Resources Information Center

Chen, Hsing-Jung; Balan, Sundari; Price, Rumi Kato

2012-01-01

Large-scale surveys have shown elevated risk for many indicators of substance abuse among Native American and Mixed-Race adolescents compared to other minority groups in the United States. This study examined underlying contextual factors associated with substance abuse among a nationally representative sample of White, Native American, and…
Teacher Training Institute for Native American Bilingual/Bicultural Education. Phase I (S.U.N.Y. Brockport, Summer, 1978).

ERIC Educational Resources Information Center

New York State Education Dept., Albany. Office of Cultural Education.

A two week teacher training institute for Native American bilingual/bicultural education was held in the summer of 1978 at Brockport State University of New York. Educational Programs for bilingual and bicultural learning environments for Native American students had been hampered by insufficient teachers and teacher trainers and the use of…

A resolution recognizing National Native American Heritage Month and celebrating the heritages and cultures of Native Americans and the contributions of Native Americans to the United States.

THOMAS, 113th Congress

Sen. Cantwell, Maria [D-WA

2013-11-20

Senate - 11/20/2013 Submitted in the Senate, considered, and agreed to without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:
A resolution recognizing National Native American Heritage Month and celebrating the heritages and cultures of Native Americans and the contributions of Native Americans to the United States.

THOMAS, 112th Congress

Sen. Akaka, Daniel K. [D-HI

2011-11-16

Senate - 11/16/2011 Submitted in the Senate, considered, and agreed to without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:
A resolution recognizing National Native American Heritage Month and celebrating the heritages and cultures of Native Americans and the contributions of Native Americans to the United States.

THOMAS, 113th Congress

Sen. Tester, Jon [D-MT

2014-11-20

Senate - 11/20/2014 Submitted in the Senate, considered, and agreed to without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:
Market perceptions and opportunities for native plant production on the southern Colorado Plateau

Treesearch

Donna L. Peppin; Peter Z. Fule; Janet C. Lynn; Anne L. Mottek-Lucas; Carolyn Hull Sieg

2010-01-01

Increases in revegetation activities have created a large demand for locally adapted native plant materials (NPM) in the southwestern United States. Currently, there is a minimal supply of local genotypes to meet this demand. We investigated the potential for the initiation of a native plant market in the southern Colorado Plateau. Through a literature search,...
The Experience of Non-Native English-Speaking Students in Academic Libraries in the United States.

ERIC Educational Resources Information Center

Onwuegbuzie, Anthony J.; Jiao, Qun G.; Daley, Christine E.

This study compared native and non-native English-speaking university students with respect to frequency of library usage and reasons for using the library, as well as differences between these groups with respect to levels of library anxiety. Findings were intended to be used in the planning and implementation of library services for…
Intelligibility of American English Vowels and Consonants Spoken by International Students in the United States

ERIC Educational Resources Information Center

Jin, Su-Hyun; Liu, Chang

2014-01-01

Purpose: The purpose of this study was to examine the intelligibility of English consonants and vowels produced by Chinese-native (CN), and Korean-native (KN) students enrolled in American universities. Method: 16 English-native (EN), 32 CN, and 32 KN speakers participated in this study. The intelligibility of 16 American English consonants and 16…
Boundaries of mass resolution in native mass spectrometry.

PubMed

Lössl, Philip; Snijder, Joost; Heck, Albert J R

2014-06-01

Over the last two decades, native mass spectrometry (MS) has emerged as a valuable tool to study intact proteins and noncovalent protein complexes. Studied experimental systems range from small-molecule (drug)-protein interactions, to nanomachineries such as the proteasome and ribosome, to even virus assembly. In native MS, ions attain high m/z values, requiring special mass analyzers for their detection. Depending on the particular mass analyzer used, instrumental mass resolution does often decrease at higher m/z but can still be above a couple of thousand at m/z 5000. However, the mass resolving power obtained on charge states of protein complexes in this m/z region is experimentally found to remain well below the inherent instrument resolution of the mass analyzers employed. Here, we inquire into reasons for this discrepancy and ask how native MS would benefit from higher instrumental mass resolution. To answer this question, we discuss advantages and shortcomings of mass analyzers used to study intact biomolecules and biomolecular complexes in their native state, and we review which other factors determine mass resolving power in native MS analyses. Recent examples from the literature are given to illustrate the current status and limitations.
Origin of native copper in the Paraná volcanic province, Brazil, integrating Cu stable isotopes in a multi-analytical approach

NASA Astrophysics Data System (ADS)

Baggio, Sérgio Benjamin; Hartmann, Léo Afraneo; Lazarov, Marina; Massonne, Hans-Joachim; Opitz, Joachim; Theye, Thomas; Viefhaus, Tillmann

2018-03-01

Different hypotheses exist on the origin of native copper mineralization in the Paraná volcanic province that invoke magmatic, late magmatic, or hydrothermal events. The average copper content in the host basalts is 200 ppm. Native copper occurs as dendrites in cooling joints, fractures, and cavities within amygdaloidal crusts. Cuprite, tenorite, chrysocolla, malachite, and azurite occur in breccias at the top of the lava flows. Chemical analyses, X-ray diffraction, Raman spectrometry, electron microprobe analyses, LA-ICP-MS, and Cu isotope analyses were used to evaluate the origin of native copper in the volcanic province. Copper contents in magnetite of the host basalt are close to 1 wt.%, whereas clinopyroxene contains up to 0.04 wt.% Cu. Cretaceous hydrothermal alteration of magnetite and clinopyroxene released copper to generate hydrothermal copper mineralization. The isotopic composition of the native copper in the Paraná volcanic province varies from -0.9‰ in the southeastern portion (Rio Grande do Sul state) to 1.9‰ in the central portion (Paraná state) of the province. This study supports a hydrothermal origin followed by supergene enrichment for native copper in the Paraná volcanic province.
Type characters of non-native plant species in Great Lakes national parks (USA)

USGS Publications Warehouse

Bennett, J.P.; Brundu, G.; Brock, J.; Camarda, I.; Child, L.; Wade, M.

2001-01-01

Non-native plant species are increasing in frequency and abundance in many natural areas in the United States. In Midwestern National Parks, as much as one third of the flora may be non-native. It was hypothesized that botanical characters of these species could be used to typify them and improve the methods of predicting invasions. Data on 19 characters of 341 non-native species from the four Great Lakes national lakeshores (Apostle Islands, Indiana Dunes, Pictured Rocks, and Sleeping Bear Dunes) and invasive non-native species for the State of Wisconsin were collected and studied. For many of the species, little data could be found, but for 139 of them, data were collected for at least 80% of the characters. The frequencies of classes of the characters were tabulated and ranked to typify the most common non-native species. This led to a description of a 'type species' just for these four National Parks. Three species of Cirsium, including Canada (C. arvense), marsh (C. palustre) and bull thistle (C. vulgare), matched the type species better than other species. C. vulgare occurs in more National Parks than the other thistles.
Soil ecosystem function under native and exotic plant assemblages as alternative states of successional grasslands

NASA Astrophysics Data System (ADS)

Spirito, Florencia; Yahdjian, Laura; Tognetti, Pedro M.; Chaneton, Enrique J.

2014-01-01

Old fields often become dominated by exotic plants establishing persistent community states. Ecosystem functioning may differ widely between such novel communities and the native-dominated counterparts. We evaluated soil ecosystem attributes in native and exotic (synthetic) grass assemblages established on a newly abandoned field, and in remnants of native grassland in the Inland Pampa, Argentina. We asked whether exotic species alter soil functioning through the quality of the litter they shed or by changing the decomposition environment. Litter decomposition of the exotic dominant Festuca arundinacea in exotic assemblages was faster than that of the native dominant Paspalum quadrifarium in native assemblages and remnant grasslands. Decomposition of a standard litter (Triticum aestivum) was also faster in exotic assemblages than in native assemblages and remnant grasslands. In a common garden, F. arundinacea showed higher decay rates than P. quadrifarium, which reflected the higher N content and lower C:N of the exotic grass litter. Soil respiration rates were higher in the exotic than in the native assemblages and remnant grasslands. Yet there were no significant differences in soil N availability or net N mineralization between exotic and native assemblages. Our results suggest that exotic grass dominance affected ecosystem function by producing a more decomposable leaf litter and by increasing soil decomposer activity. These changes might contribute to the extended dominance of fast-growing exotic grasses during old-field succession. Further, increased organic matter turnover under novel, exotic communities could reduce the carbon storage capacity of the system in the long term.
The Acculturation of Parenting Cognitions: A Comparison of South Korean, Korean Immigrant, and European American Mothers

PubMed Central

Cote, Linda R.; Kwak, Keumjoo; Putnick, Diane L.; Chung, Hyun Jin; Bornstein, Marc H.

2016-01-01

A three-culture comparison – native South Korean, Korean immigrants to the United States, and native European American mothers – of two types of parenting cognitions – attributions and self-perceptions – was undertaken to explore cultural contributions to parenting cognitions and their adaptability among immigrant mothers. Attributions and self-perceptions of parenting were chosen because they influence parenting behavior and children’s development and vary cross-culturally. One hundred seventy-nine mothers of 20-month-old children participated: 73 South Korean, 50 Korean immigrant, and 56 European American. Korean mothers differed from European American mothers on four of the five types of attributions studied and on all four self-perceptions of parenting, and these differences were largely consistent with the distinct cultural values of South Korea and the United States. Generally, Korean immigrant mothers’ attributions for parenting more closely resembled those of mothers in the United States, whereas their self-perceptions of parenting more closely resembled those of mothers in South Korea. This study provides insight into similarities and differences in cultural models of parenting, and information about the acculturation of parenting cognitions among immigrants from South Korea. PMID:26912926
Free-energy landscape of intrinsically disordered proteins investigated by all-atom multicanonical molecular dynamics.

PubMed

Higo, Junichi; Umezawa, Koji

2014-01-01

We introduce computational studies on intrinsically disordered proteins (IDPs). Especially, we present our multicanonical molecular dynamics (McMD) simulations of two IDP-partner systems: NRSF-mSin3 and pKID-KIX. McMD is one of enhanced conformational sampling methods useful for conformational sampling of biomolecular systems. IDP adopts a specific tertiary structure upon binding to its partner molecule, although it is unstructured in the unbound state (i.e. the free state). This IDP-specific property is called "coupled folding and binding". The McMD simulation treats the biomolecules with an all-atom model immersed in an explicit solvent. In the initial configuration of simulation, IDP and its partner molecules are set to be distant from each other, and the IDP conformation is disordered. The computationally obtained free-energy landscape for coupled folding and binding has shown that native- and non-native-complex clusters distribute complicatedly in the conformational space. The all-atom simulation suggests that both of induced-folding and population-selection are coupled complicatedly in the coupled folding and binding. Further analyses have exemplified that the conformational fluctuations (dynamical flexibility) in the bound and unbound states are essentially important to characterize IDP functioning.
The structures of native celluloses, and the origin of their variability

Treesearch

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...
Collapse kinetics and chevron plots from simulations of denaturant-dependent folding of globular proteins

PubMed Central

Liu, Zhenxing; Reddy, Govardhan; O’Brien, Edward P.; Thirumalai, D.

2011-01-01

Quantitative description of how proteins fold under experimental conditions remains a challenging problem. Experiments often use urea and guanidinium chloride to study folding whereas the natural variable in simulations is temperature. To bridge the gap, we use the molecular transfer model that combines measured denaturant-dependent transfer free energies for the peptide group and amino acid residues, and a coarse-grained Cα-side chain model for polypeptide chains to simulate the folding of src SH3 domain. Stability of the native state decreases linearly as [C] (the concentration of guanidinium chloride) increases with the slope, m, that is in excellent agreement with experiments. Remarkably, the calculated folding rate at [C] = 0 is only 16-fold larger than the measured value. Most importantly ln kobs (kobs is the sum of folding and unfolding rates) as a function of [C] has the characteristic V (chevron) shape. In every folding trajectory, the times for reaching the native state, interactions stabilizing all the substructures, and global collapse coincide. The value of (mf is the slope of the folding arm of the chevron plot) is identical to the fraction of buried solvent accessible surface area in the structures of the transition state ensemble. In the dominant transition state, which does not vary significantly at low [C], the core of the protein and certain loops are structured. Besides solving the long-standing problem of computing the chevron plot, our work lays the foundation for incorporating denaturant effects in a physically transparent manner either in all-atom or coarse-grained simulations. PMID:21512127
Collapse kinetics and chevron plots from simulations of denaturant-dependent folding of globular proteins.

PubMed

Liu, Zhenxing; Reddy, Govardhan; O'Brien, Edward P; Thirumalai, D

2011-05-10

Quantitative description of how proteins fold under experimental conditions remains a challenging problem. Experiments often use urea and guanidinium chloride to study folding whereas the natural variable in simulations is temperature. To bridge the gap, we use the molecular transfer model that combines measured denaturant-dependent transfer free energies for the peptide group and amino acid residues, and a coarse-grained C(α)-side chain model for polypeptide chains to simulate the folding of src SH(3) domain. Stability of the native state decreases linearly as [C] (the concentration of guanidinium chloride) increases with the slope, m, that is in excellent agreement with experiments. Remarkably, the calculated folding rate at [C] = 0 is only 16-fold larger than the measured value. Most importantly ln k(obs) (k(obs) is the sum of folding and unfolding rates) as a function of [C] has the characteristic V (chevron) shape. In every folding trajectory, the times for reaching the native state, interactions stabilizing all the substructures, and global collapse coincide. The value of (m(f) is the slope of the folding arm of the chevron plot) is identical to the fraction of buried solvent accessible surface area in the structures of the transition state ensemble. In the dominant transition state, which does not vary significantly at low [C], the core of the protein and certain loops are structured. Besides solving the long-standing problem of computing the chevron plot, our work lays the foundation for incorporating denaturant effects in a physically transparent manner either in all-atom or coarse-grained simulations.
Performance of the herb Verbascum thapsus along environmental gradients in its native and non-native ranges

Treesearch

Tim Seipel; Jake M. Alexander; Curtis C. Daehler; Lisa J. Rew; Peter J. Edwards; Pervaiz A. Dar; Keith McDougall; Bridgett Naylor; Catherine Parks; Fredric W. Pollnac; Zafar A. Reshi; Mel Schroder; Christoph Kueffer; Peter Pearman

2014-01-01

Aim We evaluated whether the performance of individuals and populations of the invasive plant Verbascum thapsus differs between its native and non-native ranges, across climate gradients, and in response to its position in a global- scaled niche model.Location India (Kashmir) and Switzerland (native range) and Australia and USA (Hawaii,...
Widening the Circle: Culturally Relevant Pedagogy for American Indian Children.

ERIC Educational Resources Information Center

Klug, Beverly J.; Whitfield, Patricia T.

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

Treesearch

Yaoqi Zhang; Indrajit Majumdar; John Schelhas

2010-01-01

Abstract: There is growing evidence suggesting that the United Statesâ roots are not in a state of pristine nature but rather in a human-modified landscape over which Native people have since long exerted vast control and use. The longleaf pine is a typical woodland use largely shaped by fires, lightning and by Native Americans. The frequent fires, which were used to...
The First Oregonians. An Illustrated Collection of Essays on Traditional Lifeways, Federal-Indian Relations, and the State's Native People Today.

ERIC Educational Resources Information Center

Buan, Carolyn M., Ed.; Lewis, Richard, Ed.

This guide focuses on the heritage of Oregon Native people by discussing their ancient habitation, their historical lifeways and the disruption of those lifeways by Euro-American settlement and federal policies, and their continuing role in the state. The guide consists of 18 essays organized into 3 sections. The first section consists of five…
Rebuilding Trust: A Community, Multiagency, State, and University Partnership to Improve Behavioral Health Care for American Indian Youth, Their Families, and Communities

ERIC Educational Resources Information Center

Goodkind, Jessica R.; Ross-Toledo, Kimberly; John, Susie; Hall, Janie Lee; Ross, Lucille; Freeland, Lance; Coletta, Ernest; Becenti-Fundark, Twila; Poola, Charlene; Roanhorse, Regina; Lee, Christopher

2011-01-01

American Indian/Alaska Native youth represent the strength and survival of many Nations and Tribes. However, the aftermath of colonialism has resulted in numerous health disparities and challenges for Native youth, including the highest rate of suicide in the United States. With the aims of elucidating the causes of behavioral health disparities,…

NTS American Indian Religious Freedom Act Compliance Program complying with AIRFA: A literature review and evaluation

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

Pippin, L.C.

The First Amendment to the United States Constitution guarantees the inherent right of all Americans to freedom of religion. However, since the religious practices of Native Americans are significantly different from those of the majority of Americans, their religious freedom has often restricted. Section 2 of the American Indian Religious Freedom Act (AIRFA) of 1978 (Public Law 95-341) directs federal agencies to consult with Native Americans to determine appropriate procedures to protect the inherent rights of Native Americans to believe, express, and exercise their traditional religions including, but not limited to access to sites, use and possession of sacred objects,more » and freedom to worship through ceremonials and traditional rites. The NTS AIRFA Compliance Program was initiated in October 1989 to assist DOE in expanding its compliance with AIRFA to incorporate all weapons testing activities on the NTS. It is directed at the development and implementation of a consultation plan designed to solicit, on behalf of DOE, Native American comments regarding the effects of the DOE's nuclear testing activities on historic properties of Native American origin and the expression and exercise of traditional Native American religions. The program has been developed around a phased approach that includes; (1) literature review and evaluation, (2) preparation of a baseline document, (3) preparation of a study design, (4) consultation with Native Americans, (5) preparation of a draft report, (6) Native American and State consultation and review, and (7) preparation of a final report.« less
NTS American Indian Religious Freedom Act Compliance Program complying with AIRFA: A literature review and evaluation

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

Pippin, L.C.

The First Amendment to the United States Constitution guarantees the inherent right of all Americans to freedom of religion. However, since the religious practices of Native Americans are significantly different from those of the majority of Americans, their religious freedom has often restricted. Section 2 of the American Indian Religious Freedom Act (AIRFA) of 1978 (Public Law 95-341) directs federal agencies to consult with Native Americans to determine appropriate procedures to protect the inherent rights of Native Americans to believe, express, and exercise their traditional religions including, but not limited to access to sites, use and possession of sacred objects,more » and freedom to worship through ceremonials and traditional rites. The NTS AIRFA Compliance Program was initiated in October 1989 to assist DOE in expanding its compliance with AIRFA to incorporate all weapons testing activities on the NTS. It is directed at the development and implementation of a consultation plan designed to solicit, on behalf of DOE, Native American comments regarding the effects of the DOE`s nuclear testing activities on historic properties of Native American origin and the expression and exercise of traditional Native American religions. The program has been developed around a phased approach that includes; (1) literature review and evaluation, (2) preparation of a baseline document, (3) preparation of a study design, (4) consultation with Native Americans, (5) preparation of a draft report, (6) Native American and State consultation and review, and (7) preparation of a final report.« less
TRIC-B channels display labile gating: evidence from the TRIC-A knockout mouse model.

PubMed

Venturi, Elisa; Matyjaszkiewicz, Antoni; Pitt, Samantha J; Tsaneva-Atanasova, Krasimira; Nishi, Miyuki; Yamazaki, Daiju; Takeshima, Hiroshi; Sitsapesan, Rebecca

2013-08-01

Sarcoplasmic/endoplasmic reticulum (SR) and nuclear membranes contain two related cation channels named TRIC-A and TRIC-B. In many tissues, both subtypes are co-expressed, making it impossible to distinguish the distinct single-channel properties of each subtype. We therefore incorporated skeletal muscle SR vesicles derived from Tric-a-knockout mice into bilayers in order to characterise the biophysical properties of native TRIC-B without possible misclassification of the channels as TRIC-A, and without potential distortion of functional properties by detergent purification protocols. The native TRIC-B channels were ideally selective for cations. In symmetrical 210 mM K(+), the maximum (full) open channel level (199 pS) was equivalent to that observed when wild-type SR vesicles were incorporated into bilayers. Analysis of TRIC-B gating revealed complex and variable behaviour. Four main sub-conductance levels were observed at approximately 80 % (161 pS), 60 % (123 pS), 46 % (93 pS), and 30 % (60 pS) of the full open state. Seventy-five percent of the channels were voltage sensitive with Po being markedly reduced at negative holding potentials. The frequent, rapid transitions between TRIC-B sub-conductance states prevented development of reliable gating models using conventional single-channel analysis. Instead, we used mean-variance plots to highlight key features of TRIC-B gating in a more accurate and visually useful manner. Our study provides the first biophysical characterisation of native TRIC-B channels and indicates that this channel would be suited to provide counter current in response to Ca(2+) release from the SR. Further experiments are required to distinguish the distinct functional properties of TRIC-A and TRIC-B and understand their individual but complementary physiological roles.
Investing in rangeland restoration in the Arid West, USA: countering the effects of an invasive weed on the long-term fire cycle.

PubMed

Epanchin-Niell, Rebecca; Englin, Jeffrey; Nalle, Darek

2009-01-01

In large areas of the arid western United States, much of which are federally managed, fire frequencies and associated management costs are escalating as flammable, invasive cheatgrass (Bromus tectorum) increases its stronghold. Cheatgrass invasion and the subsequent increase in fire frequency result in the loss of native vegetation, less predictable forage availability for livestock and wildlife, and increased costs and risk associated with firefighting. Revegetation following fire on land that is partially invaded by cheatgrass can reduce both the dominance of cheatgrass and its associated high fire rate. Thus restoration can be viewed as an investment in fire-prevention and, if native seed is used, an investment in maintaining native vegetation on the landscape. Here we develop and employ a Markov model of vegetation dynamics for the sagebrush steppe ecosystem to predict vegetation change and management costs under different intensities and types of post-fire revegetation. We use the results to estimate the minimum total cost curves for maintaining native vegetation on the landscape and for preventing cheatgrass dominance. Our results show that across a variety of model parameter possibilities, increased investment in post-fire revegetation reduces long-term fire management costs by more than enough to offset the costs of revegetation. These results support that a policy of intensive post-fire revegetation will reduce long-term management costs for this ecosystem, in addition to providing environmental benefits. This information may help justify costs associated with revegetation and raise the priority of restoration in federal land budgets.
Blood Politics, Ethnic Identity, and Racial Misclassification among American Indians and Alaska Natives

PubMed Central

Haozous, Emily A.; Strickland, Carolyn J.; Palacios, Janelle F.; Solomon, Teshia G. Arambula

2014-01-01

Misclassification of race in medical and mortality records has long been documented as an issue in American Indian/Alaska Native data. Yet, little has been shared in a cohesive narrative which outlines why misclassification of American Indian/Alaska Native identity occurs. The purpose of this paper is to provide a summary of the current state of the science in racial misclassification among American Indians and Alaska Natives. We also provide a historical context on the importance of this problem and describe the ongoing political processes that both affect racial misclassification and contribute to the context of American Indian and Alaska Native identity. PMID:24669226
Blood politics, ethnic identity, and racial misclassification among American Indians and Alaska Natives.

PubMed

Haozous, Emily A; Strickland, Carolyn J; Palacios, Janelle F; Solomon, Teshia G Arambula

2014-01-01

Misclassification of race in medical and mortality records has long been documented as an issue in American Indian/Alaska Native data. Yet, little has been shared in a cohesive narrative which outlines why misclassification of American Indian/Alaska Native identity occurs. The purpose of this paper is to provide a summary of the current state of the science in racial misclassification among American Indians and Alaska Natives. We also provide a historical context on the importance of this problem and describe the ongoing political processes that both affect racial misclassification and contribute to the context of American Indian and Alaska Native identity.
Conformational stability as a design target to control protein aggregation.

PubMed

Costanzo, Joseph A; O'Brien, Christopher J; Tiller, Kathryn; Tamargo, Erin; Robinson, Anne Skaja; Roberts, Christopher J; Fernandez, Erik J

2014-05-01

Non-native protein aggregation is a prevalent problem occurring in many biotechnological manufacturing processes and can compromise the biological activity of the target molecule or induce an undesired immune response. Additionally, some non-native aggregation mechanisms lead to amyloid fibril formation, which can be associated with debilitating diseases. For natively folded proteins, partial or complete unfolding is often required to populate aggregation-prone conformational states, and therefore one proposed strategy to mitigate aggregation is to increase the free energy for unfolding (ΔGunf) prior to aggregation. A computational design approach was tested using human γD crystallin (γD-crys) as a model multi-domain protein. Two mutational strategies were tested for their ability to reduce/increase aggregation rates by increasing/decreasing ΔGunf: stabilizing the less stable domain and stabilizing the domain-domain interface. The computational protein design algorithm, RosettaDesign, was implemented to identify point variants. The results showed that although the predicted free energies were only weakly correlated with the experimental ΔGunf values, increased/decreased aggregation rates for γD-crys correlated reasonably well with decreases/increases in experimental ΔGunf, illustrating improved conformational stability as a possible design target to mitigate aggregation. However, the results also illustrate that conformational stability is not the sole design factor controlling aggregation rates of natively folded proteins.
Impact of native plants on bird and butterfly biodiversity in suburban landscapes.

PubMed

Burghardt, Karin T; Tallamy, Douglas W; Gregory Shriver, W

2009-02-01

Managed landscapes in which non-native ornamental plants are favored over native vegetation now dominate the United States, particularly east of the Mississippi River. We measured how landscaping with native plants affects the avian and lepidopteran communities on 6 pairs of suburban properties in southeastern Pennsylvania. One property in each pair was landscaped entirely with native plants and the other exhibited a more conventional suburban mixture of plants--a native canopy with non-native groundcover and shrubs. Vegetation sampling confirmed that total plant cover and plant diversity did not differ between treatments, but non-native plant cover was greater on the conventional sites and native plant cover was greater on the native sites. Several avian (abundance, species richness, biomass, and breeding-bird abundance) and larval lepidopteran (abundance and species richness) community parameters were measured from June 2006 to August 2006. Native properties supported significantly more caterpillars and caterpillar species and significantly greater bird abundance, diversity, species richness, biomass, and breeding pairs of native species. Of particular importance is that bird species of regional conservation concern were 8 times more abundant and significantly more diverse on native properties. In our study area, native landscaping positively influenced the avian and lepidopteran carrying capacity of suburbia and provided a mechanism for reducing biodiversity losses in human-dominated landscapes.
Modeling invasive alien plant species in river systems: Interaction with native ecosystem engineers and effects on hydro-morphodynamic processes

NASA Astrophysics Data System (ADS)

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

2017-08-01

Invasive alien plant species negatively impact native plant communities by out-competing species or changing abiotic and biotic conditions in their introduced range. River systems are especially vulnerable to biological invasions, because waterways can function as invasion corridors. Understanding interactions of invasive and native species and their combined effects on river dynamics is essential for developing cost-effective management strategies. However, numerical models for simulating long-term effects of these processes are lacking. This paper investigates how an invasive alien plant species affects native riparian vegetation and hydro-morphodynamics. A morphodynamic model has been coupled to a dynamic vegetation model that predicts establishment, growth and mortality of riparian trees. We introduced an invasive alien species with life-history traits based on Japanese Knotweed (Fallopia japonica), and investigated effects of low- and high propagule pressure on invasion speed, native vegetation and hydro-morphodynamic processes. Results show that high propagule pressure leads to a decline in native species cover due to competition and the creation of unfavorable native colonization sites. With low propagule pressure the invader facilitates native seedling survival by creating favorable hydro-morphodynamic conditions at colonization sites. With high invader abundance, water levels are raised and sediment transport is reduced during the growing season. In winter, when the above-ground invader biomass is gone, results are reversed and the floodplain is more prone to erosion. Invasion effects thus depend on seasonal above- and below ground dynamic vegetation properties and persistence of the invader, on the characteristics of native species it replaces, and the combined interactions with hydro-morphodynamics.
The H2A-H2B dimeric kinetic intermediate is stabilized by widespread hydrophobic burial with few fully native interactions.

PubMed

Guyett, Paul J; Gloss, Lisa M

2012-01-20

The H2A-H2B histone heterodimer folds via monomeric and dimeric kinetic intermediates. Within ∼5 ms, the H2A and H2B polypeptides associate in a nearly diffusion limited reaction to form a dimeric ensemble, denoted I₂ and I₂*, the latter being a subpopulation characterized by a higher content of nonnative structure (NNS). The I₂ ensemble folds to the native heterodimer, N₂, through an observable, first-order kinetic phase. To determine the regions of structure in the I₂ ensemble, we characterized 26 Ala mutants of buried hydrophobic residues, spanning the three helices of the canonical histone folds of H2A and H2B and the H2B C-terminal helix. All but one targeted residue contributed significantly to the stability of I₂, the transition state and N₂; however, only residues in the hydrophobic core of the dimer interface perturbed the I₂* population. Destabilization of I₂* correlated with slower folding rates, implying that NNS is not a kinetic trap but rather accelerates folding. The pattern of Φ values indicated that residues forming intramolecular interactions in the peripheral helices contributed similar stability to I₂ and N₂, but residues involved in intermolecular interactions in the hydrophobic core are only partially folded in I₂. These findings suggest a dimerize-then-rearrange model. Residues throughout the histone fold contribute to the stability of I₂, but after the rapid dimerization reaction, the hydrophobic core of the dimer interface has few fully native interactions. In the transition state leading to N₂, more native-like interactions are developed and nonnative interactions are rearranged. Copyright © 2011 Elsevier Ltd. All rights reserved.
Geometry of proteins: hydrogen bonding, sterics, and marginally compact tubes.

PubMed

Banavar, Jayanth R; Cieplak, Marek; Flammini, Alessandro; Hoang, Trinh X; Kamien, Randall D; Lezon, Timothy; Marenduzzo, Davide; Maritan, Amos; Seno, Flavio; Snir, Yehuda; Trovato, Antonio

2006-03-01

The functionality of proteins is governed by their structure in the native state. Protein structures are made up of emergent building blocks of helices and almost planar sheets. A simple coarse-grained geometrical model of a flexible tube barely subject to compaction provides a unified framework for understanding the common character of globular proteins. We argue that a recent critique of the tube idea is not well founded.
Geometry of proteins: Hydrogen bonding, sterics, and marginally compact tubes

NASA Astrophysics Data System (ADS)

Banavar, Jayanth R.; Cieplak, Marek; Flammini, Alessandro; Hoang, Trinh X.; Kamien, Randall D.; Lezon, Timothy; Marenduzzo, Davide; Maritan, Amos; Seno, Flavio; Snir, Yehuda; Trovato, Antonio

2006-03-01

The functionality of proteins is governed by their structure in the native state. Protein structures are made up of emergent building blocks of helices and almost planar sheets. A simple coarse-grained geometrical model of a flexible tube barely subject to compaction provides a unified framework for understanding the common character of globular proteins. We argue that a recent critique of the tube idea is not well founded.
Stabilization of Proteins and Noncovalent Protein Complexes during Electrospray Ionization by Amino Acid Additives.

PubMed

Zhang, Hua; Lu, Haiyan; Chingin, Konstantin; Chen, Huanwen

2015-07-21

Ionization of proteins and noncovalent protein complexes with minimal disturbance to their native structure presents a great challenge for biological mass spectrometry (MS). In living organisms, the native structure of intracellular proteins is commonly stabilized by solute amino acids (AAs) accumulated in cells at very high concentrations. Inspired by nature, we hypothesized that AAs could also pose a stabilizing effect on the native structure of proteins and noncovalent protein complexes during ionization. To test this hypothesis, here we explored MS response for various protein complexes upon the addition of free AAs at mM concentrations into the electrospray ionization (ESI) solution. Thermal activation of ESI droplets in the MS inlet capillary was employed as a model destabilizing factor during ionization. Our results indicate that certain AAs, in particular proline (Pro), pose considerable positive effect on the stability of noncovalent protein complexes in ESI-MS without affecting the signal intensity of protein ions and original protein-ligand equilibrium, even when added at the 20 mM concentration. The data suggest that the degree of protein stabilization is primarily determined by the osmolytic and ampholytic characteristics of AA solutes. The highest stability and visibility of noncovalent protein complexes in ESI-MS are achieved using AA additives with neutral isoelectric point, moderate proton affinity, and unfavorable interaction with the native protein state. Overall, our results indicate that the simple addition of free amino acids into the working solution can notably improve the stability and accuracy of protein analysis by native ESI-MS.
Chemical Recycling of Molecules in Cometary Comae

NASA Astrophysics Data System (ADS)

Boice, Daniel C.; Kawakita, Hideyo; Shinnaka, Yoshiharu; Kobayashi, Hitomi

2015-08-01

Modeling is essential to understand the important physical and chemical processes that occur in cometary comae, especially the relationship between native and sibling molecules, such as, HCN and CN. Photochemistry is a major source of ions and electrons that further initiate key gas-phase reactions, leading to the plethora of molecules and atoms observed in comets. The effects of photoelectrons that react via impacts are important to the overall ionization in the inner coma. We have found that many molecules undergo protonation reactions with primarily water, followed by electron recombination resulting in the original molecules in a vibrationally excited state. These excited molecules spontaneously emit photons back to the ground state. We identify this series of reactions as chemical “recycling.” We discuss the importance of this mechanism for HCN, NH3, and water in comets. We also identify other relevant processes in the collision-dominated, inner coma of a comet within a global modeling framework to better understand observations and in situ measurements of cometary species, especially relationships between native and sibling molecules for the Rosetta Mission to Comet 67P/Churyumov-Gerasimenko.Acknowledgements: We appreciate support from the NSF Planetary Astronomy Program under Grant No. 0908529. This program is partially supported by the MEXT Supported Program for the Strategic Research Foundation at Private Universities, 2014-2018.
Native American tribal cultures: implications for veterinary medical education.

PubMed

Gelberg, Susan; Gelberg, Howard

2007-01-01

This article reviews the literature from veterinary medicine, tribal education, career development, and psychology to focus on the reasons that Native people are currently under-represented in the field of veterinary medicine. Educational implications and recruitment strategies are suggested. Local, state, and national resources are provided to help veterinary medical educators make their programs more culturally competent for Native veterinary students and faculty.
Sociocultural Variables That Impact High School Students' Perceptions of Native Fauna: A Study on the Species Component of the Biodiversity Concept

ERIC Educational Resources Information Center

Bermudez, Gonzalo M.; Battistón, Luisina V.; García Capocasa, María C.; De Longhi, Ana L.

2017-01-01

This study investigates the influence of school sector (private versus state schools) and student gender on knowledge of native fauna. Our main objectives were (a) to describe the knowledge of high school students from the province of Cordoba, Argentina with respect to native animal species, (b) to determine if any exotic species (introduced or…
Mothers, Fathers, Peers, and Mexican-Origin Adolescents’ Sexual Intentions

PubMed Central

Killoren, Sarah E.; Updegraff, Kimberly A.; Christopher, F. Scott; Umaña-Taylor, Adriana J.

2011-01-01

Drawing on a symbolic-interaction perspective and a compensation model, the processes linking mother-and father-adolescent relationship qualities, deviant peer affiliations, and adolescents’ sexual intentions were investigated for 246 Mexican-origin youths born in the United States and in Mexico using multiple-group structural equation models. Deviant peer affiliations significantly mediated the relations between paternal acceptance and sexual intentions and between disclosure to mothers and sexual intentions for U.S.-born youths but not for Mexico-born youths. Findings highlight the importance of examining variability as a function of youth nativity. PMID:21278903
Controlled graphene encapsulation: a nanoscale shield for characterising single bacterial cells in liquid.

PubMed

Li, Jiayao; Zheng, Changxi; Liu, Boyin; Chou, Tsengming; Kim, Yeonuk; Qiu, Shi; Li, Jian; Yan, Wenyi; Fu, Jing

2018-06-11

High-resolution single-cell imaging in their native or near-native state has received considerable interest for decades. In this research, we present an innovative approach that can be employed to study both morphological and nano-mechanical properties of hydrated single bacterial cells. The proposed strategy is to encapsulate wet cells with monolayer graphene with a newly developed water membrane approach, followed by imaging with both electron microscopy (EM) and atomic force microscopy (AFM). A computational framework was developed to provide additional insights, with the detailed nanoindentation process on graphene modeled based on finite element method. The model was first validated by calibration with polymer materials of known properties, and the contribution of graphene was then studied and corrected to determine the actual moduli of the encapsulated hydrated sample. Aapplication of the proposed approach was performed on hydrated bacterial cells (Klebsiella pneumoniae) to correlate the structural and mechanical information. EM and EDS (energy-dispersive X-ray spectroscopy) imaging confirmed that the cells in their near-native stage can be studied inside the miniatured environment enabled with graphene encapsulation. The actual moduli of the encapsulated hydrated cells were determined based on the developed computational model in parallel, with results comparable with those acquired with Wet-AFM. It is expected that the successful establishment of controlled graphene encapsulation offers a new route for probing liquid/live cells with scanning probe microscopy, as well as correlative imaging of hydrated samples for both biological and material sciences. © 2018 IOP Publishing Ltd.
Native American Indian Successes in Natural Resources, Science and Engineering: PreK through Ph.D.

NASA Astrophysics Data System (ADS)

Bolman, J. R.

2005-12-01

We are living in a definite time of change. Distinct changes are being experienced in our most sacred and natural environments. This is especially true on Native lands. Native people have lived for millennia in distinct and unique ways. The knowledge of balancing the needs of people with the needs of our natural environments is paramount in all tribal societies. This inherent knowledge has become the foundation on which to build a "blended" contemporary understanding of western science. The Dakota's and Northern California have recognized the critical need in understanding successful tribal strategies to engage educational systems (K-12 and higher education), to bring to prominence the professional development opportunities forged through working with tribal peoples and ensure the growth of Native people in STEM (Science, Technology, Engineering and Mathematics) professions. The presentation will highlight: 1) current philosophies on building a STEM Native workforce; 2) successful educational programs/activities in PreK-Ph.D. systems; 3) current Native professionals, their research and tribal applicability; and 4) forwarding thinking for creating sustainable environmental and social infrastructures for all people. South Dakota School of Mines and Technology (SDSM&T) and Humboldt State University (HSU) have been recognized nationally for their partnerships with Native communities. SDSM&T has set record numbers for graduating Native students in science and engineering. SDSM&T had 27 graduates in five years (2000-2005) and hosted more than 1000+ Native students for programs and activities. Humboldt State University is the only university in the CSU system with a program focusing specifically on Natives in natural resources, science and engineering as well as a Native American Studies degree. Both universities have designed programs to meet current needs and address challenging issues in Earth, Wind, Fire and Water. The programs are funded through NASA, NSF, NIH and others.
Forest landscape restoration: linkages with stream fishes of the southern United States

Treesearch

Melvin L. Warren

2012-01-01

With well over 600 native species, the southern United States supports one of the richest temperate freshwater fish faunas on Earth (Fig. 10.1 ). Unfortunately, an expert review revealed that 27% (188 taxa) of southern fishes are endangered, threatened, or vulnerable (Warren et al. 2000 ) and that 16â18% of native fishes are imperiled in 45 of 51 major southern river...

NCADI's 1995 National Directory of Drug Abuse and Alcoholism Treatment and Prevention Programs That Have a Special Program for American Indians/Alaska Natives.

ERIC Educational Resources Information Center

Vanderbilt, Rebecca, Comp.; Schacht, Robert M., Comp.

This state-by-state directory lists over 500 alcohol and drug abuse treatment and prevention services that target American Indians and Alaska Natives. The directory was compiled from the website of the National Clearinghouse for Alcohol and Drug Information (NCADI). Their home page on the Internet is located at http://www.health.org/index.htm. The…
Influence of the native topology on the folding barrier for small proteins

NASA Astrophysics Data System (ADS)

Prieto, Lidia; Rey, Antonio

2007-11-01

The possibility of downhill instead of two-state folding for proteins has been a very controversial topic which arose from recent experimental studies. From the theoretical side, this question has also been accomplished in different ways. Given the experimental observation that a relationship exists between the native structure topology of a protein and the kinetic and thermodynamic properties of its folding process, Gō-type potentials are an appropriate way to approach this problem. In this work, we employ an interaction potential from this family to get a better insight on the topological characteristics of the native state that may somehow determine the presence of a thermodynamic barrier in the folding pathway. The results presented here show that, indeed, the native topology of a small protein has a great influence on its folding behavior, mostly depending on the proportion of local and long range contacts the protein has in its native structure. Furthermore, when all the interactions present contribute in a balanced way, the transition results to be cooperative. Otherwise, the tendency to a downhill folding behavior increases.
Early Mathematics Achievement Trajectories: English-Language Learner and Native English-Speaker Estimates, Using the Early Childhood Longitudinal Survey

PubMed Central

Roberts, Greg; Bryant, Diane

2012-01-01

This study used data from the Early Childhood Longitudinal Survey, Kindergarten Class of 1998 –1999, to (a) estimate mathematics achievement trends through 5th grade in the population of students who are English-language proficient by the end of kindergarten, (b) compare trends across primary language groups within this English-language proficient group, (c) evaluate the effect of low socioeconomic status (SES) for English-language proficient students and within different primary language groups, and (d) estimate language-group trends in specific mathematics skill areas. The group of English-language proficient English-language learners (ELLs) was disaggregated into native Spanish speakers and native speakers of Asian languages, the 2 most prevalent groups of ELLs in the United States. Results of multilevel latent variable growth modeling suggest that primary language may be less salient than SES in explaining the mathematics achievement of English-language proficient ELLs. The study also found that mathematics-related school readiness is a key factor in explaining subsequent achievement differences and that the readiness gap is prevalent across the range of mathematics-related skills. PMID:21574702
Prediction of protein tertiary structure to low resolution: performance for a large and structurally diverse test set.

PubMed

Eyrich, V A; Standley, D M; Friesner, R A

1999-05-14

We report the tertiary structure predictions for 95 proteins ranging in size from 17 to 160 residues starting from known secondary structure. Predictions are obtained from global minimization of an empirical potential function followed by the application of a refined atomic overlap potential. The minimization strategy employed represents a variant of the Monte Carlo plus minimization scheme of Li and Scheraga applied to a reduced model of the protein chain. For all of the cases except beta-proteins larger than 75 residues, a native-like structure, usually 4-6 A root-mean-square deviation from the native, is located. For beta-proteins larger than 75 residues, the energy gap between native-like structures and the lowest energy structures produced in the simulation is large, so that low RMSD structures are not generated starting from an unfolded state. This is attributed to the lack of an explicit hydrogen bond term in the potential function, which we hypothesize is necessary to stabilize large assemblies of beta-strands. Copyright 1999 Academic Press.
State-and-transition prototype model of riparian vegetation downstream of Glen Canyon Dam, Arizona

USGS Publications Warehouse

Ralston, Barbara E.; Starfield, Anthony M.; Black, Ronald S.; Van Lonkhuyzen, Robert A.

2014-01-01

Facing an altered riparian plant community dominated by nonnative species, resource managers are increasingly interested in understanding how to manage and promote healthy riparian habitats in which native species dominate. For regulated rivers, managing flows is one tool resource managers consider to achieve these goals. Among many factors that can influence riparian community composition, hydrology is a primary forcing variable. Frame-based models, used successfully in grassland systems, provide an opportunity for stakeholders concerned with riparian systems to evaluate potential riparian vegetation responses to alternative flows. Frame-based, state-and-transition models of riparian vegetation for reattachment bars, separation bars, and the channel margin found on the Colorado River downstream of Glen Canyon Dam were constructed using information from the literature. Frame-based models can be simple spreadsheet models (created in Microsoft® Excel) or developed further with programming languages (for example, C-sharp). The models described here include seven community states and five dam operations that cause transitions between states. Each model divides operations into growing (April–September) and non-growing seasons (October–March) and incorporates upper and lower bar models, using stage elevation as a division. The inputs (operations) can be used by stakeholders to evaluate flows that may promote dynamic riparian vegetation states, or identify those flow options that may promote less desirable states (for example, Tamarisk [Tamarix sp.] temporarily flooded shrubland). This prototype model, although simple, can still elicit discussion about operational options and vegetation response.
Similarities in the Etiology of Alcohol Use Among Native American and Non-Native Young Women

PubMed Central

Komro, Kelli A.; Livingston, Melvin D.; Garrett, Brady A.; Boyd, Misty L.

2016-01-01

Objective: This study examined social- and individual- level factors associated with alcohol use among young women and tested whether differences exist between Native American and non-Native young women. Method: School-based surveys were conducted among 952 young women (ages 14–19) attending four high schools within the tribal jurisdictional service area of the Cherokee Nation in northeastern Oklahoma. Structural equation modeling using Mplus was used to assess the direct and indirect effects of social- and individual-level factors on subsequent alcohol use among Native and non-Native young women. Results: We found no differences in the level of risk and protective factors among Native and non-Native young women. Among Native and non-Native young women, alcohol access, parental communication, and best friends’ alcohol use had statistically significant direct and/or indirect effects on alcohol use. Indirect effects were mediated through alcohol expectancies and norms. A history of alcohol problems by an adult in the household and depression were not retained as independent risk factors in either model. Conclusions: We found more similarities than differences in level of and relations to alcohol use among social and individual risk and protective factors between Native American and non-Native young women from northeastern Oklahoma. The results provide support for universal prevention strategies, suggesting the importance of increasing perceptions that it is difficult to obtain alcohol and increasing parent–child communication. PMID:27588537
Similarities in the Etiology of Alcohol Use Among Native American and Non-Native Young Women.

PubMed

Komro, Kelli A; Livingston, Melvin D; Garrett, Brady A; Boyd, Misty L

2016-09-01

This study examined social-and individual-level factors associated with alcohol use among young women and tested whether differences exist between Native American and non-Native young women. School-based surveys were conducted among 952 young women (ages 14-19) attending four high schools within the tribal jurisdictional service area of the Cherokee Nation in northeastern Oklahoma. Structural equation modeling using Mplus was used to assess the direct and indirect effects of social-and individual-level factors on subsequent alcohol use among Native and non-Native young women. We found no differences in the level of risk and protective factors among Native and non-Native young women. Among Native and non-Native young women, alcohol access, parental communication, and best friends' alcohol use had statistically significant direct and/or indirect effects on alcohol use. Indirect effects were mediated through alcohol expectancies and norms. A history of alcohol problems by an adult in the household and depression were not retained as independent risk factors in either model. We found more similarities than differences in level of and relations to alcohol use among social and individual risk and protective factors between Native American and non-Native young women from northeastern Oklahoma. The results provide support for universal prevention strategies, suggesting the importance of increasing perceptions that it is difficult to obtain alcohol and increasing parent-child communication.
Differences in ecological structure, function, and native species abundance between native and invaded Hawaiian streams.

PubMed

Holitzki, Tara M; MacKenzie, Richard A; Wiegner, Tracy N; McDermid, Karla J

2013-09-01

Poeciliids, one of the most invasive species worldwide, are found on almost every continent and have been identified as an "invasive species of concern" in the United States, New Zealand, and Australia. Despite their global prevalence, few studies have quantified their impacts on tropical stream ecosystem structure, function, and biodiversity. Utilizing Hawaiian streams as model ecosystems, we documented how ecological structure, function, and native species abundance differed between poeciliid-free and poeciliid-invaded tropical streams. Stream nutrient yields, benthic biofilm biomass, densities of macroinvertebrates and fish, and community structures of benthic algae, macroinvertebrates, and fish were compared between streams with and without established poeciliid populations on the island of Hawai'i, Hawaii, USA. Sum nitrate (sigmaNO3(-) = NO3(-) + NO2(-)), total nitrogen, and total organic carbon yields were eight times, six times, and five times higher, respectively, in poeciliid streams than in poeciliid-free streams. Benthic biofilm ash-free dry mass was 1.5x higher in poeciliid streams than in poeciliid-free streams. Percentage contributions of chironomids and hydroptilid caddisflies to macroinvertebrate densities were lower in poeciliid streams compared to poeciliid-free streams, while percentage contributions of Cheumatopsyche analis caddisflies, Dugesia sp. flatworms, and oligochaetes were higher. Additionally, mean densities of native gobies were two times lower in poeciliid streams than in poeciliid-free ones, with poeciliid densities being approximately eight times higher than native fish densities. Our results, coupled with the wide distribution of invasive poeciliids across Hawaii and elsewhere in the tropics, suggest that poeciliids may negatively impact the ecosystem structure, function, and native species abundance of tropical streams they invade. This underscores the need for increased public awareness to prevent future introductions and for developing and implementing effective eradication and restoration strategies.
Recent Advances in Immobilization Strategies for Glycosidases

PubMed Central

Karav, Sercan; Cohen, Joshua L.; Barile, Daniela; de Moura Bell, Juliana Maria Leite Nobrega

2017-01-01

Glycans play important biological roles in cell-to-cell interactions, protection against pathogens, as well as in proper protein folding and stability, and are thus interesting targets for scientists. Although their mechanisms of action have been widely investigated and hypothesized, their biological functions are not well understood due to the lack of deglycosylation methods for large-scale isolation of these compounds. Isolation of glycans in their native state is crucial for the investigation of their biological functions. However, current enzymatic and chemical deglycosylation techniques require harsh pretreatment and reaction conditions (high temperature and use of detergents) that hinder the isolation of native glycan structures. Indeed, the recent isolation of new endoglycosidases that are able to cleave a wider variety of linkages and efficiently hydrolyze native proteins has opened up the opportunity to elucidate the biological roles of a higher variety of glycans in their native state. As an example, our research group recently isolated a novel Endo-β-N-acetylglucosaminidase from Bifidobacterium longum subsp. infantis ATCC 15697 (EndoBI-1) that cleaves N-N′-diacetyl chitobiose moieties found in the N-linked glycan (N-glycan) core of high mannose, hybrid, and complex N-glycans. This enzyme is also active on native proteins, which enables native glycan isolation, a key advantage when evaluating their biological activities. Efficient, stable, and economically viable enzymatic release of N-glycans requires the selection of appropriate immobilization strategies. In this review, we discuss the state-of-the-art of various immobilization techniques (physical adsorption, covalent binding, aggregation, and entrapment) for glycosidases, as well as their potential substrates and matrices. PMID:27718339
Structural and kinetic mapping of side-chain exposure onto the protein energy landscape.

PubMed

Bernstein, Rachel; Schmidt, Kierstin L; Harbury, Pehr B; Marqusee, Susan

2011-06-28

Identification and characterization of structural fluctuations that occur under native conditions is crucial for understanding protein folding and function, but such fluctuations are often rare and transient, making them difficult to study. Native-state hydrogen exchange (NSHX) has been a powerful tool for identifying such rarely populated conformations, but it generally reveals no information about the placement of these species along the folding reaction coordinate or the barriers separating them from the folded state and provides little insight into side-chain packing. To complement such studies, we have performed native-state alkyl-proton exchange, a method analogous to NSHX that monitors cysteine modification rather than backbone amide exchange, to examine the folding landscape of Escherichia coli ribonuclease H, a protein well characterized by hydrogen exchange. We have chosen experimental conditions such that the rate-limiting barrier acts as a kinetic partition: residues that become exposed only upon crossing the unfolding barrier are modified in the EX1 regime (alkylation rates report on the rate of unfolding), while those exposed on the native side of the barrier are modified predominantly in the EX2 regime (alkylation rates report on equilibrium populations). This kinetic partitioning allows for identification and placement of partially unfolded forms along the reaction coordinate. Using this approach we detect previously unidentified, rarely populated conformations residing on the native side of the barrier and identify side chains that are modified only upon crossing the unfolding barrier. Thus, in a single experiment under native conditions, both sides of the rate-limiting barrier are investigated.
Structural and kinetic mapping of side-chain exposure onto the protein energy landscape

PubMed Central

Bernstein, Rachel; Schmidt, Kierstin L.; Harbury, Pehr B.; Marqusee, Susan

2011-01-01

Identification and characterization of structural fluctuations that occur under native conditions is crucial for understanding protein folding and function, but such fluctuations are often rare and transient, making them difficult to study. Native-state hydrogen exchange (NSHX) has been a powerful tool for identifying such rarely populated conformations, but it generally reveals no information about the placement of these species along the folding reaction coordinate or the barriers separating them from the folded state and provides little insight into side-chain packing. To complement such studies, we have performed native-state alkyl-proton exchange, a method analogous to NSHX that monitors cysteine modification rather than backbone amide exchange, to examine the folding landscape of Escherichia coli ribonuclease H, a protein well characterized by hydrogen exchange. We have chosen experimental conditions such that the rate-limiting barrier acts as a kinetic partition: residues that become exposed only upon crossing the unfolding barrier are modified in the EX1 regime (alkylation rates report on the rate of unfolding), while those exposed on the native side of the barrier are modified predominantly in the EX2 regime (alkylation rates report on equilibrium populations). This kinetic partitioning allows for identification and placement of partially unfolded forms along the reaction coordinate. Using this approach we detect previously unidentified, rarely populated conformations residing on the native side of the barrier and identify side chains that are modified only upon crossing the unfolding barrier. Thus, in a single experiment under native conditions, both sides of the rate-limiting barrier are investigated. PMID:21670244
Circular permutation of a WW domain: Folding still occurs after excising the turn of the folding-nucleating hairpin

PubMed Central

Kier, Brandon L.; Anderson, Jordan M.; Andersen, Niels H.

2014-01-01

A hyperstable Pin1 WW domain has been circularly permuted via excision of the fold-nucleating turn; it still folds to form the native three-strand sheet and hydrophobic core features. Multiprobe folding dynamics studies of the normal and circularly permuted sequences, as well as their constituent hairpin fragments and comparable-length β-strand-loop-β-strand models, indicate 2-state folding for all topologies. N-terminal hairpin formation is the fold nucleating event for the wild-type sequence; the slower folding circular permutant has a more distributed folding transition state. PMID:24350581
Propensity to form amyloid fibrils is encoded as excitations in the free energy landscape of monomeric proteins.

PubMed

Zhuravlev, Pavel I; Reddy, Govardhan; Straub, John E; Thirumalai, D

2014-07-15

Protein aggregation, linked to many of diseases, is initiated when monomers access rogue conformations that are poised to form amyloid fibrils. We show, using simulations of src SH3 domain, that mechanical force enhances the population of the aggregation-prone (N(⁎)) states, which are rarely populated under force free native conditions but are encoded in the spectrum of native fluctuations. The folding phase diagrams of SH3 as a function of denaturant concentration ([C]), mechanical force (f), and temperature exhibit an apparent two-state behavior, without revealing the presence of the elusive N(⁎) states. Interestingly, the phase boundaries separating the folded and unfolded states at all [C] and f fall on a master curve, which can be quantitatively described using an analogy to superconductors in a magnetic field. The free energy profiles as a function of the molecular extension (R), which are accessible in pulling experiments, (R), reveal the presence of a native-like N(⁎) with a disordered solvent-exposed amino-terminal β-strand. The structure of the N(⁎) state is identical with that found in Fyn SH3 by NMR dispersion experiments. We show that the timescale for fibril formation can be estimated from the population of the N(⁎) state, determined by the free energy gap separating the native structure and the N(⁎) state, a finding that can be used to assess fibril forming tendencies of proteins. The structures of the N(⁎) state are used to show that oligomer formation and likely route to fibrils occur by a domain-swap mechanism in SH3 domain. Copyright © 2014 Elsevier Ltd. All rights reserved.
A global organism detection and monitoring system for non-native species

USGS Publications Warehouse

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, accessing the operating system, and to use existing libraries in C++, R, and other languages to develop the tools to track harmful species in space and time. The GODM database and system are crucial for early detection and rapid containment of invasive species. ?? 2007 Elsevier B.V. All rights reserved.
Native vegetation establishment for IDOT erosion control best management practices.

DOT National Transportation Integrated Search

2014-05-01

The objective of this report was to develop native roadside vegetation best management practices for : the Illinois Department of Transportation. A review of current practices was undertaken, along with a : review of those of other state departments ...
33 CFR 203.16 - Federally recognized Indian Tribes and the Alaska Native Corporations.

Code of Federal Regulations, 2011 CFR

2011-07-01

..., NATURAL DISASTER PROCEDURES Introduction § 203.16 Federally recognized Indian Tribes and the Alaska Native Corporations. Requests for Public Law 84-99 assistance on tribal lands held in trust by the United States, or...
Persistence and extirpation in invaded landscapes: patch characteristics and connectivity determine effects of non-native predatory fish on native salamanders

USGS Publications Warehouse

Pilliod, David S.; Arkle, Robert S.; Maxell, Bryce A.

2012-01-01

Studies have demonstrated negative effects of non-native, predatory fishes on native amphibians, yet it is still unclear why some amphibian populations persist, while others are extirpated, following fish invasion. We examined this question by developing habitat-based occupancy models for the long-toed salamander (Ambystoma macrodactylum) and nonnative fish using survey data from 1,749 water bodies across 470 catchments in the Northern Rocky Mountains, USA. We first modeled the habitat associations of salamanders at 468 fishless water bodies in 154 catchments where non-native fish were historically, and are currently, absent from the entire catchment. Wethen applied this habitat model to the complete data set to predict the probability of salamander occupancy in each water body, removing any effect of fish presence. Finally, we compared field-observed occurrences of salamanders and fish to modeled probability of salamander occupancy. Suitability models indicated that fish and salamanders had similar habitat preferences, possibly resulting in extirpations of salamander populations from entire catchments where suitable habitats were limiting. Salamanders coexisted with non-native fish in some catchments by using marginal quality, isolated (no inlet or outlet) habitats that remained fishless. They rarely coexisted with fish within individual water bodies and only where habitat quality was highest. Connectivity of water bodies via streams resulted in increased probability of fish invasion and consequently reduced probability of salamander occupancy.These results could be used to identify and prioritize catchments and water bodies where control measures would be most effective at restoring amphibian populations. Our approach could be useful as a framework for improved investigations into questions of persistence and extirpation of native species when non-native species have already become established.
The Power of Protection: A Population-Based Comparison of Native and Non-Native Youth Suicide Attempters

ERIC Educational Resources Information Center

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…
Conformational Space and Stability of ETD Charge Reduction Products of Ubiquitin

NASA Astrophysics Data System (ADS)

Lermyte, Frederik; Łącki, Mateusz Krzysztof; Valkenborg, Dirk; Gambin, Anna; Sobott, Frank

2017-01-01

Owing to its versatility, electron transfer dissociation (ETD) has become one of the most commonly utilized fragmentation techniques in both native and non-native top-down mass spectrometry. However, several competing reactions—primarily different forms of charge reduction—occur under ETD conditions, as evidenced by the distorted isotope patterns usually observed. In this work, we analyze these isotope patterns to compare the stability of nondissociative electron transfer (ETnoD) products, specifically noncovalent c/ z fragment complexes, across a range of ubiquitin conformational states. Using ion mobility, we find that more extended states are more prone to fragment release. We obtain evidence that for a given charge state, populations of ubiquitin ions formed either directly by electrospray ionization or through collapse of more extended states upon charge reduction, span a similar range of collision cross-sections. Products of gas-phase collapse are, however, less stabilized towards unfolding than the native conformation, indicating that the ions retain a memory of previous conformational states. Furthermore, this collapse of charge-reduced ions is promoted if the ions are `preheated' using collisional activation, with possible implications for the kinetics of gas-phase compaction.
Uncovering Specific Electrostatic Interactions in the Denatured States of Proteins

PubMed Central

Shen, Jana K.

2010-01-01

The stability and folding of proteins are modulated by energetically significant interactions in the denatured state that is in equilibrium with the native state. These interactions remain largely invisible to current experimental techniques, however, due to the sparse population and conformational heterogeneity of the denatured-state ensemble under folding conditions. Molecular dynamics simulations using physics-based force fields can in principle offer atomistic details of the denatured state. However, practical applications are plagued with the lack of rigorous means to validate microscopic information and deficiencies in force fields and solvent models. This study presents a method based on coupled titration and molecular dynamics sampling of the denatured state starting from the extended sequence under native conditions. The resulting denatured-state pKas allow for the prediction of experimental observables such as pH- and mutation-induced stability changes. I show the capability and use of the method by investigating the electrostatic interactions in the denatured states of wild-type and K12M mutant of NTL9 protein. This study shows that the major errors in electrostatics can be identified by validating the titration properties of the fragment peptides derived from the sequence of the intact protein. Consistent with experimental evidence, our simulations show a significantly depressed pKa for Asp8 in the denatured state of wild-type, which is due to a nonnative interaction between Asp8 and Lys12. Interestingly, the simulation also shows a nonnative interaction between Asp8 and Glu48 in the denatured state of the mutant. I believe the presented method is general and can be applied to extract and validate microscopic electrostatics of the entire folding energy landscape. PMID:20682271

Marine Science Training Program for Alaska Native Students

DTIC Science & Technology

1991-08-01

Seward Marine Center or Kasitsna Bay. In 1989 we decided that a more intensive internship with direct faculty involvement would be more effective ...at UAF provides orientation activities for prospective Native students from the states rural high schools. In addition RSS provides the Alaska Native...opportunity to explore the effects of science upon their daily lives will attract student to careers into oceanic and related sciences and further
The Native American: Warriors in the U.S. Military

DTIC Science & Technology

2011-03-10

large as 95 percent.Ŗ Europeans brought measles, smallpox, cholera , and other diseases that reduced the Native American population and wiped out...Press, 1984. Clevenger, Steven. America’s First Warriors: Native Americans and Iraq. Museum of New Mexico Press. 2010. Clodfelter, MichaeL The Dakota...Autobiography of a Winnebago Indian. Dover Publications, Inc., 1963. Vandervort, Bruce. Indian Wars of Mexico , Canada, and the United States, 1812-1900
Insights from a Learner Corpus as Opposed to a Native Corpus about Cohesive Devices in an Academic Writing Context

ERIC Educational Resources Information Center

Ersanli, Ceylan Yangin

2015-01-01

This study reports on the insights from an EFL learner corpora (a total of 151 essays and 49,690 words) generated from essays collected over the years in a Turkish state university from freshmen students enrolling in the Advanced Writing course. The comparison of cohesive devices in the non-native corpus (NNC) with those in a native corpus (NC)…
A resolution recognizing National American Indian and Alaska Native Heritage Month and celebrating the heritage and culture of American Indians and Alaska Natives and the contributions of American Indians and Alaska Natives to the United States.

THOMAS, 111th Congress

Sen. Dorgan, Byron L. [D-ND

2010-11-19

Senate - 11/19/2010 Submitted in the Senate, considered, and agreed to without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:
A resolution recognizing National American Indian and Alaska Native Heritage Month and celebrating the heritage and culture of American Indians and Alaska Natives and the contributions of American Indians and Alaska Natives to the United States.

THOMAS, 111th Congress

Sen. Dorgan, Byron L. [D-ND

2009-11-05

Senate - 11/05/2009 Submitted in the Senate, considered, and agreed to without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:
Spatial variability and macro‐scale drivers of growth for native and introduced Flathead Catfish populations

USGS Publications Warehouse

Massie, Danielle L.; Smith, Geoffrey; Bonvechio, Timothy F.; Bunch, Aaron J.; Lucchesi, David O.; Wagner, Tyler

2018-01-01

Quantifying spatial variability in fish growth and identifying large‐scale drivers of growth are fundamental to many conservation and management decisions. Although fish growth studies often focus on a single population, it is becoming increasingly clear that large‐scale studies are likely needed for addressing transboundary management needs. This is particularly true for species with high recreational value and for those with negative ecological consequences when introduced outside of their native range, such as the Flathead Catfish Pylodictis olivaris. This study quantified growth variability of the Flathead Catfish across a large portion of its contemporary range to determine whether growth differences existed between habitat types (i.e., reservoirs and rivers) and between native and introduced populations. Additionally, we investigated whether growth parameters varied as a function of latitude and time since introduction (for introduced populations). Length‐at‐age data from 26 populations across 11 states in the USA were modeled using a Bayesian hierarchical von Bertalanffy growth model. Population‐specific growth trajectories revealed large variation in Flathead Catfish growth and relatively high uncertainty in growth parameters for some populations. Relatively high uncertainty was also evident when comparing populations and when quantifying large‐scale patterns. Growth parameters (Brody growth coefficient [K] and theoretical maximum average length [L∞]) were not different (based on overlapping 90% credible intervals) between habitat types or between native and introduced populations. For populations within the introduced range of Flathead Catfish, latitude was negatively correlated with K. For native populations, we estimated an 85% probability that L∞ estimates were negatively correlated with latitude. Contrary to predictions, time since introduction was not correlated with growth parameters in introduced populations of Flathead Catfish. Results of this study suggest that Flathead Catfish growth patterns are likely shaped more strongly by finer‐scale processes (e.g., exploitation or prey abundances) as opposed to macro‐scale drivers.
Native plant naming by high-school students of different socioeconomic status: implications for botany education

NASA Astrophysics Data System (ADS)

Bermudez, Gonzalo M. A.; Díaz, Sandra; De Longhi, Ana L.

2018-01-01

People's diminished awareness of plants, affected by anthropogenic environmental deterioration, has challenged science education to overcome the obstacles impeding a better understanding of their meaning and value. The aim of this study was to investigate the influence of the socioeconomic status of high-school students, as indicated by their attendance at private or state schools, on their knowledge of native plants. In total, 321 students aged 15-18 were asked to write down 10 plants native to Córdoba, Argentina, in a freelist questionnaire. Students listed a mean of 6.8 species of a total of 165 different categories of plant names. The majority of the species named were exotic to Córdoba (63%) or Argentina (50.6%, of which 33.8% were adventitious), indicating an 'adventitious-to-native' effect by which all spontaneously reproducing plants were presumed to be native species. However, the 20 most frequently named plants were mainly native, with 'Algarrobo' (Prosopis spp.) and 'Espinillo' (Vachellia caven) being the most mentioned. Students' socioeconomic status had a significant effect on the number of species named, with the students of state schools (where the less well-off sectors of the society attend) mentioning more species and, among these, more native ones than the students from private schools. Furthermore, we defined size, colour and scent as being conspicuous traits of plant flowers that are relevant for human perception, and found that the most frequently named adventitious species, unlike the native ones, were those exhibiting big brightly-coloured flowers which ranged from being inodorous to having medium intensity scents.
A molten globule-like intermediate state detected in the thermal transition of cytochrome c under low salt concentration.

PubMed

Nakamura, Shigeyoshi; Baba, Takayuki; Kidokoro, Shun-Ichi

2007-04-01

To understand the stabilization mechanism of the transient intermediate state in protein folding, it is very important to understand the structure and stability of the molten globule state under a native condition, in which the native state exists stably. The thermal transitions of horse cytochrome c were thermodynamically evaluated by highly precise differential scanning calorimetry (DSC) at pH 3.8-5.0. The heat capacity functions were analyzed using double deconvolution and the nonlinear least-squares method. An intermediate (I) state is clearly confirmed in the thermal native (N)-to-denatured (D) transition of horse cytochrome c. The mole fraction of the intermediate state shows the largest value, 0.4, at nearly 70 degrees C at pH 4.1. This intermediate state was also detected by the circular dichroism (CD) method and was found to have the properties of the molten globule-like structure by three-state analysis of the CD data. The Gibbs free-energy change between N and I, DeltaG(NI), and that between N and D, DeltaG(ND), were evaluated to be 9-22 kJ mol(-1) and 41-45 kJ mol(-1), respectively at 15( ) degrees C and pH 4.1.
Structural Characteristic of the Initial Unfolded State on Refolding Determines Catalytic Efficiency of the Folded Protein in Presence of Osmolytes

PubMed Central

Warepam, Marina; Sharma, Gurumayum Suraj; Dar, Tanveer Ali; Khan, Md. Khurshid Alam; Singh, Laishram Rajendrakumar

2014-01-01

Osmolytes are low molecular weight organic molecules accumulated by organisms to assist proper protein folding, and to provide protection to the structural integrity of proteins under denaturing stress conditions. It is known that osmolyte-induced protein folding is brought by unfavorable interaction of osmolytes with the denatured/unfolded states. The interaction of osmolyte with the native state does not significantly contribute to the osmolyte-induced protein folding. We have therefore investigated if different denatured states of a protein (generated by different denaturing agents) interact differently with the osmolytes to induce protein folding. We observed that osmolyte-assisted refolding of protein obtained from heat-induced denatured state produces native molecules with higher enzyme activity than those initiated from GdmCl- or urea-induced denatured state indicating that the structural property of the initial denatured state during refolding by osmolytes determines the catalytic efficiency of the folded protein molecule. These conclusions have been reached from the systematic measurements of enzymatic kinetic parameters (K m and k cat), thermodynamic stability (T m and ΔH m) and secondary and tertiary structures of the folded native proteins obtained from refolding of various denatured states (due to heat-, urea- and GdmCl-induced denaturation) of RNase-A in the presence of various osmolytes. PMID:25313668
Modeling the fish community population dynamics and forecasting the eradication success of an exotic fish from an alpine stream

USGS Publications Warehouse

Laplanche, Christophe; Elger, Arnaud; Santoul, Frédéric; Thiede, Gary P.; Budy, Phaedra

2018-01-01

Management actions aimed at eradicating exotic fish species from riverine ecosystems can be better informed by forecasting abilities of mechanistic models. We illustrate this point with an example of the Logan River, Utah, originally populated with endemic cutthroat trout (Oncorhynchus clarkii utah), which compete with exotic brown trout (Salmo trutta). The coexistence equilibrium was disrupted by a large scale, experimental removal of the exotic species in 2009–2011 (on average, 8.2% of the stock each year), followed by an increase in the density of the native species. We built a spatially-explicit, reaction-diffusion model encompassing four key processes: population growth in heterogeneous habitat, competition, dispersal, and a management action. We calibrated the model with detailed long-term monitoring data (2001–2016) collected along the 35.4-km long river main channel. Our model, although simple, did a remarkable job reproducing the system steady state prior to the management action. Insights gained from the model independent predictions are consistent with available knowledge and indicate that the exotic species is more competitive; however, the native species still occupies more favorable habitat upstream. Dynamic runs of the model also recreated the observed increase of the native species following the management action. The model can simulate two possible distinct long-term outcomes: recovery or eradication of the exotic species. The processing of available knowledge using Bayesian methods allowed us to conclude that the chance for eradication of the invader was low at the beginning of the experimental removal (0.7% in 2009) and increased (20.5% in 2016) by using more recent monitoring data. We show that accessible mathematical and numerical tools can provide highly informative insights for managers (e.g., outcome of their conservation actions), identify knowledge gaps, and provide testable theory for researchers.
Unraveling protein folding mechanism by analyzing the hierarchy of models with increasing level of detail

NASA Astrophysics Data System (ADS)

Hayashi, Tomohiko; Yasuda, Satoshi; Škrbić, Tatjana; Giacometti, Achille; Kinoshita, Masahiro

2017-09-01

Taking protein G with 56 residues for a case study, we investigate the mechanism of protein folding. In addition to its native structure possessing α-helix and β-sheet contents of 27% and 39%, respectively, we construct a number of misfolded decoys with a wide variety of α-helix and β-sheet contents. We then consider a hierarchy of 8 different models with increasing level of detail in terms of the number of entropic and energetic physical factors incorporated. The polyatomic structure is always taken into account, but the side chains are removed in half of the models. The solvent is formed by either neutral hard spheres or water molecules. Protein intramolecular hydrogen bonds (H-bonds) and protein-solvent H-bonds (the latter is present only in water) are accounted for or not, depending on the model considered. We then apply a physics-based free-energy function (FEF) corresponding to each model and investigate which structures are most stabilized. This special approach taken on a step-by-step basis enables us to clarify the role of each physical factor in contributing to the structural stability and separately elucidate its effect. Depending on the model employed, significantly different structures such as very compact configurations with no secondary structures and configurations of associated α-helices are optimally stabilized. The native structure can be identified as that with lowest FEF only when the most detailed model is employed. This result is significant for at least the two reasons: The most detailed model considered here is able to capture the fundamental aspects of protein folding notwithstanding its simplicity; and it is shown that the native structure is stabilized by a complex interplay of minimal multiple factors that must be all included in the description. In the absence of even a single of these factors, the protein is likely to be driven towards a different, more stable state.
CERT tribal internship program. Final intern report: Melinda Jacquez, 1995

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

NONE

1998-09-01

The purpose of the intern project was to write a comprehensive booklet on all state legislation proposed in 1995 on Native American issues. A second purpose was to contact tribal governments and request an ordinance, law or resolution on hazardous and nuclear waste transportation. This intern report contains a summary of bills proposed in 37 state legislatures pertaining to Native American issues. Time ran out before the second project objective could be met.
Native State Mass Spectrometry, Surface Plasmon Resonance, and X-ray Crystallography Correlate Strongly as a Fragment Screening Combination.

PubMed

Woods, Lucy A; Dolezal, Olan; Ren, Bin; Ryan, John H; Peat, Thomas S; Poulsen, Sally-Ann

2016-03-10

Fragment-based drug discovery (FBDD) is contingent on the development of analytical methods to identify weak protein-fragment noncovalent interactions. Herein we have combined an underutilized fragment screening method, native state mass spectrometry, together with two proven and popular fragment screening methods, surface plasmon resonance and X-ray crystallography, in a fragment screening campaign against human carbonic anhydrase II (CA II). In an initial fragment screen against a 720-member fragment library (the "CSIRO Fragment Library") seven CA II binding fragments, including a selection of nonclassical CA II binding chemotypes, were identified. A further 70 compounds that comprised the initial hit chemotypes were subsequently sourced from the full CSIRO compound collection and screened. The fragment results were extremely well correlated across the three methods. Our findings demonstrate that there is a tremendous opportunity to apply native state mass spectrometry as a complementary fragment screening method to accelerate drug discovery.
The impact of state behavioral health reform on Native American individuals, families, and communities.

PubMed

Willging, Cathleen E; Goodkind, Jessica; Lamphere, Louise; Saul, Gwendolyn; Fluder, Shannon; Seanez, Paula

2012-07-01

In 2005, the State of New Mexico undertook a sweeping transformation of all publicly funded behavioral health services. The reform was intended to enhance the cultural responsiveness and appropriateness of these services. To examine achievement of this objective, we conducted a qualitative study of the involvement of Native Americans in reform efforts and the subsequent impacts of reform on services for Native Americans. We found that the reform was relatively unsuccessful at creating mechanisms for genuine community input or improving behavioral health care for this population. These shortcomings were related to limited understandings of administrators concerning how tribal governments and health care systems operate, and the structural limitations of a managed care system that does not allow flexibility for culturally appropriate utilization review, screening, or treatment. However, interaction between the State and tribes increased, and we conclude that aspects of the reform could be strengthened to achieve more meaningful involvement and service improvements.
Quakers and Indians in Colonial America. Lesson Plan.

ERIC Educational Resources Information Center

Carter, Max L.

1994-01-01

States that the record of relations between early American colonists and indigenous Native Americans generally shows cultural conflict. Asserts that the Society of Friends (Quakers), led by William Penn, developed a different approach to relations with the Native Americans. (CFR)
Integrated Spatial Models of Non Native Plant Invasion, Fire Risk, and Wildlife Habitat to Support Conservation of Military and Adjacent Lands in the Arid Southwest

DTIC Science & Technology

2015-12-01

FINAL REPORT Integrated spatial models of non-native plant invasion, fire risk, and wildlife habitat to support conservation of military and...as reflecting the official policy or position of the Department of Defense. Reference herein to any specific commercial product, process, or service...2. REPORT TYPE Final 3. DATES COVERED (From - To) 26/4/2010 – 25/10/2015 4. TITLE AND SUBTITLE Integrated Spatial Models of Non-Native Plant
Thermodynamic properties of an extremely rapid protein folding reaction.

PubMed

Schindler, T; Schmid, F X

1996-12-24

The cold-shock protein CspB from Bacillus subtilis is a very small beta-barrel protein, which folds with a time constant of 1 ms (at 25 degrees C) in a U reversible N two-state reaction. To elucidate the energetics of this extremely fast reaction we investigated the folding kinetics of CspB as a function of both temperature and denaturant concentration between 2 and 45 degrees C and between 1 and 8 M urea. Under all these conditions unfolding and refolding were reversible monoexponential reactions. By using transition state theory, data from 327 kinetic curves were jointly analyzed to determine the thermodynamic activation parameters delta H H2O++, delta S H2O++, delta G H2O++, and delta C p H2O++ for unfolding and refolding and their dependences on the urea concentration. 90% of the total change in heat capacity and 96% of the change in the m value (m = d delta G/d[urea]) occur between the unfolded state and the activated state. This suggests that for CspB the activated state of folding is unusually well structured and almost equivalent to the native protein in its interactions with the solvent. As a consequence of this native-like activated state a strong temperature-dependent enthalpy/entropy compensation is observed for the refolding kinetics, and the barrier to refolding shifts from being largely enthalpic at low temperature to largely entropic at high temperature. This shift originates not from the changes in the folding protein chains itself, but from the changes in the protein-solvent interactions. We speculate that the absence of intermediates and the native-like activated state in the folding of CspB are correlated with the small size and the structural type of this protein. The stabilization of a small beta-sheet as in CspB requires extensive non-local interactions, and therefore incomplete sheets are unstable. As a consequence, the critical activated state is reached only very late in folding. The instability of partially folded structure is a means to avoid misfolding prior to the rate-limiting step, and a native-like activated state reduces the risk of non-productive side reactions during the final steps to the native state.
Under What Circumstances Do Wood Products from Native Forests Benefit Climate Change Mitigation?

PubMed

Keith, Heather; Lindenmayer, David; Macintosh, Andrew; Mackey, Brendan

2015-01-01

Climate change mitigation benefits from the land sector are not being fully realised because of uncertainty and controversy about the role of native forest management. The dominant policy view, as stated in the IPCC's Fifth Assessment Report, is that sustainable forest harvesting yielding wood products, generates the largest mitigation benefit. We demonstrate that changing native forest management from commercial harvesting to conservation can make an important contribution to mitigation. Conservation of native forests results in an immediate and substantial reduction in net emissions relative to a reference case of commercial harvesting. We calibrated models to simulate scenarios of native forest management for two Australian case studies: mixed-eucalypt in New South Wales and Mountain Ash in Victoria. Carbon stocks in the harvested forest included forest biomass, wood and paper products, waste in landfill, and bioenergy that substituted for fossil fuel energy. The conservation forest included forest biomass, and subtracted stocks for the foregone products that were substituted by non-wood products or plantation products. Total carbon stocks were lower in harvested forest than in conservation forest in both case studies over the 100-year simulation period. We tested a range of potential parameter values reported in the literature: none could increase the combined carbon stock in products, slash, landfill and substitution sufficiently to exceed the increase in carbon stock due to changing management of native forest to conservation. The key parameters determining carbon stock change under different forest management scenarios are those affecting accumulation of carbon in forest biomass, rather than parameters affecting transfers among wood products. This analysis helps prioritise mitigation activities to focus on maximising forest biomass. International forest-related policies, including negotiations under the UNFCCC, have failed to recognize fully the mitigation value of native forest conservation. Our analyses provide evidence for decision-making about the circumstances under which forest management provides mitigation benefits.
NH2-terminal sequence truncation decreases the stability of bovine rhodanese, minimally perturbs its crystal structure, and enhances interaction with GroEL under native conditions.

PubMed

Trevino, R J; Gliubich, F; Berni, R; Cianci, M; Chirgwin, J M; Zanotti, G; Horowitz, P M

1999-05-14

The NH2-terminal sequence of rhodanese influences many of its properties, ranging from mitochondrial import to folding. Rhodanese truncated by >9 residues is degraded in Escherichia coli. Mutant enzymes with lesser truncations are recoverable and active, but they show altered active site reactivities (Trevino, R. J., Tsalkova, T., Dramer, G., Hardesty, B., Chirgwin, J. M., and Horowitz, P. M. (1998) J. Biol. Chem. 273, 27841-27847), suggesting that the NH2-terminal sequence stabilizes the overall structure. We tested aspects of the conformations of these shortened species. Intrinsic and probe fluorescence showed that truncation decreased stability and increased hydrophobic exposure, while near UV CD suggested altered tertiary structure. Under native conditions, truncated rhodanese bound to GroEL and was released and reactivated by adding ATP and GroES, suggesting equilibrium between native and non-native conformers. Furthermore, GroEL assisted folding of denatured mutants to the same extent as wild type, although at a reduced rate. X-ray crystallography showed that Delta1-7 crystallized isomorphously with wild type in polyethyleneglycol, and the structure was highly conserved. Thus, the missing NH2-terminal residues that contribute to global stability of the native structure in solution do not significantly alter contacts at the atomic level of the crystallized protein. The two-domain structure of rhodanese was not significantly altered by drastically different crystallization conditions or crystal packing suggesting rigidity of the native rhodanese domains and the stabilization of the interdomain interactions by the crystal environment. The results support a model in which loss of interactions near the rhodanese NH2 terminus does not distort the folded native structure but does facilitate the transition in solution to a molten globule state, which among other things, can interact with molecular chaperones.
Under What Circumstances Do Wood Products from Native Forests Benefit Climate Change Mitigation?

PubMed Central

Keith, Heather; Lindenmayer, David; Macintosh, Andrew; Mackey, Brendan

2015-01-01

Climate change mitigation benefits from the land sector are not being fully realised because of uncertainty and controversy about the role of native forest management. The dominant policy view, as stated in the IPCC’s Fifth Assessment Report, is that sustainable forest harvesting yielding wood products, generates the largest mitigation benefit. We demonstrate that changing native forest management from commercial harvesting to conservation can make an important contribution to mitigation. Conservation of native forests results in an immediate and substantial reduction in net emissions relative to a reference case of commercial harvesting. We calibrated models to simulate scenarios of native forest management for two Australian case studies: mixed-eucalypt in New South Wales and Mountain Ash in Victoria. Carbon stocks in the harvested forest included forest biomass, wood and paper products, waste in landfill, and bioenergy that substituted for fossil fuel energy. The conservation forest included forest biomass, and subtracted stocks for the foregone products that were substituted by non-wood products or plantation products. Total carbon stocks were lower in harvested forest than in conservation forest in both case studies over the 100-year simulation period. We tested a range of potential parameter values reported in the literature: none could increase the combined carbon stock in products, slash, landfill and substitution sufficiently to exceed the increase in carbon stock due to changing management of native forest to conservation. The key parameters determining carbon stock change under different forest management scenarios are those affecting accumulation of carbon in forest biomass, rather than parameters affecting transfers among wood products. This analysis helps prioritise mitigation activities to focus on maximising forest biomass. International forest-related policies, including negotiations under the UNFCCC, have failed to recognize fully the mitigation value of native forest conservation. Our analyses provide evidence for decision-making about the circumstances under which forest management provides mitigation benefits. PMID:26436916

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